@article {pmid36748704, year = {2023}, author = {Anbo, M and Jelsbak, L}, title = {A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, doi = {10.1099/mgen.0.000919}, pmid = {36748704}, issn = {2057-5858}, abstract = {High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.}, }
@article {pmid36748580, year = {2022}, author = {Wietz, M and López-Pérez, M and Sher, D and Biller, SJ and Rodriguez-Valera, F}, title = {Microbe Profile: Alteromonas macleodii - a widespread, fast-responding, 'interactive' marine bacterium.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {11}, pages = {}, doi = {10.1099/mic.0.001236}, pmid = {36748580}, issn = {1465-2080}, abstract = {Alteromonas macleodii is a marine heterotrophic bacterium with widespread distribution - from temperate to tropical oceans, and from surface to deep waters. Strains of A. macleodii exhibit considerable genomic and metabolic variability, and can grow rapidly on diverse organic compounds. A. macleodii is a model organism for the study of population genomics, physiological adaptations and microbial interactions, with individual genomes encoding diverse phenotypic traits influenced by recombination and horizontal gene transfer.}, }
@article {pmid36748576, year = {2022}, author = {Kupczok, A and Bailey, ZM and Refardt, D and Wendling, CC}, title = {Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, doi = {10.1099/mgen.0.000915}, pmid = {36748576}, issn = {2057-5858}, abstract = {Lambdoid (or Lambda-like) phages are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure, which served as the basis for the 'modular genome hypothesis'. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into 12 groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26 % of homologous protein clusters in the four known operons (i.e. the early left, early right, immunity and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be near one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the cI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, play an important role in the evolution of the modular structure of these genomes.}, }
@article {pmid36748570, year = {2023}, author = {Sengupta, S and Azad, RK}, title = {Leveraging comparative genomics to uncover alien genes in bacterial genomes.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, doi = {10.1099/mgen.0.000939}, pmid = {36748570}, issn = {2057-5858}, abstract = {A significant challenge in bacterial genomics is to catalogue genes acquired through the evolutionary process of horizontal gene transfer (HGT). Both comparative genomics and sequence composition-based methods have often been invoked to quantify horizontally acquired genes in bacterial genomes. Comparative genomics methods rely on completely sequenced genomes and therefore the confidence in their predictions increases as the databases become more enriched in completely sequenced genomes. Recent developments including in microbial genome sequencing call for reassessment of alien genes based on information-rich resources currently available. We revisited the comparative genomics approach and developed a new algorithm for alien gene detection. Our algorithm compared favourably with the existing comparative genomics-based methods and is capable of detecting both recent and ancient transfers. It can be used as a standalone tool or in concert with other complementary algorithms for comprehensively cataloguing alien genes in bacterial genomes.}, }
@article {pmid36748564, year = {2023}, author = {Colombi, E and Hill, Y and Lines, R and Sullivan, JT and Kohlmeier, MG and Christophersen, CT and Ronson, CW and Terpolilli, JJ and Ramsay, JP}, title = {Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, doi = {10.1099/mgen.0.000918}, pmid = {36748564}, issn = {2057-5858}, abstract = {Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.}, }
@article {pmid36748528, year = {2022}, author = {Tamminga, SM and Völpel, SL and Schipper, K and Stehle, T and Pannekoek, Y and van Sorge, NM}, title = {Genetic diversity of Staphylococcus aureus wall teichoic acid glycosyltransferases affects immune recognition.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, doi = {10.1099/mgen.0.000902}, pmid = {36748528}, issn = {2057-5858}, abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections and systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for S. aureus nasal colonization, phage-mediated horizontal gene transfer, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with N-acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP. TarS and TarP modify WTA with β-linked GlcNAc at the C-4 (β1,4-GlcNAc) and the C-3 position (β1,3-GlcNAc) of the RboP subunit, respectively, whereas TarM modifies WTA with α-linked GlcNAc at the C-4 position (α1,4-GlcNAc). Importantly, these WTA glycosylation patterns impact immune recognition and clearance of S. aureus. Previous studies suggest that tarS is near-universally present within the S. aureus population, whereas a smaller proportion co-contain either tarM or tarP. To gain more insight into the presence and genetic variation of tarS, tarM and tarP in the S. aureus population, we analysed a collection of 25 652 S. aureus genomes within the PubMLST database. Over 99 % of isolates contained tarS. Co-presence of tarS/tarM or tarS/tarP occurred in 37 and 7 % of isolates, respectively, and was associated with specific S. aureus clonal complexes. We also identified 26 isolates (0.1 %) that contained all three glycosyltransferase genes. At sequence level, we identified tar alleles with amino acid substitutions in critical enzymatic residues or with premature stop codons. Several tar variants were expressed in a S. aureus tar-negative strain. Analysis using specific monoclonal antibodies and human langerin showed that WTA glycosylation was severely attenuated or absent. Overall, our data provide a broad overview of the genetic diversity of the three WTA glycosyltransferases in the S. aureus population and the functional consequences for immune recognition.}, }
@article {pmid36748517, year = {2022}, author = {Greig, DR and Bird, MT and Chattaway, MA and Langridge, GC and Waters, EV and Ribeca, P and Jenkins, C and Nair, S}, title = {Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, doi = {10.1099/mgen.0.000913}, pmid = {36748517}, issn = {2057-5858}, abstract = {Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.}, }
@article {pmid36744899, year = {2023}, author = {Prasad, A and Ene, A and Jablonska, S and Du, J and Wolfe, AJ and Putonti, C}, title = {Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068722}, doi = {10.1128/msphere.00687-22}, pmid = {36744899}, issn = {2379-5042}, abstract = {Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.}, }
@article {pmid36744093, year = {2023}, author = {Qi, Q and Rajabal, V and Ghaly, TM and Tetu, SG and Gillings, MR}, title = {Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091391}, pmid = {36744093}, issn = {1664-302X}, abstract = {Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.}, }
@article {pmid36741554, year = {2022}, author = {Lombard, L and van Doorn, R and Groenewald, JZ and Tessema, T and Kuramae, EE and Etolo, DW and Raaijmakers, JM and Crous, PW}, title = {Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.}, journal = {Fungal systematics and evolution}, volume = {10}, number = {}, pages = {177-215}, pmid = {36741554}, issn = {2589-3831}, abstract = {Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.}, }
@article {pmid36740055, year = {2023}, author = {Markowicz, A}, title = {The significance of metallic nanoparticles in the emerging, development and spread of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162029}, doi = {10.1016/j.scitotenv.2023.162029}, pmid = {36740055}, issn = {1879-1026}, abstract = {An ever-increasing number of newly synthesised nanoparticles have a constantly expanding range of applications. The large-scale implementation of nanoparticles will inevitably lead to intentional or accidental contamination of various environments. Since the major benefit of using several metallic nanoparticles is antimicrobial activity, these emerging contaminants may have a potentially hazardous impact on the development and spread of antibiotic resistance - a challenge that threats infection therapy worldwide. Few studies underline that metallic nanoparticles may affect the emergence and evolution of resistance via mutations and horizontal transfer between different bacterial species. Due to the complexity of factors and mechanisms involved in disseminating antibiotic resistance, it is crucial to investigate if metallic nanoparticles play a significant role in this process through co-selection ability and pressure exerted on bacteria. The aim of this review is to summarise the current research on mutations and three main horizontal gene transfer modes facilitated by nanoparticles. Here, the current results in the field are presented, major knowledge gaps and the necessity for more environmentally relevant studies are discussed.}, }
@article {pmid36739179, year = {2023}, author = {Islam, T and Azad, RB and Kasfy, SH and Rahman, AA and Khan, TZ}, title = {Horizontal gene transfer from plant to whitefly.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2023.01.007}, pmid = {36739179}, issn = {1879-3096}, abstract = {The recent discovery of the horizontal transfer of a toxin-neutralizing gene from plant to whitefly (Bemisia tabaci), a polyphagous insect, sparked a new area of study. In this forum, we discuss some potential biotechnological applications of this newly discovered knowledge in the coevolutionary arms race between plants and whitefly.}, }
@article {pmid36738814, year = {2023}, author = {Bhowmik, P and Bharatham, N and Murakami, S and Ramachandran, V and Datta, S}, title = {Identification of key amino acid residues in OqxB mediated efflux of fluoroquinolones using site-directed mutagenesis.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104039}, doi = {10.1016/j.resmic.2023.104039}, pmid = {36738814}, issn = {1769-7123}, abstract = {OqxB belongs to the RND (Resistance-Nodulation-Division) efflux pump family, recognized widely as a major contributor towards enhancing antimicrobial resistance. It is known to be predominantly present in all Klebsiella spp. and is attributed for its role in increasing resistance against an array of antibiotics like nitrofurantoin, quinolones, β-lactams and colistin. However, the presence of oqxB encoding this efflux pump is not limited only to Klebsiella spp., but is also found to occur via horizontal gene transfer in other bacterial genera like Escherichia coli, Enterobacter cloacae and Salmonella spp. Recently, we reported the crystal structure of OqxB and its structure-function relationship required for the efflux of fluoroquinolones. Extending these findings further, we characterized the structural architecture of this efflux pump along with identifying some critical amino acids at the substrate binding domain of OqxB. Based on our in silico modelling studies, both, hydrophobic residues (F180, L280, L621, F626) and polar residues (R48, E50, E184, R157, R774) were found to be located at this site. The present work reports the importance of these key amino acid residues and the crucial ion-pair interactions at the substrate-binding pocket, thereby establishing their role in OqxB mediated efflux and the resultant resistance development against fluoroquinolones.}, }
@article {pmid36738611, year = {2023}, author = {Zhang, Y and Zhao, Z and Xu, H and Wang, L and Liu, R and Jia, X}, title = {Fate of antibiotic resistance genes and bacteria in a coupled water-processing system with wastewater treatment plants and constructed wetlands in coastal eco-industrial parks.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114606}, doi = {10.1016/j.ecoenv.2023.114606}, pmid = {36738611}, issn = {1090-2414}, abstract = {In coastal eco-industrial zones, wastewater treatment plants (WWTPs) and constructed wetlands (CWs) can alleviate the challenge of water shortage and the negative effect of sewage discharge, while the problems of antibiotic resistance genes (ARGs) have not attracted enough attention. In this research, the Wafergen SmartChip system was adopted to investigate the ARG profiles in a coupled system combined WWTPs and CWs in a coastal industrial park. Potential risks of antibiotic resistance in chemical industrial wastewater were confirmed due to the higher abundance of target ARGs (> 10[7] copies/mL). General decline with partial enrichment in absolute and relative abundance of ARGs from the WWTPs to CWs revealed the effective removal of ARGs in the coupled system, while the fate of different ARG types varied greatly. Aminoglycoside and sulfonamide ARGs were detected with higher abundance (up to 5.34 ×10[7] and 3.61 ×10[7] copies/mL), especially aac(6')-Ib and sul1. Denitrification, secondary sedimentation, and acid hydrolysis contributed to the removal of aminoglycoside, sulfonamide, β-lactamase, chloramphenicol, and multidrug ARGs. Catalytic ozonation contributed to the removal of tetracycline and MLSB ARGs. Subsurface CWs worked effectively for the removal of sulfonamide, tetracycline, and multidrug ARGs, especially tetX, cphA, tetG, and strB. Close correlations between ARGs and MGEs emphasized the vital roles of anthropogenic pollutants and horizontal gene transfer on the diffusion of ARGs. Actinobacteria, Bacteroidota, and Cyanobacteria were dominant in the CWs, while Proteobacteria, Firmicutes, and Planctomycetota were prevalent in the WWTPs. Redundancy analysis and variance partitioning analysis indicated that transposase and water quality posed greater influences on the distribution of ARGs. Co-occurrence network revealed that potential multiple antibiotic resistant pathogenic bacteria decreased in the CWs. The coupled system has a limited effect on the reduction of ARGs and potential ARG hosts, providing a comprehensive insight into the fate of ARGs in conventional water-processing systems.}, }
@article {pmid36732595, year = {2023}, author = {Bhattacharjee, AS and Schulz, F and Woyke, T and Orcutt, BN and Martínez Martínez, J}, title = {Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {10}, doi = {10.1038/s43705-022-00210-8}, pmid = {36732595}, issn = {2730-6151}, abstract = {The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNA[Tyr] gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.}, }
@article {pmid36726572, year = {2022}, author = {Calero-Cáceres, W and Rodríguez, K and Medina, A and Medina, J and Ortuño-Gutiérrez, N and Sunyoto, T and Dias, CAG and Bastidas-Caldes, C and Ramírez, MS and Harries, AD}, title = {Genomic insights of mcr-1 harboring Escherichia coli by geographical region and a One-Health perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032753}, pmid = {36726572}, issn = {1664-302X}, abstract = {The importance of the One Health concept in attempting to deal with the increasing levels of multidrug-resistant bacteria in both human and animal health is a challenge for the scientific community, policymakers, and the industry. The discovery of the plasmid-borne mobile colistin resistance (mcr) in 2015 poses a significant threat because of the ability of these plasmids to move between different bacterial species through horizontal gene transfer. In light of these findings, the World Health Organization (WHO) recommends that countries implement surveillance strategies to detect the presence of plasmid-mediated colistin-resistant microorganisms and take suitable measures to control and prevent their dissemination. Seven years later, ten different variants of the mcr gene (mcr-1 to mcr-10) have been detected worldwide in bacteria isolated from humans, animals, foods, the environment, and farms. However, the possible transmission mechanisms of the mcr gene among isolates from different geographical origins and sources are largely unknown. This article presents an analysis of whole-genome sequences of Escherichia coli that harbor mcr-1 gene from different origins (human, animal, food, or environment) and geographical location, to identify specific patterns related to virulence genes, plasmid content and antibiotic resistance genes, as well as their phylogeny and their distribution with their origin. In general, E. coli isolates that harbor mcr-1 showed a wide plethora of ARGs. Regarding the plasmid content, the highest concentration of plasmids was found in animal samples. In turn, Asia was the continent that led with the largest diversity and occurrence of these plasmids. Finally, about virulence genes, terC, gad, and traT represent the most frequent virulence genes detected. These findings highlight the relevance of analyzing the environmental settings as an integrative part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance.}, }
@article {pmid36726175, year = {2023}, author = {Petersen, C and Sørensen, T and Nielsen, MR and Sondergaard, TE and Sørensen, JL and Fitzpatrick, DA and Frisvad, JC and Nielsen, KL}, title = {Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {3}, pmid = {36726175}, issn = {2210-6340}, abstract = {The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.}, }
@article {pmid36724669, year = {2023}, author = {Adenaya, A and Berger, M and Brinkhoff, T and Ribas-Ribas, M and Wurl, O}, title = {Usage of antibiotics in aquaculture and the impact on coastal waters.}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114645}, doi = {10.1016/j.marpolbul.2023.114645}, pmid = {36724669}, issn = {1879-3363}, abstract = {For decades, coastal marine ecosystems have been threatened by a wide range of anthropogenic pollutants. Recently, there has been increasing concern about the accumulation and impacts of antibiotic compounds on marine ecosystems. However, information regarding the accumulation of antibiotics and the impacts they may have on microbial communities in coastal water bodies and on human health is sparse in literature. Antibiotics from aquacultures are constantly discharged into marine environments via rivers. Large rivers transport tons of antibiotics every year into coastal waters, e.g., 12 tons of sulfonamide by the river Mekong. Here, we discuss a potential influence of such imported antibiotics on bacterial communities in coastal waters. Potential accumulation of antibiotics in the uppermost surface layer of aquatic ecosystems, the so-called sea surface microlayer (SML), is of interest. Because of the ability of the SML to accumulate anthropogenic pollutants, it may serve as a pool for antibiotics and correspondingly also for resistant organisms. Also, due to its biofilm-like structure, the SML could serve as a hotspot for horizontal gene transfer, speeding up the spread of antibiotic resistant strains to encompassing marine environments. The emergence of antibiotic resistant bacteria is a global threat and scientists projected that it could pave the way for the next pandemic that could ravage the world in the next decades. For this reason, it is time to focus research on understanding and minimizing the impact of antibiotics on the sustainability of coastal waters and on the health of humans who depend on coastal resources for food and recreational purposes. Also, knowledge about antibiotics in the SML is necessary to understand the effects they are likely to have on bacterial abundance, diversity, and metabolic activities in coastal water bodies.}, }
@article {pmid36724283, year = {2022}, author = {Sarma, S and Bhattacharjee, A and Devi, MV and Panyang, PP and Singh, AK}, title = {Long-term adaptation of ParA, RelE/ParE partition system, replication protein and phage proteins encoding low-cost plasmids of Escherichia species isolated from diarrheic children of North East India.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxac065}, pmid = {36724283}, issn = {1365-2672}, abstract = {AIMS: The prevalent distribution of plasmid-mediated β-lactam resistance is the most pressing global problem in enteric diseases. The current work aims to characterize plasmid-carrying β-lactam resistant Enterobacteriaceae isolates from North East India for horizontal gene transfer (HGT) and plasmid adaptation study.<br><br>METHODS AND RESULTS: In vitro transconjugation and transformation showed overall high conjugation frequency (4.11&#xa0;&#xd7;&#xa0;10-1-9.2&#xa0;&#xd7;&#xa0;10-1) and moderate transformation efficiency/&#xb5;g DNA (1.02&#xa0;&#xd7;&#xa0;102 -1&#xa0;&#xd7;&#xa0;103), and the highest conjugation frequency (9.2&#xa0;&#xd7;&#xa0;10-1) and transformation efficiency (1&#xa0;&#xd7;&#xa0;103) for Escherichia species S-10. Intra/intergenus plasmid transformation efficiency was highest for the transformation of Klebsiella pneumoniae S-2 to Shigellaflexneri S-42 (1.3&#xa0;&#xd7;&#xa0;103) and lowest for Escherichia species S-10 to Escherichia fergusonii S-30 (2&#xa0;&#xd7;&#xa0;102). In the plasmid stability test, S-10 was detected with the highest plasmid carrying frequency (83.44%) and insignificant segregational loss rate (0.0004) until the 60th day with low plasmid cost on the host. The above findings were also validated by whole-plasmid sequencing of Escherichia species S-10. The genome was identified with two plasmids constituting multiple phage proteins, relaxosomal protein NikA, replication protein RepA, and the plasmid maintenance proteins (ParA, RelE/ParE), thus assisting stable plasmid maintenance.<br><br>CONCLUSIONS: The results thus indicate that the high conjugation ability and low plasmid fitness cost might lead to horizontal gene transfer of the plasmid to the environment due to their prolonged adaptation in nonselective conditions, intensifying the infection's severity.}, }
@article {pmid36722946, year = {2023}, author = {Carrilero, L and Dunn, SJ and Moran, RA and McNally, A and Brockhurst, MA}, title = {Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0071322}, doi = {10.1128/msystems.00713-22}, pmid = {36722946}, issn = {2379-5077}, abstract = {Multidrug resistance (MDR) plasmids drive the spread of antibiotic resistance between bacterial lineages. The immediate impact of MDR plasmid acquisition on fitness and cellular processes varies among bacterial lineages, but how the evolutionary processes enabling the genomic integration of MDR plasmids vary is less well understood, particularly in clinical pathogens. Using diverse Escherichia coli lineages experimentally evolved for ~700 generations, we show that the evolutionary response to gaining the MDR plasmid pLL35 was dominated by chromosomal mutations affecting metabolic and regulatory functions, with both strain-specific and shared mutational targets. The expression of several of these functions, such as anaerobic metabolism, is known to be altered upon acquisition of pLL35. Interactions with resident mobile genetic elements, notably several IS-elements, potentiated parallel mutations, including insertions upstream of hns that were associated with its upregulation and the downregulation of the plasmid-encoded extended-spectrum beta-lactamase gene. Plasmid parallel mutations targeted conjugation-related genes, whose expression was also commonly downregulated in evolved clones. Beyond their role in horizontal gene transfer, plasmids can be an important selective force shaping the evolution of bacterial chromosomes and core cellular functions. IMPORTANCE Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. Using experimental evolution with diverse E. coli lineages and a clinical multidrug resistance plasmid, we show that although plasmids drove unique evolutionary paths per lineage, there was a surprising degree of convergence in the functions targeted by mutations across lineages, dominated by metabolic functions. Remarkably, these same metabolic functions show higher evolutionary rates in MDR-lineages in nature and in some cases, like anaerobic metabolism, their expression is directly manipulated by the plasmid. Interactions with other mobile elements resident in the genomes accelerated adaptation by disrupting genes and regulatory sequences that they inserted into. Beyond their role in horizontal gene transfer, plasmids are an important selective force driving the evolution of bacterial genomes and core cellular functions.}, }
@article {pmid36586689, year = {2023}, author = {Shi, H and Hu, X and Xu, J and Hu, B and Ma, L and Lou, L}, title = {Conjugation-mediated transfer of antibiotic resistance genes influenced by primary soil components and underlying mechanisms.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161232}, doi = {10.1016/j.scitotenv.2022.161232}, pmid = {36586689}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Soil ; Bentonite ; Kaolin ; Quartz/pharmacology ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Bacteria/genetics ; Plasmids ; }, abstract = {Soil is the main natural reservoir of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Their dissemination and proliferation were largely motivated by conjugative transfer, while the influence of soil components on bacterial conjugative transfer and the underlying mechanisms remain poorly understood. In the present study, two Escherichia coli strains were exposed to soil minerals (quartz, kaolinite and montmorillonite) and organic matters (humic acid, biochar and soot) respectively to investigate their impact on ARGs conjugation. The results showed that quartz had no significant effect on conjugation; montmorillonite promoted the growth of the donor, but inhibited the recipient and conjugant; kaolinite and three organic matters significantly promoted the production of conjugant, while biochar promoted and then inhibited it with time prolong. Within the range of bacterial concentration involved in this study, the concentration of conjugant increased with the ratio of the concentration of donor and recipient (RD/R), indicating that the variation of conjugant production was mainly mediated by changing RD/R. Further observation of biochar treatment group showed that the bacterial responses such as cell membrane permeability, cell surface hydrophobicity and biofilm formation ability shifted with the exposure time, which might be a potential factor affecting conjugative transfer. Collectively, our findings suggest that the type and exposure time of soil components jointly affected conjugation, while the change of RD/R and related bacterial responses are the main underlying mechanisms.}, }
@article {pmid36720410, year = {2023}, author = {Zhao, H and Liu, X and Sun, Y and Liu, J and Waigi, MG}, title = {Effects and mechanisms of plant growth regulators on horizontal transfer of antibiotic resistance genes through plasmid-mediated conjugation.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {137997}, doi = {10.1016/j.chemosphere.2023.137997}, pmid = {36720410}, issn = {1879-1298}, abstract = {A vast number of bacteria occur in both soil and plants, with some of them harboring antibiotic resistance genes (ARGs). When bacteria congregate on the interface of soil particles or on plant root surfaces, these ARGs can be transferred between bacteria via conjugation, leading to the formation of antibiotic-resistant pathogens that threaten human health. Plant growth regulators (PGRs) are widely used in agricultural production, promoting plant growth and increasing crop yields. However, until now, little information has been known about the effects of PGRs on the horizontal gene transfer (HGT) of ARGs. In this study, with Escherichia coli DH5α (carrying RP4 plasmid with Tet[R], Amp[R], Kan[R]) as the donor and E. coli HB101 as the recipient, a series of diparental conjugation experiments were conducted to investigate the effects of indoleacetic acid (IAA), ethel (ETH) and gibberellin (GA3) on HGT of ARGs via plasmid-mediated conjugation. Furthermore, the mechanisms involved were also clarified. The results showed that all three PGRs affected the ARG transfer frequency by inducing the intracellular reactive oxygen species (ROS) formation, changing the cell membrane permeability, and regulating the gene transcription of traA, traL, trfAp, trbBp, kilA, and korA in plasmid RP4. In detail, 50-100 mg⋅L[-1] IAA, 20-50 mg⋅L[-1] ETH and 1500-2500 mg⋅L[-1] GA3 all significantly promoted the ARG conjugation. This study indicated that widespread use of PGRs in agricultural production could affect the HGT of ARGs via plasmid-mediated conjugation, and the application of reasonable concentrations of PGRs could reduce the ARG transmission in both soil environments and plants.}, }
@article {pmid36719227, year = {2023}, author = {Cesa-Luna, C and Geudens, N and Girard, L and De Roo, V and Maklad, HR and Martins, JC and Höfte, M and De Mot, R}, title = {Charting the Lipopeptidome of Nonpathogenic Pseudomonas.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0098822}, doi = {10.1128/msystems.00988-22}, pmid = {36719227}, issn = {2379-5077}, abstract = {A major source of pseudomonad-specialized metabolites is the nonribosomal peptide synthetases (NRPSs) assembling siderophores and lipopeptides. Cyclic lipopeptides (CLPs) of the Mycin and Peptin families are frequently associated with, but not restricted to, phytopathogenic species. We conducted an in silico analysis of the NRPSs encoded by lipopeptide biosynthetic gene clusters in nonpathogenic Pseudomonas genomes, covering 13 chemically diversified families. This global assessment of lipopeptide production capacity revealed it to be confined to the Pseudomonas fluorescens lineage, with most strains synthesizing a single type of CLP. Whereas certain lipopeptide families are specific for a taxonomic subgroup, others are found in distant groups. NRPS activation domain-guided peptide predictions enabled reliable family assignments, including identification of novel members. Focusing on the two most abundant lipopeptide families (Viscosin and Amphisin), a portion of their uncharted diversity was mapped, including characterization of two novel Amphisin family members (nepenthesin and oakridgin). Using NMR fingerprint matching, known Viscosin-family lipopeptides were identified in 15 (type) species spread across different taxonomic groups. A bifurcate genomic organization predominates among Viscosin-family producers and typifies Xantholysin-, Entolysin-, and Poaeamide-family producers but most families feature a single NRPS gene cluster embedded between cognate regulator and transporter genes. The strong correlation observed between NRPS system phylogeny and rpoD-based taxonomic affiliation indicates that much of the structural diversity is linked to speciation, providing few indications of horizontal gene transfer. The grouping of most NRPS systems in four superfamilies based on activation domain homology suggests extensive module dynamics driven by domain deletions, duplications, and exchanges. IMPORTANCE Pseudomonas species are prominent producers of lipopeptides that support proliferation in a multitude of environments and foster varied lifestyles. By genome mining of biosynthetic gene clusters (BGCs) with lipopeptide-specific organization, we mapped the global Pseudomonas lipopeptidome and linked its staggering diversity to taxonomy of the producers, belonging to different groups within the major Pseudomonas fluorescens lineage. Activation domain phylogeny of newly mined lipopeptide synthetases combined with previously characterized enzymes enabled assignment of predicted BGC products to specific lipopeptide families. In addition, novel peptide sequences were detected, showing the value of substrate specificity analysis for prioritization of BGCs for further characterization. NMR fingerprint matching proved an excellent tool to unequivocally identify multiple lipopeptides bioinformatically assigned to the Viscosin family, by far the most abundant one in Pseudomonas and with stereochemistry of all its current members elucidated. In-depth analysis of activation domains provided insight into mechanisms driving lipopeptide structural diversification.}, }
@article {pmid36717488, year = {2023}, author = {Ishibashi, K and Tanaka, Y and Morishita, Y}, title = {Evolutionary Overview of Aquaporin Superfamily.}, journal = {Advances in experimental medicine and biology}, volume = {1398}, number = {}, pages = {81-98}, doi = {10.1007/978-981-19-7415-1_6}, pmid = {36717488}, issn = {0065-2598}, abstract = {Aquaporins (AQPs) are present not only in three domains of life, bacteria, eukaryotes, and archaea, but also in viruses. With the accumulating arrays of AQP superfamily, the evolutional relationship has attracted much attention with multiple publications on "the genome-wide identification and phylogenetic analysis" of AQP superfamily. A pair of NPA boxes forming a pore is highly conserved throughout the evolution and renders key residues for the classification of AQP superfamily into four groups: AQP1-like, AQP3-like, AQP8-like, and AQP11-like. The complexity of AQP family has mostly been achieved in nematodes and subsequent evolution has been directed toward increasing the number of AQPs through whole-genome duplications (WGDs) to extend the tissue specific expression and regulation. The discovery of the intracellular AQP (iAQP: AQP8-like and AQP11-like) and substrate transports by the plasma membrane AQP (pAQP: AQP1-like and AQP3-like) have accelerated the AQP research much more toward the transport of substrates with complex profiles. This evolutionary overview based on a simple classification of AQPs into four subfamilies will provide putative structural, functional, and localization information and insights into the role of AQP as well as clues to understand the complex diversity of AQP superfamily.}, }
@article {pmid36715351, year = {2023}, author = {Liu, H and Huang, W and Yu, Y and Chen, D}, title = {Lightning-Rod Effect on Nanowire Tips Reinforces Electroporation and Electrochemical Oxidation: An Efficient Strategy for Eliminating Intracellular Antibiotic Resistance Genes.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.2c11811}, pmid = {36715351}, issn = {1936-086X}, abstract = {Conventional oxidative disinfection methods are usually inefficient to eliminate intracellular antibiotic resistance genes (i-ARGs) due to competitive oxidation of cellular components of antibiotic-resistant bacteria (ARB), resulting in the ubiquitous occurrence of ARGs in drinking water systems. Herein, we developed the strategy of coupling electroporation and electrochemical oxidation on a Co3O4-nanowires-modified electrode to destroy the multiresistant Escherichia coli cells and promote subsequent i-ARG (blaTEM-1 and aac(3)-II) degradation. The lightning-rod effect over nanowire tips can form finite regions with a locally enhanced electric field and highly concentrated charge density, in turn facilitating the electroporation for ARB cell damage and electrochemical reactivity for reactive chlorine/oxygen species generation. Characterization of the ARB membrane integrity and morphology revealed that electroporation-induced cell pores were further enlarged by the oxidation of reactive species, resulting in i-ARG removal at lower applied voltages and with 6-9 times lower energy consumption than the conventional electrochemical oxidation approach with a Co3O4-film-modified electrode. The satisfactory application and effective inhibition of horizontal gene transfer in tap water further demonstrated the great potential of our strategy in the control of the ARG dissemination risk in drinking water systems.}, }
@article {pmid36714980, year = {2023}, author = {Cheng, YY and Zhou, Z and Papadopoulos, JM and Zuke, JD and Falbel, TG and Anantharaman, K and Burton, BM and Venturelli, OS}, title = {Efficient plasmid transfer via natural competence in a microbial co-culture.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {e11406}, doi = {10.15252/msb.202211406}, pmid = {36714980}, issn = {1744-4292}, abstract = {The molecular and ecological factors shaping horizontal gene transfer (HGT) via natural transformation in microbial communities are largely unknown, which is critical for understanding the emergence of antibiotic-resistant pathogens. We investigate key factors shaping HGT in a microbial co-culture by quantifying extracellular DNA release, species growth, and HGT efficiency over time. In the co-culture, plasmid release and HGT efficiency are significantly enhanced than in the respective monocultures. The donor is a key determinant of HGT efficiency as plasmids induce the SOS response, enter a multimerized state, and are released in high concentrations, enabling efficient HGT. However, HGT is reduced in response to high donor lysis rates. HGT is independent of the donor viability state as both live and dead cells transfer the plasmid with high efficiency. In sum, plasmid HGT via natural transformation depends on the interplay of plasmid properties, donor stress responses and lysis rates, and interspecies interactions.}, }
@article {pmid36714722, year = {2022}, author = {Zhu, X and Chen, WJ and Bhatt, K and Zhou, Z and Huang, Y and Zhang, LH and Chen, S and Wang, J}, title = {Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1063393}, pmid = {36714722}, issn = {1664-462X}, abstract = {With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.}, }
@article {pmid36712336, year = {2022}, author = {Kuroyanagi, T and Bulasag, AS and Fukushima, K and Ashida, A and Suzuki, T and Tanaka, A and Camagna, M and Sato, I and Chiba, S and Ojika, M and Takemoto, D}, title = {Botrytis cinerea identifies host plants via the recognition of antifungal capsidiol to induce expression of a specific detoxification gene.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac274}, pmid = {36712336}, issn = {2752-6542}, abstract = {The gray mold pathogen Botrytis cinerea has a broad host range, causing disease in >400 plant species, but it is not known how this pathogen evolved this polyxenous nature. Botrytis cinerea can metabolize a wide range of phytoalexins, including the stilbenoid resveratrol in grape, and the sesquiterpenoids capsidiol in tobacco and rishitin in potato and tomato. In this study, we analyzed the metabolism of sesquiterpenoid phytoalexins by B. cinerea. Capsidiol was dehydrogenated to capsenone, which was then further oxidized, while rishitin was directly oxidized to epoxy- or hydroxyrishitins, indicating that B. cinerea has separate mechanisms to detoxify structurally similar sesquiterpenoid phytoalexins. RNA-seq analysis revealed that a distinct set of genes were induced in B. cinerea when treated with capsidiol or rishitin, suggesting that B. cinerea can distinguish structurally similar phytoalexins to activate appropriate detoxification mechanisms. The gene most highly upregulated by capsidiol treatment encoded a dehydrogenase, designated Bccpdh. Heterologous expression of Bccpdh in a capsidiol-sensitive plant symbiotic fungus, Epichloë festucae, resulted in an acquired tolerance of capsidiol and the ability to metabolize capsidiol to capsenone, while B. cinerea Δbccpdh mutants became relatively sensitive to capsidiol. The Δbccpdh mutant showed reduced virulence on the capsidiol producing Nicotiana and Capsicum species but remained fully pathogenic on potato and tomato. Homologs of Bccpdh are found in taxonomically distant Ascomycota fungi but not in related Leotiomycetes species, suggesting that B. cinerea acquired the ancestral Bccpdh by horizontal gene transfer, thereby extending the pathogenic host range of this polyxenous pathogen to capsidiol-producing plant species.}, }
@article {pmid36708845, year = {2023}, author = {Xiao, R and Huang, D and Du, L and Song, B and Yin, L and Chen, Y and Gao, L and Li, R and Huang, H and Zeng, G}, title = {Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161855}, doi = {10.1016/j.scitotenv.2023.161855}, pmid = {36708845}, issn = {1879-1026}, abstract = {As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.}, }
@article {pmid36706177, year = {2023}, author = {Melamed, JR and Yerneni, SS and Arral, ML and LoPresti, ST and Chaudhary, N and Sehrawat, A and Muramatsu, H and Alameh, MG and Pardi, N and Weissman, D and Gittes, GK and Whitehead, KA}, title = {Ionizable lipid nanoparticles deliver mRNA to pancreatic β cells via macrophage-mediated gene transfer.}, journal = {Science advances}, volume = {9}, number = {4}, pages = {eade1444}, doi = {10.1126/sciadv.ade1444}, pmid = {36706177}, issn = {2375-2548}, abstract = {Systemic messenger RNA (mRNA) delivery to organs outside the liver, spleen, and lungs remains challenging. To overcome this issue, we hypothesized that altering nanoparticle chemistry and administration routes may enable mRNA-induced protein expression outside of the reticuloendothelial system. Here, we describe a strategy for delivering mRNA potently and specifically to the pancreas using lipid nanoparticles. Our results show that delivering lipid nanoparticles containing cationic helper lipids by intraperitoneal administration produces robust and specific protein expression in the pancreas. Most resultant protein expression occurred within insulin-producing β cells. Last, we found that pancreatic mRNA delivery was dependent on horizontal gene transfer by peritoneal macrophage exosome secretion, an underappreciated mechanism that influences the delivery of mRNA lipid nanoparticles. We anticipate that this strategy will enable gene therapies for intractable pancreatic diseases such as diabetes and cancer.}, }
@article {pmid36695602, year = {2023}, author = {Anderson, REV and Chalmers, G and Murray, R and Mataseje, L and Pearl, DL and Mulvey, M and Topp, E and Boerlin, P}, title = {Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0186922}, doi = {10.1128/aem.01869-22}, pmid = {36695602}, issn = {1098-5336}, abstract = {Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.}, }
@article {pmid36692711, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X}, title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36692711}, issn = {1614-7499}, abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.}, }
@article {pmid36692352, year = {2023}, author = {Chen, M and Shao, Y and Luo, J and Yuan, L and Wang, M and Chen, M and Guo, Q}, title = {Penicillin and Cefotaxime Resistance of Quinolone-Resistant Neisseria meningitidis Clonal Complex 4821, Shanghai, China, 1965-2020.}, journal = {Emerging infectious diseases}, volume = {29}, number = {2}, pages = {341-350}, doi = {10.3201/eid2902.221066}, pmid = {36692352}, issn = {1080-6059}, abstract = {Clonal complex 4821 (CC4821) Neisseria meningitidis, usually resistant to quinolones but susceptible to penicillin and third-generation cephalosporins, is increasing worldwide. To characterize the penicillin-nonsusceptible (Pen[NS]) meningococci, we analyzed 491 meningococci and 724 commensal Neisseria isolates in Shanghai, China, during 1965-2020. The Pen[NS] proportion increased from 0.3% in 1965-1985 to 7.0% in 2005-2014 and to 33.3% in 2015-2020. Of the 26 Pen[NS] meningococci, 11 (42.3%) belonged to the CC4821 cluster; all possessed mutations in penicillin-binding protein 2, mostly from commensal Neisseria. Genetic analyses and transformation identified potential donors of 6 penA alleles. Three Pen[NS] meningococci were resistant to cefotaxime, 2 within the CC4821 cluster. With 96% of the Pen[NS] meningococci beyond the coverage of scheduled vaccination and the cefotaxime-resistant isolates all from toddlers, quinolone-resistant CC4821 has acquired penicillin and cefotaxime resistance closely related to the internationally disseminated ceftriaxone-resistant gonococcal FC428 clone, posing a greater threat especially to young children.}, }
@article {pmid36690118, year = {2023}, author = {Yue, Z and Zhang, J and Ding, C and Wang, Y and Zhou, Z and Yu, X and Zhang, T and Wang, X}, title = {Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161742}, doi = {10.1016/j.scitotenv.2023.161742}, pmid = {36690118}, issn = {1879-1026}, abstract = {Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.}, }
@article {pmid36689882, year = {2023}, author = {An, R and Qi, Y and Zhang, XX and Ma, L}, title = {Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects.}, journal = {Water research}, volume = {231}, number = {}, pages = {119629}, doi = {10.1016/j.watres.2023.119629}, pmid = {36689882}, issn = {1879-2448}, abstract = {Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.}, }
@article {pmid36688638, year = {2023}, author = {Bhandari, M and Rathnayake, IU and Huygens, F and Jennison, AV}, title = {Clinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0263122}, doi = {10.1128/spectrum.02631-22}, pmid = {36688638}, issn = {2165-0497}, abstract = {Cholera caused by pathogenic Vibrio cholerae is still considered one of the major health problems in developing countries including those in Asia and Africa. Australia is known to have unique V. cholerae strains in Queensland waterways, resulting in sporadic cholera-like disease being reported in Queensland each year. We conducted virulence and antimicrobial genetic characterization of O1 and non-O1, non-O139 V. cholerae (NOVC) strains (1983 to 2020) from Queensland with clinical significance and compared these to environmental strains that were collected as part of a V. cholerae monitoring project in 2012 of Queensland waterways. In this study, 87 V. cholerae strains were analyzed where O1 (n = 5) and NOVC (n = 54) strains from Queensland and international travel-associated NOVC (n = 2) (61 in total) strains were sequenced, characterized, and compared with seven previously sequenced O1 strains and 18 other publicly available NOVC strains from Australia and overseas to visualize the genetic context among them. Of the 61 strains, three clinical and environmental NOVC serogroup strains had cholera toxin-producing genes, namely, the CTX phage (identified in previous outbreaks) and the complete Vibrio pathogenicity island 1. Phylogenetic analysis based on core genome analysis showed more than 10 distinct clusters and interrelatedness between clinical and environmental V. cholerae strains from Australia. Moreover, 30 (55%) NOVC strains had the cholix toxin gene (chxA) while only 11 (20%) strains had the mshA gene. In addition, 18 (34%) NOVC strains from Australia had the type three secretion system and discrete expression of type six secretion system genes. Interestingly, four NOVC strains from Australia and one NOVC strain from Indonesia had intSXT, a mobile genetic element. Several strains were found to have beta-lactamase (blaCARB-9) and chloramphenicol acetyltransferase (catB9) genes. Our study suggests that Queensland waterways can harbor highly divergent V. cholerae strains and serve as a reservoir for various V. cholerae-associated virulence genes which could be shared among O1 and NOVC V. cholerae strains via mobile genetic elements or horizontal gene transfer. IMPORTANCE Australia has its own V. cholerae strains, both toxigenic and nontoxigenic, that are associated with cholera disease. This study aimed to characterize a collection of clinical and environmental NOVC strains from Australia to understand their virulence and antimicrobial resistance profile and to place strains from Australia in the genetic context of international strains. The findings from this study suggest the toxigenic V. cholerae strains in the Queensland River water system are of public health concern. Therefore, ongoing monitoring and genomic characterization of V. cholerae strains from the Queensland environment are important and would assist public health departments to track the source of cholera infection early and implement prevention strategies for future outbreaks. Understanding the genomics of V. cholerae could also inform the natural ecology and evolution of this bacterium in natural environments.}, }
@article {pmid36685277, year = {2022}, author = {Gomis-Rüth, FX and Stöcker, W}, title = {Structural and evolutionary insights into astacin metallopeptidases.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {1080836}, pmid = {36685277}, issn = {2296-889X}, abstract = {The astacins are a family of metallopeptidases (MPs) that has been extensively described from animals. They are multidomain extracellular proteins, which have a conserved core architecture encompassing a signal peptide for secretion, a prodomain or prosegment and a zinc-dependent catalytic domain (CD). This constellation is found in the archetypal name-giving digestive enzyme astacin from the European crayfish Astacus astacus. Astacin catalytic domains span ∼200 residues and consist of two subdomains that flank an extended active-site cleft. They share several structural elements including a long zinc-binding consensus sequence (HEXXHXXGXXH) immediately followed by an EXXRXDRD motif, which features a family-specific glutamate. In addition, a downstream SIMHY-motif encompasses a "Met-turn" methionine and a zinc-binding tyrosine. The overall architecture and some structural features of astacin catalytic domains match those of other more distantly related MPs, which together constitute the metzincin clan of metallopeptidases. We further analysed the structures of PRO-, MAM, TRAF, CUB and EGF-like domains, and described their essential molecular determinants. In addition, we investigated the distribution of astacins across kingdoms and their phylogenetic origin. Through extensive sequence searches we found astacin CDs in > 25,000 sequences down the tree of life from humans beyond Metazoa, including Choanoflagellata, Filasterea and Ichtyosporea. We also found < 400 sequences scattered across non-holozoan eukaryotes including some fungi and one virus, as well as in selected taxa of archaea and bacteria that are pathogens or colonizers of animal hosts, but not in plants. Overall, we propose that astacins originate in the root of Holozoa consistent with Darwinian descent and that the latter genes might be the result of horizontal gene transfer from holozoan donors.}, }
@article {pmid36684780, year = {2022}, author = {Wang, Y and Shahid, MQ}, title = {Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1035157}, pmid = {36684780}, issn = {1664-462X}, abstract = {Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.}, }
@article {pmid36680934, year = {2023}, author = {Tang, Y and Shi, Y and Jia, B and Zhang, Y and Wang, Q}, title = {Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa.}, journal = {Biochemical and biophysical research communications}, volume = {645}, number = {}, pages = {30-39}, doi = {10.1016/j.bbrc.2022.12.060}, pmid = {36680934}, issn = {1090-2104}, abstract = {Pseudomonas aeruginosa is a Gram-negative bacterium capable of widespread niches, which is also one of the main bacteria that cause patient infection. The metabolic diversity of Pseudomonas aeruginosa is an essential factor in adapting to a variety of environments. Based on the previous studies, adaptive genetic variation in the glycerol kinase GlpK, the glycerol 3-phosphotransferase, contributes to the fitness of bacteria in human bodies, such as Mycobacterium tuberculosis and Escherichia coli. Thus, this study aimed to explore the molecular evolution and function of glpK in P. aeruginosa. Using extensive population genomic data, we have identified the prevalence of two glpK copies in P. aeruginosa that clustered into distinct branches, which were later known as Clade 1 and 2. The evolution analysis revealed that glpK in Clade 1 derived from an ancestral P. aeruginosa species and the other from an ancient horizontal gene transfer event. In addition, we confirmed that the GlpK in Clade 2 still retained glycerol kinase activity but was much weaker than that of GlpK in Clade 1. We demonstrated the importance of the critical amino acid Q70 in GlpK glycerol kinase activity by point mutation. Furthermore, Co-expression network analysis implied that the two glpK copies of P. aeruginosa regulate separate networks and may be a strategy to improve fitness in P. aeruginosa.}, }
