@article {pmid38041553, year = {2023}, author = {Schmitz, M and Querques, I}, title = {DNA on the move: mechanisms, functions and applications of transposable elements.}, journal = {FEBS open bio}, volume = {}, number = {}, pages = {}, doi = {10.1002/2211-5463.13743}, pmid = {38041553}, issn = {2211-5463}, abstract = {Transposons are mobile genetic elements that have invaded all domains of life by moving between and within their host genomes. Due to their mobility (or transposition), transposons facilitate horizontal gene transfer in bacteria and foster the evolution of new molecular functions in prokaryotes and eukaryotes. As transposition can lead to detrimental genomic rearrangements, organisms have evolved a multitude of molecular strategies to control transposons, including genome defence mechanisms provided by CRISPR-Cas systems. Apart from their biological impacts on genomes, DNA transposons have been leveraged as efficient gene insertion vectors in basic research, transgenesis and gene therapy. However, the close to random insertion profile of transposon-based tools limits their programmability and safety. Despite recent advances brought by the development of CRISPR-associated genome editing nucleases, a strategy for efficient insertion of large, multi-kilobase transgenes at user-defined genomic sites is currently challenging. The discovery and experimental characterization of bacterial CRISPR-associated transposons (CASTs) led to the attractive hypothesis that these systems could be repurposed as programmable, site-specific gene integration technologies. Here, we provide a broad overview of the molecular mechanisms underpinning DNA transposition and of its biological and technological impact. The second focus of the article is to describe recent mechanistic and functional analyses of CAST transposition. Finally, current challenges and desired future advances of CAST-based genome engineering applications are briefly discussed.}, }
@article {pmid38039844, year = {2023}, author = {Harada, R and Inagaki, Y}, title = {Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data.}, journal = {Protist}, volume = {174}, number = {6}, pages = {125997}, doi = {10.1016/j.protis.2023.125997}, pmid = {38039844}, issn = {1618-0941}, abstract = {Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.}, }
@article {pmid38031909, year = {2023}, author = {Kröger, C and Lerminiaux, NA and Ershova, AS and MacKenzie, KD and Kirzinger, MW and Märtlbauer, E and Perry, BJ and Cameron, ADS and Schauer, K}, title = {Plasmid-encoded lactose metabolism and mobilized colistin resistance (mcr-9) genes in Salmonella enterica serovars isolated from dairy facilities in the 1980s.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, doi = {10.1099/mgen.0.001149}, pmid = {38031909}, issn = {2057-5858}, mesh = {*Colistin/pharmacology ; *Salmonella enterica/genetics ; Lactose ; Serogroup ; Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer by plasmids can confer metabolic capabilities that expand a host cell's niche. Yet, it is less understood whether the coalescence of specialized catabolic functions, antibiotic resistances and metal resistances on plasmids provides synergistic benefits. In this study, we report whole-genome assembly and phenotypic analysis of five Salmonella enterica strains isolated in the 1980s from milk powder in Munich, Germany. All strains exhibited the unusual phenotype of lactose-fermentation and encoded either of two variants of the lac operon. Surprisingly, all strains encoded the mobilized colistin resistance gene 9 (mcr-9), long before the first report of this gene in the literature. In two cases, the mcr-9 gene and the lac locus were linked within a large gene island that formed an IncHI2A-type plasmid in one strain but was chromosomally integrated in the other strain. In two other strains, the mcr-9 gene was found on a large IncHI1B/IncP-type plasmid, whereas the lac locus was encoded on a separate chromosomally integrated plasmidic island. The mcr-9 sequences were identical and genomic contexts could not explain the wide range of colistin resistances exhibited by the Salmonella strains. Nucleotide variants did explain phenotypic differences in motility and exopolysaccharide production. The observed linkage of mcr-9 to lactose metabolism, an array of heavy-metal detoxification systems, and other antibiotic resistance genes may reflect a coalescence of specialized phenotypes that improve the spread of colistin resistance in dairy facilities, much earlier than previously suspected.}, }
@article {pmid38013098, year = {2023}, author = {Fang, GY and Liu, XQ and Jiang, YJ and Mu, XJ and Huang, BW}, title = {Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168908}, doi = {10.1016/j.scitotenv.2023.168908}, pmid = {38013098}, issn = {1879-1026}, abstract = {Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.}, }
@article {pmid38012331, year = {2023}, author = {Zhu, H and Yu, J and Fu, Y and Mao, X and Yang, H}, title = {Two-Omics Probe on the Potential of Pseudomonas sp. GDMCC 1.1703 Under Phenol Stress.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {21}, pmid = {38012331}, issn = {1432-0991}, support = {2019YFC1803801//Key Technologies Research and Development Program/ ; 2019YFC1803800//Key Technology Research and Development Program of Shandong/ ; }, abstract = {Pseudomonas sp. harbors genetic diversity and readily adapts to environmental challenges, conferring upon it the ability to remediate. It is important to genetically determine the effects of bacterial application. The two-omics integration approach may shed more light on Pseudomonas isolates, filling the knowledge gap between genetic potential and dynamic function. In the present study, a strain from the Xi River was isolated using benzene-selective enrichment medium and phylogenetically identified as Pseudomonas sp. GDMCC 1.1703 by 16S rRNA gene sequencing. Its phenol degradability was optimally assessed at a rate of 45.7% (by statistics P < 0.05) in 12 h with a 200 mg/L concentration. Genomics and transcriptomics analyses were successively used to identify the genes and pathways responsible for phenol degradation. At least 42 genes were genomically identified to be involved in xenobiotic biodegradation. The degradative genes clustered into operons were hypothesized to have evolved through horizontal gene transfer. On the basis of genomic authentication, transcriptome analysis dynamically revealed that phenol degradation and responsive mechanisms were both upregulated as defense between the Ctrl (control) and PS (phenol-stressed) groups. Quantitative reverse transcription-PCR not only validated the key genes identified via RNA sequencing but also consistently confirmed the realistic intracellular expression. The approach of omics integration, which is effective in exploring the potential of isolates, will hopefully become an established method for determining the remediation potential of a candidate for development.}, }
@article {pmid38007474, year = {2023}, author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M}, title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {265}, pmid = {38007474}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; }, mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; }, abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.<br><br>RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G&#x2009;+&#x2009;C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G&#x2009;+&#x2009;C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G&#x2009;+&#x2009;C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.<br><br>CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.}, }
@article {pmid38007076, year = {2023}, author = {Zhang, Z and Bo, L and Wang, S and Li, C and Zhang, X and Xue, B and Yang, X and He, X and Shen, Z and Qiu, Z and Zhao, C and Wang, J}, title = {Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117739}, doi = {10.1016/j.envres.2023.117739}, pmid = {38007076}, issn = {1096-0953}, abstract = {In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.}, }
@article {pmid38006896, year = {2023}, author = {Yang, QE and Ma, X and Zeng, L and Wang, Q and Li, M and Teng, L and He, M and Liu, C and Zhao, M and Wang, M and Hui, D and Madsen, JS and Liao, H and Walsh, TR and Zhou, S}, title = {Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00227-6}, pmid = {38006896}, issn = {2666-5247}, abstract = {BACKGROUND: The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context.<br><br>METHODS: For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli.<br><br>FINDINGS: We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids.<br><br>INTERPRETATION: Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors.<br><br>FUNDING: The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.}, }
@article {pmid38006562, year = {2024}, author = {Serbus, LR}, title = {A Light in the Dark: Uncovering Wolbachia-Host Interactions Using Fluorescence Imaging.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {349-373}, pmid = {38006562}, issn = {1940-6029}, abstract = {The success of microbial endosymbionts, which reside naturally within a eukaryotic "host" organism, requires effective microbial interaction with, and manipulation of, the host cells. Fluorescence microscopy has played a key role in elucidating the molecular mechanisms of endosymbiosis. For 30 years, fluorescence analyses have been a cornerstone in studies of endosymbiotic Wolbachia bacteria, focused on host colonization, maternal transmission, reproductive parasitism, horizontal gene transfer, viral suppression, and metabolic interactions in arthropods and nematodes. Fluorescence-based studies stand to continue informing Wolbachia-host interactions in increasingly detailed and innovative ways.}, }
@article {pmid38006561, year = {2024}, author = {Bordenstein, SR}, title = {Isolation of Phage WO Particles from Wolbachia-Infected Arthropods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {337-348}, pmid = {38006561}, issn = {1940-6029}, abstract = {Nearly all arthropod-associated Wolbachia contain intact and/or genomic remnants of phage WO, temperate bacteriophages that facilitate horizontal gene transfer, genomic rearrangement of the bacterial chromosome, and symbiotic interactions between Wolbachia and their arthropod hosts. Integrated prophage WO genomes produce active, lytic particles; but the lack of a cell-free culturing system for Wolbachia render them difficult to purify and study. This chapter describes polyethylene glycol (PEG) precipitation of phage particles from Wolbachia-infected arthropods, followed by confirmation of phage WO isolation and purification using electron microscopy and PCR.}, }
@article {pmid38005943, year = {2023}, author = {Loney, RE and Delesalle, VA and Chaudry, BE and Czerpak, M and Guffey, AA and Goubet-McCall, L and McCarty, M and Strine, MS and Tanke, NT and Vill, AC and Krukonis, GP}, title = {A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations.}, journal = {Viruses}, volume = {15}, number = {11}, pages = {}, pmid = {38005943}, issn = {1999-4915}, support = {52007540/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Bacteriophages (phages) are the most numerous entities on Earth, but we have only scratched the surface of describing phage diversity. We isolated seven Bacillus subtilis phages from desert soil in the southwest United States and then sequenced and characterized their genomes. Comparative analyses revealed high nucleotide and amino acid similarity between these seven phages, which constitute a novel subcluster. Interestingly, the tail fiber and lysin genes of these phages seem to come from different origins and carry out slightly different functions. These genes were likely acquired by this subcluster of phages via horizontal gene transfer. In conjunction with host range assays, our data suggest that these phages are adapting to hosts with different cell walls.}, }
@article {pmid38005684, year = {2023}, author = {Khafizova, GV and Sierro, N and Ivanov, NV and Sokornova, SV and Polev, DE and Matveeva, TV}, title = {Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {22}, pages = {}, doi = {10.3390/plants12223787}, pmid = {38005684}, issn = {2223-7747}, support = {21-14-00050//Russian Science Foundation/ ; }, abstract = {Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due to the activity of T-DNA genes, gathered on a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, a lot of plant species are known to contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some of the genes remain intact, which leads to the conclusion of their functional role in plants. In this study, we present a comprehensive analysis of the cT-DNAs in the Nicotiana noctiflora Hook. genome, including gene expression and opine identification. Deep sequencing of the Nicotiana noctiflora genome revealed the presence of two different cT-DNAs, NnT-DNA1 and NnT-DNA2, which contain the intact genes iaaM, iaaH, acs, orf13, orf13a, and orf14. According to the expression analysis results, all these genes are most active in roots in comparison with other organs, which is consistent with data on cT-DNA gene expression in other plant species. We also used genetic engineering approaches and HPTLC and HPLC-MS methods to investigate the product of the acs gene (agrocinopine synthase), which turned out to be similar to agrocinopine A. Overall, this study expands our knowledge of cT-DNAs in plants and brings us closer to understanding their possible functions. Further research of cT-DNAs in different species and their functional implications could contribute to advancements in plant genetics and potentially unveil novel traits with practical applications in agriculture and other fields.}, }
@article {pmid38004737, year = {2023}, author = {Cai, T and Tang, H and Du, X and Wang, W and Tang, K and Wang, X and Liu, D and Wang, P}, title = {Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, doi = {10.3390/microorganisms11112725}, pmid = {38004737}, issn = {2076-2607}, support = {42188102, 91951203 and 32070175//the National Science Foundation of China/ ; 2022YFC3103600//the National Key R&amp;D Program of China/ ; 2021345//the Youth Innovation Promotion Association CAS/ ; 2019BT02Y262//the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; GJTD-2020-12//the K. C. Wong Education Foundation/ ; 2021B1212050023//the Science and Technology Planning Project of Guangdong Province of China/ ; }, abstract = {Many bacteria use the second messenger c-di-GMP to regulate exopolysaccharide production, biofilm formation, motility, virulence, and other phenotypes. The c-di-GMP level is controlled by the complex network of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that synthesize and degrade c-di-GMP. In addition to chromosomally encoded DGCs, increasing numbers of DGCs were found to be located on mobile genetic elements. Whether these mobile genetic element-encoded DGCs can modulate the physiological phenotypes in recipient bacteria after horizontal gene transfer should be investigated. In our previous study, a genomic island encoding three DGC proteins (Dgc137, Dgc139, and Dgc140) was characterized in Vibrio alginolyticus isolated from the gastric cavity of the coral Galaxea fascicularis. Here, the effect of the three DGCs in four Pseudoalteromonas strains isolated from coral Galaxea fascicularis and other marine environments was explored. The results showed that when dgc137 is present rather than the three DGC genes, it obviously modulates biofilm formation and bacterial motility in these Pseudoalteromonas strains. Our findings implied that mobile genetic element-encoded DGC could regulate the physiological status of neighboring bacteria in a microbial community by modulating the c-di-GMP level after horizontal gene transfer.}, }
@article {pmid38004480, year = {2023}, author = {Muteeb, G and Rehman, MT and Shahwan, M and Aatif, M}, title = {Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ph16111615}, pmid = {38004480}, issn = {1424-8247}, support = {xxx//King Faisal University/ ; }, abstract = {Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.}, }
@article {pmid38002987, year = {2023}, author = {Wang, B and Finazzo, M and Artsimovitch, I}, title = {Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/genes14112044}, pmid = {38002987}, issn = {2073-4425}, support = {GM067153//National Institute of Health/ ; }, abstract = {Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.}, }
@article {pmid38000736, year = {2023}, author = {Yao, N and Li, W and Hu, L and Fang, N}, title = {Do mould inhibitors alter the microbial community structure and antibiotic resistance gene profiles on textiles?.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168808}, doi = {10.1016/j.scitotenv.2023.168808}, pmid = {38000736}, issn = {1879-1026}, abstract = {Mould inhibitors are closely associated with human health and have been extensively applied to textiles to prevent mould and insect infestations. However, the impact of these mould inhibitors on the microbial community structure on textiles and antibiotic resistance gene (ARG) profiles remains largely unexplored. In this study, testing techniques, including high-throughput quantitative PCR and Illumina sequencing, were employed to analyse the effects of three types of mould inhibitors -para-dichlorobenzene (PDCB), naphthalene, and natural camphor balls-on the composition of microbial communities and ARG profiles. The microbial mechanisms underlying these effects were also investigated. The experiments revealed that PDCB reduced the diversity of bacterial communities on textiles, whereas naphthalene and natural camphor balls exerted relatively minor effects. In contrast with bacterial diversity, PDCB enhanced the diversity of fungal communities on textiles, but significantly reduced their abundance. Naphthalene had the least impact on fungal communities; however, it notably increased the relative abundance of Basidiomycota. All three types of mould inhibitors substantially altered ARG profiles. Potential mechanisms responsible for the alterations in ARG profiles include microbial community succession and horizontal gene transfer mediated by mobile genetic elements. PDCB prominently increased the abundance of ARGs, mainly attributable to the relative enrichment of potential hosts (including certain γ-Proteobacteria and Bacillales) for specific ARGs. Thus, this study has important implications for the selection of mould inhibitors, as well as the assessment of microbial safety in textiles.}, }
@article {pmid37999346, year = {2023}, author = {Marinacci, B and Krzyżek, P and Pellegrini, B and Turacchio, G and Grande, R}, title = {Latest Update on Outer Membrane Vesicles and Their Role in Horizontal Gene Transfer: A Mini-Review.}, journal = {Membranes}, volume = {13}, number = {11}, pages = {}, pmid = {37999346}, issn = {2077-0375}, abstract = {Outer membrane vesicles (OMVs) are spherical, lipid-based nano-structures, which are released by Gram-negative bacteria in both in vitro and in vivo conditions. The size and composition of OMVs depend on not only the producer bacterial species but also cells belonging to the same strain. The mechanism of vesicles' biogenesis has a key role in determining their cargo and the pattern of macromolecules exposed on their surface. Thus, the content of proteins, lipids, nucleic acids, and other biomolecules defines the properties of OMVs and their beneficial or harmful effects on human health. Many studies have provided evidence that OMVs can be involved in a plethora of biological processes, including cell-to-cell communication and bacteria-host interactions. Moreover, there is a growing body of literature supporting their role in horizontal gene transfer (HGT). During this process, OMVs can facilitate the spreading of genes involved in metabolic pathways, virulence, and antibiotic resistance, guaranteeing bacterial proliferation and survival. For this reason, a deeper understanding of this new mechanism of genetic transfer could improve the development of more efficient strategies to counteract infections sustained by Gram-negative bacteria. In line with this, the main aim of this mini-review is to summarize the latest evidence concerning the involvement of OMVs in HGT.}, }
@article {pmid37995998, year = {2023}, author = {Huang, B and Lv, X and Zheng, H and Yu, H and Zhang, Y and Zhang, C and Wang, J}, title = {Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117718}, doi = {10.1016/j.envres.2023.117718}, pmid = {37995998}, issn = {1096-0953}, abstract = {The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.}, }
@article {pmid37988660, year = {2023}, author = {Zhang, M and Tong, X and Wang, W and Wang, J and Qu, W}, title = {Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.202300521}, pmid = {37988660}, issn = {1521-4028}, support = {2022C02040//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, abstract = {This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.}, }
@article {pmid37987191, year = {2023}, author = {Garbisu, C and Alkorta, I}, title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {12}, pages = {e2300153}, doi = {10.1002/bies.202300153}, pmid = {37987191}, issn = {1521-1878}, support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; }, abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.}, }
@article {pmid37983489, year = {2023}, author = {Simmons, M and Horbelt, N and Sverko, T and Scoppola, E and Jackson, DJ and Harrington, MJ}, title = {Invasive mussels fashion silk-like byssus via mechanical processing of massive horizontally acquired coiled coils.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {48}, pages = {e2311901120}, doi = {10.1073/pnas.2311901120}, pmid = {37983489}, issn = {1091-6490}, support = {RGPIN-2018-05243//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; CRC Tier 2 950-231953//Canada Research Chairs (Chaires de recherche du Canada)/ ; 528314512//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {Zebra and quagga mussels (Dreissena spp.) are invasive freshwater biofoulers that perpetrate devastating economic and ecological impact. Their success depends on their ability to anchor onto substrates with protein-based fibers known as byssal threads. Yet, compared to other mussel lineages, little is understood about the proteins comprising their fibers or their evolutionary history. Here, we investigated the hierarchical protein structure of Dreissenid byssal threads and the process by which they are fabricated. Unique among bivalves, we found that threads possess a predominantly β-sheet crystalline structure reminiscent of spider silk. Further analysis revealed unexpectedly that the Dreissenid thread protein precursors are mechanoresponsive α-helical proteins that are mechanically processed into β-crystallites during thread formation. Proteomic analysis of the byssus secretory organ and byssus fibers revealed a family of ultrahigh molecular weight (354 to 467 kDa) asparagine-rich (19 to 20%) protein precursors predicted to form α-helical coiled coils. Moreover, several independent lines of evidence indicate that the ancestral predecessor of these proteins was likely acquired via horizontal gene transfer. This chance evolutionary event that transpired at least 12 Mya has endowed Dreissenids with a distinctive and effective fiber formation mechanism, contributing significantly to their success as invasive species and possibly, inspiring new materials design.}, }
@article {pmid37982820, year = {2023}, author = {Cheatle Jarvela, AM and Wexler, JR}, title = {Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.}, journal = {Development genes and evolution}, volume = {}, number = {}, pages = {}, pmid = {37982820}, issn = {1432-041X}, abstract = {Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.}, }
@article {pmid37982629, year = {2023}, author = {Tian, D and Zhao, M and Zheng, S and Jiang, X and Zhang, B}, title = {Involvement of Tn3 transposon in formation and transmission of hypervirulent and carbapenem-resistant Klebsiella pneumoniae.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0303823}, doi = {10.1128/spectrum.03038-23}, pmid = {37982629}, issn = {2165-0497}, abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to most common antibiotics, becoming the most important and prevalent nosocomial opportunity pathogen. Besides, K. pneumoniae can also cause severe community-acquired infections, such as primary liver abscess and endophthalmitis. These pathogens are commonly referred to as hvKp. CRKP and hvKp have evolved separately, each occupying its own clonal lineage and exhibiting a variety of properties. Our study provides important insights into the evolutionary events related to the arousal of virulence and drug resistance in K. pneumoniae through plasmid transmission, mediated by Tn3 transposon. Our study also provides evidence that multiple mechanisms contribute to the successful transfer of non-conjugative virulence plasmid, and the involvement of transposons enhances the efficiency. A good knowledge of its transmission mechanisms is fundamental to finding effective strategies to combat these threatening pathogens. Transposons are widely present in bacteria, spreading resistance and virulence genes between the environment and humans. Therefore, emerging transposon-mediated hypervirulent and carbapenem-resistant pathogens should be highly valued.}, }
@article {pmid37981687, year = {2023}, author = {Chen, X and Wang, Z and Zhang, C and Hu, J and Lu, Y and Zhou, H and Mei, Y and Cong, Y and Guo, F and Wang, Y and He, K and Liu, Y and Li, F}, title = {Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {265}, pmid = {37981687}, issn = {1741-7007}, support = {2019FY100400//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 2022YFD1401600//Key Technologies Research and Development Program/ ; LZ23C140002//Natural Science Foundation of Zhejiang Province/ ; LY22C140005//Natural Science Foundation of Zhejiang Province/ ; 32202366//National science foundation of China/ ; 32102271//National science foundation of China/ ; }, abstract = {BACKGROUND: Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved.<br><br>RESULTS: Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms.<br><br>CONCLUSIONS: Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.}, }
@article {pmid37980566, year = {2023}, author = {Lee, IPA and Eldakar, OT and Gogarten, JP and Andam, CP}, title = {Protocol for an agent-based model of recombination in bacteria playing a public goods game.}, journal = {STAR protocols}, volume = {4}, number = {4}, pages = {102733}, doi = {10.1016/j.xpro.2023.102733}, pmid = {37980566}, issn = {2666-1667}, abstract = {Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.[1].}, }
@article {pmid37980337, year = {2023}, author = {Yenew, B and Ghodousi, A and Diriba, G and Tesfaye, E and Cabibbe, AM and Amare, M and Moga, S and Alemu, A and Dagne, B and Sinshaw, W and Mollalign, H and Meaza, A and Tadesse, M and Gamtesa, DF and Abebaw, Y and Seid, G and Zerihun, B and Getu, M and Chiacchiaretta, M and Gaudin, C and Marceau, M and Didelot, X and Tolera, G and Abdella, S and Kebede, A and Getahun, M and Mehammed, Z and Supply, P and Cirillo, DM}, title = {A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7519}, pmid = {37980337}, issn = {2041-1723}, abstract = {The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.}, }
@article {pmid37976849, year = {2023}, author = {Li, YJ and Yuan, Y and Tan, WB and Xi, BD and Wang, H and Hui, KL and Chen, JB and Zhang, YF and Wang, LF and Li, RF}, title = {Antibiotic resistance genes and heavy metals in landfill: A review.}, journal = {Journal of hazardous materials}, volume = {464}, number = {}, pages = {132395}, doi = {10.1016/j.jhazmat.2023.132395}, pmid = {37976849}, issn = {1873-3336}, abstract = {Landfill is reservoir containing antibiotic resistance genes (ARGs) that pose a threat to human life and health. Heavy metals impose lasting effects on ARGs. This review investigated and analyzed the distribution, composition, and abundance of heavy metals and ARGs in landfill. The abundance ranges of ARGs detected in refuse and leachate were similar. The composition of ARG varied with sampling depth in refuse. ARG in leachate varies with the distribution of ARG in the refuse. The ARG of sulI was associated with 11 metals (Co, Pb, Mn, Zn, Cu, Cr, Ni, Sb, As, Cd, and Al). The effects of the total metal concentration on ARG abundance were masked by many factors. Low heavy metal concentrations showed positive effects on ARG diffusion; conversely, high heavy metal concentrations showed negative effects. Organic matter had a selective pressure effect on microorganisms and could provide energy for the diffusion of ARGs. Complexes of heavy metals and organic matter were common in landfill. Therefore, the hypothesis was proposed that organic matter and heavy metals have combined effects on the horizontal gene transfer (HGT) of ARGs during landfill stabilization. This work provides a new basis to better understand the HGT of ARGs in landfill.}, }
@article {pmid37976735, year = {2023}, author = {Gao, Y and Liu, J and Fang, Y and Xu, X and Wang, F and Tang, Y and Yin, D and Cookson, AL and Zhu, W and Mao, S and Zhong, R}, title = {Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables.}, journal = {Microbiological research}, volume = {278}, number = {}, pages = {127540}, doi = {10.1016/j.micres.2023.127540}, pmid = {37976735}, issn = {1618-0623}, abstract = {Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.}, }
@article {pmid37975503, year = {2023}, author = {Irby, I and Brown, SP}, title = {The social lives of viruses and other mobile genetic elements: a commentary on Leeks et al. 2023.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {11}, pages = {1582-1586}, doi = {10.1111/jeb.14239}, pmid = {37975503}, issn = {1420-9101}, support = {5R21AI156817-02/NH/NIH HHS/United States ; }, abstract = {Illustration of life-histories of phages and plasmids through horizontal and vertical transmission (see Figure 1 for more information).}, }
@article {pmid37974331, year = {2023}, author = {Zhang, Y and Ding, N and Li, Y and Ouyang, M and Fu, P and Peng, Y and Tan, Y}, title = {Transcription factor FOXM1 specifies chromatin DNA to extracellular vesicles.}, journal = {Autophagy}, volume = {}, number = {}, pages = {}, doi = {10.1080/15548627.2023.2284523}, pmid = {37974331}, issn = {1554-8635}, abstract = {Extracellular vesicle DNAs (evDNAs) hold significant diagnostic value for various diseases and facilitate transcellular transfer of genetic material. Our study identifies transcription factor FOXM1 as a mediator for directing chromatin genes or DNA fragments (termed FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 binds to MAP1LC3/LC3 in the nucleus, and FOXM1-chDNAs, such as the DUX4 gene and telomere DNA, are designated by FOXM1 binding and translocated to the cytoplasm before being released to EVs through the secretory autophagy during lysosome inhibition (SALI) process involving LC3. Disrupting FOXM1 expression or the SALI process impairs FOXM1-chDNAs incorporation into EVs. FOXM1-chDNAs can be transmitted to recipient cells via EVs and expressed in recipient cells when they carry functional genes. This finding provides an example of how chromatin DNA fragments are specified to EVs by transcription factor FOXM1, revealing its contribution to the formation of evDNAs from nuclear chromatin. It provides a basis for further exploration of the roles of evDNAs in biological processes, such as horizontal gene transfer.}, }
@article {pmid37974017, year = {2023}, author = {Thepmanee, O and Munkongwongsiri, N and Prachumwat, A and Saksmerprome, V and Jitrakorn, S and Sritunyalucksana, K and Vanichviriyakit, R and Chanarat, S and Jaroenlak, P and Itsathitphaisarn, O}, title = {Molecular and cellular characterization of four putative nucleotide transporters from the shrimp microsporidian Enterocytozoon hepatopenaei (EHP).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20008}, pmid = {37974017}, issn = {2045-2322}, support = {BRF1-054/2565//The National Science Research and Innovation Fund (NSRF)/ ; BRF1-054/2565//The National Science Research and Innovation Fund (NSRF)/ ; PRP6505030760//The Agricultural Research Development Agency/ ; PRP6505030760//The Agricultural Research Development Agency/ ; B05F640137//The Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; RGNS 65-013//Chulalongkorn University/ ; }, abstract = {Microsporidia are obligate intracellular parasites that lost several enzymes required in energy production. The expansion of transporter families in these organisms enables them to hijack ATP from hosts. In this study, nucleotide transporters of the microsporidian Enterocytozoon hepatopenaei (EHP), which causes slow growth in economically valuable Penaeus shrimp, were characterized. Analysis of the EHP genome suggested the presence of four putative nucleotide transporter genes, namely EhNTT1, EhNTT2, EhNTT3, and EhNTT4. Sequence alignment revealed four charged amino acids that are conserved in previously characterized nucleotide transporters. Phylogenetic analysis suggested that EhNTT1, 3, and 4 were derived from one horizontal gene transfer event, which was independent from that of EhNTT2. Localization of EhNTT1 and EhNTT2 using immunofluorescence analysis revealed positive signals within the envelope of developing plasmodia and on mature spores. Knockdown of EhNTT2 by double administration of sequence specific double-stranded RNA resulted in a significant reduction in EHP copy numbers, suggesting that EhNTT2 is crucial for EHP replication in shrimp. Taken together, the insight into the roles of NTTs in microsporidian proliferation can provide the biological basis for the development of alternative control strategies for microsporidian infection in shrimp.}, }
@article {pmid37973843, year = {2023}, author = {Allard, N and Collette, A and Paquette, J and Rodrigue, S and Côté, JP}, title = {Systematic investigation of recipient cell genetic requirements reveals important surface receptors for conjugative transfer of IncI2 plasmids.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1172}, pmid = {37973843}, issn = {2399-3642}, support = {5014521//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 571440//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; 314063//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; }, abstract = {Bacterial conjugation is a major horizontal gene transfer mechanism. While the functions encoded by many conjugative plasmids have been intensively studied, the contribution of recipient chromosome-encoded genes remains largely unknown. Here, we analyzed the genetic requirement of recipient cells for conjugation of IncI2 plasmid TP114, which was recently shown to transfer at high rates in the gut microbiota. We performed transfer assays with ~4,000 single-gene deletion mutants of Escherichia coli. When conjugation occurs on a solid medium, we observed that recipient genes impairing transfer rates were not associated with a specific cellular function. Conversely, transfer assays performed in broth were largely dependent on the lipopolysaccharide biosynthesis pathway. We further identified specific structures in lipopolysaccharides used as recipient cell surface receptors by PilV adhesins associated with the type IVb accessory pilus of TP114. Our strategy is applicable to study other mobile genetic elements and understand important host cell factors for their dissemination.}, }
@article {pmid37972772, year = {2023}, author = {Xin, R and Zhang, Y and Zhang, K and Yang, Y and Ma, Y and Niu, Z}, title = {Investigation of the antimicrobial susceptibility patterns of marine cyanobacteria in Bohai Bay: Cyanobacteria may be important hosts of antibiotic resistance genes in marine environment.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168516}, doi = {10.1016/j.scitotenv.2023.168516}, pmid = {37972772}, issn = {1879-1026}, abstract = {Marine cyanobacteria, as widely distributed and photosynthetically autotrophic bacteria in the ocean, may contribute to the global dissemination of antibiotic resistance genes (ARGs) and develop a different antimicrobial susceptibility pattern from heterotrophic bacteria and cyanobacteria from freshwater environments. However, studies on antimicrobial susceptibility and the carriage of ARGs in marine cyanobacteria are still very limited. In this study, the antibiotic resistance characteristics of cyanobacteria in nearshore waters were examined through field monitoring and laboratory investigations, which included PCR detection and ARG transformation. The results showed a positive correlation between marine cyanobacteria and some ARGs in the nearshore waters of Bohai Bay. Moreover, most screened cyanobacteria showed high minimum inhibitory concentration (MIC) values for polymyxins, tetracyclines, kanamycin, and sulfonamides, moderate MIC values for streptomycin, chloramphenicol, rifampicin, and norfloxacin, and low MIC values for roxithromycin and cephalosporins. The blaTEM, blaKPC, sul1, sul2, strA, tetA, tetB, tetC, tetM, mdfA, and intI1 genes were detected in the screened marine cyanobacteria. The highest detection rates were observed for blaTEM (93.3 %), sul1 (56.6 %), sul2 (90 %), and strA (73.3 %). The detection rate of tetA (33.3 %) was the highest among the tetracycline resistance genes, and mdfA, a multidrug-resistant pump gene with resistance to tetracycline, also showed a high detection level (23.3 %). Overall, most of the screened marine cyanobacteria were found to tolerate multiple antibiotics in seawater, and the condition of the ARGs carriage was serious. Furthermore, the screened marine Synechocystis sp. C12-2 demonstrated the ability to accept ARGs on the RP4 plasmid through natural transformation and showed reduced sensitivity to ampicillin, suggesting the possibility that some marine cyanobacteria could acquire ARGs from the environment through horizontal gene transfer. Thus, marine cyanobacteria may play an important role in the propagation of marine ARGs.}, }
@article {pmid37971327, year = {2023}, author = {Förster, M and Rathmann, I and Yüksel, M and Power, JJ and Maier, B}, title = {Genome-wide transformation reveals extensive exchange across closely related Bacillus species.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad1074}, pmid = {37971327}, issn = {1362-4962}, support = {CRC 1310//Deutsche Forschungsgemeinschaft/ ; //University of Cologne/ ; }, abstract = {Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.}, }
@article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0062923}, doi = {10.1128/aem.00629-23}, pmid = {37971255}, issn = {1098-5336}, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, }
@article {pmid37971242, year = {2023}, author = {Lerminiaux, N and Mitchell, R and Bartoszko, J and Davis, I and Ellis, C and Fakharuddin, K and Hota, SS and Katz, K and Kibsey, P and Leis, JA and Longtin, Y and McGeer, A and Minion, J and Mulvey, M and Musto, S and Rajda, E and Smith, SW and Srigley, JA and Suh, KN and Thampi, N and Tomlinson, J and Wong, T and Mataseje, L and , }, title = {Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0086023}, doi = {10.1128/aac.00860-23}, pmid = {37971242}, issn = {1098-6596}, abstract = {Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.}, }
@article {pmid37968548, year = {2023}, author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A}, title = {Characterization of the soil resistome and mobilome in Namib Desert soils.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37968548}, issn = {1618-1905}, abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.}, }
@article {pmid37966605, year = {2024}, author = {Chu Yuan Kee, MJ and Chen, J}, title = {Phage Transduction of Staphylococcus aureus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {263-275}, pmid = {37966605}, issn = {1940-6029}, abstract = {Bacteriophage transduction is the major mechanism of horizontal gene transfer (HGT) among many bacteria. In Staphylococcus aureus, the phage-mediated acquisition of mobile genetic elements (MGEs) that encode virulence and antibiotic resistance genes largely contribute to its evolutionary adaptation and genetic plasticity. In molecular biology, generalized transduction is routinely used as a technique to manipulate and construct bacterial strains. Here, we describe optimized protocols for generalized transduction, applicable for the transfer of plasmid or chromosomal deoxyribonucleic acid (DNA) from donor to recipient S. aureus strains.}, }
@article {pmid37966239, year = {2023}, author = {Maccario, L and Silva, AF and Nesme, J and Amador, CI and Sørensen, SJ and Cooper, VS and Røder, HL}, title = {Draft genomes of seven isolates from Danish wastewater facilities belonging to Pseudomonas, Bacillus, Pseudochrobactrum, Brevundimonas, and Pandoraea.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0052923}, doi = {10.1128/MRA.00529-23}, pmid = {37966239}, issn = {2576-098X}, abstract = {We report here seven draft genomes of bacterial strains from two Danish wastewater facilities, two of which might be characterized as a new group within the Pseudomonas and Pseudochrobactrum genera, respectively. These genomes will provide useful references for understanding bacterial interactions and horizontal gene transfer within bacterial communities.}, }
@article {pmid37965050, year = {2023}, author = {Kormos, A and Dimopoulos, G and Bier, E and Lanzaro, GC and Marshall, JM and James, AA}, title = {Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1261123}, pmid = {37965050}, issn = {2296-4185}, abstract = {The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.}, }
@article {pmid37963249, year = {2023}, author = {Goldlust, K and Ducret, A and Halte, M and Dedieu-Berne, A and Erhardt, M and Lesterlin, C}, title = {The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {47}, pages = {e2310842120}, doi = {10.1073/pnas.2310842120}, pmid = {37963249}, issn = {1091-6490}, support = {FRM-EQU202103012587//Fondation pour la Recherche M&#xe9;dicale (FRM)/ ; ANR-18-CE35-0008//Agence Nationale de la Recherche (ANR)/ ; ANR-22-CE12-0032//Agence Nationale de la Recherche (ANR)/ ; no. 113_MC_GH_MEL-BER_Erhardt_HU//Berlin University Alliance (BUA)/ ; }, abstract = {Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established that the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that while most transfer events occur between cells in direct contact, the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a unique model for conjugation that revises our understanding of the DNA transfer mechanism and the dissemination of drug resistance and virulence genes within complex bacterial communities.}, }
@article {pmid37959048, year = {2023}, author = {Qin, Y and Huang, W and Yang, J and Zhao, Y and Zhao, M and Xu, H and Zhang, M}, title = {The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {21}, pages = {}, doi = {10.3390/foods12213928}, pmid = {37959048}, issn = {2304-8158}, support = {2022D01C404//Natural Science Foundation of Xinjiang/ ; 2019Q002//Natural Science Foundation of Xinjiang/ ; 2022D01D42//Natural Science Foundation of Xinjiang/ ; }, abstract = {Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 10[8] total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.}, }
@article {pmid37955258, year = {2023}, author = {Gong, P and Liu, H and Yu, T and Jiang, C and Gou, E and Guan, J and Chen, H and Kang, H}, title = {Evaluation of resistance risk in soil due to antibiotics during application of penicillin V fermentation residue.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-33}, doi = {10.1080/09593330.2023.2283807}, pmid = {37955258}, issn = {1479-487X}, abstract = {The soil application of hydrothermally treated penicillin V fermentation residue (PFR) is attractive but challenged, due to the concern of the resistance risk in soil related to residual antibiotics. In this study, a lab-scale incubation experiment was conducted to investigate the influence of penicillin V on antibiotic resistance genes (ARGs) in PFR-amended soil via qPCR. The introduced penicillin V in soil could not be persistent, and its degradation occurred mainly within 2 days. The higher number of soil ARGs was detected under 108 mg/kg of penicillin V than lower contents (≤54 mg/kg). Additionally, the relative abundance of ARGs was higher in soil spiked with penicillin V than that in blank soil, and the great increase in the relative abundance of soil ARGs occurred earlier under 108 mg/kg of penicillin V than lower contents. The horizontal gene transfer might contribute to the shift of ARGs in PFR-amended soil. The results indicated that the residual penicillin V could cause the proliferation of soil ARGs and should be completely removed by hydrothermal treatment before soil application. The results of this study provide a comprehensive understanding of the resistance risk posed by penicillin V during the application of hydrothermally pretreated PFR.}, }
@article {pmid37953666, year = {2023}, author = {Pandey, T and Kalluraya, CA and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK}, title = {Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {e114835}, doi = {10.15252/embj.2023114835}, pmid = {37953666}, issn = {1460-2075}, support = {P40 OD010440/CD/ODCDC CDC HHS/United States ; }, abstract = {Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.}, }
@article {pmid37952399, year = {2023}, author = {Salter, C and Westrick, JA and Chaganti, SR and Birbeck, JA and Peraino, NJ and Weisener, CG}, title = {Elucidating microbial mechanisms of microcystin-LR degradation in Lake Erie beach sand through metabolomics and metatranscriptomics.}, journal = {Water research}, volume = {247}, number = {}, pages = {120816}, doi = {10.1016/j.watres.2023.120816}, pmid = {37952399}, issn = {1879-2448}, abstract = {As one of five Laurentian Great Lakes, Lake Erie ranks among the top freshwater drinking sources and ecosystems globally. Historical and current agriculture mismanagement and climate change sustains the environmental landscape for late summer cyanobacterial harmful algal blooms, and consequently, cyanotoxins such as microcystin (MC). Microcystin microbial degradation is a promising mitigation strategy, however the mechanisms controlling the breakdown of MCs in Lake Erie are not well understood. Pelee Island, Ontario, Canada is located in the western basin of Lake Erie and the bacterial community in the sand has demonstrated the capacity of metabolizing the toxin. Through a multi-omic approach, the metabolic, functional and taxonomical signatures of the Pelee Island microbial community during MC-LR degradation was investigated over a 48-hour period to comprehensively study the degradation mechanism. Cleavage of bonds surrounding nitrogen atoms and the upregulation of nitrogen deamination (dadA, alanine dehydrogenase, leucine dehydrogenase) and assimilation genes (glnA, gltB) suggests a targeted isolation of nitrogen by the microbial community for energy production. Methylotrophic pathways RuMP and H4MPT control assimilation and dissimilation of carbon, respectively and differential abundance of Methylophilales indicates an interconnected role through electron exchange of denitrification and methylotrophic pathways. The detected metabolites did not resolve a clear breakdown pathway, but rather the diversity of products in combination with taxonomic and functional results supports that a variety of strategies are applied, such as epoxidation, hydroxylation, and aromatic degradation. Annual repeated exposure to the toxin may have allowed the community to adaptatively establish a novel pathway through functional plasticity and horizontal gene transfer. The culmination of these results reveals the complexity of the Pelee Island sand community and supports a dynamic and cooperative metabolism between microbial species to achieve MC degradation.}, }
@article {pmid37951253, year = {2023}, author = {Kang, Y and Zhao, S and Cheng, H and Xu, W and You, R and Hu, J}, title = {The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168359}, doi = {10.1016/j.scitotenv.2023.168359}, pmid = {37951253}, issn = {1879-1026}, abstract = {The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.}, }
@article {pmid37944236, year = {2023}, author = {Xiao, T and Chen, R and Cai, C and Yuan, S and Dai, X and Dong, B and Xu, Z}, title = {Abatement of antibiotics and resistance genes during catalytic ozonation enhanced sludge dewatering process: Synchronized in volume and hazardousness reduction.}, journal = {Journal of hazardous materials}, volume = {463}, number = {}, pages = {132912}, doi = {10.1016/j.jhazmat.2023.132912}, pmid = {37944236}, issn = {1873-3336}, abstract = {Based on the efficiency of the catalytic ozonation techniques (HDWS+O3 and MnFe2O4 @SBC+O3) in enhancing the sludge dewaterability, the effectiveness in synchronized abatement antibiotics and antibiotic resistance genes (ARGs) was conducted to determine. The results revealed that catalytic ozonation conditioning altered the distribution of target antibiotics (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) in the dewatered filtrate, the dewatered sludge cake and the extra-microcolony/cellular polymers (EMPS/ECPS) layers, achieving the redistribution from solid-phase adsorption to liquid-phase dissolution. The total degradation rate was over 90% for TC and OTC, 72-78% for NOR and OFL; the abatement efficiency of eleven ARGs reached 1.47-3.01 log and 1.64-3.59 log, respectively, and more than four eARGs were eliminated. The effective abatement of the absolute abundance of Mobile genetic elements (MGEs) (0.91-1.89 log) demonstrated that catalytic ozonation conditioning could also significantly inhibit horizontal gene transfer (HGT). The abundance of resistant bacteria was greatly reduced and the signal transduction of the typical ARGs host bacteria was inhibited. The highly reactive oxidation species (ROS) generated were responsible for the abatement of antibiotics and ARGs. These findings provided new insights into the sludge conditioning for ideal and synchronized reduction in volume and hazardousness by catalytic ozonation processes in sludge treatment.}, }
@article {pmid37940998, year = {2023}, author = {Schaller, D and Hartmann, T and Lafond, M and Stadler, PF and Wieseke, N and Hellmuth, M}, title = {Relative timing information and orthology in evolutionary scenarios.}, journal = {Algorithms for molecular biology : AMB}, volume = {18}, number = {1}, pages = {16}, pmid = {37940998}, issn = {1748-7188}, support = {RGPIN-2019-05817//Natural Sciences and Engineering Research Council of Canada/ ; 214087123//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.<br><br>RESULTS: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.}, }
@article {pmid37938748, year = {2023}, author = {Zeldes, B and Poehlein, A and Jain, S and Baum, C and Daniel, R and Müller, V and Basen, M}, title = {DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {2}, pmid = {37938748}, issn = {2730-6151}, support = {BA 5757/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 031B0857A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857C//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0857B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.}, }
@article {pmid37935916, year = {2023}, author = {An, T and Cai, Y and Li, G and Li, S and Wong, PK and Guo, J and Zhao, H}, title = {Prevalence and transmission risk of colistin and multidrug resistance in long-distance coastal aquaculture.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {115}, pmid = {37935916}, issn = {2730-6151}, support = {U1901210//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41425015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122056//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; }, abstract = {Due to the wide use of antibiotics, intensive aquaculture farms have been recognized as a significant reservoir of antibiotic resistomes. Although the prevalence of colistin resistance genes and multidrug-resistant bacteria (MDRB) has been documented, empirical evidence for the transmission of colistin and multidrug resistance between bacterial communities in aquaculture farms through horizontal gene transfer (HGT) is lacking. Here, we report the prevalence and transmission risk of colistin and multidrug resistance in 27 aquaculture water samples from 9 aquaculture zones from over 5000 km of subtropical coastlines in southern China. The colistin resistance gene mcr-1, mobile genetic element (MGE) intl1 and 13 typical antibiotic resistance genes (ARGs) were prevalent in all the aquaculture water samples. Most types of antibiotic (especially colistin) resistance are transmissible in bacterial communities based on evidence from laboratory conjugation and transformation experiments. Diverse MDRB were detected in most of the aquaculture water samples, and a strain with high-level colistin resistance, named Ralstonia pickettii MCR, was isolated. The risk of horizontal transfer of the colistin resistance of R. pickettii MCR through conjugation and transformation was low, but the colistin resistance could be steadily transmitted to offspring through vertical transfer. The findings have important implications for the future regulation of antibiotic use in aquaculture farms globally to address the growing threat posed by antibiotic resistance to human health.}, }
@article {pmid37938682, year = {2022}, author = {Orevi, T and Sørensen, SJ and Kashtan, N}, title = {Droplet size and surface hydrophobicity enhance bacterial plasmid transfer rates in microscopic surface wetness.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {72}, pmid = {37938682}, issn = {2730-6151}, support = {#220020475//James S. McDonnell Foundation (McDonnell Foundation)/ ; #1396/19//Israel Science Foundation (ISF)/ ; NNF200C0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Conjugal plasmids constitute a major engine for horizontal gene transfer in bacteria, and are key drivers of the spread of antibiotic resistance, virulence, and metabolic functions. Bacteria in terrestrial habitats often inhabit surfaces that are not constantly water-saturated, where microscopic surface wetness (MSW), comprised of thin liquid films and microdroplets, permanently or intermittently occurs. How physical properties of microdroplets, and of the surfaces they reside on, affect plasmid transfer rates is not well understood. Here, building on microscopy-based microdroplet experiments, we examined the relation between droplet properties (size and spread) and plasmid transfer rates at single-cell and individual droplet resolution, using Pseudomonas putida as a model species. We show that transfer rates increase with droplet size, due to higher densities of cells on the surface in larger droplets, resulting from lower ratio between the area of the liquid-solid interface and droplet volumes. We further show that surface hydrophobicity promotes transfer rates via the same mechanism. Our results provide new insights into how physical properties of surfaces and MSW affect plasmid transfer rates, and more generally, microbial interactions mediated by cell-to-cell contact, with important implications for our understanding of the ecology and evolution of bacteria in unsaturated environments.}, }
@article {pmid37938745, year = {2022}, author = {Kujawska, M and Raulo, A and Millar, M and Warren, F and Baltrūnaitė, L and Knowles, SCL and Hall, LJ}, title = {Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {20}, pmid = {37938745}, issn = {2730-6151}, support = {100/974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10353//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/J004529/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/M011216/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; NE/L011867/1//NERC Environmental Bioinformatics Centre (NEBC)/ ; }, abstract = {Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.}, }
@article {pmid37934408, year = {2023}, author = {Martinez-Varela, A and Casas, G and Berrojalbiz, N and Lundin, D and Piña, B and Dachs, J and Vila-Costa, M}, title = {Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37934408}, issn = {1614-7499}, support = {CTM2015-70535-P//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CTM2015-65691-R//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2018-000794-S//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2017SGR800//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h[-1]. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.}, }
@article {pmid37931146, year = {2023}, author = {Kosterlitz, O and Grassi, N and Werner, B and McGee, RS and Top, EM and Kerr, B}, title = {Evolutionary "crowdsourcing": alignment of fitness landscapes allows for cross-species adaptation of a horizontally transferred gene.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad237}, pmid = {37931146}, issn = {1537-1719}, abstract = {Genes that undergo horizontal gene transfer (HGT) evolve in different genomic backgrounds. Despite the ubiquity of cross-species HGT, the effects of switching hosts on gene evolution remains understudied. Here, we present a framework to examine the evolutionary consequences of host switching and apply this framework to an antibiotic resistance gene commonly found on conjugative plasmids. Specifically, we determined the adaptive landscape of this gene for a small set of mutationally connected genotypes in three enteric species. We uncovered that the landscape topographies were largely aligned with minimal host-dependent mutational effects. By simulating gene evolution over the experimentally gauged landscapes, we found that the adaptive evolution of the mobile gene in one species translated to adaptation in another. By simulating gene evolution over artificial landscapes, we found that sufficient alignment between landscapes ensures such "adaptive equivalency" across species. Thus, given adequate landscape alignment within a bacterial community, vehicles of HGT such as plasmids may enable a distributed form of genetic evolution across community members, where species can 'crowdsource' adaptation.}, }
@article {pmid37930866, year = {2023}, author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, T and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC}, title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad964}, pmid = {37930866}, issn = {1362-4962}, support = {//U.S. Department of Energy/ ; //Joint Genome Institute/ ; DE-AC02-05CH11231//DOE Office of Science User Facilities/ ; 17-SC-20-SC//Exascale Computing Project/ ; //U.S. Department of Energy Office of Science/ ; //National Nuclear Security Administration/ ; MR/W02666X/1//MRC Career Development Award/ ; //Office of Science of the US Department of Science/ ; }, abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.}, }
@article {pmid37928655, year = {2023}, author = {Wang, Z and Zhang, N and Li, C and Shao, L}, title = {Diversity of antibiotic resistance genes in soils with four different fertilization treatments.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291599}, pmid = {37928655}, issn = {1664-302X}, abstract = {Although the enrichment of resistance genes in soil has been explored in recent years, there are still some key questions to be addressed regarding the variation of ARG composition in soil with different fertilization treatments, such as the core ARGs in soil after different fertilization treatments, the correlation between ARGs and bacterial taxa, etc. For soils after different fertilization treatments, the distribution and combination of ARG in three typical fertilization methods (organic fertilizer alone, chemical fertilizer alone, and conventional fertilizer) and non-fertilized soils were investigated in this study using high-throughput fluorescence quantitative PCR (HT-qPCR) technique. The application of organic fertilizers significantly increased the abundance and quantity of ARGs and their subtypes in the soil compared to the non-fertilized soil, where sul1 was the ARGs specific to organic fertilizers alone and in higher abundance. The conventional fertilizer application also showed significant enrichment of ARGs, which indicated that manure addition often had a more decisive effect on ARGs in soil than chemical fertilizers, and three bacteria, Pseudonocardia, Irregularibacter, and Castllaniella, were the key bacteria affecting ARG changes in soil after fertilization. In addition, nutrient factors and heavy metals also affect the distribution of ARGs in soil and are positively correlated. This paper reveals the possible reasons for the increase in the number of total soil ARGs and their relative abundance under different fertilization treatments, which has positive implications for controlling the transmission of ARGs through the soil-human pathway.}, }
@article {pmid37923145, year = {2023}, author = {Geoffroy, F and Uecker, H}, title = {Limits to evolutionary rescue by conjugative plasmids.}, journal = {Theoretical population biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tpb.2023.10.001}, pmid = {37923145}, issn = {1096-0325}, abstract = {Plasmids may carry genes coding for beneficial traits and thus contribute to adaptation of bacterial populations to environmental stress. Conjugative plasmids can horizontally transfer between cells, which a priori facilitates the spread of adaptive alleles. However, if the potential recipient cell is already colonized by another incompatible plasmid, successful transfer may be prevented. Competition between plasmids can thus limit horizontal transfer. Previous modeling has indeed shown that evolutionary rescue by a conjugative plasmid is hampered by incompatible resident plasmids in the population. If the rescue plasmid is a mutant variant of the resident plasmid, both plasmids transfer at the same rates. A high conjugation rate then has two, potentially opposing, effects - a direct positive effect on spread of the rescue plasmid and an increase in the fraction of resident plasmid cells. This raises the question whether a high conjugation rate always benefits evolutionary rescue. In this article, we systematically analyse three models of increasing complexity to disentangle the benefits and limits of increasing horizontal gene transfer in the presence of plasmid competition and plasmid costs. We find that the net effect can be positive or negative and that the optimal transfer rate is thus not always the highest one. These results can contribute to our understanding of the many facets of plasmid-driven adaptation and the wide range of transfer rates observed in nature.}, }
@article {pmid37923139, year = {2023}, author = {Arriaza, RH and Abiskaroon, B and Patel, M and Daneshian, L and Kluza, A and Snoeck, S and Watkins, MB and Hopkins, J and Van Leeuwen, T and Grbic, M and Grbic, V and Borowski, T and Chruszcz, M}, title = {Structural and functional studies reveal the molecular basis of substrate promiscuity of a glycosyltransferase originating from a major agricultural pest.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {105421}, doi = {10.1016/j.jbc.2023.105421}, pmid = {37923139}, issn = {1083-351X}, abstract = {The two-spotted spider mite, Tetranychus urticae, is a major cosmopolitan pest that feeds on more than 1,100 plant species. Its genome contains an unprecedentedly large number of genes involved in detoxifying and transporting xenobiotics, including 80 genes that code for uridine diphosphate (UDP) glycosyltransferases (UGTs). These enzymes were acquired via horizontal gene transfer (HGT) from bacteria after loss in the Chelicerata lineage. UGTs are well-known for their role in phase II metabolism, however, their contribution to host adaptation and acaricide resistance in arthropods, such as T. urticae, is not yet resolved. TuUGT202A2 (Tetur22g00270) has been linked to the ability of this pest to adapt to tomato plants. Moreover, it was shown that this enzyme can glycosylate a wide range of flavonoids. To understand this relationship at the molecular level, structural, functional, and computational studies were performed. Structural studies provided specific snapshots of the enzyme in different catalytically relevant stages. The crystal structure of TuUGT202A2 in complex with UDP-glucose was obtained and site directed-mutagenesis paired with molecular dynamic simulations revealed a novel lid-like mechanism involved in the binding of the activated sugar donor. Two additional TuUGT202A2 crystal complexes, UDP-(S)-naringenin and UDP-naringin, demonstrated that this enzyme has a highly plastic and open-ended acceptor binding site. Overall, this work reveals the molecular basis of substrate promiscuity of TuUGT202A2 and provides novel insights into the structural mechanism of UGTs catalysis.}, }
@article {pmid37924893, year = {2023}, author = {Stevenson, EM and Buckling, A and Cole, M and Lindeque, PK and Murray, AK}, title = {Selection for antimicrobial resistance in the plastisphere.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168234}, doi = {10.1016/j.scitotenv.2023.168234}, pmid = {37924893}, issn = {1879-1026}, abstract = {Microplastics and antimicrobials are widespread contaminants that threaten global systems and frequently co-exist in the presence of human or animal pathogens. Whilst the impact of each of these contaminants has been studied in isolation, the influence of this co-occurrence in driving antimicrobial resistance (AMR)[1] in microplastic-adhered microbial communities, known as 'the Plastisphere', is not well understood. This review proposes the mechanisms by which interactions between antimicrobials and microplastics may drive selection for AMR in the Plastisphere. These include: 1) increased rates of horizontal gene transfer in the Plastisphere compared with free-living counterparts and natural substrate controls due to the proximity of cells, co-occurrence of environmental microplastics with AMR selective compounds and the sequestering of extracellular antibiotic resistance genes in the biofilm matrix. 2) An elevated AMR selection pressure in the Plastisphere due to the adsorbing of AMR selective or co-selective compounds to microplastics at concentrations greater than those found in surrounding mediums and potentially those adsorbed to comparator particles. 3) AMR selection pressure may be further elevated in the Plastisphere due to the incorporation of antimicrobial or AMR co-selective chemicals in the plastic matrix during manufacture. Implications for both ecological functioning and environmental risk assessments are discussed, alongside recommendations for further research.}, }
@article {pmid37917352, year = {2023}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis.}, journal = {Archives of microbiology}, volume = {205}, number = {12}, pages = {366}, pmid = {37917352}, issn = {1432-072X}, support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; }, abstract = {The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.}, }
@article {pmid37909761, year = {2023}, author = {Xedzro, C and Shimamoto, T and Yu, L and Zuo, H and Sugawara, Y and Sugai, M and Shimamoto, T}, title = {Emergence of colistin-resistant Enterobacter cloacae and Raoultella ornithinolytica carrying the phosphoethanolamine transferase gene, mcr-9, derived from vegetables in Japan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0106323}, doi = {10.1128/spectrum.01063-23}, pmid = {37909761}, issn = {2165-0497}, abstract = {Colistin, a last-line antimicrobial agent, is recommended for the treatment of severe infections caused by multidrug-resistant (MDR) microorganisms. However, reports on plasmid-mediated mobilized colistin resistance (mcr) genes have prompted the importance of routine colistin resistance surveillance. Herein, we report the emergence of Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1 carrying an mcr-9.1 gene in vegetables from Japan. A total of 308 colistin-resistant isolates were retrieved from 200 fresh vegetables in Hiroshima Prefecture, Japan. PCR detection of mcr-1 to mcr-9 was conducted. While none of the isolates detected positive for mcr-1 to mcr-8 genes, we found two (0.65%) positive strains, E. cloacae CST17-2 and R. ornithinolytica CST129-1, that harbored mcr-9.1 allele. These isolates were subjected to phenotypic susceptibility testing, whole-genome sequencing (WGS), PCR-based replicon typing, and conjugation experiment. We found that both isolates had high colistin resistance [minimum inhibitory concentration (MIC) 16 or >64 µg/mL] and showed MDR phenotypes. WGS of both isolates revealed mcr-9 on a plasmid of the IncHI2/HI2A backbone. The mcr-9-bearing plasmid, pCST17-2_1, was self-transferable, although the pCST129-1_1 plasmid was not. Despite being colistin-resistant, the so-called two-component regulatory operon, qseBC, which induces polymyxin resistance, was absent from the genetic arrangements downstream of mcr-9 in R. ornithinolytica CST129-1. Nonetheless, a conjugation experiment demonstrated that mcr-9 in a Raoultella-type background is capable of mediating colistin resistance. In silico genomic analysis and comparison revealed distinct genetic structures surrounding mcr-9, especially in the downstream vicinities. The E. cloacae CST17-2 strain is of sequence-type ST738, a sequence type that has emerged in mcr-9.1-containing E. cloacae. Remarkably, we report the first mcr-9-carrying colistin-resistant Enterobacteriaceae isolated from Japanese vegetables, which is a grave public health concern. Our findings highlight the importance of strict epidemiological monitoring to track and/or prevent further dissemination of mcr homologs across the vegetable industry.IMPORTANCEPlasmid-mediated mobile colistin-resistance genes have been recognized as a global threat because they jeopardize the efficacy of colistin in therapeutic practice. Here, we described the genetic features of two mcr-9.1-carrying Gram-negative bacteria with a colistin-resistant phenotype derived from vegetables in Japan. The colistin-resistant mcr-9.1, which has never been detected in vegetables, was located on a large plasmid in Enterobacter cloacae CST17-2 and Raoultella ornithinolytica CST129-1, suggesting a high chance of horizontal gene transfer. To the best of our knowledge, this is the first report of mcr-9 in R. ornithinolytica. This study indicates that fresh vegetables might be a potential source for the transmission of mcr-9 genes encoding resistance to frontline (colistin) and clinically relevant antimicrobials. The study also provides additional consideration for colistin use and the relevance of routine surveillance in epidemiological perspective to curb the continuous spread of mcr alleles.}, }