@article {pmid36680256, year = {2023}, author = {Pchelin, IM and Tkachev, PV and Azarov, DV and Gorshkov, AN and Drachko, DO and Zlatogursky, VV and Dmitriev, AV and Goncharov, AE}, title = {A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/v15010216}, pmid = {36680256}, issn = {1999-4915}, abstract = {In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.}, }
@article {pmid36677319, year = {2022}, author = {Shivaramu, S and Tomasch, J and Kopejtka, K and Nupur,  and Saini, MK and Bokhari, SNH and Küpper, H and Koblížek, M}, title = {The Influence of Calcium on the Growth, Morphology and Gene Regulation in Gemmatimonas phototrophica.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/microorganisms11010027}, pmid = {36677319}, issn = {2076-2607}, abstract = {The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl2 L[-1]. When grown at a lower concentration of calcium (2 mg CaCl2 L[-1]) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl2 L[-1] to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species.}, }
@article {pmid36676100, year = {2023}, author = {Lila, ASA and Rajab, AAH and Abdallah, MH and Rizvi, SMD and Moin, A and Khafagy, ES and Tabrez, S and Hegazy, WAH}, title = {Biofilm Lifestyle in Recurrent Urinary Tract Infections.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/life13010148}, pmid = {36676100}, issn = {2075-1729}, abstract = {Urinary tract infections (UTIs) represent one of the most common infections that are frequently encountered in health care facilities. One of the main mechanisms used by bacteria that allows them to survive hostile environments is biofilm formation. Biofilms are closed bacterial communities that offer protection and safe hiding, allowing bacteria to evade host defenses and hide from the reach of antibiotics. Inside biofilm communities, bacteria show an increased rate of horizontal gene transfer and exchange of resistance and virulence genes. Additionally, bacterial communication within the biofilm allows them to orchestrate the expression of virulence genes, which further cements the infestation and increases the invasiveness of the infection. These facts stress the necessity of continuously updating our information and understanding of the etiology, pathogenesis, and eradication methods of this growing public health concern. This review seeks to understand the role of biofilm formation in recurrent urinary tact infections by outlining the mechanisms underlying biofilm formation in different uropathogens, in addition to shedding light on some biofilm eradication strategies.}, }
@article {pmid36675876, year = {2022}, author = {Li, Y and Qi, M and Zhang, Q and Xu, Z and Zhang, Y and Gao, Y and Qi, Y and Qiu, L and Wang, M}, title = {Phylogenesis of the Functional 1-Aminocyclopropane-1-Carboxylate Oxidase of Fungi and Plants.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/jof9010055}, pmid = {36675876}, issn = {2309-608X}, abstract = {The 1-aminocyclopropane-1-carboxylic acid (ACC) pathway that synthesizes ethylene is shared in seed plants, fungi and probably other organisms. However, the evolutionary relationship of the key enzyme ACC oxidase (ACO) in the pathway among organisms remains unknown. Herein, we cloned, expressed and characterized five ACOs from the straw mushroom (Volvariella volvacea) and the oyster mushroom (Pleurotus ostreatus): VvACO1-4 and PoACO. The five mushroom ACOs and the previously identified AbACO of the button mushroom contained all three conserved residues that bound to Fe(II) in plant ACOs. They also had variable residues that were conserved and bound to ascorbate and bicarbonate in plant ACOs and harbored only 1-2 of the five conserved ACO motifs in plant ACOs. Particularly, VvACO2 and AbACO had only one ACO motif 2. Additionally, VvACO4 shared 44.23% sequence identity with the cyanobacterium Hapalosiphon putative functional ACO. Phylogenetic analysis showed that the functional ACOs of monocotyledonous and dicotyledonous plants co-occurred in Type I, Type II and Type III, while putative functional gymnosperm ACOs also appeared in Type III. The putative functional bacterial ACO, functional fungi and slime mold ACOs were clustered in ancestral Type IV. These results indicate that ACO motif 2, ACC and Fe(II) are essential for ACO activity. The ACOs of the other organisms may come from the horizontal transfer of fungal ACOs, which were found ordinarily in basidiomycetes. It is mostly the first case for the horizontal gene transfers from fungi to seed plants. The horizontal transfer of ACOs from fungi to plants probably facilitates the fungal-plant symbioses, plant-land colonization and further evolution to form seeds.}, }
@article {pmid36671285, year = {2023}, author = {Canellas, ALB and de Oliveira, BFR and Laport, MS}, title = {Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/antibiotics12010084}, pmid = {36671285}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations' Sustainable Development Goals and, due to its multisectoral character, a holistic approach is needed to tackle this issue. Thus, the investigation of environments beyond the clinic is of utmost importance. Here, we investigated thirteen strains of antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most strains carried at least one antimicrobial resistance gene and 11 carried at least one heavy metal resistance gene. Noteworthy, four (30.7%) strains carried the blaKPC gene, coding for a carbapenemase. In particular, the whole-genome sequence of Aeromonas hydrophila strain 34SFC-3 was determined, revealing not only the presence of antimicrobial and heavy metal resistance genes but also a versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative elements, and an IncQ1 plasmid were also detected. Considering the ubiquity of Aeromonas species, their genetic promiscuity, pathogenicity, and intrinsic features to endure environmental stress, our findings reinforce the concept that A. hydrophila truly is a "Jack of all trades'' that should not be overlooked under the One Health perspective.}, }
@article {pmid36671228, year = {2022}, author = {Selvarajan, R and Obize, C and Sibanda, T and Abia, ALK and Long, H}, title = {Evolution and Emergence of Antibiotic Resistance in Given Ecosystems: Possible Strategies for Addressing the Challenge of Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/antibiotics12010028}, pmid = {36671228}, issn = {2079-6382}, abstract = {Antibiotics were once considered the magic bullet for all human infections. However, their success was short-lived, and today, microorganisms have become resistant to almost all known antimicrobials. The most recent decade of the 20th and the beginning of the 21st century have witnessed the emergence and spread of antibiotic resistance (ABR) in different pathogenic microorganisms worldwide. Therefore, this narrative review examined the history of antibiotics and the ecological roles of antibiotics, and their resistance. The evolution of bacterial antibiotic resistance in different environments, including aquatic and terrestrial ecosystems, and modern tools used for the identification were addressed. Finally, the review addressed the ecotoxicological impact of antibiotic-resistant bacteria and public health concerns and concluded with possible strategies for addressing the ABR challenge. The information provided in this review will enhance our understanding of ABR and its implications for human, animal, and environmental health. Understanding the environmental dimension will also strengthen the need to prevent pollution as the factors influencing ABR in this setting are more than just antibiotics but involve others like heavy metals and biocides, usually not considered when studying ABR.}, }
@article {pmid36669850, year = {2023}, author = {Tonkin-Hill, G and Gladstone, RA and Pöntinen, AK and Arredondo-Alonso, S and Bentley, SD and Corander, J}, title = {Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.277340.122}, pmid = {36669850}, issn = {1549-5469}, abstract = {Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.}, }
@article {pmid36669792, year = {2023}, author = {Breidenstein, A and Ter Beek, J and Berntsson, RP}, title = {Structural and functional characterization of TraI from pKM101 reveals basis for DNA processing.}, journal = {Life science alliance}, volume = {6}, number = {4}, pages = {}, doi = {10.26508/lsa.202201775}, pmid = {36669792}, issn = {2575-1077}, abstract = {Type 4 secretion systems are large and versatile protein machineries that facilitate the spread of antibiotic resistance and other virulence factors via horizontal gene transfer. Conjugative type 4 secretion systems depend on relaxases to process the DNA in preparation for transport. TraI from the well-studied conjugative plasmid pKM101 is one such relaxase. Here, we report the crystal structure of the trans-esterase domain of TraI in complex with its substrate oriT DNA, highlighting the conserved DNA-binding mechanism of conjugative relaxases. In addition, we present an apo structure of the trans-esterase domain of TraI that includes most of the flexible thumb region. This allows us for the first time to visualize the large conformational change of the thumb subdomain upon DNA binding. We also characterize the DNA binding, nicking, and religation activity of the trans-esterase domain, helicase domain, and full-length TraI. Unlike previous indications in the literature, our results reveal that the TraI trans-esterase domain from pKM101 behaves in a conserved manner with its homologs from the R388 and F plasmids.}, }
@article {pmid36669117, year = {2023}, author = {Ishikawa, M and Fujiwara, A and Kosetsu, K and Horiuchi, Y and Kamamoto, N and Umakawa, N and Tamada, Y and Zhang, L and Matsushita, K and Palfalvi, G and Nishiyama, T and Kitasaki, S and Masuda, Y and Shiroza, Y and Kitagawa, M and Nakamura, T and Cui, H and Hiwatashi, Y and Kabeya, Y and Shigenobu, S and Aoyama, T and Kato, K and Murata, T and Fujimoto, K and Benfey, PN and Hasebe, M and Kofuji, R}, title = {GRAS transcription factors regulate cell division planes in moss overriding the default rule.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {4}, pages = {e2210632120}, doi = {10.1073/pnas.2210632120}, pmid = {36669117}, issn = {1091-6490}, abstract = {Plant cells are surrounded by a cell wall and do not migrate, which makes the regulation of cell division orientation crucial for development. Regulatory mechanisms controlling cell division orientation may have contributed to the evolution of body organization in land plants. The GRAS family of transcription factors was transferred horizontally from soil bacteria to an algal common ancestor of land plants. SHORTROOT (SHR) and SCARECROW (SCR) genes in this family regulate formative periclinal cell divisions in the roots of flowering plants, but their roles in nonflowering plants and their evolution have not been studied in relation to body organization. Here, we show that SHR cell autonomously inhibits formative periclinal cell divisions indispensable for leaf vein formation in the moss Physcomitrium patens, and SHR expression is positively and negatively regulated by SCR and the GRAS member LATERAL SUPPRESSOR, respectively. While precursor cells of a leaf vein lacking SHR usually follow the geometry rule of dividing along the division plane with the minimum surface area, SHR overrides this rule and forces cells to divide nonpericlinally. Together, these results imply that these bacterially derived GRAS transcription factors were involved in the establishment of the genetic regulatory networks modulating cell division orientation in the common ancestor of land plants and were later adapted to function in flowering plant and moss lineages for their specific body organizations.}, }
@article {pmid36668832, year = {2022}, author = {Proctor, RH and Hao, G and Kim, HS and Whitaker, BK and Laraba, I and Vaughan, MM and McCormick, SP}, title = {A Novel Trichothecene Toxin Phenotype Associated with Horizontal Gene Transfer and a Change in Gene Function in Fusarium.}, journal = {Toxins}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/toxins15010012}, pmid = {36668832}, issn = {2072-6651}, abstract = {Fusarium trichothecenes are among the mycotoxins of most concern to food and feed safety. Production of these mycotoxins and presence of the trichothecene biosynthetic gene (TRI) cluster have been confirmed in only two multispecies lineages of Fusarium: the Fusarium incarnatum-equiseti (Incarnatum) and F. sambucinum (Sambucinum) species complexes. Here, we identified and characterized a TRI cluster in a species that has not been formally described and is represented by Fusarium sp. NRRL 66739. This fungus is reported to be a member of a third Fusarium lineage: the F. buharicum species complex. Cultures of NRRL 66739 accumulated only two trichothecenes, 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol. Although these are not novel trichothecenes, the production profile of NRRL 66739 is novel, because in previous reports 7-hydroxyisotrichodermin and 7-hydroxyisotrichodermol were components of mixtures of 6-8 trichothecenes produced by several Fusarium species in Sambucinum. Heterologous expression analysis indicated that the TRI13 gene in NRRL 66739 confers trichothecene 7-hydroxylation. This contrasts the trichothecene 4-hydroxylation function of TRI13 in other Fusarium species. Phylogenetic analyses suggest that NRRL 66739 acquired the TRI cluster via horizontal gene transfer from a close relative of Incarnatum and Sambucinum. These findings provide insights into evolutionary processes that have shaped the distribution of trichothecene production among Fusarium species and the structural diversity of the toxins.}, }
@article {pmid36653393, year = {2023}, author = {Couturier, A and Virolle, C and Goldlust, K and Berne-Dedieu, A and Reuter, A and Nolivos, S and Yamaichi, Y and Bigot, S and Lesterlin, C}, title = {Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {294}, pmid = {36653393}, issn = {2041-1723}, mesh = {DNA, Bacterial/genetics/metabolism ; *Escherichia coli/genetics/metabolism ; *Conjugation, Genetic ; Plasmids/genetics ; DNA ; DNA, Single-Stranded/genetics ; Gene Transfer, Horizontal ; }, abstract = {Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.}, }
@article {pmid36655280, year = {2022}, author = {Shin, H and Kim, Y and Han, S and Hur, HG}, title = {Resistome Study in Aquatic Environments.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {3}, pages = {1-11}, doi = {10.4014/jmb.2210.10044}, pmid = {36655280}, issn = {1738-8872}, abstract = {Since the first discovery of antibiotics, introduction of new antibiotics has been coupled with the occurrence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Rapid dissemination of ARB and ARGs in the aquatic environments has become a global concern. ARB and ARGs have been already disseminated in the aquatic environments via various routes. Main hosts of most of ARGs were found to belong to Gammaproteobacteria class, including clinically important potential pathogens. Transmission of ARGs also occurs by horizontal gene transfer (HGT) mechanisms between bacterial strains in the aquatic environments, resulting in ubiquity of ARGs. Thus, a few of ARGs and MGEs (e.g. strA, sul1, int1) have been suggested as indicators for global comparability of contamination level in the aquatic environments. With ARB and ARGs contamination, the occurrence of critical pathogens has been globally issued due to their widespread in the aquatic environments. Thus, active surveillance systems have been launched worldwide. In this review, we described advancement of methodologies for ARGs detection, and occurrence of ARB and ARGs and their dissemination in the aquatic environments. Even though numerous studies have been conducted for ARB and ARGs, there is still no clear strategy to tackle antibiotic resistance (AR) in the aquatic environments. At least, for consistent surveillance, a strict framework should be established for further research in the aquatic environments.}, }
@article {pmid36653270, year = {2023}, author = {Murakami, H and Sano, K and Motomura, K and Kuroda, A and Hirota, R}, title = {Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2022.12.002}, pmid = {36653270}, issn = {1347-4421}, abstract = {Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.}, }
@article {pmid36641904, year = {2023}, author = {Alnahhas, RN and Dunlop, MJ}, title = {Advances in linking single-cell bacterial stress response to population-level survival.}, journal = {Current opinion in biotechnology}, volume = {79}, number = {}, pages = {102885}, doi = {10.1016/j.copbio.2022.102885}, pmid = {36641904}, issn = {1879-0429}, abstract = {Stress response mechanisms can allow bacteria to survive a myriad of challenges, including nutrient changes, antibiotic encounters, and antagonistic interactions with other microbes. Expression of these stress response pathways, in addition to other cell features such as growth rate and metabolic state, can be heterogeneous across cells and over time. Collectively, these single-cell-level phenotypes contribute to an overall population-level response to stress. These include diversifying actions, which can be used to enable bet-hedging, and coordinated actions, such as biofilm production, horizontal gene transfer, and cross-feeding. Here, we highlight recent results and emerging technologies focused on both single-cell and population-level responses to stressors, and we draw connections about the combined impact of these effects on survival of bacterial communities.}, }
@article {pmid36639816, year = {2023}, author = {Zhu, J and Yang, F and Du, K and Wei, ZL and Wu, QF and Chen, Y and Li, WF and Li, Q and Zhou, CZ}, title = {Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {3}, pmid = {36639816}, issn = {2524-6372}, abstract = {BACKGROUND: Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.<br><br>RESULTS: Following our recently reported five cyanophages Pam1~Pam5 from Lake Chaohu in China, here we isolated another five cyanophages, termed Pan1~Pan5, which infect the cyanobacterium Pseudanabaena sp. Chao 1811. Whole-genome sequencing showed that they all contain a double-stranded DNA genome of 37.2 to 72.0&#xa0;kb in length, with less than half of the putative open reading frames annotated with known functions. Remarkably, the siphophage Pan1 encodes an auxiliary metabolic gene phoH and constitutes, together with the host, a complete queuosine modification pathway. Proteomic analyses revealed that although Pan1~Pan5 are distinct from each other in evolution, Pan1 and Pan3 are somewhat similar to our previously identified cyanophages Pam3 and Pam1 at the genomic level, respectively. Moreover, phylogenetic analyses suggested that Pan1 resembles the &#x3b1;-proteobacterial phage vB_DshS-R5C, revealing direct evidence for phage-mediated horizontal gene transfer between cyanobacteria and &#x3b1;-proteobacteria.<br><br>CONCLUSION: In addition to the previous reports of Pam1~Pam5, the present findings on Pan1~Pan5 largely enrich the library of reference freshwater cyanophages. The abundant genomic information provides a pool to identify novel genes and proteins of unknown function. Moreover, we found for the first time the evolutionary traces in the cyanophage that horizontal gene transfer might occur at the level of not only inter-species, but even inter-phylum. It indicates that the bacteriophage or cyanophage could be developed as a powerful tool for gene manipulation among various species or phyla.}, }
@article {pmid36638983, year = {2023}, author = {Yang, K and Chen, ML and Zhu, D}, title = {Exposure to benzalkonium chloride disinfectants promotes antibiotic resistance in sewage sludge microbiomes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161527}, doi = {10.1016/j.scitotenv.2023.161527}, pmid = {36638983}, issn = {1879-1026}, abstract = {Disinfectants are routinely used in human environments to control and prevent the transmission of microbial disease, and this is particularly true during the current COVID-19 crisis. However, it remains unclear whether the increased disinfectant loadings to wastewater treatment plants facilitate the dissemination of antibiotic resistance genes (ARGs) in sewage sludge microbiomes. Here, we investigated the impacts of benzalkonium chlorides (BACs), widely used disinfectants, on ARGs profiles and microbial community structures in sewage sludge by using high-throughput quantitative PCR and Illumina sequencing. A total of 147 unique ARGs and 39 mobile genetic elements (MGEs) were detected in all sewage sludge samples. Our results show that exposure to BACs disinfectants at environmentally relevant concentrations significantly promotes both the diversity and absolute abundance of ARGs in sludge microbiomes, indicating the co-selection of ARGs by BACs disinfectants. The enrichment of ARGs abundance varied from 2.15-fold to 3.63-fold compared to controls. In addition, BACs exposure significantly alters bacterial and protistan communities, resulting in dysbiosis of the sludge microbiota. The Mantel test and Procrustes analysis confirm that bacterial communities are significantly correlated with ARGs profiles under BACs treatments. The structural equation model explains 83.8 % of the total ARGs variation and further illustrates that the absolute abundance of MGEs exerts greater impacts on the variation of absolute abundance of ARGs than microbial communities under BACs exposure, suggesting BACs may promote antibiotic resistance by enhancing the horizontal gene transfer of ARGs across sludge microbiomes. Collectively, our results provide new insights into the proliferation of antibiotic resistance through disinfectant usage during the pandemic and highlight the necessity to minimize the environmental release of disinfectants into the non-target environment for combating antibiotic resistance.}, }
@article {pmid36638546, year = {2023}, author = {Gibson, PS and Veening, JW}, title = {Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae.}, journal = {Current opinion in microbiology}, volume = {72}, number = {}, pages = {102261}, doi = {10.1016/j.mib.2022.102261}, pmid = {36638546}, issn = {1879-0364}, abstract = {Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.}, }
@article {pmid36634159, year = {2023}, author = {Ryan, MP and Carraro, N and Slattery, S and Pembroke, JT}, title = {Integrative Conjugative Elements (ICEs) of the SXT/R391 family drive adaptation and evolution in γ-Proteobacteria.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/1040841X.2022.2161870}, pmid = {36634159}, issn = {1549-7828}, abstract = {Integrative Conjugative Elements (ICEs) are mosaics containing functional modules allowing maintenance by site-specific integration and excision into and from the host genome and conjugative transfer to a specific host range. Many ICEs encode a range of adaptive functions that aid bacterial survival and evolution in a range of niches. ICEs from the SXT/R391 family are found in γ-Proteobacteria. Over 100 members have undergone epidemiological and molecular characterization allowing insight into their diversity and function. Comparative analysis of SXT/R391 elements from a wide geographic distribution has revealed conservation of key functions, and the accumulation and evolution of adaptive genes. This evolution is associated with gene acquisition in conserved hotspots and variable regions within the SXT/R391 ICEs catalysed via element-encoded recombinases. The elements can carry IS elements and transposons, and a mutagenic DNA polymerase, PolV, which are associated with their evolution. SXT/R391 ICEs isolated from different niches appear to have retained adaptive functions related to that specific niche; phage resistance determinants in ICEs carried by wastewater bacteria, antibiotic resistance determinants in clinical isolates and metal resistance determinants in bacteria recovered from polluted environments/ocean sediments. Many genes found in the element hotspots are undetermined and have few homologs in the nucleotide databases.}, }
@article {pmid36629415, year = {2023}, author = {Finks, SS and Martiny, JBH}, title = {Plasmid-Encoded Traits Vary across Environments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0319122}, doi = {10.1128/mbio.03191-22}, pmid = {36629415}, issn = {2150-7511}, abstract = {Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.}, }
@article {pmid36626782, year = {2022}, author = {Sundarraj, S and Sudarmani, DNP and Samuel, P and Sevarkodiyone, SP}, title = {Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxac019}, pmid = {36626782}, issn = {1365-2672}, abstract = {AIMS: Hexavalent chromium (Cr(VI)), a toxic heavy metal, is a serious pollutant from tannery effluent, and its accumulation in soil and water causes severe environmental concerns and increasing public health issues. The present study focuses on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Ps. putida and transferred to Escherichia coli DH5α for further studies.<br><br>METHODS AND RESULTS: The bacterial cultures were kept under controlled conditions for 72&#xa0;h to observe the growth rates and bacterial resistance to chromium. When strains wild-type and transformant E. coli DH5&#x3b1; were grown in chromium-supplemented media, they revealed significant growth, but strains cured type Ps. putida and E. coli DH5&#x3b1; recorded minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5&#x3b1; and wild Ps. putida was 42.52&#xa0;&#xb1;&#xa0;1.48% and 44.46&#xa0;&#xb1;&#xa0;0.55%, respectively. The culture supernatant of the wild Ps. putida and transformant E. coli DH5&#x3b1; showed an increased reduction of Cr(VI) compared with cell extract supernatant and cell debris due to the extracellular activity of chromium reductase being responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Ps. putida and transformant E. coli DH5&#x3b1;.<br><br>CONCLUSIONS: Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.<br><br>High Cr(VI) concentration resistance and high Cr(VI) reducing the strain's ability make it suitable for bioremediation. These possible horizontal gene transfer events indicated in this study may have enabled transformant E. coli DH5&#x3b1; as a good candidate for reducing the heavy metal pollution.}, }
@article {pmid36623672, year = {2023}, author = {Sazykin, IS and Sazykina, MA}, title = {The role of oxidative stress in genome destabilization and adaptive evolution of bacteria.}, journal = {Gene}, volume = {}, number = {}, pages = {147170}, doi = {10.1016/j.gene.2023.147170}, pmid = {36623672}, issn = {1879-0038}, abstract = {The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.}, }
@article {pmid36623656, year = {2023}, author = {Wang, C and Jia, Y and Li, J and Wang, Y and Niu, H and Qiu, H and Li, X and Fang, W and Qiu, Z}, title = {Effect of bioaugmentation on tetracyclines influenced chicken manure composting and antibiotics resistance.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161457}, doi = {10.1016/j.scitotenv.2023.161457}, pmid = {36623656}, issn = {1879-1026}, abstract = {Antibiotic residue in husbandry waste has become a serious concern. In this study, contaminated chicken manure composting was conducted to reveal the bioaugmentation effect on tetracyclines residue and antibiotics resistance genes (ARGs). The bioaugmented composting removed most of the antibiotics in 7 days. Under bioaugmentation, 96.88 % of tetracycline and 92.31 % of oxytetracycline were removed, 6.32 % and 20.93 % higher than the control (P < 0.05). The high-temperature period was the most effective phase for eliminating antibiotics. The treatment showed a long high-temperature period (7 days), while no high-temperature period was in control. After composting, the treatment showed 13.87 % higher TN (26.51 g/kg) and 13.42 % higher NO3[-]-N (2.45 g/kg) than control (23.28 and 2.16 g/kg, respectively) but 12.72 % lower C/N, indicating fast decomposition and less nutrient loss. Exogenous microorganisms from bioaugmentation significantly reshaped the microbial community structure and facilitated the enrichment of genera such as Truepera and Fermentimonas, whose abundance increased by 71.10 % and 75.37 % than the control, respectively. Remarkably, ARGs, including tetC, tetG, and tetW, were enhanced by 198.77 %, 846.77 %, and 62.63 % compared with the control, while the integron gene (intl1) was elevated by 700.26 %, indicating horizontal gene transfer of ARGs. Eventually, bioaugmentation was efficient in regulating microbial metabolism, relieving antibiotic stress, and eliminating antibiotics in composting. However, the ability to remove ARGs should be further investigated. Such an approach should be further considered for treating pollutants-influenced organic waste to eliminate environmental concerns.}, }
@article {pmid36622346, year = {2023}, author = {Nieves, C and Vincent, AT and Zarantonelli, L and Picardeau, M and Veyrier, FJ and Buschiazzo, A}, title = {Horizontal transfer of the rfb cluster in Leptospira is a genetic determinant of serovar identity.}, journal = {Life science alliance}, volume = {6}, number = {2}, pages = {}, doi = {10.26508/lsa.202201480}, pmid = {36622346}, issn = {2575-1077}, abstract = {Leptospira bacteria comprise numerous species, several of which cause serious disease to a broad range of hosts including humans. These spirochetes exhibit large intraspecific variation, resulting in complex tabulations of serogroups/serovars that crisscross the species classification. Serovar identity, linked to biological/clinical phenotypes, depends on the structure of surface-exposed LPS. Many LPS biosynthesis-encoding genes reside within the chromosomic rfb gene cluster. However, the genetic basis of intraspecies variability is not fully understood, constraining diagnostics/typing methods to cumbersome serologic procedures. We now show that the gene content of the rfb cluster strongly correlates with Leptospira serovar designation. Whole-genome sequencing of pathogenic L. noguchii, including strains of different serogroups, reveals that the rfb cluster undergoes extensive horizontal gene transfer. The rfb clusters from several Leptospira species disclose a univocal correspondence between gene composition and serovar identity. This work paves the way to genetic typing of Leptospira serovars, and to pinpointing specific genes within the distinct rfb clusters, encoding host-specific virulence traits. Further research shall unveil the molecular mechanism of rfb transfer among Leptospira strains and species.}, }
@article {pmid36622251, year = {2023}, author = {Lindqvist, LL and Jarmusch, SA and Sonnenschein, EC and Strube, ML and Kim, J and Nielsen, MW and Kempen, PJ and Schoof, EM and Zhang, SD and Gram, L}, title = {Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0051722}, doi = {10.1128/msphere.00517-22}, pmid = {36622251}, issn = {2379-5042}, abstract = {In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.}, }
@article {pmid36620013, year = {2022}, author = {Lieberman, LA}, title = {Outer membrane vesicles: A bacterial-derived vaccination system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1029146}, pmid = {36620013}, issn = {1664-302X}, abstract = {Outer membrane vesicles (OMVs) are non-living spherical nanostructures that derive from the cell envelope of Gram-negative bacteria. OMVs are important in bacterial pathogenesis, cell-to-cell communication, horizontal gene transfer, quorum sensing, and in maintaining bacterial fitness. These structures can be modified to express antigens of interest using glycoengineering and genetic or chemical modification. The resulting OMVs can be used to immunize individuals against the expressed homo- or heterologous antigens. Additionally, cargo can be loaded into OMVs and they could be used as a drug delivery system. OMVs are inherently immunogenic due to proteins and glycans found on Gram negative bacterial outer membranes. This review focuses on OMV manipulation to increase vesiculation and decrease antigenicity, their utility as vaccines, and novel engineering approaches to extend their application.}, }
@article {pmid36611105, year = {2023}, author = {Aldaihani, R and Heath, LS}, title = {Connecting genomic islands across prokaryotic and phage genomes via protein families.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {344}, pmid = {36611105}, issn = {2045-2322}, abstract = {Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.}, }
@article {pmid36610752, year = {2023}, author = {Botelho, J and Cazares, A and Schulenburg, H}, title = {The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1220}, pmid = {36610752}, issn = {1362-4962}, abstract = {Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.}, }
@article {pmid36608829, year = {2023}, author = {Tan, Y and Cao, X and Chen, S and Ao, X and Li, J and Hu, K and Liu, S and Penttinen, P and Yang, Y and Yu, X and Liu, A and Liu, C and Zhao, K and Zou, L}, title = {Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161386}, doi = {10.1016/j.scitotenv.2023.161386}, pmid = {36608829}, issn = {1879-1026}, abstract = {Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.}, }
@article {pmid36608658, year = {2023}, author = {Utter, DR and Orphan, VJ}, title = {Gifts hidden in shadowy genome islands.}, journal = {Cell}, volume = {186}, number = {1}, pages = {5-7}, doi = {10.1016/j.cell.2022.12.001}, pmid = {36608658}, issn = {1097-4172}, abstract = {Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.}, }
@article {pmid36608657, year = {2023}, author = {Hackl, T and Laurenceau, R and Ankenbrand, MJ and Bliem, C and Cariani, Z and Thomas, E and Dooley, KD and Arellano, AA and Hogle, SL and Berube, P and Leventhal, GE and Luo, E and Eppley, JM and Zayed, AA and Beaulaurier, J and Stepanauskas, R and Sullivan, MB and DeLong, EF and Biller, SJ and Chisholm, SW}, title = {Novel integrative elements and genomic plasticity in ocean ecosystems.}, journal = {Cell}, volume = {186}, number = {1}, pages = {47-62.e16}, doi = {10.1016/j.cell.2022.12.006}, pmid = {36608657}, issn = {1097-4172}, abstract = {Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.}, }
@article {pmid36602323, year = {2023}, author = {Regmi, A and Tague, JG and Boas Lichty, KE and Boyd, EF}, title = {A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0187422}, doi = {10.1128/aem.01874-22}, pmid = {36602323}, issn = {1098-5336}, abstract = {Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.}, }
@article {pmid36599855, year = {2023}, author = {Cho, CH and Park, SI and Huang, TY and Lee, Y and Ciniglia, C and Yadavalli, HC and Yang, SW and Bhattacharya, D and Yoon, HS}, title = {Genome-wide signatures of adaptation to extreme environments in red algae.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {10}, pmid = {36599855}, issn = {2041-1723}, abstract = {The high temperature, acidity, and heavy metal-rich environments associated with hot springs have a major impact on biological processes in resident cells. One group of photosynthetic eukaryotes, the Cyanidiophyceae (Rhodophyta), has successfully thrived in hot springs and associated sites worldwide for more than 1 billion years. Here, we analyze chromosome-level assemblies from three representative Cyanidiophyceae species to study environmental adaptation at the genomic level. We find that subtelomeric gene duplication of functional genes and loss of canonical eukaryotic traits played a major role in environmental adaptation, in addition to horizontal gene transfer events. Shared responses to environmental stress exist in Cyanidiales and Galdieriales, however, most of the adaptive genes (e.g., for arsenic detoxification) evolved independently in these lineages. Our results underline the power of local selection to shape eukaryotic genomes that may face vastly different stresses in adjacent, extreme microhabitats.}, }
@article {pmid36598481, year = {2023}, author = {O'Leary, ML and Burbank, LP}, title = {Natural Recombination among Type I Restriction-Modification Systems Creates Diverse Genomic Methylation Patterns among Xylella fastidiosa Strains.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0187322}, doi = {10.1128/aem.01873-22}, pmid = {36598481}, issn = {1098-5336}, abstract = {Xylella fastidiosa is an important bacterial plant pathogen causing high-consequence diseases in agricultural crops around the world. Although as a species X. fastidiosa can infect many host plants, there is significant variability between strains regarding virulence on specific host plant species and other traits. Natural competence and horizontal gene transfer are believed to occur frequently in X. fastidiosa and likely influence the evolution of this pathogen. However, some X. fastidiosa strains are difficult to manipulate genetically using standard transformation techniques. Several type I restriction-modification (R-M) systems are encoded in the X. fastidiosa genome, which may influence horizontal gene transfer and recombination. Type I R-M systems themselves may undergo recombination, exchanging target recognition domains (TRDs) between specificity subunits (hsdS) to generate novel alleles with new target specificities. In this study, several conserved type I R-M systems were compared across 129 X. fastidiosa genome assemblies representing all known subspecies and 32 sequence types. Forty-four unique TRDs were identified among 50 hsdS alleles, which are arrayed in 31 allele profiles that are generally conserved within a monophyletic cluster of strains. Inactivating mutations were identified in type I R-M systems of specific strains, showing heterogeneity in the complements of functional type I R-M systems across X. fastidiosa. Genomic DNA methylation patterns were characterized in 20 X. fastidiosa strains and associated with type I R-M system allele profiles. Overall, these data suggest hsdS genes recombine among Xylella strains and/or unknown donors, and the resulting TRD reassortment establishes differential epigenetic modifications across Xylella lineages. IMPORTANCE Economic impacts on agricultural production due to X. fastidiosa have been severe in the Americas, Europe, and parts of Asia. Despite a long history of research on this pathogen, certain fundamental questions regarding the biology, pathogenicity, and evolution of X. fastidiosa have still not been answered. Wide-scale whole-genome sequencing has begun to provide more insight into X. fastidiosa genetic diversity and horizontal gene transfer, but the mechanics of genomic recombination in natural settings and the extent to which this directly influences bacterial phenotypes such as plant host range are not well understood. Genome methylation is an important factor in horizontal gene transfer and bacterial recombination that has not been comprehensively studied in X. fastidiosa. This study characterizes methylation associated with type I restriction-modification systems across a wide range of X. fastidiosa strains and lays the groundwork for a better understanding of X. fastidiosa biology and evolution through epigenetics.}, }
@article {pmid36598279, year = {2023}, author = {Xu, C and Rao, J and Xie, Y and Lu, J and Li, Z and Dong, C and Wang, L and Jiang, J and Chen, C and Chen, S}, title = {The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0350922}, doi = {10.1128/spectrum.03509-22}, pmid = {36598279}, issn = {2165-0497}, abstract = {Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.}, }
@article {pmid36597348, year = {2023}, author = {Lai, CK and Lee, YC and Ke, HM and Lu, MR and Liu, WA and Lee, HH and Liu, YC and Yoshiga, T and Kikuchi, T and Chen, PJ and Tsai, IJ}, title = {The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13752}, pmid = {36597348}, issn = {1755-0998}, abstract = {Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plant species. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides genomes have a size of 44.7-47.4 Mb and are amongst the smallest in clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants; plant HGT was especially prevalent in Bursaphelenchus mucronatus. Our results comprehensively improve the understanding of horizontal gene transfer in nematodes.}, }
@article {pmid36592614, year = {2023}, author = {Liu, Y and Chen, J and Raj, K and Baerg, L and Nathan, N and Philpott, DJ and Mahadevan, R}, title = {A Universal Strategy to Promote Secretion of G+/G- Bacterial Extracellular Vesicles and Its Application in Host Innate Immune Responses.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.2c00583}, pmid = {36592614}, issn = {2161-5063}, abstract = {Both Gram-positive and Gram-negative bacteria release nanosized extracellular vesicles called membrane vesicles (MVs, 20-400 nm), which have great potential in various biomedical applications due to their abilities to deliver effector molecules and induce therapeutic responses. To fully utilize bacterial MVs for therapeutic purposes, regulated and enhanced production of MVs would be highly advantageous. In this study, we developed a universal method to enhance MV yields in both G+/G- bacteria through an autonomous controlled peptidoglycan hydrolase (PGase) expression system. A significant increase (9.37-fold) of MV concentration was observed in engineered E. coli Nissle 1917 compared to the wild-type. With the help of this autonomous system, for the first time we experimentally confirmed horizontal gene transfer and nutrient acquisition in a cocultured bacterial consortium. Furthermore, the engineered probiotic E. coli strains with high yield of MVs showed higher activation of the innate immune responses in human embryonic kidney 293T (HEK293T) and human colorectal carcinoma cells (HCT116), thereby demonstrating the great potential of engineering probiotics in immunology and further living therapeutics in humans.}, }
@article {pmid36588930, year = {2022}, author = {Martinez-Vaz, BM and Dodge, AG and Lucero, RM and Stockbridge, RB and Robinson, AA and Tassoulas, LJ and Wackett, LP}, title = {Wastewater bacteria remediating the pharmaceutical metformin: Genomes, plasmids and products.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1086261}, pmid = {36588930}, issn = {2296-4185}, abstract = {Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. Aminobacter sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. Pseudomonas mendocina MET completely metabolized metformin and utilized all the nitrogen atoms for growth. Pseudomonas mendocina MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in Aminobacter sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in Pseudomonas mendocina MET, purified, and characterized. The Aminobacter and Pseudomonas each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.}, }
@article {pmid36587809, year = {2022}, author = {Trissi, N and Troczka, BJ and Ozsanlav-Harris, L and Singh, KS and Mallott, M and Aishwarya, V and O'Reilly, A and Bass, C and Wilding, CS}, title = {Differential regulation of the Tor gene homolog drives the red/green pigmentation phenotype in the aphid Myzuspersicae.}, journal = {Insect biochemistry and molecular biology}, volume = {}, number = {}, pages = {103896}, doi = {10.1016/j.ibmb.2022.103896}, pmid = {36587809}, issn = {1879-0240}, abstract = {In some aphid species, intraspecific variation in body colour is caused by differential carotenoid content: whilst green aphids contain only yellow carotenoids (β-, γ-, and β,γ-carotenes), red aphids additionally possess red carotenoids (torulene and 3,4-didehydrolycopene). Unusually, within animals who typically obtain carotenoids from their diet, ancestral horizontal gene transfer of carotenoid biosynthetic genes from fungi (followed by gene duplication), have imbued aphids with the intrinsic gene repertoire necessary to biosynthesise carotenoids. In the pea aphid, Acyrthosiphon pisum a lycopene (phytoene) desaturase gene (Tor) underpins the red/green phenotype, with this locus present in heterozygous form in red individuals but absent in green aphids, resulting in them being unable to convert lycopene into the red compounds 3,4-didehydrolycopene and torulene. The green peach aphid, Myzus persicae, separated from the pea aphid for ≈45MY also exists as distinct colour variable morphs, with both red and green individuals present. Here, we examined genomic data for both red and green morphs of M. persicae and identified an enlarged (compared to A. pisum) repertoire of 16 carotenoid biosynthetic genes (11 carotenoid desaturases and five carotenoid cyclase/synthase genes). From these, we identify the homolog of A. pisum Tor (here called carotene desaturase 2 or CDE-2) and show through 3D modelling that this homolog can accommodate the torulene precursor lycopene and, through RNA knockdown feeding experiments, demonstrate that disabling CDE-2 expression in red M. persicae clones results in green-coloured offspring. Unlike in A. pisum, we show that functional CDE-2 is present in the genomes of both red and green aphids. However, expression differences between the two colour morphs (350-700 fold CDE-2 overexpression in red clones), potentially driven by variants identified in upstream putative regulatory elements, underpin this phenotype. Thus, whilst aphids have a common origin of their carotenoid biosynthetic pathway, two aphid species separated for over 40MY have evolved very different drivers of intraspecific colour variation.}, }
@article {pmid36586329, year = {2022}, author = {Nnorom, MA and Saroj, D and Avery, L and Hough, R and Guo, B}, title = {A review of the impact of conductive materials on antibiotic resistance genes during the anaerobic digestion of sewage sludge and animal manure.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130628}, doi = {10.1016/j.jhazmat.2022.130628}, pmid = {36586329}, issn = {1873-3336}, abstract = {The urgent need to reduce the environmental burden of antibiotic resistance genes (ARGs) has become even more apparent as concerted efforts are made globally to tackle the dissemination of antimicrobial resistance. Concerning levels of ARGs abound in sewage sludge and animal manure, and their inadequate attenuation during conventional anaerobic digestion (AD) compromises the safety of the digestate, a nutrient-rich by-product of AD commonly recycled to agricultural land for improvement of soil quality. Exogenous ARGs introduced into the natural environment via the land application of digestate can be transferred from innocuous environmental bacteria to clinically relevant bacteria by horizontal gene transfer (HGT) and may eventually reach humans through food, water, and air. This review, therefore, discusses the prospects of using carbon- and iron-based conductive materials (CMs) as additives to mitigate the proliferation of ARGs during the AD of sewage sludge and animal manure. The review spotlights the core mechanisms underpinning the influence of CMs on the resistome profile, the steps to maximize ARG attenuation using CMs, and the current knowledge gaps. Data and information gathered indicate that CMs can profoundly reduce the abundance of ARGs in the digestate by easing selective pressure on ARGs, altering microbial community structure, and diminishing HGT.}, }
@article {pmid36583227, year = {2022}, author = {Sloan, DB and Warren, JM and Williams, AM and Kuster, SA and Forsythe, ES}, title = {Incompatibility and Interchangeability in Molecular Evolution.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evac184}, pmid = {36583227}, issn = {1759-6653}, abstract = {There is remarkable variation in the rate at which genetic incompatibilities in molecular interactions accumulate. In some cases, minor changes - even single nucleotide substitutions - create major incompatibilities when hybridization forces new variants to function in a novel genetic background from an isolated population. In other cases, genes or even entire functional pathways can be horizontally transferred between anciently divergent evolutionary lineages that span the tree of life with little evidence of incompatibilities. In this review, we explore whether there are general principles that can explain why certain genes are prone to incompatibilities while others maintain interchangeability. We summarize evidence pointing to four genetic features that may contribute to greater resistance to functional replacement: 1) function in multisubunit enzyme complexes and protein-protein interactions, 2) sensitivity to changes in gene dosage, 3) rapid rate of sequence evolution, and 4) overall importance to cell viability, which creates sensitivity to small perturbations in molecular function. We discuss the relative levels of support for these different hypotheses and lay out future directions that may help explain the striking contrasts in patterns of incompatibility and interchangeability throughout the history of molecular evolution.}, }
@article {pmid36582150, year = {2022}, author = {Manaia, CM and Aga, DS and Cytryn, E and Gaze, WH and Graham, DW and Guo, J and Leonard, AFC and Liguan, L and Murray, AK and Nunes, OC and Rodriguez-Mozaz, S and Topp, E and Zhang, T}, title = {The Complex Interplay Between Antibiotic Resistance and Pharmaceutical and Personal Care Products in the Environment.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/etc.5555}, pmid = {36582150}, issn = {1552-8618}, abstract = {Antibiotic resistant bacteria and antibiotic resistance genes are important environmental contaminants. Nonetheless, what drives the evolution, spread and transmission of antibiotic resistance dissemination is still poorly understood. The abundance of antibiotic resistant bacteria and antibiotic resistance genes is often elevated in human impacted areas, especially in environments receiving faecal wastes, or in the presence of complex mixtures of chemical contaminants, such as pharmaceuticals and personal care products (PPCPs). Self-replication, mutation, horizontal gene transfer and adaptation to different environmental conditions contribute to the persistence and proliferation of antibiotic resistant bacteria in habitats under strong anthropogenic influence. This review will discuss the interplay between chemical contaminants and antibiotic resistant bacteria and respective genes, specifically in reference to co-occurrence, potential biostimulation and selective pressure effects, and will overview mitigation by existing man-made and natural barriers. Evidence and strategies to improve the assessment of human-health risks due to environmental antibiotic resistance are also debated. This article is protected by copyright. All rights reserved. Environ Toxicol Chem 2022;00:0-0. © 2022 SETAC.}, }