@article {pmid37909043, year = {2023}, author = {Subramanian, S and Bergland Drarvik, SM and Tinney, KR and Parent, KN}, title = {Cryo-EM structure of a Shigella podophage reveals a hybrid tail and novel decoration proteins.}, journal = {Structure (London, England : 1993)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.str.2023.10.007}, pmid = {37909043}, issn = {1878-4186}, abstract = {There is a paucity of high-resolution structures of phages infecting Shigella, a human pathogen and a serious threat to global health. HRP29 is a Shigella podophage belonging to the Autographivirinae family, and has very low sequence identity to other known phages. Here, we resolved the structure of the entire HRP29 virion by cryo-EM. Phage HRP29 has a highly unusual tail that is a fusion of a T7-like tail tube and P22-like tailspikes mediated by interactions from a novel tailspike adaptor protein. Understanding phage tail structures is critical as they mediate hosts interactions. Furthermore, we show that the HRP29 capsid is stabilized by two novel, and essential decoration proteins, gp47 and gp48. Only one high resolution structure is currently available for Shigella podophages. The presence of a hybrid tail and an adapter protein suggests that it may be a product of horizontal gene transfer, and may be prevalent in other phages.}, }
@article {pmid37907163, year = {2023}, author = {Su, X and Qian, F and Bao, Y}, title = {The effect of bulk-biochar and nano-biochar amendment on the removal of antibiotic resistance genes in microplastic contaminated soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117488}, doi = {10.1016/j.envres.2023.117488}, pmid = {37907163}, issn = {1096-0953}, abstract = {Biochar amendment has significant benefits in removing antibiotic resistance genes (ARGs) in the soil. Nevertheless, there is little information on ARGs removal in microplastic contaminated soil. Herein, a 42-day soil microcosm experiment were carried out to study how two coconut shell biochars (bulk- and nano-size) eliminate soil ARGs with/without microplastic presence. The results showed that microplastic increased significantly the numbers and abundances of ARGs in soil at 14d of cultivation. And, two biochars amendment effectively inhibited soil ARGs spread whether or not microplastic was present, especially for nano-biochar which had more effective removal compared to bulk-biochar. However, microplastic weakened soil ARGs removal after applying same biochar. Two biochars removed ARGs through decreasing horizontal gene transfer (HGT) of ARGs, potential host-bacteria abundances, some bacteria crowding the eco-niche of hosts and promoting soil properties. The adverse effect of microplastic on ARGs removal was mainly caused by weakening mobile genetic elements (MGEs) removal, and by changing soil properties. Structural equation modeling (SEM) analysis indicated that biochar's effect on ARGs profile was changed by its size and microplastic presence through altering MGEs abundances. These results highlight that biochar amendment is still an effective method for ARGs removal in microplastic contaminated soil.}, }
@article {pmid37902330, year = {2023}, author = {Benigno, V and Carraro, N and Sarton-Lohéac, G and Romano-Bertrand, S and Blanc, DS and van der Meer, JR}, title = {Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0051723}, doi = {10.1128/msphere.00517-23}, pmid = {37902330}, issn = {2379-5042}, abstract = {Integrative and conjugative elements (ICEs) are widespread autonomous mobile DNA elements, containing the genes necessary for their excision, conjugative transfer, and insertion into a new host cell. ICEs can carry additional genes that are non-essential for their transfer but can confer adaptive phenotypes to the host. Our aim here was to better characterize the presence, distribution, and variation of ICEs related to the well-described ICEclc among Pseudomonas aeruginosa clinical isolates within a geographically restrained environment to understand the factors contributing to their evolution. We examined a total of 181 P. aeruginosa genome sequences obtained from patient or hospital environment isolates, most of which were obtained from a single hospital during 20 years of sampling. More than 90% of the isolates carried one or more ICEclc-like elements, with different degrees of conservation to the known ICEclc lifestyle and transfer genes. ICE clones closely matched their host clonal phylogeny, but not exclusively, indicating that both clonal evolution and ICE horizontal transfer are occurring in the hospital environment. ICEs from this singular hospital environment were mainly associated to three clone types found worldwide, suggesting an enrichment of local clones. Variable gene regions among the clinical P. aeruginosa ICEclc-type elements were notably enriched for heavy metal resistance genes, toxin-anti-toxin systems, potential efflux systems and multidrug resistance proteins, a metalloprotease and for a variety of regulatory systems, but not for specific recognizable antibiotic-resistance cassettes. Clonal persistence suggests adaptive benefits of these functional categories, and micro-patterns of gene gain and loss indicate ongoing ICE evolution within the P. aeruginosa hosts. IMPORTANCE Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.}, }
@article {pmid37901845, year = {2023}, author = {Li, L and Zhang, H and Meng, D and Yin, H}, title = {Transcriptomics of Lactobacillus paracasei: metabolism patterns and cellular responses under high-density culture conditions.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1274020}, pmid = {37901845}, issn = {2296-4185}, abstract = {Lactobacillus paracasei has significant potential for development and application in the environmental field, particularly in addressing malodor pollution. This study aims to investigate the cellular response of L. paracasei B1 under high-density culture conditions. The selected strain has previously shown effective deodorizing and bacteriostatic abilities. Transcriptomics techniques are employed to dissect the nutrient metabolism pattern of L. paracasei B1 and its response mechanism under environmental stress. The study characterizes the functions of key differentially expressed genes during growth before and after optimizing the culture conditions. The optimization of fermentation culture conditions provides a suitable growth environment for L. paracasei B1, inducing an enhancement of its phosphotransferase system for sugar source uptake and maintaining high levels of glycolysis and pyruvate metabolism. Consequently, the strain is able to grow and multiply rapidly. Under acid stress conditions, glycolysis and pyruvate metabolism are inhibited, and L. paracasei B1 generates additional energy through aerobic respiration to meet the energy demand. The two-component system and quorum sensing play roles in the response and regulation of L. paracasei B1 to adverse environments. The strain mitigates oxygen stress damage through glutathione metabolism, cysteine and methionine metabolism, base excision repair, and purine and pyrimidine metabolism. Additionally, the strain enhances lysine synthesis, the alanine, aspartate, and glutamate metabolic pathways, and relies on the ABC transport system to accumulate amino acid-compatible solutes to counteract acid stress and osmotic stress during pH regulation. These findings establish a theoretical basis for the further development and application of L. paracasei B1 for its productive properties.}, }
@article {pmid37900760, year = {2023}, author = {Yan, XM and Zhou, SS and Liu, H and Zhao, SW and Tian, XC and Shi, TL and Bao, YT and Li, ZC and Jia, KH and Nie, S and Guo, JF and Kong, L and Porth, IM and Mao, JF}, title = {Unraveling the evolutionary dynamics of the TPS gene family in land plants.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1273648}, pmid = {37900760}, issn = {1664-462X}, abstract = {Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.}, }
@article {pmid37898203, year = {2023}, author = {Jian, J and Wu, Z and Silva-Núñez, A and Li, X and Zheng, X and Luo, B and Liu, Y and Fang, X and Workman, CT and Larsen, TO and Hansen, PJ and Sonnenschein, EC}, title = {Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168042}, doi = {10.1016/j.scitotenv.2023.168042}, pmid = {37898203}, issn = {1879-1026}, abstract = {Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.}, }
@article {pmid37873201, year = {2023}, author = {Attah, V and Milner, DS and Fang, Y and Yan, X and Leonard, G and Heitman, J and Talbot, NJ and Richards, TA}, title = {Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37873201}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; }, abstract = {UNLABELLED: Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic.<br><br>SIGNIFICANCE STATEMENT: The oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.}, }
@article {pmid37894729, year = {2023}, author = {Bravo, A and Moreno-Blanco, A and Espinosa, M}, title = {One Earth: The Equilibrium between the Human and the Bacterial Worlds.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894729}, issn = {1422-0067}, support = {PID2019-104553RB-C21//Spanish Ministry of Science and Innovation (MCIN/AEI/10.13039/501100011033)/ ; }, abstract = {Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.}, }
@article {pmid37894082, year = {2023}, author = {Anton, BP and Roberts, RJ}, title = {A Survey of Archaeal Restriction-Modification Systems.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/microorganisms11102424}, pmid = {37894082}, issn = {2076-2607}, abstract = {When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m[6]A and m[4]C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m[5]C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m[6]A, m[4]C, and m[5]C DNA MTases, respectively, occur in approximately the ratio 4:2:1.}, }
@article {pmid37888586, year = {2023}, author = {Ortega-Balleza, JL and Guerrero, A and Castro-Escarpulli, G and Martínez-Vázquez, AV and Cruz-Hernández, MA and Luna-Santillana, EJ and Acosta-Cruz, E and Rodríguez-Sánchez, IP and Rivera, G and Bocanegra-García, V}, title = {Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico.}, journal = {Tropical medicine and infectious disease}, volume = {8}, number = {10}, pages = {}, pmid = {37888586}, issn = {2414-6366}, abstract = {The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.}, }
@article {pmid37887056, year = {2023}, author = {Sandmann, G}, title = {Genes and Pathway Reactions Related to Carotenoid Biosynthesis in Purple Bacteria.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, doi = {10.3390/biology12101346}, pmid = {37887056}, issn = {2079-7737}, abstract = {In purple bacteria, the genes of the carotenoid pathways are part of photosynthesis gene clusters which were distributed among different species by horizontal gene transfer. Their close organisation facilitated the first-time cloning of carotenogenic genes and promoted the molecular investigation of spheroidene and spirilloxanthin biosynthesis. This review highlights the cloning of the spheroidene and spirilloxanthin pathway genes and presents the current knowledge on the enzymes involved in the carotenoid biosynthesis of purple sulphur and non-sulphur bacteria. Mostly, spheroidene or spirilloxanthin biosynthesis exists in purple non-sulphur bacteria but both pathways operate simultaneously in Rubrivivax gelatinosus. In the following years, genes from other bacteria including purple sulphur bacteria with an okenone pathway were cloned. The individual steps were investigated by kinetic studies with heterologously expressed pathway genes which supported the establishment of the reaction mechanisms. In particular, the substrate and product specificities revealed the sequential order of the speroidene and spiriloxanthin pathways as well as their interactions. Information on the enzymes involved revealed that the phytoene desaturase determines the type of pathway by the formation of different products. By selection of mutants with amino acid exchanges in the putative substrate-binding site, the neurosporene-forming phytoene desaturase could be changed into a lycopene-producing enzyme and vice versa. Concerning the oxygen groups in neurosporene and lycopene, the tertiary alcohol group at C1 is formed from water and not by oxygenation, and the C2 or C4 keto groups are inserted differently by an oxygen-dependent or oxygen-independent ketolation reaction, respectively.}, }
@article {pmid37886666, year = {2023}, author = {Arbé-Carton, K and Rey-Sogo, A and Santos-Fernández, N and Altube, O and Garbisu, C and Arana, L and Alkorta, I}, title = {Development of a high-throughput platform to measure plasmid transfer frequency.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269732}, pmid = {37886666}, issn = {2235-2988}, abstract = {Antibiotic resistance represents one of the greatest threats to global health. The spread of antibiotic resistance genes among bacteria occurs mostly through horizontal gene transfer via conjugation mediated by plasmids. This process implies a direct contact between a donor and a recipient bacterium which acquires the antibiotic resistance genes encoded by the plasmid and, concomitantly, the capacity to transfer the acquired plasmid to a new recipient. Classical assays for the measurement of plasmid transfer frequency (i.e., conjugation frequency) are often characterized by a high variability and, hence, they require many biological and technical replicates to reduce such variability and the accompanying uncertainty. In addition, classical conjugation assays are commonly tedious and time-consuming because they typically involve counting colonies on a large number of plates for the quantification of donors, recipients, and transconjugants (i.e., the bacteria that have received the genetic material by conjugation). Due to the magnitude of the antibiotic resistance problem, it is critical to develop reliable and rapid methods for the quantification of plasmid transfer frequency that allow the simultaneous analysis of many samples. Here, we present the development of a high-throughput, reliable, quick, easy, and cost-effective method to simultaneously accomplish and measure multiple conjugation events in 96-well plates, in which the quantification of donors, recipients, and transconjugants is estimated from the time required to reach a specific threshold value (OD600 value) in the bacterial growth curves. Our method successfully discriminates different plasmid transfer frequencies, yielding results that are equivalent to those obtained by a classical conjugation assay.}, }
@article {pmid37884245, year = {2023}, author = {Zhang, Z and Li, B and Chai, Z and Yang, Z and Zhang, F and Kang, F and Ren, H and Jin, Y and Yue, J}, title = {Evolution of the ability to evade host innate immune defense by Talaromyces marneffei.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {127597}, doi = {10.1016/j.ijbiomac.2023.127597}, pmid = {37884245}, issn = {1879-0003}, abstract = {Talaromyces (Penicillium) marneffei is an intracellular pathogenic fungus. Some strains of this fungus have been misidentified due to the similarity between Talaromyces and Penicillium. T. marneffei has mainly been found to afflict immunocompromised individuals, causing respiratory, skin, and systemic mycosis. Mp1p is a key virulence factor that can help T. marneffei evade clearance by the normally functioning immune system. Understanding how novel functions arise is an intriguing question in many fields of biology. Mp1p has two homologous domains (Mp1p-LBD1 and Mp1p-LBD2). Sequence similarity searches with Mp1p-LBD sequences revealed Mp1p homologs in many other pathogenic fungi. Integrated information on the taxonomic distribution, phylogenetic relationships, and sequence similarity of Mp1p domains revealed that the ancestor of Mp1p-LBDs was acquired through horizontal gene transfer (HGT). Additional evidence revealed that Mp1p homologs have undergone extensive gene duplications in T. marneffei. Mp1p might be a result of gene fusion following gene duplication. Furthermore, we propose a new method for identifying Talaromyces and identify 4 strains with misclassification errors. Our results characterize the evolutionary mechanism of T. marneffei evasion of host innate immune defense and clearly demonstrate the role of gene duplication and HGT in the evolution of host immune escape by T. marneffei.}, }
@article {pmid37883987, year = {2023}, author = {Parthasarathy, R and Wakefield, D and Santiago, FS and Kaakoush, NO and Tedla, N}, title = {Horizontal gene transfer and endogenous retroviruses as mechanisms for molecular mimicry.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00316-6}, pmid = {37883987}, issn = {2666-5247}, }
@article {pmid37882558, year = {2023}, author = {Marti, H and Biggel, M and Shima, K and Onorini, D and Rupp, J and Charette, SJ and Borel, N}, title = {Chlamydia suis displays high transformation capacity with complete cloning vector integration into the chromosomal rrn-nqrF plasticity zone.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0237823}, doi = {10.1128/spectrum.02378-23}, pmid = {37882558}, issn = {2165-0497}, abstract = {Chlamydia, comprising several human and zoonotic pathogens, is a genus of the conserved bacterial phylum Chlamydiota. Their obligate intracellular niche serves as a barrier for natural genetic exchange via horizontal gene transfer (HGT), and further limits the development and application of genetic tools. To date, the only example for recent inter-phylum HGT among the Chlamydiota is tetracycline resistance in the potentially zoonotic species Chlamydia suis, a close phylogenetic relative of human C. trachomatis, which causes bacterial sexually transmitted infections and ocular trachoma. Tetracycline resistance in porcine C. suis strains has been described worldwide and is always part of a genomic island dividing invasin (inv), located within a chromosomal region between the rRNA operon (rrn) and the nqrF reductase. Here, we aimed to expand the still modest number of available genetic manipulation systems for Chlamydia by generating allele-replacement and integration vectors for C. suis. These vectors comprised homologous C. suis sequences of the chromosomal region of interest, an E. coli origin of replication (ori) and selection markers but lacked the native chlamydial plasmids or its ori. We first recovered allele-replacement mutants using a vector that targets the tryptophan (trp) operon of C. suis. The vector was further successfully maintained as a free plasmid in C. trachomatis without allele replacement, suggesting complex plasmid dynamics in the absence of a chlamydial ori. Moreover, we showed that the hypervariable rrn-nqrF intergenic region of C. suis is highly susceptible to transformation, resulting in complete vector integration upstream of nqrF without interruption of the targeted inv gene.IMPORTANCEThe obligate intracellular Chlamydia genus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation of Chlamydia with the opportunistic porcine pathogen Chlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer. C. suis is transmissible to humans, posing a potential public health concern. We report that C. suis can take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show that C. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed with C. suis vectors. Finally, the chromosomal region that harbors the resistance gene of C. suis is highly susceptible to complete vector integration.}, }
@article {pmid37880110, year = {2023}, author = {Tanaka, E and Wajima, T and Ota, R and Uchiya, KI}, title = {The association between transformation ability and antimicrobial resistant potential in Haemophilus influenzae.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1248/bpb.b23-00583}, pmid = {37880110}, issn = {1347-5215}, abstract = {The prevalence of quinolone low-susceptible H. influenzae has increased in Japan. Low quinolone susceptibility is caused by point mutations in target genes; however, it can also be caused by horizontal gene transfer via natural transformation. In this study, we examined whether this horizontal gene transfer could be associated with resistance to not only quinolones but also other antimicrobial agents. Horizontal transfer ability was quantified using the experimental transfer assay method for low quinolone susceptibility. Further, the association between horizontal transfer ability and resistance to β-lactams, the first-choice drugs for H. influenzae infection, was investigated. The transformation efficiency of 50 clinical isolates varied widely, ranging from 10[2] to 10[6] CFU of the colonies obtained by horizontal transfer assay. Efficiency was associated with β-lactam resistance caused by ftsI mutations, indicating that strains with high horizontal transfer ability acquired quinolone low-susceptibility as well as β-lactam resistance more easily. Strains with high transformation efficiency increased the transcript level of comA, suggesting that enhanced com operon was associated with a high DNA uptake ability. Overall, this study revealed that the transformation ability of H. influenzae was associated with multiple antimicrobial resistance. Increase in the number of strains with high horizontal transformation ability has raised concerns regarding the rapid spread of antimicrobial-resistant H. influenzae.}, }
@article {pmid37796811, year = {2023}, author = {Teixeira, M and Pillay, S and Urhan, A and Abeel, T}, title = {SHIP: identifying antimicrobial resistance gene transfer between plasmids.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {10}, pages = {}, pmid = {37796811}, issn = {1367-4811}, support = {120192//National Research Foundation of South Africa/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; Plasmids/genetics ; Escherichia coli/genetics ; Integrons/genetics ; Gene Transfer, Horizontal ; }, abstract = {MOTIVATION: Plasmids are carriers for antimicrobial resistance (AMR) genes and can exchange genetic material with other structures, contributing to the spread of AMR. There is no reliable approach to identify the transfer of AMR genes across plasmids. This is mainly due to the absence of a method to assess the phylogenetic distance of plasmids, as they show large DNA sequence variability. Identifying and quantifying such transfer can provide novel insight into the role of small mobile elements and resistant plasmid regions in the spread of AMR.<br><br>RESULTS: We developed SHIP, a novel method to quantify plasmid similarity based on the dynamics of plasmid evolution. This allowed us to find conserved fragments containing AMR genes in structurally different and phylogenetically distant plasmids, which is evidence for lateral transfer. Our results show that regions carrying AMR genes are highly mobilizable between plasmids through transposons, integrons, and recombination events, and contribute to the spread of AMR. Identified transferred fragments include a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae, and a region encoding tetracycline resistance transferred through recombination in Enterococcus faecalis.<br><br>The code developed in this work is available at https://github.com/AbeelLab/plasmidHGT.}, }
@article {pmid37875161, year = {2023}, author = {Ribes-Navarro, A and Kabeya, N and Castro, LFC and Gomes-Dos-Santos, A and Fonseca, MM and Alberts-Hubatsch, H and Hontoria, F and Navarro, JC and Monroig, &#xd3;}, title = {Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species.}, journal = {Open biology}, volume = {13}, number = {10}, pages = {230196}, doi = {10.1098/rsob.230196}, pmid = {37875161}, issn = {2046-2441}, abstract = {Previous data revealed the unexpected presence of genes encoding for long-chain polyunsaturated fatty acid (LC-PUFA) biosynthetic enzymes in transcriptomes from freshwater gammarids but not in marine species, even though closely related species were compared. This study aimed to clarify the origin and occurrence of selected LC-PUFA biosynthesis gene markers across all published gammarid transcriptomes. Through systematic searches, we confirmed the widespread occurrence of sequences from seven elongases and desaturases involved in LC-PUFA biosynthesis, in transcriptomes from freshwater gammarids but not marine species, and clarified that such occurrence is independent from the gammarid species and geographical origin. The phylogenetic analysis established that the retrieved elongase and desaturase sequences were closely related to bdelloid rotifers, confirming that multiple transcriptomes from freshwater gammarids contain contaminating rotifers' genetic material. Using the Adineta steineri genome, we investigated the genomic location and exon-intron organization of the elongase and desaturase genes, establishing they are all genome-anchored and, importantly, identifying instances of horizontal gene transfer. Finally, we provide compelling evidence demonstrating Bdelloidea desaturases and elongases enable these organisms to perform all the reactions for de novo biosynthesis of PUFA and, from them, LC-PUFA, an advantageous trait when considering the low abundance of these essential nutrients in freshwater environments.}, }
@article {pmid37875024, year = {2023}, author = {Wang, X and Qin, J and Xiang, G and Wang, C and Wang, Q and Qin, J and Wang, H and Shen, Z}, title = {Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkad326}, pmid = {37875024}, issn = {1460-2091}, support = {82272374//National Natural Science Foundation of China/ ; 22PJ1409600//Shanghai Pujiang Program/ ; RJTJ22-MS-018//Renji Hospital/ ; }, abstract = {OBJECTIVES: To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4.<br><br>METHODS: IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids.<br><br>RESULTS: We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n&#x200a;=&#x200a;3) and IMP-26 (n&#x200a;=&#x200a;2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n&#x200a;=&#x200a;9), IncHI5 (n&#x200a;=&#x200a;5), IncFII(K) (n&#x200a;=&#x200a;1) and IncFII(pKP91) (n&#x200a;=&#x200a;1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host.<br><br>CONCLUSIONS: The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.}, }
@article {pmid37873187, year = {2023}, author = {Hamrick, GS and Maddamsetti, R and Son, HI and Wilson, ML and Davis, HM and You, L}, title = {Programming dynamic division of labor using horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.10.03.560696}, pmid = {37873187}, abstract = {The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.}, }
@article {pmid37871361, year = {2023}, author = {Moussa, J and Nassour, E and Tahan, E and El Chaar, M and Jisr, T and Tokajian, S}, title = {Carbapenem resistance determinants and their transmissibility among clinically isolated Enterobacterales in Lebanon.}, journal = {Journal of infection and public health}, volume = {16}, number = {12}, pages = {1947-1953}, doi = {10.1016/j.jiph.2023.10.003}, pmid = {37871361}, issn = {1876-035X}, abstract = {BACKGROUND: The occurrence of carbapenem-resistant bacterial infections has increased significantly over the years with Gram-negative bacteria exhibiting the broadest resistance range. In this study we aimed to investigate the genomic characteristics of clinical carbapenem-resistant Enterobacterales (CRE).<br><br>METHODS: Seventeen representative multi-drug resistant (MDR) isolates from a hospital setting showing high level of resistance to carbapenems (ertapenem, meropenem and imipenem) were chosen for further characterization through whole-genome sequencing. Resistance mechanisms and transferability of plasmids carrying carbapenemase-encoding genes were also determined in silico and through conjugative mating assays.<br><br>RESULTS: We detected 18 different &#x3b2;-lactamases, including four carbapenemases (blaNDM-1, blaNDM-5, blaNDM-7, blaOXA-48) on plasmids with different Inc groups. The combined results from PBRT and in silico replicon typing revealed 20 different replicons linked to plasmids ranging in size between 80 and 200&#xa0;kb. The most prevalent Inc groups were IncFIB(K) and IncM. OXA-48, detected on 76-kb IncM1 conjugable plasmid, was the most common carbapenemase. We also detected other conjugative plasmids with different carbapenemases confirming the role of horizontal gene transfer in the dissemination of antimicrobial resistance genes.<br><br>CONCLUSION: Our findings verified the continuing spread of carbapenemases in Enterobacterales and revealed the types of mobile elements circulating in a hospital setting and contributing to the spread of resistance determinants. The occurrence and transmission of plasmids carrying carbapenemase-encoding genes call for strengthening active surveillance and prevention efforts to control antimicrobial resistance dissemination in healthcare settings.}, }
@article {pmid37870180, year = {2023}, author = {Zhang, Q and Xu, N and Lei, C and Chen, B and Wang, T and Ma, Y and Lu, T and Penuelas, J and Gillings, M and Zhu, YG and Fu, Z and Qian, H}, title = {Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2303925}, doi = {10.1002/advs.202303925}, pmid = {37870180}, issn = {2198-3844}, support = {2022YFD1700400//National Key Research and Development Program of China/ ; 21976161//National Natural Science Foundation of China/ ; 22376187//National Natural Science Foundation of China/ ; 42307158//National Natural Science Foundation of China/ ; LZ23B070001//Natural Science Foundation of Zhejiang Province/ ; TED2021-132627B-I00//Department of Local Government, Sport and cultural industries/ ; }, abstract = {The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.}, }
@article {pmid37865329, year = {2023}, author = {Ye, C and Chen, C and Zhang, K and Feng, M and Yu, X}, title = {Solar/periodate inhibits ARGs transformation by degradation of DNA without damaging cell membrane.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122766}, doi = {10.1016/j.envpol.2023.122766}, pmid = {37865329}, issn = {1873-6424}, abstract = {Antibiotic-resistant bacterial infections are a growing global threat to public health. Chlorine-based water disinfection and some advanced oxidation processes significantly increase the risk of ARGs release and transmission in the aquatic environment. Therefore, it is critical to develop or optimize disinfection methods to reduce the conversion and transmission of ARGs in natural water. This study investigated whether the solar/periodate (PI) system inhibited the natural transmission of ARGs and its mechanism. The results showed that solar/PI systems could effectively inhibit the propagation of ARGs in two simulated natural transformation systems, up to more than 100 times. By characterizing the cellular process of bacteria treated by the solar/PI system, we found that the solar/PI system could directly cause damage to DNA bases and its dual effect with almost no damage to the bacterial cell membrane, which was the main reason why this technology could inhibit natural transformation processes. Specifically, the inhibition effect of solar/PI on bacteria did not result in enhanced membrane permeability under appropriate PI dosage (<200 μM), which greatly reduced the risk of secondary contamination of eARGs released by traditional disinfection. Our findings could help improve existing disinfection strategies to ensure that antibiotic resistance is not spread in the natural water environment.}, }
@article {pmid37856455, year = {2023}, author = {Aubin, E and Llauro, C and Garrigue, J and Mirouze, M and Panaud, O and El Baidouri, M}, title = {Genome-wide analysis of horizontal transfer in non-model wild species from a natural ecosystem reveals new insights into genetic exchange in plants.}, journal = {PLoS genetics}, volume = {19}, number = {10}, pages = {e1010964}, pmid = {37856455}, issn = {1553-7404}, mesh = {*Ecosystem ; Pilot Projects ; *Genome, Plant/genetics ; Genomics ; Retroelements ; Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; }, abstract = {Horizontal transfer (HT) refers to the exchange of genetic material between divergent species by mechanisms other than reproduction. In recent years, several studies have demonstrated HTs in eukaryotes, particularly in the context of parasitic relationships and in model species. However, very little is known about HT in natural ecosystems, especially those involving non-parasitic wild species, and the nature of the ecological relationships that promote these HTs. In this work, we conducted a pilot study investigating HTs by sequencing the genomes of 17 wild non-model species from a natural ecosystem, the Massane forest, located in southern France. To this end, we developed a new computational pipeline called INTERCHANGE that is able to characterize HTs at the whole genome level without prior annotation and directly in the raw sequencing reads. Using this pipeline, we identified 12 HT events, half of which occurred between lianas and trees. We found that mainly low copy number LTR-retrotransposons from the Copia superfamily were transferred between these wild plant species, especially those of the Ivana and Ale lineages. This study revealed a possible new route for HTs between non-parasitic plants and provides new insights into the genomic characteristics of horizontally transferred DNA in plant genomes.}, }
@article {pmid37864197, year = {2023}, author = {Abante, J and Wang, PL and Salzman, J}, title = {DIVE: a reference-free statistical approach to diversity-generating and mobile genetic element discovery.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {240}, pmid = {37864197}, issn = {1474-760X}, support = {R35 GM139517/GM/NIGMS NIH HHS/United States ; }, abstract = {Diversity-generating and mobile genetic elements are key to microbial and viral evolution and can result in evolutionary leaps. State-of-the-art algorithms to detect these elements have limitations. Here, we introduce DIVE, a new reference-free approach to overcome these limitations using information contained in sequencing reads alone. We show that DIVE has improved detection power compared to existing reference-based methods using simulations and real data. We use DIVE to rediscover and characterize the activity of known and novel elements and generate new biological hypotheses about the mobilome. Building on DIVE, we develop a reference-free framework capable of de novo discovery of mobile genetic elements.}, }
@article {pmid37863223, year = {2023}, author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M}, title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167832}, doi = {10.1016/j.scitotenv.2023.167832}, pmid = {37863223}, issn = {1879-1026}, abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.}, }
@article {pmid37863060, year = {2023}, author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T}, title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2023.09.052}, pmid = {37863060}, issn = {1879-0445}, abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.}, }
@article {pmid37858689, year = {2023}, author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S}, title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117444}, doi = {10.1016/j.envres.2023.117444}, pmid = {37858689}, issn = {1096-0953}, abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.}, }
@article {pmid37856515, year = {2023}, author = {Johansson, MHK and Aarestrup, FM and Petersen, TN}, title = {Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0293169}, pmid = {37856515}, issn = {1932-6203}, abstract = {We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.}, }
@article {pmid37855620, year = {2023}, author = {Jia, C and Wang, Z and Huang, C and Teng, L and Zhou, H and An, H and Liao, S and Liu, Y and Huang, L and Tang, B and Yue, M}, title = {Mobilome-driven partitions of the resistome in Salmonella.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0088323}, doi = {10.1128/msystems.00883-23}, pmid = {37855620}, issn = {2379-5077}, abstract = {Mobile genetic elements (MGEs) or mobilomes promote the mobilization and dissemination of antimicrobial resistance genes (ARGs), serving as critical drivers for antimicrobial resistance (AMR) accumulation, interaction, and persistence. However, systematic and quantitative evaluations of the role of mobilome in spreading resistome in a bacterial pathogen remain unaddressed, partially due to the lack of closed genomes. Here, we examined MGEs across 1,817 Salmonella isolates with complete genomic sequences from 58 countries between 1911 and 2022. We found the plasmid harboring 69.8% ARGs to be the largest ARG reservoir, correlated with serovar-based evolution in most Salmonella lineages. Prophages, specifically RCS47 and SJ46, play a crucial role in the plasmids' plasticity and the acquisition of ARGs. Furthermore, distinct ARG accumulation, including resistance toward last-resort antibiotics, exhibited an MGE-favored manner. Certain socioeconomic and ecological factors, as additional layers of mediators, are associated with the preferential distribution of MGE-mediated ARGs in Salmonella. Collectively, this study demonstrated an uncharted knowledge of the segmentation of Salmonella resistome driven by mobilome, elucidating dynamic drivers and distinct mediators for resistome development that are of immediate relevance for targeted interventions. IMPORTANCE Antimicrobial resistance (AMR) has become a significant global challenge, with an estimated 10 million deaths annually by 2050. The emergence of AMR is mainly attributed to mobile genetic elements (MGEs or mobilomes), which accelerate wide dissemination among pathogens. The interaction between mobilomes and AMR genes (or resistomes) in Salmonella, a primary cause of diarrheal diseases that results in over 90 million cases annually, remains poorly understood. The available fragmented or incomplete genomes remain a significant limitation in investigating the relationship between AMR and MGEs. Here, we collected the most extensive closed Salmonella genomes (n = 1,817) from various sources across 58 countries. Notably, our results demonstrate that resistome transmission between Salmonella lineages follows a specific pattern of MGEs and is influenced by external drivers, including certain socioeconomic factors. Therefore, targeted interventions are urgently needed to mitigate the catastrophic consequences of Salmonella AMR.}, }
@article {pmid37855599, year = {2023}, author = {Feng, Z and Wang, L and Guan, Q and Chu, X and Luo, Z-Q}, title = {Acinetobacter baumannii coordinates central metabolism, plasmid dissemination, and virulence by sensing nutrient availability.}, journal = {mBio}, volume = {}, number = {}, pages = {e0227623}, doi = {10.1128/mbio.02276-23}, pmid = {37855599}, issn = {2150-7511}, abstract = {Plasmid conjugation plays an important role in the dissemination of antibiotic-resistance genes. The emergence of multidrug-resistant isolates of Acinetobacter baumannii poses grave challenges in treating infections caused by this notorious nosocomial pathogen. Yet, the composition, functionality, and regulation of conjugative machinery utilized by A. baumannii remain poorly understood. Here, we found that conjugation of the major plasmid pAB3 of A. baumannii is mediated by a type IVB secretion system similar to the Dot/Icm transporter of Legionella pneumophila. Furthermore, the expression of the structural genes of the Dot/Icm-like system is co-regulated with genes involved in central metabolism by the GacS/GacA two-component system in response to various metabolites, including intermediates of the tricarboxylic acid cycle. Loss of GacS/A also severely impaired bacterial virulence. These results establish that A. baumannii coordinates metabolism with plasmid conjugation and virulence by sensing nutrient availability, which may be exploited to develop inhibitory agents for controlling the spread of drug-resistance genes and virulence factors. IMPORTANCE Plasmid conjugation is known to be an energy-expensive process, but our understanding of the molecular linkage between conjugation and metabolism is limited. Our finding reveals that Acinetobacter baumannii utilizes a two-component system to co-regulate metabolism, plasmid transfer, and virulence by sensing reaction intermediates of key metabolic pathways, which suggests that nutrient availability dictates not only bacterial proliferation but also horizontal gene transfer. The identification of Dot/Icm-like proteins as components of a conjugation system involved in the dissemination of antibiotic-resistance genes by A. baumannii has provided important targets for the development of agents capable of inhibiting virulence and the spread of anti-microbial-resistance genes in bacterial communities.}, }
@article {pmid37850911, year = {2023}, author = {Yee, W-X and Elsener, T and Cehovin, A and Maiden, MCJ and Tang, CM}, title = {Evolution and exchange of plasmids in pathogenic Neisseria.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0044123}, doi = {10.1128/msphere.00441-23}, pmid = {37850911}, issn = {2379-5042}, abstract = {Neisseria gonorrhoeae causes sexually transmitted infection (STI) gonorrhoea and is on the WHO critical list due to increasing antimicrobial resistance (AMR). The bacterium can carry a conjugative plasmid, pConj, which prevents the use of tetracycline or doxycycline for treating gonorrhea, and is responsible for spread of a β-lactamase plasmid, pbla; over 90% of gonococcal isolates also harbor a small cryptic plasmid, pCryp. We systematically analyzed the presence of these plasmids in other Neisseria spp., including Neisseria meningitidis, which causes sepsis/meningitis. pConj is the most frequently found plasmid in the meningococcus and is in many clonal complexes. The plasmid is associated with meningococcal carriage rather than disease, indicating that pConj imposes fitness costs during systemic disease. Phylogenetic analyses reveal that pConj is genetically diverse in N. meningitidis, indicating that it shares a long evolutionary history with the meningococcus and that the plasmid has been transferred at least twice from N. meningitidis to N. gonorrhoeae. Following the first transfer, gonococcal isolates carrying the plasmid underwent clonal expansion and disseminated pConj to other gonococcal lineages. The second introduction was associated with an altered conjugation machinery which reduces conjugation efficiency. Therefore, in contrast to chromosomal resistance which has evolved through introduction of genes from commensals, gonococcal plasmid-mediated resistance has arisen through transfer from another pathogen, N. meningitidis. Further antibiotic pressure from the use of doxycycline for post-exposure prophylaxis against STIs is likely to promote plasmid-mediated AMR in both N. gonorrhoeae and N. meningitidis. IMPORTANCE Horizontal gene transfer (HGT) is a major influence in driving the spread of antimicrobial resistance (AMR) in many bacteria. A conjugative plasmid which is widespread in Neisseria gonorrhoeae, pConj, prevented the use of tetracycline/doxycycline for treating gonococcal infection. Here, we show that pConj evolved in the related pathogen, Neisseria meningitidis, and has been acquired by the gonococcus from the meningococcus on multiple occasions. Following its initial acquisition, pConj spread to different gonococcal lineages; changes in the plasmid's conjugation machinery associated with another transfer event limit spread in the gonococcal populations. Our findings have important implications for the use of doxycycline to prevent bacterial sexually transmitted disease which is likely to exacerbate the spread of AMR through HGT in pathogenic bacteria.}, }
@article {pmid37850800, year = {2023}, author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J}, title = {Orientia tsutsugamushi: comprehensive analysis of the mobilome of a highly fragmented and repetitive genome reveals the capacity for ongoing lateral gene transfer in an obligate intracellular bacterium.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0026823}, doi = {10.1128/msphere.00268-23}, pmid = {37850800}, issn = {2379-5042}, abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ~2.3-Mb genome is composed of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 93 copies, most of which are partially or heavily degraded. In this report, we analyzed RAGEs in eight fully sequenced Ot genomes and manually curated and re-annotated all RAGE-associated genes, including those encoding DNA mobilization proteins, P-type (vir), and F-type (tra) type IV secretion system (T4SS) components, ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs have led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harboring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs may play an ongoing role in lateral gene transfer within the Rickettsiales. We also identified a conserved set of gene transfer agent genes in all Ot genomes. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents, and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and virus-like elements. IMPORTANCE Obligate intracellular bacteria, or those only capable of growth inside other living cells, have limited opportunities for horizontal gene transfer with other microbes due to their isolated replicative niche. The human pathogen Ot, an obligate intracellular bacterium causing scrub typhus, encodes an unusually high copy number of a ~40 gene mobile genetic element that typically facilitates genetic transfer across microbes. This proliferated element is heavily degraded in Ot and previously assumed to be inactive. Here, we conducted a detailed analysis of this element in eight Ot strains and discovered two strains with at least one intact copy. This implies that the element is still capable of moving across Ot populations and suggests that the genome of this bacterium may be even more dynamic than previously appreciated. Our work raises questions about intracellular microbial evolution and sounds an alarm for gene-based efforts focused on diagnosing and combatting scrub typhus.}, }
@article {pmid37849012, year = {2023}, author = {Wei, Y and Gong, Z and Han, GZ}, title = {Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land.}, journal = {Mobile DNA}, volume = {14}, number = {1}, pages = {15}, pmid = {37849012}, issn = {1759-8753}, support = {31922001//National Natural Science Foundation of China/ ; }, abstract = {Mitochondrial linear plasmids have been sporadically reported in fungi and plants. Yet, much remains obscure about the diversity, distribution, and evolution of mitochondrial linear plasmids. Here, through phylogenomic analyses across 7,163 cellular organisms (including 991 plants), we find that mitochondrial linear plasmids are widely present in land plants and fungi. Phylogenetic analyses indicate that plants are likely to have acquired mitochondrial linear plasmids horizontally from fungi before or during the conquest of terrestrial environments by plants. Gene content analyses show that mitochondrial linear plasmids harbor a highly dynamic and promiscuous repertoire of genes. Our study refines the understanding of the origin and evolution of mitochondrial linear plasmids.}, }
@article {pmid37848554, year = {2023}, author = {Lücking, D and Mercier, C and Alarcón-Schumacher, T and Erdmann, S}, title = {Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {112}, pmid = {37848554}, issn = {2730-6151}, support = {Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; }, abstract = {Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.}, }
@article {pmid37845226, year = {2023}, author = {Gonzalez-Serrano, R and Rosselli, R and Roda-Garcia, JJ and Martin-Cuadrado, AB and Rodriguez-Valera, F and Dunne, M}, title = {Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6517}, pmid = {37845226}, issn = {2041-1723}, support = {PROMETEO/2019/009//Generalitat Valenciana (Regional Government of Valencia)/ ; ACIF/2016/050//Regional Government of Valencia | Conselleria de Sanitat Universal i Salut P&#xfa;blica (Conselleria de Sanitat Universal i Salut P&#xfa;blica de la Generalitat Valenciana)/ ; CRSII5_189957//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.}, }
@article {pmid37843655, year = {2023}, author = {Sudhakari, PA and Ramisetty, BCM}, title = {An Eco-evolutionary Model on Surviving Lysogeny Through Grounding and Accumulation of Prophages.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37843655}, issn = {1432-184X}, abstract = {Temperate phages integrate into the bacterial genomes propagating along with the bacterial genomes. Multiple phage elements, representing diverse prophages, are present in most bacterial genomes. The evolutionary events and the ecological dynamics underlying the accumulation of prophage elements in bacterial genomes have yet to be understood. Here, we show that the local wastewater had 7% of lysogens (hosting mitomycin C-inducible prophages), and they showed resistance to superinfection by their corresponding lysates. Genomic analysis of four lysogens and four non-lysogens revealed the presence of multiple prophages (belonging to Myoviridae and Siphoviridae) in both lysogens and non-lysogens. For large-scale comparison, 2180 Escherichia coli genomes isolated from various sources across the globe and 523 genomes specifically isolated from diverse wastewaters were analyzed. A total of 15,279 prophages were predicted among 2180 E. coli genomes and 2802 prophages among 523 global wastewater isolates, with a mean of ~ 5 prophages per genome. These observations indicate that most putative prophages are relics of past bacteria-phage conflicts; they are "grounded" prophages that cannot excise from the bacterial genome. Prophage distribution analysis based on the sequence homology suggested the random distribution of E. coli prophages within and between E. coli clades. The independent occurrence pattern of these prophages indicates extensive horizontal transfers across the genomes. We modeled the eco-evolutionary dynamics to reconstruct the events that could have resulted in the prophage accumulation accounting for infection, superinfection immunity, and grounding. In bacteria-phage conflicts, the bacteria win by grounding the prophage, which could confer superinfection immunity.}, }
@article {pmid37842006, year = {2023}, author = {López-Pérez, J and Otero, J and Sánchez-Osuna, M and Erill, I and Cortés, P and Llagostera, M}, title = {Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1266685}, pmid = {37842006}, issn = {2235-2988}, abstract = {INTRODUCTION: The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT).<br><br>METHODS: S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them.<br><br>RESULTS AND DISCUSSION: In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4&#xb0;C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.}, }
@article {pmid37841331, year = {2023}, author = {Asif, M and Li-Qun, Z and Zeng, Q and Atiq, M and Ahmad, K and Tariq, A and Al-Ansari, N and Blom, J and Fenske, L and Alodaini, HA and Hatamleh, AA}, title = {Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4647-4662}, pmid = {37841331}, issn = {2001-0370}, abstract = {Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.}, }
@article {pmid37840734, year = {2023}, author = {Li, Y and Fan, Y and Ma, X and Wang, Y and Liu, J}, title = {Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267152}, pmid = {37840734}, issn = {1664-302X}, abstract = {Sialic acids comprise a varied group of nine-carbon amino sugars found mostly in humans and other higher metazoans, playing major roles in cell interactions with external environments as well as other cells. Microbial sialic acid catabolism (SAC) has long been considered a virulence determinant, and appears to be mainly the purview of pathogenic and commensal bacterial species associated with eukaryotic hosts. Here, we used 2,521 (pre-)assembled metagenomes to evaluate the distribution of SAC in microbial communities from diverse ecosystems and human body parts. Our results demonstrated that microorganisms possessing SAC globally existed in non-host associated environments, although much less frequently than in mammal hosts. We also showed that the ecological significance and taxonomic diversity of microbial SAC have so far been largely underestimated. Phylogenetic analysis revealed a strong signal of horizontal gene transfer among distinct taxa and habitats, and also suggested a specific ecological pressure and a relatively independent evolution history in environmental communities. Our study expanded the known diversity of microbial SAC, and has provided the backbone for further studies on its ecological roles and potential pathogenesis.}, }
@article {pmid37838320, year = {2023}, author = {Wang, L and Hu, T and Li, Y and Zhao, Z and Zhu, M}, title = {Unraveling the interplay between antibiotic resistance genes and microbial communities in water and sediments of the intensive tidal flat aquaculture.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122734}, doi = {10.1016/j.envpol.2023.122734}, pmid = {37838320}, issn = {1873-6424}, abstract = {Tidal flats are formed valuably resources by the interaction of terrestrial and marine processes. Aquaculture on tidal flats has brought significant economic profits, but the over usage of antibiotics has resulted in the prevalence antibiotic resistance genes (ARGs) which pose serious threats to ecosystems. However, ARG abundances and bacterial community assemblies in the overlying water and sediments of tidal flat aquaculture areas have not been fully explored. Thus, antibiotic concentrations, ARG abundances, microbial communities and the influences of environmental factors in the Jiangsu tidal flat aquaculture ponds were investigated using high-throughput sequencing and qPCR. The concentrations of antibiotics at sampling ranged from not detectable to 2322.4 ng g[-1], and sulfamethazine and ciprofloxacin were the dominant antibiotics. The sul1 and sul2 abundances were highest and the ARG abundances were higher in sediment than in water. Meanwhile, bacterial community diversities and structures were significantly different (P < 0.05) between water and sediment samples. Network analysis identified Sphingomonadacear, Pseudomonas, and Xanthobacteraceae as potential ARG-carrying pathogens. A positive correlation between ARGs and intI1 indicated that horizontal gene transfer occurred in water, while antibiotics and TN significantly influenced ARG abundances in sediment. Neutral modeling showed that deterministic and stochastic processes contributed most to the bacterial community assemblies of water and sediment samples, respectively. This study comprehensively illustrates the prevalence of ARGs in intensive tidal flat aquaculture regions and provides an effective foundation for the management of antibiotics usage.}, }
@article {pmid37833945, year = {2023}, author = {Kuznetsova, MV and Pospelova, JS and Maslennikova, IL and Starčič Erjavec, M}, title = {Dual-Species Biofilms: Biomass, Viable Cell Ratio/Cross-Species Interactions, Conjugative Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {19}, pages = {}, doi = {10.3390/ijms241914497}, pmid = {37833945}, issn = {1422-0067}, support = {No. 19-44-590014 r_a.//Goverment of Perm Krai/ ; AAAA-A19-119112290009-1//Russian Foundation for Basic Research/ ; }, abstract = {Biofilms as a form of adaptation are beneficial for bacterial survival and may be hot spots for horizontal gene transfer, including conjugation. The aim of this research was to characterize the biofilm biomass, viable cell ratios and conjugative transfer of the pOX38 plasmid, an F-plasmid derivative, from the Escherichia coli N4i pOX38 strain (donor) into a uropathogenic E. coli DL82 strain (recipient) within dual-species biofilms with one of the following opportunistic pathogenic bacteria: Klebsiella pneumoniae, Enterococcus faecalis or Pseudomonas aeruginosa. Dual-species biofilms of E. coli with K. pneumoniae or P. aeruginosa but not E. faecalis were more massive and possessed more exopolysaccharide matrix compared to single-species biofilms of donor and recipient cells. Correlation between biofilm biomass and exopolysaccharide matrix was rs = 0.888 in dual-species biofilms. In dual-species biofilm with E. faecalis the proportion of E. coli was the highest, while in the biofilm with P. aeruginosa and K. pneumoniae, the E. coli was less abundant. The conjugative frequencies of plasmid transfer in dual-species biofilms of E. coli with E. faecalis and P. aeruginosa were reduced. A decrease in conjugative frequency was also observed when cell-free supernatants (CFSs) of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Further, the activity of the autoinducer AI-2 in the CFSs of the E. coli conjugation mixture was reduced when bacteria or CFSs of E. faecalis and P. aeruginosa were added to the E. coli conjugation mixture. Hence, the intercellular and interspecies interactions in dual-species biofilms depend on the partners involved.}, }
@article {pmid37832249, year = {2023}, author = {Wang, C and Yang, H and Liu, H and Zhang, XX and Ma, L}, title = {Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking.}, journal = {Water research}, volume = {246}, number = {}, pages = {120682}, doi = {10.1016/j.watres.2023.120682}, pmid = {37832249}, issn = {1879-2448}, abstract = {Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10[-4] to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.}, }
@article {pmid37832298, year = {2023}, author = {Chu, K and Liu, Y and Hua, Z and Lu, Y and Ye, F}, title = {Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119232}, doi = {10.1016/j.jenvman.2023.119232}, pmid = {37832298}, issn = {1095-8630}, abstract = {The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.}, }
@article {pmid37831481, year = {2023}, author = {Morgene, F and Rizoug Zeghlache, C and Feng, SY and Hauck, Y and Mirouze, N}, title = {Natural transformation and cell division delay in competent Staphylococcus aureus.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0280723}, doi = {10.1128/spectrum.02807-23}, pmid = {37831481}, issn = {2165-0497}, abstract = {Genetic competence for natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote evolution, through genomic plasticity, and foster antibiotic resistance and virulence factors spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. In this study, we investigate the transformation apparatus composition, localization, and dynamics in the human pathogen Staphylococcus aureus. We particularly show that most of the natural transformation actors co-localize in clusters. We also reveal that the localization of natural transformation proteins is dynamic, following the cell cycle. Ultimately, the natural transformation apparatus is preferentially established in the vicinity of the division septum. All these results demonstrate that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. Finally, we hypothesize that S. aureus competent cells would initiate and then block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring. IMPORTANCE Natural transformation, considered one of the three main mechanisms leading to horizontal gene transfer in bacteria, is able to promote genomic plasticity and foster antibiotic resistance spreading. Conserved machinery and actors required to perform natural transformation have been shown to accumulate at different cellular localizations depending on the model organism considered. Here, we show in the human pathogen Staphylococcus aureus that DNA binding, uptake, and recombination are spatially and temporally coordinated to ensure S. aureus natural transformation. We also reveal that localization of natural transformation proteins occurs in the vicinity of the division septum allowing S. aureus competent cells to block cell division to ensure the success of natural transformation before the final constriction of the cytokinetic ring.}, }
@article {pmid37828802, year = {2023}, author = {Zhao, J and Feng, T and An, X and Chen, X and Han, N and Wang, J and Chang, G and Hou, X}, title = {Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12778}, pmid = {37828802}, issn = {1749-4877}, support = {2019QZKK0501//Second Tibetan Plateau Scientific Expedition&#xa0;and Research Program (STEP)/ ; 32172436//National Natural Science Foundation of&#xa0;China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy&#xa0;of Science/ ; }, abstract = {With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.}, }
@article {pmid37676703, year = {2023}, author = {Avontuur, JR and Wilken, PM and Palmer, M and Coetzee, MPA and Stępkowski, T and Venter, SN and Steenkamp, ET}, title = {Complex evolutionary history of photosynthesis in Bradyrhizobium.}, journal = {Microbial genomics}, volume = {9}, number = {9}, pages = {}, pmid = {37676703}, issn = {2057-5858}, mesh = {*Bradyrhizobium/genetics ; Photosynthesis/genetics ; }, abstract = {Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae. We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.}, }
@article {pmid37820728, year = {2023}, author = {Weiss, A and Wang, T and You, L}, title = {Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities.}, journal = {Cell systems}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cels.2023.09.002}, pmid = {37820728}, issn = {2405-4720}, abstract = {Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.}, }
@article {pmid37819078, year = {2023}, author = {Svet, L and Parijs, I and Isphording, S and Lories, B and Marchal, K and Steenackers, HP}, title = {Competitive interactions facilitate resistance development against antimicrobials.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0115523}, doi = {10.1128/aem.01155-23}, pmid = {37819078}, issn = {1098-5336}, abstract = {While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates Pseudomonas rhodesiae and Raoultella terrigena influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of P. rhodesiae. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in P. rhodesiae. Whereas P. rhodesiae was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of R. terrigena was thus required for P. rhodesiae to acquire resistance, the resistance mechanisms did not depend on the presence of R. terrigena. Whole genome sequencing of resistant P. rhodesiae clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance. IMPORTANCE Antimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.}, }
@article {pmid37814055, year = {2023}, author = {Wang, Y and Gai, J and Hou, Q and Zhao, H and Shan, C and Guo, Z}, title = {Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {39}, number = {12}, pages = {337}, pmid = {37814055}, issn = {1573-0972}, support = {2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2020kypytd009//Hubei university of arts and science cultivation fund for teachers' scientific research ability: technological innovation team/ ; }, abstract = {Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.}, }
@article {pmid37808307, year = {2023}, author = {Sharma, A and Singh, RN and Song, XP and Singh, RK and Guo, DJ and Singh, P and Verma, KK and Li, YR}, title = {Genome analysis of a halophilic Virgibacillus halodenitrificans ASH15 revealed salt adaptation, plant growth promotion, and isoprenoid biosynthetic machinery.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1229955}, pmid = {37808307}, issn = {1664-302X}, abstract = {Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely "Squalene." Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.}, }
@article {pmid37806594, year = {2023}, author = {Li, N and Zheng, N and Pan, J and An, Q and Li, X and Sun, S and Chen, C and Zhu, H and Li, Z and Ji, Y}, title = {Distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167619}, doi = {10.1016/j.scitotenv.2023.167619}, pmid = {37806594}, issn = {1879-1026}, abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are both enriched in soil-vegetable systems as a consequence of the prolonged use of agricultural mulches. MPs can form unique bacterial communities and provide potential hosts for ARGs. Therefore, MPs stress may promote the spread of ARGs from soil to crops. Increasing ARGs pollution in soil-vegetable system. In our research, we investigated the distribution and major driving elements of antibiotic resistance genes in the soil-vegetable system under microplastic stress. The results showed that MPs treatment decreased the relative abundance of ARGs in non-rhizosphere soil. High concentrations of MPs promoted the enrichment of tetracycline antibiotic resistance genes in rhizosphere soil. MPs treatment promoted the enrichment of ARGs and mobile genetic elements (MGEs) in lettuce tissues, and the overall abundance of ARGs in root after 0.5 %, 1 %, and 2 % (w/w, dry weight) polyethylene (PE) administration was considerably higher compared to that in the untreated group (p < 0.05). At the same time, high PE concentrations promoted the spread of sulfa ARGs from root to leaf. MPs also impacted the bacterial communities in the soil-plant system, and the changes in ARGs as well as MGEs in each part of the soil-vegetable system were significantly correlated with the bacterial diversity index (p < 0.05). Correlation analysis and network analysis showed that bacterial communities and MGEs were the main drivers of ARGs variation in soil-lettuce systems.}, }
@article {pmid37805184, year = {2023}, author = {Roh, H and Kannimuthu, D}, title = {Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117273}, doi = {10.1016/j.envres.2023.117273}, pmid = {37805184}, issn = {1096-0953}, abstract = {The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.}, }
@article {pmid37804807, year = {2023}, author = {Xue, YM and Wang, YC and Lin, YT and Jiang, GY and Chen, R and Qin, RL and Jia, XQ and Wang, C}, title = {Engineering a Pseudomonas putida as living quorum quencher for biofilm formation inhibition, benzenes degradation, and environmental risk evaluation.}, journal = {Water research}, volume = {246}, number = {}, pages = {120690}, doi = {10.1016/j.watres.2023.120690}, pmid = {37804807}, issn = {1879-2448}, abstract = {Bacterial communication interruption based on quorum quenching (QQ) has been proven its potential in biofilm formation inhibition and biofouling control. However, it would be more satisfying if QQ could be combined with the efficient degradation of contaminants in environmental engineering. In this study, we engineered a biofilm of Pseudomonas putida through introducing a QQ synthetic gene, which achieved both biofilm formation inhibition and efficient degradation of benzene series in wastewater. The aiiO gene introduced into the P. putida by heat shock method was highly expressed to produce QQ enzyme to degrade AHL-based signal molecules. The addition of this engineered P. putida reduced the AHLs concentration, quorum sensing gene expression, and connections of the microbial community network in activated sludge and therefore inhibited the biofilm formation. Meanwhile, the sodium benzoate degradation assay indicated an enhanced benzene series removal ability of the engineering bacteria on activated sludge. Besides, we also demonstrated a controllable environmental risk of this engineered bacteria through monitoring its abundance and horizontal gene transfer test. Overall, the results of this study suggest an alternative strategy to solve multiple environmental problems through genetic engineering means and provide support for the application of engineered bacteria in environmental biotechnology.}, }