@article {pmid36575565, year = {2022}, author = {Chen, H and Tao, S and Li, N and Zhu, Q and Liu, L and Fang, Y and Xu, Y and Liang, W}, title = {Anti-restriction protein ArdA promotes clinical Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae spread and its molecular mechanism.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkac423}, pmid = {36575565}, issn = {1460-2091}, abstract = {BACKGROUND: Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has spread worldwide and has become a major threat to public health. The restriction modification system provides an innate defence of bacteria against plasmids or transposons, while many different types of plasmid encoding the anti-restriction protein ArdA can specifically affect the restriction activity in bacteria.<br><br>OBJECTIVES: To detect the codistribution of ArdA and blaKPC-2 plasmids in KPC-KP and explore the molecular mechanism of ArdA promoting KPC-KP spread.<br><br>METHODS: We collected 65 clinical CRKP isolates from Ningbo, China, and 68 cases of plasmid complete sequences in GenBank to determine the prevalence of ArdA gene on the K. pneumoniae blaKPC-2 plasmid. The anti-restriction function of ArdA in promoting horizontal gene transfer (HGT) was verified by transformation, conjugation and transduction methods, and the pull-down experiment was used to investigate the molecular mechanism of ArdA protein in vitro.<br><br>RESULTS: We found that ArdA was widely distributed in KPC-KP in 100% of cases, which was detected in 0% of drug susceptible K. pneumoniae, and the plasmids containing the ArdA gene in 90% of the 30 cases randomly retrieved from the database. We also verified that ArdA has a good anti-restriction function (P&#x200a;<&#x200a;0.05) through two aspects of HGT (transformation, transduction), and explored the non-occurrence interaction of ArdA and the hsdM subunit protein of EcoKI enzyme from the perspective of protein molecules.<br><br>CONCLUSIONS: These findings suggest that the coexistence advantage of ArdA with the blaKPC-2 plasmids may provide KPC-producing K. pneumoniae with a very efficient evasion of the restriction of type I systems, which not only favours ArdA-containing mobile genetic elements in the same species HGT between bacteria also facilitates HGT between other bacterial species.}, }
@article {pmid36573357, year = {2022}, author = {Bethke, JH and Ma, HR and Tsoi, R and Cheng, L and Xiao, M and You, L}, title = {Vertical and horizontal gene transfer tradeoffs direct plasmid fitness.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {e11300}, doi = {10.15252/msb.202211300}, pmid = {36573357}, issn = {1744-4292}, abstract = {Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.}, }
@article {pmid36572269, year = {2022}, author = {Beltrán de Heredia, I and Garbisu, C and Alkorta, I and Urra, J and González-Gaya, B and Ruiz-Romera, E}, title = {Spatio-seasonal patterns of the impact of wastewater treatment plant effluents on antibiotic resistance in river sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {120883}, doi = {10.1016/j.envpol.2022.120883}, pmid = {36572269}, issn = {1873-6424}, abstract = {There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.}, }
@article {pmid36571993, year = {2022}, author = {Su, Z and Wen, D and Gu, AZ and Zheng, Y and Tang, Y and Chen, L}, title = {Industrial effluents boosted antibiotic resistome risk in coastal environments.}, journal = {Environment international}, volume = {171}, number = {}, pages = {107714}, doi = {10.1016/j.envint.2022.107714}, pmid = {36571993}, issn = {1873-6750}, abstract = {Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.}, }
@article {pmid36571495, year = {2022}, author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL}, title = {Underexplored Viral Auxiliary Metabolic Genes in Soil: Diversity and Eco-evolutionary Significance.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16329}, pmid = {36571495}, issn = {1462-2920}, abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favorable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer (HGT), lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils. This article is protected by copyright. All rights reserved.}, }
@article {pmid36568361, year = {2022}, author = {Nayar, G and Terrizzano, I and Seabolt, E and Agarwal, A and Boucher, C and Ruiz, J and Slizovskiy, IB and Kaufman, JH and Noyes, NR}, title = {ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1024577}, pmid = {36568361}, issn = {1664-8021}, abstract = {Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.}, }
@article {pmid36567403, year = {2022}, author = {Feng, R and Duan, L and Shen, S and Cheng, Y and Wang, Y and Wang, W and Yang, S}, title = {Temporal dynamic of antibiotic resistance genes in the Zaohe-Weihe hyporheic zone: driven by oxygen and bacterial community.}, journal = {Ecotoxicology (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10646-022-02616-5}, pmid = {36567403}, issn = {1573-3017}, abstract = {The widespread spread of antibiotic resistance genes (ARGs) in hyporheic zone (HZ) has become an emerging environmental problem due to their potentially harmful nature. In this research, three different oxygen treatment systems were set up to study the effects of oxygen changes on the abundance of ARGs in the HZ. In addition, the effects of temperature and salinity on ARGs were investigated under aerobic and anaerobic systems, respectively. The bacterial community composition of sediment samples and the relationship with ARGs were analyzed. The explanation ratio and causality of the driving factors affecting ARGs were analyzed using variation partitioning analysis (VPA) and structural equation model (SEM). The relative abundance of ARGs and mobile genetic elements (MGEs) in the anaerobic system increased significantly, which was higher than that in the aerobic system and the aerobic-anaerobic interaction system. The experiment of salinity and temperature also further proved this result. There were many bacterial communities that affected tetracycline and sulfonamide ARGs in sediments, and these host bacteria are mainly concentrated in Proteobacteria, Firmicutes and Bacteroidetes. VPA and SEM further revealed that the abundance of ARGs was mainly influenced by changes in bacterial communities and oxygen conditions, and horizontal gene transfer (HGT) of MGEs also had a positive effect on the spread of ARGs. Those findings suggest that complex oxygen conditions in the HZ alter bacterial communities and promote MGEs-mediated horizontal transfer, which together lead to the spread of ARGs. This study has value as a reference for formulating effective strategies to minimize the propagation of ARGs in underground environment.}, }
@article {pmid36563663, year = {2022}, author = {Vatanen, T and Jabbar, KS and Ruohtula, T and Honkanen, J and Avila-Pacheco, J and Siljander, H and Stražar, M and Oikarinen, S and Hyöty, H and Ilonen, J and Mitchell, CM and Yassour, M and Virtanen, SM and Clish, CB and Plichta, DR and Vlamakis, H and Knip, M and Xavier, RJ}, title = {Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.}, journal = {Cell}, volume = {185}, number = {26}, pages = {4921-4936.e15}, doi = {10.1016/j.cell.2022.11.023}, pmid = {36563663}, issn = {1097-4172}, abstract = {The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.}, }
@article {pmid36561977, year = {2022}, author = {González-Villarreal, JA and González-Lozano, KJ and Aréchiga-Carvajal, ET and Morlett-Chávez, JA and Luévanos-Escareño, MP and Balagurusamy, N and Salinas-Santander, MA}, title = {Molecular mechanisms of multidrug resistance in clinically relevant enteropathogenic bacteria (Review).}, journal = {Experimental and therapeutic medicine}, volume = {24}, number = {6}, pages = {753}, pmid = {36561977}, issn = {1792-1015}, abstract = {Multidrug resistant (MDR) enteropathogenic bacteria are a growing problem within the clinical environment due to their acquired tolerance to a wide range of antibiotics, thus causing severe illnesses and a tremendous economic impact in the healthcare sector. Due to its difficult treatment, knowledge and understanding of the molecular mechanisms that confer this resistance are needed. The aim of the present review is to describe the mechanisms of antibiotic resistance from a genomic perspective observed in bacteria, including naturally acquired resistance. The present review also discusses common pharmacological and alternative treatments used in cases of infection caused by MDR bacteria, thus covering necessary information for the development of novel antimicrobials and adjuvant molecules inhibiting bacterial proliferation.}, }
@article {pmid36560776, year = {2022}, author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ}, title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/v14122772}, pmid = {36560776}, issn = {1999-4915}, support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.}, }
@article {pmid36560636, year = {2022}, author = {Ács, N and Holohan, R and Dunne, LJ and Fernandes, AR and Clooney, AG and Draper, LA and Ross, RP and Hill, C}, title = {Comparing In Vitro Faecal Fermentation Methods as Surrogates for Phage Therapy Application.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/v14122632}, pmid = {36560636}, issn = {1999-4915}, support = {SFI/15/ERCD/3189/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The human microbiome and its importance in health and disease have been the subject of numerous research articles. Most microbes reside in the digestive tract, with up to 10[12] cells per gram of faecal material found in the colon. In terms of gene number, it has been estimated that the gut microbiome harbours >100 times more genes than the human genome. Several human intestinal diseases are strongly associated with disruptions in gut microbiome composition. Less studied components of the gut microbiome are the bacterial viruses called bacteriophages that may be present in numbers equal to or greater than the prokaryotes. Their potential to lyse their bacterial hosts, or to act as agents of horizontal gene transfer makes them important research targets. In this study in vitro faecal fermentation systems were developed and compared for their ability to act as surrogates for the human colon. Changes in bacterial and viral composition occurred after introducing a high-titre single phage preparation both with and without a known bacterial host during the 24 h-long fermentation. We also show that during this timeframe 50 mL plastic tubes can provide data similar to that generated in a sophisticated faecal fermenter system. This knowledge can guide us to a better understanding of the short-term impact of bacteriophage transplants on the bacteriomes and viromes of human recipients.}, }
@article {pmid36558750, year = {2022}, author = {de Brito, FAE and de Freitas, APP and Nascimento, MS}, title = {Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/pathogens11121416}, pmid = {36558750}, issn = {2076-0817}, abstract = {Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.}, }
@article {pmid36555178, year = {2022}, author = {Janczarek, M}, title = {The Ros/MucR Zinc-Finger Protein Family in Bacteria: Structure and Functions.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, doi = {10.3390/ijms232415536}, pmid = {36555178}, issn = {1422-0067}, abstract = {Ros/MucR is a widespread family of bacterial zinc-finger-containing proteins that integrate multiple functions, such as symbiosis, virulence, transcription regulation, motility, production of surface components, and various other physiological processes in cells. This regulatory protein family is conserved in bacteria and is characterized by its zinc-finger motif, which has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure has evolved. The first prokaryotic zinc-finger domain found in the transcription regulator Ros was identified in Agrobacterium tumefaciens. In the past decades, a large body of evidence revealed Ros/MucR as pleiotropic transcriptional regulators that mainly act as repressors through oligomerization and binding to AT-rich target promoters. The N-terminal domain and the zinc-finger-bearing C-terminal region of these regulatory proteins are engaged in oligomerization and DNA binding, respectively. These properties of the Ros/MucR proteins are similar to those of xenogeneic silencers, such as H-NS, MvaT, and Lsr2, which are mainly found in other lineages. In fact, a novel functional model recently proposed for this protein family suggests that they act as H-NS-'like' gene silencers. The prokaryotic zinc-finger domain exhibits interesting structural and functional features that are different from that of its eukaryotic counterpart (a βββα topology), as it folds in a significantly larger zinc-binding globular domain (a βββαα topology). Phylogenetic analysis of Ros/MucR homologs suggests an ancestral origin of this type of protein in α-Proteobacteria. Furthermore, multiple duplications and lateral gene transfer events contributing to the diversity and phyletic distribution of these regulatory proteins were found in bacterial genomes.}, }
@article {pmid36551459, year = {2022}, author = {Lienen, T and Grobbel, M and Tenhagen, BA and Maurischat, S}, title = {Plasmid-Coded Linezolid Resistance in Methicillin-Resistant Staphylococcus&amp;nbsp;aureus from Food and Livestock in Germany.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/antibiotics11121802}, pmid = {36551459}, issn = {2079-6382}, abstract = {Resistance of methicillin-resistant Staphylococcus&amp;nbsp;aureus (MRSA) from food and livestock to last resort antibiotics such as linezolid is highly concerning, since treatment options for infections in humans might be diminished. Known mechanisms of linezolid resistance include point mutations in the 23S rRNA gene and in the ribosomal proteins L3, L4 and L22 as well as an acquisition of the cfr, optrA or poxtA gene. The objective of our study was to characterize antimicrobial resistance (AMR) determinants and phylogenetic relationships among linezolid-resistant (LR-) MRSA from food and livestock. In total, from more than 4000 incoming isolates in the years 2012 to 2021, only two strains from 2015 originating from pig samples exhibited linezolid resistance in the antimicrobial susceptibility testing with MICs of ≥8 mg/L. These LR-MRSA were characterized in detail by whole-genome sequencing and phylogenetic analyses using cgMLST. The LR-MRSA strains showed resistances to ten and eight different antibiotics, respectively. Both strains harbored plasmid-coded cfr genes mediating the linezolid resistance. The cfr genes showed identical sequences in both strains. In addition to the cfr gene, genes for phenicol and clindamycin resistance were detected on the respective plasmids, opening the possibility for a co-selection. The LR-MRSA differed distantly in the phylogenetic analyses and also to other MRSA from pig samples in the year 2015. In conclusion, the occurrence of LR-MRSA in food and livestock seems to be very rare in Germany. However, carriage of plasmids with linezolid resistance determinants could lead to further linezolid-resistant strains by horizontal gene transfer.}, }
@article {pmid36549493, year = {2022}, author = {Abudureheman, M and Ailijiang, N and Mamat, A and Feng, Y and He, C and Pu, M}, title = {Enhanced biodegradation of fluoroquinolone and the changes of bacterial communities and antibiotic-resistant genes under intermittent electrical stimulation.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115127}, doi = {10.1016/j.envres.2022.115127}, pmid = {36549493}, issn = {1096-0953}, abstract = {In this study an anaerobic-aerobic coupling system under intermittent electrical stimulation was used to improve the biodegradation of synthetic wastewater containing fluoroquinolones (FQs). The effect of electrical stimulation on FQ removal performance is more pronounced with appropriate voltage and HRT. In addition, the combination of anaerobic-anodic and aerobic-cathodic chambers is more conducive to improve the removal efficiency of FQs. Under 0.9 V, the removal efficiencies of ofloxacin, norfloxacin, ciprofloxacin, and enrofloxacin were significantly improved in the anaerobic-anodic and aerobic-cathodic system. The contribution of the anaerobic/aerobic anodic chambers to FQ removal was greater than that of the anaerobic/aerobic cathodic chambers. Electrical stimulation selectively enriched electroactive bacteria related to biodegradation (Desulfovibrio and Terrimonas), antibiotic-resistant bacteria (Atopobium and Neochlamydia), and nitrifying bacteria (SM1A02 and Reyranella). This study indicated the potential effectiveness of intermittent electrical stimulation in treating fluoroquinolone-containing wastewater in a biofilm reactor. However, electrical stimulation led to an increase in mobile genetic elements (MGEs), induced horizontal gene transfer and enriched resistant bacteria, which accelerated the spread of antibiotic-resistant genes (ARGs) in the system, indicating that the diffusion of ARGs remains a challenge.}, }
@article {pmid36539881, year = {2022}, author = {Kwun, MJ and Ion, AV and Cheng, HC and D'Aeth, JC and Dougan, S and Oggioni, MR and Goulding, DA and Bentley, SD and Croucher, NJ}, title = {Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {144}, pmid = {36539881}, issn = {1756-994X}, support = {104169/Z/14/A//Wellcome Trust/United Kingdom ; 206194//Wellcome Trust/United Kingdom ; 102169/Z/13/Z//Wellcome Trust/United Kingdom ; MR/R015600/1//Medical Research Council/United Kingdom ; BB/N002903/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).<br><br>METHODS: A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics,&#xa0;and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain's evolution.<br><br>RESULTS: GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage &#x3d5;OXC141. Prior to the introduction of PCV13, this clade's composition shifted towards a &#x3d5;OXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also &#x3d5;OXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage &#x3d5;OXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competence-stimulating peptide pheromone. This resulted in a reduction in the induction of competence for transformation.<br><br>CONCLUSION: This interference with the quorum sensing needed to induce competence reduces the risk of the prophage being deleted by homologous recombination. Hence the selfish prophage-driven alteration of a regulatory RNA limits cell-cell communication and horizontal gene transfer, complicating the interpretation of post-vaccine population dynamics.}, }
@article {pmid36537743, year = {2022}, author = {Lisboa, MP and Canal, D and Filgueiras, JPC and Turchetto-Zolet, AC}, title = {Molecular evolution and diversification of phytoene synthase (PSY) gene family.}, journal = {Genetics and molecular biology}, volume = {45}, number = {4}, pages = {e20210411}, doi = {10.1590/1678-4685-GMB-2021-0411}, pmid = {36537743}, issn = {1415-4757}, abstract = {Phytoene synthase (PSY) is a crucial enzyme required for carotenoid biosynthesis, encoded by a gene family conserved in carotenoid-producing organisms. This gene family is diversified in angiosperms through distinct duplication events. Understanding diversification patterns and the evolutionary history of the PSY gene family is important for explaining carotenogenesis in different plant tissues. This study identified 351 PSY genes in 166 species, including Viridiplantae, brown and red algae, cyanobacteria, fungi, arthropods, and bacteria. All PSY genes displayed conserved intron/exon organization. Fungi and arthropod PSY sequences were grouped with prokaryote PSY, suggesting the occurrence of horizontal gene transfer. Angiosperm PSY is split into five subgroups. One includes the putative ortholog of PSY3 (Subgroup E3) from eudicots, and the other four subgroups include PSY from both monocots and eudicots (subgroups E1, E2, M1, and M2). Expression profile analysis revealed that PSY genes are constitutively expressed across developmental stages and anatomical parts, except for the eudicot PSY3, with root-specific expression. This study elucidates the molecular evolution and diversification of the PSY gene family, furthering our understanding of variations in carotenogenesis.}, }
@article {pmid36536072, year = {2022}, author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P}, title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36536072}, issn = {1751-7370}, abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.}, }
@article {pmid36532464, year = {2022}, author = {Li, P and Luo, W and Xiang, TX and Jiang, Y and Liu, P and Wei, DD and Fan, L and Huang, S and Liao, W and Liu, Y and Zhang, W}, title = {Horizontal gene transfer via OMVs co-carrying virulence and antimicrobial-resistant genes is a novel way for the dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {945972}, pmid = {36532464}, issn = {1664-302X}, abstract = {INTRODUCTION: The rapidly increased isolation rate of CR-HvKP worldwide has brought great difficulties in controlling clinical infection. Moreover, it has been demonstrated that the transmission of drug-resistant genes among bacteria can be mediated by outer membrane vesicles (OMVs), which is a new way of horizontal gene transfer (HGT). The transmission of virulence genes among bacteria has also been well studied; however, it remains unclear whether virulence and drug-resistant genes can be co-transmitted simultaneously. Co-transmission of virulence and drug-resistant genes is essential for the formation and prevalence of CR-HvKP.<br><br>METHODS: First, we isolated OMVs from CR-HvKP by cushioned-density gradient ultracentrifugation (C-DGUC). TEM and DLS were used to examine the morphology and size of bacterial OMVs. OMV-mediated gene transfer in liquid cultures and the acquisition of the carbapenem gene and virulence gene was confirmed using colony-PCR. Antimicrobial susceptibility testing, mCIM and eCIM were conducted for the resistance of transformant. Serum killing assay, assessment of the anti-biofilm effect and galleria mellonella infection model, mucoviscosity assay, extraction and quantification of capsules were verified the virulence of transformant. Pulsed-field gel electrophoresis (PFGE), S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting hybridization confirmed the plasmid of transformant.<br><br>RESULTS: Firstly, OMVs were isolated from CR-HvKP NUHL30457 (K2, ST86). TEM and DLS analyses revealed the spherical morphology of the vesicles. Secondly, our study demonstrated that CR-HvKP delivered genetic material, incorporated DNA within the OMVs, and protected it from degradation by extracellular exonucleases. Thirdly, the vesicular lumen DNA was delivered to the recipient cells after determining the presence of virulence and carbapenem-resistant genes in the CR-HvKP OMVs. Importantly, S1-PFGE and Southern hybridization analysis of the 700603 transformant strain showed that the transformant contained both drug-resistant and virulence plasmids.<br><br>DISCUSSION: In the present study, we aimed to clarify the role of CRHvKP-OMVs in transmitting CR-HvKP among K. pneumoniae. Collectively, our findings provided valuable insights into the evolution of CR-HvKP.}, }
@article {pmid36532424, year = {2022}, author = {Pillay, S and Calderón-Franco, D and Urhan, A and Abeel, T}, title = {Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1066995}, pmid = {36532424}, issn = {1664-302X}, abstract = {The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.}, }
@article {pmid36532220, year = {2022}, author = {Boury, N and Van den Bogaard, MED and Wasendorf, C and Amon, J and Judson, S and Maroushek, SR and Peters, NT}, title = {The Use of a Multimodal Case Study To Illustrate Microbial Genetics, Metabolism, and Evolution: The Emergence of VRSA-1.}, journal = {Journal of microbiology &amp; biology education}, volume = {23}, number = {3}, pages = {}, pmid = {36532220}, issn = {1935-7877}, abstract = {Antibiotic Resistance (ABR) is a global concern and while many students are aware of this issue, many of them are unclear on the mechanisms by which ABR may emerge. The mechanism of horizontal gene transfer is something many students are not familiar with. In this curriculum contribution we present 2 versions of an 'interrupted case study' that is designed as an introduction to horizontal gene transfer for early major students and as a review case for advanced major students in biology and life sciences. The case is based on an authentic patient who developed infections with both methicillin resistant Staphylococcus aureus and vancomycin resistant S. aureus. The interrupted case study is appropriate for small and large groups and engages students while content is introduced in a highly structured way. This type of case study can be done by novice and seasoned instructors and lead to considerable learning gains in both introductory and intermediate microbiology courses.}, }
@article {pmid36528203, year = {2022}, author = {Jaiswal, S and Singh, DK and Shukla, P}, title = {Degradation effectiveness of hexachlorohexane (ϒ-HCH) by bacterial isolate Bacillus cereus SJPS-2, its gene annotation for bioremediation and comparison with Pseudomonas putida KT2440.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {120867}, doi = {10.1016/j.envpol.2022.120867}, pmid = {36528203}, issn = {1873-6424}, abstract = {Contamination of Hexachlorohexane (Lindane) in soil and water has toxic effects due toits persistent nature. In our study, an indigenous HCH (gamma isomer) degrading bacterium viz Bacillus cereus SJPS-2 was isolated from Yamuna river water using enrichment culture method. The growth curve indicated that Bacillus cereus SJPS-2 was able to degrade ϒ-HCH effectively with 80.98% degradation. Further, process was improved by using immobilization using alginate beads which showed enhanced degradation (89.34%). Interestingly, in presence of fructose, the ϒ-HCH degradation was up to 79.24% with exponential growth curve whereas the degradation was only 5.61% in presence of glucose revealing diauxic growth curve. Furthermore, The FTIR results confirmed the potential Lindane degradation capability of Bacillus cereus SJPS-2 and the bonds were recorded at wavelengths viz. 2900-2500 cm-[1], 3300-2800 cm-[1] and 785-540 cm-[1]. Similarity, the GC studies also reconfirmed the degradation potential with retention time (RT) of ethyl acetate and lindane was 2.12 and 11.0 respectively. Further, we studied the metabolic pathway involved for lindane utilization in Bacillus cereus using KEGG-KASS and functional gene annotation through Rapid Annotation using Subsystems Technology (RAST) resulted in the annotation of the lin genes (lin A, lin B, lin C, lin X, lin D, lin E) and respective encoding enzymes. The comparative ϒ-HCH degradation potential of B. cereus and P. putida KT2440 was also evaluated. The island viewer showed the different colors on circular genome indicate the coordinates of genomic islands resulted with some common genomic islands (GEIs) between both bacteria indicating the possibility of horizontal gene transfer at contaminated site or natural environment. These genomic islands (GEIs) contribute in the rearrangement genetic material or to evolve bacteria in stress conditions, as a result the metabolic pathways evolve by formation of catabolic genes. This study establishes the potential of Bacillus cereus SJPS-2 for effectual ϒ-HCH degradation.}, }
@article {pmid36527364, year = {2022}, author = {Knoop, V}, title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erac488}, pmid = {36527364}, issn = {1460-2431}, abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous "errors" that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts would not be altered by site-specific cytidine-to-uridine exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over more than 30 years. Lately this has revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that have lately contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.}, }
@article {pmid36525956, year = {2022}, author = {Liu, HW and Roisné-Hamelin, F and Beckert, B and Li, Y and Myasnikov, A and Gruber, S}, title = {DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.}, journal = {Molecular cell}, volume = {82}, number = {24}, pages = {4727-4740.e6}, doi = {10.1016/j.molcel.2022.11.015}, pmid = {36525956}, issn = {1097-4164}, abstract = {Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.}, }
@article {pmid36525447, year = {2022}, author = {Zou, X and Nguyen, M and Overbeek, J and Cao, B and Davis, JJ}, title = {Classification of bacterial plasmid and chromosome derived sequences using machine learning.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279280}, doi = {10.1371/journal.pone.0279280}, pmid = {36525447}, issn = {1932-6203}, abstract = {Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer-including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements-were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.}, }
@article {pmid36523753, year = {2022}, author = {Alam, M and Bano, N and Upadhyay, TK and Binsuwaidan, R and Alshammari, N and Sharangi, AB and Kaushal, RS and Saeed, M}, title = {Enzymatic Activity and Horizontal Gene Transfer of Heavy Metals and Antibiotic Resistant Proteus vulgaris from Hospital Wastewater: An Insight.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {3399137}, pmid = {36523753}, issn = {1712-9532}, abstract = {Globally, the issue of microbial resistance to medicines and heavy metals is getting worse. There are few reports or data available for Proteus vulgaris (P. vulgaris), particularly in India. This investigation intends to reveal the bacteria's ability to transmit genes and their level of resistance as well. The wastewater samples were taken from several hospitals in Lucknow City, India, and examined for the presence of Gram-negative bacteria that were resistant to antibiotics and heavy metals. The microbial population count in different hospital wastewaters decreases with increasing concentrations of metal and antibiotics. Among all the examined metals, Ni and Zn had the highest viable counts, whereas Hg, Cd, and Co had the lowest viable counts. Penicillin, ampicillin, and amoxicillin, among the antibiotics, demonstrated higher viable counts, whereas tetracycline and erythromycin exhibited lower viable counts. The MIC values for the P. vulgaris isolates tested ranged from 50 to 16,00 μg/ml for each metal tested. The multiple metal resistance (MMR) index, which ranged from 0.04 to 0.50, showed diverse heavy metal resistance patterns in all P. vulgaris isolates (in the case of 2-7 metals in various combinations). All of the tested isolates had methicillin resistance, whereas the least number of isolates had ofloxacin, gentamycin, or neomycin resistance. The P. vulgaris isolates displayed multidrug resistance patterns (2-12 drugs) in various antibiotic combinations. The MAR indexes were shown to be between (0.02-0.7). From the total isolates, 98%, 84%, and 80% had urease, gelatinase, and amylase activity, whereas 68% and 56% displayed protease and beta-lactamase activity. Plasmids were present in all the selected resistant isolates and varied in size from 42.5 to 57.0 kb and molecular weight from 27.2 to 37.0 MD. The transmission of the antibiotic/metal resistance genes was evaluated between a total of 7 pairs of isolates. A higher transfer frequency (4.4 × 10[-1]) was observed among antibiotics, although a lower transfer frequency (1.0 × 10[-2]) was observed against metals in both the media from the entire site tested. According to exponential decay, the population of hospital wastewater declined in the following order across all sites: Site II > Site IV > Site III > Site I for antibiotics and site IV > site II > site I >site III for metal. Different metal and antibiotic concentrations have varying effects on the population. The metal-tolerant P. vulgaris from hospital wastewater was studied in the current study had multiple distinct patterns of antibiotic resistance. It could provide cutting-edge methods for treating infectious diseases, which are essential for managing and assessing the risks associated with hospital wastewater, especially in the case of P. vulgaris.}, }
@article {pmid36261510, year = {2023}, author = {Palomino, A and Gewurz, D and DeVine, L and Zajmi, U and Moralez, J and Abu-Rumman, F and Smith, RP and Lopatkin, AJ}, title = {Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {151-162}, pmid = {36261510}, issn = {1751-7370}, support = {R15 GM143694/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Escherichia coli Infections/microbiology ; Drug Resistance, Microbial/genetics ; Conjugation, Genetic ; Gene Transfer, Horizontal ; }, abstract = {Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.}, }
@article {pmid36522135, year = {2023}, author = {Dorrell, RG and Kuo, A and Füssy, Z and Richardson, EH and Salamov, A and Zarevski, N and Freyria, NJ and Ibarbalz, FM and Jenkins, J and Pierella Karlusich, JJ and Stecca Steindorff, A and Edgar, RE and Handley, L and Lail, K and Lipzen, A and Lombard, V and McFarlane, J and Nef, C and Novák Vanclová, AM and Peng, Y and Plott, C and Potvin, M and Vieira, FRJ and Barry, K and de Vargas, C and Henrissat, B and Pelletier, E and Schmutz, J and Wincker, P and Dacks, JB and Bowler, C and Grigoriev, IV and Lovejoy, C}, title = {Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.}, journal = {Life science alliance}, volume = {6}, number = {3}, pages = {}, doi = {10.26508/lsa.202201833}, pmid = {36522135}, issn = {2575-1077}, abstract = {Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.}, }
@article {pmid36522081, year = {2023}, author = {Fan, X and Su, J and Zhou, S and An, X and Li, H}, title = {Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {508-518}, doi = {10.1016/j.jes.2022.06.006}, pmid = {36522081}, issn = {1001-0742}, abstract = {The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.}, }
@article {pmid36522071, year = {2023}, author = {Yan, X and Liu, W and Wen, S and Wang, L and Zhu, L and Wang, J and Kim, YM and Wang, J}, title = {Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {399-409}, doi = {10.1016/j.jes.2022.06.014}, pmid = {36522071}, issn = {1001-0742}, abstract = {As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10[-5], which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.}, }
@article {pmid36518176, year = {2022}, author = {Cangui-Panchi, SP and Ñacato-Toapanta, AL and Enríquez-Martínez, LJ and Reyes, J and Garzon-Chavez, D and Machado, A}, title = {Biofilm-forming microorganisms causing hospital-acquired infections from intravenous catheter: A systematic review.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100175}, doi = {10.1016/j.crmicr.2022.100175}, pmid = {36518176}, issn = {2666-5174}, abstract = {The high prevalence of nosocomial infections is related to the use of medical insertion devices such as central venous catheters (CVCs). Most of the microorganisms causing nosocomial infections are biofilm producers, this characteristic allows them to adhere to abiotic surfaces and cause initial catheter infections that can lead to bloodstream infections. Our main goal in this systematic review was to evaluate the prevalence of biofilm among CVC-related infections, particularly among Intensive Care Unit (ICU) patients, in the studies applying different in vitro and in vivo methodologies. All studies reporting clinical isolates from patients with catheter-related nosocomial infections and biofilm evaluation published up to 24 June 2022 in the PubMed and Scopus databases were included. Twenty-five studies met the eligibility criteria and were included in this systematic review for analysis. Different methodologies were applied in the assessment of biofilm-forming microorganisms including in vitro assays, catheter-infected in vitro, and in vivo mouse models. The present study showed that between 59 and 100% of clinical isolates were able to form biofilms, and the prevalence rate of biofilm formation varied significantly between studies from different countries and regions. Among the clinical isolates collected in our study set, a wide variety of microorganisms including Gram-positive strains, Gram-negative strains, and Candida albicans were found. Many authors studied resistance mechanisms and genes related to biofilm development and surface adherence properties. In some cases, the studies also evaluated biofilm inhibition assays using various kinds of catheter coatings.}, }
@article {pmid36517909, year = {2022}, author = {Vasco, K and Guevara, N and Mosquera, J and Zapata, S and Zhang, L}, title = {Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {65}, pmid = {36517909}, issn = {2524-4671}, abstract = {BACKGROUND: Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.<br><br>RESULTS: The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.<br><br>CONCLUSION: Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.}, }
@article {pmid36517527, year = {2022}, author = {Dziuba, MV and Paulus, A and Schramm, L and Awal, RP and Pósfai, M and Monteil, CL and Fouteau, S and Uebe, R and Schüler, D}, title = {Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36517527}, issn = {1751-7370}, abstract = {Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.}, }
@article {pmid36516783, year = {2022}, author = {Nishimoto, AT and Dao, TH and Jia, Q and Ortiz-Marquez, JC and Echlin, H and Vogel, P and van Opijnen, T and Rosch, JW}, title = {Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae.}, journal = {Cell reports}, volume = {41}, number = {11}, pages = {111835}, doi = {10.1016/j.celrep.2022.111835}, pmid = {36516783}, issn = {2211-1247}, abstract = {As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.}, }
@article {pmid36515883, year = {2022}, author = {Martins-Silva, P and Dias, CP and Vilar, LC and de Queiroz Silva, S and Rossi, CC and Giambiagi-deMarval, M}, title = {Dispersion and persistence of antimicrobial resistance genes among Staphylococcus spp. and Mammaliicoccus spp. isolated along a swine manure treatment plant.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36515883}, issn = {1614-7499}, abstract = {Staphylococcus spp. and Mammaliicoccus spp. colonize the skin and mucosa of humans and other animals and are responsible for several opportunistic infections. Staphylococci antibiotic resistance may be present in the environment due to the spread of treated and untreated manure from the livestock industry due to antibiotic use to disease control or growth promoter. In this work, we analyzed the species distribution and antimicrobial susceptibility of Staphylococcus and Mammaliicoccus species along different sites of a swine manure treatment plant from Southeastern Brazil. Bacterial colonies were obtained on mannitol salt agar, selected after catalase test and Gram staining, and finally identified by mass spectrometry and sequencing of the tuf gene. According to the results, S.cohnii and S. simulans were the most prevalent species. Antibiotic resistance test revealed that several strains were resistant to multiple drugs, with high levels of chloramphenicol resistance (98%), followed by erythromycin (79%), tetracycline (73%), gentamicin (46%), ciprofloxacin (42%), cefoxitin (18%), sulfamethoxazole + trimethoprim (12%), and linezolid (4%). In addition, gene detection by PCR showed that all strains carried at least 2 resistance genes and one of them carried all 11 genes investigated. Using the GTG5-PCR approach, a high genetic similarity was observed between some strains that were isolated from different points of the treatment plant. Although some were seemingly identical, differences in their resistance phenotype and genotype suggest horizontal gene transfer. The presence of resistant bacteria and resistance genes along the treatment system highlights the potential risk of contamination by people in direct contact with these animals and the soil since the effluent is used as a biofertilizer in the surrounding environment.}, }
@article {pmid36515719, year = {2022}, author = {Almalki, F and Choudhary, M and Azad, RK}, title = {Analysis of multipartite bacterial genomes using alignment free and alignment-based pipelines.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {25}, pmid = {36515719}, issn = {1432-072X}, abstract = {Since the discovery of second chromosome in Rhodobacter sphaeroides 2.4.1 in 1989, multipartite genomes have been reported in over three hundred bacterial species under nine different phyla. This has shattered the unipartite (single chromosome) genome dogma in bacteria. Since then, many questions on various aspects of multipartite genomes in bacteria have been addressed. However, our understanding of how multipartite genomes emerge and evolve is still lacking. Importantly, the knowledge of genetic factors underlying the differences in multipartite and single-chromosome genomes is lacking. In this work, we have performed comparative evolutionary and functional genomics analyses to identify molecular factors that discriminate multipartite from unipartite bacteria, with the goal to decipher taxon-specific factors, and those that are prevalent across the taxa, underlying these traits. We assessed the roles of evolutionary mechanisms, specifically gene gain, in driving the divergence of bacteria with single and multiple chromosomes. In addition, we performed functional genomic analysis to garner support for our findings from comparative evolutionary analysis. We found genes such as those encoding conserved hypothetical proteins in Deinococcus radiodurans R1, and putative phage phi-C31 gp36 major capsid like and hypothetical proteins in Rhodobacter sphaeroides 2.4.1, which are located on accessory chromosomes in these bacteria but were not found in the inferred ancestral sequences, and on the primary chromosomes, as well as were not found in their closest relatives with single chromosome within the same clade. Our study shines a new light on the potential roles of the secondary chromosomes in helping bacteria with multipartite genomes to adapt to specialized environments or growth conditions.}, }
@article {pmid36515529, year = {2022}, author = {Brennan, G and Stoian, AMM and Yu, H and Rahman, MJ and Banerjee, S and Stroup, JN and Park, C and Tazi, L and Rothenburg, S}, title = {Molecular Mechanisms of Poxvirus Evolution.}, journal = {mBio}, volume = {}, number = {}, pages = {e0152622}, doi = {10.1128/mbio.01526-22}, pmid = {36515529}, issn = {2150-7511}, abstract = {Poxviruses are often thought to evolve relatively slowly because they are double-stranded DNA pathogens with proofreading polymerases. However, poxviruses have highly adaptable genomes and can undergo relatively rapid genotypic and phenotypic change, as illustrated by the recent increase in human-to-human transmission of monkeypox virus. Advances in deep sequencing technologies have demonstrated standing nucleotide variation in poxvirus populations, which has been underappreciated. There is also an emerging understanding of the role genomic architectural changes play in shaping poxvirus evolution. These mechanisms include homologous and nonhomologous recombination, gene duplications, gene loss, and the acquisition of new genes through horizontal gene transfer. In this review, we discuss these evolutionary mechanisms and their potential roles for adaption to novel host species and modulating virulence.}, }
@article {pmid36515045, year = {2022}, author = {Oliveira-Tintino, CDM and Muniz, DF and Santos Barbosa, CRD and Silva Pereira, RL and Begnini, IM and Rebelo, RA and da Silva, LE and Mireski, SL and Nasato, MC and Lacowicz Krautler, MI and Barros Oliveira, CV and Pereira, PS and Rodrigues Teixeira, AM and Tintino, SR and de Menezes, IRA and Melo Coutinho, HD and da Silva, TG}, title = {NorA, Tet(K), MepA, and MsrA efflux pumps in Staphylococcus aureus, their inhibitors and 1,8-naphthyridine sulfonamides.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/1381612829666221212101501}, pmid = {36515045}, issn = {1873-4286}, abstract = {Antibiotic resistance can be characterized, in biochemical terms, as an antibiotic's inability to reach its bacterial target at a concentration that was previously effective. Microbial resistance to different agents can be intrinsic or acquired. Intrinsic resistance occurs due to inherent functional or structural characteristics of the bacteria, such as antibiotic-inactivating enzymes, nonspecific efflux pumps, and permeability barriers. On the other hand, bacteria can acquire resistance mechanisms via horizontal gene transfer in mobile genetic elements such as plasmids. Acquired resistance mechanisms include another category of efflux pumps with more specific substrates, which are plasmid-encoded. Efflux pumps are considered one of the main mechanisms of bacterial resistance to antibiotics and biocides, presenting themselves as integral membrane transporters. They are essential in both bacterial physiology and defense and are responsible for exporting structurally diverse substrates, falling into the following main families: ATP-binding cassette (ABC), multidrug and toxic compound extrusion (MATE), major facilitator superfamily (MFS), small multidrug resistance (SMR) and resistance-nodulation-cell division (RND). The Efflux pumps NorA and Tet(K) of the MFS family, MepA of the MATE family, and MsrA of the ABC family are some examples of specific efflux pumps that act in the extrusion of antibiotics. In this review, we address bacterial efflux pump inhibitors (EPIs), including 1,8-naphthyridine sulfonamide derivatives, given the pre-existing knowledge about the chemical characteristics that favor their biological activity. The modification and emergence of resistance to new EPIs justify further research on this theme, aiming to develop efficient compounds for clinical use.}, }
@article {pmid36512900, year = {2022}, author = {Puxty, RJ and Millard, AD}, title = {Functional ecology of bacteriophages in the environment.}, journal = {Current opinion in microbiology}, volume = {71}, number = {}, pages = {102245}, doi = {10.1016/j.mib.2022.102245}, pmid = {36512900}, issn = {1879-0364}, abstract = {Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.}, }
@article {pmid36511859, year = {2022}, author = {Kim, SK and Kim, H and Woo, SG and Kim, TH and Rha, E and Kwon, KK and Lee, H and Lee, SG and Lee, DH}, title = {CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1104}, pmid = {36511859}, issn = {1362-4962}, abstract = {Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.}, }
@article {pmid36511824, year = {2022}, author = {Chao, L and Li, Y and Chen, Y and Chen, XX and Huang, J and Rokas, A and Shen, XX}, title = {How has HGT shaped the evolution of insect genomes?.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16311}, pmid = {36511824}, issn = {1462-2920}, abstract = {As the most diverse group of animals on Earth, insects are key organisms in ecosystems. Horizontal gene transfer (HGT) refers to the transfer of genetic material between species by non-reproductive means. HGT is a major evolutionary force in prokaryotic genome evolution, but its importance in different eukaryotic groups, such as insects, has only recently begun to be understood. Genomic data from hundreds of insect species have enabled the detection of large numbers of HGT events and the elucidation of the functions of some of these foreign genes. Although quantification of the extent of HGT in insects broadens our understanding of its role in insect evolution, the scope of its influence and underlying mechanism(s) of its occurrence remain open questions for the field.}, }
@article {pmid36507660, year = {2022}, author = {Zheng, J and Liang, JL and Jia, P and Feng, SW and Lu, JL and Luo, ZH and Ai, HX and Liao, B and Li, JT and Shu, WS}, title = {Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0073622}, doi = {10.1128/msystems.00736-22}, pmid = {36507660}, issn = {2379-5077}, abstract = {Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km[2] in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.}, }
@article {pmid36507655, year = {2022}, author = {Guan, Y and Ma, L and Wang, Q and Zhao, J and Wang, S and Wu, J and Liu, Y and Sun, H and Huang, J}, title = {Horizontally acquired fungal killer protein genes affect cell development in mosses.}, journal = {The Plant journal : for cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/tpj.16060}, pmid = {36507655}, issn = {1365-313X}, abstract = {The moss Physcomitrium patens is crucial for studying plant development and evolution. Although it has been known that the P. patens genome includes genes acquired from bacteria, fungi and viruses, the functions and evolutionary significance of these acquired genes remain largely unclear. Killer protein 4 (KP4) is a well-studied toxin secreted by ascomycete fungi, such as the corn smut Ustilago maydis, that inhibits the growth of sensitive target strains by blocking their calcium uptake. Here we show that KP4 genes in mosses were acquired from fungi through at least three independent events of horizontal gene transfer (HGT). Two paralogous copies of KP4 (PpKP4-1 and PpKP4-2) exist in P. patens. Knockout mutants ppkp4-1 and ppkp4-2 showed cell death at protonemal stage, and ppkp4-2 also exhibited defects in tip growth. We provide experimental evidence that PpKP4-1/2 affects P. patens protonemal cell development by mediating cytoplasmic calcium and that KP4 genes are functionally conserved between P. patens and fungi. This study provides additional insights into the role of HGT in land plant development and evolution.}, }
@article {pmid36506112, year = {2023}, author = {Alvarez-Molina, A and Trigal, E and Prieto, M and López, M and Alvarez-Ordóñez, A}, title = {Assessment of a plasmid conjugation procedure to monitor horizontal transfer of an extended-spectrum β-lactamase resistance gene under food chain scenarios.}, journal = {Current research in food science}, volume = {6}, number = {}, pages = {100405}, pmid = {36506112}, issn = {2665-9271}, abstract = {Plasmids are relevant reservoirs of antimicrobial resistance genes (ARGs) which confer adaptive advantages to their host and can be horizontally transferred. The aims of this study were to develop a conjugation procedure to monitor the horizontal transfer of a 193 kb plasmid containing the extended-spectrum β-lactamase production gene bla CTX-M-14 between two Escherichia coli strains under a range of food chain-related scenarios, including temperature (20-37 °C), pH (5.0-9.0) or the presence of some biocidal agents (benzalkonium chloride, sodium hypochlorite or peracetic acid). The average conjugation rate in LB broth after 18 h at 37 °C was 2.09e-04 and similar rates were observed in a food matrix (cow's milk). The conjugation was reduced at temperatures below 37 °C, at alkaline pH (especially at pH 9.0) or in the presence of benzalkonium chloride. Peracetic acid and sodium hypochlorite slightly increased conjugation rates, which reached 5.59e-04 and 6.77e-03, respectively. The conjugation procedure described can be used to identify risk scenarios leading to an enhanced ARGs transmission via plasmid conjugation, as well as to identify novel intervention strategies impairing plasmid conjugation and tackling antimicrobial resistance.}, }
@article {pmid36503799, year = {2023}, author = {Wang, S and Li, S and Du, D and Abass, OK and Nasir, MS and Yan, W}, title = {Stimulants and donors promote megaplasmid pND6-2 horizontal gene transfer in activated sludge.}, journal = {Journal of environmental sciences (China)}, volume = {126}, number = {}, pages = {742-753}, doi = {10.1016/j.jes.2022.03.011}, pmid = {36503799}, issn = {1001-0742}, abstract = {The activated sludge process is characterized by high microbial density and diversity, both of which facilitate antibiotic resistance gene transfer. Many studies have suggested that antibiotic and non-antibiotic drugs at sub-inhibitory concentrations are major inducers of conjugative gene transfer. The self-transmissible plasmid pND6-2 is one of the endogenous plasmids harbored in Pseudomonas putida ND6, which can trigger the transfer of another co-occurring naphthalene-degrading plasmid pND6-1. Therefore, to illustrate the potential influence of stimulants on conjugative transfer of pND6-2, we evaluated the effects of four antibiotics (ampicillin, gentamycin, kanamycin, and tetracycline) and naphthalene, on the conjugal transfer efficiency of pND6-2 by filter-mating experiment. Our findings demonstrated that all stimulants within an optimal dose promoted conjugative transfer of pND6-2 from Pseudomonas putida GKND6 to P. putida KT2440, with tetracycline being the most effective (100 µg/L and 10 µg/L), as it enhanced pND6-2-mediated intra-genera transfer by approximately one hundred-fold. Subsequently, seven AS reactors were constructed with the addition of donors and different stimulants to further elucidate the conjugative behavior of pND6-2 in natural environment. The stimulants positively affected the conjugal process of pND6-2, while donors reshaped the host abundance in the sludge. This was likely because stimulant addition enhanced the expression levels of conjugation transfer-related genes. Furthermore, Blastocatella and Chitinimonas were identified as the potential receptors of plasmid pND6-2, which was not affected by donor types. These findings demonstrate the positive role of sub-inhibitory stimulant treatment on pND6-2 conjugal transfer and the function of donors in re-shaping the host spectrum of pND6-2.}, }
@article {pmid36502290, year = {2022}, author = {Kinateder, T and Drexler, L and Straub, K and Merkl, R and Sterner, R}, title = {Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis.}, journal = {Protein science : a publication of the Protein Society}, volume = {}, number = {}, pages = {e4536}, doi = {10.1002/pro.4536}, pmid = {36502290}, issn = {1469-896X}, abstract = {The conservation of fold and chemistry of the enzymes associated with histidine biosynthesis suggests that this pathway evolved prior to the diversification of Bacteria, Archaea, and Eukaryotes. The only exception is the histidinol phosphate phosphatase (HolPase). So far, non-homologous HolPases that possess distinct folds and belong to three different protein superfamilies have been identified in various phylogenetic clades. However, their evolution has remained unknown to date. Here, we analyzed the evolutionary history of the HolPase from γ-Proteobacteria (HisB-N). It has been argued that HisB-N and its closest homologue d-glycero-d-manno-heptose-1,7-bisphosphate 7-phosphatase (GmhB) have emerged from the same promiscuous ancestral phosphatase. GmhB variants catalyze the hydrolysis of the anomeric d-glycero-d-manno-heptose-1,7-bisphosphate (αHBP or βHBP) with a strong preference for one anomer (αGmhB or βGmhB). We found that HisB-N from Escherichia coli shows promiscuous activity for βHBP but not αHBP, while βGmhB from Crassaminicella sp. shows promiscuous activity for HolP. Accordingly, a combined phylogenetic tree of αGmhBs, βGmhBs, and HisB-N sequences revealed that HisB-Ns form a compact sub-cluster derived from βGmhBs. Ancestral sequence reconstruction and in vitro analysis revealed a promiscuous HolPase activity in the resurrected enzymes prior to functional divergence of the successors. The following increase in catalytic efficiency of the HolP turnover is reflected in the shape and electrostatics of the active site predicted by AlphaFold. An analysis of the phylogenetic tree led to a revised evolutionary model that proposes the horizontal gene transfer of a promiscuous βGmhB from δ- to γ-Proteobacteria where it evolved to the modern HisB-N. This article is protected by copyright. All rights reserved.}, }
@article {pmid36498841, year = {2022}, author = {Carpanzano, S and Santorsola, M and Nf-Core Community,  and Lescai, F}, title = {hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, doi = {10.3390/ijms232314512}, pmid = {36498841}, issn = {1422-0067}, abstract = {Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role in evolution, and has functional consequences in insects and plants. However, less is known about HGT in humans. Studies have reported bacterial integrations in cancer patients, and microbial sequences have been detected in data from well-known human sequencing projects. Few of the existing tools for investigating HGT are highly automated. Thanks to the adoption of Nextflow for life sciences workflows, and to the standards and best practices curated by communities such as nf-core, fully automated, portable, and scalable pipelines can now be developed. Here we present nf-core/hgtseq to facilitate the analysis of HGT from sequencing data in different organisms. We showcase its performance by analysing six exome datasets from five mammals. Hgtseq can be run seamlessly in any computing environment and accepts data generated by existing exome and whole-genome sequencing projects; this will enable researchers to expand their analyses into this area. Fundamental questions are still open about the mechanisms and the extent or role of horizontal gene transfer: by releasing hgtseq we provide a standardised tool which will enable a systematic investigation of this phenomenon, thus paving the way for a better understanding of HGT.}, }
@article {pmid36495587, year = {2022}, author = {Farghaly, M and Hynes, MF and Nazari, M and Checkley, SL and Liljebjelke, K}, title = {Examination of the horizontal gene transfer dynamics of an integrative and conjugative element encoding multi-drug resistance in Histophilus somni.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2021-0349}, pmid = {36495587}, issn = {1480-3275}, abstract = {Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer (HGT). A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72,914 base-pairs in length and harbours seven predicted antimicrobial resistance genes (ARG) conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycoside (APH(3'')-Ib), (APH(6)-Id), (APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to Histophilus somni and Pasteurella multocida strains. PCR assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ~ 37-fold after tetracycline exposure, and ~ 4-fold after ciprofloxacin treatment. Acquisition of ICEHs02 reduced relative fitness of H. somni transconjugants by 28% (w = 0.72 ± 0.04) and P. multocida TG relative fitness was decreased 15% (w = 0.85 ± 0.01).}, }
@article {pmid36495352, year = {2022}, author = {Kim, J and Cha, IT and Lee, KE and Son, YK and Yu, J and Seol, D}, title = {Characteristics and adaptability of Flavobacterium panici BSSL-CR3 in tidal flat revealed by comparative genomic and enzymatic analysis.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {22}, pmid = {36495352}, issn = {1432-072X}, abstract = {Tidal flat microbes play an important ecological role by removing organic pollutants and providing an energy source. However, bacteria isolated from tidal flats and their genomes have been scarcely reported, making it difficult to elucidate which genes and pathways are potentially involved in the above roles. In this study, strain BSSL-CR3, the third reported species among the tidal flat Flavobacterium was analyzed using whole-genome sequencing to investigate its adaptability and functionality in tidal flats. BSSL-CR3 is comprised of a circular chromosome of 5,972,859 bp with a GC content of 33.84%. Genome annotation and API ZYM results showed that BSSL-CR3 has a variety of secondary metabolic gene clusters and enzyme activities including α-galactosidase. BSSL-CR3 had more proteins with a low isoelectric point (pI) than terrestrial Flavobacterium strains, and several genes related to osmotic regulation were found in the genomic island (GI). Comparative genomic analysis with other tidal flat bacteria also revealed that BSSL-CR3 had the largest number of genes encoding Carbohydrate Active EnZymes (CAZymes) which are related to algae degradation. This study will provide insight into the adaptability of BSSL-CR3 to the tidal flats and contribute to facilitating future comparative analysis of bacteria in tidal flats.}, }
@article {pmid36472431, year = {2022}, author = {Brown, P and Kucerova, Z and Gorski, L and Chen, Y and Ivanova, M and Leekitcharoenphon, P and Parsons, C and Niedermeyer, J and Jackson, J and Kathariou, S}, title = {Horizontal Gene Transfer and Loss of Serotype-Specific Genes in Listeria monocytogenes Can Lead to Incorrect Serotype Designations with a Commonly-Employed Molecular Serotyping Scheme.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0274522}, doi = {10.1128/spectrum.02745-22}, pmid = {36472431}, issn = {2165-0497}, abstract = {Listeria monocytogenes is a Gram-positive, facultative intracellular foodborne pathogen capable of causing severe, invasive illness (listeriosis). Three serotypes, 1/2a, 1/2b, and 4b, are leading contributors to human listeriosis, with 4b including the major hypervirulent clones. The multiplex PCR scheme developed by Doumith and collaborators employs primers targeting specific lineages (e.g., lineage II-specific lmo0737, lineage I-specific LMOf2365_2059) or serotypes (e.g., serotype 4b-specific LMOf2365_1900). The Doumith scheme (DS) is extensively employed for molecular serotyping of L. monocytogenes due to its high accuracy, relative ease, and affordability. However, for certain strains, the DS serotype designations are in conflict with those relying on antibody-based schemes or whole-genome sequence (WGS) analysis. In the current study, all 27 tested serotype 4b strains with sequence type 782 (ST782) within the hypervirulent clonal complex 2 (CC2) were designated 1/2b/3b using the DS. These strains lacked the serotype 4b-specific gene LMOf2365_1900, while retaining LMOf2365_2059, which, together with prs, yields the DS 1/2b/3b profile. Furthermore, 15 serotype 1/2a strains of four STs, mostly from water, were designated 1/2b/3b using the DS. These strains lacked the lmo0737 cassette but harbored genomic islands with LMOf2365_2059, thus yielding the DS 1/2b/3b profile. Lastly, we investigated a novel, dual 1/2a-1/2b profile obtained using the DS with 21 serotype 1/2a strains of four STs harboring both the lmo0737 cassette and genomic islands with LMOf2365_2059. The findings suggest that for certain strains and clones of L. monocytogenes the DS designations should be viewed with caution and complemented with alternative tools, e.g., traditional serotyping or WGS analysis. IMPORTANCE Listeria monocytogenes is a foodborne pathogen responsible for severe illness (listeriosis), especially in pregnant women and their fetuses, immunocompromised individuals, and the elderly. Three serotypes, 1/2a, 1/2b, and 4b, account for most human listeriosis, with certain serotype 4b clonal complexes (CCs) overrepresented in human disease. Serotyping remains extensively employed in Listeria epidemiologic investigations, and a multiplex PCR-based serotyping scheme is widely used. However, the PCR gene targets can be lost or gained via horizontal gene transfer, leading to novel PCR profiles without known serotype designations or to incorrect serotype assignments. Thus, an entire serotype 4b clone of the hypervirulent CC2 would be misidentified as serotype 1/2b, and several strains of serotype 1/2a would be identified as serotype 1/2b. Such challenges are especially common in novel clones from underexplored habitats, e.g., wildlife and surface water. The findings suggest caution in application of molecular serotyping, while highlighting Listeria's diversity and potential for horizontal gene transfer.}, }
@article {pmid36471715, year = {2022}, author = {Wen, Y and Xie, X and Xu, P and Yang, C and Zhu, Z and Zhu, J and Lv, J and Zhang, H and Chen, L and Du, H}, title = {NDM-1 and OXA-48-Like Carbapenemases (OXA-48, OXA-181 and OXA-252) Co-Producing Shewanella xiamenensis from Hospital Wastewater, China.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6927-6938}, pmid = {36471715}, issn = {1178-6973}, abstract = {BACKGROUND: Shewanella genus, as an important carrier of resistance genes, has the potential to transmit resistance to many antimicrobials in many circumstances, especially in aquatic environment. The aim of the study was to describe the risk of Shewanella xiamenensis in hospital environment through analysis of genomic comparison and resistance status.<br><br>METHODS: Seven S. xiamenensis strains were isolated from hospital wastewater. PCR and Sanger sequencing were carried out for detection of common carbapenemase genes. Antimicrobial susceptibility testing was performed to determine the antimicrobial profile. Whole genome sequencing was applied, and sequences were further used for genomic analysis.<br><br>RESULTS: Seven Shewanella xiamenensis were all positive for bla NDM and bla OXA-48. Antimicrobial susceptibility testing showed all Shewanella xiamenensis were resistant to cefotaxime, ceftazidime, imipenem, meropenem, gentamycin and trimethoprim-sulfamethoxazole. Whole genome sequencing and phylogenetic analysis demonstrated the diversity of Shewanella xiamenensis despite isolating from one wastewater pool.<br><br>CONCLUSION: To the best of our knowledge, this is the first report of detection of three types bla OXA-48-like genes in one hospital in China. And we have detected multi-drug resistant S. xiamenensis from hospital wastewater. This emphasizes that the presence of naturally existing carbapenemases in the environment may be significantly overlooked and that the bla OXA-48-like genes in China may originate through the horizontal gene transfer from S. xiamenensis to Enterobacterales rather than import from other countries.}, }
@article {pmid36462475, year = {2022}, author = {Huang, Y and Wen, X and Li, J and Niu, Q and Tang, A and Li, Q}, title = {Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120795}, doi = {10.1016/j.envpol.2022.120795}, pmid = {36462475}, issn = {1873-6424}, abstract = {In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.}, }
@article {pmid36458228, year = {2022}, author = {Lal, D and Pandey, H and Lal, R}, title = {Phylogenetic Analyses of Microbial Hydrolytic Dehalogenases Reveal Polyphyletic Origin.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {651-657}, pmid = {36458228}, issn = {0046-8991}, abstract = {UNLABELLED: Hydrolytic dehalogenases form an important class of dehalogenases that include haloacid dehalogenase, haloalkane dehalogenase, haloacetate dehalogenase, and atrazine chlorohydrolase. These enzymes are involved in biodegradation of various environmental pollutants and therefore it is important to understand their phylogeny. In the present study, it was found that the enzymes haloalkane and haloacetate dehalogenases share a common ancestry with enzymes such as carboxyesterase, epoxide hydrolase, and lipases, which can be traced to ancestral α/β hydrolase fold enzyme. Haloacid dehalogenases and atrazine chlorohydrolases have probabaly evolved from ancestral enzymes with phosphatase and deaminases activity, respectively. These findings were supported by the similarities in the secondary structure, key catalytic motifs and placement of catalytic residues. The phylogeny of haloalkane dehalogenases and haloacid dehalogenases differs from 16S rRNA gene phylogeny, suggesting spread through horizontal gene transfer. Hydrolytic dehalogenases are polyphyletic and do not share a common evolutionay history, the functional similarities are due to convergent evolution. The present study also identifies key functional residues, mutating which, can help in generating better enzymes for clean up of the persistent environmental pollutants using enzymatic bioremediation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01043-8.}, }
@article {pmid36456543, year = {2022}, author = {Gaines, MC and Isupov, MN and Sivabalasarma, S and Haque, RU and McLaren, M and Mollat, CL and Tripp, P and Neuhaus, A and Gold, VAM and Albers, SV and Daum, B}, title = {Electron cryo-microscopy reveals the structure of the archaeal thread filament.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7411}, pmid = {36456543}, issn = {2041-1723}, mesh = {Cryoelectron Microscopy ; *Archaea ; *Electrons ; Cytoskeleton ; Software ; }, abstract = {Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism.}, }
@article {pmid36455559, year = {2022}, author = {Ruan, C and Ramoneda, J and Gogia, G and Wang, G and Johnson, DR}, title = {Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2022.11.009}, pmid = {36455559}, issn = {1879-0445}, abstract = {The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.}, }
@article {pmid36455257, year = {2022}, author = {Zhang, X and Yao, MC and Chen, L and Sheng, GP}, title = {Lewis Acid-Base Interaction Triggering Electron Delocalization to Enhance the Photodegradation of Extracellular Antibiotic Resistance Genes Adsorbed on Clay Minerals.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c05785}, pmid = {36455257}, issn = {1520-5851}, abstract = {The transformation of extracellular antibiotic resistance genes (eARGs) is largely influenced by their inevitable photodegradation in environments where they tend to be adsorbed by ubiquitous clay minerals instead of being in a free form. However, the photodegradation behaviors and mechanisms of the adsorbed eARGs may be quite different from those of the free form and still remain unclear. Herein, we found that kaolinite, a common 1:1-type clay, markedly enhanced eARG photodegradation and made eARGs undergo direct photodegradation under UVA. The decrease in the transformation efficiency of eARGs caused by photodegradation was also promoted. Spectroscopy methods combined with density functional theory calculations revealed that the Lewis acid-base interaction between P-O in eARGs and Al-OH on kaolinite delocalized electrons of eARGs, thus resulting in increased photon absorption ability of eARGs. This ultimately led to enhanced photodegradation of kaolinite-adsorbed eARGs. Additionally, divalent Ca[2+] could reduce the Lewis acid-base interaction-mediated adsorption of eARGs by kaolinite, thereby weakening the enhanced photodegradation of eARGs caused by electron delocalization. In contrast, the 2:1-type clay montmorillonite without strong Lewis acid sites was unable to delocalize the electrons to enhance the photodegradation of eARGs. This work allowed us to better evaluate eARGs' fate and risk in real aqueous environments.}, }
@article {pmid36451580, year = {2022}, author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A}, title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16292}, pmid = {36451580}, issn = {1462-2920}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.}, }
@article {pmid36451084, year = {2022}, author = {Jones, CT and Susko, E and Bielawski, JP}, title = {Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {140}, pmid = {36451084}, issn = {2730-7182}, mesh = {*Gene Transfer, Horizontal ; *RNA ; Referral and Consultation ; }, abstract = {BACKGROUND: The number of interactions between a transferable gene or its protein product and genes or gene products native to its microbial host is referred to as connectivity. Such interactions impact the tendency of the gene to be retained by evolution following horizontal gene transfer (HGT) into a microbial population. The complexity hypothesis posits that the protein product of a transferable gene with lower connectivity is more likely to function in a way that is beneficial to a new microbial host compared to the protein product of a transferable gene with higher connectivity. A gene with lower connectivity is consequently more likely to be fixed in any microbial population it enters by HGT. The more recently proposed simplicity hypothesis posits that the connectivity of a transferable gene might increase over time within any single microbial population due to gene-host coevolution, but that differential rates of colonization of microbial populations by HGT in accordance with differences in connectivity might act to counter this and even reduce connectivity over time, comprising an evolutionary trade-off.<br><br>RESULTS: We present a theoretical model that can be used to predict the conditions under which gene-host coevolution might increase or decrease the connectivity of a transferable gene over time. We show that the opportunity to enter new microbial populations by HGT can cause the connectivity of a transferable gene to evolve toward lower values, particularly in an environment that is unstable with respect to the function of the gene's protein product. We also show that a lack of such opportunity in a stable environment can cause the connectivity of a transferable gene to evolve toward higher values.<br><br>CONCLUSION: Our theoretical model suggests that the connectivity of a transferable gene can change over time toward higher values corresponding to a more sessile state of lower transferability or lower values corresponding to a more itinerant state of higher transferability, depending on the ecological milieu in which the gene exists. We note, however, that a better understanding of gene-host coevolutionary dynamics in natural microbial systems is required before any further conclusions about the veracity of the simplicity hypothesis can be drawn.}, }
@article {pmid36448285, year = {2022}, author = {Hao, C and Dewar, AE and West, SA and Ghoul, M}, title = {Gene transferability and sociality do not correlate with gene connectivity.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1987}, pages = {20221819}, doi = {10.1098/rspb.2022.1819}, pmid = {36448285}, issn = {1471-2954}, support = {834164/ERC_/European Research Council/International ; }, mesh = {*Social Behavior ; *Gene Transfer, Horizontal ; Prokaryotic Cells ; RNA ; }, abstract = {The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.}, }
@article {pmid36447017, year = {2022}, author = {Nieuwenhuis, M and Groeneveld, J and Aanen, DK}, title = {Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA.}, journal = {Current genetics}, volume = {}, number = {}, pages = {}, pmid = {36447017}, issn = {1432-0983}, abstract = {Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.}, }
@article {pmid36446404, year = {2022}, author = {Sengupta, S and Azad, RK}, title = {Reconstructing horizontal gene flow network to understand prokaryotic evolution.}, journal = {Open biology}, volume = {12}, number = {11}, pages = {220169}, pmid = {36446404}, issn = {2046-2441}, mesh = {*Gene Flow ; Phylogeny ; *Prokaryotic Cells ; Gene Regulatory Networks ; Computational Biology ; }, abstract = {Horizontal gene transfer (HGT) is a major source of phenotypic innovation and a mechanism of niche adaptation in prokaryotes. Quantification of HGT is critical to decipher its myriad roles in microbial evolution and adaptation. Advances in genome sequencing and bioinformatics have augmented our ability to understand the microbial world, particularly the direct or indirect influence of HGT on diverse life forms. Methods for detecting HGT can be classified into phylogenetic-based and parametric or composition-based approaches. Here, we exploited the complementary strengths of both the approaches to construct a high confidence horizontal gene flow network. Our network is unique in its ability to detect the transfer of native genes of a genome to genomes from other taxa, thus establishing donor and recipient organisms (taxa), rather than through a post hoc analysis as is the practice with several other approaches. The scale-free horizontal gene flow network presented here provides new insights into modes of transfer for the exchange of genetic information and also illuminates differential gene flow across phyla.}, }
@article {pmid36445094, year = {2022}, author = {Yu, Y and Cheng, W and Chen, X and Guo, Q and Cao, H}, title = {Cyanobacterial Blooms Are Not a Result of Positive Selection by Freshwater Eutrophication.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0319422}, doi = {10.1128/spectrum.03194-22}, pmid = {36445094}, issn = {2165-0497}, abstract = {Long-standing cyanobacterial harmful algal blooms (CyanoHABs) are known to result from synergistic interaction between elevated nutrients and superior ecophysiology of cyanobacteria. However, it remains to be determined whether CyanoHABs are a result of positive selection by eutrophic waters. To address this, we conducted molecular evolutionary analyses on the genomes of 9 bloom-forming cyanobacteria, combined with pangenomics and metatranscriptomics. The results showed no positive selection by water eutrophication. Instead, all homologous genes in the species are under strong purifying selection based on the ratio of divergence at nonsynonymous and synonymous sites (dN/dS) and phylogeny. The dN/dS < 0.85 (median = 0.3) for all homologous genes are similar between the genes in the pathways driving CyanoHABs and housekeeping functions. Phylogenetic support for non-positive selection comes from the mixed clustering of strains: strains of the same species from diverse geographic origins form the same clusters, while strains from the same origins form different clusters. Further support lies in the codon adaptation index (CAI) and single nucleotide polymorphism (SNP). The CAI ranged from 0.42 to 0.9 (mean = 0.75), which indicates high-level codon usage bias; the pathways for CyanoHABs and housekeeping functions showed a similar CAI. Interestingly, CAI was negatively correlated with gene expression in 3 metatranscriptomes. The numbers of SNPs were concentrated around 5 to 50. As the SNP number increases, the gene expression level decreases. These negative correlations agree with the population-level dN/dS and phylogeny in supporting purifying selection in bloom-forming cyanobacteria. In summary, superior ecophysiology appears to be acquired prior to water eutrophication. IMPORTANCE CyanoHABs are global environmental hazards, and their mechanisms of action are being intensively investigated. On an ecological scale, CyanoHABs are consequences of synergistic interactions between biological functions and elevated nutrients in eutrophic waters. On an evolutionary scale, one important question is how bloom-forming cyanobacteria acquire these superior biological functions. There are several possibilities, including adaptive evolution and horizontal gene transfer. Here, we explored the possibility of positive selection. We reasoned that there are two possible periods for cyanobacteria to acquire these functions: before the onset of water eutrophication or during water eutrophication. Either way, there should be molecular signatures in protein sequences for positive selection. Interestingly, we found no positive selection by water eutrophication, but strong purifying selection instead on nearly all the genes, suggesting these superior functions aiding CyanoHABs are acquired prior to water eutrophication.}, }
@article {pmid36443412, year = {2022}, author = {Ekhlas, D and Soro, AB and Leonard, FC and Manzanilla, EG and Burgess, CM}, title = {Examining the impact of zinc on horizontal gene transfer in Enterobacterales.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20503}, pmid = {36443412}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Gene Transfer, Horizontal ; Zinc/pharmacology ; *Gammaproteobacteria ; Conjugation, Genetic ; Ampicillin ; Escherichia coli/genetics ; }, abstract = {Antimicrobial resistance is one of the main international health concerns for humans, animals, and the environment, and substantial efforts have focused on reducing its development and spread. While there is evidence for correlations between antimicrobial usage and antimicrobial resistance development, specific information on the effect of heavy metal/antimicrobial usage on bacterial conjugation is more limited. The aim of this study was to investigate the effects of zinc and antimicrobials in different concentrations on horizontal gene transfer of an ampicillin resistance gene, using a multi-drug resistant Escherichia coli donor strain and three different Salmonella enterica serovars as recipient strains. Differences in conjugation frequencies for the different Salmonella recipients were observed, independent of the presence of zinc or the antimicrobials. Selective pressure on the recipient strains, in the form of ampicillin, resulted in a decrease in conjugation frequencies, while, the presence of rifampicin resulted in increases. Zinc exposure affected conjugation frequencies of only one of the three recipient strains, thus the effect of zinc on conjugation frequencies seemed to be concentration and strain dependent. Furthermore, differences in growth rates due to plasmid carriage were observed for one of the Salmonella strains.}, }
@article {pmid36442505, year = {2022}, author = {Ares-Arroyo, M and Coluzzi, C and P C Rocha, E}, title = {Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac1079}, pmid = {36442505}, issn = {1362-4962}, abstract = {Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.}, }
@article {pmid36439225, year = {2022}, author = {Hosseini-Giv, N and Basas, A and Hicks, C and El-Omar, E and El-Assaad, F and Hosseini-Beheshti, E}, title = {Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {962216}, pmid = {36439225}, issn = {2235-2988}, mesh = {Humans ; Anti-Bacterial Agents/metabolism ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; *Extracellular Vesicles/metabolism ; *Neoplasms/therapy/metabolism ; }, abstract = {Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.}, }
@article {pmid36437887, year = {2023}, author = {Adyari, B and Hou, L and Zhang, L and Chen, N and Ju, F and Zhu, L and Yu, CP and Hu, A}, title = {Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome.}, journal = {Environmental science and ecotechnology}, volume = {13}, number = {}, pages = {100223}, pmid = {36437887}, issn = {2666-4984}, abstract = {Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.}, }
@article {pmid36436581, year = {2022}, author = {Cuetero-Martínez, Y and Flores-Ramírez, A and De Los Cobos-Vasconcelos, D and Aguirre-Garrido, JF and López-Vidal, Y and Noyola, A}, title = {Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137383}, doi = {10.1016/j.chemosphere.2022.137383}, pmid = {36436581}, issn = {1879-1298}, abstract = {Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.}, }
@article {pmid36436244, year = {2023}, author = {Sun, W and Qian, X and Wang, X and Gu, J}, title = {Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion.}, journal = {Journal of environmental management}, volume = {326}, number = {Pt B}, pages = {116864}, doi = {10.1016/j.jenvman.2022.116864}, pmid = {36436244}, issn = {1095-8630}, mesh = {Cattle ; Animals ; *Manure/analysis ; *Anti-Bacterial Agents/pharmacology/metabolism ; Enrofloxacin/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.}, }
@article {pmid36425127, year = {2022}, author = {Memili, A and Kutchy, N and Braimah, OA and Morenikeji, OB}, title = {Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci.}, journal = {Veterinary world}, volume = {15}, number = {10}, pages = {2407-2413}, pmid = {36425127}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis.<br><br>MATERIALS AND METHODS: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro.<br><br>RESULTS: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium.<br><br>CONCLUSION: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies.}, }
@article {pmid36425042, year = {2022}, author = {Andersson, T and Makenga, G and Francis, F and Minja, DTR and Overballe-Petersen, S and Tang, ME and Fuursted, K and Baraka, V and Lood, R}, title = {Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1049110}, pmid = {36425042}, issn = {1664-302X}, abstract = {Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with bla CTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.}, }
@article {pmid36423222, year = {2022}, author = {Balparda, M and Schmitz, J and Duemmel, M and Wuthenow, IC and Schmidt, M and Alseekh, S and Fernie, AR and Lercher, MJ and Maurino, VG}, title = {Two plant glyoxalase systems with different evolutionary origins detoxify diverse reactive carbonyl species.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/plphys/kiac526}, pmid = {36423222}, issn = {1532-2548}, abstract = {Reactive carbonyl species (RCS) such as methylglyoxal (MGO) and glyoxal (GO) are highly reactive, unwanted side-products of cellular metabolism maintained at harmless intracellular levels by specific scavenging mechanisms. MGO and GO are metabolized through the glyoxalase (GLX) system, which consists of two enzymes acting in sequence, GLXI and GLXII. While plant genomes encode a number of different GLX isoforms, their specific functions and how they arose during evolution are unclear. Here, we used Arabidopsis (Arabidopsis thaliana) as a model species to investigate the evolutionary history of GLXI and GLXII in plants and whether the GLX system can protect plant cells from the toxicity of RCS other than MGO and GO. We show that plants possess two GLX systems of different evolutionary origins and with distinct structural and functional properties. The first system is shared by all eukaryotes, scavenges MGO and GO, especially during seedling establishment, and features Zn2+-type GLXI proteins with a metal co-factor preference that were present in the last eukaryotic common ancestor. GLXI and GLXII of the second system, featuring Ni2+-type GLXI, were acquired by the last common ancestor of Viridiplantae through horizontal gene transfer from proteobacteria and can together metabolize keto-D-glucose (KDG, glucosone), a glucose-derived RCS, to D-gluconate. When plants displaying loss-of-function of a Viridiplantae-specific GLXI were grown in KDG, D-gluconate levels were reduced to 10-15% of those in the wild type, while KDG levels showed an increase of 48-67%. In contrast to bacterial GLXI homologs, which are active as dimers, plant Ni2+-type GLXI proteins contain a domain duplication, are active as monomers, and have a modified second active site. The acquisition and neofunctionalization of a structurally, biochemically, and functionally distinct GLX system indicates that Viridiplantae are under strong selection to detoxify diverse RCS.}, }
@article {pmid36422324, year = {2022}, author = {Khayi, S and Chan, KG and Faure, D}, title = {Patterns of Genomic Variations in the Plant Pathogen Dickeya solani.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422324}, issn = {2076-2607}, abstract = {The plant pathogen Dickeya solani causes soft rot and blackleg diseases in several crops including Solanum tuberosum. Unveiling the patterns of its diversity contributes to understanding the emergence and virulence of this pathogen in potato agro-systems. In this study, we analyzed the genome of several D. solani strains exhibiting an atypically high number of genetic variations. Variant calling and phylogenomics support the evidence that the strains RNS10-105-1A, A623S-20A-17 and RNS05.1.2A belong to a divergent sub-group of D. solani for which we proposed RNS05.1.2A as a reference strain. In addition, we showed that the variations (1253 to 1278 snp/indels) in strains RNS13-30-1A, RNS13-31-1A and RNS13-48-1A were caused by a horizontal gene transfer event from a donor belonging to the D. solani RNS05.1.2A subgroup. The overall results highlight the patterns driving the diversification in D. solani species. This work contributes to understanding patterns and causes of diversity in the emerging pathogen D. solani.}, }
@article {pmid36422323, year = {2022}, author = {Belova, SE and Naumoff, DG and Suzina, NE and Kovalenko, VV and Loiko, NG and Sorokin, VV and Dedysh, SN}, title = {Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82[T].}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422323}, issn = {2076-2607}, abstract = {Acidisarcina polymorpha SBC82[T] is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82[T] and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82[T] by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82[T] was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.}, }
@article {pmid36422313, year = {2022}, author = {Tavares, RDS and Tacão, M and Ramalheira, E and Ferreira, S and Henriques, I}, title = {Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422313}, issn = {2076-2607}, abstract = {BACKGROUND: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a blaNDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in blaNDM-5 dissemination.<br><br>METHODS: After blaNDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed.<br><br>RESULTS: blaNDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that blaNDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of blaNDM and mcr genes. Regardless, comparative genomics confirmed the presence of blaNDM in similar complex integrons in plasmids (48/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20/41 blaNDM-positive genomes).<br><br>CONCLUSIONS: blaNDM-5 and other blaNDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of blaNDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons.}, }
@article {pmid36421375, year = {2022}, author = {Ding, H and Bi, D and Zhang, S and Han, S and Ye, Y and Yi, R and Yang, J and Liu, B and Wu, L and Zhuo, R and Kan, X}, title = {The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications.}, journal = {Biology}, volume = {11}, number = {11}, pages = {}, pmid = {36421375}, issn = {2079-7737}, abstract = {As the largest family within the order Saxifragales, Crassulaceae contains about 34 genera with 1400 species. Mitochondria play a critical role in cellular energy production. Since the first land plant mitogenome was reported in Arabidopsis, more than 400 mitogenomic sequences have been deposited in a public database. However, no entire mitogenome data have been available for species of Crassulaceae to date. To better understand the evolutionary history of the organelles of Crassulaceae, we sequenced and performed comprehensive analyses on the mitogenome of Sedum plumbizincicola. The master mitogenomic circle is 212,159 bp in length, including 31 protein-coding genes (PCGs), 14 tRNA genes, and 3 rRNA genes. We further identified totally 508 RNA editing sites in PCGs, and demonstrated that the second codon positions of mitochondrial genes are most prone to RNA editing events. Notably, by neutrality plot analyses, we observed that the mitochondrial RNA editing events have large effects on the driving forces of plant evolution. Additionally, 4 MTPTs and 686 NUMTs were detected in the mitochondrial and nuclear genomes of S. plumbizincicola, respectively. Additionally, we conducted further analyses on gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications. Therefore, the findings presented here will be helpful for future investigations on plant mitogenomes.}, }
@article {pmid36419429, year = {2022}, author = {Ding, M and Ye, Z and Liu, L and Wang, W and Chen, Q and Zhang, F and Wang, Y and Sjöling, &#xc5; and Martín-Rodríguez, AJ and Hu, R and Chen, W and Zhou, Y}, title = {Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1017092}, pmid = {36419429}, issn = {1664-302X}, abstract = {Horizontal gene transfer plays an important role in the spread of antibiotic resistance, in which plasmid-mediated conjugation transfer is the most important mechanism. While sub-minimal inhibitory concentrations (sub-MIC) of antibiotics could promote conjugation frequency, the mechanism by which sub-MIC levels of antibiotics affect conjugation frequency is not clear. Here, we used Klebsiella pneumoniae SW1780 carrying the multi-drug resistance plasmid pSW1780-KPC as the donor strain, to investigate the effects of sub-MICs of meropenem (MEM), ciprofloxacin (CIP), cefotaxime (CTX), and amikacin (AK) on conjugational transfer of pSW1780-KPC from SW1780 to Escherichia coli J53. Our results showed that the transfer frequencies increased significantly by treating SW1780 strain with sub-MIC levels of MEM, CIP, CTX and AK. Transfer frequencies at sub-MIC conditions in a Galleria mellonella were significantly higher than in vitro. To investigate gene expression and metabolic effects, RT-qPCR and LC-MS-based metabolome sequencing were performed. Transcript levels of T4SS genes virB1, virB2, virB4, virB8, and conjugation-related genes traB, traK, traE, and traL were significantly upregulated by exposure to sub-MICs of MEM, CIP, CTX, and AK. Metabolome sequencing revealed nine differentially regulated metabolites. Our findings are an early warning for a wide assessment of the roles of sub-MIC levels of antibiotics in the spread of antibiotic resistance.}, }
@article {pmid36418956, year = {2022}, author = {Lu, J and Duan, J and Han, Y and Gou, M and Li, J and Li, Q and Pang, Y}, title = {A novel serum spherical lectin from lamprey reveals a more efficient mechanism of immune initiation and regulation in jawless vertebrates.}, journal = {Cellular &amp; molecular biology letters}, volume = {27}, number = {1}, pages = {102}, pmid = {36418956}, issn = {1689-1392}, mesh = {Animals ; *Lampreys/metabolism ; *Lectins/metabolism ; Phylogeny ; Mannose-Binding Protein-Associated Serine Proteases/genetics/metabolism ; Mannose-Binding Lectins ; Mammals ; }, abstract = {The innate immune system is the body's first line of defense against pathogens and involves antibody and complement system-mediated antigen removal. Immune-response-related complement molecules have been identified in lamprey, and the occurrence of innate immune response via the mannose-binding lectin-associated serine proteases of the lectin cascade has been reported. We have previously shown that lamprey (Lampetra japonica) serum can efficiently and specifically eliminate foreign pathogens. Therefore, we aimed to understand the immune mechanism of lamprey serum in this study. We identified and purified a novel spherical lectin (LSSL) from lamprey serum. LSSL had two structural calcium ions coordinated with conserved amino acids, as determined through cryogenic electron microscopy. LSSL showed high binding capacity with microbial and mammalian glycans and demonstrated agglutination activity against bacteria. Phylogenetic analysis revealed that LSSL was transferred from phage transposons to the lamprey genome via horizontal gene transfer. Furthermore, LSSL was associated with mannose-binding lectin-associated serine protease 1 and promoted the deposition of the C3 fragment on the surface of target cells upon binding. These results led us to conclude that LSSL initiates and regulates agglutination, resulting in exogenous pathogen and tumor cell eradication. Our observations will give a greater understanding of the origin and evolution of the complement system in higher vertebrates and lead to the identification of novel immune molecules and pathways for defense against pathogens and tumor cells.}, }
@article {pmid36417430, year = {2022}, author = {Gozashti, L and Roy, SW and Thornlow, B and Kramer, A and Ares, M and Corbett-Detig, R}, title = {Transposable elements drive intron gain in diverse eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2209766119}, doi = {10.1073/pnas.2209766119}, pmid = {36417430}, issn = {1091-6490}, support = {R35GM128932/GF/NIH HHS/United States ; }, mesh = {Animals ; Introns/genetics ; *Eukaryota/genetics ; *DNA Transposable Elements/genetics ; Phylogeny ; Eukaryotic Cells ; }, abstract = {There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.}, }
@article {pmid36416260, year = {2022}, author = {Stanton, IC and Tipper, HJ and Chau, K and Klümper, U and Subirats, J and Murray, AK}, title = {Does Environmental Exposure to Pharmaceutical and Personal Care Product Residues Result in the Selection of Antimicrobial-Resistant Microorganisms, and is this Important in Terms of Human Health Outcomes?.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/etc.5498}, pmid = {36416260}, issn = {1552-8618}, abstract = {The environment plays a critical role in the development, dissemination, and transmission of antimicrobial resistance (AMR). Pharmaceuticals and personal care products (PPCPs) enter the environment through direct application to the environment and through anthropogenic pollution. Although there is a growing body of evidence defining minimal selective concentrations (MSCs) of antibiotics and the role antibiotics play in horizontal gene transfer (HGT), there is limited evidence on the role of non-antibiotic PPCPs. Existing data show associations with the development of resistance or effects on bacterial growth rather than calculating selective endpoints. Research has focused on laboratory-based systems rather than in situ experiments, although PPCP concentrations found throughout wastewater, natural water, and soil environments are often within the range of laboratory-derived MSCs and at concentrations shown to promote HGT. Increased selection and HGT of AMR by PPCPs will result in an increase in total AMR abundance in the environment, increasing the risk of exposure and potential transmission of environmental AMR to humans. There is some evidence to suggest that humans can acquire resistance from environmental settings, with water environments being the most frequently studied. However, because this is currently limited, we recommend that more evidence be gathered to understand the risk the environment plays in regard to human health. In addition, we recommend that future research efforts focus on MSC-based experiments for non-antibiotic PPCPS, particularly in situ, and investigate the effect of PPCP mixtures on AMR. Environ Toxicol Chem 2022;00:1-14. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, }
@article {pmid36414122, year = {2022}, author = {Oyanedel, D and Rojas, R and Brokordt, K and Schmitt, P}, title = {Crassostrea gigas oysters from a non-intensive farming area naturally harbor potentially pathogenic vibrio strains.}, journal = {Journal of invertebrate pathology}, volume = {196}, number = {}, pages = {107856}, doi = {10.1016/j.jip.2022.107856}, pmid = {36414122}, issn = {1096-0805}, abstract = {Farming intensification and climate change are inevitably linked to pathogen emergence in aquaculture. In this context, infectious diseases associated with vibrios span all developmental stages of the Pacific Oyster Crassostrea gigas. Moreover, virulence factors associated with pathogenicity spread among the vibrio community through horizontal gene transfer as part of the natural eco-evolutive dynamic of this group. Therefore, risk factors associated with the emergence of pathogens should be assessed before the appearance of mass mortalities in developing rearing areas. In this context, we characterized the vibrios community associated with oysters cultured in a non-intensive area free of massive mortalities located at Tongoy bay, Chile, through a culture-dependent approach. We taxonomically affiliated our isolates at the species level through the partial sequencing of the heat shock protein 60 gene and estimated their virulence potential through experimental infection of juvenile C. gigas. The vibrio community belonged almost entirely to the Splendidus clade, with Vibrio lentus being the most abundant species. The virulence potential of selected isolates was highly contrasted with oyster survival ranging between 100 and 30 %. Moreover, different vibrio species affected oyster survival at different rates, for instance V. splendidus TO2_12 produced most mortalities just 24 h after injection, while the V. lentus the most virulent strain TO6_11 produced sustained mortalities reaching 30 % of survival at day 4 after injection. Production of enzymes associated with pathogenicity was detected and hemolytic activity was positive for 50 % of the virulent strains and negative for 90 % of non-virulent strains, representing the phenotype that better relates to the virulence status of strains. Overall, results highlight that virulence is a trait present in the absence of disease expression, and therefore the monitoring of potentially pathogenic groups such as vibrios is essential to anticipate and manage oyster disease emergence in both established and under-development rearing areas.}, }
@article {pmid36412071, year = {2022}, author = {Shimpi, GG and Bentlage, B}, title = {Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2200190}, doi = {10.1002/bies.202200190}, pmid = {36412071}, issn = {1521-1878}, abstract = {In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.}, }
@article {pmid36410487, year = {2023}, author = {Deng, Y and Jiang, J and Huang, Y and Cheng, C and Lin, Z and Liu, G and Guo, Z and Feng, J}, title = {Hypoxia triggers the proliferation of antibiotic resistance genes in a marine aquaculture system.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160305}, doi = {10.1016/j.scitotenv.2022.160305}, pmid = {36410487}, issn = {1879-1026}, abstract = {The transmission of antibiotic resistance genes (ARGs) affects the safety of aquaculture animals. Dissolved oxygen (DO) can affect the transmission of ARGs, but its mechanism of action in this process is unclear. We conducted laboratory breeding experiment with low and control DO groups. Combined quantitative PCR and 16S rRNA sequencing to study the effect of DO on the spread of ARGs. Hypoxia treatment significantly increased the accumulation of ammonium and nitrite in aquaculture water, and it increased the relative abundances of ARGs and mobile genetic elements (MGEs), especially the ARGs resistant to drugs in the categories of sulfonamide, (flor)/(chlor)/(am)phenicol, and MLSB (macrolide, lincosamide and streptogramin B) and the MGE intI-1(clinic), by 2.39-95.69 % in 28 days relative to the control DO treatment. Though the abundance of ARG carries, especially the Rhodocyclaceae, Caldilineaceae, Cyclobacteriaceae, Saprospiraceae, Enterobacteriaceae, Sphingomonadaceae families, showed higher abundance in low DO groups, relating to the vertical transmission of ARGs. Hypoxia treatment is more likely to promote the horizontal gene transfer (HGT)-related pathways, including ABC transporters, two component system, and quorum sensing, thus to induce the HGT of ARGs. The changed bacterial proliferation also altered the abundance of MGEs, especially intI-1(clinic), which induced HGT of ARGs as well. Additionally, pearson correlation results revealed that the succession of bacterial community function played the strongest role in ARG proliferation, followed by bacterial community structure and MGEs. Our results highlight the importance of suitable DO concentration in controlling the spread of ARGs especially the HGT of ARGs. In the context of global attention to food safety, our results provide important information for ensuring the safety of aquatic products and the sustainable development of aquaculture.}, }