@article {pmid37804524, year = {2023}, author = {Wang, YZ and Ye, YX and Lu, JB and Wang, X and Lu, HB and Zhang, ZL and Ye, ZX and Lu, YW and Sun, ZT and Chen, JP and Li, JM and Zhang, CX and Huang, HJ}, title = {Horizontally transferred salivary protein promotes insect feeding by suppressing ferredoxin-mediated plant defenses.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad221}, pmid = {37804524}, issn = {1537-1719}, abstract = {Herbivorous insects such as whiteflies, planthoppers, and aphids secrete abundant orphan proteins to facilitate feeding. Yet, how these genes are recruited and evolve to mediate plant-insect interaction remains unknown. In this study, we report a horizontal gene transfer (HGT) event from fungi to an ancestor of Aleyrodidae insects approximately 42-190 million years ago. BtFTSP1 is a salivary protein that is secreted into host plants during Bemisia tabaci feeding. It targets a defensive ferredoxin 1 in Nicotiana tabacum (NtFD1) and disrupts the NtFD1-NtFD1 interaction in plant cytosol, leading to the degradation of NtFD1 in a ubiquitin-dependent manner. Silencing BtFTSP1 has negative effects on B. tabaci feeding, while overexpressing BtFTSP1 in N. tabacum benefits insects and rescues the adverse effect caused by NtFD1 overexpression. The association between BtFTSP1 and NtFD1 is newly evolved after HGT, with the homologous FTSP in its fungal donor failing to interact and destabilize NtFD1. Our study illustrates the important roles of horizontally transferred genes in plant-insect interactions and suggests the potential origin of orphan salivary genes.}, }
@article {pmid37803310, year = {2023}, author = {Kawabe, Y and Du, Q and Narita, TB and Bell, C and Schilde, C and Kin, K and Schaap, P}, title = {Emerging roles for diguanylate cyclase during the evolution of soma in dictyostelia.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {60}, pmid = {37803310}, issn = {2730-7182}, support = {BB/K000799/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/K000799/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid social amoebas acquired diguanylate cyclase (dgcA) by horizontal gene transfer. Dictyostelium discoideum (Ddis) in taxon group 4 uses c-di-GMP as a secreted signal to induce differentiation of stalk cells, the ancestral somatic cell type that supports the propagating spores. We here investigated how this role for c-di-GMP evolved in Dictyostelia by exploring dgcA function in the group 2 species Polysphondylium pallidum (Ppal) and in Polysphondylium violaceum (Pvio), which resides in a small sister clade to group 4.<br><br>RESULTS: Similar to Ddis, dgcA is upregulated after aggregation in Ppal and Pvio and predominantly expressed in the anterior region and stalks of emerging fruiting bodies. DgcA null mutants in Ppal and Pvio made fruiting bodies with very long and thin stalks and only few spores and showed delayed aggregation and larger aggregates, respectively. Ddis dgcA- cells cannot form stalks at all, but showed no aggregation defects. The long, thin stalks of Ppal and Pvio dgcA- mutants were also observed in acaA- mutants in these species. AcaA encodes adenylate cyclase A, which mediates the effects of c-di-GMP on stalk induction in Ddis. Other factors that promote stalk formation in Ddis are DIF-1, produced by the polyketide synthase StlB, low ammonia, facilitated by the ammonia transporter AmtC, and high oxygen, detected by the oxygen sensor PhyA (prolyl 4-hydroxylase). We deleted the single stlB, amtC and phyA genes in Pvio wild-type and dgcA- cells. Neither of these interventions affected stalk formation in Pvio wild-type and not or very mildly exacerbated the long thin stalk phenotype of Pvio dgcA- cells.<br><br>CONCLUSIONS: The study reveals a novel role for c-di-GMP in aggregation, while the reduced spore number in Pvio and Ppal dgcA- is likely an indirect effect, due to depletion of the cell pool by the extended stalk formation. The results indicate that in addition to c-di-GMP, Dictyostelia ancestrally used an as yet unknown factor for induction of stalk formation. The activation of AcaA by c-di-GMP is likely conserved throughout Dictyostelia.}, }
@article {pmid37801563, year = {2023}, author = {Liu, L and Zhang, QH and Li, RT}, title = {In Situ and Individual-Based Analysis of the Influence of Polystyrene Microplastics on Escherichia coli Conjugative Gene Transfer at the Single-Cell Level.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c05476}, pmid = {37801563}, issn = {1520-5851}, abstract = {The impact of microplastic particles of micro- and nanometer sizes on microbial horizontal gene transfer (HGT) remains a controversial topic. Existing studies rely on traditional approaches, which analyze population behavior, leading to conflicting conclusions and a limited understanding. The present study addressed these limitations by employing a novel microfluidic chamber system for in situ visualization and precise quantification of the effects of different concentrations of polystyrene (PS) microbeads on microbial HGT at the single-cell level. The statistical analysis indicated no significant difference in the division times of both the donor and recipient bacteria across different PS microbead concentrations. However, as the concentration of PS microbeads increased from 0 to 2000 mg L[-1], the average conjugation frequency of Escherichia coli decreased from 0.028 ± 0.015 to 0.004 ± 0.003. Our observations from the microfluidic experiments revealed that 500 nm PS microbeads created a barrier effect on bacterial conjugative transfer. The presence of microbeads resulted in reduced contact and interaction between the donor and recipient strains, thereby causing a decrease in the conjugation transfer frequency. These findings were validated by an individual-based modeling framework parameterized by the data from the individual-level microfluidic experiments. Overall, this study offers a fresh perspective and strategy for investigating the risks associated with the dissemination of antibiotic resistance genes related to microplastics.}, }
@article {pmid37797823, year = {2023}, author = {Lagune, M and Kremer, L and Herrmann, JL}, title = {Mycobacterium abscessus, a complex of three fast-growing subspecies sharing virulence traits with slow-growing mycobacteria.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2023.08.036}, pmid = {37797823}, issn = {1469-0691}, abstract = {BACKGROUND: Mycobacterium abscessus belongs to the largest group of mycobacteria, the rapid-growing saprophytic mycobacteria (RGM), and is one of the most difficult-to-treat opportunistic pathogen. Several features pertain to the high adaptability of M. abscessus to the host. These include the capacity to survive and persist within amoebae, to transition from a smooth to a rough morphotype that occurs during the course of the disease and to express of a wide array of virulence factors.<br><br>OBJECTIVES: The main objective of this narrative review consists to report major assets of M. abscessus that contribute to the virulence of this RGM. Strikingly, many of these determinants, whether they are from a mycobacterial origin or acquired by horizontal gene transfer, are known virulence factors found in slow-growing and strict pathogens for humans and animals.<br><br>SOURCES: In the light of recent published work in the field we attempted to highlight major features characterizing M. abscessus pathogenicity and to explain why this led to the emergence of this mycobacterial species in cystic fibrosis patients.<br><br>CONTENT: M. abscessus genome plasticity, the smooth-to-rough transition, and the expression of a panel of enzymes associated with virulence in other bacteria are key players in M. abscessus virulence. In addition, the very large repertoire of lipid transporters, known as MmpL and MmpS, deeply influences the pathogenicity of M. abscessus, as exemplified here for some of them.<br><br>IMPLICATIONS: All these traits largely contribute to make M. abscessus a unique mycobacterium regarding to its pathophysiological processes, ranging from the early colonization steps to the establishment of severe and chronic pulmonary diseases.}, }
@article {pmid37797771, year = {2023}, author = {Liu, Q and Li, Y and Sun, Y and Xie, K and Zeng, Q and Hao, Y and Yang, Q and Pu, Y and Shi, S and Gong, Z}, title = {Deterioration of sludge characteristics and promotion of antibiotic resistance genes spread with the co-existing of polyvinylchloride microplastics and tetracycline in the sequencing batch reactor.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167544}, doi = {10.1016/j.scitotenv.2023.167544}, pmid = {37797771}, issn = {1879-1026}, abstract = {With the continuous increase in microplastics (MPs) and tetracycline (TC) entering wastewater treatment plants (WWTPs) along with sewage, the co-existence of MPs and TC in the biological treatment of wastewater has attracted extensive attention. This study investigated the effect of 1 mg/L polyvinyl chloride (PVC) MPs and 100 ng/L TC co-existing on sequencing batch reactors (SBRs) (S2) treating phenol wastewater in contrast to the control with TC alone (S1). The phenol removal efficiency was significantly inhibited by the co-existence of PVC MPs and TC. Sludge characteristics were also distinctively influenced. The decreased zone sludge velocity (ZSV) and increased sludge volume index (SVI) indicated that the combined effect of PVC MPs and TC deteriorated sludge settleability, which had positive and negative linear correlations with extracellular polymeric substances (EPS) content and the protein (PN)/polysaccharide (PS) ratio, respectively. Moreover, the decreased and increased relative abundances of potential phenol-degraders and antibiotic resistance gene (ARG) carriers may elucidate the inhibition of phenol removal and promotion of ARGs propagation with the co-occurrence of PVC MPs and TC. In addition, the enhanced potential ARGs hosts, loss of the EPS protective effect, and increased membrane permeability induced by reactive oxygen species (ROS) jointly promoted ARGs dissemination in the co-existence of PVC MPs and TC. Notably, the co-occurrence of ARGs and mobile genetic element (MGEs) indicated that the co-existence of PVC MPs and TC promoted the spread of some transposase-associated ARGs mediated by horizontal gene transfer (HGT).}, }
@article {pmid37796250, year = {2023}, author = {Jung, H and Lee, D and Lee, S and Kong, HJ and Park, J and Seo, YS}, title = {Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.}, journal = {Microbial genomics}, volume = {9}, number = {10}, pages = {}, doi = {10.1099/mgen.0.001108}, pmid = {37796250}, issn = {2057-5858}, abstract = {Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.}, }
@article {pmid37793435, year = {2023}, author = {Raimondeau, P and Bianconi, ME and Pereira, L and Parisod, C and Christin, PA and Dunning, LT}, title = {Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19272}, pmid = {37793435}, issn = {1469-8137}, support = {NE/T011025/1//Natural Environment Research Council/ ; NE/V000012/1//Natural Environment Research Council/ ; URF/R/180022//Royal Society/ ; }, abstract = {Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.}, }
@article {pmid37792894, year = {2023}, author = {Pompei, S and Bella, E and Weitz, JS and Grilli, J and Lagomarsino, MC}, title = {Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer.}, journal = {PLoS computational biology}, volume = {19}, number = {10}, pages = {e1011532}, doi = {10.1371/journal.pcbi.1011532}, pmid = {37792894}, issn = {1553-7358}, abstract = {The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.}, }
@article {pmid37791787, year = {2023}, author = {Taton, A and Gilderman, TS and Ernst, DC and Omaga, CA and Cohen, LA and Rey-Bedon, C and Golden, JW and Golden, SS}, title = {Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids.}, journal = {mBio}, volume = {}, number = {}, pages = {e0184323}, doi = {10.1128/mbio.01843-23}, pmid = {37791787}, issn = {2150-7511}, abstract = {The cyanobacterium Synechococcus elongatus PCC 7942 produces an active prokaryotic Argonaute nuclease, SeAgo, whose function is unknown. Here, we show that SeAgo reduces natural transformation and prevents the maintenance of RSF1010 replicons in S. elongatus. In addition, a Cas4-like nuclease and two other proteins, UvrD and RecJcy (cyanobacterial lineage), were found to reduce the transfer or maintenance of RSF1010 replicons. Like other prokaryotic Argonautes, our results indicate that SeAgo provides defense against invading DNA. An S. elongatus ago deletion strain shares the same morphology, growth rate, and circadian gene expression as the wild type, has higher transformation efficiency, and enables the use of RSF1010-based plasmids for genetic engineering. IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.}, }
@article {pmid37788575, year = {2023}, author = {Coluzzi, C and Guillemet, M and Mazzamurro, F and Touchon, M and Godfroid, M and Achaz, G and Glaser, P and Rocha, EPC}, title = {Chance favors the prepared genomes: horizontal transfer shapes the emergence of antibiotic resistance mutations in core genes.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad217}, pmid = {37788575}, issn = {1537-1719}, abstract = {Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multi-drug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be key to the success of adaptation processes.}, }
@article {pmid37786731, year = {2023}, author = {Liao, J and Wei, X and Tao, K and Deng, G and Shu, J and Qiao, Q and Chen, G and Wei, Z and Fan, M and Saud, S and Fahad, S and Chen, S}, title = {Phenoloxidases: catechol oxidase - the temporary employer and laccase - the rising star of vascular plants.}, journal = {Horticulture research}, volume = {10}, number = {7}, pages = {uhad102}, pmid = {37786731}, issn = {2662-6810}, abstract = {Phenolics are vital for the adaptation of plants to terrestrial habitats and for species diversity. Phenoloxidases (catechol oxidases, COs, and laccases, LACs) are responsible for the oxidation and polymerization of phenolics. However, their origin, evolution, and differential roles during plant development and land colonization are unclear. We performed the phylogeny, domain, amino acids, compositional biases, and intron analyses to clarify the origin and evolution of COs and LACs, and analysed the structure, selective pressure, and chloroplast targeting to understand the species-dependent distribution of COs. We found that Streptophyta COs were not homologous to the Chlorophyta tyrosinases (TYRs), and might have been acquired by horizontal gene transfer from bacteria. COs expanded in bryophytes. Structural-functionality and selective pressure were partially responsible for the species-dependent retention of COs in embryophytes. LACs emerged in Zygnemaphyceae, having evolved from ascorbate oxidases (AAOs), and prevailed in the vascular plants and strongly expanded in seed plants. COs and LACs coevolved with the phenolic metabolism pathway genes. These results suggested that TYRs and AAOs were the first-stage phenoloxidases in Chlorophyta. COs might be the second key for the early land colonization. LACs were the third one (dominating in the vascular plants) and might be advantageous for diversified phenol substrates and the erect growth of plants. This work provided new insights into how phenoloxidases evolved and were devoted to plant evolution.}, }
@article {pmid37786723, year = {2023}, author = {Mukherjee, A and Kizziah, JL and Hawkins, NC and Nasef, MO and Parker, LK and Dokland, T}, title = {Structure of the portal complex from Staphylococcus aureus pathogenicity island 1 transducing particles in situ and in solution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.18.557803}, pmid = {37786723}, abstract = {Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high- resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a structural basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.}, }
@article {pmid37779688, year = {2023}, author = {González, D and Morales-Olavarria, M and Vidal-Veuthey, B and Cárdenas, JP}, title = {Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238580}, pmid = {37779688}, issn = {1664-302X}, abstract = {Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.}, }
@article {pmid37768051, year = {2023}, author = {Li, L and Liu, Z and Meng, D and Liu, Y and Liu, T and Jiang, C and Yin, H}, title = {Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0072023}, doi = {10.1128/msystems.00720-23}, pmid = {37768051}, issn = {2379-5077}, abstract = {Dissimilatory ferrous iron [Fe(II)] oxidation is a well-established microbial energy generation strategy. This study aims to comprehensively investigate the distribution and evolution of recognized Fe(II) oxidation pathways through comparative analysis. Interestingly, we have discovered a wide range of taxonomic groups that harbor homologs to known Fe(II) oxidation proteins. The presence of these homologs among phylogenetically distant lineages and their frequent association with mobile genetic elements strongly suggest horizontal gene transfer events involving Fe(II) oxidation proteins, such as the rus operon of Acidithiobacillus and Cyc572 from Leptospirillum lineages belonging to classes Gammaproteobacteria and Betaproteobacteria often present at the hub positions of the protein sequence similarity networks from which homologs of other taxa are derived. In addition, RoseTTAFold predictions have provided valuable insights into the structural characteristics of previously unknown Fe(II) oxidation components. Despite having limited sequence identity, a significant number of acknowledged proteins involved in different Fe(II) oxidation pathways exhibit close structural similarities, including Cyc2 and Cyc572. Collectively, this study significantly enhances our understanding of the distribution and evolution of microbial ferrous iron oxidation pathways. IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.}, }
@article {pmid37762674, year = {2023}, author = {Iasakov, T}, title = {Evolution End Classification of tfd Gene Clusters Mediating Bacterial Degradation of 2,4-Dichlorophenoxyacetic Acid (2,4-D).}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, doi = {10.3390/ijms241814370}, pmid = {37762674}, issn = {1422-0067}, support = {23-24-00480//Russian Science Foundation (RSF)/ ; }, abstract = {The tfd (tfdI and tfdII) are gene clusters originally discovered in plasmid pJP4 which are involved in the bacterial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) via the ortho-cleavage pathway of chlorinated catechols. They share this activity, with respect to substituted catechols, with clusters tcb and clc. Although great effort has been devoted over nearly forty years to exploring the structural diversity of these clusters, their evolution has been poorly resolved to date, and their classification is clearly obsolete. Employing comparative genomic and phylogenetic approaches has revealed that all tfd clusters can be classified as one of four different types. The following four-type classification and new nomenclature are proposed: tfdI, tfdII, tfdIII and tfdIV(A,B,C). Horizontal gene transfer between Burkholderiales and Sphingomonadales provides phenomenal linkage between tfdI, tfdII, tfdIII and tfdIV type clusters and their mosaic nature. It is hypothesized that the evolution of tfd gene clusters proceeded within first (tcb, clc and tfdI), second (tfdII and tfdIII) and third (tfdIV(A,B,C)) evolutionary lineages, in each of which, the genes were clustered in specific combinations. Their clustering is discussed through the prism of hot spots and driving forces of various models, theories, and hypotheses of cluster and operon formation. Two hypotheses about series of gene deletions and displacements are also proposed to explain the structural variations across members of clusters tfdII and tfdIII, respectively. Taking everything into account, these findings reconstruct the phylogeny of tfd clusters, have delineated their evolutionary trajectories, and allow the contribution of various evolutionary processes to be assessed.}, }
@article {pmid37760664, year = {2023}, author = {Xia, X}, title = {Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/antibiotics12091367}, pmid = {37760664}, issn = {2079-6382}, support = {RGPIN/2018-03878//Natural Sciences and Engineering Research Council/ ; }, abstract = {Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.}, }
@article {pmid37760663, year = {2023}, author = {Al-Sarawi, HA and Habibi, N and Uddin, S and Jha, AN and Al-Sarawi, MA and Lyons, BP}, title = {Antibiotic Resistance Mediated by Escherichia coli in Kuwait Marine Environment as Revealed through Genomic Analysis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/antibiotics12091366}, pmid = {37760663}, issn = {2079-6382}, abstract = {Antibiotic-resistance gene elements (ARGEs) such as antibiotic-resistance genes (ARGs), integrons, and plasmids are key to the spread of antimicrobial resistance (AMR) in marine environments. Kuwait's marine area is vulnerable to sewage contaminants introduced by numerous storm outlets and indiscriminate waste disposal near recreational beaches. Therefore, it has become a significant public health issue and warrants immediate investigation. Coliforms, especially Gram-negative Escherichia coli, have been regarded as significant indicators of recent fecal pollution and carriers of ARGEs. In this study, we applied a genome-based approach to identify ARGs' prevalence in E. coli isolated from mollusks and coastal water samples collected in a previous study. In addition, we investigated the plasmids and intl1 (class 1 integron) genes coupled with the ARGs, mediating their spread within the Kuwait marine area. Whole-genome sequencing (WGS) identified genes resistant to the drug classes of beta-lactams (blaCMY-150, blaCMY-42, blaCTX-M-15, blaDHA-1, blaMIR-1, blaOKP-B-15, blaOXA-1, blaOXA-48, blaTEM-1B, blaTEM-35), trimethoprim (dfrA14, dfrA15, dfrA16, dfrA1, dfrA5, dfrA7), fluroquinolone (oqxA, oqxB, qnrB38, qnrB4, qnrS1), aminoglycoside (aadA2, ant(3'')-Ia, aph(3'')-Ib, aph(3')-Ia, aph(6)-Id), fosfomycin (fosA7, fosA_6, fosA, fosB1), sulfonamide (sul1, sul2, sul3), tetracycline (tet-A, tet-B), and macrolide (mph-A). The MFS-type drug efflux gene mdf-A is also quite common in E. coli isolates (80%). The plasmid ColRNAI was also found to be prevalent in E. coli. The integron gene intI1 and gene cassettes (GC) were reported to be in 36% and 33%, respectively, of total E. coli isolates. A positive and significant (p < 0.001) correlation was observed between phenotypic AMR-intl1 (r = 0.311) and phenotypic AMR-GC (r = 0.188). These findings are useful for the surveillance of horizontal gene transfer of AMR in the marine environments of Kuwait.}, }
@article {pmid37759643, year = {2023}, author = {Li, J and Cullis, C}, title = {Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures.}, journal = {Biology}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/biology12091244}, pmid = {37759643}, issn = {2079-7737}, support = {No Grant Number//Department of Biology, Case Western Reserve University./ ; }, abstract = {Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.}, }
@article {pmid37759383, year = {2023}, author = {Hafez, M and Gourlie, R and McDonald, M and Telfer, M and Carmona, M and Sautua, F and Moffat, C and Moolhuijzen, P and See, PT and Aboukhaddour, R}, title = {Evolution of the ToxB gene in Pyrenophora tritici-repentis and related species.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-08-23-0114-FI}, pmid = {37759383}, issn = {0894-0282}, abstract = {Pyrenophora tritici-repentis is a destructive pathogen of wheat with global impact. It possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene, ToxB, across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Among ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a ~5.6 Kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in Ptr. Additionally, a microsatellite with 25-nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation. Exploring ToxB-like protein distribution in other Ascomycetes revealed their presence in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared to a phylogenetic tree, suggesting a past horizontal gene transfer event.}, }
@article {pmid37757562, year = {2023}, author = {Sharma, M and Singh, DN and Uttam, G and Sharma, P and Meena, SA and Verma, AK and Negi, RK}, title = {Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132545}, doi = {10.1016/j.jhazmat.2023.132545}, pmid = {37757562}, issn = {1873-3336}, abstract = {Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.}, }
@article {pmid37755994, year = {2023}, author = {Shikov, AE and Savina, IA and Nizhnikov, AA and Antonets, KS}, title = {Recombination in Bacterial Genomes: Evolutionary Trends.}, journal = {Toxins}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/toxins15090568}, pmid = {37755994}, issn = {2072-6651}, support = {075-15-2021-1055//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.}, }
@article {pmid37754275, year = {2023}, author = {Ma, J and Zhao, H and Mo, S and Li, J and Ma, X and Tang, Y and Li, H and Liu, Z}, title = {Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii.}, journal = {Microbial genomics}, volume = {9}, number = {9}, pages = {}, doi = {10.1099/mgen.0.001107}, pmid = {37754275}, issn = {2057-5858}, abstract = {Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.}, }
@article {pmid37752971, year = {2023}, author = {Tekle, YI and Tran, H and Wang, F and Singla, M and Udu, I}, title = {Omics of an Enigmatic Marine Amoeba Uncovers Unprecedented Gene Trafficking from Giant Viruses and Provides Insights into Its Complex Life Cycle.}, journal = {Microbiology research}, volume = {14}, number = {2}, pages = {656-672}, pmid = {37752971}, issn = {2036-7473}, abstract = {Amoebozoa include lineages of diverse ecology, behavior, and morphology. They are assumed to encompass members with the largest genome sizes of all living things, yet genomic studies in the group are limited. Trichosphaerium, a polymorphic, multinucleate, marine amoeba with a complicated life cycle, has puzzled experts for over a century. In an effort to explore the genomic diversity and investigate extraordinary behavior observed among the Amoebozoa, we used integrated omics approaches to study this enigmatic marine amoeba. Omics data, including single-cell transcriptomics and cytological data, demonstrate that Trichosphaerium sp. possesses the complete meiosis toolkit genes. These genes are expressed in life stages of the amoeba including medium and large cells. The life cycle of Trichosphaerium sp. involves asexual processes via binary fission and multiple fragmentation of giant cells, as well as sexual-like processes involving genes implicated in sexual reproduction and polyploidization. These findings are in stark contrast to a life cycle previously reported for this amoeba. Despite the extreme morphological plasticity observed in Trichosphaerium, our genomic data showed that populations maintain a species-level intragenomic variation. A draft genome of Trichosphaerium indicates elevated lateral gene transfer (LGT) from bacteria and giant viruses. Gene trafficking in Trichosphaerium is the highest within Amoebozoa and among the highest in microbial eukaryotes.}, }
@article {pmid37752398, year = {2023}, author = {Liu, H and Shi, B and Liu, W and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37752398}, issn = {1614-7499}, support = {42277039//National Natural Science Foundation of China/ ; 42207026//National Natural Science Foundation of China/ ; ZR202111290386//Natural Science Foundation of Shandong Province/ ; }, abstract = {Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).}, }
@article {pmid37748307, year = {2023}, author = {Gao, J and Xing, X and Cai, W and Li, Z and Shi, G and Chen, Y and Liang, H and Chen, C and Ma, K and Chen, J and Hu, C}, title = {Effect of micropollutants on disinfection byproducts and antibiotic resistance genes in drinking water in the process of biological activated carbon treatment.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132304}, doi = {10.1016/j.jhazmat.2023.132304}, pmid = {37748307}, issn = {1873-3336}, abstract = {The biofilm stress response of biological activated carbon (BAC) was investigated under prolonged exposure to sulfadiazine and 2,4-Dichlorophenoxyacetic acid, simulating complex emerging organic contaminants (EOCs) that are mainly involved in the formation of nitrogenous disinfection byproducts (N-DBPs) and antibiotic resistance genes (ARGs). Under trace complex EOCs condition (2 µg/L), N-DBP precursors and abundance of ARGs increased significantly in BAC effluent. The total formation potential of haloacetonitriles (HANs) and halonitromethanes (HNMs) was 751.47 ± 2.98 ng/L, which was much higher than the control group (440.67 ± 13.38 ng/L without EOCs). Similarly, the relative abundance of ARGs was more than twice that in the control group. The complex EOCs induce excessive extracellular polymeric substance secretion (EPS), thereby causing more N-DBP precursors and stronger horizontal gene transfer. Metagenome analysis revealed that functional amino acid and protein biosynthesis genes were overexpressed compared to the control group, causing more EPS to be secreted into the external environment. Complex EOCs promote Cobetia, Clostridium, and Streptomyces dominance, contributing to the production of N-DBP precursors and ARGs. For the first time, in addition to the direct hazards of the EOCs, this study successfully revealed the indirect water quality risks of complex EOCs from the microbial stress response during BAC treatment. Synergistic regulation of EOCs and microorganisms is important for tap water security.}, }
@article {pmid37746224, year = {2022}, author = {Schalamun, M and Schmoll, M}, title = {Trichoderma - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {1002161}, pmid = {37746224}, issn = {2673-6128}, abstract = {The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.}, }
@article {pmid37745407, year = {2023}, author = {Gonçalves, C and Harrison, MC and Steenwyk, JL and Opulente, DA and LaBella, AL and Wolters, JF and Zhou, X and Shen, XX and Groenewald, M and Hittinger, CT and Rokas, A}, title = {Diverse signatures of convergent evolution in cacti-associated yeasts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.14.557833}, pmid = {37745407}, abstract = {Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ∼17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.}, }
@article {pmid37743870, year = {2023}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S}, title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240138}, pmid = {37743870}, issn = {2235-2988}, abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.<br><br>METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, &amp; Grind room) of three beef-processing plants (Plant A, B &amp; C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.<br><br>RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.<br><br>CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.}, }
@article {pmid37744100, year = {2021}, author = {Stabel, M and Hagemeister, J and Heck, Z and Aliyu, H and Ochsenreither, K}, title = {Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {692804}, pmid = {37744100}, issn = {2673-6128}, abstract = {Degradation of lignocellulosic materials to release fermentable mono- and disaccharides is a decisive step toward a sustainable bio-based economy, thereby increasing the demand of robust and highly active lignocellulolytic enzymes. Anaerobic fungi of the phylum Neocallimastigomycota are potent biomass degraders harboring a huge variety of such enzymes. Compared to cellulose, hemicellulose degradation has received much less attention; therefore, the focus of this study has been the enzymatic xylan degradation of anaerobic fungi as these organisms produce some of the most effective known hydrolytic enzymes. We report the heterologous expression of a GH43 xylosidase, Xyl43Nc, and a GH11 endoxylanase, X11Nc, from the anaerobic fungus Neocallimastix californiae in Escherichia coli. The enzymes were identified by screening of the putative proteome. Xyl43Nc was highly active against 4-Nitrophenol-xylopyranosides with a Km of 0.72 mM, a kcat of 29.28 s[-1], a temperature optimum of 32°C and a pH optimum of 6. When combined, Xyl43Nc and X11Nc released xylose from beechwood xylan and arabinoxylan from wheat. Phylogenetic analysis revealed that Xyl43Nc shares common ancestry with enzymes from Spirochaetes and groups separately from Ascomycete sequences in our phylogeny, highlighting the importance of horizontal gene transfer in the evolution of the anaerobic fungi.}, }
@article {pmid37742882, year = {2023}, author = {Gu, X}, title = {Genome Distance and Phylogenetic Inference Accommodating Gene Duplication, Loss and New Gene Input.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {107916}, doi = {10.1016/j.ympev.2023.107916}, pmid = {37742882}, issn = {1095-9513}, abstract = {With the rapid growth of entire genome data, phylogenomics focuses on analyzing evolutionary histories and relationships of species, i.e., the tree of life. For decades it has been realized that the genome-wide phylogenetic inference can be approached based upon the dynamic pattern of gene content (the presence/absence of gene families), or extended gene content (absence, presence as a single-copy, or duplicates). Those methods, conceptually or technically, invoked the birth-and-death process to model the evolutionary process (gene duplication or gene loss. One common drawback is that the mechanism of new gene input, including de novo origin of new genes and the lateral gene transfer, has not been explicitly considered. In this paper, the author developed a new genome distance approach for genome phylogeny inference under the origin-birth-death stochastic process. The model takes gene duplication, gene loss and new gene input into account simultaneously. Computer simulations found that the two-genome approach is statistically difficult to distinguish between two proliferation parameters, i.e., the rate of gene duplication and the rate of new gene input. Nevertheless, it has also demonstrated the statistical feasibility for using the loss-genome distance to infer the genome phylogeny, which can avoid the large sampling problem. The strategy to study the universal tree of life was discussed and exemplified by an example.}, }
@article {pmid37741386, year = {2023}, author = {Shen, Y and Liu, Y and Du, Y and Wang, X and Guan, J and Jia, X and Xu, F and Song, Z and Gao, H and Zhang, B and Guo, P}, title = {Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167279}, doi = {10.1016/j.scitotenv.2023.167279}, pmid = {37741386}, issn = {1879-1026}, abstract = {The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.}, }
@article {pmid37739550, year = {2023}, author = {Khambhati, K and Bhattacharjee, G and Gohil, N and Maurya, R and Singh, V}, title = {Exploring the potential of phage and their applications.}, journal = {Progress in molecular biology and translational science}, volume = {200}, number = {}, pages = {1-12}, doi = {10.1016/bs.pmbts.2023.04.001}, pmid = {37739550}, issn = {1878-0814}, abstract = {Antibiotic resistant microorganisms are significantly increasing due to horizontal gene transfer, mutation and overdose of antibiotics leading to serious health conditions globally. Several multidrug resistant microorganisms have shown resistance to even the last line of antibiotics making it very difficult to treat them. Besides using antibiotics, an alternative approach to treat such resistant bacterial pathogens through the use of bacteriophage (phage) was used in the early 1900s which however declined and vanished after the discovery of antibiotics. In recent times, phage has emerged and gained interest as an alternative approach to antibiotics to treat MDR pathogens. Phage can self-replicate by utilizing cellular machinery of bacterial host by following lytic and lysogenic life cycles and therefore suitable for rapid regeneration. Application of phage for detection of bacterial pathogens, elimination of bacteria, agents for controlling food spoilage, treating human disease and several others entitles phage as a futuristic antibacterial armamentarium.}, }
@article {pmid37739079, year = {2023}, author = {Wu, L and Wu, Q and Xu, J and Rong, L and Y, X and Cai, C and Huang, X and Zou, X}, title = {Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167247}, doi = {10.1016/j.scitotenv.2023.167247}, pmid = {37739079}, issn = {1879-1026}, abstract = {The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.}, }
@article {pmid37738943, year = {2023}, author = {Zhang, J and Xu, Z and Chu, W and Ju, F and Jin, W and Li, P and Xiao, R}, title = {Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems.}, journal = {Water research}, volume = {245}, number = {}, pages = {120635}, doi = {10.1016/j.watres.2023.120635}, pmid = {37738943}, issn = {1879-2448}, abstract = {During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.}, }
@article {pmid37734313, year = {2023}, author = {Wang, YZ and An, XL and Fan, XT and Pu, Q and Li, H and Liu, WZ and Chen, Z and Su, JQ}, title = {Visible light-activated photosensitizer inhibits the plasmid-mediated horizontal gene transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132564}, doi = {10.1016/j.jhazmat.2023.132564}, pmid = {37734313}, issn = {1873-3336}, abstract = {Inhibition of plasmid transfer, including transformation and conjugation, is essential to prevent the spread of plasmid-encoded antimicrobial resistance. Photosensitizers have been successfully used in the treatment of serious infectious diseases, however, the effects of photosensitizers on the plasmid transfer are still elusive. In this study, we determined the transformation and conjugation efficiency of plasmid pUC19 and pRP4, respectively, when exposed to a photosensitizer (Visible Light-activated Rose Bengal, VLRB). The results showed that the activation of VLRB resulted in up to a 580-fold decrease in the transformation frequency of pUC19 and a 10-fold decrease in the conjugation frequency of pRP4 compared with the non-VLRB control. The inhibition of pUC19 transformation by VLRB exhibited a dose-dependent manner and was attributed to the changes in the plasmid conformation. The inhibition of pRP4 conjugation was associated with the generation of extracellular free radicals, induced oxidative stress, suppression of the mating pair formation gene (trbBp) and DNA transfer and replication gene (trfAp), and enhanced expression of the global regulatory genes (korA, korB, and trbA). These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes.}, }
@article {pmid37733747, year = {2023}, author = {Caygill, S and Dolan, L}, title = {ATP binding cassette transporters and uridine diphosphate glycosyltransferases are ancient protein families that evolved roles in herbicide resistance through exaptation.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0287356}, doi = {10.1371/journal.pone.0287356}, pmid = {37733747}, issn = {1932-6203}, abstract = {ATP-binding cassette (ABC) transporters actively transport various substances across membranes, while uridine diphosphate (UDP) glycosyltransferases (UGTs) are proteins that catalyse the chemical modification of various organic compounds. Both of these protein superfamilies have been associated with conferring herbicide resistance in weeds. Little is known about the evolutionary history of these protein families in the Archaeplastida. To infer the evolutionary histories of these protein superfamilies, we compared protein sequences collected from 10 species which represent distinct lineages of the Archaeplastida-the lineage including glaucophyte algae, rhodophyte algae, chlorophyte algae and the streptophytes-and generated phylogenetic trees. We show that ABC transporters were present in the last common ancestor of the Archaeplastida which lived 1.6 billion years ago, and the major clades identified in extant plants were already present then. Conversely, we only identified UGTs in members of the streptophyte lineage, which suggests a loss of these proteins in earlier diverging Archaeplastida lineages or arrival of UGTs into a common ancestor of the streptophyte lineage through horizontal gene transfer from a non-Archaeplastida eukaryote lineage. We found that within the streptophyte lineage, most diversification of the UGT protein family occurred in the vascular lineage, with 17 of the 20 clades identified in extant plants present only in vascular plants. Based on our findings, we conclude that ABC transporters and UGTs are ancient protein families which diversified during Archaeplastida evolution, which may have evolved for developmental functions as plants began to occupy new environmental niches and are now being selected to confer resistance to a diverse range of herbicides in weeds.}, }
@article {pmid37733635, year = {2023}, author = {Luo, T and Dai, X and Wei, W and Xu, Q and Ni, BJ}, title = {Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c02815}, pmid = {37733635}, issn = {1520-5851}, abstract = {Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.}, }
@article {pmid37732760, year = {2023}, author = {Wirth, NT and Rohr, K and Danchin, A and Nikel, PI}, title = {Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440.}, journal = {mBio}, volume = {}, number = {}, pages = {e0108123}, doi = {10.1128/mbio.01081-23}, pmid = {37732760}, issn = {2150-7511}, abstract = {Thymidylate kinases (TMPKs) play an essential role in DNA biosynthesis across all domains of life by catalyzing dTMP phosphorylation to dTDP. In Pseudomonas putida KT2440, a model Gram-negative soil bacterium, tmk is disrupted by a 65-kb genomic island (GI), posing questions about the origin of the essential TMPK function. To solve this long-standing evolutionary riddle, we addressed three competing hypotheses: (i) assembly of two Tmk segments into a functional protein, (ii) complementation by a deoxynucleotide monophosphate kinase encoded within the GI, or (iii) fulfillment of the essential function by the product of PP_3363, yet another gene annotated as "thymidylate kinase." Systematic genome engineering, quantitative physiology and targeted proteomics, complementation assays, phylogenetic analysis, and structure homology modeling were combined to investigate the role of genes within the GI. Our findings revealed that the GI-encoded dNMPK gene PP_1964 plays a critical role in complementing the disrupted TMPK function-exposing a non-essential character for the native PP_3363 gene and the tmk pseudogene. This dNMPK was found to be structurally related to that of bacteriophage T4, as part of a distinct evolutionary domain connected to mobile genetic elements and phages. The recursive genome reduction approach in this work deepens our understanding of the genetic architecture of a model bacterium while it provides evidence that the essential TMPK function has been acquired by horizontal gene transfer. Furthermore, the insights gained in the present study have broader implications for understanding the essentiality and functionality of dNMPK homologs in other bacteria. IMPORTANCE Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.}, }
@article {pmid37730038, year = {2023}, author = {Shen, M and Zhao, Y and Liu, S and Tao, S and Li, T and Long, H}, title = {Can microplastics and disinfectant resistance genes pose conceivable threats to water disinfection process?.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167192}, doi = {10.1016/j.scitotenv.2023.167192}, pmid = {37730038}, issn = {1879-1026}, abstract = {Microplastic pollution in the environment has aroused widespread concerns, however, the potential environmental risks caused by excessive use of disinfectants are still unknown. Disinfectants with doses below the threshold can enhance the communication of resistance genes in pathogenic microorganisms, promoting the development and spread of antimicrobial activity. Problematically, the intensification of microplastic pollution and the increase of disinfectant consumption will become a key driving force for the growth of disinfectant resistance bacteria (DRB) and disinfectant resistance genes (DRGs) in the environment. Disinfection plays a crucial role in ensuring water safety, however, the presence of microplastics and DRGs seriously disturb the water disinfection process. Microplastics can reduce the concentration of disinfectant in the local environment around microorganisms and improve their tolerance. Microorganisms can improve their resistance to disinfectants or generate resistance genes via phenotypic adaptation, gene mutations, and horizontal gene transfer. However, very limited information is available on the impact of DRB and DRGs on disinfection process. In this paper, the contribution of microplastics to the migration and transmission of DRGs was analyzed. The challenges posed by the presence of microplastics and DRGs on conventional disinfection were thoroughly discussed. The knowledge gaps faced by relevant current research and further research priorities have been proposed in order to provide a scientific basis in the future.}, }
@article {pmid37728942, year = {2023}, author = {Subirats, J and Sharpe, H and Tai, V and Fruci, M and Topp, E}, title = {Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0104723}, doi = {10.1128/aem.01047-23}, pmid = {37728942}, issn = {1098-5336}, abstract = {Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics. IMPORTANCE The United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.}, }
@article {pmid37724865, year = {2023}, author = {Sabatino, R and Sbaffi, T and Sivalingam, P and Corno, G and Fontaneto, D and Di Cesare, A}, title = {Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0110123}, doi = {10.1128/spectrum.01101-23}, pmid = {37724865}, issn = {2165-0497}, abstract = {Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae, Padoviridae, and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfrB6, rpoB mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated. IMPORTANCE WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.}, }
@article {pmid37724858, year = {2023}, author = {Derbyshire, KM and Salfinger, M}, title = {Plasmid-mediated drug resistance in mycobacteria: the tip of the iceberg?.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0062823}, doi = {10.1128/jcm.00628-23}, pmid = {37724858}, issn = {1098-660X}, abstract = {Macrolides, such as clarithromycin, are crucial in the treatment of nontuberculous mycobacteria (NTM). NTM are notoriously innately drug resistant, which has made the dependence on macrolides for their treatment even more important. Not surprisingly, resistance to macrolides has been documented in some NTM, including Mycobacterium avium and Mycobacterium abscessus, which are the two NTM species most often identified in clinical isolates. Resistance is mediated by point mutations in the 23S ribosomal RNA or by methylation of the rRNA by a methylase (encoded by an erm gene). Chromosomally encoded erm genes have been identified in many of the macrolide-resistant isolates, but not in Mycobacterium chelonae. Now, Brown-Elliott et al. (J Clin Microbiol 61:e00428-23, 2023, https://doi.org/10.1128/JCM.00428-23) describe the identification of a new erm variant, erm(55), which was found either on the chromosome or on a plasmid in highly macrolide-resistant clinical isolates of M. chelonae. The chromosomal erm(55) gene appears to be associated with mobile elements; one gene is within a putative transposon and the second is in a large (37 kb) insertion/deletion. The plasmid carrying erm(55) also encodes type IV and type VII secretion systems, which are often linked on large mycobacterial plasmids and are hypothesized to mediate plasmid transfer. While the conjugative transfer of the erm(55)-containing plasmid between NTM has yet to be demonstrated, the inferences are clear, as evidenced by the dissemination of plasmid-mediated drug resistance in other medically important bacteria. Here, we discuss the findings of Brown-Elliott et al., and the potential ramifications on treatment of NTM infections.}, }
@article {pmid37720149, year = {2023}, author = {Bhat, BA and Mir, RA and Qadri, H and Dhiman, R and Almilaibary, A and Alkhanani, M and Mir, MA}, title = {Integrons in the development of antimicrobial resistance: critical review and perspectives.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1231938}, doi = {10.3389/fmicb.2023.1231938}, pmid = {37720149}, issn = {1664-302X}, abstract = {Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.}, }
@article {pmid37718237, year = {2023}, author = {You, L and Jin, H and Kwok, LY and Lv, R and Zhao, Z and Bilige, M and Sun, Z and Liu, W and Zhang, H}, title = {Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2023.09.001}, pmid = {37718237}, issn = {2095-9281}, abstract = {Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.}, }
@article {pmid37716694, year = {2023}, author = {Savin, M and Hammerl, JA and Hassa, J and Hembach, N and Kalinowski, J and Schwartz, T and Droop, F and Mutters, NT}, title = {Free-floating extracellular DNA (exDNA) in different wastewaters: Status quo on exDNA-associated antimicrobial resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122560}, doi = {10.1016/j.envpol.2023.122560}, pmid = {37716694}, issn = {1873-6424}, abstract = {Wastewater treatment plants (WWTPs) have been reported as major anthropogenic reservoirs for the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) into the environment, worldwide. While most studies mainly focus on the intracellular DNA (iDNA), extracellular DNA (exDNA) accounting for a significant proportion of the total DNA in wastewater, was usually neglected. Following the One Health approach, this study focuses on wastewaters of municipal, clinical, and livestock origins (n = 45) that undergo different treatment processes (i.e., conventional activated sludge, ultrafiltration, and ozonation). Water samples were analysed for 12 ARGs as indicators of the different compartments associated with iDNA and exDNA by quantitative real-time PCR (qPCR). Taxonomic profiling of exDNA-fractions, obtained using nucleic acid adsorption particles, was conducted by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Notified exDNA concentrations varied between on-site WWTPs and treatment stages, and ranged from 314.0 ± 70.2 ng/mL in untreated livestock wastewater down to 0.7 ± 0.1 ng/mL in effluents after ultrafiltration. In general, influents exhibited higher concentrations compared to effluents, while wastewater treated by advanced treatment processes (i.e., ultrafiltration and ozonation) showed the lowest exDNA concentrations. Despite the lower concentrations, free-floating exDNA accounted for up to 80.0 ± 5.8% of the total DNA in effluents. Target ARGs were more common in the iDNA (100%, n = 45/45), compared to the exDNA-fractions (51.1%, n = 23/45), whereas exDNA-ARGs were mostly detected in clinical and slaughterhouse wastewaters as well as in the municipal influents. Compared to the iDNA-ARGs, the concentrations of exDNA-ARGs were in general lower. Nevertheless, significant higher concentrations for exDNA-associated genes were measured in clinical wastewaters for blaNDM (4.07 ± 0.15 log gene copies (GC)/L) and blaVIM-2 (6.0 ± 0.2 log GC/L). Overall, our results suggest that depending on the origin of wastewater and its treatment methods, exDNA represents an important reservoir for ARGs, particularly in clinical wastewater.}, }
@article {pmid37716437, year = {2023}, author = {Rodríguez-Pallares, S and Mateo-Vargas, MA and Rodríguez-Iglesias, MA and Galán-Sánchez, F}, title = {Molecular Characterization of consecutive isolates of OXA-48-producing Klebsiella pneumoniae: Changes in the virulome using next-generation sequencing (NGS).}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105217}, doi = {10.1016/j.micinf.2023.105217}, pmid = {37716437}, issn = {1769-714X}, abstract = {Little is known about the clonality of consecutive OXA-48 producing-Klebsiella pneumoniae isolates from the same patient and the possibility of changes in their virulomes over time. We studied the molecular characteristics of twenty OXA-48-producing K. pneumoniae consecutive isolates from six patients using whole-genome sequencing. The genomes were screened for antimicrobial resistance and virulence factor genes and for replicon groups. MLST and SNPs analysis was performed. MLST analysis found 3 STs: ST11 (n=13; 65.0%); ST4975 (n=5, 25.0%); ST307 (n=2; 10.0%). AcrAb efflux pump, siderophore enterobactin and rcsAB capsule synthesis regulator were detected in all sequenced isolates. The regulator of mucoid phenotype A (rmpA) and rmpA2 were not detected. Isolates also carried type 3 fimbriae (n=19; 95.0%), yersiniabactin (n=15; 75.0%) and type 1 fimbriae (7; 35.0%). Type 3 fimbriae and yersiniabactin were lost and recovered in consecutive isolates of two patients, probably acquired by horizontal gene transfer. Our findings reveal that recurrent infections are due to the same isolate, with an average of 2.69 SNPs per month, with different virulence profiles, and that the acquisition of virulence factor genes over time is possible.}, }
@article {pmid37715312, year = {2023}, author = {Xi, Y and Zhao, J and Zhang, J and Jin, Y and Yang, H and Duan, G and Chen, S and Long, J}, title = {Analysis of the features of 105 confirmed CRISPR loci in 487 Klebsiella variicola.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovad108}, pmid = {37715312}, issn = {1472-765X}, abstract = {Klebsiella variicola (K. variicola), an emerging human pathogen, poses a threat to public health. The horizontal gene transfer (HGT) of plasmids is an important driver of the emergence of multiple antibiotic-resistant K. variicola. Clustered regularly interspersed short palindromic repeats (CRISPR) coupled with CRISPR-associated genes (CRISPR/Cas) constitute an adaptive immune system in bacteria, and can provide acquired immunity against HGT. However, the information about the CRISPR/Cas system in K. variicola is still limited. In this study, 487 genomes of K. variicola obtained from the National Center for Biotechnology Information database were used to analyze the characteristics of CRISPR/Cas systems. Approximately 21.56% of genomes (105/487) harbor at least one confirmed CRISPR array. Three types of CRISPR/Cas systems, namely, the types I-E, I-E*, and IV-A systems, were identified among 105 strains. Spacer origin analysis further revealed that approximately one-third of spacers significantly match plasmids or phages, which demonstrates the implication of CRISPR/Cas systems in controlling HGT. Moreover, spacers in K. variicola tend to target mobile genetic elements from K. pneumoniae. This finding provides new evidence of the interaction of K. variicola and K. pneumoniae during their evolution. Collectively, our results provide valuable insights into the role of CRISPR/Cas systems in K. variicola.}, }
@article {pmid36944262, year = {2023}, author = {Milner, DS and Galindo, LJ and Irwin, NAT and Richards, TA}, title = {Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {45-66}, doi = {10.1146/annurev-micro-032421-115538}, pmid = {36944262}, issn = {1545-3251}, abstract = {Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.}, }
@article {pmid37705515, year = {2023}, author = {Abdelbary, ER and Elsaghier, AM and Abd El-Baky, RM and Waly, NGFM and Ramadan, M and Abd-Elsamea, FS and Ali, ME and Alzahrani, HA and Salah, M}, title = {First Emergence of NDM-5 and OqxAB Efflux Pumps Among Multidrug-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Assiut, Egypt.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5965-5976}, doi = {10.2147/IDR.S421978}, pmid = {37705515}, issn = {1178-6973}, abstract = {INTRODUCTION: New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae poses a high risk, especially among Egyptian pediatric patients who consume carbapenems antibiotics very widely and without adequate diagnostic sources. In addition, presence of efflux pump genes such as OqxAB increases resistance against many groups of antimicrobials which exacerbates the problem faced for human health. This study aimed to determine NDM variants among K. pneumoniae strains isolated from pediatric patients in Egypt, analyze the presence of OqxAB genes, and molecular characterization of blaNDM-5-positive K. pneumoniae.<br><br>METHODS: Fifty-six K. pneumoniae&#xa0;isolates were recovered from pediatric patients, and tested for carbapenemase by modified carbapenem inactivation methods (mCIM) test. Minimum inhibitory concentrations of meropenem and colistin were determined by meropenem E-test strips and broth microdilution, respectively. PCR was used for the detection of the resistant genes (ESBL gene (blaCTX-M), carbapenemase genes (blaNDM, blaKPC) colistin resistant (mcr1, mcr2)) and genes for efflux pump (oqxA and oqxB). BlaNDM was sequenced. The effect of efflux pump in NDM-5-producing isolates was assessed by measuring MIC of ciprofloxacin and meropenem before and after exposure to the carbonyl cyanide 3-chlorophenylhydrazone (CCCP). The horizontal gene transfer ability of&#xa0;blaNDM-5 was determined using liquid mating assay and PCR-based replicon typing (PBRT) was done to determine the major plasmid incompatibility group.<br><br>RESULTS: Twenty-nine isolates were positive for blaNDM-1, nine isolates were positive for blaNDM-5, and 15 isolates were positive for blaKPC. There is a significant increase of meropenem MIC of NDM-5-positive isolates compared with NDM-1-positive isolates. In addition, 38 isolates were positive for CTX-M, and 15 isolates were positive for mcr1. Both OqxA and OqxB were detected in 26 isolates and 13 isolates were positive for OqxA while 11 isolates were positive for OqxB only. All NDM-5-producing isolates except one isolate could transfer their plasmids by conjugation to their corresponding transconjugants (E. coli J53). Plasmid replicon typing showed that FII was predominant in NDM-5-producing K. pneumoniae. Similar strains were found between the three isolates and similarity was also detected between the two isolates.<br><br>CONCLUSION: The highly resistant K. pneumoniae producing blaNDM-5 type was firstly isolated from pediatric patients. The association of efflux pump genes such as OqxAB is involved in resistance to ciprofloxacin. This highlighted the severity risk of&#xa0;blaNDM-5-positive&#xa0;K. pneumonia as it could transfer blaNDM-5 to other bacteria and has more resistance against carbapenems. This underlines the importance of continuous monitoring of infection control guidelines, and the urgent need for a national antimicrobial stewardship plan in Egyptian hospitals.}, }
@article {pmid37700871, year = {2023}, author = {Nasir, A and Caetano-Anollés, G and Claverie, JM}, title = {Editorial: Viruses, genetic exchange, and the tree of life, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1271181}, doi = {10.3389/fmicb.2023.1271181}, pmid = {37700871}, issn = {1664-302X}, }
@article {pmid37700035, year = {2023}, author = {Lin, X and Zhang, C and Han, R and Li, S and Peng, H and Zhou, X and Huang, L and Xu, Y}, title = {Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37700035}, issn = {1751-7370}, support = {42277260//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41977340//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.}, }
@article {pmid37697273, year = {2023}, author = {El-Sabeh, A and Mlesnita, AM and Munteanu, IT and Honceriu, I and Kallabi, F and Boiangiu, RS and Mihasan, M}, title = {Characterisation of the Paenarthrobacter nicotinovorans ATCC 49919 genome and identification of several strains harbouring a highly syntenic nic-genes cluster.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {536}, pmid = {37697273}, issn = {1471-2164}, support = {PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; PN-III-P4-ID-PCE-2020-0656//Romanian Ministry of Education and Research/ ; }, abstract = {BACKGROUND: Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids.<br><br>RESULTS: In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway.<br><br>CONCLUSIONS: The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.}, }
@article {pmid37693864, year = {2023}, author = {Doughty, EL and Liu, H and Moran, RA and Hua, X and Ba, X and Guo, F and Chen, X and Zhang, L and Holmes, M and van Schaik, W and McNally, A and Yu, Y}, title = {Endemicity and diversification of carbapenem-resistant Acinetobacter baumannii in an intensive care unit.}, journal = {The Lancet regional health. Western Pacific}, volume = {37}, number = {}, pages = {100780}, doi = {10.1016/j.lanwpc.2023.100780}, pmid = {37693864}, issn = {2666-6065}, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations.<br><br>METHODS: A three-month cross-sectional observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 5068 samples were collected from the hospital environment (n&#xa0;=&#xa0;3985), patients (n&#xa0;=&#xa0;964) and staff (n&#xa0;=&#xa0;119). CRAB isolates were obtained from 10.5% of these samples (n&#xa0;=&#xa0;532). All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing.<br><br>FINDINGS: The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.6%) sampling occasions but from patients on only 72/299 (24.1%) occasions. CRAB was spread to adjacent bed units and rooms, and following re-location of patients within the ICU. We also observed three horizontal gene transfer events between CRAB strains in the ICU, involving three different plasmids.<br><br>INTERPRETATION: The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology and the unique challenges in containing the spread of CRAB in ICUs where this important multidrug-resistant pathogen is endemic.<br><br>FUNDING: This work was undertaken as part of the DETECTIVE research project funded by the Medical Research Council (MR/S013660/1), National Natural Science Foundation of China (81861138054, 32011530116, 31970128, 31770142), Zhejiang Province Medical Platform Backbone Talent Plan (2020RC075), and the National Key Research and Development Program of China grant (2018YFE0102100). W.v.S was also supported by a Wolfson Research Merit Award (WM160092).}, }
@article {pmid37693574, year = {2023}, author = {Fox, BW and Helf, MJ and Burkhardt, RN and Artyukhin, AB and Curtis, BJ and Palomino, DF and Chaturbedi, A and Tauffenberger, A and Wrobel, CJJ and Zhang, YK and Lee, SS and Schroeder, FC}, title = {Evolutionarily related host and microbial pathways regulate fat desaturation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.31.555782}, pmid = {37693574}, abstract = {Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression [1-4] , but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans . Untargeted metabolomics of a β-oxidation mutant, acdh-11 , in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β- cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli . Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1 , that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.}, }
@article {pmid37693541, year = {2023}, author = {Li, Z and Xue, AZ and Maeda, GP and Li, Y and Nabity, PD and Moran, NA}, title = {Phylloxera and aphids show distinct features of genome evolution despite similar reproductive modes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.28.555181}, pmid = {37693541}, abstract = {Genomes of aphids (family Aphididae) show several unusual evolutionary patterns. In particular, within the XO sex determination system of aphids, the X chromosome exhibits a lower rate of interchromosomal rearrangements, fewer highly expressed genes, and faster evolution at nonsynonymous sites compared to the autosomes. In contrast, other hemipteran lineages have similar rates of interchromosomal rearrangement for autosomes and X chromosomes. One possible explanation for these differences is the aphid's life cycle of cyclical parthenogenesis, where multiple asexual generations alternate with one sexual generation. If true, we should see similar features in the genomes of Phylloxeridae, an outgroup of aphids which also undergoes cyclical parthenogenesis. To investigate this, we generated a chromosome-level assembly for the grape phylloxera, an agriculturally important species of Phylloxeridae, and identified its single X chromosome. We then performed synteny analysis using the phylloxerid genome and 30 high-quality genomes of aphids and other hemipteran species. Unexpectedly, we found that the phylloxera does not share aphids' patterns of chromosome evolution. By estimating interchromosomal rearrangement rates on an absolute time scale, we found that rates are elevated for aphid autosomes compared to their X chromosomes, but this pattern does not extend to the phylloxera branch. Potentially, the conservation of X chromosome gene content is due to selection on XO males that appear in the sexual generation. We also examined gene duplication patterns across Hemiptera and uncovered horizontal gene transfer events contributing to phylloxera evolution.}, }
@article {pmid37692203, year = {2023}, author = {Chang, H and Bai, J and Zhang, H and Huang, R and Chu, H and Wang, Q and Liu, H and Cheng, J and Jiang, H}, title = {Origin and evolution of the main starch biosynthetic enzymes.}, journal = {Synthetic and systems biotechnology}, volume = {8}, number = {3}, pages = {462-468}, doi = {10.1016/j.synbio.2023.05.006}, pmid = {37692203}, issn = {2405-805X}, abstract = {Starch, a semi-crystalline energy storage form primarily found in plant plastids plays a crucial role in various food or no-food applications. Despite the starch biosynthetic pathway's main enzymes have been characterized, their origin and evolution remained a subject of debate. In this study, we conducted the comprehensive phylogenetic and structural analysis of three types of starch biosynthetic enzymes: starch synthase (SS), starch branching enzyme (SBE) and isoamylase-type debranching enzyme (ISA) from 51,151 annotated genomes. Our findings provide valuable insights into the possible scenario for the origin and evolution of the starch biosynthetic pathway. Initially, the ancestor of SBE can be traced back to an unidentified bacterium that existed before the formation of the last eukaryotic common ancestor (LECA) via horizontal gene transfer (HGT). This transfer event likely provided the eukaryote ancestor with the ability to synthesize glycogen. Furthermore, during the emergence of Archaeplastida, one clade of SS was transferred from Deltaproteobacteria by HGT, while ISA and the other clade of SS originated from Chlamydiae through endosymbiosis gene transfer (EGT). Both these transfer events collectively contributed to the establishment of the original starch biosynthetic pathway. Subsequently, after the divergence of Viridiplantae from Rhodophyta, all three enzymes underwent multiple duplications and N-terminus extension domain modifications, resulting in the formation of functionally specialized isoforms and ultimately leading to the complete starch biosynthetic pathway. By shedding light on the evolutionary origins of key enzymes involved in the starch biosynthetic pathway, this study provides important insights into the evolutionary events of plants.}, }
@article {pmid37690629, year = {2023}, author = {Haghjooy Javanmard, S and Rafiee, L and Bahri Najafi, M and Khorsandi, D and Hasan, A and Vaseghi, G and Makvandi, P}, title = {Microfluidic-based technologies in cancer liquid biopsy: Unveiling the role of horizontal gene transfer (HGT) materials.}, journal = {Environmental research}, volume = {}, number = {}, pages = {117083}, doi = {10.1016/j.envres.2023.117083}, pmid = {37690629}, issn = {1096-0953}, abstract = {Liquid biopsy includes the isolating and analysis of non-solid biological samples enables us to find new ways for molecular profiling, prognostic assessment, and better therapeutic decision-making in cancer patients. Despite the conventional theory of tumor development, a non-vertical transmission of DNA has been reported among cancer cells and between cancer and normal cells. The phenomenon referred to as horizontal gene transfer (HGT) has the ability to amplify the advancement of tumors by disseminating genes that encode molecules conferring benefits to the survival or metastasis of cancer cells. Currently, common liquid biopsy approaches include the analysis of extracellular vesicles (EVs) and tumor-free DNA (tfDNA) derived from primary tumors and their metastatic sites, which are well-known HGT mediators in cancer cells. Current technological and molecular advances expedited the high-throughput and high-sensitive HGT materials analyses by using new technologies, such as microfluidics in liquid biopsies. This review delves into the convergence of microfluidic-based technologies and the investigation of Horizontal Gene Transfer (HGT) materials in cancer liquid biopsy. The integration of microfluidics offers unprecedented advantages such as high sensitivity, rapid analysis, and the ability to analyze rare cell populations. These attributes are instrumental in detecting and characterizing CTCs, circulating nucleic acids, and EVs, which are carriers of genetic cargo that could potentially undergo HGT. The phenomenon of HGT in cancer has raised intriguing questions about its role in driving genomic diversity and acquired drug resistance. By leveraging microfluidic platforms, researchers have been able to capture and analyze individual cells or genetic material with enhanced precision, shedding light on the potential transfer of genetic material between cancer cells and surrounding stromal cells. Furthermore, the application of microfluidics in single-cell sequencing has enabled the elucidation of the genetic changes associated with HGT events, providing insights into the evolution of tumor genomes. This review also discusses the challenges and opportunities in studying HGT materials using microfluidic-based technologies. In conclusion, microfluidic-based technologies have significantly advanced the field of cancer liquid biopsy, enabling the sensitive and accurate detection of HGT materials. As the understanding of HGT's role in tumor evolution and therapy resistance continues to evolve, the synergistic integration of microfluidics and HGT research promises to provide valuable insights into cancer biology, with potential implications for precision oncology and therapeutic strategies.}, }