@article {pmid36409903, year = {2022}, author = {Liu, B and Liu, Y and Yang, B and Wang, Q and Liu, X and Qin, J and Zhao, K and Li, F and Feng, X and Li, L and Wu, P and Liu, M and Zhu, S and Feng, L and Wang, L}, title = {Escherichia coli O157:H7 senses microbiota-produced riboflavin to increase its virulence in the gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2212436119}, doi = {10.1073/pnas.2212436119}, pmid = {36409903}, issn = {1091-6490}, mesh = {Animals ; Humans ; Mice ; *Enterohemorrhagic Escherichia coli/genetics ; *Escherichia coli O157/genetics ; *Microbiota ; Riboflavin ; Virulence/genetics ; Intestines ; }, abstract = {Riboflavin is produced by most commensal bacteria in the human colon, where enterohemorrhagic Escherichia coli (EHEC) colonizes and causes diseases. Sensing environmental signals to site-specifically express the type-III secretion system (T3SS), which injects effectors into host cells leading to intestinal colonization and disease, is key to the pathogenesis of EHEC. Here, we reveal that EHEC O157:H7, a dominant EHEC serotype frequently associated with severe diseases, acquired a previously uncharacterized two-component regulatory system rbfSR, which senses microbiota-produced riboflavin to directly activate the expression of LEE genes encoding the T3SS in the colon. rbfSR is present in O157:H7 and O145:H28 but absent from other EHEC serotypes. The binding site of RbfR through which it regulates LEE gene expression was identified and is conserved in all EHEC serotypes and Citrobacter rodentium, a surrogate for EHEC in mice. Introducing rbfSR into C. rodentium enabled bacteria to sense microbiota-produced riboflavin in the mouse colon to increase the expression of LEE genes, causing increased disease severity in mice. Phylogenic analysis showed that the O55:H7 ancestor of O157:H7 obtained rbfSR which has been kept in O157:H7 since then. Thus, acquiring rbfSR represents an essential step in the evolution of the highly pathogenic O157:H7. The expression of LEE genes and cell attachment ability of other EHEC serotypes in the presence of riboflavin significantly increased when rbfSR was introduced into them, indicating that those serotypes are ready to use RbfSR to increase their pathogenicity. This may present a potential public health issue as horizontal gene transfer is frequent in enteric bacteria.}, }
@article {pmid36407614, year = {2022}, author = {Li, L and Peng, S and Wang, Z and Zhang, T and Li, H and Xiao, Y and Li, J and Liu, Y and Yin, H}, title = {Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1025122}, pmid = {36407614}, issn = {1664-462X}, abstract = {Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na[+]/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.}, }
@article {pmid36406448, year = {2022}, author = {Hinnekens, P and Fayad, N and Gillis, A and Mahillon, J}, title = {Conjugation across Bacillus cereus and kin: A review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1034440}, pmid = {36406448}, issn = {1664-302X}, abstract = {Horizontal gene transfer (HGT) is a major driving force in shaping bacterial communities. Key elements responsible for HGT are conjugation-like events and transmissible plasmids. Conjugative plasmids can promote their own transfer as well as that of co-resident plasmids. Bacillus cereus and relatives harbor a plethora of plasmids, including conjugative plasmids, which are at the heart of the group species differentiation and specification. Since the first report of a conjugation-like event between strains of B. cereus sensu lato (s.l.) 40 years ago, many have studied the potential of plasmid transfer across the group, especially for plasmids encoding major toxins. Over the years, more than 20 plasmids from B. cereus isolates have been reported as conjugative. However, with the increasing number of genomic data available, in silico analyses indicate that more plasmids from B. cereus s.l. genomes present self-transfer potential. B. cereus s.l. bacteria occupy diverse environmental niches, which were mimicked in laboratory conditions to study conjugation-related mechanisms. Laboratory mating conditions remain nonetheless simplistic compared to the complex interactions occurring in natural environments. Given the health, economic and ecological importance of strains of B. cereus s.l., it is of prime importance to consider the impact of conjugation within this bacterial group.}, }
@article {pmid36404338, year = {2022}, author = {Orata, FD and Hussain, NAS and Liang, KYH and Hu, D and Boucher, YF}, title = {Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {42}, pmid = {36404338}, issn = {1757-4749}, abstract = {BACKGROUND: Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).<br><br>RESULTS: The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (<&#x2009;3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).<br><br>CONCLUSION: V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.}, }
@article {pmid36400772, year = {2022}, author = {Kim, HJ and Black, M and Edwards, RA and Peillard-Fiorente, F and Panigrahi, R and Klingler, D and Eidelpes, R and Zeindl, R and Peng, S and Su, J and Omar, AR and MacMillan, AM and Kreutz, C and Tollinger, M and Charpentier, X and Attaiech, L and Glover, JNM}, title = {Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7076}, pmid = {36400772}, issn = {2041-1723}, mesh = {*RNA-Binding Proteins/metabolism ; *RNA, Small Untranslated/genetics ; }, abstract = {The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail.}, }
@article {pmid36400617, year = {2022}, author = {Zhai, Z and Cui, C and Li, X and Yan, J and Sun, E and Wang, C and Guo, H and Hao, Y}, title = {Prevalence, antimicrobial susceptibility, and antibiotic resistance gene transfer of Bacillus strains isolated from pasteurized milk.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2022-22199}, pmid = {36400617}, issn = {1525-3198}, abstract = {Pasteurization is carried out in dairy industries to kill harmful bacteria present in raw milk. However, endospore-forming bacteria, such as Bacillus, cannot be completely eliminated by pasteurization. In this study, a total of 114 Bacillus strains were isolated from 133 pasteurized milk samples. Antibiotic susceptibility tests showed that the percentage of Bacillus with intrinsic resistance to ampicillin and penicillin were 80 and 86%, respectively. Meanwhile, some Bacillus isolates had acquired resistance, including trimethoprim-sulfamethoxazole resistance (10 isolates), clindamycin resistance (8 isolates), erythromycin resistance (2 isolates), and tetracycline resistance (1 isolate). To further locate these acquired resistance genes, the plasmids were investigated in these 16 Bacillus strains. The plasmid profile indicated that Bacillus cereus BA008, BA117, and BA119 harbored plasmids, respectively. Subsequently, the Illumina Novaseq PE150 was applied for the genomic and plasmid DNA sequencing. Notably, the gene tetL encoding tetracycline efflux protein was found to be located on plasmid pBC46-TL of B. cereus BA117. In vitro conjugative transfer indicated that pBC46-TL can be transferred into Bacillus invictae BA142, Bacillus safensis BA143, and Bacillus licheniformis BA130. The frequencies were of 1.5 × 10[-7] to 1.7 × 10[-5] transconjugants per donor cells. Therefore, Bacillus strains with acquired antibiotic resistance may represent a potential risk for the spread of antibiotic resistance between Bacillus and other clinical pathogens via horizontal gene transfer.}, }
@article {pmid36386695, year = {2022}, author = {Gerlach, D and Sieber, RN and Larsen, J and Krusche, J and De Castro, C and Baumann, J and Molinaro, A and Peschel, A}, title = {Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951333}, pmid = {36386695}, issn = {1664-302X}, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones.}, }
@article {pmid36386682, year = {2022}, author = {Pan, X and Zhou, Z and Liu, B and Wu, Z}, title = {A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1037389}, pmid = {36386682}, issn = {1664-302X}, abstract = {Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a "reservoir" of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.}, }
@article {pmid36386654, year = {2022}, author = {Guzman-Otazo, J and Joffré, E and Agramont, J and Mamani, N and Jutkina, J and Boulund, F and Hu, YOO and Jumilla-Lorenz, D and Farewell, A and Larsson, DGJ and Flach, CF and Iñiguez, V and Sjöling, &#xc5;}, title = {Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {997849}, pmid = {36386654}, issn = {1664-302X}, abstract = {Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.}, }
@article {pmid36386652, year = {2022}, author = {de la Higuera, I and Lázaro, E}, title = {Viruses in astrobiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032918}, pmid = {36386652}, issn = {1664-302X}, abstract = {Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.}, }
@article {pmid36384846, year = {2022}, author = {Wang, YJ and Tang, YJ and Zhang, YP and Zhang, MY and Chu, SS and Qiu, RL}, title = {[Retarding potential of biochar on antibiotic resistance genes in soil and the mechanisms: A review.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {11}, pages = {3116-3126}, doi = {10.13287/j.1001-9332.202211.014}, pmid = {36384846}, issn = {1001-9332}, mesh = {Humans ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; *Metals, Heavy/analysis ; Bacteria/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) in soil pose a major challenge to global environment and health. The development of effective technologies to reduce their negative effects has implications for maintaining soil health and human health. Biochar would be a suitable control material due to its characteristics of high carbon content, large surface area, excellent adsorption capacity, and economic advantages. There are three mechanisms underlying its negative effects on the abundance of ARGs: 1) adsorption of certain pollutants (e.g., antibiotics and heavy metals) to reduce the co-selective pressure of ARGs; 2) alteration of microbial composition through altering soil physico-chemical properties, and thereby limiting the ability of bacteria to undergo horizontal transfer of ARGs; 3) direct impairment of horizontal gene transfer by the adsorption of horizontal transfer vectors such as plasmids, transposons, and integrons. However, the negative effect of biochar depends on the source of material, pyrolysis process, and its amount added. Furthermore, field aging of biochar may reduce its ability to block ARGs. Endogenous contaminants of biochar, such as polycyclic aromatic hydrocarbons and heavy metals, may cause the enrichment of specific antibiotic-resistant bacteria in the environment or induce horizontal gene transfer. In further studies, suitable biochar should be selected according to soil environments, and biochar aging control measures should be taken to improve its retarding effect on ARGs.}, }
@article {pmid36384625, year = {2022}, author = {Wang, YJ and Si, YM and Li, YJ}, title = {[Research progress on the application of quorum sensing in the colonization and degradation enhancement of bioaugmentation functional bacteria].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {10}, pages = {2871-2880}, doi = {10.13287/j.1001-9332.202210.031}, pmid = {36384625}, issn = {1001-9332}, mesh = {Quorum Sensing/physiology ; Sewage ; Bacteria/genetics ; *Water Purification ; *Environmental Pollutants/metabolism ; }, abstract = {Due to the impacts of refractory organic pollutants and environment on the water treatment system, the sewage quality can not reach the standard. It is an effective measure to improve the efficiency of wastewater treatment by introducing exogenous engineering strains with relevant functional genes and the ability of horizontal gene transfer. In sewage treatment system, there are bacteria secreting signal molecules with quorum sensing. When population density reaches induction threshold, the bacteria would activate the related genes expression (such as biofilm formation, bioluminescent, antibiotics synthesis and virulence factor expression, etc.) through releasing signaling molecules, and thus trigger the behavior of other groups. Previously, researches about quorum sensing mainly concentrated on signal transduction, microbial social behavior, and medical microbiology. In recent years, stu-dies found that quorum sensing plays an important role in wastewater biological treatment and affects the colonization of the microorganism strain and pollutants degradation. Therefore, the regulation of quorum-sensing behavior is the key factor in the bioaugmentation performance. Here, we review the signaling molecules mechanism, the release of signaling molecules and its influence factors, the colonization of microbial community and the removal of pollutants. We further discussed the research from the perspective of quorum sensing biological process. The aim was to provide new idea for the effective implementation of bioaugmentation technology and the improvement of wastewater treatment efficiency, and to provide a theoretical reference for the in-depth understanding of quorum sensing regulation behavior in the process of bioaugmentation.}, }
@article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, }
@article {pmid36381231, year = {2022}, author = {Benites, LF and Stephens, TG and Bhattacharya, D}, title = {Multiple waves of viral invasions in Symbiodiniaceae algal genomes.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac101}, pmid = {36381231}, issn = {2057-1577}, abstract = {Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.}, }
@article {pmid36377945, year = {2022}, author = {Aytan-Aktug, D and Grigorjev, V and Szarvas, J and Clausen, PTLC and Munk, P and Nguyen, M and Davis, JJ and Aarestrup, FM and Lund, O}, title = {SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0264122}, doi = {10.1128/spectrum.02641-22}, pmid = {36377945}, issn = {2165-0497}, abstract = {High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.}, }
@article {pmid36375055, year = {2022}, author = {Wu, C and Tang, D and Dai, J and Tang, X and Bao, Y and Ning, J and Zhen, Q and Song, H and St Leger, RJ and Fang, W}, title = {Bioremediation of mercury-polluted soil and water by the plant symbiotic fungus Metarhizium robertsii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {47}, pages = {e2214513119}, pmid = {36375055}, issn = {1091-6490}, mesh = {Biodegradation, Environmental ; Water ; *Mercury/toxicity ; *Methylmercury Compounds ; Phylogeny ; Ecosystem ; *Metarhizium/genetics ; Soil ; }, abstract = {Fungi are central to every terrestrial and many aquatic ecosystems, but the mechanisms underlying fungal tolerance to mercury, a global pollutant, remain unknown. Here, we show that the plant symbiotic fungus Metarhizium robertsii degrades methylmercury and reduces divalent mercury, decreasing mercury accumulation in plants and greatly increasing their growth in contaminated soils. M. robertsii does this by demethylating methylmercury via a methylmercury demethylase (MMD) and using a mercury ion reductase (MIR) to reduce divalent mercury to volatile elemental mercury. M. robertsii can also remove methylmercury and divalent mercury from fresh and sea water even in the absence of added nutrients. Overexpression of MMD and MIR significantly improved the ability of M. robertsii to bioremediate soil and water contaminated with methylmercury and divalent mercury. MIR homologs, and thereby divalent mercury tolerance, are widespread in fungi. In contrast, MMD homologs were patchily distributed among the few plant associates and soil fungi that were also able to demethylate methylmercury. Phylogenetic analysis suggests that fungi could have acquired methylmercury demethylase genes from bacteria via two independent horizontal gene transfer events. Heterologous expression of MMD in fungi that lack MMD homologs enabled them to demethylate methylmercury. Our work reveals the mechanisms underlying mercury tolerance in fungi, and may provide a cheap and environmentally friendly means of cleaning up mercury pollution.}, }
@article {pmid36374836, year = {2022}, author = {Kurlovs, AH and De Beer, B and Ji, M and Vandenhole, M and De Meyer, T and Feyereisen, R and Clark, RM and Van Leeuwen, T}, title = {Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae.}, journal = {PLoS genetics}, volume = {18}, number = {11}, pages = {e1010333}, pmid = {36374836}, issn = {1553-7404}, mesh = {Animals ; *Tetranychidae/genetics ; Herbivory ; Gene Transfer, Horizontal ; Adaptation, Physiological ; Plants ; *Pesticides ; }, abstract = {The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness as is commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, or in some cases synergism of cis and trans, in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggests modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects.}, }
@article {pmid36374047, year = {2022}, author = {Kogay, R and Zhaxybayeva, O}, title = {Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0089222}, doi = {10.1128/msystems.00892-22}, pmid = {36374047}, issn = {2379-5077}, abstract = {Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.}, }
@article {pmid36371907, year = {2022}, author = {Zhao, CX and Su, XX and Xu, MR and An, XL and Su, JQ}, title = {Uncovering the diversity and contents of gene cassettes in class 1 integrons from the endophytes of raw vegetables.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114282}, doi = {10.1016/j.ecoenv.2022.114282}, pmid = {36371907}, issn = {1090-2414}, mesh = {Humans ; *Integrons/genetics ; *Endophytes/genetics ; Vegetables/genetics ; Anti-Bacterial Agents/pharmacology ; Integrases/genetics ; }, abstract = {Rapid spread of antibiotic resistance genes (ARGs) in pathogens is threatening human health. Integrons allow bacteria to integrate and express foreign genes, facilitating horizontal transfer of ARGs in environments. Consumption of raw vegetables represents a pathway for human exposure to environmental ARGs. However, few studies have focused on integron-associated ARGs in the endophytes of raw vegetables. Here, based on the approach of qPCR and clone library, we quantified the abundance of integrase genes and analyzed the diversity and contents of resistance gene cassettes in class 1 integrons from the endophytes of six common raw vegetables. The results revealed that integrase genes for class 1 integron were most prevalent compared with class 2 and class 3 integron integrase genes (1-2 order magnitude, P < 0.05). The cucumber endophytes harbored a higher absolute abundance of integrase genes than other vegetables, while the highest bacterial abundance was detected in cabbage and cucumber endophytes. Thirty-two unique resistance gene cassettes were detected, the majority of which were associated with the genes encoding resistance to beta-lactam and aminoglycoside. Antibiotic resistance gene cassettes accounted for 52.5 % of the functionally annotated gene cassettes, and blaTEM-157 and aadA2 were the most frequently detected resistance cassettes. Additionally, carrot endophytes harbored the highest proportion of antibiotic resistance gene cassettes in the class 1 integrons. Collectively, these results provide an in-depth view of acquired resistance genes by integrons in the raw vegetable endophytes and highlight the potential health risk of the transmission of ARGs via the food chain.}, }
@article {pmid36371221, year = {2022}, author = {Uruén, C and García, C and Fraile, L and Tommassen, J and Arenas, J}, title = {How Streptococcus suis escapes antibiotic treatments.}, journal = {Veterinary research}, volume = {53}, number = {1}, pages = {91}, pmid = {36371221}, issn = {1297-9716}, mesh = {Humans ; Swine ; Animals ; *Streptococcus suis/genetics ; *Streptococcal Infections/drug therapy/veterinary ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Macrolides ; *Swine Diseases/drug therapy/prevention &amp; control ; }, abstract = {Streptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.}, }
@article {pmid36370776, year = {2023}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Charles, S and Srinivasan, V and Sajith, V and Subila, KP and Haritha, P}, title = {Metagenomics indicates abundance of biofilm related genes and horizontal transfer of multidrug resistant genes among bacterial communities in nano zinc oxide polluted soil.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160032}, doi = {10.1016/j.scitotenv.2022.160032}, pmid = {36370776}, issn = {1879-1026}, abstract = {The unsafe and reckless disposal of metal oxide nanoparticles like ZnO (nZnO) into the soil could seriously impact bacterial behavioural responses and functions. Under such stress, biofilm formation is considered to be a robust mechanism for bacterial survival in soil. We examined the response of bacterial metagenomes in soils exposed to varying levels of Zn (50, 200, 500 and 1000 mg kg[-1]) as nano Zn oxide (nZnO) in terms of biofilm genesis and regulation and their co-occurrences with multidrug resistance genes (MDRGs) and mobile genetic elements (MGEs). The size-specific effects of nZnO were verified using its bulk counterpart (bZnO). Both nZnO and bZnO facilitated profusion of biofilm related genes (BGs) especially at higher Zn levels (500 and 1000 mg kg[-1] Zn), though maximum abundance was registered at a comparatively lower level under nZnO. In general, nZnO favoured an enhancement of genes involved in exopolysaccharide biosynthesis and attachment, while bZnO favoured genes related to capsule formation, chemotaxis and biofilm dispersion. Co-occurrence network analysis revealed significant positive correlations between abundances of BGs, MDRGs and MGEs, indicating an enhanced probability for horizontal gene transfer of MDRGs in nZnO polluted soils.}, }
@article {pmid36370236, year = {2022}, author = {Kerber-Diaz, JC and Leos-Ramírez, MA and Flores-Ceron, AA and Ponce-Mendoza, A and Estrada-de Los Santos, P and Ibarra, JA}, title = {Distribution of CRISPR-Cas systems in the Burkholderiaceae family and its biological implications.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {703}, pmid = {36370236}, issn = {1432-072X}, mesh = {CRISPR-Cas Systems ; *Burkholderiaceae/genetics ; Plasmids ; Computational Biology ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function of these systems. Their function has been mostly related to "genetic immunity" against foreign genetic material, among other roles. Interest in them increased after their use in genetic manipulation was uncovered and surveys to find and classify them have been done in several bacterial groups. To determine the presence of these genetic elements in the Burkholderiaceae family members, a bioinformatic approach was followed. Attention in this family comes as it is formed by a great diversity of microorganisms that include opportunistic and true pathogens, and symbiotic and saprophytic organisms, among others. Results show that, in contrast to other bacterial groups, only 8.4% of family members harbor complete CRISPR-Cas systems and the rest either do not have one or have remains or sections of one. Analyses of the spacer sequences indicated that most of them have identity to sections of the same genomes they were found, while a few had identities with either plasmids or phages. The genus with the higher proportion of self-directed spacers is Ralstonia, and their possible roles are discussed. Most of the systems (60%) belong to the class I subtype I-E and a few to subtypes I-C (13.3%), I-F (18.3%), II-C (5%), IV-A (1.7%) and V-C (1.7%). To the best of our knowledge, this is the first study to uncover the CRISPR-Cas system for the whole Burkholderiaceae family.}, }
@article {pmid36368125, year = {2022}, author = {Ropars, J and Giraud, T}, title = {Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102236}, doi = {10.1016/j.mib.2022.102236}, pmid = {36368125}, issn = {1879-0364}, mesh = {Humans ; *Cheese/microbiology ; Fungi/genetics ; Meat ; Gene Transfer, Horizontal ; Genomics ; }, abstract = {Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.}, }
@article {pmid36361992, year = {2022}, author = {Larrea, E and Fernández-Rubio, C and Peña-Guerrero, J and Guruceaga, E and Nguewa, PA}, title = {The BRCT Domain from the Homologue of the Oncogene PES1 in Leishmania major (LmjPES) Promotes Malignancy and Drug Resistance in Mammalian Cells.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361992}, issn = {1422-0067}, mesh = {Animals ; Humans ; Mice ; Adaptor Proteins, Signal Transducing/metabolism ; CARD Signaling Adaptor Proteins/metabolism ; HEK293 Cells ; *Leishmania major/genetics/metabolism ; Mammals/metabolism ; Oncogenes ; Proteins/metabolism ; *RNA-Binding Proteins/genetics ; Leishmaniasis/complications ; *Drug Resistance, Neoplasm/genetics ; *Carcinogenesis/genetics ; }, abstract = {Around 15% of cancer cases are attributable to infectious agents. Epidemiological studies suggest that an association between leishmaniasis and cancer does exist. Recently, the homologue of PES1 in Leishmania major (LmjPES) was described to be involved in parasite infectivity. Mammalian PES1 protein has been implicated in cellular processes like cell cycle regulation. Its BRCT domain has been identified as a key factor in DNA damage-responsive checkpoints. This work aimed to elucidate the hypothetical oncogenic implication of BRCT domain from LmjPES in host cells. We generated a lentivirus carrying this BRCT domain sequence (lentiBRCT) and a lentivirus expressing the luciferase protein (lentiLuc), as control. Then, HEK293T and NIH/3T3 mammalian cells were infected with these lentiviruses. We observed that the expression of BRCT domain from LmjPES conferred to mammal cells in vitro a greater replication rate and higher survival. In in vivo experiments, we observed faster tumor growth in mice inoculated with lentiBRCT respect to lentiLuc HEK293T infected cells. Moreover, the lentiBRCT infected cells were less sensitive to the genotoxic drugs. Accordingly, gene expression profiling analysis revealed that BRCT domain from LmjPES protein altered the expression of proliferation- (DTX3L, CPA4, BHLHE41, BMP2, DHRS2, S100A1 and PARP9), survival- (BMP2 and CARD9) and chemoresistance-related genes (DPYD, Dok3, DTX3L, PARP9 and DHRS2). Altogether, our results reinforced the idea that in eukaryotes, horizontal gene transfer might be also achieved by parasitism like Leishmania infection driving therefore to some crucial biological changes such as proliferation and drug resistance.}, }
@article {pmid36360308, year = {2022}, author = {Bernelot-Moens, R and Beatty, JT}, title = {DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360308}, issn = {2073-4425}, mesh = {*Rhodobacter capsulatus/genetics/metabolism ; Topoisomerase II Inhibitors/pharmacology ; Gene Expression Regulation, Bacterial ; *Bacteriophages ; Novobiocin/pharmacology/metabolism ; Ecosystem ; Bacterial Proteins/metabolism ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.}, }
@article {pmid36360197, year = {2022}, author = {Yushchuk, O and Binda, E and Fedorenko, V and Marinelli, F}, title = {Occurrence of vanHAX and Related Genes beyond the Actinobacteria Phylum.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360197}, issn = {2073-4425}, mesh = {*Bacteria ; Anti-Bacterial Agents ; Gene Transfer, Horizontal ; Glycopeptides ; Firmicutes ; *Actinobacteria/genetics ; }, abstract = {Clinically relevant glycopeptide antibiotics remain among the most successful classes of natural antibacterials. This success, however, is endangered by the spread of glycopeptide resistance genes, also known as van genes. Thus, it is important to trace and comprehend possible routes of van gene dissemination. In the current work, we present a comprehensive bioinformatic analysis aimed at mapping the occurrence of van genes beyond the Actinobacteria phylum-the most likely natural reservoir of van genes. We show that two additional classes of Gram-positive bacteria, Erysipelotrichia and Ktedonobacteria, as well as one class of Gram-negative bacteria, Anaerolineae, carry van genes. Additionally, we demonstrate that various new genera belonging to the classes Clostridia and Bacilli also carry van genes. The majority of discovered van loci are co-localized with MGE-related genes of various types. Finally, we propose a phylogeny-based scenario for the spread of van genes, unraveling a network of consequential horizontal gene transfer events linking the phylum Actinobacteria with the five other bacterial classes carrying van genes.}, }
@article {pmid36357451, year = {2022}, author = {Downing, T and Rahm, A}, title = {Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19203}, pmid = {36357451}, issn = {2045-2322}, mesh = {*Protein Interaction Maps/genetics ; Plasmids/genetics ; *Gene Transfer, Horizontal ; Bacteria/genetics ; Bacterial Proteins/genetics ; }, abstract = {Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode proteins performing non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded proteins across representative specimens from most bacteria using all available plasmids. We found that plasmid-encoded genes constitute ~ 0.65% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks' connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in > 96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail.}, }
@article {pmid36356515, year = {2023}, author = {Jin, X and Liu, S and Zhang, Z and Liu, T and Li, N and Liang, Y and Zheng, J and Peng, N}, title = {Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130261}, doi = {10.1016/j.jhazmat.2022.130261}, pmid = {36356515}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Astacoidea/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Ecosystem ; Enrofloxacin/pharmacology ; Genes, Bacterial ; *Ponds/analysis ; Geologic Sediments ; }, abstract = {Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.}, }
@article {pmid36354153, year = {2022}, author = {Wang, H and Li, Y and Zhang, Z and Zhong, B}, title = {Horizontal gene transfer: Driving the evolution and adaptation of plants.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13407}, pmid = {36354153}, issn = {1744-7909}, abstract = {As a mechanism of genetic transmission, horizontal gene transfer (HGT) greatly contributes to the diversification and long-term evolution of green plants. Recent studies suggest that HGT events drive the evolution and adaptation of charophyte green algae and land plants. This article is protected by copyright. All rights reserved.}, }
@article {pmid36351400, year = {2022}, author = {Hua, M and Dai, D and Du, P and Chen, N and Duan, A and Yue, J and Jia, H and Rong, C and Li, A and Zeng, H and Chen, C}, title = {A chromosome-encoded T4SS independently contributes to horizontal gene transfer in Enterococcus faecalis.}, journal = {Cell reports}, volume = {41}, number = {6}, pages = {111609}, doi = {10.1016/j.celrep.2022.111609}, pmid = {36351400}, issn = {2211-1247}, mesh = {*Enterococcus faecalis/genetics/metabolism ; *Gene Transfer, Horizontal/genetics ; Plasmids/genetics ; Type IV Secretion Systems/metabolism ; Chromosomes/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Bacterial type IV secretion systems (T4SSs) are the specific devices that mediate the dissemination of antibiotic resistant genes via horizontal gene transfer (HGT). Multi-drug-resistant Enterococcus faecalis (E. faecalis) represents a clinical public health threat because of its transferable plasmid with a functional plasmid-encoded (PE)-T4SS. Here, we report a chromosome-encoded (CE)-T4SS that exists in 40% of E. faecalis isolates. Compared with the PE-T4SS, CE-T4SS displays distinct characteristics in protein architecture and is capable of mediating large and genome-wide gene transfer in an imprecise manner. Reciprocal exchange of CE-T4SS- or PE-T4SS-associated origin of transfer (oriT) could disrupt HGT function, indicating that CE-T4SS is an independent system compared with PE-T4SS. Taken together, the CE-T4SS sheds light on the knowledge of HGT in gram-positive bacteria and triggers us to explore more evolutionary mechanisms in E. faecalis.}, }
@article {pmid36350852, year = {2022}, author = {Koutsovoulos, GD and Granjeon Noriot, S and Bailly-Bechet, M and Danchin, EGJ and Rancurel, C}, title = {AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers.}, journal = {PLoS computational biology}, volume = {18}, number = {11}, pages = {e1010686}, pmid = {36350852}, issn = {1553-7358}, mesh = {*Gene Transfer, Horizontal/genetics ; Phylogeny ; *Biological Evolution ; Genome ; Software ; Evolution, Molecular ; }, abstract = {Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.}, }
@article {pmid36350849, year = {2022}, author = {Coyte, KZ and Stevenson, C and Knight, CG and Harrison, E and Hall, JPJ and Brockhurst, MA}, title = {Horizontal gene transfer and ecological interactions jointly control microbiome stability.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001847}, pmid = {36350849}, issn = {1545-7885}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics ; }, abstract = {Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.}, }
@article {pmid36350646, year = {2022}, author = {Choi, Y and Ahn, S and Park, M and Lee, S and Cho, S and Kim, H}, title = {HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkac929}, pmid = {36350646}, issn = {1362-4962}, abstract = {HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.}, }
@article {pmid36350115, year = {2022}, author = {Koppenhöfer, S and Tomasch, J and Lang, AS}, title = {Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, doi = {10.1099/mgen.0.000890}, pmid = {36350115}, issn = {2057-5858}, mesh = {*Alphaproteobacteria/genetics ; Gene Transfer, Horizontal ; *Rhodobacter capsulatus/genetics ; Prophages/genetics ; Genomics ; }, abstract = {Gene transfer agents (GTAs) are phage-like particles that transfer pieces of cellular genomic DNA to other cells. Homologues of the Rhodobacter capsulatus GTA (RcGTA) structural genes are widely distributed in the Alphaproteobacteria and particularly well conserved in the order Rhodobacterales. Possible reasons for their widespread conservation are still being discussed. It has been suggested that these alphaproteobacterial elements originate from a prophage that was present in an ancestral bacterium and subsequently evolved into a GTA that is now widely maintained in extant descendant lineages. Here, we analysed genomic properties that might relate to the conservation of these alphaproteobacterial GTAs. This revealed that the chromosomal locations of the GTA gene clusters are biased. They primarily occur on the leading strand of DNA replication, at large distances from long repetitive elements, and thus are in regions of lower plasticity, and in areas of extreme GC skew, which also accumulate core genes. These extreme GC skew regions arise from the preferential use of codons with an excess of G over C, a distinct phenomenon from the elevated GC content that has previously been found to be associated with GTA genes. The observed properties, along with their high level of conservation, show that GTA genes share multiple features with core genes in the examined lineages of the Alphaproteobacteria.}, }
@article {pmid36346786, year = {2022}, author = {Lang, AS}, title = {Virus-derived gene transfer agents benefit host cells by providing templates for DNA repair.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001874}, pmid = {36346786}, issn = {1545-7885}, mesh = {Prophages/genetics ; Gene Transfer, Horizontal ; *Caulobacter crescentus ; *Bacteriophages/genetics ; DNA Repair ; }, abstract = {The potential benefits of producing gene transfer agents (GTAs) have long been speculated. A new study in PLOS Biology shows that DNA transfer by these phage-like elements allows cells with DNA damage to perform DNA repair and survive.}, }
@article {pmid36345550, year = {2022}, author = {Shokrollahi, P and Hasani, A and Aghazadeh, M and Memar, MY and Hasani, A and Zaree, M and Rezaee, MA and Sadeghi, J}, title = {Contribution of Arginine Catabolic Mobile Element and Copper and Mercury Resistance Element in Methicillin-Resistant Staphylococcus aureus: A Vantage Point.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {9916255}, pmid = {36345550}, issn = {1712-9532}, abstract = {Different clones of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are dominating geographically. One of the significant, hypervirulent, CA-MRSA and a significant health concern clones is USA3000, found worldwide regionally with varying frequencies. The clone harbors several mobile genetic elements (MGEs) including, arginine catabolic mobile element (ACME) and copper and mercury resistance genes (COMER), accomplished by horizontal gene transfer from S. epidermidis. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. This review highlights the comprehensive view on ACME and COMER structure, their distribution, and the mechanism of action along with pathogenetic features of USA3000 encompassing their role in biofilm formation, adhesion, quorum sensing, resistance to antibiotics, chemotaxis, and nutrient uptake. We also provided an insight into the role of ACME and COMER genes in the survival of bacterium. Our results shed light on the emergence of two independent clones possessing ACME (North American) and COMER (South American) elements which later disseminated to other regions. ACME and COMER both are adjacent to staphylococcal cassette chromosome mec type IV (SCCmec IV). The acquisition of mecA, followed by COMER or ACME has been shown as a significant factor in the rise and fall of MRSA strains and their complex ability to adapt to hostile environments. The presence of ACME increases fitness, thereby allowing bacteria to colonize the skin and mucous membrane while COMER contributes to genetic stability by knocking over the copper-mediated killing in macrophages. Evidence suggests that ACME and COMER have a more prominent role in enhancing biofilm capacity and ultimately persistent infections. Interestingly, ACME strains have been shown to possess the ability to counteract skin acidity, thereby allowing increased skin colonization. A profound understanding of MGEs in S. aureus plays an important role in the prevention of epidemic clones.}, }
@article {pmid36343341, year = {2022}, author = {Wang, R and Xiao, J and Wang, Q and Zhao, W and Liu, X and Liu, Y and Fu, S}, title = {Genomic analysis of a new type VI secretion system in Vibrio parahaemolyticus and its implications for environmental adaptation in shrimp ponds.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2022-0096}, pmid = {36343341}, issn = {1480-3275}, abstract = {The type VI secretion system (T6SS) in Vibrio spp. is often used to kill heteroclonal neighbors by direct injection of toxic effectors, but its strategies in aquacultural environments receive limited attention. In this study, we conducted genomic analysis for a T6SS-harboring plasmid in V. parahaemolyticus strain VP157. Coculture assays were further conducted to verify its antibacterial function. The results showed that strain VP157 harbored a 132-kb plasmid, pVP157-1, which consists of two fragments: an 87.8-kb fragment identical to plasmid pTJ114-1 and a 44.2-kb T6SS gene cluster with only 4% DNA identity to T6SS1 in the V. parahaemolyticus reference genome. Gene-by-gene analysis of six genes representing core T6SS components suggested that each gene has distinct evolutionary origins. In vitro experimental evolution revealed that pVP157-1 can excise from the VP157 genome with an excision rate of 4%. A coculture assay suggested that strain VP157 had significantly higher antibacterial activity against Bacillus pumilus and V. cholerae than the strain without pVP157-1(VP157[∆T6SS]). In contrast, a rapid decline was observed for the proportion of VP157[∆] [T6SS] in a mock microbial community, which decreased from 10.7% to 2.1% in 5 days. The results highlighted that the acquisition of T6SS fostered the fitness of V . parahaemolyticus in a complex environment.}, }
@article {pmid36342184, year = {2022}, author = {Tran, F and Gangan, MS and Weaver, BP and Boedicker, JQ}, title = {Membrane-Binding Biomolecules Influence the Rate of Vesicle Exchange between Bacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0134622}, doi = {10.1128/aem.01346-22}, pmid = {36342184}, issn = {1098-5336}, abstract = {The exchange of bacterial extracellular vesicles facilitates molecular exchange between cells, including the horizontal transfer of genetic material. Given the implications of such transfer events on cell physiology and adaptation, some bacterial cells have likely evolved mechanisms to regulate vesicle exchange. Past work has identified mechanisms that influence the formation of extracellular vesicles, including the production of small molecules that modulate membrane structure; however, whether these mechanisms also modulate vesicle uptake and have an overall impact on the rate of vesicle exchange is unknown. Here, we show that membrane-binding molecules produced by microbes influence both the formation and uptake of extracellular vesicles and have the overall impact of increasing the vesicle exchange rate within a bacterial coculture. In effect, production of compounds that increase vesicle exchange rates encourage gene exchange between neighboring cells. The ability of several membrane-binding compounds to increase vesicle exchange was demonstrated. Three of these compounds, nisin, colistin, and polymyxin B, are antimicrobial peptides added at sub-inhibitory concentrations. These results suggest that a potential function of exogenous compounds that bind to membranes may be the regulation of vesicle exchange between cells. IMPORTANCE The exchange of bacterial extracellular vesicles is one route of gene transfer between bacteria, although it was unclear if bacteria developed strategies to modulate the rate of gene transfer within vesicles. In eukaryotes, there are many examples of specialized molecules that have evolved to facilitate the production, loading, and uptake of vesicles. Recent work with bacteria has shown that some small molecules influence membrane curvature and induce vesicle formation. Here, we show that similar compounds facilitate vesicle uptake, thereby increasing the overall rate of vesicle exchange within bacterial populations. The addition of membrane-binding compounds, several of them antibiotics at subinhibitory concentrations, to a bacterial coculture increased the rate of horizontal gene transfer via vesicle exchange.}, }
@article {pmid36342139, year = {2022}, author = {Fidopiastis, PM and Childs, C and Esin, JJ and Stellern, J and Darin, A and Lorenzo, A and Mariscal, VT and Lorenz, J and Gopan, V and McAnulty, S and Visick, KL}, title = {Vibrio fischeri Possesses Xds and Dns Nucleases That Differentially Influence Phosphate Scavenging, Aggregation, Competence, and Symbiotic Colonization of Squid.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0163522}, pmid = {36342139}, issn = {1098-5336}, support = {R35 GM130355/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Aliivibrio fischeri/genetics ; *Decapodiformes/microbiology ; Symbiosis ; Phosphates ; Biofilms ; }, abstract = {Cells of Vibrio fischeri colonize the light organ of Euprymna scolopes, providing the squid bioluminescence in exchange for nutrients and protection. The bacteria encounter DNA-rich mucus throughout their transition to a symbiotic lifestyle, leading us to hypothesize a role for nuclease activity in the colonization process. In support of this, we detected abundant extracellular nuclease activity in growing cells of V. fischeri. To discover the gene(s) responsible for this activity, we screened a V. fischeri transposon mutant library for nuclease-deficient strains. Interestingly, only one strain, whose transposon insertion mapped to nuclease gene VF_1451, showed complete loss of nuclease activity in our screens. A database search revealed that VF_1451 is homologous to the nuclease-encoding gene xds in Vibrio cholerae. However, V. fischeri strains lacking xds eventually revealed slight nuclease activity on plates after 72 h. This led us to hypothesize that a second secreted nuclease, identified through a database search as VF_0437, a homolog of V. cholerae dns, might be responsible for the residual nuclease activity. Here, we show that Xds and/or Dns are involved in essential aspects of V. fischeri biology, including natural transformation, aggregation, and phosphate scavenging. Furthermore, strains lacking either nuclease were outcompeted by the wild type for squid colonization. Understanding the specific role of nuclease activity in the squid colonization process represents an intriguing area of future research. IMPORTANCE From soil and water to host-associated secretions such as mucus, environments that bacteria inhabit are awash in DNA. Extracellular DNA (eDNA) is a nutritious resource that microbes dedicate significant energy to exploit. Calcium binds eDNA to promote cell-cell aggregation and horizontal gene transfer. eDNA hydrolysis impacts construction of and dispersal from biofilms. Strategies in which pathogens use nucleases to avoid phagocytosis or disseminate by degrading host secretions are well documented; significantly less is known about nucleases in mutualistic associations. This study describes the role of nucleases in the mutualism between V. fischeri and its squid host, Euprymna scolopes. We find that nuclease activity is an important determinant of colonization in V. fischeri, broadening our understanding of how microbes establish and maintain beneficial associations.}, }
@article {pmid36341518, year = {2022}, author = {Kessler, C and Hou, J and Neo, O and Buckner, MMC}, title = {In situ, in vivo and in vitro approaches for studying AMR plasmid conjugation in the gut microbiome.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuac044}, pmid = {36341518}, issn = {1574-6976}, abstract = {Antimicrobial resistance (AMR) is a global threat, with evolution and spread of resistance to frontline antibiotics outpacing the development of novel treatments. The spread of AMR is perpetuated by transfer of antimicrobial resistance genes (ARGs) between bacteria, notably those encoded by conjugative plasmids. The human gut microbiome is a known 'melting pot' for plasmid conjugation, with ARG transfer in this environment widely documented. There is a need to better understand the factors affecting the incidence of these transfer events, and to investigate methods of potentially counteracting the spread of ARGs. This review describes the use and potential of three approaches to studying conjugation in the human gut: observation of in situ events in hospitalized patients, modelling of the microbiome in vivo predominantly in rodent models, and the use of in vitro models of various complexities. Each has brought unique insights to our understanding of conjugation in the gut. The use and development of these systems, and combinations thereof, will be pivotal in better understanding the significance, prevalence and manipulability of horizontal gene transfer in the gut microbiome.}, }
@article {pmid36340844, year = {2022}, author = {Lynch, T and Nandi, T and Jayaprakash, T and Gregson, D and Church, DL}, title = {Genomic analysis of group A Streptococcus isolated during a correctional facility outbreak of MRSA in 2004.}, journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada}, volume = {7}, number = {1}, pages = {23-35}, pmid = {36340844}, issn = {2371-0888}, abstract = {BACKGROUND: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus.<br><br>METHODS: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes.<br><br>RESULTS: Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections.<br><br>CONCLUSIONS: GAS recovered from invasive and non-invasive sources were not genetically distinguishable. Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.}, }
@article {pmid36338125, year = {2022}, author = {Yu, W and Li, S and Zhang, G and Xu, HHK and Zhang, K and Bai, Y}, title = {New frontiers of oral sciences: Focus on the source and biomedical application of extracellular vesicles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1023700}, pmid = {36338125}, issn = {2296-4185}, abstract = {Extracellular vesicles (EVs) are a class of nanoparticles that are derived from almost any type of cell in the organism tested thus far and are present in all body fluids. With the capacity to transfer "functional cargo and biological information" to regulate local and distant intercellular communication, EVs have developed into an attractive focus of research for various physiological and pathological conditions. The oral cavity is a special organ of the human body. It includes multiple types of tissue, and it is also the beginning of the digestive tract. Moreover, the oral cavity harbors thousands of bacteria. The importance and particularity of oral function indicate that EVs derived from oral cavity are quite complex but promising for further research. This review will discuss the extensive source of EVs in the oral cavity, including both cell sources and cell-independent sources. Besides, accumulating evidence supports extensive biomedical applications of extracellular vesicles in oral tissue regeneration and development, diagnosis and treatment of head and neck tumors, diagnosis and therapy of systemic disease, drug delivery, and horizontal gene transfer (HGT). The immune cell source, odontoblasts and ameloblasts sources, diet source and the application of EVs in tooth development and HGT were reviewed for the first time. In conclusion, we concentrate on the extensive source and potential applications offered by these nanovesicles in oral science.}, }
@article {pmid36338046, year = {2022}, author = {Yang, C and Han, J and Berglund, B and Zou, H and Gu, C and Zhao, L and Meng, C and Zhang, H and Ma, X and Li, X}, title = {Dissemination of bla NDM-5 and mcr-8.1 in carbapenem-resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae in an animal breeding area in Eastern China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1030490}, pmid = {36338046}, issn = {1664-302X}, abstract = {Animal farms have become one of the most important reservoirs of carbapenem-resistant Klebsiella spp. (CRK) owing to the wide usage of veterinary antibiotics. "One Health"-studies observing animals, the environment, and humans are necessary to understand the dissemination of CRK in animal breeding areas. Based on the concept of "One-Health," 263 samples of animal feces, wastewater, well water, and human feces from 60 livestock and poultry farms in Shandong province, China were screened for CRK. Five carbapenem-resistant Klebsiella pneumoniae (CRKP) and three carbapenem-resistant Klebsiella quasipneumoniae (CRKQ) strains were isolated from animal feces, human feces, and well water. The eight strains were characterized by antimicrobial susceptibility testing, plasmid conjugation assays, whole-genome sequencing, and bioinformatics analysis. All strains carried the carbapenemase-encoding gene bla NDM-5, which was flanked by the same core genetic structure (IS5-bla NDM-5-ble MBL-trpF-dsbD-IS26-ISKox3) and was located on highly related conjugative IncX3 plasmids. The colistin resistance gene mcr-8.1 was carried by three CRKP and located on self-transmissible IncFII(K)/IncFIA(HI1) and IncFII(pKP91)/IncFIA(HI1) plasmids. The genetic context of mcr-8.1 consisted of IS903-orf-mcr-8.1-copR-baeS-dgkA-orf-IS903 in three strains. Single nucleotide polymorphism (SNP) analysis confirmed the clonal spread of CRKP carrying-bla NDM-5 and mcr-8.1 between two human workers in the same chicken farm. Additionally, the SNP analysis showed clonal expansion of CRKP and CRKQ strains from well water in different farms, and the clonal CRKP was clonally related to isolates from animal farms and a wastewater treatment plant collected in other studies in the same province. These findings suggest that CRKP and CRKQ are capable of disseminating via horizontal gene transfer and clonal expansion and may pose a significant threat to public health unless preventative measures are taken.}, }
@article {pmid36338036, year = {2022}, author = {Kraemer, SA and Barbosa da Costa, N and Oliva, A and Huot, Y and Walsh, DA}, title = {A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {995418}, pmid = {36338036}, issn = {1664-302X}, abstract = {Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs - under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.}, }