@article {pmid37689422, year = {2023}, author = {Hull, DM and Harrel, E and Harden, L and Thakur, S}, title = {Detection of resistance and virulence plasmids in Campylobacter coli and Campylobacter jejuni isolated from North Carolina food animal production, 2018-2019.}, journal = {Food microbiology}, volume = {116}, number = {}, pages = {104348}, doi = {10.1016/j.fm.2023.104348}, pmid = {37689422}, issn = {1095-9998}, abstract = {Campylobacter remains the leading cause of bacterial foodborne illness in the U.S. and worldwide. Campylobacter plasmids may play a significant role in antimicrobial resistance (AMR) and virulence factor distribution, and potentially drive rapid adaptation. C. coli (n = 345) and C. jejuni (n = 199) isolates collected from live cattle, swine, turkey, and chickens, poultry carcasses at production, and retail meat in N.C. were analyzed to determine plasmid prevalence, extrachromosomal virulence and AMR genes, and the phylogeny of assembled plasmids. Putative plasmids ranging from <2 kb to 237kb were identified with virulence factors present in 66.1% (228/345) C. coli and 88.4% (176/199) C. jejuni plasmids (promoting adherence, invasion, exotoxin production, immune modulation, chemotaxis, mobility, and the type IV secretion system). AMR genes were identified in 21.2% (73/345) C. coli and 28.1% C. jejuni plasmids (conferring resistance to tetracyclines, aminoglycosides, beta-lactams, nucleosides, and lincosamides). Megaplasmids (>100 kb) were present in 25.7% (140/544) of the isolates and carried genes previously recognized to be involved with interspecies recombination. Our study highlights the extensive distribution and diversity of Campylobacter plasmids in food animal production and their role in the dissemination of biomedically important genes. Characterizing Campylobacter plasmids within the food animal production niche is important to understanding the epidemiology of potential emerging strains.}, }
@article {pmid37680975, year = {2023}, author = {Ashy, RA}, title = {Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {10}, pages = {103789}, doi = {10.1016/j.sjbs.2023.103789}, pmid = {37680975}, issn = {1319-562X}, abstract = {The study aimed to reveal the structure and function of phageome existing in soil rhizobiome of Abutilon fruticosum in order to detect accidentally-packaged bacterial genes that encode Carbohydrate-Active enZymes (or CAZymes) and those that confer antibiotic resistance (e.g., antibiotic resistance genes or ARGs). Highly abundant genes were shown to mainly exist in members of the genera Pseudomonas, Streptomyces, Mycobacterium and Rhodococcus. Enriched CAZymes belong to glycoside hydrolase families GH4, GH6, GH12, GH15 and GH43 and mainly function in D-glucose biosynthesis via 10 biochemical passages. Another enriched CAZyme, e.g., alpha-galactosidase, of the GH4 family is responsible for the wealth of different carbohydrate forms in rhizospheric soil sink of A. fruticosum. ARGs of this phageome include the soxR and OleC genes that participate in the "antibiotic efflux pump" resistance mechanism, the parY mutant gene that participates in the "antibiotic target alteration" mechanism and the arr-1, iri, and AAC(3)-Ic genes that participate in the "antibiotic inactivation" mechanism. It is claimed that the genera Streptomyces, which harbors phages with oleC and parY mutant genes, and Pseudomonas, which harbors phages with soxR and AAC(3)-Ic genes, are approaching multidrug resistance via newly disseminating phages. These ARGs inhibit many antibiotics including oleandomycin, tetracycline, rifampin and aminoglycoside. The study highlights the possibility of accidental packaging of these ARGs in soil phageome and the risk of their horizontal transfer to human gut pathogens through the food chain as detrimental impacts of soil phageome of A. fruticosum. The study also emphasizes the beneficial impacts of phageome on soil microbiome and plant interacting in storing carbohydrates in the soil sink for use by the two entities upon carbohydrate deprivation.}, }
@article {pmid37486104, year = {2023}, author = {Hallal Ferreira Raro, O and Poirel, L and Tocco, M and Nordmann, P}, title = {Impact of veterinary antibiotics on plasmid-encoded antibiotic resistance transfer.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {78}, number = {9}, pages = {2209-2216}, pmid = {37486104}, issn = {1460-2091}, support = {/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Oxytetracycline/pharmacology ; Edaravone/pharmacology ; Reactive Oxygen Species ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; }, abstract = {OBJECTIVES: Resistance genes can be genetically transmitted and exchanged between commensal and pathogenic bacterial species, and in different compartments including the environment, or human and animal guts (One Health concept). The aim of our study was to evaluate whether subdosages of antibiotics administered in veterinary medicine could enhance plasmid transfer and, consequently, resistance gene exchange in gut microbiota.<br><br>METHODS: Conjugation frequencies were determined with Escherichia coli strains carrying IncL- (blaOXA-48) or IncI1-type (blaCTX-M-1) plasmids subjected to a series of subinhibitory concentrations of antibiotics used in veterinary medicine, namely amoxicillin, ceftiofur, apramycin, neomycin, enrofloxacin, colistin, erythromycin, florfenicol, lincomycin, oxytetracycline, sulfamethazine, tiamulin and the ionophore narasin. Treatments with subinhibitory dosages were performed with and without supplementation with the antioxidant edaravone, known as a mitigator of the inducibility effect of several antibiotics on plasmid conjugation frequency (PCF). Expression of SOS-response associated genes and fluorescence-based reactive oxygen species (ROS) detection assays were performed to evaluate the stress oxidative response.<br><br>RESULTS: Increased PCFs were observed for both strains when treating with florfenicol and oxytetracycline. Increased expression of the SOS-associated recA gene also occurred concomitantly, as well as increased ROS production. Addition of edaravone to the treatments reduced their PCF and also showed a decreasing effect on SOS and ROS responses for both plasmid scaffolds.<br><br>CONCLUSIONS: We showed here that some antibiotics used in veterinary medicine may induce transfer of plasmid-encoded resistance and therefore may contribute to the worldwide spread of antibiotic resistance genes.}, }
@article {pmid37670002, year = {2023}, author = {Natarajan, S and Pucker, B and Srivastava, S}, title = {Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14614}, pmid = {37670002}, issn = {2045-2322}, support = {CR22230114BTHLSS008458//Cytiva/ ; CR21221810BTLNTE008458//L&amp;T/ ; }, abstract = {Camptothecin is an important anticancer alkaloid produced by particular plant species. No suitable synthetic route has been established for camptothecin production yet, imposing a stress on plant-based production systems. Endophytes associated with these camptothecin-producing plants have been reported to also produce camptothecin and other high-value phytochemicals. A previous study identified a fungal endophyte Alternaria burnsii NCIM 1409, isolated from Nothapodytes nimmoniana, to be a sustainable producer of camptothecin. Our study provides key insights on camptothecin biosynthesis in this recently discovered endophyte. The whole genome sequence of A. burnsii NCIM 1409 was assembled and screened for biosynthetic gene clusters. Comparative studies with related fungi supported the identification of candidate genes involved in camptothecin synthesis and also helped to understand some aspects of the endophyte's defense against the toxic effects of camptothecin. No evidence for horizontal gene transfer of the camptothecin biosynthetic genes from the host plant to the endophyte was detected suggesting an independent evolution of the camptothecin biosynthesis in this fungus.}, }
@article {pmid37665285, year = {2024}, author = {Takahashi, T and Kim, H and Kim, HS and Kim, HS and Song, W and Kim, JS}, title = {Comparative Genomic Analysis of Staphylococcal Cassette Chromosome mec Type V Staphylococcus aureus Strains and Estimation of the Emergence of SCCmec V Clinical Isolates in Korea.}, journal = {Annals of laboratory medicine}, volume = {44}, number = {1}, pages = {47-55}, doi = {10.3343/alm.2024.44.1.47}, pmid = {37665285}, issn = {2234-3814}, abstract = {BACKGROUND: Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock. Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains.<br><br>METHODS: Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Ranger-dtl was applied to 818 SCCmec V strains using publicly available whole-genome data.<br><br>RESULTS: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000-2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors.<br><br>CONCLUSIONS: Most Korean SCCmec V strains may have emerged during 2000-2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.}, }
@article {pmid37664620, year = {2023}, author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T}, title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107508}, pmid = {37664620}, issn = {2589-0042}, abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.}, }
@article {pmid37662302, year = {2023}, author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ}, title = {DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.22.554363}, pmid = {37662302}, abstract = {Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.}, }
@article {pmid37662235, year = {2023}, author = {Pandey, T and Kalluraya, C and Wang, B and Xu, T and Huang, X and Guang, S and Daugherty, MD and Ma, DK}, title = {Acquired stress resilience through bacteria-to-nematode horizontal gene transfer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.20.554039}, pmid = {37662235}, abstract = {Natural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode gene rml-3 , which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins in C. elegans . Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides. C. elegans rml-3 is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly, rml-3 deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterial rml-3 homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.}, }
@article {pmid37662009, year = {2023}, author = {Li, Z and Zhou, X and Liao, D and Liu, R and Zhao, X and Wang, J and Zhong, Q and Zeng, Z and Peng, Y and Tan, Y and Yang, Z}, title = {Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180194}, pmid = {37662009}, issn = {2235-2988}, abstract = {INTRODUCTION: Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.<br><br>METHODS: This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.<br><br>RESULTS: General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.<br><br>DISUCSSION: This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.}, }
@article {pmid37658677, year = {2023}, author = {Clark, JW}, title = {Genome evolution in plants and the origins of innovation.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19242}, pmid = {37658677}, issn = {1469-8137}, support = {RPG-2019-004//Leverhulme Trust/ ; }, abstract = {Plant evolution has been characterised by a series of major novelties in their vegetative and reproductive traits that have led to greater complexity. Underpinning this diversification has been the evolution of the genome. When viewed at the scale of the plant kingdom, plant genome evolution has been punctuated by conspicuous instances of gene and whole-genome duplication, horizontal gene transfer and extensive gene loss. The periods of dynamic genome evolution often coincide with the evolution of key traits, demonstrating the coevolution of plant genomes and phenotypes at a macroevolutionary scale. Conventionally, plant complexity and diversity have been considered through the lens of gene duplication and the role of gene loss in plant evolution remains comparatively unexplored. However, in light of reductive evolution across multiple plant lineages, the association between gene loss and plant phenotypic diversity warrants greater attention.}, }
@article {pmid37657315, year = {2023}, author = {Zhao, Y and Hu, Z and Xie, H and Wu, H and Wang, Y and Xu, H and Liang, S and Zhang, J}, title = {Size-dependent promotion of micro(nano)plastics on the horizontal gene transfer of antibiotic resistance genes in constructed wetlands.}, journal = {Water research}, volume = {244}, number = {}, pages = {120520}, doi = {10.1016/j.watres.2023.120520}, pmid = {37657315}, issn = {1879-2448}, abstract = {Constructed wetlands (CWs) have been identified as significant sources of micro(nano)plastics (MPs/NPs) and antibiotic resistance genes (ARGs) in aquatic environments. However, little is known about the impact of MPs/NPs exposure on horizontal gene transfer (HGT) of ARGs and shaping the corresponding ARG hosts' community. Herein, the contribution of polystyrene (PS) particles (control, 4 mm, 100 μm, and 100 nm) to ARG transfer was investigated by adding an engineered fluorescent Escherichia coli harboring RP4 plasmid-encoded ARGs into CWs. It was found MPs/NPs significantly promoted ARG transfer in a size-dependent manner in each CW medium (p < 0.05). The 100 μm-sized PS exhibited the most significant promotion of ARG transfer (p < 0.05), whereas 100 nm-sized PS induced limited promotion due to its inhibitory activity on microbes. The altered RP4-carrying bacterial communities suggested that MPs/NPs, especially 100 µm-PS, could recruit pathogenic and nitrifying bacteria to acquire ARGs. The increased sharing of RP4-carrying core bacteria in CW medium further suggested that ARGs can spread into CW microbiome using MPs/NPs as carriers. Overall, our results highlight the high risks of ARG dissemination induced by MPs/NPs exposure and emphasize the need for better control of plastic disposal to prevent the potential health threats.}, }
@article {pmid37651790, year = {2023}, author = {Katsburg, M and Brombach, J and Hanke, D and Aubry, E and Lübke-Becker, A and Fulde, M}, title = {New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa.}, journal = {Veterinary microbiology}, volume = {285}, number = {}, pages = {109869}, doi = {10.1016/j.vetmic.2023.109869}, pmid = {37651790}, issn = {1873-2542}, abstract = {Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.}, }
@article {pmid37653049, year = {2023}, author = {Johnson, ET and Bowman, MJ and Gomes, RP and Carneiro, LC and Dunlap, CA}, title = {Identification of 2,4-diacetylphloroglucinol production in the genus Chromobacterium.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14292}, pmid = {37653049}, issn = {2045-2322}, abstract = {The compound 2,4-diacetylphloroglucinol (DAPG) is a broad-spectrum antibiotic that is primarily produced by Pseudomonas spp. DAPG plays an important role in the biocontrol disease suppressing activity of Pseudomonas spp. In the current study, we report the discovery of the DAPG biosynthetic cluster in strains of Chromobacterium vaccinii isolated from Brazilian aquatic environments and the distribution of the biosynthetic cluster in the Chromobacterium genus. Phylogenetic analysis of the phlD protein suggests the biosynthetic cluster probably entered the genus of Chromobacterium after a horizontal gene transfer event with a member of the Pseudomonas fluorescens group. We were able to detect trace amounts of DAPG in wild type cultures and confirm the function of the cluster with heterologous expression in Escherichia coli. In addition, we identified and verified the presence of other secondary metabolites in these strains. We also confirmed the ability of C. vaccinii strains to produce bioactive pigment violacein and bioactive cyclic depsipeptide FR900359. Both compounds have been reported to have antimicrobial and insecticidal activities. These compounds suggest strains of C. vaccinii should be further explored for their potential as biocontrol agents.}, }
@article {pmid37647945, year = {2023}, author = {Goodman, RN and Tansirichaiya, S and Roberts, AP}, title = {Development of pBACpAK entrapment vector derivatives to detect intracellular transfer of mobile genetic elements within chloramphenicol resistant bacterial isolates.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {106813}, doi = {10.1016/j.mimet.2023.106813}, pmid = {37647945}, issn = {1872-8359}, abstract = {Antimicrobial resistance disseminates throughout bacterial populations via horizontal gene transfer, driven mainly by mobile genetic elements (MGEs). Entrapment vectors are key tools in determining MGE movement within a bacterial cell between different replicons or between sites within the same replicon. The pBACpAK entrapment vector has been previously used to study intracellular transfer in Gram-negative bacteria however since pBACpAK contains a chloramphenicol resistance gene, it cannot be used in bacterial isolates which are already resistant to chloramphenicol. Therefore, we developed new derivatives of the pBACpAK entrapment vector to determine intracellular transfer of MGEs in an Escherichia coli DH5α transconjugant containing the chloramphenicol resistance plasmid pD25466. The catA1 of pBACpAK was replaced by both mcr-1 in pBACpAK-COL and aph(3')-Ia in pBACpAK-KAN, allowing it to be used in chloramphenicol resistant strains. The plasmid constructs were verified and then used to transform the E. coli DH5α/pD25466 transconjugants in order to detect intracellular movement of the MGEs associated with the pD25466 plasmid. Here we report on the validation of the expanded suite of pBACpAK vectors which can be used to study the intracellular transfer of MGEs between, and within, replicons in bacteria with different antimicrobial resistance profiles.}, }
@article {pmid37649002, year = {2023}, author = {Ye, J and Jin, L and Li, Y and Xu, H and Lin, Y and Zhou, T and Zheng, B and Wang, M and Wang, Z}, title = {Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {506}, pmid = {37649002}, issn = {1471-2164}, support = {82102457//the National Natural Science Foundation of China/ ; LQ22H200004//the Zhejiang Provincial Natural Science Foundation of China/ ; Y20210110//the Planned Science and Technology Project of Wenzhou/ ; 2019QD011//Start-up Funding for Talent Research Program in the First Affiliated Hospital of Wenzhou Medical University/ ; 2023RC046//the Zhejiang Provincial Science and Technology Plan Project of China/ ; 2022E10022//Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province/ ; }, abstract = {BACKGROUND: The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections.<br><br>RESULTS: Antimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene.<br><br>CONCLUSIONS: The data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.}, }
@article {pmid37648730, year = {2023}, author = {Xiong, L and Li, Y and Yu, H and Wei, Y and Li, H and Ji, X}, title = {Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14190}, pmid = {37648730}, issn = {2045-2322}, support = {32160294//National Natural Science Foundation of China/ ; 31860147//National Natural Science Foundation of China/ ; }, abstract = {Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.}, }
@article {pmid37645846, year = {2023}, author = {Youngblom, MA and Imhoff, MR and Smyth, LM and Mohamed, MA and Pepperell, CS}, title = {Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.18.553882}, pmid = {37645846}, abstract = {UNLABELLED: Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus . We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a 'sink' for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists.<br><br>DATA SUMMARY: Raw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics .<br><br>IMPACT STATEMENT: It is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.}, }
@article {pmid37645731, year = {2023}, author = {Lucero, RM and Demirer, K and Yeh, TJ and Stockbridge, RB}, title = {Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.10.552832}, pmid = {37645731}, abstract = {UNLABELLED: Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMR Gdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMR Gdx homologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMR Gdx homologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMR Gdx homologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMR Gdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.<br><br>SUMMARY: Using solid supported membrane electrophysiology, structural biology, and binding assays, we characterize binding and transport of metformin metabolites by bacterial SMR transporters, including proteins associated with horizontal gene transfer in wastewater bacteria that degrade metformin.}, }
@article {pmid37640834, year = {2023}, author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB}, title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {90}, pmid = {37640834}, issn = {2730-6151}, abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.}, }
@article {pmid37634776, year = {2023}, author = {Zámocký, M and Feranc, P}, title = {Discovering the deep evolutionary roots of serum amyloid A protein family.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {126537}, doi = {10.1016/j.ijbiomac.2023.126537}, pmid = {37634776}, issn = {1879-0003}, abstract = {Deep evolutionary origin of the conserved animal serum amyloid A (SAA) apolipoprotein family leading to yet unknown highly similar SAA-like sequences occurring in certain bacterial genomes is demonstrated in this contribution. Horizontal gene transfer event of corresponding genes between gut bacteria and non-vertebrate animals was discovered in the reconstructed phylogenetic tree obtained with maximum likelihood and neighbor-joining method, respectively. This detailed phylogeny based on totally 128 complete sequences comprised diverse serum amyloid A isoforms from various animal vertebrate and non-vertebrate phyla and also corresponding genes coding for highly similar proteins from animal gut bacteria. Typical largely conserved sequence motifs and a peculiar structural fold consisting mainly of four α-helix in a bundle within all reconstructed clades of the SAA protein family are discussed with respect to their supposed biological functions in various organisms that contain corresponding genes.}, }
@article {pmid37632379, year = {2023}, author = {Sabar, MA and Van Huy, T and Sugie, Y and Wada, H and Zhao, B and Matsuura, N and Ihara, M and Watanabe, T and Tanaka, H and Honda, R}, title = {Antimicrobial resistome and mobilome in the urban river affected by combined sewer overflows and wastewater treatment effluent.}, journal = {Journal of water and health}, volume = {21}, number = {8}, pages = {1032-1050}, doi = {10.2166/wh.2023.073}, pmid = {37632379}, issn = {1477-8920}, abstract = {The dissemination of antimicrobial resistance in the environment is an emerging global health problem. Wastewater treatment effluent and combined sewer overflows (CSOs) are major sources of antimicrobial resistance in urban rivers. This study aimed to clarify the effect of municipal wastewater treatment effluent and CSO on antimicrobial resistance genes (ARGs), mobile gene elements, and the microbial community in an urban river. The ARG abundance per 16S-based microbial population in the target river was 0.37-0.54 and 0.030-0.097 during the CSO event and dry weather, respectively. During the CSO event, the antimicrobial resistome in the river shifted toward a higher abundance of ARGs to clinically important drug classes, including macrolide, fluoroquinolone, and β-lactam, whereas ARGs to sulfonamide and multidrug by efflux pump were relatively abundant in dry weather. The abundance of intI1 and tnpA genes were highly associated with the total ARG abundance, suggesting their potential application as an indicator for estimating resistome contamination. Increase of prophage during the CSO event suggested that impact of CSO has a greater potential for horizontal gene transfer (HGT) via transduction. Consequently, CSO not only increases the abundance of ARGs to clinically important antimicrobials but also possibly enhances potential of HGT in urban rivers.}, }
@article {pmid37632043, year = {2023}, author = {Kozlova, AP and Saksaganskaia, AS and Afonin, AM and Muntyan, VS and Vladimirova, ME and Dzyubenko, EA and Roumiantseva, ML}, title = {A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/v15081701}, pmid = {37632043}, issn = {1999-4915}, support = {075-15-2022-320//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s-1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.}, }
@article {pmid37627664, year = {2023}, author = {Bonsaglia, ECR and Calvo, GH and Sordelli, DO and Silva, NCC and Rall, VLM and Casas, A and Buzzola, F}, title = {The Impact of Low-Level Benzalkonium Chloride Exposure on Staphylococcus spp. Strains and Control by Photoinactivation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/antibiotics12081244}, pmid = {37627664}, issn = {2079-6382}, support = {PICT2019-2883//Agencia Nacional de Promoci&#xf3;n de la Ciencia y Tecnolog&#xed;a (ANPCyT)/ ; PIP2021-11220200102843CO and PUE085//CONICET/ ; }, abstract = {Exposure of bacteria to low concentrations of biocides can facilitate horizontal gene transfer, which may lead to bacterial adaptive responses and resistance to antimicrobial agents. The emergence of antibacterial resistance not only poses a significant concern to the dairy industry but also adds to the complexity and cost of mastitis treatment. This study was aimed to evaluate how selective stress induced by benzalkonium chloride (BC) promotes antibiotic non-susceptibility in Staphylococcus spp. In addition, we investigated the efficacy of photodynamic inactivation (PDI) in both resistant and susceptible strains. The study determined the minimum inhibitory concentration (MIC) of BC using the broth microdilution method for different Staphylococcus strains. The experiments involved pairing strains carrying the qacA/qacC resistance genes with susceptible strains and exposing them to subinhibitory concentrations of BC for 72 h. The recovered isolates were tested for MIC BC and subjected to disc diffusion tests to assess changes in susceptibility patterns. The results demonstrated that subinhibitory concentrations of BC could select strains with reduced susceptibility and antibiotic resistance, particularly in the presence of S. pasteuri. The results of PDI mediated by toluidine blue (100 µM) followed by 60 min irradiation (total light dose of 2.5 J/cm[2]) were highly effective, showing complete inactivation for some bacterial strains and a reduction of up to 5 logs in others.}, }
@article {pmid37616556, year = {2023}, author = {Farrell, AA and Nesbø, CL and Zhaxybayeva, O}, title = {Early divergence and gene exchange highways in the evolutionary history of Mesoaciditogales.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad156}, pmid = {37616556}, issn = {1759-6653}, abstract = {The placement of a non-hyperthermophilic order Mesoaciditogales as the earliest branching clade within the Thermotogota phylum challenges the prevailing hypothesis that the last common ancestor of Thermotogota was a hyperthermophile. Yet, given the long branch leading to the only two Mesoaciditogales described to-date, the phylogenetic position of the order may be due to the long branch attraction artifact. By testing various models and applying data recoding in phylogenetic reconstructions, we observed that early branching of Mesoaciditogales within Thermotogota is strongly supported by the conserved marker genes assumed to be vertically inherited. However, based on the taxonomic content of 1,181 gene families and a phylogenetic analysis of 721 gene family trees, we also found that a substantial number of Mesoaciditogales genes are more closely related to species from the order Petrotogales. These genes contribute to coenzyme transport and metabolism, fatty acid biosynthesis, genes known to respond to heat and cold stressors, and include many genes of unknown functions. The Petrotogales comprise moderately thermophilic and mesophilic species with similar temperature tolerances to that of Mesoaciditogales. Our findings hint at extensive horizontal gene transfer between, or parallel independent gene gains by, the two ecologically similar lineages, and suggest that the exchanged genes may be important for adaptation to comparable temperature niches.}, }
@article {pmid37611393, year = {2023}, author = {Deng, WK and He, JL and Chen, JY and Wu, RT and Xing, SC and Liao, XD}, title = {Effects of microplastics on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132288}, doi = {10.1016/j.jhazmat.2023.132288}, pmid = {37611393}, issn = {1873-3336}, abstract = {Microplastics (MPs), as a new type of pollutant, widely exist in livestock and poultry breeding and agricultural soils. However, research on MPs pollution on greenhouse gas emissions in combined planting and breeding systems is lacking, especially from the perspective of phage horizontal gene transfer. Therefore, this paper explores the effects of MPs on functional genes related to CH4 and N2O metabolism in bacteriophages during manure composting and its planting applications. The results of the study indicated that the addition of MPs had an impact on both the physicochemical properties and microbial community structure of manure during the composting process and on the compost-applied rhizosphere soil of lactuca (Lactuca sativa). Specifically, on day 7 of composting, mcrA/pmoA and (nirS+nirK) levels in bacteria in the MP group significantly increased. Additionally, it was observed that the MP group had higher average temperatures during the high-temperature period of composting, which led to a rapid reduction in phages. However, the phage levels quickly recovered during the cooling period. Furthermore, the addition of MPs to the rhizosphere soil resulted in higher levels of nirK. These changes may affect greenhouse gas emissions.}, }
@article {pmid37610250, year = {2023}, author = {Zhao, Y and Kuang, W and An, Q and Li, J and Wang, Y and Deng, Z}, title = {Cryo-EM structures of African swine fever virus topoisomerase.}, journal = {mBio}, volume = {}, number = {}, pages = {e0122823}, doi = {10.1128/mbio.01228-23}, pmid = {37610250}, issn = {2150-7511}, abstract = {Type II topoisomerases ubiquitously exist in cellular organisms, where they play an essential role in resolving the topological problems of DNA. The viral type II topoisomerase encoded by the African swine fever virus (ASFV) is critical for viral replication and infection, thus representing an attractive target for antiviral drug development. Here we report two cryo-EM structures of ASFV topoisomerase P1192R in distinct conformations at an overall resolution of 3.16 Å and 3.13 Å, respectively. P1192R assembles as a homodimer with the C-gate formed by the coiled-coil domain adopting a closed or open conformation before reaction, providing the first visual evidence for the dynamic motions of the C-gate of type II topoisomerase. Comparative structural comparisons of eukaryotic homologs and P1192R reveal the unique structural features of P1192R, including the active site configuration, a flexible loop in the TOPRIM domain, an additionally inserted α-helix in the tower domain, and a pin-like structure in the C-terminal coiled-coil domain, which are important for enzyme activity and protein folding. These findings provide important insights into the structure and function of viral topoisomerases and may guide the efficient development of anti-ASFV drugs. Moreover, our study also offers structural evidence to support the scenario of the viral origin of eukaryotic type IIA topoisomerases. IMPORTANCE African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.}, }
@article {pmid37609252, year = {2023}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling novel lateral gene transfer events in the human microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.08.552500}, pmid = {37609252}, abstract = {Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (∼2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle .}, }
@article {pmid37605076, year = {2023}, author = {Baig, MIR and Kadu, P and Bawane, P and Nakhate, KT and Yele, S and Ojha, S and Goyal, SN}, title = {Mechanisms of emerging resistance associated with non-antibiotic antimicrobial agents: a state-of-the-art review.}, journal = {The Journal of antibiotics}, volume = {}, number = {}, pages = {}, pmid = {37605076}, issn = {1881-1469}, abstract = {Although the development of resistance by microorganisms to antimicrobial drugs has been recognized as a global public health concern, the contribution of various non-antibiotic antimicrobial agents to the development of antimicrobial resistance (AMR) remains largely neglected. The present review discusses various chemical substances and factors other than typical antibiotics, such as preservatives, disinfectants, biocides, heavy metals and improper chemical sterilization that contribute to the development of AMR. Furthermore, it encompasses the mechanisms like co-resistance and co-selection, horizontal gene transfer, changes in the composition and permeability of cell membrane, efflux pumps, transposons, biofilm formation and enzymatic degradation of antimicrobial chemicals which underlie the development of resistance to various non-antibiotic antimicrobial agents. In addition, the review addresses the resistance-associated changes that develops in microorganisms due to these agents, which ultimately contribute to the development of resistance to antibiotics. In order to prevent the indiscriminate use of chemical substances and create novel therapeutic agents to halt resistance development, a more holistic scientific approach might provide diversified views on crucial factors contributing to the persistence and spread of AMR. The review illustrates the common and less explored mechanisms contributing directly or indirectly to the development of AMR by non-antimicrobial agents that are commonly used.}, }
@article {pmid37595132, year = {2023}, author = {Kobayashi, N and Dang, TA and Kieu, PTM and Gómez Luciano, LB and Van Ba, V and Izumitsu, K and Shimizu, M and Ikeda, KI and Li, WH and Nakayashiki, H}, title = {Horizontally transferred DNA in the genome of the fungus Pyricularia oryzae is associated with repressive histone modifications.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad186}, pmid = {37595132}, issn = {1537-1719}, abstract = {Horizontal gene transfer (HGT) is a means of exchanging genetic material asexually. The process by which horizontally transferred genes are domesticated by the host genome is of great interest but is not well understood. In this study, we determined the telomere-to-telomere genome sequence of the wheat-infecting Pyricularia oryzae strain Br48. SNP analysis indicated that the Br48 strain is a hybrid of wheat- and Brachiaria-infecting strains by a sexual or parasexual cross. Comparative genomic analysis identified several megabase-scale "insertions" in the Br48 genome, some of which were possibly gained by HGT-related events from related species, such as P. pennisetigena or P. grisea. Notably, the mega-insertions often contained genes whose phylogeny is not congruent with the species phylogeny. Moreover, some of the genes have a close homolog even in distantly related organisms, such as basidiomycetes or prokaryotes, implying the involvement of multiple HGT events. Interestingly, the levels of the silent epigenetic marks H3K9me3 and H3K27me3 in a genomic region, tended to be negatively correlated with the phylogenetic concordance of genes in the same region, suggesting that horizontally transferred DNA is preferentially targeted for epigenetic silencing. Indeed, the putative HGT-derived genes were activated when MoKmt6, the gene responsible for H3K27me3 modification, was deleted. Notably, these genes also tended to be up-regulated during infection, suggesting that they are now under host control and has contributed to establishing a fungal niche. In conclusion, this study suggests that epigenetic modifications have played an important role in the domestication of HGT-derived genes in the P. oryzae genome.}, }
@article {pmid37594001, year = {2023}, author = {Yang, C and Xiang, Y and Qiu, S}, title = {Resistance in Enteric Shigella and nontyphoidal Salmonella: emerging concepts.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000000960}, pmid = {37594001}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: The emergence of globally resistant enteric Shigella and nontyphoidal Salmonella strains (NTS) has limited the selection of effective drugs, which has become a major challenge for the treatment of infections. The purpose of this review is to provide the current opinion on the antimicrobial-resistant enteric Shigella and nontyphoidal Salmonella.<br><br>RECENT FINDINGS: Enteric Shigella and NTS are resistant to almost all classes of antimicrobials in recent years. Those with co-resistance to ciprofloxacin, azithromycin and ceftriaxone, the first-line antibiotics for the treatment of infectious diarrhoea have emerged worldwide. Some of them have caused interregional and international spread by travel, trade, MSM, and polluted water sources. Several strains have even developed resistance to colistin, the last-resort antibiotic used for treatment of multidrug-resistant Gram-negative bacteria infections.<br><br>SUMMARY: The drug resistance of enteric Shigella and NTS is largely driven by the use of antibiotics and horizontal gene transfer of mobile genetic elements. These two species show various drug resistance patterns in different regions and serotypes. Hence treatment decisions for Shigella and Salmonella infections need to take into consideration prevalent antimicrobial drug resistance patterns. It is worth noting that the resistance genes such as blaCTX,mph, ermB, qnr and mcr, which can cause resistance to ciprofloxacin, cephalosporin, azithromycin and colistin are widespread because of transmission by IncFII, IncI1, IncI2 and IncB/O/K/Z plasmids. Therefore, continuous global monitoring of resistance in Shigella and Salmonella is imperative.}, }
@article {pmid37369704, year = {2023}, author = {Huang, J and Dai, X and Wu, Z and Hu, X and Sun, J and Tang, Y and Zhang, W and Han, P and Zhao, J and Liu, G and Wang, X and Mao, S and Wang, Y and Call, DR and Liu, J and Wang, L}, title = {Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1467-1481}, pmid = {37369704}, issn = {1751-7370}, support = {32072915//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31872517//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172917//National Natural Science Foundation of China (National Science Foundation of China)/ ; BK20170710//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; BK20210402//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Prophages/genetics ; Virulence/genetics ; Streptococcus/genetics ; *Anti-Infective Agents ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids ; Conjugation, Genetic ; }, abstract = {Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.}, }
@article {pmid37592233, year = {2023}, author = {Zhang, X and Xiao, L and Liu, J and Tian, Q and Xie, J}, title = {Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {462}, pmid = {37592233}, issn = {1471-2164}, support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.<br><br>RESULTS: To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.<br><br>CONCLUSIONS: Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.}, }
@article {pmid37586197, year = {2023}, author = {Shen, C and He, M and Zhang, J and Liu, J and Su, J and Dai, J}, title = {Effects of the coexistence of antibiotics and heavy metals on the fate of antibiotic resistance genes in chicken manure and surrounding soils.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115367}, doi = {10.1016/j.ecoenv.2023.115367}, pmid = {37586197}, issn = {1090-2414}, abstract = {Both heavy metals and antibiotics exert selection pressure on bacterial resistance, and as they are commonly co-contaminated in the environment, they may play a larger role in bacterial resistance. This study examined how breeding cycles affect antibiotic resistance genes (ARGs) in chicken manure and the surrounding topsoils at 20, 50, 100, 200, and 300 m from twelve typical laying hen farms in the Ningxia Hui Autonomous Region of northwest China. Six antibiotics, seven heavy metals, ten mobile genetic elements (MGEs), and microbial community affected the ARGs profile in chicken dung and soil samples. Tetracycline antibiotic residues were prevalent in chicken manure, as were relatively high content of aureomycin during each culture period. Zinc (Zn) content was highest among the seven heavy metals in chicken feces. Chicken dung also enriched aminoglycosides, MLSB, and tetracycline ARGs, notably during brooding and high production. The farm had a minimal influence on antibiotics in the surrounding soil, but its effect on ARGs and MGEs closer to the farm (50 m) was stronger, and several ARGs and MGEs increased with distance. Manure microbial composition differed dramatically throughout breeding cycles and sampling distances. ARGs were more strongly related with antibiotics and heavy metals in manure than soil, whereas MGEs were the reverse. Antibiotics, heavy metals, MGEs, and bacteria in manure accounted 12.28%, 22.25%, 0.74%, and 0.19% of ARGs composition variance, respectively, according to RDA and VPA. Bacteria (2.89%) and MGEs (2.82%) only affected soil ARGs composition. These findings showed that heavy metals and antibiotics are the main factors affecting faecal ARGs and bacteria and MGEs soil ARGs. This paper includes antibiotic resistance data for large-scale laying hen husbandry in northwest China and a theoretical framework for decreasing antibiotic resistance.}, }
@article {pmid37584599, year = {2023}, author = {Mi-Ichi, F and Tsugawa, H and Yoshida, H and Arita, M}, title = {Unique features of Entamoeba histolytica glycerophospholipid metabolism; has the E. histolytica lipid metabolism network evolved through gene loss and gain to enable parasitic life cycle adaptation?.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0017423}, doi = {10.1128/msphere.00174-23}, pmid = {37584599}, issn = {2379-5042}, abstract = {Entamoeba histolytica, a protozoan parasite, causes amoebiasis, which is a global public health problem. During the life cycle of this parasite, the properties of the cell membrane are changed markedly. To clarify the mechanism of membrane lipid changes, we exploited state-of-the-art untargeted lipidomic analysis, and atypical features of glycerophospholipids, lysoglycerophospholipids, and sphingolipids were observed compared with human equivalents. Here, we overview an entire E. histolytica glycerophospholipid metabolic pathway based on re-evaluated whole lipidome and genome along with the results of metabolic labeling experiments. We also discuss whether the E. histolytica lipid metabolism network, including the glycerophospholipid metabolic pathway, has unique features necessary for parasitic life cycle adaptation through gene loss and/or gain, and raise important questions involving biochemistry, molecular cell biology, and physiology underlying this network. Answering these questions will advance the understanding of Entamoeba physiology and will provide potential targets to develop new anti-amoebiasis drugs.}, }
@article {pmid37584505, year = {2023}, author = {Boyer, C and Lefeuvre, P and Richard, D and Lobin, KK and Pruvost, O}, title = {Complete genome sequence of a copper-resistant Xanthomonas campestris pv. campestris strain isolated from broccoli in Mauritius suggests adaptive gene gain through horizontal gene transfer.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-05-23-0177-SC}, pmid = {37584505}, issn = {0031-949X}, abstract = {Bacterial adaptation is facilitated by the presence of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) of genes, such as those coding for virulence factors or resistance to antimicrobial compounds. A hybrid assembly of Nanopore MinIon long read and Illumina short read data was produced from a copper-resistant Xanthomonas campestris pv. campestris (Xcc) strain isolated from symptomatic broccoli leaves in Mauritius. We obtained a 5.2 Mb high-quality chromosome and no plasmid. We found four genomic islands, three of which were characterized as integrative conjugative elements or integrative mobilizable elements. These genomic islands carried type III effectors and the copper resistance copLABMGF system involved in pathogenicity and environmental adaptation, respectively.}, }
@article {pmid37582866, year = {2023}, author = {}, title = {Horizontal gene transfer explains unusual traits of Armillaria fungi.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37582866}, issn = {2058-5276}, }
@article {pmid37459818, year = {2023}, author = {Kelleher, ES}, title = {Jack of all trades versus master of one: how generalist versus specialist strategies of transposable elements relate to their horizontal transfer between lineages.}, journal = {Current opinion in genetics &amp; development}, volume = {81}, number = {}, pages = {102080}, doi = {10.1016/j.gde.2023.102080}, pmid = {37459818}, issn = {1879-0380}, mesh = {*DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genomics ; }, abstract = {Transposable elements (TEs) are obligate genomic parasites, relying on host germline cells to ensure their replication and passage to future generations. While some TEs exhibit high fidelity to their host genome, being passed from parent to offspring through vertical transmission for millions of years, others frequently invade new and distantly related hosts through horizontal transfer. In this review, I highlight how the complexity of interactions between TE and host required for transposition may be an important determinant of horizontal transfer: with TEs with more complex regulatory requirements being less able to invade new host genomes.}, }
@article {pmid37578142, year = {2023}, author = {Luo, G and Liang, B and Cui, H and Kang, Y and Zhou, X and Tao, Y and Lu, L and Fan, L and Guo, J and Wang, A and Gao, SH}, title = {Determining the Contribution of Micro/Nanoplastics to Antimicrobial Resistance: Challenges and Perspectives.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c01128}, pmid = {37578142}, issn = {1520-5851}, abstract = {Microorganisms colonizing the surfaces of microplastics form a plastisphere in the environment, which captures miscellaneous substances. The plastisphere, owning to its inherently complex nature, may serve as a "Petri dish" for the development and dissemination of antibiotic resistance genes (ARGs), adding a layer of complexity in tackling the global challenge of both microplastics and ARGs. Increasing studies have drawn insights into the extent to which the proliferation of ARGs occurred in the presence of micro/nanoplastics, thereby increasing antimicrobial resistance (AMR). However, a comprehensive review is still lacking in consideration of the current increasingly scattered research focus and results. This review focuses on the spread of ARGs mediated by microplastics, especially on the challenges and perspectives on determining the contribution of microplastics to AMR. The plastisphere accumulates biotic and abiotic materials on the persistent surfaces, which, in turn, offers a preferred environment for gene exchange within and across the boundary of the plastisphere. Microplastics breaking down to smaller sizes, such as nanoscale, can possibly promote the horizontal gene transfer of ARGs as environmental stressors by inducing the overgeneration of reactive oxygen species. Additionally, we also discussed methods, especially quantitatively comparing ARG profiles among different environmental samples in this emerging field and the challenges that multidimensional parameters are in great necessity to systematically determine the antimicrobial dissemination risk in the plastisphere. Finally, based on the biological sequencing data, we offered a framework to assess the AMR risks of micro/nanoplastics and biocolonizable microparticles that leverage multidimensional AMR-associated messages, including the ARGs' abundance, mobility, and potential acquisition by pathogens.}, }
@article {pmid37577532, year = {2023}, author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT}, title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.07.28.551029}, pmid = {37577532}, abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae , but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae , exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.}, }
@article {pmid37577448, year = {2023}, author = {Bonatelli, ML and Rohwerder, T and Popp, D and Liu, Y and Akay, C and Schultz, C and Liao, KP and Ding, C and Reemtsma, T and Adrian, L and Kleinsteuber, S}, title = {Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1223838}, pmid = {37577448}, issn = {1664-302X}, abstract = {Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.}, }
@article {pmid37574851, year = {2023}, author = {Chandler, M and Ross, K and Varani, AM}, title = {The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15140}, pmid = {37574851}, issn = {1365-2958}, abstract = {Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.}, }
@article {pmid37567328, year = {2023}, author = {Andrade-Oliveira, AL and Rodrigues, GL and Pereira, MF and Bahia, AC and Machado, EA and Rossi, CC and Giambiagi-deMarval, M}, title = {Tenebrio molitor as a model system to study Staphylococcus spp virulence and horizontal gene transfer.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106304}, doi = {10.1016/j.micpath.2023.106304}, pmid = {37567328}, issn = {1096-1208}, abstract = {Invertebrates can provide a valuable alternative to traditional vertebrate animal models for studying bacterial and fungal infections. This study aimed to establish the larvae of the coleoptera Tenebrio molitor (mealworm) as an in vivo model for evaluating virulence and horizontal gene transfer between Staphylococcus spp. After identifying the best conditions for rearing T. molitor, larvae were infected with different Staphylococcus species, resulting in dose-dependent killing curves. All species tested killed the insects at higher doses, with S. nepalensis and S. aureus being the most and least virulent, respectively. However, only S. nepalensis was able to kill more than 50% of larvae 72 h post-infection at a low amount of 10[5] CFU. Staphylococcus infection also stimulated an increase in the concentration of hemocytes present in the hemolymph, which was proportional to the virulence. To investigate T. molitor's suitability as an in vivo model for plasmid transfer studies, we used S. aureus strains as donor and recipient of a plasmid containing the gentamicin resistance gene aac(6')-aph(2″). By inoculating larvae with non-lethal doses of each, we observed conjugation, and obtained transconjugant colonies with a frequency of 1.6 × 10[-5] per donor cell. This study demonstrates the potential of T. molitor larvae as a reliable and cost-effective model for analyzing the virulence of Staphylococcus and, for the first time, an optimal environment for the plasmid transfer between S. aureus carrying antimicrobial resistance genes.}, }
@article {pmid37565764, year = {2023}, author = {Yin, L and Wang, X and Xu, H and Yin, B and Wang, X and Zhang, Y and Li, X and Luo, Y and Chen, Z}, title = {Unrecognized risk of perfluorooctane sulfonate in promoting conjugative transfers of bacterial antibiotic resistance genes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0053323}, doi = {10.1128/aem.00533-23}, pmid = {37565764}, issn = {1098-5336}, abstract = {Antibiotic resistance is a major global health crisis facing humanity, with horizontal gene transfer (HGT) as a principal dissemination mechanism in the natural and clinical environments. Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse effects on humans. However, it is unknown whether PFASs affect the HGT of bacterial antibiotic resistance. Using a genetically engineered Escherichia coli MG1655 as the donor of plasmid-encoded antibiotic resistance genes (ARGs), E. coli J53 and soil bacterial community as two different recipients, this study demonstrated that the conjugation frequency of ARGs between two E. coli strains was (1.45 ± 0.17) × 10[-5] and perfluorooctane sulfonate (PFOS) at environmentally relevant concentrations (2-50 μg L[-1]) increased conjugation transfer between E. coli strains by up to 3.25-fold. Increases in reactive oxygen species production, cell membrane permeability, biofilm formation capacity, and cell contact in two E. coli strains were proposed as major promotion mechanisms from PFOS exposure. Weighted gene co-expression network analysis of transcriptome data identified a series of candidate genes whose expression changes could contribute to the increase in conjugation transfer induced by PFOS. Furthermore, PFOS also generally increased the ARG transfer into the studied soil bacterial community, although the uptake ability of different community members of the plasmid either increased or decreased upon PFOS exposure depending on specific bacterial taxa. Overall, this study reveals an unrecognized risk of PFOS in accelerating the dissemination of antibiotic resistance. IMPORTANCE Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse health effects. Although the influence of environmental pollutants on the spread of antibiotic resistance, one of the biggest threats to global health, has attracted increasing attention in recent years, it is unknown whether environmental residues of PFASs affect the dissemination of bacterial antibiotic resistance. Considering PFASs, often called "forever" compounds, have significantly higher environmental persistence than most emerging organic contaminants, exploring the effect of PFASs on the spread of antibiotic resistance is more environmentally relevant and has essential ecological and health significance. By systematically examining the influence of perfluorooctane sulfonate on the antibiotic resistance gene conjugative transfer, not only at the single-strain level but also at the community level, this study has uncovered an unrecognized risk of PFASs in promoting conjugative transfers of bacterial antibiotic resistance genes, which could be incorporated into the risk assessment framework of PFASs.}, }
@article {pmid37440531, year = {2023}, author = {Gulay, A and Fournier, G and Smets, BF and Girguis, PR}, title = {Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation.}, journal = {Molecular biology and evolution}, volume = {40}, number = {8}, pages = {}, doi = {10.1093/molbev/msad161}, pmid = {37440531}, issn = {1537-1719}, abstract = {Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.}, }
@article {pmid37561843, year = {2023}, author = {Cooper, RM and Wright, JA and Ng, JQ and Goyne, JM and Suzuki, N and Lee, YK and Ichinose, M and Radford, G and Ryan, FJ and Kumar, S and Thomas, EM and Vrbanac, L and Knight, R and Woods, SL and Worthley, DL and Hasty, J}, title = {Engineered bacteria detect tumor DNA.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6658}, pages = {682-686}, doi = {10.1126/science.adf3974}, pmid = {37561843}, issn = {1095-9203}, abstract = {Synthetic biology has developed sophisticated cellular biosensors to detect and respond to human disease. However, biosensors have not yet been engineered to detect specific extracellular DNA sequences and mutations. Here, we engineered naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells, organoids, and tumors. We characterized the functionality of the biosensors in vitro with coculture assays and then validated them in vivo with sensor bacteria delivered to mice harboring colorectal tumors. We observed horizontal gene transfer from the tumor to the sensor bacteria in our mouse model of CRC. This cellular assay for targeted, CRISPR-discriminated horizontal gene transfer (CATCH) enables the biodetection of specific cell-free DNA.}, }
@article {pmid37557975, year = {2023}, author = {Weaver, RJ and McDonald, AE}, title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {}, number = {}, pages = {149003}, doi = {10.1016/j.bbabio.2023.149003}, pmid = {37557975}, issn = {1879-2650}, abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.}, }
@article {pmid37557016, year = {2023}, author = {Veremeichik, GN and Gorpenchenko, TY and Rusapetova, TV and Brodovskaya, EV and Tchernoded, GK and Bulgakov, DV and Shkryl, YN and Bulgakov, VP}, title = {Auxin-dependent regulation of growth via rolB-induced modulation of the ROS metabolism in the long-term cultivated pRiA4-transformed Rubiacordifolia L. calli.}, journal = {Plant physiology and biochemistry : PPB}, volume = {202}, number = {}, pages = {107932}, doi = {10.1016/j.plaphy.2023.107932}, pmid = {37557016}, issn = {1873-2690}, abstract = {Gene transfer from Agrobacterium to plants is the best studied example of horizontal gene transfer (HGT) between prokaryotes and eukaryotes. The rol genes of A. rhizogenes (Rhizobium rhizogenes) provide uncontrolled root growth, or "hairy root" syndrome, the main diagnostic feature. In the present study, we investigated the stable pRiA4-transformed callus culture of Rubia cordifolia L. While untransformed callus cultures need PGRs (plant growth regulators) as an obligatory supplement, pRiA4 calli is able to achieve long-term PGR-free cultivation. For the first time, we described the pRiA4-transformed callus cultures' PGR-dependent ROS status, growth, and specialized metabolism. As we have shown, expression of the rolA and rolB but not the rolC genes is contradictory in a PGR-dependent manner. Moreover, a PGR-free pRiA4 transformed cell line is characterised as more anthraquinone (AQ) productive than an untransformed cell culture. These findings pertain to actual plant biotechnology: it could be the solution to troubles in choosing the best PGR combination for the cultivation of some rare, medicinal, and woody plants; wild-type Ri-plants and tissue cultures may become freed from legal controls on genetically modified organisms in the future. We propose possible PGR-dependent relationships between rolA and rolB as well as ROS signalling targets. The present study highlighted the high importance of the rolA gene in the regulation of combined rol gene effects and the large knowledge gap in rolA action.}, }
@article {pmid37549546, year = {2023}, author = {Ren, CY and Xu, QJ and Alvarez, PJJ and Zhu, L and Zhao, HP}, title = {Simultaneous antibiotic removal and mitigation of resistance induction by manganese bio-oxidation process.}, journal = {Water research}, volume = {244}, number = {}, pages = {120442}, doi = {10.1016/j.watres.2023.120442}, pmid = {37549546}, issn = {1879-2448}, abstract = {Microbial degradation to remove residual antibiotics in wastewater is of growing interest. However, biological treatment of antibiotics may cause resistance dissemination by mutations and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). In this study, a Mn(Ⅱ)-oxidizing bacterium (MnOB), Pseudomonas aeruginosa MQ2, simultaneously degraded antibiotics, decreased HGT, and mitigated antibiotic resistance mutation. Intracellular Mn(II) levels increased during manganese oxidation, and biogenic manganese oxides (BioMnOx, including Mn(II), Mn(III) and Mn(IV)) tightly coated the cell surface. Mn(II) bio-oxidation mitigated antibiotic resistance acquisition from an E. coli ARG donor and mitigated antibiotic resistance inducement by decreasing conjugative transfer and mutation, respectively. BioMnOx also oxidized ciprofloxacin (1 mg/L) and tetracycline (5 mg/L), respectively removing 93% and 96% within 24 h. Transcriptomic analysis revealed that two new multicopper oxidase and one peroxidase genes are involved in Mn(II) oxidation. Downregulation of SOS response, multidrug resistance and type Ⅳ secretion system related genes explained that Mn(II) and BioMnOx decreased HGT and mitigated resistance mutation by alleviating oxidative stress, which makes recipient cells more vulnerable to ARG acquisition and mutation. A manganese bio-oxidation based reactor was constructed and completely removed tetracycline with environmental concentration within 4-hour hydraulic retention time. Overall, this study suggests that Mn (II) bio-oxidation process could be exploited to control antibiotic contamination and mitigate resistance propagation during water treatment.}, }
@article {pmid37550759, year = {2023}, author = {Pas, C and Latka, A and Fieseler, L and Briers, Y}, title = {Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {174}, pmid = {37550759}, issn = {1743-422X}, support = {1S79422N//Fonds Wetenschappelijk Onderzoek/ ; 1240021N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups.<br><br>METHODS: Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution.<br><br>RESULTS: We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages.<br><br>CONCLUSION: The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.}, }
@article {pmid37550506, year = {2023}, author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG}, title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37550506}, issn = {2058-5276}, support = {758161//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LP2019-13/2019//Magyar Tudom&#xe1;nyos Akad&#xe9;mia (Hungarian Academy of Sciences)/ ; }, abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.}, }
@article {pmid37548082, year = {2023}, author = {Zackova Suchanova, J and Bilcke, G and Romanowska, B and Fatlawi, A and Pippel, M and Skeffington, A and Schroeder, M and Vyverman, W and Vandepoele, K and Kröger, N and Poulsen, N}, title = {Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19145}, pmid = {37548082}, issn = {1469-8137}, support = {GOA01G01323//Bijzonder Onderzoeksfonds UGent/ ; INST 269/731-1 FUGG//Deutsche Forschungsgemeinschaft/ ; KR 1853/9-1//Deutsche Forschungsgemeinschaft/ ; PO 2256/1-1//Deutsche Forschungsgemeinschaft/ ; 100232736//European Regional Development Fund/ ; 1228423N//Fonds Wetenschappelijk Onderzoek/ ; 03Z22EB1//German Federal Ministry of Education and Research/ ; }, abstract = {Biofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit intertidal substrata. The development of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. However, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown. Here, we have used proteomics, immunolocalization, comparative genomics, phylogenetics and structural homology analysis to investigate the evolutionary history and function of diatom adhesive proteins. Our study identified eight proteins from the adhesive trails of Craspedostauros australis, of which four form a new protein family called Trailins that contain an enigmatic Choice-of-Anchor A (CAA) domain, which was acquired through horizontal gene transfer from bacteria. Notably, the CAA-domain shares a striking structural similarity with one of the most widespread domains found in ice-binding proteins (IPR021884). Our work offers new insights into the molecular basis for diatom biofilm formation, shedding light on the function and evolution of diatom adhesive proteins. This discovery suggests that there is a transition in the composition of biomolecules required for initial surface colonization and those utilized for 3D biofilm matrix formation.}, }
@article {pmid37541538, year = {2023}, author = {Nielsen, TK and Winther-Have, CS and Thomsen, IM and Jackson, RW and Rabiey, M and Hennessy, RC and Bak, F and Kot, W and Nicolaisen, MH and Carstens, AB and Hansen, LH}, title = {Genetic rearrangements in Pseudomonas amygdali pathovar aesculi shape coronatine plasmids.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105486}, doi = {10.1016/j.meegid.2023.105486}, pmid = {37541538}, issn = {1567-7257}, abstract = {Plant pathogenic Pseudomonas species use multiple classes of toxins and virulence factors during host infection. The genes encoding these pathogenicity factors are often located on plasmids and other mobile genetic elements, suggesting that they are acquired through horizontal gene transfer to confer an evolutionary advantage for successful adaptation to host infection. However, the genetic rearrangements that have led to mobilization of the pathogenicity genes are not fully understood. In this study, we have sequenced and analyzed the complete genome sequences of four Pseudomonas amygdali pv. aesculi (Pae), which infect European horse chestnut trees (Aesculus hippocastanum) and belong to phylogroup 3 of the P. syringae species complex. The four investigated genomes contain six groups of plasmids that all encode pathogenicity factors. Effector genes were found to be mostly associated with insertion sequence elements, suggesting that virulence genes are generally mobilized and potentially undergo horizontal gene transfer after transfer to a conjugative plasmid. We show that the biosynthetic gene cluster encoding the phytotoxin coronatine was recently transferred from a chromosomal location to a mobilizable plasmid that subsequently formed a co-integrate with a conjugative plasmid.}, }
@article {pmid37541493, year = {2023}, author = {Li, S and Li, X and Chang, H and Zhong, N and Ren, N and Ho, SH}, title = {Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166029}, doi = {10.1016/j.scitotenv.2023.166029}, pmid = {37541493}, issn = {1879-1026}, abstract = {With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.}, }
@article {pmid37537271, year = {2023}, author = {Lund, D and Coertze, RD and Parras-Moltó, M and Berglund, F and Flach, CF and Johnning, A and Larsson, DGJ and Kristiansson, E}, title = {Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {812}, pmid = {37537271}, issn = {2399-3642}, support = {2018-02835//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-05771//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-03482//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, abstract = {Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.}, }
@article {pmid37533411, year = {2023}, author = {Groisman, EA and Choi, J}, title = {Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2300062}, doi = {10.1002/bies.202300062}, pmid = {37533411}, issn = {1521-1878}, abstract = {Horizontal gene transfer advances bacterial evolution. To benefit from horizontally acquired genes, enteric bacteria must overcome silencing caused when the widespread heat-stable nucleoid structuring (H-NS) protein binds to AT-rich horizontally acquired genes. This ability had previously been ascribed to both anti-silencing proteins outcompeting H-NS for binding to AT-rich DNA and RNA polymerase initiating transcription from alternative promoters. However, we now know that pathogenic Salmonella enterica serovar Typhimurium and commensal Escherichia coli break down H-NS when this silencer is not bound to DNA. Curiously, both species use the same protease - Lon - to destroy H-NS in distinct environments. Anti-silencing proteins promote the expression of horizontally acquired genes without binding to them by displacing H-NS from AT-rich DNA, thus leaving H-NS susceptible to proteolysis and decreasing H-NS amounts overall. Conserved amino acid sequences in the Lon protease and H-NS cleavage site suggest that diverse bacteria degrade H-NS to exploit horizontally acquired genes.}, }