@article {pmid36335713, year = {2022}, author = {Newson, JP and Gaissmaier, MS and McHugh, SC and Hardt, WD}, title = {Studying antibiotic persistence in vivo using the model organism Salmonella Typhimurium.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102224}, doi = {10.1016/j.mib.2022.102224}, pmid = {36335713}, issn = {1879-0364}, mesh = {Animals ; *Salmonella typhimurium/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Gene Transfer, Horizontal ; Virulence ; }, abstract = {Antibiotic persistence permits a subpopulation of susceptible bacteria to survive lethal concentrations of bactericidal antibiotics. This prolongs antibiotic therapy, promotes the evolution of antibiotic-resistant pathogen strains and can select for pathogen virulence within infected hosts. Here, we review the literature exploring antibiotic persistence in vivo, and describe the consequences of recalcitrant subpopulations, with a focus on studies using the model pathogen Salmonella Typhimurium. In vitro studies have established a concise set of features distinguishing true persisters from other forms of bacterial recalcitrance to bactericidal antibiotics. We discuss how animal infection models are useful for exploring these features in vivo, and describe how technical challenges can sometimes prevent the conclusive identification of true antibiotic persistence within infected hosts. We propose using two complementary working definitions for studying antibiotic persistence in vivo: the strict definition for studying the mechanisms of persister formation, and an operative definition for functional studies assessing the links between invasive virulence and persistence as well as the consequences for horizontal gene transfer, or the emergence of antibiotic-resistant mutants. This operative definition will enable further study of how antibiotic persisters arise in vivo, and of how surviving populations contribute to diverse downstream effects such as pathogen transmission, horizontal gene transfer and the evolution of virulence and antibiotic resistance. Ultimately, such studies will help to improve therapeutic control of antibiotic- recalcitrant populations.}, }
@article {pmid36334179, year = {2022}, author = {Tripathi, S and Purchase, D and Govarthanan, M and Chandra, R and Yadav, S}, title = {Regulatory and innovative mechanisms of bacterial quorum sensing-mediated pathogenicity: a review.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {1}, pages = {75}, pmid = {36334179}, issn = {1573-2959}, mesh = {Humans ; *Quorum Sensing/physiology ; Virulence ; Environmental Monitoring ; Bacteria ; Biofilms ; Anti-Bacterial Agents/toxicity/metabolism ; *Anti-Infective Agents/metabolism ; }, abstract = {Quorum sensing (QS) is a system of bacteria in which cells communicate with each other; it is linked to cell density in the microbiome. The high-density colony population can provide enough small molecular signals to enable a range of cellular activities, gene expression, pathogenicity, and antibiotic resistance that cause damage to the hosts. QS is the basis of chronic illnesses in human due to microbial sporulation, expression of virulence factors, biofilm formation, secretion of enzymes, or production of membrane vesicles. The transfer of antimicrobial resistance gene (ARG) among antibiotic resistance bacteria is a major public health concern. QS-mediated biofilm is a hub for ARG horizontal gene transfer. To develop innovative approach to prevent microbial pathogenesis, it is essential to understand the role of QS especially in response to environmental stressors such as exposure to antibiotics. This review provides the latest knowledge on the relationship of QS and pathogenicity and explore the novel approach to control QS via quorum quenching (QQ) using QS inhibitors (QSIs) and QQ enzymes. The state-of-the art knowledge on the role of QS and the potential of using QQ will help to overcome the threats of rapidly emerging bacterial pathogenesis.}, }
@article {pmid36332408, year = {2022}, author = {Zhou, M and Cai, Q and Zhang, C and Ouyang, P and Yu, L and Xu, Y}, title = {Antibiotic resistance bacteria and antibiotic resistance genes survived from the extremely acidity posing a risk on intestinal bacteria in an in vitro digestion model by horizontal gene transfer.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114247}, doi = {10.1016/j.ecoenv.2022.114247}, pmid = {36332408}, issn = {1090-2414}, mesh = {Humans ; *Gene Transfer, Horizontal ; *Angiotensin Receptor Antagonists ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Digestion ; }, abstract = {Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants posing risk to human health. To investigate the pathogenic ARBs and the horizontal gene transfer (HGT) via both extracellular ARGs (eARGs) and intracellular ARGs (iARGs), an in vitro digestion simulation system was established to monitoring the ARB and ARGs passing through the artificial digestive tract. The results showed that ARB was mostly affected by the acidity of the gastric fluid with about 99% ARB (total population of 2.45 × 10[9]-2.54 × 10[9]) killed at pH 2.0 and severe damage of bacterial cell membrane. However, more than 80% ARB (total population of 2.71 × 10[9]-3.90 × 10[9]) survived the challenge when the pH of the gastric fluid was 3.0 and above. Most ARB died from the high acidity, but its ARGs, intI1 and 16 S rRNA could be detected. The eARGs (accounting for 0.03-24.56% of total genes) were less than iARGs obviously. The eARGs showed greater HGT potential than that of iARGs, suggesting that transformation occurred more easily than conjugation. The transferring potential followed: tet (100%) > sul (75%) > bla (58%), related to the high correlation of intI1 with tetA and sul2 (p < 0.01). Moreover, gastric juice of pH 1.0 could decrease the transfer frequency of ARGs by 2-3 order of magnitude compared to the control, but still posing potential risks to human health. Under the treatment of digestive fluid, ARGs showed high gene horizontal transfer potential, suggesting that food-borne ARBs pose a great risk of horizontal transfer of ARGs to intestinal bacteria.}, }
@article {pmid36328265, year = {2023}, author = {Li, H and Dechesne, A and He, Z and Jensen, MM and Song, HL and Smets, BF}, title = {Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159846}, doi = {10.1016/j.scitotenv.2022.159846}, pmid = {36328265}, issn = {1879-1026}, mesh = {*Disinfection ; Gene Transfer, Horizontal ; Angiotensin Receptor Antagonists/pharmacology ; Reactive Oxygen Species ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Plasmids ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Current in the milliampere range can be used for electrochemical inactivation of bacteria. Yet, bacteria-including antibiotic resistant bacteria (ARB) may be subjected to sublethal conditions due to imperfect mixing or energy savings measures during electrochemical disinfection. It is not known whether such sublethal current intensities have the potential to stimulate plasmid transfer from ARB. In this study, conjugal transfer of plasmid pKJK5 was investigated between Pseudomonas putida strains under conditions reflecting electrochemical disinfection. Although the abundance of culturable and membrane-intact donor and recipient cells decreased with applied current (0-60 mA), both transconjugant density and transconjugant frequency increased. Both active chlorine and superoxide radicals were generated electrolytically, and ROS generation was induced. In addition, we detected significant over expression of a core oxidative stress defense gene (ahpCF) with current. Expression of selected conjugation related genes (traE, traI, trbJ, and trbL) also significantly correlated with current intensity. ROS accumulation, SOS response and subsequent derepression of conjugation are therefore the plausible consequence of sublethal current exposure. These findings suggest that sublethal intensities of current can enhance conjugal plasmid transfer, and that it is essential that conditions of electrochemical disinfection (applied voltage, current density, time and mixing) are carefully controlled to avoid conjugal ARG transmission.}, }
@article {pmid36327832, year = {2023}, author = {Kothari, A and Kumar, P and Gaurav, A and Kaushal, K and Pandey, A and Yadav, SRM and Jain, N and Omar, BJ}, title = {Association of antibiotics and heavy metal arsenic to horizontal gene transfer from multidrug-resistant clinical strains to antibiotic-sensitive environmental strains.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130260}, doi = {10.1016/j.jhazmat.2022.130260}, pmid = {36327832}, issn = {1873-3336}, mesh = {Humans ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Arsenic/toxicity ; Drug Resistance, Multiple, Bacterial/genetics ; *Metals, Heavy/toxicity ; Plasmids ; Bacteria/genetics ; Water ; }, abstract = {The emergence of multidrug-resistant bacteria is currently posing a significant threat to global public health. By testing for resistance to different antibiotic classes, we discovered that the majority of clinical bacteria are multidrug-resistant. These clinical multidrug-resistant species have antibiotic resistance genes on their plasmids that can be horizontally transferred to various antibiotic susceptible environmental bacterial species, resulting in antibiotic-resistant transconjugates. Furthermore, we discovered that the presence of an optimal concentration of antibiotics or heavy metal (arsenic) facilitates horizontal gene transfer through the formation of transconjugants. Notably, the addition of a conjugation inhibitor (2-hexadecynoic acid, a synthetic fatty acid) completely blocked the formation of antibiotic or arsenic-induced transconjugants. We discovered a high level of arsenic in water from the Shukratal region, Uttarakhand, India, which corresponded to a high serum level of arsenic in clinically infected individuals from the Shukratal region compared to other locations in Uttarakhand. Importantly, bacterial strains isolated from infected people who drink water from the Shukratal region with high arsenic levels were found to be more antibiotic-resistant than strains isolated from other sites. We discovered that bacterial strains isolated from individuals with high serum arsenic levels are significantly more resistant to antibiotics than individuals with low serum arsenic levels within the Shurkratal. This research sheds light on imminent threats to global health in which improper clinical, industrial, and other waste disposal, increased antibiotic concentrations in the environment, and increased human interference can easily transform commensal and pathogenic bacteria found in environmental niches into life-threatening multidrug-resistant superbugs.}, }
@article {pmid36327744, year = {2022}, author = {Carr, M and Leadbeater, BSC}, title = {Re-evaluating Loricate Choanoflagellate Phylogenetics: Molecular Evidence Points to the Paraphyly of Tectiform Species.}, journal = {Protist}, volume = {173}, number = {6}, pages = {125924}, doi = {10.1016/j.protis.2022.125924}, pmid = {36327744}, issn = {1618-0941}, mesh = {*Choanoflagellata/genetics ; Phylogeny ; }, abstract = {Lorica-bearing choanoflagellates belong to the order Acanthoecida, a taxon which has been consistently recovered as monophyletic in molecular phylogenies. Based upon differences in lorica development and morphology, as well as the presence or absence of a motile dispersal stage, species are labelled as either nudiform or tectiform. Whilst Acanthoecida is robustly resolved in molecular phylogenies, the placement of the root of the clade is less certain with two different positions identified in past studies. One recovered root has been placed between the nudiform family Acanthoecidae and the tectiform family Stephanoecidae. An alternative root placement falls within the tectiform species, recovering the monophyletic Acanthoecidae nested within a paraphyletic Stephanoecidae. Presented here is a 14-gene phylogeny, based upon nucleotide and amino acid sequences, which strongly supports tectiform paraphyly. The horizontal transfer of a ribosomal protein gene, from a possible SAR donor, into a subset of acanthoecid species provides further, independent, support for this root placement. Differing patterns of codon usage bias across the choanoflagellates are proposed as the cause of artefactual phylogenetic signals that lead to the recovery of tectiform monophyly.}, }
@article {pmid36327213, year = {2022}, author = {Gozzi, K and Tran, NT and Modell, JW and Le, TBK and Laub, MT}, title = {Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001790}, pmid = {36327213}, issn = {1545-7885}, support = {BBS/E/J/000PR9791/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 GM082899/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Prophages/genetics/metabolism ; *Caulobacter crescentus/genetics/metabolism ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial ; DNA Repair/genetics ; Bacterial Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.}, }
@article {pmid36326505, year = {2022}, author = {Wilson, A and Molinar, J and Aldrich, J and Chintala, G and Smit, K and Miller, K and Bollivar, DW and Alvey, RM}, title = {Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0087922}, doi = {10.1128/mra.00879-22}, pmid = {36326505}, issn = {2576-098X}, abstract = {We report the genome sequences of 24 newly discovered bacteriophages that infect Rhodobacter capsulatus, a model for photosynthesis and horizontal gene transfer studies. All have substantial relatedness to previously reported siphovirus bacteriophages. Most are categorized in known clusters (RcB, RcC, RcD, and RcF), with one forming a new cluster, RcG.}, }
@article {pmid36325933, year = {2022}, author = {Corning, PA}, title = {The synergism hypothesis (revisited): a theory whose time has come?.}, journal = {Theoretical biology forum}, volume = {115}, number = {1-2}, pages = {85-97}, doi = {10.19272/202211402006}, pmid = {36325933}, issn = {2282-2593}, mesh = {*Biological Evolution ; Selection, Genetic ; *Heredity ; Hybridization, Genetic ; Gene Transfer, Horizontal ; }, abstract = {A major theoretical issue in evolutionary biology over the past two decades has concerned the rise of complexity over time in the natural world, and a search has been underway for "a Grand Unified Theory" - as biologist Daniel McShea characterized it - that is consistent with Darwin's great vision. As it happens, such a theory already exists. It was first proposed many years ago in The Synergism Hypothesis: A Theory of Progressive Evolution, and it involves an economic (or perhaps bioeconomic) theory of complexity. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects - synergies - with functional advantages that may, in turn, become direct causes of natural selection. In other words, the Synergism Hypothesis is a theory about the unique combined effects produced by the relationships between things. I refer to it as Holistic Darwinism; it is entirely con - sistent with natural selection theory, properly understood. Because the Synergism Hypothesis was first proposed during a time when the genecentric, neo-Darwinist paradigm was domi nant in evolutionary biology, it was largely overlooked. But times have changed. Biologist Richard Michod has concluded that "cooperation is now seen as the primary creative force behind ever greater levels of complexity and organization in all of biology." And Martin Nowak has called cooperation "the master architect of evolution." Here I will revisit this theory in the light of the many theoretical developments and research findings in recent years that are supportive of it, including the role of symbiogenesis in evolution, the phenomenon of hybridization, lateral gene transfer in prokaryotes, "developmental plasticity" (evo-devo), epigenetic inheritance, the role of behaviour (and teleonomy) in evolution, and gene-culture coevolution. The Synergism Hypothesis is especially relevant to the evolution of humankind.}, }
@article {pmid36324140, year = {2022}, author = {Slizovskiy, IB and Oliva, M and Settle, JK and Zyskina, LV and Prosperi, M and Boucher, C and Noyes, NR}, title = {Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {185}, pmid = {36324140}, issn = {2049-2618}, support = {1R01AI141810-01/NH/NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).<br><br>RESULTS: Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher&#xa0;ARG&#xa0;recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.<br><br>CONCLUSIONS: TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.}, }
@article {pmid36322896, year = {2022}, author = {Huang, H and Lin, L and Bu, F and Su, Y and Zheng, X and Chen, Y}, title = {Reductive Stress Boosts the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes: The Neglected Side of the Intracellular Redox Spectrum.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {22}, pages = {15594-15606}, doi = {10.1021/acs.est.2c04276}, pmid = {36322896}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Escherichia coli/genetics ; Plasmids/genetics ; Drug Resistance, Microbial/genetics ; *Pseudomonas putida ; Oxidation-Reduction ; Conjugation, Genetic ; }, abstract = {The dissemination of plasmid-borne antibiotic resistance genes (ARGs) among bacteria is becoming a global challenge to the "One Health" concept. During conjugation, the donor/recipient usually encounter diverse stresses induced by the surrounding environment. Previous studies mainly focused on the effects of oxidative stress on plasmid conjugation, but ignored the potential contribution of reductive stress (RS), the other side of the intracellular redox spectrum. Herein, we demonstrated for the first time that RS induced by dithiothreitol could significantly boost the horizontal transfer of plasmid RP4 from Escherichia coli K12 to different recipients (E. coli HB101, Salmonella Typhimurium, and Pseudomonas putida KT2440). Phenotypic and genotypic tests confirmed that RS upregulated genes encoding the transfer apparatus of plasmid RP4, which was attributed to the promoted consumption of intracellular glutamine in the donor rather than the widely reported SOS response. Moreover, RS was verified to benefit ATP supply by activating glycolysis (e.g., GAPDH) and the respiratory chain (e.g., appBC), triggering the deficiency of intracellular free Mg[2+] by promoting its binding, and reducing membrane permeability by stimulating cardiolipin biosynthesis, all of which were beneficial to the functioning of transfer apparatus. Overall, our findings uncovered the neglected risks of RS in ARG spreading and updated the regulatory mechanism of plasmid conjugation.}, }
@article {pmid36314801, year = {2022}, author = {Jiang, W and Zhang, M and Gao, S and Zhu, Q and Qiu, J and Yan, X and Xin, F and Jiang, M and Hong, Q}, title = {Comparative Genomic Analysis of Carbofuran-Degrading Sphingomonads Reveals the Carbofuran Catabolism Mechanism in Sphingobium sp. Strain CFD-1.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0102422}, pmid = {36314801}, issn = {1098-5336}, mesh = {*Carbofuran/metabolism ; *Insecticides/metabolism ; Biodegradation, Environmental ; *Sphingomonadaceae/metabolism ; Genomics ; Phenols/metabolism ; }, abstract = {The worldwide use of the carbamate insecticide carbofuran has caused considerable concern about its environmental fate. Degradation of carbofuran by Sphingobium sp. strain CFD-1 is initiated via the hydrolysis of its ester bond by carbamate hydrolase CehA to form carbofuran phenol. In this study, another carbofuran-degrading strain, Sphingobium sp. CFD-2, was isolated. Subsequently, a cfd gene cluster responsible for the catabolism of carbofuran phenol was predicted by comparing the genomes of strains CFD-1, CFD-2, and Novosphingobium sp. strain KN65.2. The key genes verified to be involved in the catabolism of carbofuran phenol within the cfd cluster include the hydroxylase gene cfdC, epoxide hydrolase gene cfdF, and ring cleavage dioxygenase gene cfdE and are responsible for the successive conversion of carbofuran phenol, resulting in complete ring cleavage. These carbofuran-catabolic genes (cehA and the cfd cluster) are distributed on two plasmids in strain CFD-1 and are highly conserved among the carbofuran-degrading sphingomonad strains. The mobile genetic element IS6100 flanks cehA and the cfd gene cluster, indicating the importance of horizontal gene transfer in the formation of carbofuran degradation gene clusters. The elucidation of the molecular mechanism of carbofuran catabolism provides insights into the evolutionary scenario of the conserved carbofuran catabolic pathway. IMPORTANCE Owing to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. In this study, the cfd gene cluster, responsible for the catabolism of carbofuran phenol, was predicted by comparing sphingomonad genomes. The function of key enzymatic genes in this gene cluster was identified. Furthermore, the carbamate hydrolase gene cehA and the cfd gene cluster are highly conserved in different carbofuran-degrading strains. Additionally, the horizontal gene transfer elements flanking the cfd gene cluster were investigated. These findings help elucidate the molecular mechanism of microbial carbofuran degradation and enhance our understanding of the evolutionary mechanism of the carbofuran catabolic pathway.}, }
@article {pmid36313567, year = {2022}, author = {Cellier, MFM}, title = {Nramp: Deprive and conquer?.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {988866}, pmid = {36313567}, issn = {2296-634X}, abstract = {Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H[+])-dependent manganese (Mn[2+]) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)'s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries 'eukaryotic signature' marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H[+]-dependent Mn[2+] acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn[2+]-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn[2+] sequestering defense perhaps favoring intracellular growth-competent bacteria.}, }
@article {pmid36312970, year = {2022}, author = {Wang, X and Wang, T and Guo, M and Zhang, C and Bo, Z and Wu, Y and Chao, G}, title = {The large plasmid carried class 1 integrons mediated multidrug resistance of foodborne Salmonella Indiana.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {991326}, pmid = {36312970}, issn = {1664-302X}, abstract = {Salmonella enterica serovar Indiana (S. Indiana) has aroused widespread concern as an important zoonotic pathogen. The molecular mechanism of multidrug resistance (MDR) in S. Indiana is not known and should be assessed. We aim to investigate the molecular mechanism of MDR and the importance of large plasmids carried class 1 integrons in the MDR of foodborne S. Indiana. Class 1 integrons in 48 S. Indiana isolates and 200 isolates of 7 other Salmonella serotypes were detected by polymerase chain reaction (PCR). To analyze the antimicrobial resistance genes (ARGs) of two S. Indiana isolates, designated S. Indiana 15 and S. Indiana 222, next-generation sequencing (NGS) was performed, and the resulting sequences were compared with the complete nucleotide sequences of S. Indiana D90 and S. Indiana C629. Comparative functional analysis was conducted between the intI1 (1,014 bp) of S. Indiana 222 and the intI1 (699 bp) of S. Indiana 15. Plasmid conjugation transfer analysis was performed to analyze the horizontal gene transfer of the integrons-related resistance genes with integron-positive and integron-negative Salmonella isolates. 64.58% of S. Indiana isolates carried class 1 integrons, which was significantly higher than that of other Salmonella serotypes (p < 0.001). The NGS results showed that the S. Indiana 15 and S. Indiana 222 isolates carried a large plasmid with a class 1 integron and multiple ARGs, similar to S. Indiana D90 and S. Indiana C629. Two integrases found in S. Indiana isolates belong to class 1 integrases and could integrate resistance genes into specific integration sites of the integrons. The conjugation frequency of intI1 (1,014 bp) was 6.08 × 10[-5], which was significantly higher than that of intI1 (699 bp) (p < 0.01). The large plasmids carrying a class 1 integron and the number of ARGs were strongly correlated (p < 0.001). The conjugation frequency of integron-positive S. Indiana recipient isolates was significantly higher than that of integron-negative recipient isolates (p < 0.05). S. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones. Graphical abstractS. Indiana containing large plasmids carrying a class 1 integron more easily captured resistance genes from other bacteria (S. Enteritidis and S. Derby), which could be an important cause of the emerging pandemic of MDR clones.}, }
@article {pmid36309447, year = {2023}, author = {Alonso García, E and Benomar, N and Lavilla Lerma, L and de la Fuente Ordoñez, JJ and Knapp, CW and Abriouel, H}, title = {Changes in resistome profile of potential probiotic Lactiplantibacillus pentosus in response to edible oil adaptation.}, journal = {Food microbiology}, volume = {109}, number = {}, pages = {104148}, doi = {10.1016/j.fm.2022.104148}, pmid = {36309447}, issn = {1095-9998}, mesh = {Food Microbiology ; Fermentation ; *Lactobacillus pentosus/metabolism ; *Probiotics/metabolism ; *Olea ; Anti-Bacterial Agents/pharmacology/metabolism ; Oils ; }, abstract = {Despite increasing interest to investigate horizontal gene transfer as a leading cause of antibiotic resistance spread, the resistome is not only influenced by the influx and efflux of genes in different environments. Rather, the expression of existing genes under different stress conditions requires special attention. This study determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils influence their phenotypic and genotypic responses to antibiotics. This has significant diet, food matrix, gut health, and food safety concerns. Pre-adapting L. pentosus strains to oils significantly changed their susceptibility profile to antibiotics. However, results generally differed among the three strains; although changes in the Minimum Inhibitory Concentration (MIC) of antibiotics occurred, it depended on the L. pentosus strain and the oil used for adaptation. The pre-adaptation of L. pentosus strains with olive, sunflower, argan and linseed oils induced gene expressions (e.g., rpsL, recA and uvrB) in several stress responses. Thus, to analyze this fact in-depth, transcriptional changes were reported in the selected potential probiotic L. pentosus CF2-10 adapted with olive or sunflower, rerouting its metabolic pathways to export toxic molecules through efflux pumps and ABC transporters. Pre-adaptation of some lactobacilli with olive or sunflower oils may represent a novel approach for manufacturing probiotic products with improved stability, functionality and robustness.}, }
@article {pmid36308932, year = {2023}, author = {Ye, C and Zhang, K and Wu, X and Wan, K and Cai, WF and Feng, M and Yu, X}, title = {Uncovering novel disinfection mechanisms of solar light/periodate system: The dominance of singlet oxygen and metabolomic insights.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130177}, doi = {10.1016/j.jhazmat.2022.130177}, pmid = {36308932}, issn = {1873-3336}, mesh = {Humans ; Disinfection ; Singlet Oxygen ; Escherichia coli ; Pandemics ; *COVID-19 ; *Water Purification ; Water/pharmacology ; }, abstract = {Disinfection plays an essential role in waterborne pathogen control and disease prevention, especially during the COVID-19 pandemic. Catalyst-free solar light/periodate (PI) system has recently presented great potential in water disinfection, whereas the in-depth chemical and microbiological mechanisms for efficient bacterial inactivation remain unclear. Our work delineated firstly the critical role of singlet oxygen, instead of reported hydroxyl radicals and superoxide radicals, in dominating bacterial inactivation by the PI/simulated sunlight (SSL) system. Multi-evidence demonstrated the prominent disinfection performance of this system for Staphylococcus aureus in terms of culturability (> 6 logs CFU), cellular integrity, and metabolic activity. Particularly, the excellent intracellular DNA removal (> 95%) indicated that PI/SSL system may function as a selective disinfection strategy to diminish bacterial culturability without damaging the cell membrane. The PI/SSL system could also effectively inhibit bacterial regrowth for > 5 days and horizontal gene transfer between E. coli genera. Nontargeted metabolomic analysis suggested that PI/SSL system inactivated bacteria by triggering the accumulation of intracellular reactive oxygen species and the depletion of reduced glutathione. Additionally, the PI/SSL system could accomplish simultaneous micropollutant removal and bacterial inactivation, suggesting its versatility in water decontamination. Overall, this study deciphers more comprehensive antibacterial mechanisms of this environmentally friendly disinfection system, facilitating the technical development and application of the selective disinfection strategy in environmental pathogen control.}, }
@article {pmid36308328, year = {2022}, author = {Golparian, D and Jacobsson, S and Sánchez-Busó, L and Bazzo, ML and Lan, PT and Galarza, P and Ohnishi, M and Unemo, M}, title = {GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jac/dkac366}, pmid = {36308328}, issn = {1460-2091}, abstract = {OBJECTIVES: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global threat and novel treatment alternatives are imperative. Herein, susceptibility to the novel antimicrobial zoliflodacin, currently in a global Phase 3 randomized controlled clinical trial for gonorrhoea treatment, was investigated by screening for zoliflodacin GyrB target mutations in publicly available gonococcal genomes and, where feasible, determination of the associated zoliflodacin MIC.<br><br>METHODS: The European Nucleotide Archive was queried using the search term 'Taxon: 485'. DNA sequences from 27&#x200a;151 gonococcal isolates were analysed and gyrB, gyrA, parC and parE alleles characterized.<br><br>RESULTS: GyrB amino acid alterations were rare (97.0% of isolates had a wild-type GyrB sequence). GyrB V470L (2.7% of isolates) was the most prevalent alteration, followed by S467N (0.12%), N. meningitidis GyrB (0.092%), V470I (0.059%), Q468R/P (0.015%), A466T (0.0074%), L425I&#x200a;+&#x200a;L465I (0.0037%), L465I (0.0037%), G482S (0.0037%) and D429V (0.0037%). Only one isolate (0.0037%) carried a substitution in a resistance-associated GyrB codon (D429V), resulting in a zoliflodacin MIC of 8&#x2005;mg/L. None of the other detected gyrB, gyrA, parC or parE mutations caused a zoliflodacin MIC outside the wild-type MIC distribution.<br><br>CONCLUSIONS: The zoliflodacin target GyrB was highly conserved among 27&#x200a;151 global gonococcal isolates cultured in 1928-2021. The single zoliflodacin-resistant clinical isolate (0.0037%) was cultured from a male patient in Japan in 2000. Evidently, this strain has not clonally expanded nor has the gyrB zoliflodacin-resistance mutation disseminated through horizontal gene transfer to other strains. Phenotypic and genomic surveillance, including gyrB mutations, of zoliflodacin susceptibility are imperative.}, }
@article {pmid36307484, year = {2022}, author = {Tran, HNH and Thu, TNH and Nguyen, PH and Vo, CN and Doan, KV and Nguyen Ngoc Minh, C and Nguyen, NT and Ta, VND and Vu, KA and Hua, TD and Nguyen, TNT and Van, TT and Pham Duc, T and Duong, BL and Nguyen, PM and Hoang, VC and Pham, DT and Thwaites, GE and Hall, LJ and Slade, DJ and Baker, S and Tran, VH and Chung The, H}, title = {Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {87}, pmid = {36307484}, issn = {2055-5008}, support = {218726/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 215515/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Fusobacterium/genetics ; Genomics ; *Microbiota ; *Colorectal Neoplasms/microbiology ; Asian People ; }, abstract = {Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.}, }
@article {pmid36306437, year = {2022}, author = {Kronmiller, BA and Feau, N and Shen, D and Tabima, JF and Ali, SS and Armitage, AD and Arredondo, FD and Bailey, BA and Bollmann, SR and Dale, A and Harrison, R and Hrywkiw, K and Kasuga, T and McDougal, R and Nellist, CF and Panda, P and Tripathy, S and Williams, NM and Ye, W and Wang, Y and Hamelin, RC and Grunwald, NJ}, title = {Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {}, doi = {10.1094/MPMI-06-22-0133-R}, pmid = {36306437}, issn = {0894-0282}, abstract = {Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts including crops, trees, and ornamentals. We sequenced 31 individual Phytophthora species genomes and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, as well as plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine learning approach to identify horizontally transferred genes with bacterial or fungal origin we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthoras. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in Phytophthora.}, }
@article {pmid36303123, year = {2022}, author = {Vaughan, AL and Altermann, E and Glare, TR and Hurst, MRH}, title = {Genome sequence of the entomopathogenic Serratia entomophila isolate 626 and characterisation of the species specific itaconate degradation pathway.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {728}, pmid = {36303123}, issn = {1471-2164}, mesh = {Animals ; *Serratia/genetics ; Virulence/genetics ; Plasmids ; *Coleoptera/genetics ; Larva ; Serratia marcescens/genetics ; }, abstract = {BACKGROUND: Isolates of Serratia entomophila and S. proteamaculans (Yersiniaceae) cause disease specific to the endemic New Zealand pasture pest, Costelytra giveni (Coleoptera: Scarabaeidae). Previous genomic profiling has shown that S. entomophila isolates appear to have conserved genomes and, where present, conserved plasmids. In the absence of C. giveni larvae, S. entomophila prevalence reduces in the soil over time, suggesting that S. entomophila has formed a host-specific relationship with C. giveni. To help define potential genetic mechanisms driving retention of the chronic disease of S. entomophila, the genome of the isolate 626 was sequenced, enabling the identification of unique chromosomal properties, and defining the gain/loss of accessory virulence factors relevant to pathogenicity to C. giveni larvae.<br><br>RESULTS: We report the complete sequence of S. entomophila isolate 626, a causal agent of amber disease in C. giveni larvae. The genome of S. entomophila 626 is 5,046,461&#xa0;bp, with 59.1% G&#x2009;+&#x2009;C content and encoding 4,695 predicted CDS. Comparative analysis with five previously sequenced Serratia species, S. proteamaculans 336X, S. marcescens Db11, S. nematodiphila DH-S01, S. grimesii BXF1, and S. ficaria NBRC 102596, revealed a core of 1,165 genes shared. Further comparisons between S. entomophila 626 and S. proteamaculans 336X revealed fewer predicted phage-like regions and genomic islands in 626, suggesting less horizontally acquired genetic material. Genomic analyses revealed the presence of a four-gene itaconate operon, sharing a similar gene order as the Yersinia pestis ripABC complex. Assessment of a constructed 626::RipC mutant revealed that the operon confer a possible metabolic advantage to S. entomophila in the initial stages of C. giveni infection.<br><br>CONCLUSIONS: Evidence is presented where, relative to S. proteamaculans 336X, S. entomophila 626 encodes fewer genomic islands and phages, alluding to limited horizontal gene transfer in S. entomophila. Bioassay assessments of a S. entomophila-mutant with a targeted mutation of the itaconate degradation region unique to this species, found the mutant to have a reduced capacity to replicate post challenge of the C. giveni larval host, implicating the itaconate operon in establishment within the host.}, }
@article {pmid36301081, year = {2022}, author = {Castro-Gutierrez, V and Fuller, E and Garcillán-Barcia, MP and Helgason, T and Hassard, F and Moir, J}, title = {Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36301081}, issn = {2057-5858}, mesh = {*Proteobacteria/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; DNA Transposable Elements/genetics ; *Sphingomonadaceae/genetics ; Escherichia coli/genetics ; }, abstract = {Bioremediation of metaldehyde from drinking water using metaldehyde-degrading strains has recently emerged as a promising alternative. Whole-genome sequencing was used to obtain full genomes for metaldehyde degraders Acinetobacter calcoaceticus E1 and Sphingobium CMET-H. For the former, the genetic context of the metaldehyde-degrading genes had not been explored, while for the latter, none of the degrading genes themselves had been identified. In A. calcoaceticus E1, IS91 and IS6-family insertion sequences (ISs) were found surrounding the metaldehyde-degrading gene cluster located in plasmid pAME76. This cluster was located in closely-related plasmids and associated to identical ISs in most metaldehyde-degrading β- and γ-Proteobacteria, indicating horizontal gene transfer (HGT). For Sphingobium CMET-H, sequence analysis suggested a phytanoyl-CoA family oxygenase as a metaldehyde-degrading gene candidate due to its close homology to a previously identified metaldehyde-degrading gene known as mahX. Heterologous gene expression in Escherichia coli alongside degradation tests verified its functional significance and the degrading gene homolog was henceforth called mahS. It was found that mahS is hosted within the conjugative plasmid pSM1 and its genetic context suggested a crossover between the metaldehyde and acetoin degradation pathways. Here, specific replicons and ISs responsible for maintaining and dispersing metaldehyde-degrading genes in α, β and γ-Proteobacteria through HGT were identified and described. In addition, a homologous gene implicated in the first step of metaldehyde utilisation in an α-Proteobacteria was uncovered. Insights into specific steps of this possible degradation pathway are provided.}, }
@article {pmid36298845, year = {2022}, author = {Harrison, RL and Rowley, DL}, title = {The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298845}, issn = {1999-4915}, mesh = {Animals ; *Nucleopolyhedroviruses ; Phylogeny ; Genome, Viral ; GTP Phosphohydrolases/genetics ; Open Reading Frames ; *Moths ; Nucleotides ; }, abstract = {We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.}, }
@article {pmid36298721, year = {2022}, author = {Lal, A and Kil, EJ and Vo, TTB and Wira Sanjaya, IGNP and Qureshi, MA and Nattanong, B and Ali, M and Shuja, MN and Lee, S}, title = {Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298721}, issn = {1999-4915}, mesh = {*Geminiviridae/genetics ; DNA, Viral/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Pakistan ; Plant Diseases ; *Begomovirus ; Sequence Analysis, DNA ; Genome, Viral ; }, abstract = {Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch's postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name 'Chenopodium leaf distortion virus' (CLDV).}, }
@article {pmid36296271, year = {2022}, author = {Navarro, A and Rodea, GE and Castelán-Sánchez, HG and Saucedo-Pastrana, HA and Licona-Moreno, D and Eslava-Campos, C and Tirado-Gómez, LL and Vilchis-Reyes, A and García de la Torre, G and Cruz-Licea, V}, title = {Importance of Microbiome of Fecal Samples Obtained from Adolescents with Different Weight Conditions on Resistance Gene Transfer.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296271}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) is a relevant public health problem worldwide, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. The microbiome of fecal samples from Mexican adolescents were analyzed and correlated with eating habits, and the presence of AMR genes on bacteria in the microbiome was evaluated. Fecal samples from adolescents were collected and processed to extract genomic DNA. An Illumina HiSeq 1500 system was used to determine resistance genes and the microbiome of adolescents through the amplification of gene resistance and the V3-V4 regions of RNA, respectively. Analysis of the microbiome from fecal samples taken from 18 obese, overweight, and normal-weight adolescents revealed that the Firmicutes was the most frequent phylum, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The following species were detected as the most frequent in the samples: F. prausnitzii, P. cori, B. adolescentis, E. coli and A. muciniphila. The presence of Bacteroides, Prevotella and Ruminococcus was used to establish the enterotype; enterotype 1 was more common in women and enterotype 2 was more common in men. Twenty-nine AMR genes were found for β-lactamases, fluoroquinolones, aminoglycosides, macrolide, lincosamides, streptogramin (MLS), tetracyclines and sulfonamides. The presence of microorganisms in fecal samples that harbor AMR genes that work against antimicrobials frequently used for the treatment of microbial infections such as b-lactams, macrolides, aminoglycosides, MLS, and tetracyclines is of great concern, as these organisms may be an important reservoir for horizontal AMR gene transfer.}, }
@article {pmid36292780, year = {2022}, author = {Li, M and Chen, Q and Wu, C and Li, Y and Wang, S and Chen, X and Qiu, B and Li, Y and Mao, D and Lin, H and Yu, D and Cao, Y and Huang, Z and Cui, C and Zhong, Z}, title = {A Novel Module Promotes Horizontal Gene Transfer in Azorhizobium caulinodans ORS571.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292780}, issn = {2073-4425}, mesh = {*Azorhizobium caulinodans/genetics ; Gene Transfer, Horizontal ; *Sesbania/microbiology ; Integrases/metabolism ; Flavonoids/metabolism ; Soil ; }, abstract = {Azorhizobium caulinodans ORS571 contains an 87.6 kb integrative and conjugative element (ICE[Ac]) that conjugatively transfers symbiosis genes to other rhizobia. Many hypothetical redundant gene fragments (rgfs) are abundant in ICE[Ac], but their potential function in horizontal gene transfer (HGT) is unknown. Molecular biological methods were employed to delete hypothetical rgfs, expecting to acquire a minimal ICE[Ac] and consider non-functional rgfs as editable regions for inserting genes related to new symbiotic functions. We determined the significance of rgf4 in HGT and identified the physiological function of genes designated rihF1a (AZC_3879), rihF1b (AZC_RS26200), and rihR (AZC_3881). In-frame deletion and complementation assays revealed that rihF1a and rihF1b work as a unit (rihF1) that positively affects HGT frequency. The EMSA assay and lacZ-based reporter system showed that the XRE-family protein RihR is not a regulator of rihF1 but promotes the expression of the integrase (intC) that has been reported to be upregulated by the LysR-family protein, AhaR, through sensing host's flavonoid. Overall, a conservative module containing rihF1 and rihR was characterized, eliminating the size of ICE[Ac] by 18.5%. We propose the feasibility of constructing a minimal ICE[Ac] element to facilitate the exchange of new genetic components essential for symbiosis or other metabolic functions between soil bacteria.}, }
@article {pmid36291676, year = {2022}, author = {Mocchetti, E and Morette, L and Mulliert, G and Mathiot, S and Guillot, B and Dehez, F and Chauvat, F and Cassier-Chauvat, C and Brochier-Armanet, C and Didierjean, C and Hecker, A}, title = {Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291676}, issn = {2218-273X}, mesh = {*Glutathione Transferase/metabolism ; *Synechocystis/genetics/metabolism ; Pyruvaldehyde ; Glutathione/metabolism ; Protein Structure, Secondary ; }, abstract = {Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site ([10]SRAS[13] in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.}, }
@article {pmid36289972, year = {2022}, author = {Cherak, Z and Loucif, L and Bendjama, E and Moussi, A and Benbouza, A and Grainat, N and Rolain, JM}, title = {Dissemination of Carbapenemases and MCR-1 Producing Gram-Negative Bacteria in Aquatic Environments in Batna, Algeria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289972}, issn = {2079-6382}, abstract = {Antibiotic-resistant-bacteria are being considered as emerging environmental contaminants where the importance of the surrounding environment in their emergence and dissemination has been emphasized. The aim of this study was to screen for the presence and diversity of carbapenem- and colistin-resistant Gram-negative bacteria (GNBs) in different aquatic environments. Water samples were collected in Batna, Algeria. Carbapenem- and colistin-resistant GNBs were selectively isolated and then identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. After phenotypic antibiotic susceptibility testing, the molecular mechanisms of β-lactams and colistin-resistance were investigated by PCR and sequencing. The clonality of mcr-1 positive Escherichia coli was determined by multi-locus sequence typing. We noticed a high level of resistance in both tap water and wastewater. The most commonly found carbapenem-resistance mechanism was the OXA-48 enzyme, but other carbapenemases were also detected. In addition, the mcr-1 gene was detected in 18 E. coli of different sequence types. Our findings highlight the role of aquatic environments in the dissemination of resistant-bacteria, especially considering that water is a connecting medium between different ecological systems and can easily transmit resistant-bacteria and promote horizontal gene transfer. Thus, the development of effective treatment strategies for eliminating antibiotic-resistance is seriously needed.}, }
@article {pmid36289941, year = {2022}, author = {Sekizuka, T and Tanaka, R and Hashino, M and Yatsu, K and Kuroda, M}, title = {Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36289941}, issn = {2079-6382}, abstract = {To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.}, }
@article {pmid36287061, year = {2022}, author = {Li, Y and Shi, X and Zuo, Y and Li, T and Liu, L and Shen, Z and Shen, J and Zhang, R and Wang, S}, title = {Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0229722}, doi = {10.1128/spectrum.02297-22}, pmid = {36287061}, issn = {2165-0497}, abstract = {Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 10[4]-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.}, }
@article {pmid36286524, year = {2022}, author = {Akob, DM and Sutton, JM and Bushman, TJ and Baesman, SM and Klein, E and Shrestha, Y and Andrews, R and Fierst, JL and Kolton, M and Gushgari-Doyle, S and Oremland, RS and Freeman, JL}, title = {Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {22}, pages = {e0121922}, pmid = {36286524}, issn = {1098-5336}, mesh = {*Bradyrhizobium ; *Trichloroethylene/metabolism ; Nitrogen Fixation/genetics ; Soil/chemistry ; Acetylene/metabolism ; Phylogeny ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Root Nodules, Plant/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.}, }
@article {pmid36285389, year = {2022}, author = {Hulin, MT and Rabiey, M and Zeng, Z and Vadillo Dieguez, A and Bellamy, S and Swift, P and Mansfield, JW and Jackson, RW and Harrison, RJ}, title = {Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18573}, pmid = {36285389}, issn = {1469-8137}, support = {BB/P006272/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010568/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010746/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.}, }
@article {pmid36282569, year = {2022}, author = {Cerqueira de Araujo, A and Josse, T and Sibut, V and Urabe, M and Asadullah, A and Barbe, V and Nakai, M and Huguet, E and Periquet, G and Drezen, JM}, title = {Chelonus inanitus bracovirus encodes lineage-specific proteins and truncated immune IκB-like factors.}, journal = {The Journal of general virology}, volume = {103}, number = {10}, pages = {}, doi = {10.1099/jgv.0.001791}, pmid = {36282569}, issn = {1465-2099}, mesh = {Humans ; Animals ; *Polydnaviridae/genetics ; Phylogeny ; *Wasps/genetics ; Viral Proteins/genetics ; Biological Evolution ; }, abstract = {Bracoviruses and ichnoviruses are endogenous viruses of parasitic wasps that produce particles containing virulence genes expressed in host tissues and necessary for parasitism success. In the case of bracoviruses the particles are produced by conserved genes of nudiviral origin integrated permanently in the wasp genome, whereas the virulence genes can strikingly differ depending on the wasp lineage. To date most data obtained on bracoviruses concerned species from the braconid subfamily of Microgastrinae. To gain a broader view on the diversity of virulence genes we sequenced the genome packaged in the particles of Chelonus inanitus bracovirus (CiBV) produced by a wasp belonging to a different subfamily: the Cheloninae. These are egg-larval parasitoids, which means that they oviposit into the host egg and the wasp larvae then develop within the larval stages of the host. We found that most of CiBV virulence genes belong to families that are specific to Cheloninae. As other bracoviruses and ichnoviruses however, CiBV encode v-ank genes encoding truncated versions of the immune cactus/IκB factor, which suggests these proteins might play a key role in host-parasite interactions involving domesticated endogenous viruses. We found that the structures of CiBV V-ANKs are different from those previously reported. Phylogenetic analysis supports the hypothesis that they may originate from a cactus/IκB immune gene from the wasp genome acquired by the bracovirus. However, their evolutionary history is different from that shared by other V-ANKs, whose common origin probably reflects horizontal gene transfer events of virus sequences between braconid and ichneumonid wasps.}, }
@article {pmid36282171, year = {2022}, author = {Koonin, EV and Krupovic, M}, title = {A life LINE for large viruses.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36282171}, issn = {2050-084X}, mesh = {*Retroelements ; *Poxviridae/genetics ; Vaccinia virus/genetics ; Virus Replication ; }, abstract = {As long suspected, poxviruses capture host genes through a reverse-transcription process now shown to be mediated by retrotransposons.}, }
@article {pmid36280316, year = {2022}, author = {Paul, D and Das, B}, title = {Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens.}, journal = {Progress in molecular biology and translational science}, volume = {192}, number = {1}, pages = {1-31}, doi = {10.1016/bs.pmbts.2022.07.009}, pmid = {36280316}, issn = {1878-0814}, mesh = {Humans ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Ecosystem ; Bacteria/genetics ; Gene Transfer, Horizontal ; }, abstract = {The human gastrointestinal tract is home to a complex and dynamic community of microorganisms known as gut microbiota, which provide the host with important metabolic, signaling, and immunomodulatory functions. Both the commensal and pathogenic members of the gut microbiome serve as reservoirs of antimicrobial-resistance genes (ARG), which can cause potential health threats to the host and can transfer the ARGs to the susceptible microbes and into the environment. Antimicrobial resistance is becoming a major burden on human health and is widely recognized as a global challenge. The diversity and abundance of ARGs in the gut microbiome are variable and depend on the exposure to healthcare-associated antibiotics, usage of antibiotics in veterinary and agriculture, and the migration of the population. The transfer frequency of the ARGs through horizontal gene transfer (HGT) with the help of mobile genetic elements (MGEs) like plasmids, transposons, or phages is much higher among bacteria living in the GI tract compared to other microbial ecosystems. HGT in gut bacteria is facilitated through multiple gene transfer mechanisms, including transformation, conjugation, transduction, and vesicle fusion. It is the need of the hour to implement strict policies to limit indiscriminate antibiotic usage when needed. Developing rapid diagnostic tests for resistance determination and alternatives to antibiotics like vaccination, probiotics, and bacteriophage therapy should have the highest priority in the research and development sectors. Collective actions for sustainable development against resistant pathogens by promoting endogenous gut microbial growth and diversity through interdisciplinary research and findings are key to overcoming the current antimicrobial resistance crisis.}, }