@article {pmid37533217, year = {2023}, author = {Shin, NR and Pauchet, Y}, title = {First evidence of a horizontally-acquired GH-7 cellobiohydrolase from a longhorned beetle genome.}, journal = {Archives of insect biochemistry and physiology}, volume = {}, number = {}, pages = {e22039}, doi = {10.1002/arch.22039}, pmid = {37533217}, issn = {1520-6327}, support = {//Max Planck Society/ ; PA2808/4-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Xylophagous larvae of longhorned beetles (Coleoptera; Cerambycidae) efficiently break down polysaccharides of the plant cell wall, which make the bulk of their food, using a range of carbohydrate-active enzymes (CAZymes). In this study, we investigated the function and evolutionary history of the first identified example of insect-encoded members of glycoside hydrolase family 7 (GH7) derived from the Lamiinae Exocentrus adspersus. The genome of this beetle contained two genes encoding GH7 proteins located in tandem and flanked by transposable elements. Phylogenetic analysis revealed that the GH7 sequences of E. adspersus were closely related to those of Ascomycete fungi, suggesting that they were acquired through horizontal gene transfer (HGT) from fungi. However, they were more distantly related to those encoded by genomes of Crustacea and of protist symbionts of termites and cockroaches, supporting that the same enzyme family was recruited several times independently in Metazoa during the course of their evolution. The recombinant E. adspersus GH7 was found to primarily break down cellulose polysaccharides into cellobiose, indicating that it is a cellobiohydrolase, and could also use smaller cellulose oligomers as substrates. Additionally, the cellobiohydrolase activity was boosted by the presence of calcium chloride. Our findings suggest that the combination of GH7 cellobiohydrolases with other previously characterized endo-β-1,4-glucanases and β-glucosidases allows longhorned beetles like E. adspersus to efficiently break down cellulose into monomeric glucose.}, }
@article {pmid37531380, year = {2023}, author = {Pinder, C and Lebedinec, R and Levine, TP and Birch, M and Oliver, JD}, title = {Characterisation of putative class 1A DHODH-like proteins from Mucorales and dematiaceous mould species.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289441}, doi = {10.1371/journal.pone.0289441}, pmid = {37531380}, issn = {1932-6203}, abstract = {Olorofim is a new antifungal in clinical development which has a novel mechanism of action against dihydroorotate dehydrogenase (DHODH). DHODH form a ubiquitous family of enzymes in the de novo pyrimidine biosynthetic pathway and are split into class 1A, class 1B and class 2. Olorofim specifically targets the fungal class 2 DHODH present in a range of pathogenic moulds. The nature and number of DHODH present in many fungal species have not been addressed for large clades of this kingdom. Mucorales species do not respond to olorofim; previous work suggests they have only class 1A DHODH and so lack the class 2 target that olorofim inhibits. The dematiaceous moulds have mixed susceptibility to olorofim, yet previous analyses imply that they have class 2 DHODH. As this is at odds with their intermediate susceptibility to olorofim, we hypothesised that these pathogens may maintain a second class of DHODH, facilitating pyrimidine biosynthesis in the presence of olorofim. The aim of this study was to investigate the DHODH repertoire of clinically relevant species of Mucorales and dematiaceous moulds to further characterise these pathogens and understand variations in olorofim susceptibility. Using bioinformatic analysis, S. cerevisiae complementation and biochemical assays of recombinant protein, we provide the first evidence that two representative members of the Mucorales have only class 1A DHODH, substantiating a lack of olorofim susceptibility. In contrast, bioinformatic analyses initially suggested that seven dematiaceous species appeared to harbour both class 1A-like and class 2-like DHODH genes. However, further experimental investigation of the putative class 1A-like genes through yeast complementation and biochemical assays characterised them as dihydrouracil oxidases rather than DHODHs. These data demonstrate variation in dematiaceous mould olorofim susceptibility is not due to a secondary DHODH and builds on the growing picture of fungal dihydrouracil oxidases as an example of horizontal gene transfer.}, }
@article {pmid37526972, year = {2023}, author = {Winter, M and Harms, K and Johnsen, PJ and Buckling, A and Vos, M}, title = {Testing for the fitness benefits of natural transformation during community-embedded evolution.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, doi = {10.1099/mic.0.001375}, pmid = {37526972}, issn = {1465-2080}, abstract = {Natural transformation is a process where bacteria actively take up DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. The evolutionary benefits of transformation are still under debate. One main explanation is that foreign allele and gene uptake facilitates natural selection by increasing genetic variation, analogous to meiotic sex. However, previous experimental evolution studies comparing fitness gains of evolved transforming- and isogenic non-transforming strains have yielded mixed support for the 'sex hypothesis.' Previous studies testing the sex hypothesis for natural transformation have largely ignored species interactions, which theory predicts provide conditions favourable to sex. To test for the adaptive benefits of bacterial transformation, the naturally transformable wild-type Acinetobacter baylyi and a transformation-deficient ∆comA mutant were evolved for 5 weeks. To provide strong and potentially fluctuating selection, A. baylyi was embedded in a community of five other bacterial species. DNA from a pool of different Acinetobacter strains was provided as a substrate for transformation. No effect of transformation ability on the fitness of evolved populations was found, with fitness increasing non-significantly in most treatments. Populations showed fitness improvement in their respective environments, with no apparent costs of adaptation to competing species. Despite the absence of fitness effects of transformation, wild-type populations evolved variable transformation frequencies that were slightly greater than their ancestor which potentially could be caused by genetic drift.}, }
@article {pmid37526649, year = {2023}, author = {Rodrigues, JA and Blankenship, HM and Cha, W and Mukherjee, S and Sloup, RE and Rudrik, JT and Soehnlen, M and Manning, SD}, title = {Pangenomic analyses of antibiotic-resistant Campylobacter jejuni reveal unique lineage distributions and epidemiological associations.}, journal = {Microbial genomics}, volume = {9}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001073}, pmid = {37526649}, issn = {2057-5858}, abstract = {Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of Campylobacter jejuni, a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index P<0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of C. jejuni, while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of C. jejuni. They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.}, }
@article {pmid37517232, year = {2023}, author = {Zheng, Z and Huang, Y and Liu, L and Wang, L and Tang, J}, title = {Interaction between microplastic biofilm formation and antibiotics: Effect of microplastic biofilm and its driving mechanisms on antibiotic resistance gene.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132099}, doi = {10.1016/j.jhazmat.2023.132099}, pmid = {37517232}, issn = {1873-3336}, abstract = {As two pollutants with similar transport pathways, microplastics (MPs) and antibiotics (ATs) inevitably co-exist in water environments, and their interaction has become a topic of intense research interest for scholars over the past few years. This paper comprehensively and systematically reviews the current interaction between MPs and ATs, in particular, the role played by biofilm developed MPs (microplastic biofilm). A summary of the formation process of microplastic biofilm and its unique microbial community structure is presented in the paper. The formation of microplastic biofilm can enhance the adsorption mechanisms of ATs on primary MPs. Moreover, microplastic biofilm system is a diverse and vast reservoir of genetic material, and this paper reviews the mechanisms by which microplastics with biofilm drive the production of antibiotic resistance genes (ARGs) and the processes that selectively enrich for more ARGs. Meanwhile, the enrichment of ARGs may lead to the development of microbial resistance and the gradual loss of the antimicrobial effect of ATs. The transfer pathways of ARGs affected by microplastic biofilm are outlined, and ARGs dependent transfer of antibiotic resistance bacteria (ARB) is mainly through horizontal gene transfer (HGT). Furthermore, the ecological implications of the interaction between microplastic biofilm and ATs and perspectives for future research are reviewed. This review contributes to a new insight into the aquatic ecological environmental risks and the fate of contaminants (MPs, ATs), and is of great significance for controlling the combined pollution of these two pollutants.}, }
@article {pmid37513735, year = {2023}, author = {Nath, J and De, J and Sur, S and Banerjee, P}, title = {Interaction of Microbes with Microplastics and Nanoplastics in the Agroecosystems-Impact on Antimicrobial Resistance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/pathogens12070888}, pmid = {37513735}, issn = {2076-0817}, support = {2020-70020-33033//National Institute of Food and Agriculture/ ; 2022-70020-37590//National Institute of Food and Agriculture/ ; }, abstract = {Microplastics (MPs) and nanoplastics (NPs) are hotspots for the exchange of antimicrobial resistance genes (ARGs) between different bacterial taxa in the environment. Propagation of antimicrobial resistance (AMR) is a global public health issue that needs special attention concerning horizontal gene transfer (HGT) under micro-nano plastics (MNPs) pressure. Interactions between MNPs and microbes, or mere persistence of MNPs in the environment (either water or soil), influence microbial gene expressions, affecting autochthonous microbiomes, their resistomes, and the overall ecosystem. The adsorption of a range of co-contaminants on MNPs leads to the increased interaction of pollutants with microbes resulting in changes in AMR, virulence, toxin production, etc. However, accurately estimating the extent of MNP infestation in agroecosystems remains challenging. The main limitation in estimating the level of MNPs contamination in agroecosystems, surface and subsurface waters, or sediments is the lack of standardized protocols for extraction of MPs and analytical detection methods from complex high organic content matrices. Nonetheless, recent advances in MPs detection from complex matrices with high organic matter content are highly promising. This review aims to provide an overview of relevant information available to date and summarize the already existing knowledge about the mechanisms of MNP-microbe interactions including the different factors with influence on HGT and AMR. In-depth knowledge of the enhanced ARGs propagation in the environment under the influence of MNPs could raise the needed awareness, about future consequences and emergence of multidrug-resistant bacteria.}, }
@article {pmid37513616, year = {2023}, author = {Fan, X and Lu, Y and Zhao, Y and Miao, H and Qi, K and Wang, R}, title = {An Insight into the Exploration of Antibiotic Resistance Genes in Calorie Restricted Diet Fed Mice.}, journal = {Nutrients}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/nu15143198}, pmid = {37513616}, issn = {2072-6643}, support = {7212143//Natural Science Foundation of Beijing/ ; 81803214, 81800750, 82003432//National Natural Science Foundation of China/ ; }, abstract = {Antibiotic resistance genes (ARGs) threaten the success of modern drugs against multidrug resistant infections. ARGs can be transferred to opportunistic pathogens by horizontal gene transfer (HGT). Many studies have investigated the characteristics of ARGs in various chemical stressors. Studies on the effects of dietary nutrition and dietary patterns on ARGs are rare. The study first demonstrated the effect of calorie restricted (CR) diet on the ARGs and mobile genetic elements (MGEs) in mouse feces and explored their relationship with gut microbiota and their functions. The results showed that the abundance of the total ARGs in mouse feces of the CR group increased, especially tetracycline ARGs (tetW-01). The abundance of the MLSB ARGs (ermB) decreased evidently in mouse feces of the CR group. In addition, the total abundance of MGEs decreased evidently in the CR group, especially tnpA-03. In the meantime, the abundance of Lactobacillus and Bifidobacterium in mouse feces of the CR group increased remarkably. The Spearman correlation analysis between gut microbiota and ARGs showed that several probiotics were significantly positively correlated with ARGs (tetW-01), which might be the main contribution to the increase in ARGs of the CR group.}, }
@article {pmid37513002, year = {2023}, author = {Gryganskyi, AP and Golan, J and Muszewska, A and Idnurm, A and Dolatabadi, S and Mondo, SJ and Kutovenko, VB and Kutovenko, VO and Gajdeczka, MT and Anishchenko, IM and Pawlowska, J and Tran, NV and Ebersberger, I and Voigt, K and Wang, Y and Chang, Y and Pawlowska, TE and Heitman, J and Vilgalys, R and Bonito, G and Benny, GL and Smith, ME and Reynolds, N and James, TY and Grigoriev, IV and Spatafora, JW and Stajich, JE}, title = {Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned?.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/microorganisms11071830}, pmid = {37513002}, issn = {2076-2607}, abstract = {The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.}, }
@article {pmid37512869, year = {2023}, author = {Zinno, P and Perozzi, G and Devirgiliis, C}, title = {Foodborne Microbial Communities as Potential Reservoirs of Antimicrobial Resistance Genes for Pathogens: A Critical Review of the Recent Literature.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/microorganisms11071696}, pmid = {37512869}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is a global and increasing threat to human health. Several genetic determinants of AMR are found in environmental reservoirs, including bacteria naturally associated with widely consumed fermented foods. Through the food chain, these bacteria can reach the gut, where horizontal gene transfer (HGT) can occur within the complex and populated microbial environment. Numerous studies on this topic have been published over the past decades, but a conclusive picture of the potential impact of the non-pathogenic foodborne microbial reservoir on the spread of AMR to human pathogens has not yet emerged. This review critically evaluates a comprehensive list of recent experimental studies reporting the isolation of AMR bacteria associated with fermented foods, focusing on those reporting HGT events, which represent the main driver of AMR spread within and between different bacterial communities. Overall, our analysis points to the methodological heterogeneity as a major weakness impairing determination or a causal relation between the presence of AMR determinants within the foodborne microbial reservoir and their transmission to human pathogens. The aim is therefore to highlight the main gaps and needs to better standardize future studies addressing the potential role of non-pathogenic bacteria in the spread of AMR.}, }
@article {pmid37512822, year = {2023}, author = {Di Pierro, F and Campedelli, I and De Marta, P and Fracchetti, F and Del Casale, A and Cavecchia, I and Matera, M and Cazzaniga, M and Bertuccioli, A and Guasti, L and Zerbinati, N}, title = {Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/microorganisms11071649}, pmid = {37512822}, issn = {2076-2607}, abstract = {Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of B. breve (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of B. breve PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (rpoB and erm(X)) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the erm(X) gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis.}, }
@article {pmid37511529, year = {2023}, author = {Kordiš, D and Turk, V}, title = {Origin and Early Diversification of the Papain Family of Cysteine Peptidases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, doi = {10.3390/ijms241411761}, pmid = {37511529}, issn = {1422-0067}, support = {P1-0207, P1-0140, J1-2473//Slovenian Research Agency/ ; }, abstract = {Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.}, }
@article {pmid37511216, year = {2023}, author = {Kim, YK and Jo, S and Cheon, SH and Hong, JR and Kim, KJ}, title = {Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae).}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, doi = {10.3390/ijms241411448}, pmid = {37511216}, issn = {1422-0067}, support = {NRF-2021R1A2C1013731//National Research Foundation of Korea/ ; NRF-2020R1A6A3A01100512//National Research Foundation of Korea/ ; }, abstract = {Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.}, }
@article {pmid37508388, year = {2023}, author = {Zuber, NE and Fornasero, LV and Erdozain Bagolín, SA and Lozano, MJ and Sanjuán, J and Del Papa, MF and Lagares, A}, title = {Diversity, Genomics and Symbiotic Characteristics of Sinorhizobia That Nodulate Desmanthus spp. in Northwest Argentina.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/biology12070958}, pmid = {37508388}, issn = {2079-7737}, support = {PICT-2019-01021//Ministerio de Ciencia Tecnololog&#xed;a e Innovaci&#xf3;n Productiva - MinCyT, Argentina/ ; PIP 2022-2024-11220210100367CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas - CONICET, Argentina/ ; ATN-RF-18786-RG//FONTAGRO/ ; }, abstract = {Desmanthus spp. are legumes with the ability to associate with diverse α-proteobacteria-a microsymbiont-in order to establish nitrogen-fixing root nodules. A previous investigation from our laboratory revealed that the main bacteria associated with Desmanthus paspalaceus in symbiosis in central Argentina (Province of Santa Fe) were quite diverse and belonged to the genera Rhizobium and Mesorhizobium. To achieve a more extensive view of the local microsymbionts associated with Desmanthus spp., we sampled three different sites in Jujuy and Salta, in northwest Argentina. Matrix-assisted Laser-Desorption-Ionization Time-of-Flight mass spectrometry (MALDI-TOF) typing, 16S-rDNA analysis, and genome sequencing demonstrated that the dominant root-nodule microsymbionts belonged to the genus Sinorhizobium, with some sequenced genomes related to Sinorhizobium mexicanum, Sinorhizobium chiapanecum, and Sinorhizobium psoraleae. An analysis of nodA and nodC markers indicated that, in some of the isolates, horizontal gene transfer appeared to be responsible for the lack of congruence between the phylogenies of the chromosome and of the symbiotic region. These results revealed diverse evolutionary strategies for reaching the current Desmanthus-microsymbiont diversity. What is remarkable beside their observed genetic diversity is that the tolerance profiles of these isolates to abiotic stresses (temperature, salt concentration, pH) were quite coincident with the separation of the sinorhizobia according to place of origin, suggesting possible ecoedaphic adaptations. This observation, together with the higher aerial dry-weight matter that some isolates generated in Desmanthus virgatus cv. Marc when compared to the biomass generated by the commercial strain Sinorhizobium terangae CB3126, distinguish the collected sinorhizobia as constituting valuable germplasm for evaluation in local fields to select for more efficient symbiotic pairs.}, }
@article {pmid37508321, year = {2023}, author = {Zaghen, F and Sora, VM and Meroni, G and Laterza, G and Martino, PA and Soggiu, A and Bonizzi, L and Zecconi, A}, title = {Epidemiology of Antimicrobial Resistance Genes in Staphyloccocus aureus Isolates from a Public Database in a One Health Perspective-Sample Characteristics and Isolates' Sources.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/antibiotics12071225}, pmid = {37508321}, issn = {2079-6382}, support = {Programma di Sviluppo Rurale 2014-2020 Misura 16.1 project MOOH//FEASR/ ; 2017MZ5KWM_001 project "SAFE MILK: OMICS SCIENCE FOR MILK SAFETY AND QUALITY"//PRIN/ ; PSR2021 line 6 One Health Action Hub//University of Milan/ ; }, abstract = {Staphylococcus aureus is considered one of the most widespread bacterial pathogens for both animals and humans, being the causative agent of various diseases like food poisoning, respiratory tract infections, nosocomial bacteremia, and surgical site and cardiovascular infections in humans, as well as clinical and subclinical mastitis, dermatitis, and suppurative infections in animals. Thanks to their genetic flexibility, several virulent and drug-resistant strains have evolved mainly due to horizontal gene transfer and insurgence of point mutations. Infections caused by the colonization of such strains are particularly problematic due to frequently occurring antibiotic resistance, particulary methicillin-resistant S. aureus (MRSA), and are characterized by increased mortality, morbidity, and hospitalization rates compared to those caused by methicillin-sensitive S. aureus (MSSA). S. aureus infections in humans and animals are a prime example of a disease that may be managed by a One Health strategy. In fact, S. aureus is a significant target for control efforts due to its zoonotic potential, the frequency of its illnesses in both humans and animals, and the threat posed by S. aureus antibiotic resistance globally. The results of an epidemiological analysis on a worldwide public database (NCBI Pathogen Detection Isolate Browser; NPDIB) of 35,026 S. aureus isolates were described. We considered the diffusion of antibiotic resistance genes (ARGs), in both human and animal setting, and the results may be considered alarming. The result of this study allowed us to identify the presence of clusters with specific ARG patterns, and that these clusters are associated with different sources of isolation (e.g., human, non-human).}, }
@article {pmid37508250, year = {2023}, author = {Liu, S and Liu, B and Zhu, Y and Qiu, Y and Li, B}, title = {The Spatial-Temporal Effects of Bacterial Growth Substrates on Antibiotic Resistance Gene Spread in the Biofilm.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/antibiotics12071154}, pmid = {37508250}, issn = {2079-6382}, support = {2020YFC19092-05, 2022YFC32031-04//Ministry of Science and Technology/ ; FRF-TP-20-011A3//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Biofilm is considered as the hotspot of antibiotic resistance gene (ARG) dissemination. Bacterial growth substrates are important factors for biofilm formation, but its spatial-temporal effects on ARG spread in biofilm is still unclear. In this study, microfluidics combined with microscopic observation were used to reveal spatial-temporal effects of bacterial growth substrates on ARG transfer at real time. The initial horizontal gene transfer events were found to be independent of substrate levels. However, subsequent transfer processes varied greatly depending on the availability of growth substrates. The proportion of transconjugants was much higher (~12%) when observed in substrate-rich regions (under the channel) at 24 h, followed by an exponential decline, with the distance far from the channel. Furthermore, three-dimensional observation revealed that vertical gene transfer influenced by the concentrations of bacterial growth substrates was important for ARG spread in biofilm. The transfer frequency was 8.2 times higher in the high substrate concentration (50×) compared to low concentration (0.5×) in simulated sewage, underscoring the substantial impact of bacterial growth substrate variability on ARG dissemination. This study is helpful for in-depth understanding of ARG dissemination through biofilms and indicates that reducing pollutant emission is important for ARG control in the environment.}, }
@article {pmid37508224, year = {2023}, author = {Guidotti-Takeuchi, M and Melo, RT and Ribeiro, LNM and Dumont, CF and Ribeiro, RAC and Brum, BA and de Amorim Junior, TLIF and Rossi, DA}, title = {Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/antibiotics12071127}, pmid = {37508224}, issn = {2079-6382}, abstract = {Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.}, }
@article {pmid37508213, year = {2023}, author = {Anyanwu, MU and Jaja, IF and Okpala, COR and Njoga, EO and Okafor, NA and Oguttu, JW}, title = {Mobile Colistin Resistance (mcr) Gene-Containing Organisms in Poultry Sector in Low- and Middle-Income Countries: Epidemiology, Characteristics, and One Health Control Strategies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/antibiotics12071117}, pmid = {37508213}, issn = {2079-6382}, abstract = {Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs.}, }
@article {pmid37505810, year = {2023}, author = {Dewan, I and Uecker, H}, title = {A mathematician's guide to plasmids: an introduction to plasmid biology for modellers.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {7}, pages = {}, doi = {10.1099/mic.0.001362}, pmid = {37505810}, issn = {1465-2080}, abstract = {Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.}, }
@article {pmid37503831, year = {2023}, author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA}, title = {Beyond parasitic convergence: unraveling the evolution of the organellar genomes in holoparasites.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcad108}, pmid = {37503831}, issn = {1095-8290}, abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been extensively studied, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and comprises approximately 10% of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.<br><br>SCOPE: This review summarizes the current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.<br><br>CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition, and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.}, }
@article {pmid37502928, year = {2023}, author = {Hu, K and Chou, CW and Wilke, CO and Finkelstein, IJ}, title = {Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.03.531003}, pmid = {37502928}, abstract = {CRISPR-associated transposons (CASTs) co-opt CRISPR-Cas proteins and Tn7-family transposons for RNA-guided vertical and horizontal transmission. CASTs encode minimal CRISPR arrays but can't acquire new spacers. Here, we show that CASTs instead co-opt defense-associated CRISPR arrays for horizontal transmission. A bioinformatic analysis shows that all CAST sub-types co-occur with defense-associated CRISPR-Cas systems. Using an E. coli quantitative transposition assay, we show that CASTs use CRISPR RNAs (crRNAs) from these defense systems for horizontal gene transfer. A high-resolution structure of the type I-F CAST-Cascade in complex with a type III-B crRNA reveals that Cas6 recognizes direct repeats via sequence-independent π - π interactions. In addition to using heterologous CRISPR arrays, type V CASTs can also transpose via a crRNA-independent unguided mechanism, even when the S15 co-factor is over-expressed. Over-expressing S15 and the trans-activating CRISPR RNA (tracrRNA) or a single guide RNA (sgRNA) reduces, but does not abrogate, off-target integration for type V CASTs. Exploiting new spacers in defense-associated CRISPR arrays explains how CASTs horizontally transfer to new hosts. More broadly, this work will guide further efforts to engineer the activity and specificity of CASTs for gene editing applications.}, }
@article {pmid37499542, year = {2023}, author = {Chen, X and Zhu, Y and Chen, J and Yan, S and Xie, S}, title = {Multi-omic profiling of a novel activated sludge strain Sphingobacterium sp. WM1 reveals the mechanism of tetracycline biodegradation and its merits of potential application.}, journal = {Water research}, volume = {243}, number = {}, pages = {120397}, doi = {10.1016/j.watres.2023.120397}, pmid = {37499542}, issn = {1879-2448}, abstract = {As an emerging pollutant, the antibiotic tetracycline (TC) has been consistently detected in wastewater and activated sludge. Biodegradation represents a potentially crucial pathway to dissipate TC contamination. However, few efficient TC-degrading bacteria have been isolated and a comprehensive understanding of the molecular mechanisms underlying TC degradation is still lacking. In this study, a novel TC-degrading bacterium, designated as Sphingobacterium sp. WM1, was successfully isolated from activated sludge. Strain WM1 exhibited a remarkable performance in degrading 50 mg/L TC within 1 day under co-metabolic conditions. Genomic analysis of the strain WM1 unveiled the presence of three functional tetX genes. Unraveling the complex molecular mechanisms, transcriptome analysis highlighted the role of upregulated transmembrane transport and accelerated electron transport in facilitating TC degradation. Proteomics confirmed the up-regulation of proteins involved in cellular biosynthesis/metabolism and ribosomal processes. Crucially, the tetX gene-encoding protein showed a significant upregulation, indicating its role in TC degradation. Heterologous expression of the tetX gene resulted in TC dissipation from an initial 51.9 mg/L to 4.2 mg/L within 24 h. The degradation pathway encompassed TC hydroxylation, transforming into TP461 and subsequent metabolites, which effectively depleted TC's inhibitory activity. Notably, the tetX genes in strain WM1 showed limited potential for horizontal gene transfer. Collectively, strain WM1's potent TC degradation capacity signals a promise for enhancing TC clean-up strategies.}, }
@article {pmid37499413, year = {2023}, author = {Ma, R and Wang, J and Liu, Y and Wang, G and Yang, Y and Liu, Y and Kong, Y and Lin, J and Li, Q and Li, G and Yuan, J}, title = {Dynamics of antibiotic resistance genes and bacterial community during pig manure, kitchen waste, and sewage sludge composting.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118651}, doi = {10.1016/j.jenvman.2023.118651}, pmid = {37499413}, issn = {1095-8630}, abstract = {Organic solid wastes (OSWs) are important reservoirs for antibiotic resistance genes (ARGs). Aerobic composting transforms OSWs into fertilizers. In this study, we investigated ARGs dynamics and their driving mechanisms in three OSW composts: pig manure (PM), kitchen waste (KC), and sewage sludge (SG). The dominant ARGs were different in each OSW, namely tetracycline, aminoglycoside, and macrolide resistance (PM); tetracyclines and aminoglycosides (KC); and sulfonamides (SG). ARGs abundance decreased in PM (71%) but increased in KC (5.9-fold) and SG (1.3-fold). Interestingly, the ARGs abundance was generally similar in all final composts, which was contributed to the similar bacterial community in final composts. In particular, sulfonamide and β-lactam resistant genes removed (100%) in PM, while sulfonamide in KC (38-fold) and tetracycline in SG (5-fold) increased the most. Additionally, ARGs abundance rebounded during the maturation period in all treatments. Firmicutes, Proteobacteria, and Actinobacteria were the main ARGs hosts. Several persistent and high-risk genes included tetW, aadA, aadE, tetX, strB, tetA, mefA, intl1, and intl2. The structural equation models showed ARGs removal was mainly affected by physicochemical parameters and bacterial communities in PM, the ARGs enrichment in KC composting correlated with increased mobile genetic elements (MGEs). In general, thermophilic aerobic composting can inhibit the vertical gene transfer (VGT) of pig manure and horizontal gene transfer (HGT) of sludge, but it increases the HGT of kitchen waste, resulting in a dramatic increase of ARGs in KC compost. More attention should be paid to the ARGs risk of kitchen waste composting.}, }
@article {pmid37494793, year = {2023}, author = {Wang, H and Xu, K and Wang, J and Feng, C and Chen, Y and Shi, J and Ding, Y and Deng, C and Liu, X}, title = {Microplastic biofilm: An important microniche that may accelerate the spread of antibiotic resistance genes via natural transformation.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132085}, doi = {10.1016/j.jhazmat.2023.132085}, pmid = {37494793}, issn = {1873-3336}, abstract = {Microplastic (MP) biofilms provide a specific microniche for microbial life and are a potential hotspot for the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Nevertheless, the acquisition of ARGs in MP biofilms via natural transformation mediated by extracellular DNA (eDNA) has been rarely explored. This study demonstrated that MP biofilms promoted the natural transformation of extracellular ARGs at the single-cell and multi-species levels, compared to natural substrate (NS) biofilms and bacterioplankton. The transformation frequency on MP biofilms was up to 1000-fold compare to that on NS. The small MPs and aged MPs enhanced the ARG transformation frequencies up to 77.16-fold and 32.05-fold, respectively, compared with the large MPs and pristine MPs. The transformation frequencies on MP biofilms were significantly positively correlated with the bacterial density and extracellular polymeric substance (EPS) content (P < 0.05). Furthermore, MPs significantly increased the expression of the biofilm formation related genes (motA and pgaA) and DNA uptake related genes (pilX and comA) compared to NS and bacterioplankton. The more transformants colonized on MPs contributed to the enhanced transformation frequencies at the community-wide level. Overall, eDNA-mediated transformation in MP biofilms may be an important path of ARG spread, which was promoted by heterogeneous biofilm.}, }
@article {pmid37495486, year = {2023}, author = {Soler-Bistué, A}, title = {Restriction-methylation systems regulate transformation in Acinetobacter baumannii.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.07.009}, pmid = {37495486}, issn = {1878-4380}, abstract = {Antimicrobial resistance in Acinetobacter baumannii is a major concern. Natural transformation remains understudied as a horizontal gene transfer (HGT) mechanism for the spread of resistance genes. Recent work (Vesel et al.) reveals a profound impact of the state of donor DNA methylation with strong implications for HGT of resistance determinants in this worrisome pathogen.}, }
@article {pmid37485539, year = {2023}, author = {Li, L and Liu, Y and Xiao, Q and Xiao, Z and Meng, D and Yang, Z and Deng, W and Yin, H and Liu, Z}, title = {Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1173748}, pmid = {37485539}, issn = {1664-302X}, abstract = {The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.}, }
@article {pmid37483384, year = {2023}, author = {Wang, M}, title = {Editorial: Antimicrobial resistance dissemination and horizontal gene transfer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240680}, pmid = {37483384}, issn = {2235-2988}, }
@article {pmid37478933, year = {2023}, author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G}, title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {165672}, doi = {10.1016/j.scitotenv.2023.165672}, pmid = {37478933}, issn = {1879-1026}, abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.}, }
@article {pmid37478352, year = {2023}, author = {Deng, Z and Chen, H and Wang, J and Zhang, N and Han, Z and Xie, Y and Zhang, X and Fang, X and Yu, H and Zhang, D and Yue, Z and Zhang, C}, title = {Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c03738}, pmid = {37478352}, issn = {1520-5851}, abstract = {Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.}, }
@article {pmid37476668, year = {2023}, author = {Agarwal, V and Stubits, R and Nassrullah, Z and Dillon, MM}, title = {Pangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213261}, pmid = {37476668}, issn = {1664-302X}, abstract = {The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.}, }
@article {pmid37475746, year = {2023}, author = {Bhatia, RP and Kirit, HA and Lewis, CM and Sankaranarayanan, K and Bollback, JP}, title = {Evolutionary barriers to horizontal gene transfer in macrophage-associated Salmonella.}, journal = {Evolution letters}, volume = {7}, number = {4}, pages = {227-239}, pmid = {37475746}, issn = {2056-3744}, abstract = {Horizontal gene transfer (HGT) is a powerful evolutionary force facilitating bacterial adaptation and emergence of novel phenotypes. Several factors, including environmental ones, are predicted to restrict HGT, but we lack systematic and experimental data supporting these predictions. Here, we address this gap by measuring the relative fitness of 44 genes horizontally transferred from Escherichia coli to Salmonella enterica in infection-relevant environments. We estimated the distribution of fitness effects in each environment and identified that dosage-dependent effects across different environments are a significant barrier to HGT. The majority of genes were found to be deleterious. We also found longer genes had stronger negative fitness consequences than shorter ones, showing that gene length was negatively associated with HGT. Furthermore, fitness effects of transferred genes were found to be environmentally dependent. In summary, a substantial fraction of transferred genes had a significant fitness cost on the recipient, with both gene characteristics and the environment acting as evolutionary barriers to HGT.}, }
@article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, }
@article {pmid37468904, year = {2023}, author = {Liu, B and Warnow, T}, title = {Weighted ASTRID: fast and accurate species trees from weighted internode distances.}, journal = {Algorithms for molecular biology : AMB}, volume = {18}, number = {1}, pages = {6}, pmid = {37468904}, issn = {1748-7188}, abstract = {BACKGROUND: Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance.<br><br>RESULTS: Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets.<br><br>CONCLUSIONS: Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .}, }
@article {pmid37467272, year = {2023}, author = {Li, XL and Sun, Y and Yin, Y and Zhan, S and Wang, C}, title = {A bacterial-like Pictet-Spenglerase drives the evolution of fungi to produce β-carboline glycosides together with separate genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {30}, pages = {e2303327120}, doi = {10.1073/pnas.2303327120}, pmid = {37467272}, issn = {1091-6490}, support = {32021001 and 32230087//MOST | National Natural Science Foundation of China (NSFC)/ ; }, abstract = {Diverse β-carboline (βC) alkaloids are produced by microbes, plants, and animals with myriad bioactivities and drug potentials. However, the biosynthetic mechanism of βCs remains largely elusive, especially regarding the hydroxyl and glucosyl modifications of βCs. Here, we report the presence of the bacterial-like Pictet-Spenglerase gene Fcs1 in the entomopathogenic Beauveria fungi that can catalyze the biosynthesis of the βC skeleton. The overexpression of Fcs1 in Beauveria bassiana led to the identification of six βC methyl glycosides, termed bassicarbosides (BCSs) A-F. We verified that the cytochrome P450 (CYP) genes adjacent to Fcs1 cannot oxidize βCs. Alternatively, the separated CYP684B2 family gene Fcs2 was identified to catalyze βC hydroxylation together with its cofactor gene Fcs3. The functional homologue of Fcs2 is only present in the Fcs1-containing fungi and highly similar to the Fcs1-connected yet nonfunctional CYP. Both evolved quicker than those from fungi without Fcs1 homologues. Finally, the paired methyl/glucosyl transferase genes were verified to mediate the production of BCSs from hydroxy-βCs. All these functionally verified genes are located on different chromosomes of Beauveria, which is in contrast to the typical content-clustered feature of fungal biosynthetic gene clusters (BGCs). We also found that the production of BCSs selectively contributed to fungal infection of different insect species. Our findings shed light on the biosynthetic mechanism of βC glycosides, including the identification of a βC hydroxylase. The results of this study also propose an evolving process of fungal BGC formation following the horizontal transfer of a bacterial gene to fungi.}, }
@article {pmid37467082, year = {2023}, author = {Jen, FE and Abrahams, JL and Schulz, BL and Lamelas, A and Pluschke, G and Jennings, MP}, title = {High-Frequency Changes in Pilin Glycosylation Patterns during Neisseria meningitidis Serogroup a Meningitis Outbreaks in the African Meningitis Belt.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.3c00149}, pmid = {37467082}, issn = {2373-8227}, abstract = {In the meningitis belt of sub-Saharan Africa, there are cyclic meningococcal epidemics that coincide with clonal waves of Neisseria meningitidis carriage and invasive disease. In the framework of longitudinal colonization and disease studies in Ghana and Burkina Faso, meningococcal isolates belonging to the closely related hypervirulent A:ST-5, A:ST-7, and A:ST-2859 clones have been collected from 1998 to 2011 during meningococcal outbreaks. A comparative whole-genome sequencing study with 100 of these isolates identified the pilin glycosylation (pgl) locus as one hot spot of recombination. Frequent exchange of pgl genes in N. meningitidis by lateral gene transfer results in differences in the glycosylation patterns of pilin and other cell surface glycoproteins. In this study, we looked at both recombination and phase variation of the pgl genes of these clinical isolates and analyzed the glycan structures resulting from different pgl alleles and their variable expression. Our results indicate that the basal O-linked sugar of the glycans expressed by these isolates is masked by various additional mono- or disaccharide structures whose expression is highly variable due to the phase-variable expression of pgl genes. We also observed a distinct glycoform in two isolates with pgl loci that were modified by recombination. These data suggest that variation in N. meningitidis protein glycosylation could be crucial for bacterial adaptation to evade herd immunity in semi-immune populations. Investigating pilin glycosylation in N. meningitidis can shed light on the mechanisms by which this pathogen evades the host immune response, and may help identify potential targets for novel therapies and vaccines.}, }
@article {pmid37462915, year = {2023}, author = {Alav, I and Buckner, MMC}, title = {Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/1040841X.2023.2233603}, pmid = {37462915}, issn = {1549-7828}, abstract = {Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.}, }
@article {pmid37461575, year = {2023}, author = {Asad, A and Jahan, I and Munni, MA and Begum, R and Mukta, MA and Saif, K and Faruque, SN and Hayat, S and Islam, Z}, title = {Increasing trend of antibiotic resistance in Shigella in Bangladesh: a plasmid-mediated transfer of mphA macrolide resistance gene.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3080386/v1}, pmid = {37461575}, abstract = {Shigellosis remains a common gastrointestinal disease mostly in children <5 years of age in developing countries. Azithromycin (AZM), a macrolide, is currently the first-line treatment for shigellosis in Bangladesh; ciprofloxacin (CIP) and ceftriaxone (CRO) are also used frequently. We aimed to evaluate the current epidemiology of antimicrobial resistance (AMR) and mechanism(s) of increasing macrolide resistance in Shigella in Bangladesh. A total of 2407 clinical isolates of Shigella from 2009 to 2016 were studied. Over the study period, Shigella sonnei was gradually increasing and become predominant (55%) over Shigella flexneri (36%) by 2016. We used CLSI-guided epidemiological cut-off value (ECV) for AZM in Shigella to set resistance breakpoints (zone-diameter ≤ 15 mm for S. flexneri and ≤ 11 mm for S. sonnei). Between 2009 and 2016, AZM resistance increased from 22% to approximately 60%, CIP resistance increased by 40%, and CRO resistance increased from zero to 15%. The mph A gene was the key macrolide resistance factor in Shigella ; a 63MDa conjugative middle-range plasmid was harboring AZM and CRO resistance factors. Our findings show that, especially after 2014, there has been a rapid increase in resistance to the three most effective antibiotics. The rapid spread of macrolide (AZM) resistance genes among Shigella are driven by horizontal gene transfer rather than direct lineage.}, }
@article {pmid37460464, year = {2023}, author = {Morreale, DP and Porsch, EA and Kern, BK and St Geme, JW and Planet, PJ}, title = {Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4281}, pmid = {37460464}, issn = {2041-1723}, abstract = {The bacterial genus Kingella includes two pathogenic species, namely Kingella kingae and Kingella negevensis, as well as strictly commensal species. Both K. kingae and K. negevensis secrete a toxin called RtxA that is absent in the commensal species. Here we present a phylogenomic study of the genus Kingella, including new genomic sequences for 88 clinical isolates, genotyping of another 131 global isolates, and analysis of 52 available genomes. The phylogenetic evidence supports that the toxin-encoding operon rtxCA was acquired by a common ancestor of the pathogenic Kingella species, and that a preexisting type-I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% of K. kingae strains containing two copies of the rtxA toxin gene. The rtxA duplication is largely clonal and is associated with invasive disease. Assays with isogenic strains show that a single copy of rtxA is associated with reduced cytotoxicity in vitro. Thus, our study identifies key steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.}, }
@article {pmid37452100, year = {2023}, author = {Koch, L}, title = {Maverick - top gun of horizontal gene transfer.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {37452100}, issn = {1471-0064}, }
@article {pmid37450185, year = {2023}, author = {Loret, S and Habib, B and Romain, P and Roba, A and Reboul, A}, title = {Prevention of horizontal transfer of laboratory plasmids to environmental bacteria: comparison of the effectiveness of a few disinfection approaches to degrade DNA.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37450185}, issn = {1614-7499}, support = {Grant Recipient/ Boutaina HABIB//UNamur GRant for Foreign PhD Students/ ; }, abstract = {The routine work of any molecular biology laboratory includes the daily use of microorganisms, including strains of E. coli, transformed with a variety of plasmids expressing at least one antibiotic resistance gene (ARG). Therefore, to avoid the accidental release of ARGs into environmental water, methods for disinfection of liquid laboratory waste must be effective in destroying nucleic acids. In support of this recommendation, the origin of replication of Enterobacteriaceae plasmids has been detected in strains of non-Enterobacteriaceae bacteria isolated from wastewater from laboratories and research institutes, suggesting that interspecific transfer of laboratory plasmids had occurred. Using quantitative polymerase chain reaction, we determined the decimal reduction value (D value, expressed as concentration of disinfectant or length of physical treatment) of several decontamination methods for their DNA degradation effect on cultures of E. coli Top10 transformed with a kanamycin resistant plasmid (pET28A + or pEGFP-C2). The estimated D values were 0.7 M for sulfuric acid, 6.3% for a commercial P3 disinfectant, 25 min for steam sterilization at 121 °C, and 49 min for disinfection by UVC. A 20-min treatment of bacteria cultures with a final concentration of 1-10% sodium hypochlorite was found to be ineffective in completely destroying a bacteria plasmid gene marker (coding for the pBR322 origin of replication). Residual DNA from NaClO-treated cells was 60%, while it decreased under 10% using the commercial disinfectant P3 diluted at 5%. As the degradation was incomplete in both cases, we recommend avoiding discharge of disinfected liquid waste to wastewater (even after chemical neutralization) without additional plasmid destruction treatment, to prevent horizontal transfer of laboratory ARGs to environmental bacteria.}, }
@article {pmid37445761, year = {2023}, author = {Xiao, Y and Zhang, Y and Xie, F and Olsen, RH and Shi, L and Li, L}, title = {Inhibition of Plasmid Conjugation in Escherichia coli by Targeting rbsB Gene Using CRISPRi System.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, doi = {10.3390/ijms241310585}, pmid = {37445761}, issn = {1422-0067}, abstract = {Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic-resistant genes (ARGs) among human pathogens. The spread of ARGs can be halted or diminished by interfering with the conjugation process. In this study, we explored the possibility of using an rbsB gene as a single target to inhibit plasmid-mediated horizontal gene transfer in Escherichia coli by CRISPR interference (CRISPRi) system. Three single-guide RNAs (sgRNAs) were designed to target the rbsB gene. The transcriptional levels of the rbsB gene, the conjugation-related genes, and the conjugation efficiency in the CRISPRi strain were tested. We further explored the effect of the repressed expression of the rbsB gene on the quorum sensing (QS) system and biofilm formation. The results showed that the constructed CRISPRi system was effective in repressing the transcriptional level of the rbsB gene at a rate of 66.4%. The repressed expression of the rbsB gene resulted in the reduced conjugation rate of RP4 plasmid by 88.7%, which significantly inhibited the expression of the conjugation-related genes (trbBp, trfAp, traF and traJ) and increased the global regulator genes (korA, korB and trbA). The repressed rbsB gene expression reduced the depletion of autoinducer 2 signals (AI-2) by 12.8% and biofilm formation by a rate of 68.2%. The results of this study indicated the rbsB gene could be used as a universal target for the inhibition of conjugation. The constructed conjugative CRISPRi system has the potential to be used in ARG high-risk areas.}, }
@article {pmid37442321, year = {2023}, author = {van Hamelsve Ld, S and Kurenbach, B and Paull, DJ and Godsoe, WA and Ferguson, GC and Heinemann, JA}, title = {Indigenous food sources as vectors of Escherichia coli and antibiotic resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122155}, doi = {10.1016/j.envpol.2023.122155}, pmid = {37442321}, issn = {1873-6424}, abstract = {The contamination of surface waters by fecal bacteria, measured by the number of Escherichia coli, is a significant public health issue. When these bacteria are also resistant to antimicrobials, infections are more complicated to treat. While water is regularly tested at recreational sites, wild-harvested foods, known as mahinga kai by the indigenous Māori people of Aotearoa New Zealand, are commonly overlooked as a source of exposure to potential pathogens and antimicrobial resistance (AMR). We investigate two likely sources of risk from harvesting aquatic wild foods. The first is water contact, and the second is contact with/ingestion of the harvest. We used E. coli as a proxy for microbial water quality at harvesting sites. Two popular mahinga kai species were also harvested and assessed. We found antibiotic-resistant bacteria on watercress (Nasturtium officinale) and cockles (Austrovenus stutchburyi). One-third of E. coli isolates were conjugative donors of at least one resistance phenotype. Tank experiments were used to track the internalization of E. coli by Greenshell/lip mussels (Perna canaliculus). Greenshell mussels kept at environmentally relevant concentrations of E. coli were colonized to levels considered unsafe for human consumption in 24 h. Finally, we measured horizontal gene transfer between bacteria within the shellfish, what we termed 'intra-shellular' conjugation. The transmission frequency of plasmid RP4 was significantly higher in mussels than in water alone. Our results indicate that shellfish could promote the dissemination of antibiotic resistance. They highlight the need to limit or reduce human pathogenic bacteria where food is gathered.}, }
@article {pmid37440893, year = {2023}, author = {Brenner, E and Sreevatsan, S}, title = {Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1204838}, doi = {10.3389/fmicb.2023.1204838}, pmid = {37440893}, issn = {1664-302X}, abstract = {Bacterial CRISPR/Cas systems target foreign genetic elements such as phages and regulate gene expression by some pathogens, even in the host. The system is a marker for evolutionary history and has been used for inferences in Mycobacterium tuberculosis for 30 years. However, knowledge about mycobacterial CRISPR/Cas systems remains limited. It is believed that Type III-A Cas systems are exclusive to Mycobacterium canettii and the M. tuberculosis complex (MTBC) of organisms and that very few of the >200 diverse species of non-tuberculous mycobacteria (NTM) possess any CRISPR/Cas system. This study sought unreported CRISPR/Cas loci across NTM to better understand mycobacterial evolution, particularly in species phylogenetically near the MTBC. An analysis of available mycobacterial genomes revealed that Cas systems are widespread across Mycobacteriaceae and that some species contain multiple types. The phylogeny of Cas loci shows scattered presence in many NTM, with variation even within species, suggesting gains/losses of these loci occur frequently. Cas Type III-A systems were identified in pathogenic Mycobacterium heckeshornense and the geological environmental isolate Mycobacterium SM1. In summary, mycobacterial CRISPR/Cas systems are numerous, Type III-A systems are unreliable as markers for MTBC evolution, and mycobacterial horizontal gene transfer appears to be a frequent source of genetic variation.}, }
@article {pmid37440885, year = {2023}, author = {Verhaegen, M and Bergot, T and Liebana, E and Stancanelli, G and Streissl, F and Mingeot-Leclercq, MP and Mahillon, J and Bragard, C}, title = {On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1221478}, doi = {10.3389/fmicb.2023.1221478}, pmid = {37440885}, issn = {1664-302X}, abstract = {Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.}, }
@article {pmid37439570, year = {2023}, author = {Diorio-Toth, L and Wallace, MA and Farnsworth, CW and Wang, B and Gul, D and Kwon, JH and Andleeb, S and Burnham, CD and Dantas, G}, title = {Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0020623}, doi = {10.1128/msystems.00206-23}, pmid = {37439570}, issn = {2379-5077}, abstract = {Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.}, }
@article {pmid37437616, year = {2023}, author = {Li, H and Wang, K and Xu, J and Wu, H and Ma, Y and Zou, R and Song, HL}, title = {Enhanced removal of antibiotic and antibiotic resistance genes by coupling biofilm electrode reactor and manganese ore substrate up-flow microbial fuel cell constructed wetland system.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {139461}, doi = {10.1016/j.chemosphere.2023.139461}, pmid = {37437616}, issn = {1879-1298}, abstract = {Manganese ore substrate up-flow microbial fuel cell constructed wetland (UCW-MFC(Mn)) as an innovative wastewater treatment technology for purifying antibiotics and electricity generation with few antibiotic resistance genes (ARGs) generation has attracted attention. However, antibiotic purifying effects should be further enhanced. In this study, a biofilm electrode reactor (BER) that needs direct current driving was powered by a Mn ore anode (UCW-MFC(Mn)) to form a coupled system without requiring direct-current source. Removal efficiencies of sulfadiazine (SDZ), ciprofloxacin (CIP) and the corresponding ARGs in the coupled system were compared with composite (BER was powered by direct-current source) and anaerobic systems (both of BER and UCW-MFC were in open circuit mode). The result showed that higher antibiotic removal efficiency (94% for SDZ and 99.1% for CIP) in the coupled system was achieved than the anaerobic system (88.5% for SDZ and 98.2% for CIP). Moreover, electrical stimulation reduced antibiotic selective pressure and horizontal gene transfer potential in BER, and UCW-MFC further reduced ARG abundances by strengthening the electro-adsorption of ARG hosts determined by Network analysis. Bacterial community diversity continuously decreased in BER while it increased in UCW-MFC, indicating that BER mitigated the toxicity of antibiotic. Degree of modularity, some functional bacteria (antibiotic degrading bacteria, fermentative bacteria and EAB), and P450 enzyme related to antibiotic and xenobiotics biodegradation genes were enriched in electric field existing UCW-MFC, accounting for the higher degradation efficiency. In conclusion, this study provided an effective strategy for removing antibiotics and ARGs in wastewater by operating a BER-UCW-MFC coupled system.}, }
@article {pmid37436868, year = {2023}, author = {Mondal, A and Bansal, MS}, title = {Generalizing the Domain-Gene-Species Reconciliation Framework to Microbial Genes and Domains.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/TCBB.2023.3294480}, pmid = {37436868}, issn = {1557-9964}, abstract = {Protein domains play an important role in the function and evolution of many gene families. Previous studies have shown that domains are frequently lost or gained during gene family evolution. Yet, most computational approaches for studying gene family evolution do not account for domain-level evolution within genes. To address this limitation, a new three-level reconciliation framework, called the Domain-Gene-Species (DGS) reconciliation model, has been recently developed to simultaneously model the evolution of a domain family inside one or more gene families and the evolution of those gene families inside a species tree. However, the existing model applies only to multi-cellular eukaryotes where horizontal gene transfer is negligible. In this work, we generalize the existing DGS reconciliation model by allowing for the spread of genes and domains across species boundaries through horizontal transfer. We show that the problem of computing optimal generalized DGS reconciliations, though NP-hard, is approximable to within a constant factor, where the specific approximation ratio depends on the "event costs" used. We provide two different approximation algorithms for the problem and demonstrate the impact of the generalized framework using both simulated and real biological data. Our results show that our new algorithms result in highly accurate reconstructions of domain family evolution for microbes.}, }
@article {pmid37434470, year = {2023}, author = {Bucknell, AH and McDonald, MC}, title = {That's no moon, it's a Starship: Giant transposons driving fungal horizontal gene transfer.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15118}, pmid = {37434470}, issn = {1365-2958}, support = {//Royal Society of Biology/ ; //the School of Biosciences at the University of Birmingham/ ; }, abstract = {To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.}, }
@article {pmid37434168, year = {2023}, author = {Li, KL and Nakashima, K and Hisata, K and Satoh, N}, title = {Expression and possible functions of a horizontally transferred glycosyl hydrolase gene, GH6-1, in Ciona embryogenesis.}, journal = {EvoDevo}, volume = {14}, number = {1}, pages = {11}, pmid = {37434168}, issn = {2041-9139}, abstract = {BACKGROUND: The Tunicata or Urochordata is the only animal group with the ability to synthesize cellulose directly and cellulose is a component of the tunic that covers the entire tunicate body. The genome of Ciona intestinalis type A contains a cellulose synthase gene, CesA, that it acquired via an ancient, horizontal gene transfer. CesA is expressed in embryonic epidermal cells and functions in cellulose production. Ciona CesA is composed of both a glycosyltransferase domain, GT2, and a glycosyl hydrolase domain, GH6, which shows a mutation at a key position and seems functionless. Interestingly, the Ciona genome contains a glycosyl hydrolase gene, GH6-1, in which the GH6 domain seems intact. This suggests expression and possible functions of GH6-1 during Ciona embryogenesis. Is GH6-1 expressed during embryogenesis? If so, in what tissues is the gene expressed? Does GH6-1 serve a function? If so, what is it? Answers to these questions may advance our understanding of evolution of this unique animal group.<br><br>RESULTS: Quantitative reverse transcription PCR and in situ hybridization revealed that GH6-1 is expressed in epidermis of tailbud embryos and in early swimming larvae, a pattern similar to that of CesA. Expression is downregulated at later stages and becomes undetectable in metamorphosed juveniles. The GH6-1 expression level is higher in the anterior-trunk region and caudal-tip regions of late embryos. Single-cell RNA sequencing analysis of the late tailbud stage showed that cells of three clusters with epidermal identity express GH6-1, and that some of them co-express CesA. TALEN-mediated genome editing was used to generate GH6-1 knockout Ciona larvae. Around half of TALEN-electroporated larvae showed abnormal development of adhesive papillae and altered distribution of surface cellulose. In addition, three-fourths of TALEN-electroporated animals failed to complete larval metamorphosis.<br><br>CONCLUSIONS: This study showed that tunicate GH6-1, a gene that originated by horizontal gene transfer of a prokaryote gene, is recruited into the ascidian genome, and that it is expressed and functions in epidermal cells of ascidian embryos. Although further research is required, this observation demonstrates that both CesA and GH6-1 are involved in tunicate cellulose metabolism, impacting tunicate morphology and ecology.}, }
@article {pmid37429971, year = {2023}, author = {Heo, S and Oh, SE and Lee, G and Lee, J and Ha, NC and Jeon, CO and Jeong, K and Lee, JH and Jeong, DW}, title = {Staphylococcus equorum plasmid pKS1030-3 encodes auxiliary biofilm formation and trans-acting gene mobilization systems.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11108}, pmid = {37429971}, issn = {2045-2322}, support = {NRF-2019R1A2C1003639//National Research Foundation of Korea/ ; }, abstract = {The foodborne bacterium Staphylococcus equorum strain KS1030 harbours plasmid pSELNU1, which encodes a lincomycin resistance gene. pSELNU1 undergoes horizontal transfer between bacterial strains, thus spreading antibiotic resistance. However, the genes required for horizontal plasmid transfer are not encoded in pSELNU1. Interestingly, a relaxase gene, a type of gene related to horizontal plasmid transfer, is encoded in another plasmid of S. equorum KS1030, pKS1030-3. The complete genome of pKS1030-3 is 13,583 bp long and encodes genes for plasmid replication, biofilm formation (the ica operon), and horizontal gene transfer. The replication system of pKS1030-3 possesses the replication protein-encoding gene repB, a double-stranded origin of replication, and two single-stranded origins of replication. The ica operon, relaxase gene, and a mobilization protein-encoding gene were detected in pKS1030-3 strain-specifically. When expressed in S. aureus RN4220, the ica operon and relaxase operon of pKS1030-3 conferred biofilm formation ability and horizontal gene transfer ability, respectively. The results of our analyses show that the horizontal transfer of pSELNU1 of S. equorum strain KS1030 depends on the relaxase encoded by pKS1030-3, which is therefore trans-acting. Genes encoded in pKS1030-3 contribute to important strain-specific properties of S. equorum KS1030. These results could contribute to preventing the horizontal transfer of antibiotic resistance genes in food.}, }
@article {pmid37428925, year = {2023}, author = {Walker, AA and Robinson, SD and Merritt, DJ and Cardoso, FC and Goudarzi, MH and Mercedes, RS and Eagles, DA and Cooper, P and Zdenek, CN and Fry, BG and Hall, DW and Vetter, I and King, GF}, title = {Horizontal gene transfer underlies the painful stings of asp caterpillars (Lepidoptera: Megalopygidae).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {29}, pages = {e2305871120}, doi = {10.1073/pnas.2305871120}, pmid = {37428925}, issn = {1091-6490}, support = {DP200102867//Australian Research Council/ ; CE200100012//Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science/ ; APP2017461//Australian National Health and Medical Research Council/ ; }, abstract = {Larvae of the genus Megalopyge (Lepidoptera: Zygaenoidea: Megalopygidae), known as asp or puss caterpillars, produce defensive venoms that cause severe pain. Here, we present the anatomy, chemistry, and mode of action of the venom systems of caterpillars of two megalopygid species, the Southern flannel moth Megalopyge opercularis and the black-waved flannel moth Megalopyge crispata. We show that megalopygid venom is produced in secretory cells that lie beneath the cuticle and are connected to the venom spines by canals. Megalopygid venoms consist of large aerolysin-like pore-forming toxins, which we have named megalysins, and a small number of peptides. The venom system differs markedly from those of previously studied venomous zygaenoids of the family Limacodidae, suggestive of an independent origin. Megalopygid venom potently activates mammalian sensory neurons via membrane permeabilization and induces sustained spontaneous pain behavior and paw swelling in mice. These bioactivities are ablated by treatment with heat, organic solvents, or proteases, indicating that they are mediated by larger proteins such as the megalysins. We show that the megalysins were recruited as venom toxins in the Megalopygidae following horizontal transfer of genes from bacteria to the ancestors of ditrysian Lepidoptera. Megalopygids have recruited aerolysin-like proteins as venom toxins convergently with centipedes, cnidarians, and fish. This study highlights the role of horizontal gene transfer in venom evolution.}, }
@article {pmid37427782, year = {2023}, author = {Tang, X and Shang, J and Ji, Y and Sun, Y}, title = {PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad578}, pmid = {37427782}, issn = {1362-4962}, support = {9678241//City University of Hong Kong/ ; //Hong Kong Innovation and Technology Commission/ ; }, abstract = {Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.}, }
@article {pmid37425999, year = {2023}, author = {Sun, D and Sun, X and Hu, Y and Yamaichi, Y}, title = {Editorial: Horizontal gene transfer mediated bacterial antibiotic resistance, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1221606}, pmid = {37425999}, issn = {1664-302X}, }
@article {pmid37425898, year = {2023}, author = {Culbertson, EM and Levin, TC}, title = {Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.27.546753}, pmid = {37425898}, abstract = {Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to anti-phage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due to the long evolutionary distances separating animal and bacterial proteins, which obscures their relationships. Here, we tackle this problem for three innate immune families (CD-NTases [including cGAS], STINGs, and Viperins) by deeply sampling protein diversity across eukaryotes. We find that Viperins are truly ancient immune proteins, likely inherited since the last eukaryotic common ancestor and possibly longer. In contrast, we find other immune proteins that arose via at least five independent events of horizontal gene transfer (HGT) from bacteria. Two of these events allowed algae to acquire new bacterial viperins, while three more HGT events gave rise to distinct superfamilies of eukaryotic CD-NTases: the OAS superfamily, which is widespread across eukaryotes; the Mab21 superfamily (containing cGAS) which has diversified via a series of animal-specific duplications, and a previously undefined eSMODS superfamily, which more closely resembles bacterial CD-NTases. Finally, we found that cGAS and STING proteins have substantially different histories, with STINGs arising via convergent domain shuffling in bacteria and eukaryotes. Overall, our findings paint a picture of eukaryotic innate immunity as highly dynamic, where eukaryotes build upon their ancient antiviral repertoires through the reuse of protein domains and by repeatedly sampling a rich reservoir of bacterial anti-phage genes.}, }
@article {pmid37424546, year = {2023}, author = {Sharon, BM and Hulyalkar, NV and Zimmern, PE and Palmer, KL and De Nisco, NJ}, title = {Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464.}, journal = {Access microbiology}, volume = {5}, number = {6}, pages = {}, pmid = {37424546}, issn = {2516-8290}, abstract = {Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.}, }
@article {pmid37424042, year = {2023}, author = {Wang, B and Xu, J and Wang, Y and Stirling, E and Zhao, K and Lu, C and Tan, X and Kong, D and Yan, Q and He, Z and Ruan, Y and Ma, B}, title = {Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2301980}, doi = {10.1002/advs.202301980}, pmid = {37424042}, issn = {2198-3844}, support = {42090060//National Natural Science Foundation of China/ ; 42277283//National Natural Science Foundation of China/ ; 41991334//National Natural Science Foundation of China/ ; 2023C02004//Key R&amp;D Program of Zhejjiang Province/ ; 2023C02015//Key R&amp;D Program of Zhejjiang Province/ ; }, abstract = {Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.}, }
@article {pmid37406030, year = {2023}, author = {Rhoads, DD and Pummil, J and Ekesi, NS and Alrubaye, AAK}, title = {Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0283914}, pmid = {37406030}, issn = {1932-6203}, mesh = {Female ; Animals ; Cattle ; Humans ; *Staphylococcus aureus/genetics ; Chickens/genetics ; Virulence/genetics ; Genomic Islands/genetics ; Phylogeny ; *Staphylococcal Infections/veterinary/genetics ; Gene Transfer, Horizontal ; }, abstract = {Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.}, }