@article {pmid36279613, year = {2022}, author = {Yang, J and Xiang, J and Xie, Y and Yu, K and Li, J and Wang, H and Li, P and Gin, KY and He, Y}, title = {Removal behavior and key drivers of antibiotic resistance genes in two full-scale leachate treatment plants.}, journal = {Water research}, volume = {226}, number = {}, pages = {119239}, doi = {10.1016/j.watres.2022.119239}, pmid = {36279613}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; Bioreactors ; Bacteria/genetics ; }, abstract = {Leachate is a critical reservoir of antibiotic resistance genes (ARGs) and its proper treatment is closely related to human health and ecosystem safety. Here, we used high-throughput qPCR to explore the removal behavior of ARGs in two full-scale leachate treatment plants (LTPs) where biological treatment and membrane filtration processes were integrated. A total of 286 ARGs and 55 mobile genetic elements (MGEs) were detected, with aminoglycoside, multidrug and MLSB resistance genes being the most prevalent and abundant. Anaerobic digestion was found to be an important pretreatment process for leachate, while anoxic/aerobic tanks in membrane bioreactor (MBR) acted as incubators for ARGs due to their significant proliferation effect on ARGs. Integrated membrane filtration (UF-NF-RO) excelled in ARGs removal with absolute abundances reduced by 3 to 6 orders of magnitude, from about 10[9] copies/mL in raw leachate to 10[3]-10[5] copies/mL in effluents. Our results also showed that leachate treatment processes significantly altered the composition of ARGs and bacterial communities. Procrustes analysis and network analysis revealed strong associations between microbes and ARGs, with several hub genes and bacterial genera identified. Structural equation models (SEMs) indicated that bacterial composition, MGEs and basic water properties were the key drivers shaping ARGs dynamics in the raw leachate, biological system and filtration system, respectively. Notably, several pathogens (e.g., Klebsiella, Vibrio, Aeromonas) were closely correlated with ARGs in raw leachate and may amplify the dissemination risks of ARGs. Moreover, insertion sequences in biological systems would accelerate the horizontal gene transfer of ARGs. In short, this study provides new insights into the mechanisms of ARGs removal and dissemination behavior in industrial-scale LTPs.}, }
@article {pmid36275512, year = {2022}, author = {Wang, X and Yoo, E and Lee, S and Cho, GT and Lee, GA and Yi, JY and Du, X and Han, S and Hyun, DY and Ro, N and Kim, KM}, title = {Classification of 17 species Aegilops using DNA barcoding and SNPs, reveals gene flow among Aegilops biuncialis, Aegilops juvenalis, and Aegilops columnaris.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {984825}, pmid = {36275512}, issn = {1664-462X}, abstract = {Rapid changes in agricultural environments caused by global warming pose a major challenge to food production and safety. Common wheat (Triticum aestivum) is a hexaploid plant (AABBDD) that shares large numbers of quantitative traits and resistance genes with B and D genomes of Aegilops species, which are responsible for several metabolic functions and biosynthetic processes, particularly in plant adaptation to biotic as well as abiotic stresses. Comparatively, the abundance of the Aegilops gene pool is much higher than that of Triticum. Therefore, we used four universal DNA barcodes for plants (ITS2, matK, rbcL, and psbM-petN) to construct a phylogenetic tree to classify the genus Aegilops. Fourteen species were distinguished among a total of 17 representative species. Aegilops biuncialis, Aegilops juvenalis, and Aegilops umbellulata could not be grouped into any of the clusters in the phylogenetic tree, indicating that these three species could not be distinguished by four DNA barcodes. Therefore, from 2408 SNPs obtained using genotyping by sequencing (GBS), we manually screened 30 SNPs that could be potentially used to classify these three species. The results of gene flow and genetic differentiation index (Fst) showed that the genetic differentiation among the three species was small, and there was bidirectional horizontal gene transfer between the three species, which was consistent with our results that the three species were difficult to classify by DNA barcode.}, }
@article {pmid36271797, year = {2022}, author = {Wisniewska, A and Wons, E and Potrykus, K and Hinrichs, R and Gucwa, K and Graumann, PL and Mruk, I}, title = {Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage.}, journal = {Nucleic acids research}, volume = {50}, number = {19}, pages = {10964-10980}, pmid = {36271797}, issn = {1362-4962}, mesh = {*Transcription Factors/genetics/metabolism ; *DNA Restriction-Modification Enzymes/genetics ; Prophages/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Escherichia coli/genetics/metabolism ; Gene Regulatory Networks ; }, abstract = {Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.}, }
@article {pmid36270189, year = {2023}, author = {Yu, Y and Xie, Z and Yang, J and Yang, R and Li, Y and Zhu, Y and Zhao, Y and Yang, Q and Chen, J and Alwathnani, HA and Feng, R and Rensing, C and Herzberg, M}, title = {Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130184}, doi = {10.1016/j.jhazmat.2022.130184}, pmid = {36270189}, issn = {1873-3336}, mesh = {Antimony/toxicity ; *Arsenites ; *Arsenic ; *Metalloids ; *Bacteriophages/genetics ; Citrobacter/genetics ; }, abstract = {Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.}, }
@article {pmid36268794, year = {2022}, author = {McLellan, LK and Anderson, ME and Grossman, AD}, title = {TnSmu1 is a functional integrative and conjugative element in Streptococcus mutans that when expressed causes growth arrest of host bacteria.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14992}, pmid = {36268794}, issn = {1365-2958}, support = {R35 GM122538/GM/NIGMS NIH HHS/United States ; R35 GM122538/GM/NIGMS NIH HHS/United States ; }, abstract = {Integrative and conjugative elements (ICEs) are major drivers of horizontal gene transfer in bacteria. They mediate their own transfer from host cells (donors) to recipients and allow bacteria to acquire new phenotypes, including pathogenic and metabolic capabilities and drug resistances. Streptococcus mutans, a major causative agent of dental caries, contains a putative ICE, TnSmu1, integrated at the 3' end of a leucyl tRNA gene. We found that TnSmu1 is a functional ICE, containing all the genes necessary for ICE function. It excised from the chromosome and excision was stimulated by DNA damage. We identified the DNA junctions generated by excision of TnSmu1, defined the ends of the element, and detected the extrachromosomal circle. We found that TnSmu1 can transfer from S. mutans donors to recipients when co-cultured on solid medium. The presence of TnSmu1 in recipients inhibited successful acquisition of another copy and this inhibition was mediated, at least in part, by the likely transcriptional repressor encoded by the element. Using microscopy to track individual cells, we found that activation of TnSmu1 caused an arrest of cell growth. Our results demonstrate that TnSmu1 is a functional ICE that affects the biology of its host cells.}, }
@article {pmid36267172, year = {2022}, author = {Fernanda, PA and Liu, S and Yuan, T and Ramalingam, B and Lu, J and Sekar, R}, title = {Diversity and abundance of antibiotic resistance genes and their relationship with nutrients and land use of the inflow rivers of Taihu Lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009297}, pmid = {36267172}, issn = {1664-302X}, abstract = {Taihu Lake is the third largest freshwater lake in China and an important source for drinking water, flood protection, aquaculture, agriculture, and other activities. This lake is connected to many principal and small rivers with inflow from west and outflow on the eastern side of the lake and these inflow rivers are believed to significantly contribute to the water pollution of the lake. This study was aimed at assessing the diversity and abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and their relationship with water quality parameters and land use patterns. Water samples were collected from 10 major inflow rivers and the source water protection area of the Taihu Lake in spring and summer 2019. High-throughput profiling was used to detect and quantify 384 ARGs and MGEs and in addition, 11 water quality parameters were analyzed. The results showed that the number of ARGs/MGEs detected in each inflow river ranged from 105 to 185 in spring and 107 to 180 in summer. The aminoglycoside resistance genes were the most dominant types ARGs detected followed by beta-lactam resistance, multidrug resistance, macrolide-lincosamide-streptogramin B (MLSB) resistance genes, which contributed to 65% of the ARGs. The water quality parameters showed significant correlation with absolute abundance of ARGs. Furthermore, significant correlation between ARGs and MGEs were also observed which demonstrates potential gene transfer among organisms through horizontal gene transfer via MGEs. ARGs showed strong positive correlation with cultivated and industrial lands whereas, negative correlation was observed with river, lake, forest, land for green buffer, and land for port and harbor. The overall results indicate that the inflow rivers of Taihu Lake are polluted by various sources including multiple nutrients and high abundance of ARGs, which needs attention for better management of the inflow rivers of this lake.}, }
@article {pmid36264827, year = {2022}, author = {Zürcher, JF and Robertson, WE and Kappes, T and Petris, G and Elliott, TS and Salmond, GPC and Chin, JW}, title = {Refactored genetic codes enable bidirectional genetic isolation.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6619}, pages = {516-523}, doi = {10.1126/science.add8943}, pmid = {36264827}, issn = {1095-9203}, support = {/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acids/genetics ; *Codon/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genetic Code ; Protein Biosynthesis/genetics ; Genome, Bacterial ; *Cell Engineering ; }, abstract = {The near-universal genetic code defines the correspondence between codons in genes and amino acids in proteins. We refactored the structure of the genetic code in Escherichia coli and created orthogonal genetic codes that restrict the escape of synthetic genetic information into natural life. We developed orthogonal and mutually orthogonal horizontal gene transfer systems, which permit the transfer of genetic information between organisms that use the same genetic code but restrict the transfer of genetic information between organisms that use different genetic codes. Moreover, we showed that locking refactored codes into synthetic organisms completely blocks invasion by mobile genetic elements, including viruses, which carry their own translation factors and successfully invade organisms with canonical and compressed genetic codes.}, }
@article {pmid36261788, year = {2022}, author = {Chong, SL and Tan, JL and Ngeow, YF}, title = {The resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {715}, pmid = {36261788}, issn = {1471-2164}, mesh = {Humans ; *Mycobacterium abscessus/genetics ; Gene Transfer, Horizontal ; Phylogeny ; beta-Lactams ; Anti-Bacterial Agents ; Aminoglycosides ; }, abstract = {BACKGROUND: Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico.<br><br>RESULTS: From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes.<br><br>CONCLUSION: Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC.}, }
@article {pmid36261416, year = {2022}, author = {Siddique, S and Radakovic, ZS and Hiltl, C and Pellegrin, C and Baum, TJ and Beasley, H and Bent, AF and Chitambo, O and Chopra, D and Danchin, EGJ and Grenier, E and Habash, SS and Hasan, MS and Helder, J and Hewezi, T and Holbein, J and Holterman, M and Janakowski, S and Koutsovoulos, GD and Kranse, OP and Lozano-Torres, JL and Maier, TR and Masonbrink, RE and Mendy, B and Riemer, E and Sobczak, M and Sonawala, U and Sterken, MG and Thorpe, P and van Steenbrugge, JJM and Zahid, N and Grundler, F and Eves-van den Akker, S}, title = {The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6190}, pmid = {36261416}, issn = {2041-1723}, mesh = {Animals ; *Parasites ; Pantothenic Acid ; Transcriptome ; *Tylenchida ; *Cysts ; }, abstract = {Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.}, }
@article {pmid36259734, year = {2022}, author = {Zhao, D and Zhang, S and Kumar, S and Zhou, H and Xue, Q and Sun, W and Zhou, J and Xiang, H}, title = {Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota".}, journal = {mSystems}, volume = {}, number = {}, pages = {e0066922}, doi = {10.1128/msystems.00669-22}, pmid = {36259734}, issn = {2379-5077}, abstract = {Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.}, }
@article {pmid36256808, year = {2022}, author = {Eppley, JM and Biller, SJ and Luo, E and Burger, A and DeLong, EF}, title = {Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2212722119}, pmid = {36256808}, issn = {1091-6490}, mesh = {*Bacteriophages/genetics ; Seawater/microbiology ; Oceans and Seas ; *Viruses/genetics ; Virion/genetics ; Genome, Viral/genetics ; }, abstract = {Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage immunity, and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, bacteriophage-induced cell mortality and cellular host and virus productivity. Given that marine phage satellites cannot be distinguished from bona fide viral particles via commonly used microscopic techniques, their predicted numbers (∼3.2 × 10[26] in the ocean) may influence current estimates of virus densities, production, and virus-induced mortality. In total, the data suggest that marine phage satellites have potential to significantly impact the ecology and evolution of bacteria and their viruses throughout the oceans. We predict that any habitat that harbors bacteriophage will also harbor similar phage satellites, making them a ubiquitous feature of most microbiomes on Earth.}, }
@article {pmid36255244, year = {2022}, author = {Zhu, N and Sun, S and Leng, F and Fan, W and Chen, J and Ma, J and He, H and Yang, G and Wang, Y}, title = {Identification of Key Genes during Ca[2+]-Induced Genetic Transformation in Escherichia coli by Combining Multi-Omics and Gene Knockout Techniques.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {21}, pages = {e0058722}, pmid = {36255244}, issn = {1098-5336}, mesh = {*Escherichia coli/genetics ; Gene Knockout Techniques ; Plasmids ; *Gene Transfer, Horizontal ; Transformation, Genetic ; }, abstract = {The molecular mechanism of the Ca[2+]-mediated formation of competent cells in Escherichia coli remains unclear. In this study, transcriptome and proteomics techniques were used to screen genes in response to Ca[2+] treatment. A total of 333 differentially expressed genes (317 upregulated and 16 downregulated) and 145 differentially expressed proteins (54 upregulated and 91 downregulated) were obtained. These genes and proteins are mainly enriched in cell membrane components, transmembrane transport, and stress response-related functional terms. Fifteen genes with these functions, including yiaW, ygiZ, and osmB, are speculated to play a key role in the cellular response to Ca[2+]. Three single-gene deletion strains were constructed with the Red homologous recombination method to verify its function in genetic transformation. The transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. None of the three gene deletion strains changed in size, which is one of the main elements of microscopic morphology, but they exhibited different membrane permeabilities and transformation efficiencies. This study demonstrates that Ca[2+]-mediated competence formation in E. coli is not a simple physicochemical process and may involve the regulation of genes in response to Ca[2+]. This study lays the foundation for further in-depth analyses of the molecular mechanism of Ca[2+]-mediated transformation. IMPORTANCE Using transcriptome and proteome techniques and association analysis, we identified several key genes involved in the formation of Ca[2+]-mediated E. coli DH5α competent cells. We used Red homologous recombination technology to construct three single-gene deletion strains and found that the transformation efficiencies of yiaW, ygiZ, and osmB deletion strains for different-size plasmids were significantly increased. These results proved that the genetic transformation process is not only a physicochemical process but also a reaction process involving multiple genes. These results suggest ways to improve the horizontal gene transfer mechanism of foodborne microorganisms and provide new ideas for ensuring the safety of food preservation and processing.}, }
@article {pmid36252757, year = {2022}, author = {Li, S and Gao, M and Dong, H and Jiang, Y and Liang, W and Jiang, J and Ho, SH and Li, F}, title = {Deciphering the fate of antibiotic resistance genes in norfloxacin wastewater treated by a bio-electro-Fenton system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128110}, doi = {10.1016/j.biortech.2022.128110}, pmid = {36252757}, issn = {1873-2976}, abstract = {The misuse of antibiotics has increased the prevalence of antibiotic resistance genes (ARGs), considered a class of critical environmental contaminants due to their ubiquitous and persistent nature. Previous studies reported the potentiality of bio-electro-Fenton processes for antibiotic removal and ARGs control. However, the production and fate of ARGs in bio-electro-Fenton processes triggered by microbial fuel cells are rare. In this study, the norfloxacin (NFLX) average residual concentrations within two days were 2.02, 6.07 and 14.84 mg/L, and the average removal efficiency of NFLX was 79.8%, 69.6% and 62.9% at the initial antibiotic concentrations of 10, 20 and 40 mg/L, respectively. The most prevalent resistance gene type in all processes was the fluoroquinolone antibiotic gene. Furthermore, Proteobacteria was the dominant ARG-carrying bacteria. Overall, this study can provide theoretical support for the efficient treatment of high antibiotics-contained wastewater by bio-electro-Fenton systems to better control ARGs from the perspective of ecological security.}, }
@article {pmid36251935, year = {2022}, author = {Lu, J and Yu, Z and Ding, P and Guo, J}, title = {Triclosan Promotes Conjugative Transfer of Antibiotic Resistance Genes to Opportunistic Pathogens in Environmental Microbiome.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {15108-15119}, doi = {10.1021/acs.est.2c05537}, pmid = {36251935}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Microbiota ; Plasmids ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; *Triclosan/pharmacology ; }, abstract = {Although triclosan, as a widely used antiseptic chemical, is known to promote the transmission of antibiotic resistance to diverse hosts in pure culture, it is still unclear whether and how triclosan could affect the transmission of broad-host-range plasmids among complex microbial communities. Here, bacterial culturing, fluorescence-based cell sorting, and high-throughput 16S rRNA gene amplicon sequencing were combined to investigate contributions of triclosan on the transfer rate and range of an IncP-type plasmid from a proteobacterial donor to an activated sludge microbiome. Our results demonstrate that triclosan significantly enhances the conjugative transfer of the RP4 plasmid among activated sludge communities at environmentally relevant concentrations. High-throughput 16S rRNA gene sequencing on sorted transconjugants demonstrates that triclosan not only promoted the intergenera transfer but also the intragenera transfer of the RP4 plasmid among activated sludge communities. Moreover, triclosan mediated the transfer of the RP4 plasmid to opportunistic human pathogens, for example, Legionella spp. The mechanism of triclosan-mediated conjugative transfer is primarily associated with excessive oxidative stress, followed by increased membrane permeability and provoked SOS response. Our findings offer insights into the impacts of triclosan on the dissemination of antibiotic resistance in the aquatic environmental microbiome.}, }
@article {pmid36246261, year = {2022}, author = {Dela Ahator, S and Liu, Y and Wang, J and Zhang, LH}, title = {The virulence factor regulator and quorum sensing regulate the type I-F CRISPR-Cas mediated horizontal gene transfer in Pseudomonas aeruginosa.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {987656}, pmid = {36246261}, issn = {1664-302X}, abstract = {Pseudomonas aeruginosa is capable of thriving in diverse environments due to its network of regulatory components for effective response to stress factors. The survival of the bacteria is also dependent on the ability to discriminate between the acquisition of beneficial and non-beneficial genetic materials via horizontal gene transfer (HGT). Thus, bacteria have evolved the CRISPR-Cas adaptive immune system for defense against the deleterious effect of phage infection and HGT. By using the transposon mutagenesis approach, we identified the virulence factor regulator (Vfr) as a key regulator of the type I-F CRISPR-Cas system in P. aeruginosa. We showed that Vfr influences the expression of the CRISPR-Cas system through two signaling pathways in response to changes in calcium levels. Under calcium-rich conditions, Vfr indirectly regulates the CRISPR-Cas system via modulation of the AHL-QS gene expression, which could be vital for defense against phage infection at high cell density. When encountering calcium deficiency, however, Vfr can directly regulate the CRISPR-Cas system via a cAMP-dependent pathway. Furthermore, we provide evidence that mutation of vfr reduces the CRISPR-Cas spacer acquisition and interference of HGT. The results from this study add to the regulatory network of factors controlling the CRISPR-Cas system in response to abiotic factors in the environment. The findings may facilitate the design of effective and reliable phage therapies against P. aeruginosa infections, as targeting Vfr could prevent the development of the CRISPR-Cas mediated phage resistance.}, }
@article {pmid36244140, year = {2022}, author = {Liu, J and Bao, Z and Wang, C and Wei, J and Wei, Y and Chen, M}, title = {Understanding of mercury and methylmercury transformation in sludge composting by metagenomic analysis.}, journal = {Water research}, volume = {226}, number = {}, pages = {119204}, doi = {10.1016/j.watres.2022.119204}, pmid = {36244140}, issn = {1879-2448}, mesh = {*Methylmercury Compounds ; *Mercury ; Sewage ; *Composting ; Metagenome ; Bacteria/genetics/metabolism ; Bacteroidetes ; }, abstract = {Municipal sewage especially the produced sewage sludge is a significant source releasing mercury (Hg) to the environment. However, the Hg speciation especially methylmercury (MeHg) transformation in sewage sludge treatment process remains poorly understood. This study investigated the transformation of Hg speciation especially MeHg in sludge composting. The distribution of Hg transformation related gene pairs hgcAB and merAB, and their putative microbial hosts were comprehensively analyzed. Both Hg (from 3.16±0.22 mg/kg to 3.20±0.19 mg/kg) and MeHg content (from 4.77±0.64 ng/g to 4.36±0.37 ng/g) were not obviously changed before and after composting, but about 19.69% of Hg and 27.36% of MeHg were lost according to mass balance calculation. The metagenomic analysis further revealed that anaerobes (Desulfobacterota and Euryarchaeota) were the mainly putative Hg methylators especially carrying high abundance of hgcA gene in the initial periods of composting. Among the 151 reconstructed metagenome-assembled genomes (MAGs), only 4 hgcA gene carriers (Myxococcota, Firmicutes, Cyclobacteriaceae, and Methanothermobacter) and 16 merB gene carriers were identified. But almost all of the MAGs carried hgcB gene and merA gene. The merA gene was widely distributed in genomes, which indicated the widespread functionality of microbes for reducing Hg(II) to Hg(0). The hgcA carrying microbes tends to present the similar metabolic pathways including methanogenesis and sulfur metabolism. Besides, both the irregular distribution of hgcA in various species (including Actinobacteria, Archaea, Bacteroidetes, Desulfobacterota, Euryarchaeota, and Nitrospirae, etc.) and opposite evolution trends between hgcA gene abundance and its host genome abundance can be an indication of horizontal gene transfer or gene deletions of hgcA during composting. Our findings thus revealed that sludge composting is not only a hotspot for Hg speciation transformation, but also a potential hotspot for MeHg transformation.}, }
@article {pmid36243187, year = {2022}, author = {Yun, Y and Su, T and Gui, Z and Tian, X and Chen, Y and Cao, Y and Yang, S and Xie, J and Anwar, N and Li, M and Li, G and Ma, T}, title = {Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {315}, number = {}, pages = {120355}, doi = {10.1016/j.envpol.2022.120355}, pmid = {36243187}, issn = {1873-6424}, mesh = {*Oil and Gas Fields ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Tetracycline ; Anti-Bacterial Agents/analysis ; *Microbiota ; }, abstract = {As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.}, }
@article {pmid36228898, year = {2022}, author = {Yuasa, HJ}, title = {Metazoan tryptophan indole-lyase: Are they still active?.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {263}, number = {}, pages = {110801}, doi = {10.1016/j.cbpb.2022.110801}, pmid = {36228898}, issn = {1879-1107}, abstract = {Tryptophan indole-lyase (TIL), also known as tryptophanase, is a pyridoxal-5'-phosphate dependent bacterial enzyme that catalyzes the reversible hydrolytic cleavage of l-tryptophan (l-Trp) to indole and ammonium pyruvate. TIL is also found in some metazoans, and they may have been acquired by horizontal gene transfer. In this study, two metazoans, Nematostella vectensis (starlet sea anemone) and Bradysia coprophila (fungus gnat) TILs were bacterially expressed and characterized. The kcat values of metazoan TILs were low, < 1/200 of the kcat of Escherichia coli TIL. By contrast, metazoan TILs showed lower Km values than the TILs of common bacteria, indicating that their affinity for l-Trp is higher than that of bacterial TILs. Analysis of a series of chimeric enzymes based on B. coprophila and bacterial TILs revealed that the low Km value of B. coprophila TIL is not accidental due to the substitution of a single residue, but is due to the cooperative effect of multiple residues. This suggests that high affinity for l-Trp was positively selected during the molecular evolution of metazoan TIL. This is the first report that metazoan TILs have low but obvious activity.}, }
@article {pmid36228885, year = {2022}, author = {Al Mamun, AAM and Kissoon, K and Kishida, K and Shropshire, WC and Hanson, B and Christie, PJ}, title = {IncFV plasmid pED208: Sequence analysis and evidence for translocation of maintenance/leading region proteins through diverse type IV secretion systems.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102652}, doi = {10.1016/j.plasmid.2022.102652}, pmid = {36228885}, issn = {1095-9890}, mesh = {*Type IV Secretion Systems/genetics ; Plasmids/genetics ; *Escherichia coli/genetics ; F Factor ; Sequence Analysis ; Conjugation, Genetic ; Bacterial Proteins/metabolism ; }, abstract = {Two phylogenetically distantly-related IncF plasmids, F and pED208, serve as important models for mechanistic and structural studies of F-like type IV secretion systems (T4SSFs) and F pili. Here, we present the pED208 sequence and compare it to F and pUMNF18, the closest match to pED208 in the NCBI database. As expected, gene content of the three cargo regions varies extensively, although the maintenance/leading regions (MLRs) and transfer (Tra) regions also carry novel genes or motifs with predicted modulatory effects on plasmid stability, dissemination and host range. By use of a Cre recombinase assay for translocation (CRAfT), we recently reported that pED208-carrying donors translocate several products of the MLR (ParA, ParB1, ParB2, SSB, PsiB, PsiA) intercellularly through the T4SSF. Here, we extend these findings by reporting that pED208-carrying donors translocate 10 additional MLR proteins during conjugation. In contrast, two F plasmid-encoded toxin components of toxin-antitoxin (TA) modules, CcdB and SrnB, were not translocated at detectable levels through the T4SSF. Remarkably, most or all of the pED208-encoded MLR proteins and CcdB and SrnB were translocated through heterologous T4SSs encoded by IncN and IncP plasmids pKM101 and RP4, respectively. Together, our sequence analyses underscore the genomic diversity of the F plasmid superfamily, and our experimental data demonstrate the promiscuous nature of conjugation machines for protein translocation. Our findings raise intriguing questions about the nature of T4SS translocation signals and of the biological and evolutionary consequences of conjugative protein transfer.}, }
@article {pmid36227733, year = {2022}, author = {Acar Kirit, H and Bollback, JP and Lagator, M}, title = {The Role of the Environment in Horizontal Gene Transfer.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36227733}, issn = {1537-1719}, mesh = {*Gene Transfer, Horizontal ; *Escherichia coli/genetics ; Salmonella typhimurium/genetics ; Bacteria/genetics ; Environment ; }, abstract = {Gene-by-environment interactions play a crucial role in horizontal gene transfer by affecting how the transferred genes alter host fitness. However, how the environment modulates the fitness effect of transferred genes has not been tested systematically in an experimental study. We adapted a high-throughput technique for obtaining very precise estimates of bacterial fitness, in order to measure the fitness effects of 44 orthologs transferred from Salmonella Typhimurium to Escherichia coli in six physiologically relevant environments. We found that the fitness effects of individual genes were highly dependent on the environment, while the distributions of fitness effects across genes were not, with all tested environments resulting in distributions of same shape and spread. Furthermore, the extent to which the fitness effects of a gene varied between environments depended on the average fitness effect of that gene across all environments, with nearly neutral and nearly lethal genes having more consistent fitness effects across all environments compared to deleterious genes. Put together, our results reveal the unpredictable nature of how environmental conditions impact the fitness effects of each individual gene. At the same time, distributions of fitness effects across environments exhibit consistent features, pointing to the generalizability of factors that shape horizontal gene transfer of orthologous genes.}, }
@article {pmid36226968, year = {2022}, author = {Jana, B and Keppel, K and Fridman, CM and Bosis, E and Salomon, D}, title = {Multiple T6SSs, Mobile Auxiliary Modules, and Effectors Revealed in a Systematic Analysis of the Vibrio parahaemolyticus Pan-Genome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0072322}, doi = {10.1128/msystems.00723-22}, pmid = {36226968}, issn = {2379-5077}, abstract = {Type VI secretion systems (T6SSs) play a major role in interbacterial competition and in bacterial interactions with eukaryotic cells. The distribution of T6SSs and the effectors they secrete vary between strains of the same bacterial species. Therefore, a pan-genome investigation is required to better understand the T6SS potential of a bacterial species of interest. Here, we performed a comprehensive, systematic analysis of T6SS gene clusters and auxiliary modules found in the pan-genome of Vibrio parahaemolyticus, an emerging pathogen widespread in marine environments. We identified 4 different T6SS gene clusters within genomes of this species; two systems appear to be ancient and widespread, whereas the other 2 systems are rare and appear to have been more recently acquired via horizontal gene transfer. In addition, we identified diverse T6SS auxiliary modules containing putative effectors with either known or predicted toxin domains. Many auxiliary modules are possibly horizontally shared between V. parahaemolyticus genomes, since they are flanked by DNA mobility genes. We further investigated a DUF4225-containing protein encoded on an Hcp auxiliary module, and we showed that it is an antibacterial T6SS effector that exerts its toxicity in the bacterial periplasm, leading to cell lysis. Computational analyses of DUF4225 revealed a widespread toxin domain associated with various toxin delivery systems. Taken together, our findings reveal a diverse repertoire of T6SSs and auxiliary modules in the V. parahaemolyticus pan-genome, as well as novel T6SS effectors and toxin domains that can play a major role in the interactions of this species with other cells. IMPORTANCE Gram-negative bacteria employ toxin delivery systems to mediate their interactions with neighboring cells. Vibrio parahaemolyticus, an emerging pathogen of humans and marine animals, was shown to deploy antibacterial toxins into competing bacteria via the type VI secretion system (T6SS). Here, we analyzed 1,727 V. parahaemolyticus genomes and revealed the pan-genome T6SS repertoire of this species, including the T6SS gene clusters, horizontally shared auxiliary modules, and toxins. We also identified a role for a previously uncharacterized domain, DUF4225, as a widespread antibacterial toxin associated with diverse toxin delivery systems.}, }
@article {pmid36224268, year = {2022}, author = {Rathmann, I and Förster, M and Yüksel, M and Horst, L and Petrungaro, G and Bollenbach, T and Maier, B}, title = {Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36224268}, issn = {1751-7370}, abstract = {Bacterial transformation, a common mechanism of horizontal gene transfer, can speed up adaptive evolution. How its costs and benefits depend on the growth environment is poorly understood. Here, we characterize the distributions of fitness effects (DFE) of transformation in different conditions and test whether they predict in which condition transformation is beneficial. To determine the DFEs, we generate hybrid libraries between the recipient Bacillus subtilis and different donor species and measure the selection coefficient of each hybrid strain. In complex medium, the donor Bacillus vallismortis confers larger fitness effects than the more closely related donor Bacillus spizizenii. For both donors, the DFEs show strong effect beneficial transfers, indicating potential for fast adaptive evolution. While some transfers of B. vallismortis DNA show pleiotropic effects, various transfers are beneficial only under a single growth condition, indicating that the recipient can benefit from a variety of donor genes to adapt to varying growth conditions. We scrutinize the predictive value of the DFEs by laboratory evolution under different growth conditions and show that the DFEs correctly predict the condition at which transformation confers a benefit. We conclude that transformation has a strong potential for speeding up adaptation to varying environments by profiting from a gene pool shared between closely related species.}, }
@article {pmid36223775, year = {2022}, author = {Wang, B and Pandey, T and Long, Y and Delgado-Rodriguez, SE and Daugherty, MD and Ma, DK}, title = {Co-opted genes of algal origin protect C. elegans against cyanogenic toxins.}, journal = {Current biology : CB}, volume = {32}, number = {22}, pages = {4941-4948.e3}, pmid = {36223775}, issn = {1879-0445}, support = {R35 GM133633/GM/NIGMS NIH HHS/United States ; R35 GM139618/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics/metabolism ; *Amygdalin/metabolism ; Phylogeny ; *Caenorhabditis elegans Proteins/metabolism ; Cyanides/metabolism ; }, abstract = {Amygdalin is a cyanogenic glycoside enriched in the tissues of many edible plants, including seeds of stone fruits such as cherry (Prunus avium), peach (Prunus persica), and apple (Malus domestica). These plants biosynthesize amygdalin in defense against herbivore animals, as amygdalin generates poisonous cyanide upon plant tissue destruction.[1][,][2][,][3][,][4] Poisonous to many animals, amygdalin-derived cyanide is detoxified by potent enzymes commonly found in bacteria and plants but not most animals.[5] Here we show that the nematode C. elegans can detoxify amygdalin by a genetic pathway comprising cysl-1, egl-9, hif-1, and cysl-2. A screen of a natural product library for hypoxia-independent regulators of HIF-1 identifies amygdalin as a potent activator of cysl-2, a HIF-1 transcriptional target that encodes a cyanide detoxification enzyme in C. elegans. As a cysl-2 paralog similarly essential for amygdalin resistance, cysl-1 encodes a protein homologous to cysteine biosynthetic enzymes in bacteria and plants but functionally co-opted in C. elegans. We identify exclusively HIF-activating egl-9 mutations in a cysl-1 suppressor screen and show that cysl-1 confers amygdalin resistance by regulating HIF-1-dependent cysl-2 transcription to protect against amygdalin toxicity. Phylogenetic analysis indicates that cysl-1 and cysl-2 were likely acquired from green algae through horizontal gene transfer (HGT) and functionally co-opted in protection against amygdalin. Since acquisition, these two genes evolved division of labor in a cellular circuit to detect and detoxify cyanide. Thus, algae-to-nematode HGT and subsequent gene function co-option events may facilitate host survival and adaptation to adverse environmental stresses and biogenic toxins.}, }
@article {pmid36215219, year = {2022}, author = {Ali, A and Imran, M and Sial, S and Khan, A}, title = {Effective antibiotic dosing in the presence of resistant strains.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275762}, pmid = {36215219}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria ; Follow-Up Studies ; Gene Transfer, Horizontal ; Models, Theoretical ; }, abstract = {Mathematical models can be very useful in determining efficient and successful antibiotic dosing regimens. In this study, we consider the problem of determining optimal antibiotic dosing when bacteria resistant to antibiotics are present in addition to susceptible bacteria. We consider two different models of resistance acquisition, both involve the horizontal transfer (HGT) of resistant genes from a resistant to a susceptible strain. Modeling studies on HGT and study of optimal antibiotic dosing protocols in the literature, have been mostly focused on transfer of resistant genes via conjugation, with few studies on HGT via transformation. We propose a deterministic ODE based model of resistance acquisition via transformation, followed by a model that takes into account resistance acquisition through conjugation. Using a numerical optimization algorithm to determine the 'best' antibiotic dosing strategy. To illustrate our optimization method, we first consider optimal dosing when all the bacteria are susceptible to the antibiotic. We then consider the case where resistant strains are present. We note that constant periodic dosing may not always succeed in eradicating the bacteria while an optimal dosing protocol is successful. We determine the optimal dosing strategy in two different scenarios: one where the total bacterial population is to be minimized, and the next where we want to minimize the bacterial population at the end of the dosing period. We observe that the optimal strategy in the first case involves high initial dosing with dose tapering as time goes on, while in the second case, the optimal dosing strategy is to increase the dosing at the beginning of the dose cycles followed by a possible dose tapering. As a follow up study we intend to look at models where 'persistent' bacteria may be present in additional to resistant and susceptible strain and determine the optimal dosing protocols in this case.}, }
@article {pmid36214559, year = {2022}, author = {Matilla, MA and Monson, RE and Murphy, A and Schicketanz, M and Rawlinson, A and Duncan, C and Mata, J and Leeper, F and Salmond, GPC}, title = {Solanimycin: Biosynthesis and Distribution of a New Antifungal Antibiotic Regulated by Two Quorum-Sensing Systems.}, journal = {mBio}, volume = {}, number = {}, pages = {e0247222}, doi = {10.1128/mbio.02472-22}, pmid = {36214559}, issn = {2150-7511}, abstract = {The increasing emergence of drug-resistant fungal infections has necessitated a search for new compounds capable of combating fungal pathogens of plants, animals, and humans. Microorganisms represent the main source of antibiotics with applicability in agriculture and in the clinic, but many aspects of their metabolic potential remain to be explored. This report describes the discovery and characterization of a new antifungal compound, solanimycin, produced by a hybrid polyketide/nonribosomal peptide (PKS/NRPS) system in Dickeya solani, the enterobacterial pathogen of potato. Solanimycin was active against a broad range of plant-pathogenic fungi of global economic concern and the human pathogen Candida albicans. The genomic cluster responsible for solanimycin production was defined and analyzed to identify the corresponding biosynthetic proteins, which include four multimodular PKS/NRPS proteins and several tailoring enzymes. Antifungal production in D. solani was enhanced in response to experimental conditions found in infected potato tubers and high-density fungal cultures. Solanimycin biosynthesis was cell density dependent in D. solani and was controlled by both the ExpIR acyl-homoserine lactone and Vfm quorum-sensing systems of the bacterial phytopathogen. The expression of the solanimycin cluster was also regulated at the post-transcriptional level, with the regulator RsmA playing a major role. The solanimycin biosynthetic cluster was conserved across phylogenetically distant bacterial genera, and multiple pieces of evidence support that the corresponding gene clusters were acquired by horizontal gene transfer. Given its potent broad-range antifungal properties, this study suggests that solanimycin and related molecules may have potential utility for agricultural and clinical exploitation. IMPORTANCE Fungal infections represent a major clinical, agricultural, and food security threat worldwide, which is accentuated due to the difficult treatment of these infections. Microorganisms represent a prolific source of antibiotics, and current data support that this enormous biosynthetic potential has been scarcely explored. To improve the performance in the discovery of novel antimicrobials, there is a need to diversify the isolation niches for new antibiotic-producing microorganisms as well as to scrutinize novel phylogenetic positions. With the identification of the antifungal antibiotic solanimycin in a broad diversity of phytopathogenic Dickeya spp., we provide further support for the potential of plant-associated bacteria for the biosynthesis of novel antimicrobials. The complex regulatory networks involved in solanimycin production reflect the high metabolic cost of bacterial secondary metabolism. This metabolic regulatory control makes many antibiotics cryptic under standard laboratory conditions, and mimicking environmental conditions, as shown here, is a strategy to activate cryptic antibiotic clusters.}, }
@article {pmid36214558, year = {2022}, author = {Suchland, RJ and Carrell, SJ and Ramsey, SA and Hybiske, K and Debrine, AM and Sanchez, J and Celum, C and Rockey, DD}, title = {Genomic Analysis of MSM Rectal Chlamydia trachomatis Isolates Identifies Predicted Tissue-Tropic Lineages Generated by Intraspecies Lateral Gene Transfer-Mediated Evolution.}, journal = {Infection and immunity}, volume = {90}, number = {11}, pages = {e0026522}, pmid = {36214558}, issn = {1098-5522}, support = {R21 AI144865/AI/NIAID NIH HHS/United States ; R03 AI156514/AI/NIAID NIH HHS/United States ; R01 AI126785/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Male ; *Chlamydia Infections/microbiology ; Chlamydia trachomatis/genetics ; Gene Transfer, Horizontal ; Genome-Wide Association Study ; Genomics ; *Homosexuality, Male ; }, abstract = {Chlamydia trachomatis is an obligate intracellular bacterium that causes serious diseases in humans. Rectal infection and disease caused by this pathogen are important yet understudied aspects of C. trachomatis natural history. The University of Washington Chlamydia Repository has a large collection of male-rectal-sourced strains (MSM rectal strains) isolated in Seattle, USA and Lima, Peru. Initial characterization of strains collected over 30 years in both Seattle and Lima led to an association of serovars G and J with male rectal infections. Serovar D, E, and F strains were also collected from MSM patients. Genome sequence analysis of a subset of MSM rectal strains identified a clade of serovar G and J strains that had high overall genomic identity. A genome-wide association study was then used to identify genomic loci that were correlated with tissue tropism in a collection of serovar-matched male rectal and female cervical strains. The polymorphic membrane protein PmpE had the strongest correlation, and amino acid sequence alignments identified a set of PmpE variable regions (VRs) that were correlated with host or tissue tropism. Examination of the positions of VRs by the protein structure-predicting Alphafold2 algorithm demonstrated that the VRs were often present in predicted surface-exposed loops in both PmpE and PmpH protein structure. Collectively, these studies identify possible tropism-predictive loci for MSM rectal C. trachomatis infections and identify predicted surface-exposed variable regions of Pmp proteins that may function in MSM rectal versus cervical tropism differences.}, }
@article {pmid36212863, year = {2022}, author = {Han, B and Ma, L and Yu, Q and Yang, J and Su, W and Hilal, MG and Li, X and Zhang, S and Li, H}, title = {The source, fate and prospect of antibiotic resistance genes in soil: A review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {976657}, pmid = {36212863}, issn = {1664-302X}, abstract = {Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.}, }
@article {pmid36212841, year = {2022}, author = {Neira, G and Vergara, E and Holmes, DS}, title = {Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900531}, pmid = {36212841}, issn = {1664-302X}, abstract = {Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2-3) and moderately thermophilic conditions (50-60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including "first line of defense" mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the "second line of defense" where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.}, }
@article {pmid36212306, year = {2022}, author = {Zhong, Y and Yu, R and Chen, J and Liu, Y and Zhou, R}, title = {Highly active repeat-mediated recombination in the mitogenome of the holoparasitic plant Aeginetia indica.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {988368}, pmid = {36212306}, issn = {1664-462X}, abstract = {Mitogenomes of most flowering plants evolve slowly in sequence, but rapidly in structure. The rearrangements in structure are mainly caused by repeat-mediated recombination. However, patterns of repeat-mediated recombination vary substantially among plants, and to provide a comprehensive picture, characterization of repeat-mediated recombination should extend to more plant species, including parasitic plants with a distinct heterotrophic lifestyle. Here we assembled the mitogenome of the holoparasitic plant Aeginetia indica (Orobanchaceae) using Illumina sequencing reads. The mitogenome was assembled into a circular chromosome of 420,362 bp, 18,734 bp longer than that of another individual of A. indica which was assembled before as a linear molecule. Synteny analysis between the two mitogenomes revealed numerous rearrangements, unique regions of each individual and 0.2% sequence divergence in their syntenic regions. The A. indica mitogenome contains a gene content typical of flowering plants (33 protein-coding, 3 rRNA, and 17 tRNA genes). Repetitive sequences >30 bp in size totals 57,060 bp, representing 13.6% of the mitogenome. We examined recombination mediated by repeats >100 bp in size and found highly active recombination for all the repeats, including a very large repeat of ~16 kb. Recombination between these repeats can form much smaller subgenomic circular chromosomes, which may lead to rapid replication of mitochondrial DNA and thus be advantageous for A. indica with a parasitic lifestyle. In addition, unlike some other parasitic plants, A. indica shows no evidence for horizontal gene transfer of protein-coding genes in its mitogenome.}, }
@article {pmid36206680, year = {2022}, author = {Xu, C and Lu, J and Shen, C and Wang, J and Li, F}, title = {Deciphering the mechanisms shaping the plastisphere antibiotic resistome on riverine microplastics.}, journal = {Water research}, volume = {225}, number = {}, pages = {119192}, doi = {10.1016/j.watres.2022.119192}, pmid = {36206680}, issn = {1879-2448}, mesh = {*Microplastics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Plastics ; Vancomycin ; Polyethylene Terephthalates ; Bacteria/genetics ; *Rifamycins ; Water ; }, abstract = {Microplastics in urban rivers provide bacterial niches and serve as dispersal vectors for antibiotic resistant genes (ARGs) dissemination, which may exacerbate risks in the aquatic systems. However, whether MPs in the river would also selectively enrich ARGs and the underlying mechanisms shaping the resistome on MPs remains largely unknown. In this study, we explored the occurrence of ARGs, bacterial communities, and mobile genetic elements (MGEs) on MPs and in waters from the Huangpu River in China. Microplastics were widely distributed in the river (1.78 ± 0.84 items/L), with overwhelming percentages of polyethylene terephthalate fibers. Although reduced ARG abundances were observed on MPs than in waters, MPs selectively enriched the ARGs resistant to Rifamycin and Vancomycin. A clear variation for ARG profiles was elucidated between water and MPs samples. Network analysis suggested that MPs created a unique niche for the genus Afipia to colonize, potentially contributing to the vertical dissemination of ARGs. Additionally, the co-occurrence between ARGs and MGEs revealed that the MPs favor the propagation of some plasmid-associated ARGs mediated by horizontal gene transfer. The null model-based stochasticity ratio and the neutral community model suggested that the ARG assembly on MPs was dominantly driven by stochastic process. The results further indicated that microbial communities and MGEs played significant roles in shaping ARG profiles and dynamics on MPs. Our findings provided new insights into the ecological processes of antibiotic resistome of the aquatic plastisphere.}, }