@article {pmid37410611, year = {2023}, author = {Shetty, VP and Akshay, SD and Rai, P and Deekshit, VK}, title = {Integrons as the potential targets for combating multidrug resistance in Enterobacteriaceae using CRISPR- Cas9 technique.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad137}, pmid = {37410611}, issn = {1365-2672}, abstract = {The emergence of multi-drug resistance (MDR) to pan-drug resistance (PDR) in Enterobacteriaceae has made treatment extremely challenging. Genetic mutations and horizontal gene transfer (HGT) through mobile genetic elements (MGEs) were frequently associated mechanisms of drug resistance in pathogens. However, transposons, plasmids, and integrons transfer MDR genes in bacterium via HGT much faster. Integrons are dsDNA segment that plays a crucial role in the adaptation and evolution of bacteria. They contain multiple gene cassettes that code for antibiotic resistance determinants that are expressed by a single promoter (Pc). Integrons are the cause of drug resistance in Enterobacteriaceae. Although alternatives to antibiotics such as bacteriophages, phage proteins, antimicrobial peptides, and natural compounds have been widely used to treat MDR infections, there have been limited efforts to reverse the antibiotic resistance ability of bacteria. Thus, silencing the genes harboured on MGEs achieved by Gene Editing Techniques (GETs) might prevent the spread of MDR. One such GETs, which has a simple design, good repeatability, low cost, and high efficiency, is CRISPR- Cas9 system. Thus, this review is a first of the kind that focuses on utilizing the structure of an integron to make it an ideal target for GETs like CRISPR- Cas9 systems.}, }
@article {pmid37409977, year = {2023}, author = {Fan, Q and Zhang, J and Shi, H and Chang, S and Hou, F}, title = {Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0064523}, doi = {10.1128/aem.00645-23}, pmid = {37409977}, issn = {1098-5336}, abstract = {Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.}, }
@article {pmid37408640, year = {2023}, author = {Kumari, K and Rawat, V and Shadan, A and Sharma, PK and Deb, S and Singh, RP}, title = {In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140249}, pmid = {37408640}, issn = {1664-302X}, abstract = {A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.}, }
@article {pmid37404190, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0017723}, doi = {10.1128/aem.00177-23}, pmid = {37404190}, issn = {1098-5336}, abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.}, }
@article {pmid37396349, year = {2023}, author = {Chen, F and Wang, D and Lu, T and Li, S}, title = {Identification of a novel type II-C Cas9 from the fish pathogen Flavobacterium psychrophilum.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1181303}, pmid = {37396349}, issn = {1664-302X}, abstract = {Flavobacterium psychrophilum is the causative agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish worldwide. As an important fish pathogen, F. psychrophilum is frequently exposed to multiple invading genetic elements in natural environments. Endonuclease Cas9 provides bacteria with adaptive interference against invading genetic elements. Previous studies revealed that several F. psychrophilum strains harbored a type II-C Cas9 called Fp1Cas9, but little is known about the potential role of this endonuclease against invading genetic elements. In this work, we identified a gene encoding a novel type II-C Cas9 called Fp2Cas9 from F. psychrophilum strain CN46. Through bacterial RNA sequencing, we demonstrated active transcription of both Fp2Cas9 and pre-crRNAs in strain CN46. Bioinformatics analysis further revealed that the transcription of Fp2Cas9 and pre-crRNAs was driven by a newly integrated promoter sequence and a promoter element embedded within each CRISPR repeat, respectively. To formally demonstrate that Fp2Cas9 and associated crRNAs yielded functional interference in strain CN46, a plasmid interference assay was performed, resulting in adaptive immunity to target DNA sequences in Flavobacterium bacteriophages. Phylogenetic analysis demonstrated that Fp2Cas9 was present only in several F. psychrophilum isolates. Phylogenetic analysis revealed that this novel endonuclease was probably acquired through horizontal gene transfer from the CRISPR-Cas9 system in an unidentified Flavobacterium species. Comparative genomics analysis further showed that the Fp2Cas9 was integrated into the type II-C CRISPR-Cas locus in strain CN38 instead of the original Fp1Cas9. Taken together, our results shed light on the origin and evolution of Fp2Cas9 gene and demonstrated that this novel endonuclease provided adaptive interference against bacteriophage infections.}, }
@article {pmid37395521, year = {2023}, author = {Meng, PQ and Zhang, Q and Ding, Y and Lin, JX and Chen, F}, title = {Evolutionary and Pan-genome Analysis of Three Important Black-pigmented Periodontal Pathogens.}, journal = {The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA)}, volume = {26}, number = {2}, pages = {93-104}, doi = {10.3290/j.cjdr.b4128023}, pmid = {37395521}, issn = {1867-5646}, abstract = {OBJECTIVE: To analyse the pan-genome of three black-pigmented periodontal pathogens: Porphyromonas gingivalis, Prevotella intermedia and Prevotella nigrescens.<br><br>METHODS: Pan-genome analyses of 66, 33 and 5 publicly available whole-genome sequences of P. gingivalis, P. intermedia and P. nigrescens, respectively, were performed using Pan-genome Analysis Pipeline software (version 1.2.1; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China). Phylogenetic trees were constructed based on the entire pan-genome and single nucleotide polymorphisms within the core genome. The distribution and abundance of virulence genes in the core and dispensable genomes were also compared in the three species.<br><br>RESULTS: All three species possess an open pan-genome. The core genome of P. gingivalis, P. intermedia and P. nigrescens included 1001, 1514 and 1745 orthologous groups, respectively, which were mainly related to basic cellular functions such as metabolism. The dispensable genome of P. gingivalis, P. intermedia and P. nigrescens was composed of 2814, 2689 and 906 orthologous groups, respectively, and it was enriched in genes involved in pathogenicity or with unknown functions. Phylogenetic trees presented a clear separation of P. gingivalis, P. intermedia and P. nigrescens, verifying the reclassification of the black-pigmented species. Furthermore, the three species shared almost the same virulence factors involved in adhesion, proteolysis and evasion of host defences. Some of these virulence genes were conserved across species whereas others belonged to the dispensable genome, which might be acquired through horizontal gene transfer.<br><br>CONCLUSION: This study highlighted the usefulness of pan-genome analysis to infer evolutionary cues for black-pigmented species, indicating their homology and phylogenomic diversity.}, }
@article {pmid37395112, year = {2023}, author = {Lloyd, GS and Thomas, CM}, title = {Microbial Primer: The logic of bacterial plasmids.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {7}, pages = {}, doi = {10.1099/mic.0.001336}, pmid = {37395112}, issn = {1465-2080}, abstract = {This short primer is intended to give an overview of bacterial plasmids for those not yet familiar with these fascinating genetic elements. It covers their basic properties but does not attempt to cover the diversity of phenotypic properties that can be encoded by plasmids, and includes suggestions for further reading.}, }
@article {pmid37394042, year = {2023}, author = {Mohammad Mirsoleimani Azizi, S and Zakaria, BS and Haffiez, N and Kumar, A and Ranjan Dhar, B}, title = {Pilot-scale investigation of conductive carbon cloth amendment for enhancing high-solids anaerobic digestion and mitigating antibiotic resistance.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129411}, doi = {10.1016/j.biortech.2023.129411}, pmid = {37394042}, issn = {1873-2976}, abstract = {This study examined the effectiveness of introducing conductive carbon cloth into a pilot-scale high-solids anaerobic digestion (HSAD) system. Adding carbon cloth increased methane production by 22% and improved the maximum methane production rate by 39%. Microbial community characterization indicated a possible direct interspecies electron transfer-based syntrophic association among microbes. Using carbon cloth also enhanced microbial richness, diversity, and evenness. Carbon cloth effectively reduced the total abundance of antibiotic resistance genes (ARGs) by 44.6%, mainly by inhibiting horizontal gene transfer, as shown by the significant decrease in the relative abundance of integron genes (particularly intl1). The multivariate analysis further demonstrated strong correlations of intl1 with most of the targeted ARGs. These findings suggest that carbon cloth amendment can promote efficient methane production and attenuate the spread of ARGs in HSAD systems.}, }
@article {pmid37392596, year = {2023}, author = {Evans, D and Sundermann, A and Griffith, M and Rangachar Srinivasa, V and Mustapha, M and Chen, J and Dubrawski, A and Cooper, V and Harrison, L and Van Tyne, D}, title = {Empirically derived sequence similarity thresholds to study the genomic epidemiology of plasmids shared among healthcare-associated bacterial pathogens.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104681}, doi = {10.1016/j.ebiom.2023.104681}, pmid = {37392596}, issn = {2352-3964}, abstract = {BACKGROUND: Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to apply whole-genome sequencing to systematically resolve and track plasmids carried by nosocomial pathogens in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.<br><br>METHODS: We performed an observational study of plasmids circulating among bacterial isolates infecting patients at a large hospital. We first examined plasmids carried by isolates sampled from the same patient over time and isolates that caused clonal outbreaks in the same hospital to develop thresholds with which horizontal plasmid transfer within a tertiary hospital could be inferred. We then applied those sequence similarity thresholds to perform a systematic screen of 3074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal links between patients infected with bacteria encoding plasmids of interest.<br><br>FINDINGS: Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content and accumulated fewer than 15 SNPs per 100&#xa0;kb of plasmid sequence. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids that potentially circulated among clinical isolates. Ten highly preserved plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes.<br><br>INTERPRETATION: Evidence suggests that the horizontal transfer of plasmids among nosocomial bacterial pathogens appears to be frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital.<br><br>FUNDING: This research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine.}, }
@article {pmid37389331, year = {2023}, author = {Bromfield, ESP and Cloutier, S and Hynes, MF}, title = {Ensifer canadensis sp. nov. strain T173[T] isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1195755}, doi = {10.3389/fmicb.2023.1195755}, pmid = {37389331}, issn = {1664-302X}, abstract = {A bacterial strain, designated T173[T], was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173[T] was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173[T]. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173[T] in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04[T] as the closest relative. The highest digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173[T] compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95-96% for bacterial species circumscription. The genome of strain T173[T] has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173[T]. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173[T]. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173[T] (= LMG 32374[T] = HAMBI 3766[T]) as the species type strain.}, }
@article {pmid37384706, year = {2023}, author = {Widen, SA and Bes, IC and Koreshova, A and Pliota, P and Krogull, D and Burga, A}, title = {Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6652}, pages = {eade0705}, doi = {10.1126/science.ade0705}, pmid = {37384706}, issn = {1095-9203}, abstract = {Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.}, }
@article {pmid37384391, year = {2023}, author = {Römling, U and Cao, LY and Bai, FW}, title = {Evolution of cyclic di-GMP signalling on a short and long term time scale.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {6}, pages = {}, doi = {10.1099/mic.0.001354}, pmid = {37384391}, issn = {1465-2080}, abstract = {Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.}, }
@article {pmid37379503, year = {2023}, author = {Duan, JL and Ma, JY and Sun, XD and Liu, XY and Wang, Y and Du, L and Xia, PF and Yuan, XZ}, title = {Bubbles Expand the Dissemination of Antibiotic Resistance in the Aquatic Environment.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c02935}, pmid = {37379503}, issn = {1520-5851}, abstract = {Antibiotic resistance is a global health challenge, and the COVID-19 pandemic has amplified the urgency to understand its airborne transmission. The bursting of bubbles is a fundamental phenomenon in natural and industrial processes, with the potential to encapsulate or adsorb antibiotic-resistant bacteria (ARB). However, there is no evidence to date for bubble-mediated antibiotic resistance dissemination. Here, we show that bubbles can eject abundant bacteria to the air, form stable biofilms over the air-water interface, and provide opportunities for cell-cell contact that facilitates horizontal gene transfer at and over the air-liquid interface. The extracellular matrix (ECM) on bacteria can increase bubble attachment on biofilms, increase bubble lifetime, and, thus, produce abundant small droplets. We show through single-bubble probe atomic force microscopy and molecular dynamics simulations that hydrophobic interactions with polysaccharides control how the bubble interacts with the ECM. These results highlight the importance of bubbles and its physicochemical interaction with ECM in facilitating antibiotic resistance dissemination and fulfill the framework on antibiotic resistance dissemination.}, }
@article {pmid37378525, year = {2023}, author = {Tan, Q and Li, R and Liu, L and Wang, D and Dai, XF and Song, LM and Zhang, DD and Kong, ZQ and Klosterman, SJ and Usami, T and Subbarao, KV and Liang, WX and Chen, JY}, title = {Functional Characterization of Verticillium dahliae Race 3-Specific Gene VdR3e in Virulence and Elicitation of Plant Immune Responses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0108323}, doi = {10.1128/spectrum.01083-23}, pmid = {37378525}, issn = {2165-0497}, abstract = {Verticillium dahliae is a soilborne fungal pathogen that causes disease on many economically important crops. Based on the resistance or susceptibility of differential cultivars in tomato, isolates of V. dahliae are divided into three races. Avirulence (avr) genes within the genomes of the three races have also been identified. However, the functional role of the avr gene in race 3 isolates of V. dahliae has not been characterized. In this study, bioinformatics analysis showed that VdR3e, a cysteine-rich secreted protein encoded by the gene characterizing race 3 in V. dahliae, was likely obtained by horizontal gene transfer from the fungal genus Bipolaris. We demonstrate that VdR3e causes cell death by triggering multiple defense responses. In addition, VdR3e localized at the periphery of the plant cell and triggered immunity depending on its subcellular localization and the cell membrane receptor BAK1. Furthermore, VdR3e is a virulence factor and shows differential pathogenicity in race 3-resistant and -susceptible hosts. These results suggest that VdR3e is a virulence factor that can also interact with BAK1 as a pathogen-associated molecular pattern (PAMP) to trigger immune responses. IMPORTANCE Based on the gene-for-gene model, research on the function of avirulence genes and resistance genes has had an unparalleled impact on breeding for resistance in most crops against individual pathogens. The soilborne fungal pathogen, Verticillium dahliae, is a major pathogen on many economically important crops. Currently, avr genes of the three races in V. dahliae have been identified, but the function of avr gene representing race 3 has not been described. We investigated the characteristics of VdR3e-mediated immunity and demonstrated that VdR3e acts as a PAMP to activate a variety of plant defense responses and induce plant cell death. We also demonstrated that the role of VdR3e in pathogenicity was host dependent. This is the first study to describe the immune and virulence functions of the avr gene from race 3 in V. dahliae, and we provide support for the identification of genes mediating resistance against race 3.}, }
@article {pmid37374993, year = {2023}, author = {Caliskan-Aydogan, O and Alocilja, EC}, title = {A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061491}, pmid = {37374993}, issn = {2076-2607}, support = {1012975//United States Department of Agriculture/ ; 2022-67017-36982.//USDA-NIFA/ ; }, abstract = {Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.}, }
@article {pmid37374909, year = {2023}, author = {Harris, M and Fasolino, T and Ivankovic, D and Davis, NJ and Brownlee, N}, title = {Genetic Factors That Contribute to Antibiotic Resistance through Intrinsic and Acquired Bacterial Genes in Urinary Tract Infections.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061407}, pmid = {37374909}, issn = {2076-2607}, abstract = {The overprescribing and misuse of antibiotics have led to the rapid development of multidrug-resistant bacteria, such as those that cause UTIs. UTIs are the most common outpatient infections and are mainly caused by Escherichia coli and Klebsiella spp., although some Gram-positive bacteria, such as Pseudomonas aeruginosa, have been isolated in many cases. The rise of antimicrobial-resistant bacteria is a major public health concern, as it is predicted to lead to increased healthcare costs and poor patient outcomes and is expected to be the leading cause of global mortality by 2050. Antibiotic resistance among bacterial species can arise from a myriad of factors, including intrinsic and acquired resistance mechanisms, as well as mobile genetic elements, such as transposons, integrons, and plasmids. Plasmid-mediated resistance is of major concern as drug-resistance genes can quickly and efficiently spread across bacterial species via horizontal gene transfer. The emergence of extended-spectrum β-lactamases (ESBLs) such as NDM-1, OXA, KPC, and CTX-M family members has conferred resistance to many commonly used antibiotics in the treatment of UTIs, including penicillins, carbapenems, cephalosporins, and sulfamethoxazole. This review will focus on plasmid-mediated bacterial genes, especially those that encode ESBLs, and how they contribute to antibiotic resistance. Early clinical detection of these genes in patient samples will provide better treatment options and reduce the threat of antibiotic resistance.}, }
@article {pmid37372483, year = {2023}, author = {Shymialevich, D and Wójcicki, M and Świder, O and Średnicka, P and Sokołowska, B}, title = {Characterization and Genome Study of a Newly Isolated Temperate Phage Belonging to a New Genus Targeting Alicyclobacillus acidoterrestris.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/genes14061303}, pmid = {37372483}, issn = {2073-4425}, abstract = {The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The inactivation of Alicyclobacillus spp. constitutes a challenge because it is resistant to environmental factors, such as high temperatures, and active acidity. However, the use of bacteriophages seems to be a promising approach. In this study, we aimed to isolate and comprehensively characterize a novel bacteriophage targeting Alicyclobacillus spp. The Alicyclobacillus phage strain KKP 3916 was isolated from orchard soil against the Alicyclobacillus acidoterrestris strain KKP 3133. The bacterial host's range and the effect of phage addition at different rates of multiplicity of infections (MOIs) on the host's growth kinetics were determined using a Bioscreen C Pro growth analyzer. The Alicyclobacillus phage strain KKP 3916, retained its activity in a wide range of temperatures (from 4 °C to 30 °C) and active acidity values (pH from 3 to 11). At 70 °C, the activity of the phage decreased by 99.9%. In turn, at 80 °C, no activity against the bacterial host was observed. Thirty minutes of exposure to UV reduced the activity of the phages by almost 99.99%. Based on transmission-electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the Alicyclobacillus phage strain KKP 3916 was classified as a tailed bacteriophage. The genomic sequencing revealed that the newly isolated phage had linear double-stranded DNA (dsDNA) with sizes of 120 bp and 131 bp and 40.3% G+C content. Of the 204 predicted proteins, 134 were of unknown function, while the remainder were annotated as structural, replication, and lysis proteins. No genes associated with antibiotic resistance were found in the genome of the newly isolated phage. However, several regions, including four associated with integration into the bacterial host genome and excisionase, were identified, which indicates the temperate (lysogenic) life cycle of the bacteriophage. Due to the risk of its potential involvement in horizontal gene transfer, this phage is not an appropriate candidate for further research on its use in food biocontrol. To the best of our knowledge, this is the first article on the isolation and whole-genome analysis of the Alicyclobacillus-specific phage.}, }
@article {pmid37372055, year = {2023}, author = {Gheibzadeh, MS and Manyumwa, CV and Tastan Bishop, &#xd6; and Shahbani Zahiri, H and Parkkila, S and Zolfaghari Emameh, R}, title = {Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems.}, journal = {Biology}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/biology12060770}, pmid = {37372055}, issn = {2079-7737}, support = {737//National Institute of Genetic Engineering and Biotechnology/ ; M/75137//Ministry of Science, Research and Technology/ ; 111212//National Research Foundation/ ; }, abstract = {Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.}, }
@article {pmid37369847, year = {2023}, author = {Steenwyk, JL and Li, Y and Zhou, X and Shen, XX and Rokas, A}, title = {Incongruence in the phylogenomics era.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {37369847}, issn = {1471-0064}, abstract = {Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.}, }
@article {pmid37368881, year = {2023}, author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C}, title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.}, journal = {PLoS biology}, volume = {21}, number = {6}, pages = {e3002177}, doi = {10.1371/journal.pbio.3002177}, pmid = {37368881}, issn = {1545-7885}, abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.}, }
@article {pmid37368681, year = {2023}, author = {Boss, L and Kędzierska, B}, title = {Bacterial Toxin-Antitoxin Systems' Cross-Interactions-Implications for Practical Use in Medicine and Biotechnology.}, journal = {Toxins}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/toxins15060380}, pmid = {37368681}, issn = {2072-6651}, support = {UGrants-first 533-D000-GF68-23//University of Gda&#x144;sk/ ; }, abstract = {Toxin-antitoxin (TA) systems are widely present in bacterial genomes. They consist of stable toxins and unstable antitoxins that are classified into distinct groups based on their structure and biological activity. TA systems are mostly related to mobile genetic elements and can be easily acquired through horizontal gene transfer. The ubiquity of different homologous and non-homologous TA systems within a single bacterial genome raises questions about their potential cross-interactions. Unspecific cross-talk between toxins and antitoxins of non-cognate modules may unbalance the ratio of the interacting partners and cause an increase in the free toxin level, which can be deleterious to the cell. Moreover, TA systems can be involved in broadly understood molecular networks as transcriptional regulators of other genes' expression or modulators of cellular mRNA stability. In nature, multiple copies of highly similar or identical TA systems are rather infrequent and probably represent a transition stage during evolution to complete insulation or decay of one of them. Nevertheless, several types of cross-interactions have been described in the literature to date. This implies a question of the possibility and consequences of the TA system cross-interactions, especially in the context of the practical application of the TA-based biotechnological and medical strategies, in which such TAs will be used outside their natural context, will be artificially introduced and induced in the new hosts. Thus, in this review, we discuss the prospective challenges of system cross-talks in the safety and effectiveness of TA system usage.}, }
@article {pmid37367481, year = {2023}, author = {Fakhar, AZ and Liu, J and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {The Lost and Found: Unraveling the Functions of Orphan Genes.}, journal = {Journal of developmental biology}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/jdb11020027}, pmid = {37367481}, issn = {2221-3759}, support = {IOS-2038872//National Science Foundation/ ; }, abstract = {Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.}, }
@article {pmid37367332, year = {2023}, author = {Fallon, AM and Carroll, EM}, title = {Virus-like Particles from Wolbachia-Infected Cells May Include a Gene Transfer Agent.}, journal = {Insects}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/insects14060516}, pmid = {37367332}, issn = {2075-4450}, abstract = {Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head-tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.}, }
@article {pmid37360531, year = {2023}, author = {Gaballa, A and Wiedmann, M and Carroll, LM}, title = {More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1060519}, doi = {10.3389/fcimb.2023.1060519}, pmid = {37360531}, issn = {2235-2988}, abstract = {Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.}, }
@article {pmid37360032, year = {2023}, author = {Fleming, JF and Valero-Gracia, A and Struck, TH}, title = {Identifying and addressing methodological incongruence in phylogenomics: A review.}, journal = {Evolutionary applications}, volume = {16}, number = {6}, pages = {1087-1104}, doi = {10.1111/eva.13565}, pmid = {37360032}, issn = {1752-4571}, abstract = {The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning-one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one-size-fits-all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.}, }
@article {pmid37358464, year = {2023}, author = {Binsker, U and Oelgeschläger, K and Neumann, B and Werner, G and Käsbohrer, A and Hammerl, JA}, title = {Genomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0101523}, doi = {10.1128/spectrum.01015-23}, pmid = {37358464}, issn = {2165-0497}, abstract = {Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function. IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.}, }
@article {pmid37353919, year = {2023}, author = {Frazão, N and Gordo, I}, title = {Ecotype formation and prophage domestication during gut bacterial evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2300063}, doi = {10.1002/bies.202300063}, pmid = {37353919}, issn = {1521-1878}, abstract = {How much bacterial evolution occurs in our intestines and which factors control it are currently burning questions. The formation of new ecotypes, some of which capable of coexisting for long periods of time, is highly likely in our guts. Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals.}, }
@article {pmid37350784, year = {2023}, author = {Fujihara, H and Hirose, J and Suenaga, H}, title = {Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168246}, doi = {10.3389/fmicb.2023.1168246}, pmid = {37350784}, issn = {1664-302X}, abstract = {A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.}, }
@article {pmid37348862, year = {2023}, author = {Moradigaravand, D and Li, L and Dechesne, A and Nesme, J and de la Cruz, R and Ahmad, H and Banzhaf, M and Sørensen, SJ and Smets, BF and Kreft, JU}, title = {Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rRNA Sequences by Machine Learning.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad400}, pmid = {37348862}, issn = {1367-4811}, abstract = {MOTIVATION: Wastewater Treatment Plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for Horizontal Gene Transfer (HGT) of antimicrobial resistance determinants. This facilitates the transmission of clinically important genes between, e.g., enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped.<br><br>RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e., the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 (95% CI: 0.44, 0.55), 0.43 for pKJK5 (0.95% CI: 0.41, 0.49) and 0.53 for RP4 (0.95% CI: 0.48, 0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of antimicrobial resistance (AMR) pollution in wastewater systems.<br><br>The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.}, }
@article {pmid37339822, year = {2023}, author = {Arkhipova, IR and Yushenova, IA and Rodriguez, F}, title = {Shaping eukaryotic epigenetic systems by horizontal gene transfer.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {7}, pages = {e2200232}, doi = {10.1002/bies.202200232}, pmid = {37339822}, issn = {1521-1878}, abstract = {DNA methylation constitutes one of the pillars of epigenetics, relying on covalent bonds for addition and/or removal of chemically distinct marks within the major groove of the double helix. DNA methyltransferases, enzymes which introduce methyl marks, initially evolved in prokaryotes as components of restriction-modification systems protecting host genomes from bacteriophages and other invading foreign DNA. In early eukaryotic evolution, DNA methyltransferases were horizontally transferred from bacteria into eukaryotes several times and independently co-opted into epigenetic regulatory systems, primarily via establishing connections with the chromatin environment. While C5-methylcytosine is the cornerstone of plant and animal epigenetics and has been investigated in much detail, the epigenetic role of other methylated bases is less clear. The recent addition of N4-methylcytosine of bacterial origin as a metazoan DNA modification highlights the prerequisites for foreign gene co-option into the host regulatory networks, and challenges the existing paradigms concerning the origin and evolution of eukaryotic regulatory systems.}, }
@article {pmid37339743, year = {2023}, author = {Takeuchi, N and Hamada-Zhu, S and Suzuki, H}, title = {Prophages and plasmids can display opposite trends in the types of accessory genes they carry.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20231088}, doi = {10.1098/rspb.2023.1088}, pmid = {37339743}, issn = {1471-2954}, abstract = {Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.}, }
@article {pmid37337195, year = {2023}, author = {Zhang, Y and Miao, J and Zhang, N and Wang, X and Li, Z and Richard, OA and Li, B}, title = {The analysis of the function, diversity, and evolution of the Bacillus phage genome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {170}, pmid = {37337195}, issn = {1471-2180}, abstract = {BACKGROUND: Phages play a pivotal role in the evolution of microbial populations. The interactions between phages and their hosts are complex and may vary in response to host physiology and environmental conditions. Here, we have selected the genomes of some representative Bacillus prophages and lysosomes from the NCBI database for evolutionary analysis. We explored their evolutionary relationships and analyzed the protein information encoded by hundreds of Bacillus phages.<br><br>RESULTS: We obtained the following conclusions: First, Bacillus phages carried some known functional gene fragments and a large number of unknown functional gene fragments, which might have an important impact on Bacillus populations, such as the formation of spores and biofilms and the transmission of virulence factors. Secondly, the Bacillus phage genome showed diversity, with a clear genome boundary between Bacillus prophages and Bacillus lytic phages. Furthermore, genetic mutations, sequence losses, duplications, and host-switching have occurred during the evolution of the Bacillus phage, resulting in low genome similarity between the Bacillus phages. Finally, the lysis module played an important influence on the process of Bacillus phage cross-species infestation.<br><br>CONCLUSIONS: This study systematically described their protein function, diversity, and genome evolution, and the results of this study provide a basis for evolutionary diversity, horizontal gene transfer and co-evolution with the host in Bacillus phages.}, }
@article {pmid37336594, year = {2023}, author = {Shafiq, M and Bilal, H and Permana, B and Xu, D and Cai, G and Li, X and Zeng, M and Yuan, Y and Jiao, X and Yao, F}, title = {Characterization of antibiotic resistance genes and mobile elements in extended-spectrum β-lactamase-producing Escherichia coli strains isolated from hospitalized patients in Guangdong, China.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad125}, pmid = {37336594}, issn = {1365-2672}, abstract = {AIM: This study aimed to investigate the high-resolution phenotypic and genotypic characterization of extended-spectrum β-lactamase (ESBL)-producing E. coli strains isolated from hospitalized patients to explore the resistance genes and mobile genetic elements (MGEs) involved in horizontal dissemination.<br><br>METHODS: Between May and September 2021, a total of 216 ESBL-producing E. coli isolates were recovered from multiple departments. The identification of strains was performed using MALDI-TOF mass spectrometry and PCR, while antibiotic susceptibility testing was carried out using the Vitek 2 COMPACT system to determine resistance patterns, while PCR was used to detect different resistance genes and MGEs. In addition, a conjugation assay was performed to investigate the horizontal gene transfer of resistance genes. Selected isolates underwent whole-genome sequencing using the Illumina MiSeq platform.<br><br>RESULTS: A total of 216 out of 409 E. coli isolates recovered from a tertiary hospital were observed to be ESBL-producing, giving a carriage rate of 52.8%, as determined by phenotypic screening. The most frequent sources of ESBL-producing E. coli isolates were urine (129/216, 59.72%,) and blood (50/216, 23.14%). The most prevalent ESBL genes identified were blaCTX-M (60.18%), blaTEM (40.27%), and blaSHV (18.05%). Three E. coli isolates were found to carry the genes blaNDM, mcr-1, and fosA3 genes. The most prevalent MGEs were IS26 (95.37%), Int (87.03%), and IncFIB (76.85%). Whole-genome sequencing analysis of eight MDR E. coli strains revealed that these isolates belonged to eight different sequence types (STs) and serotypes and were found to harbor multiple plasmid replicons and virulence factors.<br><br>CONCLUSION: This study highlights a high incidence of antibiotic resistance genes and MGEs associated with the dissemination of ESBLs and other resistance genes.}, }
@article {pmid37336333, year = {2023}, author = {Xia, Y and Zuo, S and Zheng, Y and Yang, W and Tang, X and Ke, X and Zhuo, Q and Yang, X and Li, Y and Liu, H and Fan, B}, title = {Extended one generation reproductive toxicity study and effect on gut flora of genetically modified rice rich in β-carotene in wistar rats.}, journal = {Reproductive toxicology (Elmsford, N.Y.)}, volume = {}, number = {}, pages = {108424}, doi = {10.1016/j.reprotox.2023.108424}, pmid = {37336333}, issn = {1873-1708}, abstract = {To evaluate the reproductive toxicity of gene modified rice generated by introducing phytoene synthase (Psy) and bacterial phytoene desaturase (CrtI) from maize and Erwinia uredovora, Wistar rats were allocated into 3 groups and fed with Psy and CrtI gene modified rice mixture diet (GM group), non-gene modified rice mixture diet (non-GM group), and AIN-93 diet (Blank control group) from parental generation (F0) to the offsprings (F1). GM rice, Heijinmi (HJM) and Non-GM rice, Heishuai (HS), were both formulated into diets at ratios of 73.5% and 75.5% according to the AIN93 diet for rodent animals, respectively. Relative to the non-GM group, no biologically relevant differences were observed in GM group rats concerning reproductive performance such as fertility rate, gestation rate, mean duration, hormone level, and reproductive organ pathology. The developmental parameters results were not significantly different from the non-GM group such as body weight, food consumption, developmental neurotoxicity, behavior, hematology, and serum chemistry. In terms of immunotoxicity, the IgG indicators of offspring from the GM group improved in contrast with the non-GM group. Additional gut flora analysis of F0 generation rats resulted as that the treatment elicited an increased gut microflora diversity of F0 rats. And no horizontal gene transfer of Psy and CrtI genes in rats fed a GM rice HJM diet. In conclusion, we found no adverse effects related to GM rice in the extended one-generation reproductive toxicity study, indicating that GM rice is a safe alternative for its counterpart rice regarding reproductive toxicity.}, }
@article {pmid37333098, year = {2023}, author = {Grodner, B and Shi, H and Farchione, O and Vill, AC and Ntekas, I and Diebold, PJ and Zipfel, WR and Brito, IL and De Vlaminck, I}, title = {Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.09.544291}, pmid = {37333098}, abstract = {The frequent exchange of mobile genetic elements (MGEs) between bacteria accelerates the spread of functional traits, including antimicrobial resistance, within the human microbiome. Yet, progress in understanding these intricate processes has been hindered by the lack of tools to map the spatial spread of MGEs in complex microbial communities, and to associate MGEs to their bacterial hosts. To overcome this challenge, we present an imaging approach that pairs single molecule DNA Fluorescence In Situ Hybridization (FISH) with multiplexed ribosomal RNA FISH, thereby enabling the simultaneous visualization of both MGEs and host bacterial taxa. We used this methodology to spatially map bacteriophage and antimicrobial resistance (AMR) plasmids in human oral biofilms, and we studied the heterogeneity in their spatial distributions and demonstrated the ability to identify their host taxa. Our data revealed distinct clusters of both AMR plasmids and prophage, coinciding with densely packed regions of host bacteria in the biofilm. These results suggest the existence of specialized niches that maintain MGEs within the community, possibly acting as local hotspots for horizontal gene transfer. The methods introduced here can help advance the study of MGE ecology and address pressing questions regarding antimicrobial resistance and phage therapy.}, }
@article {pmid37332513, year = {2022}, author = {Morson, N and Molenda, O and Picott, KJ and Richardson, RE and Edwards, EA}, title = {Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac021}, pmid = {37332513}, issn = {2633-6685}, abstract = {Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of Dehalococcoides.}, }
@article {pmid37334233, year = {2021}, author = {Liguori, R and Rommel, SH and Bengtsson-Palme, J and Helmreich, B and Wurzbacher, C}, title = {Microbial retention and resistances in stormwater quality improvement devices treating road runoff.}, journal = {FEMS microbes}, volume = {2}, number = {}, pages = {xtab008}, pmid = {37334233}, issn = {2633-6685}, abstract = {Current knowledge about the microbial communities that occur in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials used to remove dissolved heavy metals from two different SQIDs were analyzed to determine microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated with intl1 and with microbial genera. The filter media itself was enriched with Intl1 gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g. czrA, czcA, silP, mexW and mexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.}, }
@article {pmid37329912, year = {2023}, author = {Eleni, K and Chiara, P and Panagiotis, KA and Apostolia, S and Eleni, P and Athanasia, K and Panagiota, L and Smaragda, S and Fabrice, ML and Sotirios, V and Dimitrios, KG}, title = {Accelerated dissipation, soil microbial toxicity and dispersal of antimicrobial resistance in soils repeatedly exposed to tiamulin, tilmicosin and sulfamethoxazole.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164817}, doi = {10.1016/j.scitotenv.2023.164817}, pmid = {37329912}, issn = {1879-1026}, abstract = {The application of manures leads to the contamination of agricultural soils with veterinary antibiotics (VAs). These might exert toxicity on the soil microbiota and threaten environmental quality, and public health. We obtained mechanistic insights about the impact of three VAs, namely, sulfamethoxazole (SMX), tiamulin (TIA) and tilmicosin (TLM), on the abundance of key soil microbial groups, antibiotic resistance genes (ARGs) and class I integron integrases (intl1). In a microcosm study, we repeatedly treated two soils (differing in pH and VA dissipation capacity) with the studied VAs, either directly or via fortified manure. This application scheme resulted in accelerated dissipation of TIA, but not of SMX, and accumulation of TLM. Potential nitrification rates (PNR), and the abundance of ammonia-oxidizing microorganism (AOM) were reduced by SMX and TIA, but not by TLM. VAs strongly impacted the total prokaryotic and AOM communities, whereas manure addition was the main determinant of the fungal and protist communities. SMX stimulated sulfonamide resistance, while manure stimulated ARGs and horizontal gene transfer. Correlations identified opportunistic pathogens like Clostridia, Burkholderia-Caballeronia-Paraburkholderia, and Nocardioides as potential ARG reservoirs in soil. Our results provide unprecedented evidence about the effects of understudied VAs on soil microbiota and highlight risks posed by VA-contaminated manures. ENVIRONMENTAL IMPLICATION: The dispersal of veterinary antibiotics (VAs) through soil manuring enhances antimicrobial resistance (AMR) development and poses a threat to the environment and the public health. We provide insights about the impact of selected VAs on their: (i) microbially-mediated dissipation in soil; (ii) ecotoxicity on the soil microbial communities; (iii) capacity to stimulate AMR. Our results (i) demonstrate the effects of VAs and their application-mode on the bacterial, fungal, and protistan communities, and on the soil ammonia oxidizers; (ii) describe natural attenuation processes against VA dispersal, (iii) depict potential soil microbial AMR reservoirs, essential for the development of risk assessment strategies.}, }
@article {pmid37327521, year = {2023}, author = {Zhu, S and Yang, B and Wang, Z and Liu, Y}, title = {Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors.}, journal = {Ecotoxicology and environmental safety}, volume = {262}, number = {}, pages = {115124}, doi = {10.1016/j.ecoenv.2023.115124}, pmid = {37327521}, issn = {1090-2414}, abstract = {The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.}, }
@article {pmid37325804, year = {2023}, author = {Woods, RJ and Barbosa, C and Koepping, L and Raygoza, JA and Mwangi, M and Read, AF}, title = {The evolution of antibiotic resistance in an incurable and ultimately fatal infection: A retrospective case study.}, journal = {Evolution, medicine, and public health}, volume = {11}, number = {1}, pages = {163-173}, pmid = {37325804}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: The processes by which pathogens evolve within a host dictate the efficacy of treatment strategies designed to slow antibiotic resistance evolution and influence population-wide resistance levels. The aim of this study is to describe the underlying genetic and phenotypic changes leading to antibiotic resistance within a patient who died as resistance evolved to available antibiotics. We assess whether robust patterns of collateral sensitivity and response to combinations existed that might have been leveraged to improve therapy.<br><br>METHODOLOGY: We used whole-genome sequencing of nine isolates taken from this patient over 279 days of a chronic infection with Enterobacter hormaechei, and systematically measured changes in resistance against five of the most relevant drugs considered for treatment.<br><br>RESULTS: The entirety of the genetic change is consistent with de novo mutations and plasmid loss events, without acquisition of foreign genetic material via horizontal gene transfer. The nine isolates fall into three genetically distinct lineages, with early evolutionary trajectories being supplanted by previously unobserved multi-step evolutionary trajectories. Importantly, although the population evolved resistance to all the antibiotics used to treat the infection, no single isolate was resistant to all antibiotics. Evidence of collateral sensitivity and response to combinations therapy revealed inconsistent patterns across this diversifying population.<br><br>CONCLUSIONS: Translating antibiotic resistance management strategies from theoretical and laboratory data to clinical situations, such as this, will require managing diverse population with unpredictable resistance trajectories.}, }
@article {pmid37323902, year = {2023}, author = {Nguyen, QH and Le, TTH and Nguyen, ST and Nguyen, KT and Quyen, DV and Hayer, J and Bañuls, AL and Tran, TTT}, title = {Large-scale analysis of putative plasmids in clinical multidrug-resistant Escherichia coli isolates from Vietnamese patients.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1094119}, pmid = {37323902}, issn = {1664-302X}, abstract = {INTRODUCTION: In the past decades, extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant (CR) Escherichia coli isolates have been detected in Vietnamese hospitals. The transfer of antimicrobial resistance (AMR) genes carried on plasmids is mainly responsible for the emergence of multidrug-resistant E. coli strains and the spread of AMR genes through horizontal gene transfer. Therefore, it is important to thoroughly study the characteristics of AMR gene-harboring plasmids in clinical multidrug-resistant bacterial isolates.<br><br>METHODS: The profiles of plasmid assemblies were determined by analyzing previously published whole-genome sequencing data of 751 multidrug-resistant E. coli isolates from Vietnamese hospitals in order to identify the risk of AMR gene horizontal transfer and dissemination.<br><br>RESULTS: The number of putative plasmids in isolates was independent of the sequencing coverage. These putative plasmids originated from various bacterial species, but mostly from the Escherichia genus, particularly E. coli species. Many different AMR genes were detected in plasmid contigs of the studied isolates, and their number was higher in CR isolates than in ESBL-producing isolates. Similarly, the blaKPC-2, blaNDM-5, blaOXA-1, blaOXA-48, and blaOXA-181 &#x3b2;-lactamase genes, associated with resistance to carbapenems, were more frequent in CR strains. Sequence similarity network and genome annotation analyses revealed high conservation of the &#x3b2;-lactamase gene clusters in plasmid contigs that carried the same AMR genes.<br><br>DISCUSSION: Our study provides evidence of horizontal gene transfer in multidrug-resistant E. coli isolates via conjugative plasmids, thus rapidly accelerating the emergence of resistant bacteria. Besides reducing antibiotic misuse, prevention of plasmid transmission also is essential to limit antibiotic resistance.}, }
@article {pmid37321361, year = {2023}, author = {Zhang, J and Zhang, C and Zan, T and Nan, P and Li, L and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Host shift promotes divergent evolution between closely related holoparasitic species.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {107842}, doi = {10.1016/j.ympev.2023.107842}, pmid = {37321361}, issn = {1095-9513}, abstract = {Distinct hosts have been hypothesized to possess the potential for affecting species differentiation and genome evolution of parasitic organisms. However, what host shift history is experienced by the closely related parasites and whether disparate evolution of their genomes occur remain largely unknown. Here, we screened horizontal gene transfer (HGT) events in a pair of sister species of holoparasitic Boschniakia (Orobanchaceae) having obligate hosts from distinct families to recall the former host-parasite associations and performed a comparative analysis to investigate the difference of their organelle genomes. Except those from the current hosts (Ericaceae and Betulaceae), we identified a number of HGTs from Rosaceae supporting the occurrence of unexpected ancient host shifts. Different hosts transfer functional genes which changed nuclear genomes of this sister species. Likewise, different donors transferred sequences to their mitogenomes, which vary in size due to foreign and repetitive elements rather than other factors found in other parasites. The plastomes are both severely reduced, and the degree of difference in reduction syndrome reaches the intergeneric level. Our findings provide new insights into the genome evolution of parasites adapting to different hosts and extend the mechanism of host shift promoting species differentiation to parasitic plant lineages.}, }
@article {pmid37317293, year = {2023}, author = {Shelenkov, A and Mikhaylova, Y and Voskanyan, S and Egorova, A and Akimkin, V}, title = {Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051314}, pmid = {37317293}, issn = {2076-2607}, abstract = {Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.}, }
@article {pmid37315610, year = {2023}, author = {Pires, J and Santos, R and Monteiro, S}, title = {Antibiotic resistance genes in bacteriophages from wastewater treatment plant and hospital wastewaters.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164708}, doi = {10.1016/j.scitotenv.2023.164708}, pmid = {37315610}, issn = {1879-1026}, abstract = {Antibiotic resistant bacteria (ARB) are a major health risk caused particularly by anthropogenic activities. Acquisition of antibiotic resistances by bacteria is known to have happened before the discovery of antibiotics and can occur through different routes. Bacteriophages are thought to have an important contribution to the dissemination of antibiotic resistance genes (ARGs) in the environment. In this study, seven ARGs (blaTEM, blaSHV, blaCTX-M, blaCMY, mecA, vanA, and mcr-1) were investigated, in the bacteriophage fraction, in raw urban and hospital wastewaters. The genes were quantified in 58 raw wastewater samples collected at five WWTPs (n = 38) and hospitals (n = 20). All genes were detected in the phage DNA fraction, with the bla genes found in higher frequency. On the other hand, mecA and mcr-1 were the least frequently detected genes. Concentrations varied between 10[2] copies/L and 10[6] copies/L. The gene coding for the resistance to colistin (mcr-1), a last-resort antibiotic for the treatment of multidrug-resistant Gram-negative infections, was identified in raw urban and hospital wastewaters with positivity rates of 19 % and 10 %, respectively. ARGs patterns varied between hospital and raw urban wastewaters, and within hospitals and WWTP. This study suggests that phages are reservoirs of ARGs, and that ARGs (with particularly emphasis on resistance to colistin and vancomycin) in the phage fraction are already widely widespread in the environment with potential large implications for public health.}, }
@article {pmid37314210, year = {2023}, author = {Nguyen, M and Elmore, Z and Ihle, C and Moen, FS and Slater, AD and Turner, BN and Parrello, B and Best, AA and Davis, JJ}, title = {Predicting variable gene content in Escherichia coli using conserved genes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0005823}, doi = {10.1128/msystems.00058-23}, pmid = {37314210}, issn = {2379-5077}, abstract = {Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.}, }
@article {pmid37311294, year = {2023}, author = {Zhang, Q and Zhou, L and Zhao, Y and Gao, S and Yang, Y and Chen, Q and Li, W and Qi, Q and Dong, Q and Lei, J and Guo, X and Gao, Q and Yang, Y}, title = {Uncovering the virome and its interaction with antibiotic resistome during compost fertilization.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131763}, doi = {10.1016/j.jhazmat.2023.131763}, pmid = {37311294}, issn = {1873-3336}, abstract = {Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.}, }
@article {pmid37310285, year = {2023}, author = {Cohen, H and Fridman, CM and Gerlic, M and Salomon, D}, title = {A Vibrio T6SS-Mediated Lethality in an Aquatic Animal Model.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0109323}, doi = {10.1128/spectrum.01093-23}, pmid = {37310285}, issn = {2165-0497}, abstract = {Bacteria belonging to the genus Vibrio include many known and emerging pathogens. Horizontal gene transfer of pathogenicity islands is a major contributor to the emergence of new pathogenic Vibrio strains. Here, we use the brine shrimp Artemia salina as a model and show that the marine bacterium Vibrio proteolyticus uses a horizontally shared type VI secretion system, T6SS3, to intoxicate a eukaryotic host. Two T6SS3 effectors, which were previously shown to induce inflammasome-mediated pyroptotic cell death in mammalian phagocytic cells, contribute to this toxicity. Furthermore, we find a novel T6SS3 effector that also contributes to the lethality mediated by this system against Artemia salina. Therefore, our results reveal a T6SS that is shared among diverse vibrios and mediates host lethality, indicating that it can lead to the emergence of new pathogenic strains. IMPORTANCE The rise in sea surface temperature has been linked to the spread of bacteria belonging to the genus Vibrio and the human illnesses associated with them. Since vibrios often share virulence traits horizontally, a better understanding of their virulence potential and determinants can prepare us for new emerging pathogens. In this work, we showed that a toxin delivery system found in various vibrios mediates lethality in an aquatic animal. Taken together with previous reports showing that the same system induces inflammasome-mediated cell death in mammalian phagocytic cells, our findings suggest that this delivery system and its associated toxins may contribute to the emergence of pathogenic strains.}, }
@article {pmid37310275, year = {2023}, author = {Saati-Santamaría, Z}, title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0152323}, doi = {10.1128/spectrum.01523-23}, pmid = {37310275}, issn = {2165-0497}, abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.}, }
@article {pmid37307358, year = {2023}, author = {Marr, RA and Moore, J and Formby, S and Martiniuk, JT and Hamilton, J and Ralli, S and Konwar, K and Rajasundaram, N and Hahn, A and Measday, V}, title = {Whole Genome Sequencing of Canadian Saccharomyces cerevisiae strains isolated from spontaneous wine fermentations reveals a new Pacific West Coast Wine Clade.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkad130}, pmid = {37307358}, issn = {2160-1836}, abstract = {Vineyards in wine regions around the world are reservoirs of yeast with oenological potential. Saccharomyces cerevisiae ferments grape sugars to ethanol and generates flavour and aroma compounds in wine. Wineries place a high value on identifying yeast native to their region to develop a region-specific wine program. Commercial wine strains are genetically very similar due to a population bottleneck and in-breeding compared to the diversity of S. cerevisiae from the wild and other industrial processes. We have isolated and microsatellite typed hundreds of S. cerevisiae strains from spontaneous fermentations of grapes from the Okanagan Valley wine region in British Columbia, Canada. We chose 75 S. cerevisiae strains, based on our microsatellite clustering data, for whole genome sequencing using Illumina paired end reads. Phylogenetic analysis shows that British Columbian S. cerevisiae strains cluster into four clades: Wine/European, Transpacific Oak, Beer 1/Mixed Origin and a new clade that we have designated as Pacific West Coast Wine. The Pacific West Coast Wine clade has high nucleotide diversity and shares genomic characteristics with wild North American oak strains but also has gene flow from Wine/European and Ecuadorian clades. We analyzed gene copy number variations to find evidence of domestication and found that strains in the Wine/European and Pacific West Coast Wine clades have gene copy number variation reflective of adaptations to the wine making environment. The 'wine circle/Region B', a cluster of five genes acquired by horizontal gene transfer into the genome of commercial wine strains is also present in the majority of the British Columbian strains in the Wine/European clade but in a minority of the Pacific West Coast Wine clade strains. Previous studies have shown that S. cerevisiae strains isolated from Mediterranean Oak trees may be the living ancestors of European wine yeast strains. This study is the first to isolate S. cerevisiae strains with genetic similarity to non-vineyard North American Oak strains from spontaneous wine fermentations.}, }
@article {pmid37302657, year = {2023}, author = {Wu, T and Mao, H and Hai, D and Cheng, J and Fu, Y and Lin, Y and Jiang, D and Xie, J}, title = {Molecular characterization of a novel fungal alphaflexivirus reveals potential inter-species horizontal gene transfer.}, journal = {Virus research}, volume = {}, number = {}, pages = {199151}, doi = {10.1016/j.virusres.2023.199151}, pmid = {37302657}, issn = {1872-7492}, abstract = {Sclerotinia sclerotiorum is a notorious phytopathogenic fungus that harbors diverse mycoviruses. A novel positive-sense single-stranded RNA virus, Sclerotinia sclerotiorum alphaflexivirus 2 (SsAFV2), was isolated from the hypovirulent strain 32-9 of S. sclerotiorum, and its complete genome was determined. The SsAFV2 genome contains 7,162 nucleotides (nt), excluding the poly (A) structure, and is composed of four open reading frames (ORF1-4). ORF1 encodes a polyprotein that contains three conserved domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). The ORF3 putative encodes coat proteins (CP), with ORF2 and ORF4 encoding hypothetical proteins of unknown functions. Phylogenetic analysis revealed that SsAFV2 clustered with Botrytis virus X (BVX) based on multiple alignments of helicase, RdRp, and CP, but the methyltransferase of SsAFV2 was most closely related to Sclerotinia sclerotiorum alphaflexivirus 1, suggesting that SsAFV2 is a new member of the Botrexvirus genus within the Alphaflexiviridae family, and also revealed the occurrence of potential inter-species horizontal gene transfer events within the Botrexvirus genus during the evolutionary process. Our results contribute to the current knowledge regarding the evolution and divergence of Botrexviruses.}, }
@article {pmid37296404, year = {2023}, author = {Mehta, RS and Petit, RA and Read, TD and Weissman, DB}, title = {Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {243}, pmid = {37296404}, issn = {1471-2105}, support = {AI139188/NH/NIH HHS/United States ; 214626/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.}, }
@article {pmid37294009, year = {2023}, author = {Manoharan-Basil, SS and Gestels, Z and Abdellati, S and Akomoneh, EA and Kenyon, C}, title = {Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis.}, journal = {Microbial genomics}, volume = {9}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001041}, pmid = {37294009}, issn = {2057-5858}, }
@article {pmid37289828, year = {2023}, author = {Walsh, SK and Imrie, RM and Matuszewska, M and Paterson, GK and Weinert, LA and Hadfield, JD and Buckling, A and Longdon, B}, title = {The host phylogeny determines viral infectivity and replication across Staphylococcus host species.}, journal = {PLoS pathogens}, volume = {19}, number = {6}, pages = {e1011433}, doi = {10.1371/journal.ppat.1011433}, pmid = {37289828}, issn = {1553-7374}, abstract = {Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non-S. aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods-plaque assays, optical density (OD) assays, and quantitative (q)PCR-we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S. aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.}, }
@article {pmid37286020, year = {2023}, author = {Lapadula, WJ and Juri Ayub, M}, title = {Ribosome Inactivating Proteins in Insects: HGT, gene expression, and functional implications.}, journal = {Gene}, volume = {}, number = {}, pages = {147547}, doi = {10.1016/j.gene.2023.147547}, pmid = {37286020}, issn = {1879-0038}, abstract = {Ribosome-inactivating proteins (RIPs) are RNA N-glycosidases that depurinate an adenine residue in the conserved alpha-sarcin/ricin loop (SRL) of rRNA, inhibiting protein synthesis. Previously, we reported the existence of these toxins in insects, whose presence is restricted to mosquitoes from the Culicinae subfamily (e.g., Aedes aegypti) and whiteflies from the Aleyrodidae family (e.g., Bemisia tabaci). Both groups of genes are derived from two independent horizontal gene transfer (HGT) events and are evolved under purifying selection. Here, we report and characterize the occurrence of a third HGT event in the Sciaroidea superfamily, which supports the recurrent acquisition of RIP genes by insects. Transcriptomic experiments, available in databases, allowed us to describe the temporal and spatial expression profiles for these foreign genes in these organisms. Furthermore, we found that RIP expression is induced after infection with pathogens and provided, for the first time, transcriptomic evidence of parasite SRL depurination. This evidence suggests a possible role of these foreign genes as immune effectors in insects.}, }
@article {pmid37283901, year = {2023}, author = {Abubaker, KT and Anwar, KA}, title = {Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15429}, pmid = {37283901}, issn = {2167-8359}, abstract = {BACKGROUND: Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer.<br><br>OBJECTIVES: This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq.<br><br>PATIENTS AND METHODS: Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum &#x3b2;-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI).<br><br>RESULTS: The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3[rd] generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed.<br><br>CONCLUSION: Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.}, }
@article {pmid37283060, year = {2023}, author = {Yang, L and Mai, G and Hu, Z and Zhou, H and Dai, L and Deng, Z and Ma, Y}, title = {Global transmission of broad-host-range plasmids derived from the human gut microbiome.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad498}, pmid = {37283060}, issn = {1362-4962}, abstract = {Broad-host-range (BHR) plasmids in human gut bacteria are of considerable interest for their ability to mediate horizontal gene transfer (HGT) across large phylogenetic distance. However, the human gut plasmids, especially the BHR plasmids, remain largely unknown. Here, we identified the plasmids in the draft genomes of gut bacterial isolates from Chinese and American donors, resulting in 5372 plasmid-like clusters (PLCs), of which, 820 PLCs (comPLCs) were estimated with > 60% completeness genomes and only 155 (18.9%) were classified to known replicon types (n = 37). We observed that 175 comPLCs had a broad host range across distinct bacterial genera, of which, 71 were detected in at least two human populations of Chinese, American, Spanish, and Danish, and 13 were highly prevalent (>10%) in at least one human population. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments. In conclusion, we obtained a large collection of plasmid sequences in human gut bacteria and demonstrated that a subset of the BHR plasmids can be transmitted globally, thus facilitating extensive HGT (e.g. antibiotic resistance genes) events. This study highlights the potential implications of the plasmids for global human health.}, }
@article {pmid37279941, year = {2023}, author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H}, title = {A novel group of dynamin-related proteins shared by eukaryotes and giant viruses is able to remodel mitochondria from within the matrix.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad134}, pmid = {37279941}, issn = {1537-1719}, abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted, but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action is contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.}, }
@article {pmid37279818, year = {2023}, author = {Wang, X and Zhang, L and Gu, J and Feng, Y and He, K and Jiang, H}, title = {Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121950}, doi = {10.1016/j.envpol.2023.121950}, pmid = {37279818}, issn = {1873-6424}, abstract = {Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3[-]-N 14.7% and NH4[+]-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.}, }
@article {pmid37280593, year = {2023}, author = {Guo, X and Hu, X and Li, J and Shao, B and Wang, Y and Wang, L and Li, K and Lin, D and Wang, H and Gao, Z and Jiao, Y and Wen, Y and Ji, H and Ma, C and Ge, S and Jiang, W and Jin, X}, title = {The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {134}, pmid = {37280593}, issn = {1741-7007}, abstract = {BACKGROUND: Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses.<br><br>RESULTS: The genome of S. himalayana is&#x2009;~&#x2009;1.92&#xa0;Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~&#x2009;54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host.<br><br>CONCLUSIONS: Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.}, }
@article {pmid37278656, year = {2023}, author = {Huo, W and Price, VJ and Sharifi, A and Zhang, MQ and Palmer, KL}, title = {Enterococcus faecalis Strains with Compromised CRISPR-Cas Defense Emerge under Antibiotic Selection for a CRISPR-Targeted Plasmid.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0012423}, doi = {10.1128/aem.00124-23}, pmid = {37278656}, issn = {1098-5336}, abstract = {Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged that are replete with mobile genetic elements (MGEs). Non-MDR E. faecalis strains frequently possess CRISPR-Cas systems, which reduce the frequency of MGE acquisition. We demonstrated in previous studies that E. faecalis populations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-type E. faecalis populations but not E. faecalis populations that lacked the cas9 gene. Our results indicate that E. faecalis CRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer. IMPORTANCE Enterococcus faecalis is a leading cause of hospital-acquired infections and disseminator of antibiotic resistance plasmids among Gram-positive bacteria. We have previously shown that E. faecalis strains with an active CRISPR-Cas system can prevent plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. However, CRISPR-Cas is not a perfect barrier. In this study, we observed populations of E. faecalis with transient coexistence of CRISPR-Cas and one of its plasmid targets. Our experimental data demonstrate that antibiotic selection results in compromised E. faecalis CRISPR-Cas function, thereby facilitating the acquisition of additional resistance plasmids by E. faecalis.}, }
@article {pmid37278068, year = {2023}, author = {Guinet, B and Lepetit, D and Charlat, S and Buhl, PN and Notton, DG and Cruaud, A and Rasplus, JY and Stigenberg, J and de Vienne, DM and Boussau, B and Varaldi, J}, title = {Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.85993}, pmid = {37278068}, issn = {2050-084X}, abstract = {The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.}, }
@article {pmid37272817, year = {2023}, author = {Castellanos, A and Restrepo, L and Bajaña, L and Betancourt, I and Bayot, B and Reyes, A}, title = {Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0485122}, doi = {10.1128/spectrum.04851-22}, pmid = {37272817}, issn = {2165-0497}, abstract = {Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirAB[vp] genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirAB[vp] toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.}, }
@article {pmid37271423, year = {2023}, author = {Feyereisen, R and Urban, JM and Nelson, DR}, title = {Aliens in the CYPome of the black fungus gnat, Bradysia coprophila.}, journal = {Insect biochemistry and molecular biology}, volume = {}, number = {}, pages = {103965}, doi = {10.1016/j.ibmb.2023.103965}, pmid = {37271423}, issn = {1879-0240}, abstract = {The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.}, }
@article {pmid37270585, year = {2023}, author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q}, title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37270585}, issn = {1751-7370}, abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.}, }
@article {pmid37270161, year = {2023}, author = {Sharma, HK and Gupta, P and Nagpal, D and Mukherjee, M and Parmar, VS and Lather, V}, title = {Virtual screening and antimicrobial evaluation for identification of natural compounds as the prospective inhibitors of antibacterial drug resistance targets in Staphylococcus aureus.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {105554}, doi = {10.1016/j.fitote.2023.105554}, pmid = {37270161}, issn = {1873-6971}, abstract = {Infectious diseases have remained a burgeoning cause of death and disability since long. Staphylococcus aureus (S. aureus) is a severe bacterial pathogen causing nosocomial and community infections. It exhibits widespread resistance to antibiotics posing a significant threat to their efficacy. For combating this challenge, different strategies may include modifying existing antibiotics, developing new antibacterial agents, and combining treatments with resistance mechanism inhibitors. Resistance in S. aureus occurs through horizontal gene transfer or chromosomal mutations. Acquisition mechanisms involve enzymatic modification, efflux, target bypass, and drug displacement. Mutations can impact drug targets, activate efflux pumps, or alter cell wall composition to impede drug access. Overcoming S. aureus resistance requires innovative approaches to preserve antibiotic effectiveness. The present study involves the virtual screening of phytochemicals of diverse chemical classes from Zinc database against the antibiotic resistant targets of S. aureus like β-Lactamase, Penicillin Binding Protein 2a (PBP2a), Dihydrofolate reductase (DHFR), DNA gyrase, Multidrug ABC transporter SAV1866, Undecaprenyl diphosphate synthase (UPPS), etc. Thymol, eugenol, gallic acid, l-ascorbic acid, curcumin, berberine and quercetin were identified as potential molecules based on their docking score, binding interactions. These molecules were further analyzed for the ADMET and drug likeness properties using pkCSM, SwissADME and Qikprop tools. Further in vitro evaluation of these molecules against antibiotic-resistant strains of S. aureus, both alone and in combination with antibiotics revealed significant findings. Curcumin demonstrated the lowest MIC values (31.25-62.5 μg/ml) when tested individually. Thymol, berberine, and quercetin displayed MIC values within the range of 125-250 μg/ml, while eugenol and gallic acid exhibited MIC values ranging from 500 to 1000 μg/ml. Notably, thymol exhibited potent synergy with all four antibiotics against clinical isolates of S. aureus, with Fractional inhibitory concentration index (FICI) values consistently below 0.5, highlighting its exceptional antibacterial activity, especially in combination with amoxicillin.}, }
@article {pmid37270129, year = {2023}, author = {Xu, Y and Liu, Q and Meng, G and Dong, C}, title = {Horizontal gene transfer of Cccyt contributes to virulence of mycoparasite Calcarisporium cordycipiticola by interacting with a host heat shock protein.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {124927}, doi = {10.1016/j.ijbiomac.2023.124927}, pmid = {37270129}, issn = {1879-0003}, abstract = {Horizontal gene transfer (HGT) is an important driving force for virulence evolution of pathogens, however, functions of these transferred genes are still not fully investigated. Here, an HGT effector, CcCYT was reported to contribute to virulence of a mycoparasite, Calcarisporium cordycipiticola to the host Cordyceps militaris, an important mushroom. Cccyt was predicted to be horizontally transferred from Actinobacteria ancestor by phylogenetic, synteny, GC content and codon usage pattern analyses. The transcript of Cccyt was sharply up-regulated at the early stage of infecting C. militaris. This effector was localized to the cell wall and contributed to the virulence of C. cordycipiticola without affecting its morphology, mycelial growth, conidiation, and resistance to abiotic stress. CcCYT can firstly bind the septa, and finally cytoplasm of the deformed hyphal cells of C. militaris. Pull-down assay coupled mass spectrometry revealed that proteins with which CcCYT interacted were related to protein process, folding and degradation. GST-Pull down assay confirmed that C. cordycipiticola effector CcCYT can interact with host protein CmHSP90 to inhibit the immune response of host. The results provided functional evidence that HGT is an important driving force for the virulence evolution and will be helpful for revealing the interaction between mycoparasite and mushroom host.}, }
@article {pmid37269713, year = {2023}, author = {Dai, X and Zhao, J and Sun, J and Chen, L and Han, P and Wang, X and Huang, J and Wang, L}, title = {ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis.}, journal = {Veterinary microbiology}, volume = {283}, number = {}, pages = {109795}, doi = {10.1016/j.vetmic.2023.109795}, pmid = {37269713}, issn = {1873-2542}, abstract = {Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10[-5]. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.}, }
@article {pmid37268165, year = {2023}, author = {Kameswaran, S and Ramesh, B}, title = {Quenching and Quorum Sensing in Bacterial Bio-films.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104085}, doi = {10.1016/j.resmic.2023.104085}, pmid = {37268165}, issn = {1769-7123}, abstract = {Quorum sensing (QS) is the ability of bacteria to monitor their population density and adjust gene expression accordingly. QS-regulated processes include host-microbe interactions, horizontal gene transfer, and multicellular behaviours (such as the growth and development of biofilm). The creation, transfer, and perception of bacterial chemicals known as autoinducers or QS signals are necessary for QS signalling (e.g. N-acylhomoserine lactones). Quorum quenching (QQ), another name for the disruption of QS signalling, comprises a wide range of events and mechanisms that are described and analysed in this study. In order to better comprehend the targets of the QQ phenomena that organisms have naturally developed and are currently being actively researched from practical perspectives, we first surveyed the diversity of QS-signals and QS-associated responses. Next, the mechanisms, molecular players, and targets related to QS interference are discussed, with a focus on natural QQ enzymes and compounds that function as QS inhibitors. To illustrate the processes and biological functions of QS inhibition in microbe-microbe and host-microbe interactions, a few QQ paradigms are described in detail. Finally, certain QQ techniques are offered as potential instruments in a variety of industries, including agriculture, medical, aquaculture, crop production, and anti-biofouling areas.}, }
@article {pmid37267763, year = {2023}, author = {Sun, S and Wang, Q and Wang, N and Yang, S and Qi, H}, title = {High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118296}, doi = {10.1016/j.jenvman.2023.118296}, pmid = {37267763}, issn = {1095-8630}, abstract = {Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.}, }
@article {pmid37267681, year = {2023}, author = {Carlsen, L and Büttner, H and Christner, M and Cordts, L and Franke, G and Hoffmann, A and Knobling, B and Lütgehetmann, M and Nakel, J and Werner, T and Knobloch, JK}, title = {Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany.}, journal = {Journal of infection and public health}, volume = {16}, number = {8}, pages = {1142-1148}, doi = {10.1016/j.jiph.2023.05.029}, pmid = {37267681}, issn = {1876-035X}, abstract = {BACKGROUND: Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages.<br><br>METHODS: In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n&#xa0;=&#xa0;59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n&#xa0;=&#xa0;240).<br><br>RESULTS: Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum &#x3b2;-lactamases decreased over time.<br><br>CONCLUSIONS: This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.}, }
@article {pmid37263036, year = {2023}, author = {Wu, C and Zhang, G and Zhang, K and Sun, J and Cui, Z and Guo, Y and Liu, H and Xu, W}, title = {Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118132}, doi = {10.1016/j.jenvman.2023.118132}, pmid = {37263036}, issn = {1095-8630}, abstract = {Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.}, }
@article {pmid37261234, year = {2023}, author = {Fatima, S and Ishaq, Z and Irfan, M and AlAsmari, AF and Achakzai, JK and Zaheer, T and Ali, A and Akbar, A}, title = {Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1151805}, pmid = {37261234}, issn = {2296-2565}, abstract = {INTRODUCTION: Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden.<br><br>METHODS: In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization.<br><br>RESULTS AND DISCUSSION: MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.}, }
@article {pmid37258869, year = {2023}, author = {Abdelrazik, E and El-Hadidi, M}, title = {Tracking Antibiotic Resistance from the Environment to Human Health.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {289-301}, pmid = {37258869}, issn = {1940-6029}, abstract = {Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.}, }
@article {pmid37257204, year = {2023}, author = {Chen, P and Yu, K and He, Y}, title = {The dynamics and transmission of antibiotic resistance associated with plant microbiomes.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107986}, doi = {10.1016/j.envint.2023.107986}, pmid = {37257204}, issn = {1873-6750}, abstract = {Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.}, }
@article {pmid37256324, year = {2023}, author = {Oliveira, GS and Lentz, SA and Wink, PL and Martins, AF}, title = {Molecular typing of mcr-1 Escherichia coli isolates from pigs and farm environment based on fumC and fimH alleles.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2022-0173}, pmid = {37256324}, issn = {1746-0921}, abstract = {Background: The dissemination of polymyxin resistance represents a significant threat to public health. Materials &amp; methods: Sequence-based typing was performed by 53 mcr-1 Escherichia coli isolates using fumC/fimH (CH) genes to characterize clones spreading from pig farming. Furthermore, 12 isolates had their whole genome sequenced for phylogenetic study. Results: The isolates were classified into 22 distinct CH types, and two novel CH types (CH41-1578 and CH4-1579) and one sequence type (ST12652) was also described. According to phylogenetic study, both multilocus sequence typing and CH methods grouped the isolates similarly. Conclusion: Our findings suggest that the dissemination of the mcr-1 gene in pig farming has occurred mainly by horizontal gene transfer, and CH typing proved to be a good tool to characterize E. coli clones.}, }
@article {pmid37254648, year = {2023}, author = {Rana, R and Jaiswal, G and Bansal, K and Patil, PB}, title = {Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13164}, pmid = {37254648}, issn = {1758-2229}, abstract = {Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.}, }
@article {pmid37252660, year = {2023}, author = {Tokuda, R and Iwabuchi, N and Kitazawa, Y and Nijo, T and Suzuki, M and Maejima, K and Oshima, K and Namba, S and Yamaji, Y}, title = {Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1132432}, pmid = {37252660}, issn = {1664-8021}, abstract = {Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.}, }
@article {pmid37251586, year = {2023}, author = {Scott, TW and West, SA and Dewar, AE and Wild, G}, title = {Is cooperation favored by horizontal gene transfer?.}, journal = {Evolution letters}, volume = {7}, number = {3}, pages = {113-120}, pmid = {37251586}, issn = {2056-3744}, abstract = {It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.}, }
@article {pmid37250807, year = {2023}, author = {Mwakyoma, AA and Kidenya, BR and Minja, CA and Mushi, MF and Sandeman, A and Sabiti, W and Holden, MTG and Mshana, SE}, title = {Comparison of Horizontal blaCTX-M Gene Transfer via Conjugation among Extended Spectrum β-Lactamases Producing Escherichia coli Isolates from Patients with Urinary Tract Infection, Their Animals, and Environment.}, journal = {Archives of molecular biology and genetics}, volume = {2}, number = {1}, pages = {1-8}, pmid = {37250807}, issn = {2831-6754}, abstract = {BACKGROUND: The dissemination of the extended spectrum β-lactamases (ESBL) producing E. coli poses a significant public health problem. Understanding the efficiency and frequency of horizontal gene transfer via conjugation of ESBL producing E. coli is imperative towards devising prevention and control measures. This study compared the frequencies and efficiencies of horizontal blaCTX-M gene transfer via conjugation among Escherichia coli isolates from urine and gastrointestinal tract (GIT) of patients with urinary tract infection (UTI), their animals and environment.<br><br>METHODS: Horizontal blaCTX-M gene transfer via conjugation by a broth mating experiment was performed using 50 confirmed ESBL producing E. coli isolates as donors and Escherichia coli J53 (F[-], met, pro, Az[r]), as the recipient. The transconjugants were detected and their frequencies and efficiencies of conjugation were measured and compared between ESBL producing E. coli isolates multi-sourced from urine, GIT, animals and environment. Antimicrobial susceptibility testing of all resulting transconjugants was performed. DNA was extracted from all transconjugants to confirm the presence and the acquisition of blaCTX-M gene.<br><br>RESULTS: Out of 50 ESBL producing E. coli isolates harboring blaCTX-M gene, 37 (74.0%) successfully exercised horizontal gene transfer through conjugation. All transconjugants were confirmed phenotypically and genotypically by PCR. Of note, all of the isolates from environment 100.0% (7/7) performed conjugation, exhibiting the highest transfer efficiency, followed by isolates from urine and animals, with the conjugation transfer efficiency of 77.8% (14/18) and 76.1% (10/13), respectively. The isolates from the environment conjugated with a significant more efficiency than those from the GIT [Two-sample test of proportions; p-value = 0.0119]. The overall conjugation transfer frequencies ranged from 0.4 &#xd7; 10[-14] - 5.5 &#xd7; 10[-11] per donor cells with the highest median conjugation transfer frequency observed among isolates from animal (3.23 &#xd7; 10[-12] [IQR: 0.70 &#xd7; 10[-12] - 7.22 &#xd7; 10[-12]]) followed by that of isolates from the environment (1.60 &#xd7; 10[-12] [IQR: 0.30 &#xd7; 10[-12] - 5.0 &#xd7; 10[-12]]).<br><br>CONCLUSION: ESBL producing E. coli from human, animals and environment exercises horizontal blaCTX-M gene transfer efficiently with the highest occurrence among isolates from the environment and animals. The antimicrobial resistance control and prevention strategies should be widened up to explore strategies to prevent horizontal AMR gene transfer.}, }
@article {pmid37246713, year = {2023}, author = {Jowsey, WJ and Morris, CRP and Hall, DA and Sullivan, JT and Fagerlund, RD and Eto, KY and Solomon, PD and Mackay, JP and Bond, CS and Ramsay, JP and Ronson, CW}, title = {DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad457}, pmid = {37246713}, issn = {1362-4962}, abstract = {Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.}, }
@article {pmid37246198, year = {2023}, author = {Shafique, MS and Guo, W and Chen, X and Zhao, K and Liu, Y and Wang, C and Ji, Z}, title = {Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice.}, journal = {Functional &amp; integrative genomics}, volume = {23}, number = {2}, pages = {189}, pmid = {37246198}, issn = {1438-7948}, }
@article {pmid37243281, year = {2023}, author = {Arnau, V and Díaz-Villanueva, W and Mifsut Benet, J and Villasante, P and Beamud, B and Mompó, P and Sanjuan, R and González-Candelas, F and Domingo-Calap, P and Džunková, M}, title = {Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/v15051196}, pmid = {37243281}, issn = {1999-4915}, abstract = {The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.}, }
@article {pmid37239594, year = {2023}, author = {Tuvo, B and Scarpaci, M and Bracaloni, S and Esposito, E and Costa, AL and Ioppolo, M and Casini, B}, title = {Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {10}, pages = {}, doi = {10.3390/ijerph20105868}, pmid = {37239594}, issn = {1660-4601}, abstract = {The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.}, }
@article {pmid37239483, year = {2023}, author = {Alim, NTB and Koppenhöfer, S and Lang, AS and Beatty, JT}, title = {Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/genes14051124}, pmid = {37239483}, issn = {2073-4425}, abstract = {A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.}, }
@article {pmid37239397, year = {2023}, author = {Dey, S and Gaur, M and Sykes, EME and Prusty, M and Elangovan, S and Dixit, S and Pati, S and Kumar, A and Subudhi, E}, title = {Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/genes14051037}, pmid = {37239397}, issn = {2073-4425}, abstract = {BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.<br><br>METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.<br><br>RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.<br><br>CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.}, }
@article {pmid37237011, year = {2023}, author = {Negeri, AA and Mamo, H and Gahlot, DK and Gurung, JM and Seyoum, ET and Francis, MS}, title = {Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8595}, pmid = {37237011}, issn = {2045-2322}, abstract = {CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.}, }
@article {pmid37236960, year = {2023}, author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H}, title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {5}, pages = {1415-1429}, doi = {10.13287/j.1001-9332.202305.032}, pmid = {37236960}, issn = {1001-9332}, abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.}, }
@article {pmid37236388, year = {2023}, author = {Song, D and Tang, X and Tariq, A and Pan, K and Li, D}, title = {Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116233}, doi = {10.1016/j.envres.2023.116233}, pmid = {37236388}, issn = {1096-0953}, abstract = {Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 10[5] to 6.22 × 10[7] copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.}, }
@article {pmid37232518, year = {2023}, author = {Burch, CL and Romanchuk, A and Kelly, M and Wu, Y and Jones, CD}, title = {Empirical evidence that complexity limits horizontal gene transfer.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad089}, pmid = {37232518}, issn = {1759-6653}, abstract = {Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein-protein interactions in which the gene participates, i.e., its connectivity. Two non-exclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the Complexity Hypothesis (Jain, Rivera, &amp; Lake, 1999) and the Balance Hypothesis (Papp, Pál, &amp; Hurst, 2003). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologues to make normal protein-protein interactions or from gene mis-expression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into E. coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the Complexity Hypotheses explains all three of these observations, the Balance Hypothesis explains only the first one.}, }
@article {pmid37115189, year = {2023}, author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR}, title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37115189}, issn = {2057-5858}, support = {U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.}, }
@article {pmid37227565, year = {2023}, author = {Chettri, U and Nongkhlaw, M and Joshi, SR}, title = {Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.}, journal = {Current microbiology}, volume = {80}, number = {7}, pages = {226}, pmid = {37227565}, issn = {1432-0991}, abstract = {Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.}, }
@article {pmid37227251, year = {2023}, author = {Tonkin-Hill, G and Corander, J and Parkhill, J}, title = {Challenges in prokaryote pangenomics.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001021}, pmid = {37227251}, issn = {2057-5858}, abstract = {Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.}, }
@article {pmid37223257, year = {2021}, author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P}, title = {Extracellular membrane vesicles and nanotubes in Archaea.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab007}, pmid = {37223257}, issn = {2633-6693}, abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.}, }
@article {pmid37223255, year = {2021}, author = {Afonina, I and Tien, B and Nair, Z and Matysik, A and Lam, LN and Veleba, M and Jie, AKJ and Rashid, R and Cazenave-Gassiot, A and Wenk, M and Wai, SN and Kline, KA}, title = {The composition and function of Enterococcus faecalis membrane vesicles.}, journal = {microLife}, volume = {2}, number = {}, pages = {uqab002}, pmid = {37223255}, issn = {2633-6693}, abstract = {Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.}, }
@article {pmid37221009, year = {2023}, author = {Shaferman, M and Gencel, M and Alon, N and Alasad, K and Rotblat, B and Serohijos, AWR and Alfonta, L and Bershtein, S}, title = {The fitness effects of codon composition of the horizontally transferred antibiotic resistance genes intensify at sub-lethal antibiotic levels.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad123}, pmid = {37221009}, issn = {1537-1719}, abstract = {The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced E. coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5'-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5'-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.}, }
@article {pmid37219457, year = {2023}, author = {Murthy, AC and Aleksanyan, N and Morton, GM and Toyoda, HC and Kalashyan, M and Chen, S and Ragucci, AE and Broulidakis, MP and Swerdlow, KJ and Bui, MNN and Muccioli, M and Berkmen, MB}, title = {Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0003323}, doi = {10.1128/jb.00033-23}, pmid = {37219457}, issn = {1098-5530}, abstract = {Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.}, }
@article {pmid37218693, year = {2023}, author = {Bejenari, M and Sondergaard, TE and Sørensen, JL}, title = {6-MSA, a secondary metabolite distribution hub with multiple fungal destinations.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxad107}, pmid = {37218693}, issn = {1365-2672}, abstract = {6-methylsalicylic acid is a small, simple polyketide produced by a broad spectrum of fungal species. Since fungi obtained the ability to synthesize 6-MSA from bacteria through a horizontal gene transfer event, it has developed into a multipurpose metabolic hub from where numerous complex compounds are produced. The most relevant metabolite from a human perspective is the small lactone patulin as it is one of the most potent mycotoxins. Other important end products derived from 6-MSA include the small quinone epoxide terreic acid and the prenylated yanuthones. The most advanced modification of 6-MSA is observed in the aculin biosynthetic pathway, which is mediated by a non-ribosomal peptide synthase and a terpene cyclase. In this short review, we summarize for the first time all the possible pathways that takes their onset from 6-MSA and provide a synopsis of the responsible gene clusters and derive the resulting biosynthetic pathways.}, }
@article {pmid37078595, year = {2023}, author = {Botelho, J}, title = {Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance.}, journal = {Nucleic acids research}, volume = {51}, number = {9}, pages = {4385-4397}, pmid = {37078595}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents ; Virulence/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.}, }
@article {pmid37217185, year = {2023}, author = {Maruyama, M and Kagamoto, T and Matsumot, Y and Onum, R and Miyagishima, SY and Tanifuj, G and Nakazawa, M and Kashiyama, Y}, title = {Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcad044}, pmid = {37217185}, issn = {1471-9053}, abstract = {While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified the gene RvNaRL, which had sequence similarity to nitrate reductases found in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify its function of the protein product RvNaRL, we established a RNAi mediated knockdown and a CRISPR-Cas9-mediated knockout experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knockdown and knockout cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to acquisition of the nitrate assimilation by the horizontal gene transfer.}, }
@article {pmid37215039, year = {2023}, author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J}, title = {Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.11.540415}, pmid = {37215039}, abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ∼2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.}, }
@article {pmid37213501, year = {2023}, author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X}, title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1145315}, pmid = {37213501}, issn = {1664-302X}, abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.}, }
@article {pmid37213168, year = {2023}, author = {Youngblom, MA and Shockey, AC and Callaghan, MM and Dillard, JP and Pepperell, CS}, title = {The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.000985}, pmid = {37213168}, issn = {2057-5858}, abstract = {The incidence of gonorrhoea is increasing at an alarming pace, and therapeutic options continue to narrow as a result of worsening drug resistance. Neisseria gonorrhoeae is naturally competent, allowing the organism to adapt rapidly to selection pressures including antibiotics. A sub-population of N. gonorrhoeae carries the Gonococcal Genetic Island (GGI), which encodes a type IV secretion system (T4SS) that secretes chromosomal DNA. Previous research has shown that the GGI increases transformation efficiency in vitro, but the extent to which it contributes to horizontal gene transfer (HGT) during infection is unknown. Here we analysed genomic data from clinical isolates of N. gonorrhoeae to better characterize GGI+ and GGI- sub-populations and to delineate patterns of variation at the locus itself. We found the element segregating at an intermediate frequency (61%), and it appears to act as a mobile genetic element with examples of gain, loss, exchange and intra-locus recombination within our sample. We further found evidence suggesting that GGI+ and GGI- sub-populations preferentially inhabit distinct niches with different opportunities for HGT. Previously, GGI+ isolates were reported to be associated with more severe clinical infections, and our results suggest this could be related to metal-ion trafficking and biofilm formation. The co-segregation of GGI+ and GGI- isolates despite mobility of the element suggests that both niches inhabited by N. gonorrhoeae remain important to its overall persistence as has been demonstrated previously for cervical- and urethral-adapted sub-populations. These data emphasize the complex population structure of N. gonorrhoeae and its capacity to adapt to diverse niches.}, }
@article {pmid37213139, year = {2023}, author = {C Silva-de-Jesus, A and Rossi, CC and Pereira-Ribeiro, PM and Guaraldi, AL and Giambiagi-deMarval, M}, title = {Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2022-0225}, pmid = {37213139}, issn = {1746-0921}, abstract = {Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials &amp; methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.}, }
@article {pmid37210032, year = {2023}, author = {Yin, Y and Lou, T and Song, W and Wang, C and Wang, J}, title = {Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129180}, doi = {10.1016/j.biortech.2023.129180}, pmid = {37210032}, issn = {1873-2976}, abstract = {The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.}, }
@article {pmid37209559, year = {2023}, author = {Yuan, B and Zhang, Y and Zhang, Z and Lin, Z and Ma, Y and Sun, Y}, title = {Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131659}, doi = {10.1016/j.jhazmat.2023.131659}, pmid = {37209559}, issn = {1873-3336}, abstract = {Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.}, }
@article {pmid37204585, year = {2023}, author = {Lü, W and Ren, H and Ding, W and Li, H and Yao, X and Jiang, X}, title = {Rapid shifts in pond sediment microbiota in response to high ambient temperature in a water-sediment microcosm.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-023-26823-7}, pmid = {37204585}, issn = {1614-7499}, abstract = {Unlike the extensive research on the response of soil microorganisms to high ambient temperature (HTA), the response of sediment microorganisms to HTA remains unclear. Understanding the response of sediment microorganisms to HTA is important to forecast their impacts on ecosystems and climate warming under projected climate change scenarios. Against the background of climate warming and frequent high ambient temperatures in summer, we conducted a laboratory incubation experiment to clarify the unique assembly characteristics of pond sediment bacterial communities at different temperatures (4, 10, 15, 25, 30 and 35 °C). The results showed that the structure and function of the microbial community in pond sediments at 35 °C were different from those under other temperatures; the microbial community structure at 35 °C had the most large modules and an average module size. Temperature and dissolved oxygen influenced the microbial community network modularity. The CO2 emission rates of pond sediments at 35 °C were significantly higher than those at other temperatures. At 35 °C, heterogeneous selection was the most important assembly process. Additionally, warming altered the microbial network structure and ecosystem functioning but not the microbial diversity or community composition, which may be related to horizontal gene transfer. Revealing the rapid response of pond sediment microorganisms to HTA is important for identifying their role in nutrient cycling and assessing the ecological impacts of climate warming and high ambient temperatures on inland water sediments.}, }
@article {pmid37201375, year = {2023}, author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC}, title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.}, journal = {Water research}, volume = {239}, number = {}, pages = {120061}, doi = {10.1016/j.watres.2023.120061}, pmid = {37201375}, issn = {1879-2448}, abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.}, }
@article {pmid37196739, year = {2023}, author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y}, title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129190}, doi = {10.1016/j.biortech.2023.129190}, pmid = {37196739}, issn = {1873-2976}, abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.}, }
@article {pmid37191574, year = {2023}, author = {Zhu, Q and Gao, S and Xiao, B and He, Z and Hu, S}, title = {Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0464522}, doi = {10.1128/spectrum.04645-22}, pmid = {37191574}, issn = {2165-0497}, abstract = {Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.}, }
@article {pmid37187278, year = {2023}, author = {Zhou, Q and Zhang, J and Fang, Q and Zhang, M and Wang, X and Zhang, D and Pan, X}, title = {Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121828}, doi = {10.1016/j.envpol.2023.121828}, pmid = {37187278}, issn = {1873-6424}, abstract = {MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.}, }
@article {pmid37185344, year = {2023}, author = {Riccardi, C and Koper, P and Innocenti, G and diCenzo, GC and Fondi, M and Mengoni, A and Perrin, E}, title = {Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001025}, pmid = {37185344}, issn = {2057-5858}, abstract = {Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.}, }
@article {pmid37178001, year = {2023}, author = {Vesel, N and Iseli, C and Guex, N and Lemopoulos, A and Blokesch, M}, title = {DNA modifications impact natural transformation of Acinetobacter baumannii.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad377}, pmid = {37178001}, issn = {1362-4962}, support = {407240_167061/SNSF_/Swiss National Science Foundation/Switzerland ; 55008726/HHMI/Howard Hughes Medical Institute/United States ; }, abstract = {Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.}, }
@article {pmid37177929, year = {2023}, author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F}, title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2551-2561}, doi = {10.13227/j.hjkx.202206267}, pmid = {37177929}, issn = {0250-3301}, abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.}, }
@article {pmid37173437, year = {2023}, author = {Feng, SY and Hauck, Y and Morgene, F and Mohammedi, R and Mirouze, N}, title = {The complex regulation of competence in Staphylococcus aureus under microaerobic conditions.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {512}, pmid = {37173437}, issn = {2399-3642}, abstract = {To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.}, }
@article {pmid37173063, year = {2023}, author = {Ayllón, MA and Vainio, EJ}, title = {Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle.}, journal = {Advances in virus research}, volume = {115}, number = {}, pages = {1-86}, doi = {10.1016/bs.aivir.2023.02.002}, pmid = {37173063}, issn = {1557-8399}, abstract = {Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.}, }
@article {pmid37172383, year = {2023}, author = {Liu, YJ and Li, ZH and He, YT and Yuan, L and Sheng, GP}, title = {Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131587}, doi = {10.1016/j.jhazmat.2023.131587}, pmid = {37172383}, issn = {1873-3336}, abstract = {Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.}, }
@article {pmid37172034, year = {2023}, author = {Green, VE and Klancher, CA and Yamamoto, S and Dalia, AB}, title = {The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae.}, journal = {PLoS genetics}, volume = {19}, number = {5}, pages = {e1010767}, doi = {10.1371/journal.pgen.1010767}, pmid = {37172034}, issn = {1553-7404}, abstract = {Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.}, }
@article {pmid37168121, year = {2023}, author = {Tao, S and Zhou, D and Chen, H and Li, N and Zheng, L and Fang, Y and Xu, Y and Jiang, Q and Liang, W}, title = {Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177841}, doi = {10.3389/fmicb.2023.1177841}, pmid = {37168121}, issn = {1664-302X}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.}, }
@article {pmid37167868, year = {2023}, author = {Cai, P and Chen, Q and Du, W and Yang, S and Li, J and Cai, H and Zhao, X and Sun, W and Xu, N and Wang, J}, title = {Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131567}, doi = {10.1016/j.jhazmat.2023.131567}, pmid = {37167868}, issn = {1873-3336}, abstract = {Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.}, }
@article {pmid37166501, year = {2023}, author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A}, title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37166501}, issn = {1432-184X}, abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.}, }
@article {pmid37164096, year = {2023}, author = {Gao, Y and Luo, W and Zhang, H and Chen, Y and Li, Z and Wei, G and Chen, W}, title = {Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163933}, doi = {10.1016/j.scitotenv.2023.163933}, pmid = {37164096}, issn = {1879-1026}, abstract = {Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.}, }
@article {pmid37158891, year = {2023}, author = {Tapia, SM and Macías, LG and Pérez-Torrado, R and Daroqui, N and Manzanares, P and Querol, A and Barrio, E}, title = {A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {102}, pmid = {37158891}, issn = {1741-7007}, abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.<br><br>RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.<br><br>CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.}, }
@article {pmid37156401, year = {2023}, author = {Gartzonika, K and Politi, L and Mavroidi, A and Tsantes, AG and Spanakis, N and Priavali, E and Vrioni, G and Tsakris, A}, title = {High prevalence of clonally-related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {106837}, doi = {10.1016/j.ijantimicag.2023.106837}, pmid = {37156401}, issn = {1872-7913}, abstract = {NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were consecutively recovered. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined-disk tests for carbapenemase production, PCR and sequencing for resistance genes, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments, genotyping by multilocus sequence typing, whole genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST ST (ST182), whereas single isolates belonged to different STs (ST190, ST269, ST443, ST743). PFGE analysis has revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates of the study period. All ST182 blaNDM-1-carrying isolates also harbored the blaACT-16 AmpC gene, while blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most of the cases. In all clonal isolates the blaNDM-1 gene was located on an IncA/C-type plasmid and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. Our study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.}, }
@article {pmid37156383, year = {2023}, author = {Tyrrell, C and Do, TT and Leigh, RJ and Burgess, CM and Brennan, FP and Walsh, F}, title = {Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163926}, doi = {10.1016/j.scitotenv.2023.163926}, pmid = {37156383}, issn = {1879-1026}, abstract = {Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus. We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.}, }
@article {pmid37156983, year = {2023}, author = {Calderón-Franco, D and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG}, title = {Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.}, journal = {Antonie van Leeuwenhoek}, volume = {}, number = {}, pages = {}, pmid = {37156983}, issn = {1572-9699}, abstract = {The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L[-1]). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L[-1]). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.}, }
@article {pmid37155884, year = {2023}, author = {Kinsella, CM and van der Hoek, L}, title = {Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {20}, pages = {e2303844120}, doi = {10.1073/pnas.2303844120}, pmid = {37155884}, issn = {1091-6490}, abstract = {Among cressdnaviruses, only the family Circoviridae is recognized to infect vertebrates, while many others have unknown hosts. Detection of virus-to-host horizontal gene transfer is useful for solving such virus-host relationships. Here, we extend this utility to an unusual case of virus-to-virus horizontal transfer, showing multiple ancient captures of cressdnavirus Rep genes by avipoxviruses-large dsDNA pathogens of birds and other saurians. As gene transfers must have occurred during virus coinfections, saurian hosts were implied for the cressdnavirus donor lineage. Surprisingly, phylogenetic analysis revealed that donors were not members of the vertebrate-infecting Circoviridae, instead belonging to a previously unclassified family that we name Draupnirviridae. While draupnirviruses still circulate today, we show that those in the genus Krikovirus infected saurian vertebrates at least 114 Mya, leaving endogenous viral elements inside snake, lizard, and turtle genomes throughout the Cretaceous Period. Endogenous krikovirus elements in some insect genomes and frequent detection in mosquitoes imply that spillover to vertebrates was arthropod mediated, while ancestral draupnirviruses likely infected protists before their emergence in animals. A modern krikovirus sampled from an avipoxvirus-induced lesion shows that their interaction with poxviruses is ongoing. Captured Rep genes in poxvirus genomes often have inactivated catalytic motifs, yet near-total presence across the Avipoxvirus genus, and evidence of both expression and purifying selection on them suggests currently unknown functions.}, }
@article {pmid37155541, year = {2023}, author = {Jiang, Y and Zhao, L and Li, JD and Sun, J and Miao, R and Shao, B and Wu, P}, title = {The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer.}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {1}, pages = {103-112}, doi = {10.5455/javar.2023.j658}, pmid = {37155541}, issn = {2311-7710}, abstract = {OBJECTIVES: This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts.<br><br>MATERIALS AND METHODS: Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed.<br><br>RESULTS: The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs.<br><br>CONCLUSIONS: The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.}, }
@article {pmid37154532, year = {2023}, author = {Cai, L}, title = {Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e16174}, doi = {10.1002/ajb2.16174}, pmid = {37154532}, issn = {1537-2197}, abstract = {The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.}, }
@article {pmid37152757, year = {2023}, author = {Nie, Z and Tang, K and Wang, W and Wang, P and Guo, Y and Wang, Y and Kao, SJ and Yin, J and Wang, X}, title = {Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138751}, pmid = {37152757}, issn = {1664-302X}, abstract = {Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.}, }
@article {pmid37071810, year = {2023}, author = {Paulat, NS and Storer, JM and Moreno-Santillán, DD and Osmanski, AB and Sullivan, KAM and Grimshaw, JR and Korstian, J and Halsey, M and Garcia, CJ and Crookshanks, C and Roberts, J and Smit, AFA and Hubley, R and Rosen, J and Teeling, EC and Vernes, SC and Myers, E and Pippel, M and Brown, T and Hiller, M and ,  and Rojas, D and Dávalos, LM and Lindblad-Toh, K and Karlsson, EK and Ray, DA}, title = {Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37071810}, issn = {1537-1719}, mesh = {Animals ; *DNA Transposable Elements/genetics ; *Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny ; }, abstract = {Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.}, }
@article {pmid37149187, year = {2023}, author = {Li, LG and Zhang, T}, title = {Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163870}, doi = {10.1016/j.scitotenv.2023.163870}, pmid = {37149187}, issn = {1879-1026}, abstract = {Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.}, }
@article {pmid37148762, year = {2023}, author = {Jiang, H and Zhang, L and Wang, X and Gu, J and Song, Z and Wei, S and Guo, H and Xu, L and Qian, X}, title = {Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118071}, doi = {10.1016/j.jenvman.2023.118071}, pmid = {37148762}, issn = {1095-8630}, abstract = {Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.}, }
@article {pmid37146969, year = {2023}, author = {Takada, H and Katoh, T and Sakanaka, M and Odamaki, T and Katayama, T}, title = {GH20 and GH84 β-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {104781}, doi = {10.1016/j.jbc.2023.104781}, pmid = {37146969}, issn = {1083-351X}, abstract = {Intestinal mucus layers mediate symbiosis and dysbiosis of host-microbe interactions. These interactions are influenced by the mucin O-glycan degrading ability of several gut microbes. The identities and prevalence of many glycoside hydrolyses (GHs) involved in microbial mucin O-glycan breakdown have been previously reported; however, the exact mechanisms and extent to which these GHs are dedicated to mucin O-glycan degradation pathways warrant further research. Here, using Bifidobacterium bifidum as a model mucinolytic bacterium, we revealed that two β-N-acetylglucosaminidases belonging to the GH20 (BbhI) and GH84 (BbhIV) families play important roles in mucin O-glycan degradation. Using substrate specificity analysis of natural oligosaccharides and O-glycomic analysis of porcine gastric mucin (PGM) incubated with purified enzymes or B. bifidum carrying bbhI and/or bbhIV mutations, we showed that BbhI and BbhIV are highly specific for β-(1→3)- and β-(1→6)-GlcNAc linkages of mucin core structures, respectively. Interestingly, we found that efficient hydrolysis of the β-(1→3)-linkage by BbhI of the mucin core 4 structure [GlcNAcβ1-3(GlcNAcβ1-6)GalNAcα-O-Thr] required prior removal of the β-(1→6)-GlcNAc linkage by BbhIV. Consistent with this, inactivation of bbhIV markedly decreased the ability of B. bifidum to release GlcNAc from PGM. When combined with a bbhI mutation, we observed that the growth of the strain on PGM was reduced. Finally, phylogenetic analysis suggests that GH84 members may have gained diversified functions through microbe-microbe and host-microbe horizontal gene transfer events. Taken together, these data strongly suggest GH84 family members in host glycan breakdown.}, }
@article {pmid37144438, year = {2023}, author = {Hu, X and Xu, Y and Liu, S and Gudda, FO and Ling, W and Qin, C and Gao, Y}, title = {Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2301177}, doi = {10.1002/smll.202301177}, pmid = {37144438}, issn = {1613-6829}, abstract = {Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.}, }
@article {pmid36933870, year = {2023}, author = {Yang, Q and Zhu, Y and Schwarz, S and Wang, L and Liu, W and Yang, W and Liu, S and Zhang, W}, title = {Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E.}, journal = {International journal of antimicrobial agents}, volume = {61}, number = {5}, pages = {106793}, doi = {10.1016/j.ijantimicag.2023.106793}, pmid = {36933870}, issn = {1872-7913}, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Streptococcus/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; }, abstract = {Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.}, }
@article {pmid37143068, year = {2023}, author = {Valach, M and Moreira, S and Petitjean, C and Benz, C and Butenko, A and Flegontova, O and Nenarokova, A and Prokopchuk, G and Batstone, T and Lapébie, P and Lemogo, L and Sarrasin, M and Stretenowich, P and Tripathi, P and Yazaki, E and Nara, T and Henrissat, B and Lang, BF and Gray, MW and Williams, TA and Lukeš, J and Burger, G}, title = {Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {99}, pmid = {37143068}, issn = {1741-7007}, support = {BB/R016437/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.<br><br>RESULTS: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The&#x2009;~&#x2009;280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.<br><br>CONCLUSIONS: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.}, }
@article {pmid37138596, year = {2023}, author = {Zhao, Y and Wei, HM and Yuan, JL and Xu, L and Sun, JQ}, title = {A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177951}, pmid = {37138596}, issn = {1664-302X}, abstract = {Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.}, }
@article {pmid37137974, year = {2023}, author = {Ikhimiukor, OO and Souza, SSR and Marcovici, MM and Nye, GJ and Gibson, R and Andam, CP}, title = {Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {482}, pmid = {37137974}, issn = {2399-3642}, abstract = {Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.}, }
@article {pmid37133439, year = {2023}, author = {Tran, NN and Morrisette, T and Jorgensen, SCJ and Orench-Benvenutti, JM and Kebriaei, R}, title = {Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections.}, journal = {Pharmacotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1002/phar.2806}, pmid = {37133439}, issn = {1875-9114}, abstract = {Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies and reported alternatives are discussed.}, }
@article {pmid37126651, year = {2023}, author = {Akmal, M and Akatsuka, M and Nishiki, I and Yoshida, T}, title = {Resistance and genomic characterization of a plasmid pkh2101 harbouring erm(B) isolated from emerging fish pathogen Lactococcus garvieae serotype II in Japan.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.13793}, pmid = {37126651}, issn = {1365-2761}, abstract = {The emergence of antibiotic-resistant pathogenic strains of Lactococcus garvieae serotype II isolated from fish in Japan has become a growing concern in recent years. The data on drug susceptibility and its associated resistance mechanism are limited. Therefore, the present study was conducted to determine the minimum inhibitory concentrations (MICs) of chemotherapeutic agents against 98 pathogenic strains of emerging Lactococcus garvieae serotype II isolated from fish from six different prefectures in Japan from 2018 to 2021. The tested strains were resistant to erythromycin, lincomycin and tiamulin. PCR amplification revealed the presence of erm(B) in all erythromycin-resistant strains, while a conjugation experiment confirmed that these strains carried erm(B) that could be transferred to recipient Enterococcus faecalis OG1RF with frequencies from 10[-4] to 10[-6] per donor cells. Nucleotide sequencing of the representative isolated plasmid pkh2101 from an erythromycin-resistant strain showed that it was a 26,850 bp molecule with an average GC content of 33.49%, comprising 31 CDSs, 13 of which remained without any functional annotation. Comparative genomic analysis suggested that pkh2101 shared the highest similarity (97.57% identity) with the plasmid pAMbeta1, which was previously isolated clinically from Enterococcus faecalis DS-5. This study provides potential evidence that the plasmid harbouring erm(B) could be a source of antibiotic resistance transmission in emerging L. garvieae infection in aquaculture.}, }
@article {pmid37125932, year = {2023}, author = {Quan, J and Hu, H and Zhang, H and Meng, Y and Liao, W and Zhou, J and Han, X and Shi, Q and Zhao, D and Wang, Q and Jiang, Y and Yu, Y}, title = {Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0355422}, doi = {10.1128/spectrum.03554-22}, pmid = {37125932}, issn = {2165-0497}, abstract = {The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.}, }
@article {pmid37125466, year = {2023}, author = {Castanheira, M and Mendes, RE and Gales, AC}, title = {Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {Supplement_2}, pages = {S166-S178}, doi = {10.1093/cid/ciad109}, pmid = {37125466}, issn = {1537-6591}, abstract = {Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.}, }
@article {pmid37121291, year = {2023}, author = {Kosterlitz, O and Huisman, JS}, title = {Guidelines for the estimation and reporting of plasmid conjugation rates.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102685}, doi = {10.1016/j.plasmid.2023.102685}, pmid = {37121291}, issn = {1095-9890}, abstract = {Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.}, }
@article {pmid37120693, year = {2023}, author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K}, title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {42}, pmid = {37120693}, issn = {2730-6151}, abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.}, }
@article {pmid37120212, year = {2023}, author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P}, title = {Lebanese fermented goat milk products: From tradition to meta-omics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {168}, number = {}, pages = {112762}, doi = {10.1016/j.foodres.2023.112762}, pmid = {37120212}, issn = {1873-7145}, abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.}, }
@article {pmid37120023, year = {2023}, author = {Adomako, MO and Yu, FH}, title = {Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163760}, doi = {10.1016/j.scitotenv.2023.163760}, pmid = {37120023}, issn = {1879-1026}, abstract = {Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.}, }
@article {pmid37119017, year = {2023}, author = {Shin, NR and Okamura, Y and Kirsch, R and Pauchet, Y}, title = {Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12844}, pmid = {37119017}, issn = {1365-2583}, abstract = {With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.}, }
@article {pmid37116631, year = {2023}, author = {Garcillán-Barcia, MP and Redondo-Salvo, S and de la Cruz, F}, title = {Plasmid classifications.}, journal = {Plasmid}, volume = {}, number = {}, pages = {102684}, doi = {10.1016/j.plasmid.2023.102684}, pmid = {37116631}, issn = {1095-9890}, abstract = {Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).}, }
@article {pmid37110299, year = {2023}, author = {Qi, Q and Kamruzzaman, M and Iredell, JR}, title = {A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040878}, pmid = {37110299}, issn = {2076-2607}, abstract = {Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.}, }
@article {pmid37110264, year = {2023}, author = {Vittorakis, E and Vică, ML and Zervaki, CO and Vittorakis, E and Maraki, S and Mavromanolaki, VE and Schürger, ME and Neculicioiu, VS and Papadomanolaki, E and Sinanis, T and Giannoulaki, G and Xydaki, E and Kastanakis, SG and Junie, LM}, title = {Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040841}, pmid = {37110264}, issn = {2076-2607}, abstract = {S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020-2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections.}, }
@article {pmid37110261, year = {2023}, author = {Karnachuk, OV and Beletsky, AV and Rakitin, AL and Ikkert, OP and Avakyan, MR and Zyusman, VS and Napilov, A and Mardanov, AV and Ravin, NV}, title = {Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040838}, pmid = {37110261}, issn = {2076-2607}, abstract = {Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.}, }
@article {pmid37107701, year = {2023}, author = {Wu, L and Fan, P and Zhou, J and Li, Y and Xu, Z and Lin, Y and Wang, Y and Song, J and Yao, H}, title = {Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/genes14040943}, pmid = {37107701}, issn = {2073-4425}, abstract = {Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.}, }
@article {pmid37104544, year = {2023}, author = {Brual, T and Effantin, G and Baltenneck, J and Attaiech, L and Grosbois, C and Royer, M and Cigna, J and Faure, D and Hugouvieux-Cotte-Pattat, N and Gueguen, E}, title = {A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria.}, journal = {PLoS genetics}, volume = {19}, number = {4}, pages = {e1010725}, doi = {10.1371/journal.pgen.1010725}, pmid = {37104544}, issn = {1553-7404}, abstract = {The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.}, }
@article {pmid37102089, year = {2023}, author = {Shao, M and Liu, L and Liu, B and Zheng, H and Meng, W and Liu, Y and Zhang, X and Ma, X and Sun, C and Luo, X and Li, F and Xing, B}, title = {Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus.}, journal = {ACS environmental Au}, volume = {3}, number = {2}, pages = {105-120}, pmid = {37102089}, issn = {2694-2518}, abstract = {Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.}, }
@article {pmid37099912, year = {2023}, author = {Sun, X and Kong, T and Huang, D and Chen, Z and Kolton, M and Yang, J and Huang, Y and Cao, Y and Gao, P and Yang, N and Li, B and Liu, H and Sun, W}, title = {Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots.}, journal = {Journal of hazardous materials}, volume = {454}, number = {}, pages = {131458}, doi = {10.1016/j.jhazmat.2023.131458}, pmid = {37099912}, issn = {1873-3336}, abstract = {Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.}, }
@article {pmid37095096, year = {2023}, author = {Ahmad, M and Prensky, H and Balestrieri, J and ElNaggar, S and Gomez-Simmonds, A and Uhlemann, AC and Traxler, B and Singh, A and Lopatkin, AJ}, title = {Tradeoff between lag time and growth rate drives the plasmid acquisition cost.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2343}, pmid = {37095096}, issn = {2041-1723}, mesh = {Plasmids ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.}, }
@article {pmid37062264, year = {2023}, author = {Jin, C and Cao, J and Zhang, K and Zhang, X and Cao, Z and Zou, W}, title = {Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil.}, journal = {Ecotoxicology and environmental safety}, volume = {256}, number = {}, pages = {114913}, doi = {10.1016/j.ecoenv.2023.114913}, pmid = {37062264}, issn = {1090-2414}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Molybdenum/pharmacology ; Genes, Bacterial ; Soil ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Plasmids ; }, abstract = {The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5-10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.}, }
@article {pmid37098416, year = {2023}, author = {Gong, H and Huang, X and Zhu, W and Chen, J and Huang, Y and Zhao, Z and Weng, J and Che, Y and Wang, J and Wang, X}, title = {Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104249}, doi = {10.1016/j.fm.2023.104249}, pmid = {37098416}, issn = {1095-9998}, abstract = {Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.}, }
@article {pmid37098287, year = {2023}, author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J}, title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.}, journal = {Water research}, volume = {237}, number = {}, pages = {119986}, doi = {10.1016/j.watres.2023.119986}, pmid = {37098287}, issn = {1879-2448}, abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.}, }
@article {pmid37097444, year = {2023}, author = {Bibi, S and Weis, K and Kaur, A and Bhandari, R and Goss, EM and Jones, JB and Potnis, N}, title = {A Brief Evaluation of Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen, Xanthomonas euvesicatoria pv. perforans.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-02-23-0077-SC}, pmid = {37097444}, issn = {0031-949X}, abstract = {Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple Xanthomonas euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility including both phage related genes and transposase. Among copper tolerant strains of Xanthomonas euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid borne resistance.}, }
@article {pmid37097343, year = {2023}, author = {Francis, A and Steel, M}, title = {Labellable Phylogenetic Networks.}, journal = {Bulletin of mathematical biology}, volume = {85}, number = {6}, pages = {46}, pmid = {37097343}, issn = {1522-9602}, abstract = {Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations) and non-tree-like 'reticulate' processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper, we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of 'expanding covers' of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.}, }
@article {pmid36778249, year = {2023}, author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE}, title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778249}, support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; }, abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species and recently demonstrated to occur in rare instances from one human generation to the next. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeatedmeasures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous 2 numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.}, }
@article {pmid37094448, year = {2023}, author = {Zhu, S and Yang, B and Jia, Y and Yu, F and Wang, Z and Liu, Y}, title = {Comprehensive analysis of disinfectants on the horizontal transfer of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131428}, doi = {10.1016/j.jhazmat.2023.131428}, pmid = {37094448}, issn = {1873-3336}, abstract = {The propagation of antimicrobial resistance (AMR) is constantly paralyzing our healthcare systems. In addition to the pressure of antibiotic selection, the roles of non-antibiotic compounds in disseminating antibiotic resistance genes (ARGs) are a matter of great concerns. This study aimed to explore the impact of different disinfectants on the horizontal transfer of ARGs and their underlying mechanisms. First, the effects of different kinds of disinfectants on the conjugative transfer of RP4-7 plasmid were evaluated. Results showed that quaternary ammonium salt, organic halogen, alcohol and guanidine disinfectants significantly facilitated the conjugative transfer. Conversely, heavy-metals, peroxides and phenols otherwise displayed an inhibitory effect. Furthermore, we deciphered the mechanism by which guanidine disinfectants promoted conjugation, which includes increased cell membrane permeability, over-production of ROS, enhanced SOS response, and altered expression of conjugative transfer-related genes. More critically, we also revealed that guanidine disinfectants promoted bacterial energy metabolism by enhancing the activity of electron transport chain (ETC) and proton force motive (PMF), thus promoting ATP synthesis and flagellum motility. Overall, our findings reveal the promotive effects of disinfectants on the transmission of ARGs and highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.}, }
@article {pmid37093956, year = {2023}, author = {Baumdicker, F and Kupczok, A}, title = {Tackling the pangenome dilemma requires the concerted analysis of multiple population genetic processes.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad067}, pmid = {37093956}, issn = {1759-6653}, abstract = {The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory genes of low and intermediate frequencies. Different population genetics processes contribute to the shape of these pangenomes, namely selection and fitness-independent-processes such as gene transfer, gene loss, and migration. However, their relative importance is unknown and highly debated. Here we argue that the debate around prokaryotic pangenomes arose due to the imprecise application of population genetics models. Most importantly, two different processes of horizontal gene transfer act on prokaryotic populations, which are frequently confused, despite their fundamentally different behavior. Genes acquired from distantly related organisms (termed here acquiring gene transfer, AGT) is most comparable to mutation in nucleotide sequences. In contrast, gene gain within the population (termed here spreading gene transfer, SGT) has an effect on gene frequencies that is identical to the effect of positive selection on single genes. We thus show that selection and fitness-independent population genetic processes affecting pangenomes are indistinguishable at the level of single gene dynamics. Nevertheless, population genetics processes are fundamentally different when considering the joint distribution of all accessory genes across individuals of a population. We propose that, to understand to which degree the different processes shaped pangenome diversity, the development of comprehensive models and simulation tools is mandatory. Furthermore, we need to identify summary statistics and measurable features that can distinguish between the processes, where considering the joint distribution of accessory genes across individuals of a population will be particularly relevant.}, }
@article {pmid37092000, year = {2023}, author = {Han, Z and Xu, S and Gao, T}, title = {Unexpected complex horizontal gene transfer in teleost fish.}, journal = {Current zoology}, volume = {69}, number = {2}, pages = {222-223}, pmid = {37092000}, issn = {1674-5507}, }
@article {pmid37091576, year = {2022}, author = {Varner, PM and Allemann, MN and Michener, JK and Gunsch, CK}, title = {The effect of bacterial growth strategies on plasmid transfer and naphthalene degradation for bioremediation.}, journal = {Environmental technology &amp; innovation}, volume = {28}, number = {}, pages = {}, pmid = {37091576}, issn = {2352-1864}, abstract = {Mobilizable plasmids are extra-chromosomal, circular DNA that have contributed to the rapid evolution of bacterial genomes and have been used in environmental, biotechnological, and medicinal applications. Degradative plasmids with genetic capabilities to degrade organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs), have the potential to be useful for more environmentally friendly and cost-effective remediation technologies compared to existing physical remediation methods. Genetic bioaugmentation, the addition of catabolic genes into well-adapted communities via plasmid transfer (conjugation), is being explored as a remediation approach that is sustainable and long-lasting. Here, we explored the effect of the ecological growth strategies of plasmid donors and recipients on conjugation and naphthalene degradation of two PAH-degrading plasmids, pNL1 and NAH7. Overall, both pNL1 and NAH7 showed conjugation preferences towards a slow-growing ecological growth strategy, except when NAH7 was in a mixed synthetic community. These conjugation preferences were partially described by a combination of growth strategy, GC content, and phylogenetic relatedness. Further, removal of naphthalene via plasmid-mediated degradation was consistently higher in a community consisting of recipients with a slow-growing ecological growth strategy compared to a mixed community or a community consisting of fast-growing ecological growth strategy. Understanding plasmid conjugation and degradative preferences has the capacity to influence future remediation technology design and has broad implications in biomedical, environmental, and health fields.}, }
@article {pmid37087920, year = {2023}, author = {Zheng, CW and Luo, YH and Long, X and Gu, H and Cheng, J and Zhang, L and Lai, YJS and Rittmann, BE}, title = {The structure of biodegradable surfactants shaped the microbial community, antimicrobial resistance, and potential for horizontal gene transfer.}, journal = {Water research}, volume = {236}, number = {}, pages = {119944}, doi = {10.1016/j.watres.2023.119944}, pmid = {37087920}, issn = {1879-2448}, abstract = {While most household surfactants are biodegradable in aerobic conditions, their biodegradability may obscure their environmental risks. The presence of surfactants in a biological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in the biomass. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation ARG. Cationic hexadecyltrimethyl-ammonium (CTAB), anionic sodium dodecyl sulfate (SDS), and zwitterionic 3-(decyldimethylammonio)-propanesulfonate inner salt (DAPS) were used to represent the three classes of surfactants in domestic household clean-up products. This study focused on the removal of these surfactants by the O2-based Membrane Biofilm Reactor (O2-MBfR) for hotspot scenarios (∼1 mM) and how the three classes of surfactants affected the microbial community's structure and ARG. Given sufficient O2 delivery, the MBfR provided at least 98% surfactant removal. The presence and biodegradation for each surfactant uniquely shaped the biofilms' microbial communities and the presence of ARG. CTAB had by far the strongest impact and the higher ARG abundance. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also led to more functional genes relevant to the Type-IV secretion system and protection against oxidative stress, which also could encourage horizontal gene transfer. Our findings highlight that the biodegradation of quaternary ammonium surfactants, while beneficial, can pose public health concerns from its ability to promote the proliferation of ARG.}, }
@article {pmid37083586, year = {2023}, author = {Maphosa, S and Moleleki, LN and Motaung, TE}, title = {Bacterial secretion system functions: evidence of interactions and downstream implications.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {4}, pages = {}, doi = {10.1099/mic.0.001326}, pmid = {37083586}, issn = {1465-2080}, abstract = {Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.}, }
@article {pmid37083356, year = {2023}, author = {Wu, J and Zhou, JH and Liu, DF and Wu, J and He, RL and Cheng, ZH and Li, HH and Li, WW}, title = {Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c09491}, pmid = {37083356}, issn = {1520-5851}, abstract = {Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.}, }
@article {pmid37079454, year = {2023}, author = {Gulliver, EL and Adams, V and Marcelino, VR and Gould, J and Rutten, EL and Powell, DR and Young, RB and D'Adamo, GL and Hemphill, J and Solari, SM and Revitt-Mills, SA and Munn, S and Jirapanjawat, T and Greening, C and Boer, JC and Flanagan, KL and Kaldhusdal, M and Plebanski, M and Gibney, KB and Moore, RJ and Rood, JI and Forster, SC}, title = {Extensive genome analysis identifies novel plasmid families in Clostridium perfringens.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000995}, pmid = {37079454}, issn = {2057-5858}, abstract = {Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfringens strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464 C. perfringens genomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported from Clostridium botulinum. We sequenced and archived 102 new C. perfringens genomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11 C. perfringens strains representing all toxinotypes (A-G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across the C. perfringens isolates. Plasmids and plasmid diversity play an essential role in C. perfringens pathogenicity and broader biology. We have expanded the C. perfringens genome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novel C. perfringens plasmids whilst providing a comprehensive understanding of species diversity.}, }
@article {pmid37072776, year = {2023}, author = {Hernández, M and Roy, S and Keevil, CW and Dumont, MG}, title = {Identification of diverse antibiotic resistant bacteria in agricultural soil with H2[18]O stable isotope probing combined with high-throughput sequencing.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {34}, pmid = {37072776}, issn = {2524-6372}, abstract = {BACKGROUND: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in [18]O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.<br><br>RESULTS: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with [18]O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.<br><br>CONCLUSIONS: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.}, }
@article {pmid37072330, year = {2023}, author = {Fokina, AS and Karyagina, AS and Rusinov, IS and Moshensky, DM and Spirin, SA and Alexeevski, AV}, title = {Evolution of Restriction-Modification Systems Consisting of One Restriction Endonuclease and Two DNA Methyltransferases.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {2}, pages = {253-261}, doi = {10.1134/S0006297923020086}, pmid = {37072330}, issn = {1608-3040}, abstract = {Some restriction-modification systems contain two DNA methyltransferases. In the present work, we have classified such systems according to the families of catalytic domains present in the restriction endonucleases and both DNA methyltransferases. Evolution of the restriction-modification systems containing an endonuclease with a NOV_C family domain and two DNA methyltransferases, both with DNA_methylase family domains, was investigated in detail. Phylogenetic tree of DNA methyltransferases from the systems of this class consists of two clades of the same size. Two DNA methyltransferases of each restriction-modification system of this class belong to the different clades. This indicates independent evolution of the two methyltransferases. We detected multiple cross-species horizontal transfers of the systems as a whole, as well as the cases of gene transfer between the systems.}, }
@article {pmid37070987, year = {2023}, author = {Dai, X and Sun, J and Zhu, B and Lv, M and Chen, L and Chen, L and Wang, X and Huang, J and Wang, L}, title = {Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0487522}, doi = {10.1128/spectrum.04875-22}, pmid = {37070987}, issn = {2165-0497}, abstract = {The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.}, }
@article {pmid37070984, year = {2023}, author = {Wu, HY and Wei, ZL and Shi, DY and Li, HB and Li, XM and Yang, D and Zhou, SQ and Peng, XX and Yang, ZW and Yin, J and Chen, TJ and Li, JW and Jin, M}, title = {Simulated Gastric Acid Promotes the Horizontal Transfer of Multidrug Resistance Genes across Bacteria in the Gastrointestinal Tract at Elevated pH Levels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0482022}, doi = {10.1128/spectrum.04820-22}, pmid = {37070984}, issn = {2165-0497}, abstract = {The assessment of factors that can promote the transmission of antibiotic resistance genes (ARGs) across bacteria in the gastrointestinal tract is in great demand to understand the occurrence of infections related to antibiotic-resistant bacteria (ARB) in humans. However, whether acid-resistant enteric bacteria can promote ARG transmission in gastric fluid under high-pH conditions remains unknown. This study assessed the effects of simulated gastric fluid (SGF) at different pH levels on the RP4 plasmid-mediated conjugative transfer of ARGs. Moreover, transcriptomic analysis, measurement of reactive oxygen species (ROS) levels, assessment of cell membrane permeability, and real-time quantitative assessment of the expression of key genes were performed to identify the underlying mechanisms. The frequency of conjugative transfer was the highest in SGF at pH 4.5. Antidepressant consumption and certain dietary factors further negatively impacted this situation, with 5.66-fold and 4.26-fold increases in the conjugative transfer frequency being noted upon the addition of sertraline and 10% glucose, respectively, compared with that in the control group without any additives. The induction of ROS generation, the activation of cellular antioxidant systems, increases in cell membrane permeability, and the promotion of adhesive pilus formation were factors potentially contributing to the increased transfer frequency. These findings indicate that conjugative transfer could be enhanced under certain circumstances in SGF at elevated pH levels, thereby facilitating ARG transmission in the gastrointestinal tract. IMPORTANCE The low pH of gastric acid kills unwanted microorganisms, in turn affecting their inhabitation in the intestine. Hence, studies on the factors that influence antibiotic resistance gene (ARG) propagation in the gastrointestinal tract and on the underlying mechanisms are limited. In this study, we constructed a conjugative transfer model in the presence of simulated gastric fluid (SGF) and found that SGF could promote the dissemination of ARGs under high-pH conditions. Furthermore, antidepressant consumption and certain dietary factors could negatively impact this situation. Transcriptomic analysis and a reactive oxygen species assay revealed the overproduction of reactive oxygen species as a potential mechanism by which SGF could promote conjugative transfer. This finding can help provide a comprehensive understanding of the bloom of antibiotic-resistant bacteria in the body and create awareness regarding the risk of ARG transmission due to certain diseases or an improper diet and the subsequent decrease in gastric acid levels.}, }
@article {pmid37065212, year = {2023}, author = {Wang, H and Cheng, H and Huang, B and Hu, X and Chen, Y and Zheng, L and Yang, L and Deng, J and Wang, Q}, title = {Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1116172}, pmid = {37065212}, issn = {2235-2988}, mesh = {Humans ; Child ; Azithromycin/pharmacology ; *Salmonella enterica/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Salmonella Infections/microbiology ; Salmonella/genetics ; Plasmids/genetics ; Microbial Sensitivity Tests ; Chloramphenicol/pharmacology ; Drug Resistance, Multiple, Bacterial ; }, abstract = {INTRODUCTION: Samonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied.<br><br>METHODS: This study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children's Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools.<br><br>RESULTS: In total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 &#xb5;g/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters.<br><br>CONCLUSION: mphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.}, }
@article {pmid37061654, year = {2023}, author = {Elbehery, AHA and Beason, E and Siam, R}, title = {Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {195}, pmid = {37061654}, issn = {1432-072X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Indian Ocean ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.}, }
@article {pmid37061183, year = {2023}, author = {Gilbert, C and Maumus, F}, title = {Sidestepping Darwin: horizontal gene transfer from plants to insects.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101035}, doi = {10.1016/j.cois.2023.101035}, pmid = {37061183}, issn = {2214-5753}, abstract = {Horizontal transfer of genetic material (HT) is the passage of DNA between organisms by means other than reproduction. Increasing numbers of HT are reported in insects, with bacteria, fungi, plants and insects acting as the main sources of these transfers. Here, we provide a detailed account of plant-to-insect HT events. At least 14 insect species belonging to 6 orders are known to have received plant genetic material through HT. One of them, the whitefly Bemisia tabaci (MEAM1), concentrates most of these transfers, with no less than 28 HT events yielding 55 plant-derived genes in this species. Several plant-to-insect HT events reported so far involve gene families known to play a role in plant-parasite interactions. We highlight methodological approaches that may further help characterize these transfers. We argue that plant-to-insect HT is likely more frequent than currently appreciated and that in-depth studies of these transfers will shed new light on plant-insect interactions.}, }
@article {pmid37055994, year = {2023}, author = {Li, B and Jeon, MK and Li, X and Yan, T}, title = {Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130590}, doi = {10.1016/j.jhazmat.2022.130590}, pmid = {37055994}, issn = {1873-3336}, mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/analysis ; Genes, Bacterial ; Salinity ; Drug Resistance, Microbial/genetics ; }, abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, blaTEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and blaTEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and blaTEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.}, }
@article {pmid37054673, year = {2023}, author = {Moura de Sousa, J and Lourenço, M and Gordo, I}, title = {Horizontal gene transfer among host-associated microbes.}, journal = {Cell host &amp; microbe}, volume = {31}, number = {4}, pages = {513-527}, doi = {10.1016/j.chom.2023.03.017}, pmid = {37054673}, issn = {1934-6069}, mesh = {*Gene Transfer, Horizontal ; Bacteria/genetics ; Biological Evolution ; *Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.}, }
@article {pmid37052605, year = {2023}, author = {Calder, A and Snyder, LAS}, title = {Diversity of the type VI secretion systems in the Neisseria spp.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000986}, pmid = {37052605}, issn = {2057-5858}, mesh = {Humans ; *Type VI Secretion Systems/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Complete Type VI Secretion Systems were identified in the genome sequence data of Neisseria subflava isolates sourced from throat swabs of human volunteers. The previous report was the first to describe two complete Type VI Secretion Systems in these isolates, both of which were distinct in terms of their gene organization and sequence homology. Since publication of the first report, Type VI Secretion System subtypes have been identified in Neisseria spp. The characteristics of each type in N. subflava are further investigated here and in the context of the other Neisseria spp., including identification of the lineages containing the different types and subtypes. Type VI Secretion Systems use VgrG for delivery of toxin effector proteins; several copies of vgrG and associated effector / immunity pairs are present in Neisseria spp. Based on sequence similarity between strains and species, these core Type VI Secretion System genes, vgrG, and effector / immunity genes may diversify via horizontal gene transfer, an instrument for gene acquisition and repair in Neisseria spp.}, }
@article {pmid37052502, year = {2023}, author = {Tang, B and Yang, A and Liu, P and Wang, Z and Jian, Z and Chen, X and Yan, Q and Liang, X and Liu, W}, title = {Outer Membrane Vesicles Transmitting blaNDM-1 Mediate the Emergence of Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0144422}, doi = {10.1128/aac.01444-22}, pmid = {37052502}, issn = {1098-6596}, abstract = {Dissemination of hypervirulent and carbapenem-resistant Klebsiella pneumoniae (CRKP) has been reported worldwide, posing a serious threat to antimicrobial therapy and public health. Outer membrane vesicles (OMVs) act as vectors for the horizontal transfer of virulence and resistance genes. However, K. pneumoniae OMVs that transfer carbapenem resistance genes into hypervirulent K. pneumoniae (hvKP) have been insufficiently investigated. Therefore, this study investigates the transmission of the blaNDM-1 gene encoding resistance via OMVs released from CRKP and the potential mechanism responsible for the carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) emergence. OMVs were isolated via ultracentrifugation from CRKP with or without meropenem selective pressure. OMVs were then used to transform classical K. pneumoniae (ckp) ATCC 10031, extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae ATCC 700603, and hvKP NTUH-K2044. Our results showed that meropenem treatment resulted in changes in the number and diameter of OMVs secreted by CRKP. OMVs derived from CRKP mediated the transfer of blaNDM-1 to ckp and hvKP, thereby increasing the carbapenem MIC of transformants. Further experiments confirmed that NTUH-K2044 transformants exhibited hypervirulence. Our study demonstrates, for the first time, that OMVs derived from CRKP can carry blaNDM-1 and deliver resistance genes to other K. pneumoniae strains, even hvKP. The transfer of carbapenem genes into hypervirulent strains may promote the emergence and dissemination of CR-hvKP. This study elucidates a new mechanism underlying the formation of CR-hvKP.}, }
@article {pmid37047476, year = {2023}, author = {Msaddak, A and Mars, M and Quiñones, MA and Lucas, MM and Pueyo, JJ}, title = {Lupin, a Unique Legume That Is Nodulated by Multiple Microsymbionts: The Role of Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047476}, issn = {1422-0067}, mesh = {*Fabaceae/genetics/microbiology ; *Lupinus/genetics/microbiology ; Root Nodules, Plant/microbiology ; Phylogeny ; Gene Transfer, Horizontal ; Health Promotion ; DNA, Bacterial/genetics ; Vegetables/genetics ; *Rhizobium/genetics ; *Bradyrhizobium/genetics ; Symbiosis/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lupin is a high-protein legume crop that grows in a wide range of edaphoclimatic conditions where other crops are not viable. Its unique seed nutrient profile can promote health benefits, and it has been proposed as a phytoremediation plant. Most rhizobia nodulating Lupinus species belong to the genus Bradyrhizobium, comprising strains that are phylogenetically related to B. cytisi, B. hipponenese, B. rifense, B. iriomotense/B. stylosanthis, B. diazoefficiens, B. japonicum, B. canariense/B. lupini, and B. retamae/B. valentinum. Lupins are also nodulated by fast-growing bacteria within the genera Microvirga, Ochrobactrum, Devosia, Phyllobacterium, Agrobacterium, Rhizobium, and Neorhizobium. Phylogenetic analyses of the nod and nif genes, involved in microbial colonization and symbiotic nitrogen fixation, respectively, suggest that fast-growing lupin-nodulating bacteria have acquired their symbiotic genes from rhizobial genera other than Bradyrhizobium. Horizontal transfer represents a key mechanism allowing lupin to form symbioses with bacteria that were previously considered as non-symbiotic or unable to nodulate lupin, which might favor lupin's adaptation to specific habitats. The characterization of yet-unstudied Lupinus species, including microsymbiont whole genome analyses, will most likely expand and modify the current lupin microsymbiont taxonomy, and provide additional knowledge that might help to further increase lupin's adaptability to marginal soils and climates.}, }
@article {pmid37043515, year = {2023}, author = {Novelo, M and Dutra, HL and Metz, HC and Jones, MJ and Sigle, LT and Frentiu, FD and Allen, SL and Chenoweth, SF and McGraw, EA}, title = {Dengue and chikungunya virus loads in the mosquito Aedes aegypti are determined by distinct genetic architectures.}, journal = {PLoS pathogens}, volume = {19}, number = {4}, pages = {e1011307}, doi = {10.1371/journal.ppat.1011307}, pmid = {37043515}, issn = {1553-7374}, abstract = {Aedes aegypti is the primary vector of the arboviruses dengue (DENV) and chikungunya (CHIKV). These viruses exhibit key differences in their vector interactions, the latter moving more quicky through the mosquito and triggering fewer standard antiviral pathways. As the global footprint of CHIKV continues to expand, we seek to better understand the mosquito's natural response to CHIKV-both to compare it to DENV:vector coevolutionary history and to identify potential targets in the mosquito for genetic modification. We used a modified full-sibling design to estimate the contribution of mosquito genetic variation to viral loads of both DENV and CHIKV. Heritabilities were significant, but higher for DENV (40%) than CHIKV (18%). Interestingly, there was no genetic correlation between DENV and CHIKV loads between siblings. These data suggest Ae. aegypti mosquitoes respond to the two viruses using distinct genetic mechanisms. We also examined genome-wide patterns of gene expression between High and Low CHIKV families representing the phenotypic extremes of viral load. Using RNAseq, we identified only two loci that consistently differentiated High and Low families: a long non-coding RNA that has been identified in mosquito screens post-infection and a distant member of a family of Salivary Gland Specific (SGS) genes. Interestingly, the latter gene is also associated with horizontal gene transfer between mosquitoes and the endosymbiotic bacterium Wolbachia. This work is the first to link the SGS gene to a mosquito phenotype. Understanding the molecular details of how this gene contributes to viral control in mosquitoes may, therefore, also shed light on its role in Wolbachia.}, }
@article {pmid37037946, year = {2023}, author = {Yang, P and Zhu, X and Ning, K}, title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {391}, pmid = {37037946}, issn = {2399-3642}, mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; }, abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.}, }
@article {pmid37037312, year = {2023}, author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M}, title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115866}, doi = {10.1016/j.envres.2023.115866}, pmid = {37037312}, issn = {1096-0953}, abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.}, }
@article {pmid37036996, year = {2023}, author = {Kalluraya, CA and Weitzel, AJ and Tsu, BV and Daugherty, MD}, title = {Bacterial origin of a key innovation in the evolution of the vertebrate eye.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2214815120}, doi = {10.1073/pnas.2214815120}, pmid = {37036996}, issn = {1091-6490}, support = {R35 GM133633/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Genes, Bacterial ; *Vertebrates/metabolism ; Eye Proteins/genetics ; Retinoids/metabolism ; Invertebrates/genetics ; Vision, Ocular/genetics ; }, abstract = {The vertebrate eye was described by Charles Darwin as one of the greatest potential challenges to a theory of natural selection by stepwise evolutionary processes. While numerous evolutionary transitions that led to the vertebrate eye have been explained, some aspects appear to be vertebrate specific with no obvious metazoan precursor. One critical difference between vertebrate and invertebrate vision hinges on interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3), which enables the physical separation and specialization of cells in the vertebrate visual cycle by promoting retinoid shuttling between cell types. While IRBP has been functionally described, its evolutionary origin has remained elusive. Here, we show that IRBP arose via acquisition of novel genetic material from bacteria by interdomain horizontal gene transfer (iHGT). We demonstrate that a gene encoding a bacterial peptidase was acquired prior to the radiation of extant vertebrates >500 Mya and underwent subsequent domain duplication and neofunctionalization to give rise to vertebrate IRBP. Our phylogenomic analyses on >900 high-quality genomes across the tree of life provided the resolution to distinguish contamination in genome assemblies from true instances of horizontal acquisition of IRBP and led us to discover additional independent transfers of the same bacterial peptidase gene family into distinct eukaryotic lineages. Importantly, this work illustrates the evolutionary basis of a key transition that led to the vertebrate visual cycle and highlights the striking impact that acquisition of bacterial genes has had on vertebrate evolution.}, }
@article {pmid37036995, year = {2023}, author = {Verster, KI and Cinege, G and Lipinszki, Z and Magyar, LB and Kurucz, &#xc9; and Tarnopol, RL and Ábrahám, E and Darula, Z and Karageorgi, M and Tamsil, JA and Akalu, SM and Andó, I and Whiteman, NK}, title = {Evolution of insect innate immunity through domestication of bacterial toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2218334120}, doi = {10.1073/pnas.2218334120}, pmid = {37036995}, issn = {1091-6490}, support = {R35 GM119816/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Domestication ; *Bacterial Toxins/metabolism ; Drosophila/genetics/metabolism ; Gene Transfer, Horizontal ; *Wasps/metabolism ; Immunity, Innate/genetics ; }, abstract = {Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B (cdtB) and apoptosis-inducing protein of 56 kDa (aip56), were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular (cdtB) or fused copies (cdtB::aip56) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo's serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.}, }
@article {pmid37036347, year = {2023}, author = {Lewis, AM and Willard, DJ and H Manesh, MJ and Sivabalasarma, S and Albers, SV and Kelly, RM}, title = {Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin.}, journal = {mBio}, volume = {}, number = {}, pages = {e0005323}, doi = {10.1128/mbio.00053-23}, pmid = {37036347}, issn = {2150-7511}, abstract = {A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.}, }
@article {pmid37036197, year = {2023}, author = {Mota-Bravo, L and Camps, M and Muñoz-Gutiérrez, I and Tatarenkov, A and Warner, C and Suarez, I and Cortés-Cortés, G}, title = {Detection of Horizontal Gene Transfer Mediated by Natural Conjugative Plasmids in E. coli.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/64523}, pmid = {37036197}, issn = {1940-087X}, mesh = {*Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Conjugation, Genetic ; Plasmids/genetics ; Anti-Bacterial Agents ; }, abstract = {Conjugation represents one of the main mechanisms facilitating horizontal gene transfer in Gram-negative bacteria. This work describes methods for the study of the mobilization of naturally occurring conjugative plasmids, using two naturally-occurring plasmids as an example. These protocols rely on the differential presence of selectable markers in donor, recipient, and conjugative plasmid. Specifically, the methods described include 1) the identification of natural conjugative plasmids, 2) the quantification of conjugation rates in solid culture, and 3) the diagnostic detection of the antibiotic resistance genes and plasmid replicon types in transconjugant recipients by polymerase chain reaction (PCR). The protocols described here have been developed in the context of studying the evolutionary ecology of horizontal gene transfer, to screen for the presence of conjugative plasmids carrying antibiotic-resistance genes in bacteria found in the environment. The efficient transfer of conjugative plasmids observed in these experiments in culture highlights the biological relevance of conjugation as a mechanism promoting horizontal gene transfer in general and the spread of antibiotic resistance in particular.}, }
@article {pmid37033775, year = {2023}, author = {Alborzi, A and Hosseini, M and Bahrami, S and Ghorbanpoor, M and Tabandeh, M}, title = {Evaluation of hematological changes, oxidant/antioxidant status and immuno-logical responses in sheep and goats naturally infected with Linguatula serrata.}, journal = {Veterinary research forum : an international quarterly journal}, volume = {14}, number = {3}, pages = {161-167}, pmid = {37033775}, issn = {2008-8140}, abstract = {Linguatula serrata is a worldwide zoonotic food-borne parasite. The parasite is responsible for linguatulosis and poses a concern to human and animal health in endemic regions. This study investigated the hematological changes, oxidant/antioxidant status and immunological responses in goats and sheep naturally infected with L. serrata. Hematological changes, antioxidant enzymes and malondialdehyde (MDA) levels were measured. The level of inter-leukin-2 (IL-2), IL-4, IL-5, IL-10, and tumor necrosis factor alpha (TNF-α) mRNA expression was investigated in lymph nodes. According to the hemogram results, eosinophils were significantly increased in the infected goats and sheep, and Horizontal Gene Transfer (HGT), hematocrit (HCT), and mean corpuscular hemoglobin concentration (MCHC) were significantly decreased. The levels of MDA and the activity of glutathione peroxidase (GPx) were significantly higher in infected animals than in non-infected animals. However, the activity of superoxide dismutase (SOD) and catalase (CAT) was significantly lower in infected animals than in non-infected animals. A comparison of the cytokine mRNA expression in lymph nodes from infected and non-infected animals showed higher cytokine expression in the infected animals. Infection with L. serrata caused microcytic hypochromic and normocytic hypochromic anemia in goats and sheep. The inconsistent results of immunological changes were found in infected goats and sheep. In both animals, oxidative stress occurred and led to an increase in lipid peroxidation. L. serrata created a cytokine microenvironment biased towards the type 2 immune responses.}, }
@article {pmid37030228, year = {2023}, author = {Chen, J and Xia, H and Huang, K and Li, J and Xie, J}, title = {Earthworms restructure the distribution of extracellular antibiotics resistance genes of sludge by modifying the structure of extracellular polymeric substances during vermicomposting.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131315}, doi = {10.1016/j.jhazmat.2023.131315}, pmid = {37030228}, issn = {1873-3336}, abstract = {The role of earthworms in reducing the antibiotic resistance genes (ARGs) in sludge vermicompost remains unclear. The structure of extracellular polymeric substance (EPS) of sludge may be associated with the horizontal gene transfer behavior of ARGs in the vermicomposting of sludge. Therefore, this study aimed to investigate the effects of earthworms on the structural characteristics of EPS associated with the fate of ARGs in EPS during the vermicomposting of sludge. The results showed vermicomposting could diminish the abundance of ARGs and mobile genetic elements (MGEs) in the EPS of sludge by 47.93 % and 7.75 %, compared to the control, respectively. Relative to the control, vermicomposting also led to the reduction of MGEs abundances in the soluble EPS of 40.04 %, lightly bound EPS of 43.53 %, and tightly bound EPS of 70.49 %, respectively. The total abundances of certain ARGs dramatically diminished 95.37 % in tightly bound EPS of sludge during vermicomposting. In vermicomposting, the main influencing factor of ARGs distribution was the proteins in LB-EPS, accounting for 48.5 % of the variation. This study suggests that the earthworms lower the total abundances of ARGs by regulating the microbial community and modifying the microbial metabolic pathways associated with ARGs and MGEs in the EPS of sludge.}, }
@article {pmid37023995, year = {2023}, author = {Botts, RT and Page, DM and Bravo, JA and Brown, ML and Castilleja, CC and Guzman, VL and Hall, S and Henderson, JD and Kenney, SM and Lensink, ME and Paternoster, MV and Pyle, SL and Ustick, L and Walters-Laird, CJ and Top, EM and Cummings, DE}, title = {Polluted wetlands contain multidrug-resistance plasmids encoding CTX-M-type extended-spectrum β-lactamases.}, journal = {Plasmid}, volume = {126}, number = {}, pages = {102682}, doi = {10.1016/j.plasmid.2023.102682}, pmid = {37023995}, issn = {1095-9890}, abstract = {While most detailed analyses of antibiotic resistance plasmids focus on those found in clinical isolates, less is known about the vast environmental reservoir of mobile genetic elements and the resistance and virulence factors they encode. We selectively isolated three strains of cefotaxime-resistant Escherichia coli from a wastewater-impacted coastal wetland. The cefotaxime-resistant phenotype was transmissible to a lab strain of E. coli after one hour, with frequencies as high as 10[-3] transconjugants per recipient. Two of the plasmids also transferred cefotaxime resistance to Pseudomonas putida, but these were unable to back-transfer this resistance from P. putida to E. coli. In addition to the cephalosporins, E. coli transconjugants inherited resistance to at least seven distinct classes of antibiotics. Complete nucleotide sequences revealed large IncF-type plasmids with globally distributed replicon sequence types F31:A4:B1 and F18:B1:C4 carrying diverse antibiotic resistance and virulence genes. The plasmids encoded extended-spectrum β-lactamases blaCTX-M-15 or blaCTX-M-55, each associated with the insertion sequence ISEc9, although in different local arrangements. Despite similar resistance profiles, the plasmids shared only one resistance gene in common, the aminoglycoside acetyltransferase aac(3)-IIe. Plasmid accessory cargo also included virulence factors involved in iron acquisition and defense against host immunity. Despite their sequence similarities, several large-scale recombination events were detected, including rearrangements and inversions. In conclusion, selection with a single antibiotic, cefotaxime, yielded conjugative plasmids conferring multiple resistance and virulence factors. Clearly, efforts to limit the spread of antibiotic resistance and virulence among bacteria must include a greater understanding of mobile elements in the natural and human-impacted environments.}, }
@article {pmid37023132, year = {2023}, author = {Urquhart, AS and Vogan, AA and Gardiner, DM and Idnurm, A}, title = {Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2214521120}, pmid = {37023132}, issn = {1091-6490}, mesh = {*DNA Transposable Elements/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Recombinases/genetics ; Tyrosine/genetics ; Evolution, Molecular ; }, abstract = {Transposable elements in eukaryotic organisms have historically been considered "selfish," at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are, in some cases, predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA "Captain" tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfers of Starships, implying that they jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defense, thereby having implications on the evolutionary stability of such elements.}, }
@article {pmid37023131, year = {2023}, author = {Benz, F and Hall, AR}, title = {Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2212147120}, pmid = {37023131}, issn = {1091-6490}, mesh = {Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; *Anti-Bacterial Agents/pharmacology ; Models, Theoretical ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance encoded on plasmids is a pressing global health problem. Predicting which plasmids spread in the long term remains very challenging, even though some key parameters influencing plasmid stability have been identified, such as plasmid growth costs and horizontal transfer rates. Here, we show these parameters evolve in a strain-specific way among clinical plasmids and bacteria, and this occurs rapidly enough to alter the relative likelihoods of different bacterium-plasmid combinations spreading. We used experiments with Escherichia coli and antibiotic-resistance plasmids isolated from patients, paired with a mathematical model, to track long-term plasmid stability (beyond antibiotic exposure). Explaining variable stability across six bacterium-plasmid combinations required accounting for evolutionary changes in plasmid stability traits, whereas initial variation of these parameters was a relatively poor predictor of long-term outcomes. Evolutionary trajectories were specific to particular bacterium-plasmid combinations, as evidenced by genome sequencing and genetic manipulation. This revealed epistatic (here, strain-dependent) effects of key genetic changes affecting horizontal plasmid transfer. Several genetic changes involved mobile elements and pathogenicity islands. Rapid strain-specific evolution can thus outweigh ancestral phenotypes as a predictor of plasmid stability. Accounting for strain-specific plasmid evolution in natural populations could improve our ability to anticipate and manage successful bacterium-plasmid combinations.}, }
@article {pmid37022443, year = {2023}, author = {Stentz, R and Cheema, J and Philo, M and Carding, SR}, title = {A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {37022443}, issn = {1432-1432}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.}, }
@article {pmid37022212, year = {2023}, author = {Tóth, AG and Judge, MF and Nagy, S&#xc1; and Papp, M and Solymosi, N}, title = {A survey on antimicrobial resistance genes of frequently used probiotic bacteria, 1901 to 2022.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {14}, pages = {}, doi = {10.2807/1560-7917.ES.2023.28.14.2200272}, pmid = {37022212}, issn = {1560-7917}, mesh = {*Gram-Positive Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Probiotics ; Bifidobacterium animalis/drug effects/genetics ; Lactobacillales/drug effects/genetics ; Genome, Bacterial ; *Genes, Bacterial ; }, abstract = {BackgroundAntimicrobial resistance (AMR) is caused by AMR determinants, mainly genes (ARGs) in the bacterial genome. Bacteriophages, integrative mobile genetic elements (iMGEs) or plasmids can allow ARGs to be exchanged among bacteria by horizontal gene transfer (HGT). Bacteria, including bacteria with ARGs, can be found in food. Thus, it is conceivable that in the gastrointestinal tract, bacteria from the gut flora could take up ARGs from food.AimThe study objective was to gain insight into the ARG set carried by commonly used probiotic bacteria that may enter the human body with non-fermented foods, fermented foods, or probiotic dietary supplements (FFPs) and to assess ARG mobility.MethodsNext generation sequencing whole genome data from 579 isolates of 12 commonly employed probiotic bacterial species were collected from a public repository. Using bioinformatical tools, ARGs were analysed and linkage with mobile genetic elements assessed.ResultsResistance genes were found in eight bacterial species. The ratios of ARG positive/negative samples per species were: Bifidobacterium animalis (65/0), Lactiplantibacillus plantarum (18/194), Lactobacillus delbrueckii (1/40), Lactobacillus helveticus (2/64), Lactococcus lactis (74/5), Leucoconstoc mesenteroides (4/8), Levilactobacillus brevis (1/46), Streptococcus thermophilus (4/19). In 66% (112/169) of the ARG-positive samples, at least one ARG could be linked to plasmids or iMGEs. No bacteriophage-linked ARGs were found.ConclusionThe finding of potentially mobile ARGs in probiotic strains for human consumption raises awareness of a possibility of ARG HGT in the gastrointestinal tract. In addition to existing recommendations, screening FFP bacterial strains for ARG content and mobility characteristics might be considered.}, }
@article {pmid37020720, year = {2023}, author = {Liu, Q and Yang, LL and Xin, YH}, title = {Diversity of the genus Cryobacterium and proposal of 19 novel species isolated from glaciers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115168}, pmid = {37020720}, issn = {1664-302X}, abstract = {The bacterial genus Cryobacterium includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of Cryobacterium with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of Cryobacterium. Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature (T max) of ≤ 20°C and a T max of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The T max parameter had a strong phylogenetic signal, indicating that the temperature adaptation of Cryobacterium was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus Cryobacterium by the following 19 names: Cryobacterium serini sp. nov., Cryobacterium lactosi sp. nov., Cryobacterium gelidum sp. nov., Cryobacterium suzukii sp. nov., Cryobacterium fucosi sp. nov., Cryobacterium frigoriphilum sp. nov., Cryobacterium cryoconiti sp. nov., Cryobacterium lyxosi sp. nov., Cryobacterium sinapicolor sp. nov., Cryobacterium sandaracinum sp. nov., Cryobacterium cheniae sp. nov., Cryobacterium shii sp. nov., Cryobacterium glucosi sp. nov., Cryobacterium algoritolerans sp. nov., Cryobacterium mannosilyticum sp. nov., Cryobacterium adonitolivorans sp. nov., Cryobacterium algoricola sp. nov., Cryobacterium tagatosivorans sp. nov., and Cryobacterium glaciale sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of Cryobacterium.}, }
@article {pmid37019751, year = {2023}, author = {Dart, E and Ahlgren, NA}, title = {New tRNA-targeting transposons that hijack phage and vesicles.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2023.03.004}, pmid = {37019751}, issn = {0168-9525}, abstract = {Genomic islands are hotspots for horizontal gene transfer (HGT) in bacteria, but, for Prochlorococcus, an abundant marine cyanobacterium, how these islands form has puzzled scientists. With the discovery of tycheposons, a new family of transposons, Hackl et al. provide evidence for elegant new mechanisms of gene rearrangement and transfer among Prochlorococcus and bacteria more broadly.}, }
@article {pmid37018030, year = {2023}, author = {Jerez, SA and Plaza, N and Bravo, V and Urrutia, IM and Blondel, CJ}, title = {Vibrio type III secretion system 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000973}, pmid = {37018030}, issn = {2057-5858}, mesh = {Humans ; Type III Secretion Systems ; *Vibrionaceae ; Phylogeny ; *Vibrio Infections/microbiology ; *Vibrio parahaemolyticus/genetics ; }, abstract = {Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, type III secretion system (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host-cell processes, critical for V. parahaemolyticus to colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness of V. parahaemolyticus in its interaction with bacterivorous protists; hence, it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes in Vibrio and non-Vibrio species, suggesting that the T3SS2 gene cluster is not restricted to the Vibrionaceae and can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define six T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of the T3SS2 gene clusters (subgroup VI) that lacks most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond the family Vibrionaceae and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacterium that has acquired the Vibrio T3SS2 gene cluster.}, }
@article {pmid37017542, year = {2023}, author = {Joglekar, P and Ferrell, BD and Jarvis, T and Haramoto, K and Place, N and Dums, JT and Polson, SW and Wommack, KE and Fuhrmann, JJ}, title = {Spontaneously Produced Lysogenic Phages Are an Important Component of the Soybean Bradyrhizobium Mobilome.}, journal = {mBio}, volume = {}, number = {}, pages = {e0029523}, doi = {10.1128/mbio.00295-23}, pmid = {37017542}, issn = {2150-7511}, abstract = {The ability of Bradyrhizobium spp. to nodulate and fix atmospheric nitrogen in soybean root nodules is critical to meeting humanity's nutritional needs. The intricacies of soybean bradyrhizobia-plant interactions have been studied extensively; however, bradyrhizobial ecology as influenced by phages has received somewhat less attention, even though these interactions may significantly impact soybean yield. In batch culture, four soybean bradyrhizobia strains, Bradyrhizobium japonicum S06B (S06B-Bj), B. japonicum S10J (S10J-Bj), Bradyrhizobium diazoefficiens USDA 122 (USDA 122-Bd), and Bradyrhizobium elkanii USDA 76[T] (USDA 76-Be), spontaneously (without apparent exogenous chemical or physical induction) produced tailed phages throughout the growth cycle; for three strains, phage concentrations exceeded cell numbers by ~3-fold after 48 h of incubation. Phage terminase large-subunit protein phylogeny revealed possible differences in phage packaging and replication mechanisms. Bioinformatic analyses predicted multiple prophage regions within each soybean bradyrhizobia genome, preventing accurate identification of spontaneously produced prophage (SPP) genomes. A DNA sequencing and mapping approach accurately delineated the boundaries of four SPP genomes within three of the soybean bradyrhizobia chromosomes and suggested that the SPPs were capable of transduction. In addition to the phages, S06B-Bj and USDA 76-Be contained three to four times more insertion sequences (IS) and large, conjugable, broad host range plasmids, both of which are known drivers of horizontal gene transfer (HGT) in soybean bradyrhizobia. These factors indicate that SPP along with IS and plasmids participate in HGT, drive bradyrhizobia evolution, and play an outsized role in bradyrhizobia ecology. IMPORTANCE Previous studies have shown that IS and plasmids mediate HGT of symbiotic nodulation (nod) genes in soybean bradyrhizobia; however, these events require close cell-to-cell contact, which could be limited in soil environments. Bacteriophage-assisted gene transduction through spontaneously produced prophages provides a stable means of HGT not limited by the constraints of proximal cell-to-cell contact. These phage-mediated HGT events may shape soybean bradyrhizobia population ecology, with concomitant impacts on soybean agriculture.}, }
@article {pmid37017538, year = {2023}, author = {Jonsdottir, I and Given, C and Penttinen, R and Jalasvuori, M}, title = {Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0010723}, doi = {10.1128/msphere.00107-23}, pmid = {37017538}, issn = {2379-5042}, abstract = {Conjugative plasmids can confer antimicrobial resistance (AMR) to their host bacterium. The plasmids disperse even between distantly related host species, rescuing the host from otherwise detrimental effects of antibiotics. Little is known about the role of these plasmids in the spread of AMR during antibiotic treatment. One unstudied question is whether the past evolutionary history of a plasmid in a particular species creates host specificity in its rescue potential or if interspecific coevolution can improve interspecific rescues. To study this, we coevolved the plasmid RP4 under three different host settings; solely Escherichia coli or Klebsiella pneumoniae, or alternating between both of them. The ability of evolved plasmids in bacterial biofilm to rescue susceptible planktonic host bacteria of either the same or different species during beta-lactam treatment was tested. The interspecific coevolution seemed to decrease rescue potential for the RP4 plasmid, while the K. pneumoniae evolved plasmid became more host specific. Large deletion in the region encoding the mating pair formation (Tra2) apparatus was detected in the plasmids evolved with K. pneumoniae. This adaptation resulted in the exapted evolution of resistance against a plasmid-dependent bacteriophage PRD1. Further, previous studies have suggested that mutations in this region completely abolish the plasmid's ability to conjugate; however, our study shows it is not essential for conjugation but rather affects the host-specific conjugation efficiency. Overall, the results suggest that previous evolutionary history can result in the separation of host-specific plasmid lineages that may be further amplified by unselected exaptations such as phage resistance. IMPORTANCE Antimicrobial resistance (AMR) is a major global public health threat which can rapidly spread in microbial communities via conjugative plasmids. Here, we advance with evolutionary rescue via conjugation in a more natural setting, namely, biofilm, and incorporate a broad-host range plasmid RP4 to test whether intra- and interspecific host histories affect its transfer potential. Escherichia coli and Klebsiella pneumoniae hosts were seen to elicit different evolutionary influences on the RP4 plasmid, leading to clear differences in the rescue potential and underlining the significant role of the plasmid-host interactions in the spread of AMR. We also contradicted previous reports that established certain conjugal transfer genes of RP4 as essential. This work enhances the understanding of how plasmid host range evolve in different host settings and further, the potential effects it may have on the horizontal spread of AMR in complex environments such as biofilms.}, }
@article {pmid37014461, year = {2023}, author = {Talat, A and Miranda, C and Poeta, P and Khan, AU}, title = {Farm to table: colistin resistance hitchhiking through food.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {167}, pmid = {37014461}, issn = {1432-072X}, mesh = {Animals ; Humans ; *Colistin/pharmacology ; Farms ; Chickens/microbiology ; Escherichia coli/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Poultry/microbiology ; *Escherichia coli Proteins/genetics ; Plasmids ; Microbial Sensitivity Tests ; }, abstract = {Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.}, }
@article {pmid37009500, year = {2023}, author = {Nodari, CS and Opazo-Capurro, A and Castillo-Ramirez, S and Mattioni Marchetti, V}, title = {Editorial: Mobile genetic elements as dissemination drivers of multidrug-resistant Gram-negative bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180510}, pmid = {37009500}, issn = {2235-2988}, mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Gram-Negative Bacteria/genetics ; Interspersed Repetitive Sequences ; }, }
@article {pmid37007505, year = {2023}, author = {Apari, P and Földvári, G}, title = {Domestication and microbiome succession may drive pathogen spillover.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1102337}, pmid = {37007505}, issn = {1664-302X}, abstract = {Emerging infectious diseases have posed growing medical, social and economic threats to humanity. The biological background of pathogen spillover or host switch, however, still has to be clarified. Disease ecology finds pathogen spillovers frequently but struggles to explain at the molecular level. Contrarily, molecular biological traits of host-pathogen relationships with specific molecular binding mechanisms predict few spillovers. Here we aim to provide a synthetic explanation by arguing that domestication, horizontal gene transfer even between superkingdoms as well as gradual exchange of microbiome (microbiome succession) are essential in the whole scenario. We present a new perspective at the molecular level which can explain the observations of frequent pathogen spillover events at the ecological level. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. We also highlight the importance of systematic monitoring of virulence genes across taxonomical categories and in the whole biosphere as it helps prevent future epidemics and pandemics. We conclude that that the processes of domestication, horizontal gene transfer and microbial succession might be important mechanisms behind the many spillover events driven and accelerated by climate change, biodiversity loss and globalization.}, }
@article {pmid37004306, year = {2023}, author = {Deng, X and Yuan, J and Chen, L and Chen, H and Wei, C and Nielsen, PH and Wuertz, S and Qiu, G}, title = {CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter.}, journal = {Water research}, volume = {235}, number = {}, pages = {119906}, doi = {10.1016/j.watres.2023.119906}, pmid = {37004306}, issn = {1879-2448}, mesh = {Prophages/genetics ; CRISPR-Cas Systems ; *Bacteriophages/genetics ; Phylogeny ; Wastewater ; *Betaproteobacteria ; }, abstract = {Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.}, }
@article {pmid37002975, year = {2023}, author = {Stockdale, SR and Hill, C}, title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102307}, doi = {10.1016/j.mib.2023.102307}, pmid = {37002975}, issn = {1879-0364}, abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.}, }
@article {pmid37001724, year = {2023}, author = {Boiten, KE and Kuijper, EJ and Schuele, L and van Prehn, J and Bode, LGM and Maat, I and van Asten, SAV and Notermans, DW and Rossen, JWA and Veloo, ACM}, title = {Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands.}, journal = {Anaerobe}, volume = {81}, number = {}, pages = {102722}, doi = {10.1016/j.anaerobe.2023.102722}, pmid = {37001724}, issn = {1095-8274}, abstract = {OBJECTIVES: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization.<br><br>METHODS: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs).<br><br>RESULTS: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance.<br><br>CONCLUSIONS: Novel CTns, Tns, and plasmids were encountered in the five MDR B.&#xa0;fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.}, }
@article {pmid36996986, year = {2023}, author = {Cheng, Y and Wang, X and Zhao, L and Zhang, X and Kong, Q and Li, H and You, X and Li, Y}, title = {Wheat straw pyrochar more efficiently decreased enantioselective uptake of dinotefuran by lettuce and dissemination of antibiotic resistance genes than pyrochar in an agricultural soil.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163088}, doi = {10.1016/j.scitotenv.2023.163088}, pmid = {36996986}, issn = {1879-1026}, abstract = {Remediation of soils pollution caused by dinotefuran, a chiral pesticide, is indispensable for ensuring human food security. In comparison with pyrochar, the effect of hydrochar on enantioselective fate of dinotefuran, and antibiotic resistance genes (ARGs) profiles in the contaminated soils remain poorly understood. Therefore, wheat straw hydrochar (SHC) and pyrochar (SPC) were prepared at 220 and 500 °C, respectively, to investigate their effects and underlying mechanisms on enantioselective fate of dinotefuran enantiomers and metabolites, and soil ARG abundance in soil-plant ecosystems using a 30-day pot experiment planted with lettuce. SPC showed a greater reduction effect on the accumulation of R- and S-dinotefuran and metabolites in lettuce shoots than SHC. This was mainly resulted from the lowered soil bioavailability of R- and S-dinotefuran due to adsorption/immobilization by chars, together with the char-enhanced pesticide-degrading bacteria resulted from increased soil pH and organic matter content. Both SPC and SHC efficiently reduced ARG levels in soils, owing to lowered abundance of ARG-carrying bacteria and declined horizontal gene transfer induced by decreased dinotefuran bioavailability. The above results provide new insights for optimizing char-based sustainable technologies to mitigate pollution of dinotefuran and spread of ARGs in agroecosystems.}, }
@article {pmid36996977, year = {2023}, author = {Zhang, C and Wang, C and Zhao, X and Hakizimana, I}, title = {Effect of resistance difference on distribution of antibiotics in bacterial cell and conjugative gene transfer risks during electrochemical flow through reaction.}, journal = {The Science of the total environment}, volume = {878}, number = {}, pages = {163142}, doi = {10.1016/j.scitotenv.2023.163142}, pmid = {36996977}, issn = {1879-1026}, abstract = {The occurrences and spread of antibiotic resistance (AR) mediated by horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) in aquatic environment have been aggravated because of the abuse of antibiotics. While the pressure of different antibiotics is known to induce the spread of AR in bacteria, whether distribution of different antibiotics in cell structure could affect HGT risks is not clear. Here, a significant difference between the distribution of tetracycline hydrochloride (Tet) and sulfamethoxazole (Sul) in cell structure during electrochemical flow through reaction (EFTR) process was firstly reported. Meanwhile, EFTR treatment possessed excellent disinfection performance and consequently controlled the HGT risks. The intracellular Tet (iTet) was discharged through efflux pumps to increase the content of extracellular Tet (eTet) due to the resistance of donor E. coli DH5α under the selective pressure of Tet, declining the damage of donor and plasmid RP4. The HGT frequency was 8.18-fold increase compared with that by EFTR treatment alone. While the secretion of intracellular Sul (iSul) was inhibited by blocking the formation of efflux pumps to inactivate the donor under the Sul pressure, and the total content of iSul and adsorbed Sul (aSul) to be 1.36-fold higher than that of eSul. Therefore, the reactive oxygen species (ROS) generation and cell membrane permeability were improved to release ARGs, and •OH attacked plasmid RP4 in the EFTR process, inhibiting the HGT risks. This study advances the awareness of the interaction between distribution of different antibiotics in cell structure and the HGT risks in the EFTR process.}, }
@article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0466722}, doi = {10.1128/spectrum.04667-22}, pmid = {36995244}, issn = {2165-0497}, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, }
@article {pmid36995224, year = {2023}, author = {Piscon, B and Pia Esposito, E and Fichtman, B and Samburski, G and Efremushkin, L and Amselem, S and Harel, A and Rahav, G and Zarrilli, R and Gal-Mor, O}, title = {The Effect of Outer Space and Other Environmental Cues on Bacterial Conjugation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0368822}, doi = {10.1128/spectrum.03688-22}, pmid = {36995224}, issn = {2165-0497}, abstract = {Bacterial conjugation is one of the most abundant horizontal gene transfer (HGT) mechanisms, playing a fundamental role in prokaryote evolution. A better understanding of bacterial conjugation and its cross talk with the environment is needed for a more complete understanding of HGT mechanisms and to fight the dissemination of malicious genes between bacteria. Here, we studied the effect of outer space, microgravity, and additional key environmental cues on transfer (tra) gene expression and conjugation efficiency, using the under studied broad-host range plasmid pN3, as a model. High resolution scanning electron microscopy revealed the morphology of the pN3 conjugative pili and mating pair formation during conjugation. Using a nanosatellite carrying a miniaturized lab, we studied pN3 conjugation in outer space, and used qRT-PCR, Western blotting and mating assays to determine the effect of ground physicochemical parameters on tra gene expression and conjugation. We showed for the first time that bacterial conjugation can occur in outer space and on the ground, under microgravity-simulated conditions. Furthermore, we demonstrated that microgravity, liquid media, elevated temperature, nutrient depletion, high osmolarity and low oxygen significantly reduce pN3 conjugation. Interestingly, under some of these conditions we observed an inverse correlation between tra gene transcription and conjugation frequency and found that induction of at least traK and traL can negatively affect pN3 conjugation frequency in a dose-dependent manner. Collectively, these results uncover pN3 regulation by various environmental cues and highlight the diversity of conjugation systems and the different ways in which they may be regulated in response to abiotic signals. IMPORTANCE Bacterial conjugation is a highly ubiquitous and promiscuous process, by which a donor bacterium transfers a large portion of genetic material to a recipient cell. This mechanism of horizontal gene transfer plays an important role in bacterial evolution and in the ability of bacteria to acquire resistance to antimicrobial drugs and disinfectants. Bacterial conjugation is a complex and energy-consuming process, that is tightly regulated and largely affected by various environmental signals sensed by the bacterial cell. Comprehensive knowledge about bacterial conjugation and the ways it is affected by environmental cues is required to better understand bacterial ecology and evolution and to find new effective ways to counteract the threating dissemination of antibiotic resistance genes between bacterial populations. Moreover, characterizing this process under stress or suboptimal growth conditions such as elevated temperatures, high salinity or in the outer space, may provide insights relevant to future habitat environmental conditions.}, }
@article {pmid36993299, year = {2023}, author = {Quinones-Olvera, N and Owen, SV and McCully, LM and Marin, MG and Rand, EA and Fan, AC and Martins Dosumu, OJ and Paul, K and Sanchez Castaño, CE and Petherbridge, R and Paull, JS and Baym, M}, title = {Diverse and abundant viruses exploit conjugative plasmids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993299}, support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection. While the majority of bacterial viruses, phages, use chromosomally-encoded cell surface structures as receptors, plasmid dependent-phages exploit plasmid-encoded conjugation proteins, making their host range dependent on horizontal transfer of the plasmid. Despite their unique biology and biotechnological significance, only a small number of plasmid-dependent phages have been characterized. Here we systematically search for new plasmid-dependent phages using a targeted discovery platform, and find that they are in fact common and abundant in nature, and vastly unexplored in terms of their genetic diversity. Plasmid-dependent tectiviruses have highly conserved genetic architecture but show profound differences in their host range which do not reflect bacterial phylogeny. Finally, we show that plasmid-dependent tectiviruses are missed by metaviromic analyses, showing the continued importance of culture-based phage discovery. Taken together, these results indicate plasmid-dependent phages play an unappreciated evolutionary role in constraining horizontal gene transfer.}, }
@article {pmid36990411, year = {2023}, author = {Sánchez-Arroyo, A and Plaza-Vinuesa, L and Rivas, BL and Mancheño, JM and Muñoz, R}, title = {The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986[T] is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity.}, journal = {International journal of biological macromolecules}, volume = {237}, number = {}, pages = {124230}, doi = {10.1016/j.ijbiomac.2023.124230}, pmid = {36990411}, issn = {1879-0003}, abstract = {The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986[T] (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.}, }
@article {pmid36989191, year = {2023}, author = {Rathnapala, JMSN and Ragab, W and Kawato, S and Furukawa, M and Nozaki, R and Kondo, H and Hirono, I}, title = {Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.13786}, pmid = {36989191}, issn = {1365-2761}, abstract = {Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V. nig2, and TUMSAT-V. nig3) to explore opportunities for disease management. Putative virulence factors and mobile genetic elements were detected while evaluating the phylogenetic relationship of each isolated strain. The genomes consisted of two circular chromosomes (I and II) plus one or two plasmids. The size of chromosome I ranged from 4.02 to 4.07 Mb with an average GC content of 46%, while the number of predicted CDSs ranged from 3563 to 3644. The size of chromosome II ranged from 2.16 to 2.18 Mb, with an average GC content of 45.5%, and the number of predicted CDSs ranged from 1970 to 1987. Numerous virulence genes were identified related to adherence, antiphagocytosis, chemotaxis, motility, iron uptake, quorum sensing, secretion systems, and toxins in all three genomes. Higher numbers of prophages and genomic islands found in TUMSAT-V. nig1 suggest that the strain has experienced numerous horizontal gene transfer events. The presence of antimicrobial resistance genes suggests that the strains have multidrug resistance. Comparative genomic analysis showed that all three strains belonged to the same clade.}, }
@article {pmid36989040, year = {2023}, author = {Sanow, S and Kuang, W and Schaaf, G and Huesgen, P and Schurr, U and Roessner, U and Watt, M and Arsova, B}, title = {Molecular mechanisms of Pseudomonas assisted plant nitrogen uptake - opportunities for modern agriculture.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-10-22-0223-CR}, pmid = {36989040}, issn = {0894-0282}, abstract = {Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT and Pseudomonas sp. K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which in turn have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N), and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signalling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions, and differs at sufficient and deficient N. The molecular controls behind different plant response are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas driven nitrogen fixation and to point to possible agricultural solutions.}, }
@article {pmid36988519, year = {2023}, author = {Low, WW and Seddon, C and Beis, K and Frankel, G}, title = {The Interaction of the F-Like Plasmid-Encoded TraN Isoforms with Their Cognate Outer Membrane Receptors.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0006123}, doi = {10.1128/jb.00061-23}, pmid = {36988519}, issn = {1098-5530}, abstract = {Horizontal gene transfer via conjugation plays a major role in bacterial evolution. In F-like plasmids, efficient DNA transfer is mediated by close association between donor and recipient bacteria. This process, known as mating pair stabilization (MPS), is mediated by interactions between the plasmid-encoded outer membrane (OM) protein TraN in the donor and chromosomally-encoded OM proteins in the recipient. We have recently reported the existence of 7 TraN sequence types, which are grouped into 4 structural types, that we named TraNα, TraNβ, TraNγ, and TraNδ. Moreover, we have shown specific pairing between TraNα and OmpW, TraNβ and OmpK36 of Klebsiella pneumoniae, TraNγ and OmpA, and TraNδ and OmpF. In this study, we found that, although structurally similar, TraNα encoded by the Salmonella enterica pSLT plasmid (TraNα2) binds OmpW in both Escherichia coli and Citrobacter rodentium, while TraNα encoded by the R100-1 plasmid (TraNα1) only binds OmpW in E. coli. AlphaFold2 predictions suggested that this specificity is mediated by a single amino acid difference in loop 3 of OmpW, which we confirmed experimentally. Moreover, we show that single amino acids insertions into loop 3 of OmpK36 affect TraNβ-mediated conjugation efficiency of the K. pneumoniae resistance plasmid pKpQIL. Lastly, we report that TraNβ can also mediate MPS by binding OmpK35, making it the first TraN variant that can bind more than one OM protein in the recipient. Together, these data show that subtle sequence differences in the OM receptors can impact TraN-mediated conjugation efficiency. IMPORTANCE Conjugation plays a central role in the spread of antimicrobial resistance genes among bacterial pathogens. Efficient conjugation is mediated by formation of mating pairs via a pilus, followed by mating pair stabilization (MPS), mediated by tight interactions between the plasmid-encoded outer membrane protein (OMP) TraN in the donor (of which there are 7 sequence types grouped into the 4 structural isoforms α, β, γ, and δ), and an OMP receptor in the recipient (OmpW, OmpK36, OmpA, and OmpF, respectively). In this study, we found that subtle differences in OmpW and OmpK36 have significant consequences on conjugation efficiency and specificity, highlighting the existence of selective pressure affecting plasmid-host compatibility and the flow of horizontal gene transfer in bacteria.}, }
@article {pmid36985115, year = {2023}, author = {Gummalla, VS and Zhang, Y and Liao, YT and Wu, VCH}, title = {The Role of Temperate Phages in Bacterial Pathogenicity.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985115}, issn = {2076-2607}, abstract = {Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage-bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments.}, }
@article {pmid36983453, year = {2023}, author = {Urquhart, AS and Idnurm, A}, title = {A Polyphasic Approach including Whole Genome Sequencing Reveals Paecilomyces paravariotii sp. nov. as a Cryptic Sister Species to P. variotii.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983453}, issn = {2309-608X}, abstract = {Whole genome sequencing is rapidly increasing phylogenetic resolution across many groups of fungi. To improve sequencing coverage in the genus Paecilomyces (Eurotiales), we report nine new Paecilomyces genomes representing five different species. Phylogenetic comparison between these genomes and those reported previously showed that Paecilomyces paravariotii is a distinct species from its close relative P. variotii. The independence of P. paravariotii is supported by analysis of overall gene identify (via BLAST), differences in secondary metabolism and an inability to form ascomata when paired with a fertile P. variotii strain of opposite mating type. Furthermore, whole genome sequencing resolves the P. formosus clade into three separate species, one of which lacked a valid name that is now provided.}, }
@article {pmid36982992, year = {2023}, author = {Liu, W and Huang, Y and Zhang, H and Liu, Z and Huan, Q and Xiao, X and Wang, Z}, title = {Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982992}, issn = {1422-0067}, mesh = {Drug Resistance, Microbial ; *Intestines ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Plasmids/genetics ; Conjugation, Genetic ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.}, }
@article {pmid36980919, year = {2023}, author = {Weltzer, ML and Wall, D}, title = {Social Diversification Driven by Mobile Genetic Elements.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980919}, issn = {2073-4425}, mesh = {*Bacteria/genetics ; *Myxococcales/genetics ; Biological Evolution ; Genome ; Interspersed Repetitive Sequences/genetics ; }, abstract = {Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.}, }
@article {pmid36975806, year = {2023}, author = {Desingu, PA and Nagarajan, K and Sundaresan, NR}, title = {Unique Tandem Repeats in the Inverted Terminal Repeat Regions of Monkeypox Viruses.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0319922}, pmid = {36975806}, issn = {2165-0497}, abstract = {The genetic diversity, especially in noncoding regions between clade I, clade IIa, and clade IIb monkeypox viruses (MPXVs), is still not fully understood. Here, we report that unique 16-nucleotide-length tandem repeats in MPXVs viruses are located in the noncoding regions of inverted terminal repeats (ITR), and the copy number of this repeat is different among clade I, clade IIa, and clade IIb viruses. It is noteworthy that tandem repeats containing these specific sequences (AACTAACTTATGACTT) are only present in MPXVs and are not found in other poxviruses. Also, the tandem repeats containing these specific sequences (AACTAACTTATGACTT) do not correspond to the tandem repeats present in the human and rodent (mice and rat) genomes. On the other hand, some of the reported tandem repeats in the human and rodent (mice and rat) genomes are present in the clade IIb-B.1 lineage of MPXV. In addition, it is noteworthy that the genes flanking these tandem repeats are lost and gained compared between clade I, clade IIa, and clade IIb MPXV. IMPORTANCE The different groups of MPXVs contain unique tandem repeats with different copy numbers in the ITR regions, and these repeats may be likely to play a role in the genetic diversity of the virus. Clade IIb (B) MPXV contains 38 and 32 repeats similar to the Tandem repeats reported in the human and rodent genome, respectively. However, none of these 38 (human) and 32 (rodent) tandem repeats matched the tandem repeats (AACTAACTTATGACTT) found in the present study. Finally, when developing attenuated or modified MPXV vaccine strains, these repeats in noncoding genomic regions can be exploited to incorporate foreign proteins (adjuvants/other virus proteins/racking fluorescent proteins such as green fluorescent protein) to carry out studies such as vaccine production and virus pathogenesis.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36964199}, issn = {1751-7370}, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36961781, year = {2023}, author = {Belal, NA and Heath, LS}, title = {A complete theoretical framework for inferring horizontal gene transfers using partial order sets.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0281824}, pmid = {36961781}, issn = {1932-6203}, mesh = {Phylogeny ; *Gene Transfer, Horizontal ; *Evolution, Molecular ; }, abstract = {We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.}, }
@article {pmid36958858, year = {2023}, author = {Bird, SM and Ford, S and Thompson, CMA and Little, R and Hall, JPJ and Jackson, RW and Malone, J and Harrison, E and Brockhurst, MA}, title = {Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {4}, pages = {}, pmid = {36958858}, issn = {1574-6941}, support = {BB/R014884/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014884/2/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R018154/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Rhizosphere ; Plasmids/genetics ; Mutation ; *Pseudomonas fluorescens/genetics ; }, abstract = {Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here, we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens SBW25 in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their environmental niche.}, }
@article {pmid36958158, year = {2023}, author = {Saha, S and Xiong, JQ and Patil, SM and Ha, GS and Hoh, JK and Park, HK and Chung, W and Chang, SW and Khan, MA and Park, HB and Jeon, BH}, title = {Dissemination of sulfonamide resistance genes in digester microbiome during anaerobic digestion of food waste leachate.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131200}, doi = {10.1016/j.jhazmat.2023.131200}, pmid = {36958158},