@article {pmid36205822, year = {2022}, author = {Deb, S}, title = {Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {38}, number = {12}, pages = {231}, pmid = {36205822}, issn = {1573-0972}, mesh = {*Bifidobacterium/genetics ; Carbohydrates ; Evolution, Molecular ; *Genome, Bacterial/genetics ; Humans ; Phylogeny ; }, abstract = {Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.}, }
@article {pmid36205197, year = {2022}, author = {Gontier, N and Sukhoverkhov, A}, title = {Reticulate evolution underlies synergistic trait formation in human communities.}, journal = {Evolutionary anthropology}, volume = {}, number = {}, pages = {}, doi = {10.1002/evan.21962}, pmid = {36205197}, issn = {1520-6505}, abstract = {This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; and (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits.}, }
@article {pmid36203131, year = {2022}, author = {Somee, MR and Amoozegar, MA and Dastgheib, SMM and Shavandi, M and Maman, LG and Bertilsson, S and Mehrshad, M}, title = {Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {690}, pmid = {36203131}, issn = {1471-2164}, mesh = {*Archaea ; Bacteria ; Biodegradation, Environmental ; Carbon/metabolism ; Hydrocarbons/metabolism ; Hydrogen/metabolism ; *Petroleum/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. RESULTS: Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.<br><br>CONCLUSION: Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.}, }
@article {pmid36202926, year = {2022}, author = {Barnum, TP and Coates, JD}, title = {Chlorine redox chemistry is widespread in microbiology.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36202926}, issn = {1751-7370}, abstract = {Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2[-]) by converting it to chloride (Cl[-]) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4[-]) or chlorate (ClO3[-]), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.}, }
@article {pmid36200778, year = {2022}, author = {da Silva Barreira, D and Lapaquette, P and Novion Ducassou, J and Couté, Y and Guzzo, J and Rieu, A}, title = {Spontaneous Prophage Induction Contributes to the Production of Membrane Vesicles by the Gram-Positive Bacterium Lacticaseibacillus casei BL23.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0237522}, pmid = {36200778}, issn = {2150-7511}, mesh = {*Peptidoglycan ; Virus Activation ; *Lacticaseibacillus casei/genetics ; Prophages/genetics ; N-Acetylmuramoyl-L-alanine Amidase ; Anti-Bacterial Agents/pharmacology ; Mitomycins ; beta-Lactams ; }, abstract = {The formation of membrane vesicles (MVs) by Gram-positive bacteria has gained increasing attention over the last decade. Recently, models of vesicle formation have been proposed and involve the digestion of the cell wall by prophage-encoded or stress-induced peptidoglycan (PG) hydrolases and the inhibition of PG synthesis by β-lactam antibiotics. The impact of these mechanisms on vesicle formation is largely dependent on the strain and growth conditions. To date, no information on the production of vesicles by the lactobacilli family has been reported. Here, we aimed to characterize the MVs released by the Gram-positive bacteria Lacticaseibacillus casei BL23 and also investigated the mechanisms involved in vesicle formation. Using electron microscopy, we established that the size of the majority of L. casei BL23 vesicles ranged from 50 to 100 nm. Furthermore, we showed that the vesicles were released consistently throughout the growth of the bacteria in standard culture conditions. The protein composition of the vesicles released in the supernatant was identified and a significant number of prophage proteins was detected. Moreover, using a mutant strain harboring a defective PLE2 prophage, we were able to show that the spontaneous and mitomycin-triggered induction of the prophage PLE2 contribute to the production of MVs by L. casei BL23. Finally, we also demonstrated the influence of prophages on the membrane integrity of bacteria. Overall, our results suggest a key role of the prophage PLE2 in the production of MVs by L. casei BL23 in the absence or presence of genotoxic stress. IMPORTANCE The last few decades have demonstrated that membrane vesicles (MVs) produced by microorganisms can have a wide variety of functions. This diversity places MVs at the crossroads of major research topics in current microbiology such as antibiotic resistance, horizontal gene transfer, cell communication, biofilm development, bacteriophage resistance, and pathogenesis. In particular, vesicles produced by probiotic strains have been shown to play a significant role in their beneficial effects. Thus, the study of vesicle biogenesis is a key element for promoting and improving their release. Overall, our results suggest a key role of spontaneous and mitomycin-triggered prophage induction in MV production by the Gram-positive bacteria Lacticaseibacillus casei BL23. This phenomenon is of great interest as prophage-induced MVs could potentially influence bacterial behavior, stress resistance, and vesicle functions.}, }
@article {pmid36200773, year = {2022}, author = {Sattler, J and Tsvetkov, T and Stelzer, Y and Schäfer, S and Sommer, J and Noster, J and Göttig, S and Hamprecht, A}, title = {Emergence of Tn1999.7, a New Transposon in blaOXA-48-Harboring Plasmids Associated with Increased Plasmid Stability.}, journal = {Antimicrobial agents and chemotherapy}, volume = {66}, number = {11}, pages = {e0078722}, pmid = {36200773}, issn = {1098-6596}, mesh = {*Bacterial Proteins/genetics ; *beta-Lactamases/genetics/metabolism ; *DNA Transposable Elements/genetics ; Europe ; Germany ; *Plasmids/genetics ; Enterobacteriaceae/genetics/pathogenicity ; Genetic Variation ; }, abstract = {OXA-48 is the most common carbapenemase in Enterobacterales in Germany and many other European countries. Depending on the genomic location of blaOXA-48, OXA-48-producing isolates vary in phenotype and intra- and interspecies transferability of blaOXA-48. In most bacterial isolates, blaOXA-48 is located on one of seven variants of Tn1999 (Tn1999.1 to Tn1999.6 and invTn1999.2). Here, a novel Tn1999 variant, Tn1999.7, is described, which was identified in 11 clinical isolates from 2016 to 2020. Tn1999.7 differs from Tn1999.1 by the insertion of the 8,349-bp Tn3 family transposon Tn7442 between the lysR gene and blaOXA-48 open reading frame. Tn7442 carries genes coding for a restriction endonuclease and a DNA methyltransferase as cargo, forming a type III restriction modification system. Tn1999.7 was carried on an ~71-kb IncL plasmid in 9/11 isolates. In one isolate, Tn1999.7 was situated on an ~76-kb plasmid, harboring an additional insertion sequence in the plasmid backbone. In one isolate, the plasmid size is only ~63 kb due to a deletion adjacent to Tn7442 that extends into the plasmid backbone. Mean conjugation rates of the Tn1999.7-harboring plasmids in J53 ranged from 4.47 × 10[-5] to 2.03 × 10[-2], similar to conjugation rates of other pOXA-48-type IncL plasmids. The stability of plasmids with Tn1999.7 was significantly higher than that of a Tn1999.2-harboring plasmid in vitro. This increase in stability could be related to the insertion of a restriction-modification system, which can promote postsegregational killing. The increased plasmid stability associated with Tn1999.7 could contribute to the further spread of OXA-48.}, }
@article {pmid36198712, year = {2022}, author = {Faddetta, T and Vassallo, A and Del Duca, S and Gallo, G and Fani, R and Puglia, AM}, title = {Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16651}, pmid = {36198712}, issn = {2045-2322}, mesh = {Bacteria/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial ; Lipids ; *Nucleic Acids/metabolism ; RNA/metabolism ; *Streptomyces coelicolor/genetics/metabolism ; }, abstract = {Membrane vesicles (MVs) are spherical particles with nanoscale dimensions and characterized by the presence of diverse cargos, such as nucleic acids, proteins, lipids, and cellular metabolites. Many examples of (micro)organisms producing MVs are reported in literature. Among them, bacterial MVs are of particular interest because they are now considered as the fourth mechanism of horizontal gene transfer. Streptomyces bacteria are well-known for their ecological roles and ability to synthesize bioactive compounds, with Streptomyces coelicolor being the model organism. It was previously demonstrated that it can produce distinct populations of MVs characterized by different protein and metabolite cargos. In this work we demonstrated for the first time that MVs of S. coelicolor carry both DNA and RNA and that their DNA content represents the entire chromosome of the bacterium. These findings suggest that MV DNA could have a role in the evolution of Streptomyces genomes and that MVs could be exploited in new strain engineering strategies.}, }
@article {pmid36195901, year = {2022}, author = {Kelly, JB and Carlson, DE and Low, JS and Thacker, RW}, title = {Novel trends of genome evolution in highly complex tropical sponge microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {164}, pmid = {36195901}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Evolution, Molecular ; *Lipopolysaccharides ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Steroids ; Sterols ; }, abstract = {BACKGROUND: Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.<br><br>RESULTS: A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.<br><br>CONCLUSIONS: These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.}, }
@article {pmid36194009, year = {2022}, author = {Cook, D and Flannigan, MD and Candra, BV and Compton, KD and Hare, JM}, title = {The DdrR Coregulator of the Acinetobacter baumannii Mutagenic DNA Damage Response Potentiates UmuDAb Repression of Error-Prone Polymerases.}, journal = {Journal of bacteriology}, volume = {204}, number = {11}, pages = {e0016522}, pmid = {36194009}, issn = {1098-5530}, support = {P20 RR016481/RR/NCRR NIH HHS/United States ; R15 GM085722/GM/NIGMS NIH HHS/United States ; P20 GM103436/GM/NIGMS NIH HHS/United States ; }, mesh = {*Acinetobacter baumannii/genetics/metabolism ; Mutagens ; DNA-Directed DNA Polymerase/genetics/metabolism ; Mutagenesis ; DNA Damage ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Acinetobacter baumannii strain 17978 is an opportunistic pathogen with a unique DNA damage repair response that lacks the LexA repressor but induces ~150 genes after DNA damage. It uses the UmuD homolog UmuDAb and the small protein DdrR, unique to Acinetobacter, to repress multiple horizontally acquired umuDC error-prone polymerase genes through an unknown mechanism. We used reverse transcription-quantitative PCR and immunoblotting to elucidate UmuDAb regulatory requirements and DdrR contributions to the corepression of this specialized regulon. Mutations in the putative UmuDAb helix-turn-helix (HTH) domain could not repress the expression of the UmuDAb/DdrR regulon. A ddrR insertion mutation in these HTH mutant backgrounds produced even greater derepression of the regulon, suggesting that DdrR exerts an additional level of control over this mutagenic response. These ddrR HTH mutant A. baumannii cells overexpressed UmuDAb, cleaving it after treatment with the DNA-damaging agent mitomycin C. This showed that DdrR was not required for UmuDAb self-cleavage and that UmuDAb repression and self-cleavage actions were independent. An uncleavable umuDAb mutant with an A-to-Y change at position 83 (A83Y) could neither induce the UmuDAb/DdrR regulon nor conduct SOS mutagenesis. However, a prophage-encoded umuDrumB operon was still partially induced after DNA damage in this mutant. Surprisingly, that prophage's putative repressor was dispensable for prophage-encoded umuDrumB induction, implying another repressor's involvement. This study revealed that UmuDAb behaves like LexA, requiring an N-terminal HTH motif for repression and C-terminal self-cleavage for gene induction and subsequent SOS mutagenesis, and DdrR cooperates with it to exert an additional level of repressive control on this pathogen's mutagenic response to DNA damage. IMPORTANCE Acinetobacter baumannii is a nosocomial pathogen that acquires antibiotic resistance genes through conjugative transfer and carries out a robust mutagenic DNA damage response. After exposure to conditions typically encountered in health care settings, such as antibiotics, UV light, and desiccation, this species induces error-prone UmuD'2C polymerases. This mutagenic capability increases A. baumannii survival and virulence and is regulated by the UmuDAb/DdrR corepressor system unique to the Acinetobacter genus. Our study has revealed that the DdrR protein provides an additional layer of control in preventing mutagenic polymerase expression by enhancing UmuDAb repression actions. Understanding these repressors could lead to new drug targets, as multidrug resistance in hospital-acquired infections has decreased treatment options, with limited new drugs being developed.}, }
@article {pmid36187977, year = {2022}, author = {Shami, AY and Abulfaraj, AA and Refai, MY and Barqawi, AA and Binothman, N and Tashkandi, MA and Baeissa, HM and Baz, L and Abuauf, HW and Ashy, RA and Jalal, RS}, title = {Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990169}, pmid = {36187977}, issn = {1664-302X}, abstract = {Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.}, }
@article {pmid36186424, year = {2022}, author = {Walker, AR and Shields, RC}, title = {Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {997341}, pmid = {36186424}, issn = {1664-8021}, support = {R03 DE029882/DE/NIDCR NIH HHS/United States ; }, abstract = {CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. S. mutans strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and 'openness' of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.}, }
@article {pmid36186036, year = {2022}, author = {Perez Saura, P and Chabi, M and Corato, A and Cardol, P and Remacle, C}, title = {Cell adaptation of the extremophilic red microalga Galdieria sulphuraria to the availability of carbon sources.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {978246}, pmid = {36186036}, issn = {1664-462X}, abstract = {Global energy demand and fossil fuels impact on climate can be partially managed by an increase in the use of biofuels for transports and industries. Biodiesel production is generally preceded by a transesterification process of the green biomass triacylglycerols that generates large amounts of glycerol as a by-product. In this study, the extremophilic red microalga Galdieria sulphuraria 074W was cultivated in heterotrophy. The microalgal growth parameters and biomass composition were compared when grown on an equivalent molar concentration of carbon of either glucose or glycerol as unique carbon source. The maximal biomass reached in these two conditions was not significantly different (∼2.5 g.L[-1]). Fatty acid profile, protein and storage carbohydrate contents were also statistically similar, irrespectively of the metabolized carbon source. We also observed that the pigment content of G. sulphuraria cells decreased during heterotrophic growth compared to photoautotrophic cultivated cells, and that this diminution was more important in the presence of glucose than glycerol: cells were yellowish in the presence of glucose and green in the presence of glycerol. The pigmentation was restored when glucose was totally consumed in the medium, suggesting that the presence of glucose repressed pigment synthesis. Based on this observation, a transcriptome analysis was performed in order to better understand the mechanisms involved in the loss of color mediated by darkness and by glucose in G. sulphuraria. Three conditions were analyzed: heterotrophy with glycerol or glucose and phototrophy. This allowed us to understand the transcriptional response of cells to light and dark environments both at the nuclear and chloroplast levels, and to show that transcription of gene families, acquired by horizontal gene transfer, such as sugar, amino acid, or acetate transporters, were involved in the response to the availability of different (in)organic sources.}, }
@article {pmid36183960, year = {2022}, author = {Sharma, V and Sood, A and Ray, P and Angrup, A}, title = {Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii.}, journal = {Microbial pathogenesis}, volume = {173}, number = {Pt A}, pages = {105811}, doi = {10.1016/j.micpath.2022.105811}, pmid = {36183960}, issn = {1096-1208}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial ; Metronidazole ; Drug Resistance, Bacterial/genetics ; Genomics ; *Anti-Infective Agents/pharmacology ; }, abstract = {Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.}, }
@article {pmid36181826, year = {2023}, author = {Ren, Z and Zhao, Y and Han, S and Li, X}, title = {Regulatory strategies for inhibiting horizontal gene transfer of ARGs in paddy and dryland soil through computer-based methods.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159096}, doi = {10.1016/j.scitotenv.2022.159096}, pmid = {36181826}, issn = {1879-1026}, mesh = {*Soil ; *Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Computers ; }, abstract = {Antibiotic resistance genes (ARGs) have been regarded as emerging pollutants due to their potential risk of resistance. Horizontal gene transfer (HGT) is the main pathway for ARGs to lead to environmental threats. Therefore, the inhabitation of ARGs' HGT can effectively inhibit ARGs' potential drug resistance risk within a single strain. In this paper, the characteristics of ARGs' HGT in paddy and dryland soils were identified and regulated by a combination of ARGs' HGT feature identification, transfer mechanism analysis and transfer process regulation. The homology modeling algorithm was used to simulate the construction of the Tn5 plasmid transposase of Escherichia coli (E. coli) for identifying ARGs' HGT characteristics. The GCG (212.617 Å) was thus determined as the target codon. Through integrated computer-based methods, results showed that the most important environmental disturbance factors for the HGT of ARGs in the paddy and dryland soils were rough farmyard manure/sewage irrigation and mining pollution, respectively. Under the disturbance of key environmental factors, the inhibitory effect of HGT of ARGs in paddy and dryland soil was reduced by 35.01 % and 34.74 %, respectively. Results demonstrated that the proposed theoretical mechanism and control strategies could effectively inhibit the HGT of E. coli ARGs in the soil environment.}, }
@article {pmid36181435, year = {2022}, author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M}, title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36181435}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; }, abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.}, }
@article {pmid36177458, year = {2022}, author = {Choufa, C and Tidjani, AR and Gauthier, A and Harb, M and Lao, J and Leblond-Bourget, N and Vos, M and Leblond, P and Bontemps, C}, title = {Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {970179}, pmid = {36177458}, issn = {1664-302X}, abstract = {Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.}, }
@article {pmid36177035, year = {2022}, author = {Martínez-Vicente, P and Poblador, F and Leitner, J and Farré, D and Steinberger, P and Engel, P and Angulo, A}, title = {Discovery of the first PD-1 ligand encoded by a pathogen.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1007334}, pmid = {36177035}, issn = {1664-3224}, mesh = {*B7-H1 Antigen/metabolism ; DNA ; Ligands ; Membrane Glycoproteins/metabolism ; *Programmed Cell Death 1 Ligand 2 Protein/metabolism ; Programmed Cell Death 1 Receptor/genetics ; Viral Proteins ; }, abstract = {Large double-stranded DNA viruses deploy multiple strategies to subvert host immune defenses. Some of these tactics are mediated by viral gene products acquired by horizontal gene transfer from the corresponding hosts and shaped throughout evolution. The programmed death-1 (PD-1) receptor and its ligands, PD-L1 and PD-L2, play a pivotal role attenuating T-cell responses and regulating immune tolerance. In this study, we report the first functional PD-L1 homolog gene (De2) found in a pathogen. De2, captured by a γ-herpesvirus from its host during co-evolution around 50 million years ago, encodes a cell-surface glycoprotein that interacts with high affinity and stability with host PD-1. We also find that mutations evolved by the viral protein result in a significant loss of its ability to interact in cis with CD80, an interaction that for PD-L1:CD80 has been reported to block PD-1 inhibitory pathways. Furthermore, we demonstrate that the viral protein strongly inhibits T-cell signaling. Our observations suggest that PD-L1 homologs may enable viruses to evade T cell responses, favor their replication, and prevent excessive tissue damage. Altogether, our findings reveal a novel viral immunosuppressive strategy and highlight the importance of the modulation of the PD-1/PD-L1 axis during viral infections.}, }
@article {pmid36175544, year = {2022}, author = {Harris, BJ and Clark, JW and Schrempf, D and Szöllősi, GJ and Donoghue, PCJ and Hetherington, AM and Williams, TA}, title = {Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {11}, pages = {1634-1643}, pmid = {36175544}, issn = {2397-334X}, support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; *Embryophyta/genetics ; Phylogeny ; Plants/genetics ; Fossils ; *Tracheophyta ; }, abstract = {The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.}, }
@article {pmid36173309, year = {2022}, author = {Gan, X and Li, M and Xu, J and Yan, S and Wang, W and Li, F}, title = {Emerging of Multidrug-Resistant Cronobacter sakazakii Isolated from Infant Supplementary Food in China.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0119722}, pmid = {36173309}, issn = {2165-0497}, mesh = {*Cronobacter sakazakii/genetics ; Food Microbiology ; *Cronobacter/genetics ; Infant Formula/microbiology ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol ; Tetracycline ; Virulence Factors/genetics ; Trimethoprim ; Ampicillin ; Sulfamethoxazole ; Adenosine Monophosphate ; }, abstract = {Cronobacter is a foodborne pathogen associated with severe infections in restricted populations and particularly with high mortality in neonates and infants. The prevalence and antimicrobial resistance (AMR) phenotype of Cronobacter cultured from powdered infant formula and supplementary food were studied. The virulence factors, AMR genes, and genomic environments of the multidrug-resistant isolates were further studied. A total of 1,055 Cronobacter isolates were recovered from 12,105 samples of powdered infant formula and supplementary food collected from 29 provinces between 2018 and 2019 in China. Among these, 1,048 isolates were from infant supplementary food and 7 were from powdered infant formula. Regarding antimicrobial resistance susceptibility, 11 (1.0%) isolates were resistant and two showed resistance to four antimicrobials (ampicillin [AMP], tetracycline [TET], sulfamethoxazole-trimethoprim [SXT], and chloramphenicol [CHL]), defined as MDR. These two MDR isolates were subsequently identified as Cronobacter sakazakii sequence type 4 (ST4) (C. sakazakii Crono-589) and ST40 (C. sakazakii Crono-684). Both MDR isolates contain 11 types of virulence genes and 7 AMR genes on their genomes. Meanwhile, the IncFIB plasmids of both MDR C. sakazakii isolates also harbored 2 types of virulence genes. Results of the genomic comparative analysis indicated that food-associated C. sakazakii could acquire antimicrobial resistance determinants through horizontal gene transfer (HGT). IMPORTANCE As a foodborne pathogen, Cronobacter can cause serious infections in restricted populations and lead to death or chronic sequelae. Although a number of investigations showed that Cronobacter isolates are susceptible to most antimicrobial agents, MDR Cronobacter isolates, isolated mainly from clinical cases but occasionally from foods, have been reported in recent years. In this study, we successfully identified two MDR Cronobacter sakazakii isolates from infant foods based on nationwide surveillance and genome sequencing in China. Genomic analysis revealed that these two MDR C. sakazakii strains acquired resistance genes from other species via different evolution and transmission routes. It is important to monitor MDR C. sakazakii isolates in infant foods, and appropriate control measures should be taken to reduce the contamination with and transmission of this MDR bacterium.}, }
@article {pmid36161953, year = {2022}, author = {Kirsch, R and Okamura, Y and Haeger, W and Vogel, H and Kunert, G and Pauchet, Y}, title = {Metabolic novelty originating from horizontal gene transfer is essential for leaf beetle survival.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2205857119}, pmid = {36161953}, issn = {1091-6490}, mesh = {Animals ; *Coleoptera/enzymology/genetics ; Gene Knockout Techniques ; *Gene Transfer, Horizontal ; Pectins/metabolism ; Phylogeny ; Plants/chemistry ; *Polygalacturonase/genetics ; }, abstract = {Horizontal gene transfer (HGT) provides an evolutionary shortcut for recipient organisms to gain novel functions. Although reports of HGT in higher eukaryotes are rapidly accumulating, in most cases the evolutionary trajectory, metabolic integration, and ecological relevance of acquired genes remain unclear. Plant cell wall degradation by HGT-derived enzymes is widespread in herbivorous insect lineages. Pectin is an abundant polysaccharide in the walls of growing parts of plants. We investigated the significance of horizontally acquired pectin-digesting polygalacturonases (PGs) of the leaf beetle Phaedon cochleariae. Using a CRISPR/Cas9-guided gene knockout approach, we generated a triple knockout and a quadruple PG-null mutant in order to investigate the enzymatic, biological, and ecological effects. We found that pectin-digestion 1) is exclusively linked to the horizontally acquired PGs from fungi, 2) became fixed in the host genome by gene duplication leading to functional redundancy, 3) compensates for nutrient-poor diet by making the nutritious cell contents more accessible, and 4) facilitates the beetles development and survival. Our analysis highlights the selective advantage PGs provide to herbivorous insects and demonstrate the impact of HGT on the evolutionary success of leaf-feeding beetles, major contributors to species diversity.}, }
@article {pmid36161931, year = {2022}, author = {Choi, J and Schmukler, M and Groisman, EA}, title = {Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2210239119}, pmid = {36161931}, issn = {1091-6490}, support = {R01 AI049561/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics/metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; Mammals/metabolism ; Mice ; *Protease La/genetics/metabolism ; }, abstract = {Horizontal gene transfer drives bacterial evolution. To confer new properties, horizontally acquired genes must overcome gene silencing by nucleoid-associated proteins, such as the heat-stable nucleoid structuring (H-NS) protein. Enteric bacteria possess proteins that displace H-NS from foreign genes, form nonfunctional oligomers with H-NS, and degrade H-NS, raising the question of whether any of these mechanisms play a role in overcoming foreign gene silencing in vivo. To answer this question, we mutagenized the hns gene and identified a variant specifying an H-NS protein that binds foreign DNA and silences expression of the corresponding genes, like wild-type H-NS, but resists degradation by the Lon protease. Critically, Escherichia coli expressing this variant alone fails to produce curli, which are encoded by foreign genes and required for biofilm formation, and fails to colonize the murine gut. Our findings establish that H-NS proteolysis is a general mechanism of derepressing foreign genes and essential for colonization of mammalian hosts.}, }
@article {pmid36161739, year = {2022}, author = {Riley, AB and Grillo, MA and Epstein, B and Tiffin, P and Heath, KD}, title = {Discordant population structure among rhizobium divided genomes and their legume hosts.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16704}, pmid = {36161739}, issn = {1365-294X}, abstract = {Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprising multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont, which forms a root nodule symbiosis with the host plant Medicago truncatula. S. meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements, pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. Given limited recombination on the chromosome, compared to the symbiosis elements, distinct population structures may result from differences in effective gene flow. Alternatively, positive or purifying selection, with little recombination, may explain distinct geographical patterns at the chromosome. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.}, }
@article {pmid36161197, year = {2022}, author = {Amábile-Cuevas, CF}, title = {Phage Therapies: Lessons (Not) Learned from the "Antibiotic Era".}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {1}, pages = {12-14}, pmid = {36161197}, issn = {2641-6549}, abstract = {The use of phages as therapeutic or prophylactic approaches is gaining increased interest amid the growing menace of antibiotic resistance. Phages, along with other new anti-infective strategies, are certainly welcome as much needed additions to the medicinal arsenal. However, we can easily make with phages the same mistakes we made with antibiotics, which caused the current resistance crisis. The oversimplification of the ecological role of antibiotics, neglecting ancient resistance and the role of horizontal gene transfer; the active search for wide spectrum, and the massive agricultural abuse; and, most importantly, the financial greed behind the development and use of antibiotics; these are all trends that are now visible in phage research. Should we bring phages to the same track that wasted antibiotics, we could be looking at a "postphage era" in our near future.}, }
@article {pmid36160247, year = {2022}, author = {Soliman, AM and Ramadan, H and Yu, L and Hisatsune, J and Sugai, M and Elnahriry, SS and Nariya, H and El-Domany, RA and Shimamoto, T and Jackson, CR and Shimamoto, T}, title = {Complete genome sequences of two Escherichia coli clinical isolates from Egypt carrying mcr-1 on IncP and IncX4 plasmids.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {989045}, pmid = {36160247}, issn = {1664-302X}, abstract = {Colistin is a last-resort antibiotic used in the treatment of multidrug resistant Gram-negative bacteria. However, the activity and efficacy of colistin has been compromised by the worldwide spread of the mobile colistin resistance genes (mcr-1 to mcr-10). In this study, two clinical Escherichia coli strains, named EcCAI51, and EcCAI73, harbored mcr-1, showed multidrug-resistant phenotypes (with colistin MIC = 4 μg/ml), and belonged to phylogroup D: multilocus sequence type 1011 (ST1011) and phylogroup A: ST744, respectively. Findings revealed the existence of mcr-1 gene on two conjugable plasmids, pAMS-51-MCR1 (∼122 kb IncP) and pAMS-73-MCR1 (∼33 kb IncX4), in EcCAI51, and EcCAI73, respectively. The mcr-1-pap2 element was detected in the two plasmids. Additionally, the composite transposon (ISApl1-IS5D-pap2-mcr-1-ISApl1) was identified only in pAMS-51-MCR1 suggesting the potential for horizontal gene transfer. The two strains carried from 16 to 18 different multiple acquired antimicrobial resistance genes (ARGs). Additionally, two different multireplicon virulence plasmids (∼117 kb pAMS-51-Vr and ∼226 kb pAMS-73-Vr) carrying the sit operon, the Salmochelin siderophore iroBCDE operon and other several virulence genes were identified from the two strains. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of EcCAI73, and EcCAI51 with global E. coli lineages at HC levels of 50 (HC50) to 100 (HC100) core genome allelic differences. To the best of our knowledge, this study presented the first complete genomic sequences of mcr-1-carrying IncP and IncX4 plasmids from human clinical E. coli isolates in Egypt. In addition, the study illustrated the mcr-1 broad dissemination in diverse plasmids and dissimilar E. coli clones.}, }
@article {pmid36159637, year = {2022}, author = {Yu, Z and Zhang, Z and Shi, L and Hua, S and Luan, T and Lin, Q and Zheng, Z and Feng, X and Liu, M and Li, X}, title = {In silico characterization of IncX3 plasmids carrying bla OXA-181 in Enterobacterales.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {988236}, pmid = {36159637}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems ; *DNA Transposable Elements ; Escherichia coli/genetics/metabolism ; Humans ; Microbial Sensitivity Tests ; Plasmids/genetics ; *Type IV Secretion Systems ; beta-Lactamases/genetics/metabolism ; }, abstract = {Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring bla OXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of bla OXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring bla OXA-181 in Enterobacterales, we identified 81 bla OXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored bla OXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of bla OXA-181 among the 66 bla OXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring bla OXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring bla OXA-181 were human origin. Almost all the bla OXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both bla OXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of bla OXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading bla OXA-181 genes in Enterobacterales.}, }
@article {pmid36155788, year = {2022}, author = {Gilbert, C and Maumus, F}, title = {Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci.}, journal = {Genome biology and evolution}, volume = {14}, number = {10}, pages = {}, pmid = {36155788}, issn = {1759-6653}, mesh = {Animals ; *Hemiptera/genetics ; Genes, Plant ; Gene Transfer, Horizontal ; }, abstract = {The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula WJ, Mascotti ML, Juri Ayub M. 2020. Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep. 10(1):15503; Xia J, et al. 2021. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184(7):1693-1705 e1617.). Here, we uncovered a total of 49 plant-like genes deriving from at least 24 independent HGT events in the genome of the Middle East Asia Minor 1 (MEAM1) whitefly. Orthologs of these genes are present in three cryptic B. tabaci species, they are phylogenetically nested within plant sequences, they are expressed and have evolved under purifying selection. The predicted functions of these genes suggest that most of them are involved in plant-insect interactions. Thus, substantial plant-to-insect HGT may have facilitated the evolution of B. tabaci toward adaptation to a large host spectrum. Our study shows that eukaryote-to-eukaryote HGT may be relatively common in some lineages and it provides new candidate genes that may be targeted to improve current control strategies against whiteflies.}, }
@article {pmid36155273, year = {2022}, author = {Bhargav, A and Gupta, S and Seth, S and James, S and Fatima, F and Chaurasia, P and Ramachandran, S}, title = {Knowledgebase of potential multifaceted solutions to antimicrobial resistance.}, journal = {Computational biology and chemistry}, volume = {101}, number = {}, pages = {107772}, doi = {10.1016/j.compbiolchem.2022.107772}, pmid = {36155273}, issn = {1476-928X}, mesh = {Humans ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria ; *Anti-Infective Agents/pharmacology ; Knowledge Bases ; }, abstract = {Antimicrobial resistance (AMR), a top threat to global health, challenges preventive and treatment strategies of infections. AMR strains of microbial pathogens arise through multiple mechanisms. The underlying "antibiotic resistance genes" (ARGs) spread through various species by lateral gene transfer thereby causing global dissemination. Human methods also augment this process through inappropriate use, non-compliance to treatment schedule, and environmental waste. Worldwide significant efforts are being invested to discover novel therapeutic solutions for tackling resistant pathogens. Diverse therapeutic strategies have evolved over recent years. In this work we have developed a comprehensive knowledgebase by collecting alternative antimicrobial therapeutic strategies from literature data. Therapeutic strategies against bacteria, virus, fungus and parasites were extracted from PubMed literature using text mining. We have used a subjective (sentimental) approach for data mining new strategies, resulting in broad coverage of novel entities and subsequently add objective data like entity name (including IUPAC), potency, and safety information. The extracted data was organized in a freely accessible web platform, KOMBAT. The KOMBAT comprises 1104 Chemical compounds, 220 of newly identified antimicrobial peptides, 42 bacteriophages, 242 phytochemicals, 106 nanocomposites, and 94 novel entities for phototherapy. Entities tested and evaluated on AMR pathogens are included. We envision that this database will be useful for developing future therapeutics against AMR pathogens. The database can be accessed through http://kombat.igib.res.in/.}, }
@article {pmid36154280, year = {2022}, author = {Goytia, M and Wadsworth, CB}, title = {Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0199122}, pmid = {36154280}, issn = {2150-7511}, mesh = {Humans ; Azithromycin/pharmacology ; Drug Resistance, Bacterial/genetics ; Penicillin-Binding Proteins/metabolism ; Neisseria/genetics ; DNA Gyrase ; Neisseria gonorrhoeae ; *Gonorrhea/epidemiology ; Anti-Bacterial Agents/pharmacology/metabolism ; Ciprofloxacin/pharmacology ; *Anti-Infective Agents/metabolism ; beta-Lactams/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance (AMR) is widespread within Neisseria gonorrhoeae populations. Recent work has highlighted the importance of commensal Neisseria (cN) as a source of AMR for their pathogenic relatives through horizontal gene transfer (HGT) of AMR alleles, such as mosaic penicillin binding protein 2 (penA), multiple transferable efflux pump (mtr), and DNA gyrase subunit A (gyrA) which impact beta-lactam, azithromycin, and ciprofloxacin susceptibility, respectively. However, nonpathogenic commensal species are rarely characterized. Here, we propose that surveillance of the universally carried commensal Neisseria may play the role of the "canary in the coal mine," and reveal circulating known and novel antimicrobial resistance determinants transferable to pathogenic Neisseria. We summarize the current understanding of commensal Neisseria as an AMR reservoir, and call to increase research on commensal Neisseria species, through expanding established gonococcal surveillance programs to include the collection, isolation, antimicrobial resistance phenotyping, and whole-genome sequencing (WGS) of commensal isolates. This will help combat AMR in the pathogenic Neisseria by: (i) determining the contemporary AMR profile of commensal Neisseria, (ii) correlating AMR phenotypes with known and novel genetic determinants, (iii) qualifying and quantifying horizontal gene transfer (HGT) for AMR determinants, and (iv) expanding commensal Neisseria genomic databases, perhaps leading to the identification of new drug and vaccine targets. The proposed modification to established Neisseria collection protocols could transform our ability to address AMR N. gonorrhoeae, while requiring minor modifications to current surveillance practices. IMPORTANCE Contemporary increases in the prevalence of antimicrobial resistance (AMR) in Neisseria gonorrhoeae populations is a direct threat to global public health and the effective treatment of gonorrhea. Substantial effort and financial support are being spent on identifying resistance mechanisms circulating within the gonococcal population. However, these surveys often overlook a known source of resistance for gonococci-the commensal Neisseria. Commensal Neisseria and pathogenic Neisseria frequently share DNA through horizontal gene transfer, which has played a large role in rendering antibiotic therapies ineffective in pathogenic Neisseria populations. Here, we propose the expansion of established gonococcal surveillance programs to integrate a collection, AMR profiling, and genomic sequencing pipeline for commensal species. This proposed expansion will enhance the field's ability to identify resistance in and from nonpathogenic reservoirs and anticipate AMR trends in pathogenic Neisseria.}, }
@article {pmid36149586, year = {2022}, author = {Gonçalves, OS and de Assis, JCS and Santana, MF}, title = {Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes.}, journal = {Functional &amp; integrative genomics}, volume = {22}, number = {6}, pages = {1139-1145}, pmid = {36149586}, issn = {1438-7948}, mesh = {Workflow ; *Genome, Bacterial ; *Gene Transfer, Horizontal ; }, }
@article {pmid36145457, year = {2022}, author = {Crestani, C and Seligsohn, D and Forde, TL and Zadoks, RN}, title = {How GBS Got Its Hump: Genomic Analysis of Group B Streptococcus from Camels Identifies Host Restriction as well as Mobile Genetic Elements Shared across Hosts and Pathogens.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36145457}, issn = {2076-0817}, support = {BB/R012075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Group B Streptococcus (GBS) literature largely focuses on humans and neonatal disease, but GBS also affects numerous animals, with significant impacts on health and productivity. Spill-over events occur between humans and animals and may be followed by amplification and evolutionary adaptation in the new niche, including changes in the core or accessory genome content. Here, we describe GBS from one-humped camels (Camelus dromedarius), a relatively poorly studied GBS host of increasing importance for food security in arid regions. Genomic analysis shows that virtually all GBS from camels in East Africa belong to a monophyletic clade, sublineage (SL)609. Capsular types IV and VI, including a new variant of type IV, were over-represented compared to other host species. Two genomic islands with signatures of mobile elements contained most camel-associated genes, including genes for metal and carbohydrate utilisation. Lactose fermentation genes were associated with milk isolates, albeit at lower prevalence in camel than bovine GBS. The presence of a phage with high identity to Streptococcus pneumoniae and Streptococcus suis suggests lateral gene transfer between GBS and bacterial species that have not been described in camels. The evolution of camel GBS appears to combine host restriction with the sharing of accessory genome content across pathogen and host species.}, }
@article {pmid36144411, year = {2022}, author = {García-Ríos, E and Guillamón, JM}, title = {Genomic Adaptations of Saccharomyces Genus to Wine Niche.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144411}, issn = {2076-2607}, abstract = {Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.}, }
@article {pmid36144405, year = {2022}, author = {Sowah, RA and Molina, M and Georgacopoulos, O and Snyder, B and Cyterski, M}, title = {Sources and Drivers of ARGs in Urban Streams in Atlanta, Georgia, USA.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144405}, issn = {2076-2607}, abstract = {The spread of antibiotic resistance genes (ARGs) in the aquatic environment is an emerging concern in the interest of protecting public health. Stemming the environmental dissemination of ARGs will require a better understanding of the sources and drivers of ARGs in the water environment. In this study, we used direct measurement of sewage-associated molecular markers, the class 1 integron gene, standard water quality parameters, and watershed characteristics to evaluate the sources and drivers of ARGs in an urban watershed impacted by a gradient of human activities. Quantitative polymerase chain reaction (qPCR) was used to quantify the abundance of the sewage-associated HF183, the E. coli fecal indicator, class 1 integron gene (int1), and the ARGs sulI, sulII, tetW, tetM, ampC, and blaSHV in stream water samples collected from the Proctor Creek watershed in Atlanta, Georgia. Our findings show that ARGs were widely distributed, with detection frequencies of 96% (sulI and sulII), 82% (tetW and tetM), and 49% (ampC and blaSHV). All the ARGs were positively and significantly correlated (r > 0.5) with the HF183 and E. coli markers. Non-linear machine learning models developed using generalized boosting show that more than 70% of the variation in ARG loads in the watershed could be explained by fecal source loading, with other factors such as class 1 integron, which is associated with acquired antibiotic resistance, and environmental factors contributing < 30% to ARG variation. These results suggest that input from fecal sources is a more critical driver of ARG dissemination than environmental stressors or horizontal gene transfer in aquatic environments highly impacted by anthropogenic pollution. Finally, our results provide local watershed managers and stakeholders with information to mitigate the burden of ARGs and fecal bacteria in urban streams.}, }
@article {pmid36142804, year = {2022}, author = {Maslova, O and Mindlin, S and Beletsky, A and Mardanov, A and Petrova, M}, title = {Plasmids as Key Players in Acinetobacter Adaptation.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142804}, issn = {1422-0067}, mesh = {*Acinetobacter/genetics ; *Acinetobacter baumannii/genetics ; Anti-Bacterial Agents ; *Arsenic ; *Metals, Heavy ; Plasmids/genetics ; }, abstract = {This review briefly summarizes the data on the mechanisms of development of the adaptability of Acinetobacters to various living conditions in the environment and in the clinic. A comparative analysis of the genomes of free-living and clinical strains of A. lwoffii, as well as the genomes of A. lwoffii and A. baumannii, has been carried out. It has been shown that plasmids, both large and small, play a key role in the formation of the adaptability of Acinetobacter to their living conditions. In particular, it has been demonstrated that the plasmids of various strains of Acinetobacter differ from each other in their structure and gene composition depending on the lifestyle of their host bacteria. Plasmids of modern strains are enriched with antibiotic-resistant genes, while the content of genes involved in resistance to heavy metals and arsenic is comparable to plasmids from modern and ancient strains. It is concluded that Acinetobacter plasmids may ensure the survival of host bacteria under conditions of various types of environmental and clinical stresses. A brief overview of the main mechanisms of horizontal gene transfer on plasmids inherent in Acinetobacter strains is also given.}, }
@article {pmid36140010, year = {2022}, author = {Riva, V and Patania, G and Riva, F and Vergani, L and Crotti, E and Mapelli, F}, title = {Acinetobacter baylyi Strain BD413 Can Acquire an Antibiotic Resistance Gene by Natural Transformation on Lettuce Phylloplane and Enter the Endosphere.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36140010}, issn = {2079-6382}, abstract = {Antibiotic resistance spread must be considered in a holistic framework which comprises the agri-food ecosystems, where plants can be considered a bridge connecting water and soil habitats with the human microbiome. However, the study of horizontal gene transfer events within the plant microbiome is still overlooked. Here, the environmental strain Acinetobacter baylyi BD413 was used to study the acquisition of extracellular DNA (exDNA) carrying an antibiotic resistance gene (ARG) on lettuce phylloplane, performing experiments at conditions (i.e., plasmid quantities) mimicking those that can be found in a water reuse scenario. Moreover, we assessed how the presence of a surfactant, a co-formulant widely used in agriculture, affected exDNA entry in bacteria and plant tissues, besides the penetration and survival of bacteria into the leaf endosphere. Natural transformation frequency in planta was comparable to that occurring under optimal conditions (i.e., temperature, nutrient provision, and absence of microbial competitors), representing an entrance pathway of ARGs into an epiphytic bacterium able to penetrate the endosphere of a leafy vegetable. The presence of the surfactant determined a higher presence of culturable transformant cells in the leaf tissues but did not significantly increase exDNA entry in A. baylyi BD413 cells and lettuce leaves. More research on HGT (Horizontal Gene Transfer) mechanisms in planta should be performed to obtain experimental data on produce safety in terms of antibiotic resistance.}, }
@article {pmid36138780, year = {2022}, author = {Chitayat Levi, L and Rippin, I and Ben Tulila, M and Galron, R and Tuller, T}, title = {Modulating Gene Expression within a Microbiome Based on Computational Models.}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138780}, issn = {2079-7737}, abstract = {Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core property influencing this process is horizontal gene transfer between members of the bacterial community used to maintain genetic variation. The essential effect of this mechanism is the exposure of genetic information to a wide array of members of the community, creating an additional "layer" of information in the microbiome named the "plasmidome". From an engineering perspective, introduction of genetic information to an environment must be facilitated into chosen species which will be able to carry out the desired effect instead of competing and inhibiting it. Moreover, this process of information transfer imposes concerns for the biosafety of genetic engineering of microbiomes as exposure of genetic information into unwanted hosts can have unprecedented ecological impacts. Current technologies are usually experimentally developed for a specific host/environment, and only deal with the transformation process itself at best, ignoring the impact of horizontal gene transfer and gene-microbiome interactions that occur over larger periods of time in uncontrolled environments. The goal of this research was to design new microbiome-specific versions of engineered genetic information, providing an additional layer of compatibility to existing engineering techniques. The engineering framework is entirely computational and is agnostic to the selected microbiome or gene by reducing the problem into the following set up: microbiome species can be defined as wanted or unwanted hosts of the modification. Then, every element related to gene expression (e.g., promoters, coding regions, etc.) and regulation is individually examined and engineered by novel algorithms to provide the defined expression preferences. Additionally, the synergistic effect of the combination of engineered gene blocks facilitates robustness to random mutations that might occur over time. This method has been validated using both computational and experimental tools, stemming from the research done in the iGEM 2021 competition, by the TAU group.}, }
@article {pmid36138049, year = {2022}, author = {Zielezinski, A and Loch, JI and Karlowski, WM and Jaskolski, M}, title = {Massive annotation of bacterial L-asparaginases reveals their puzzling distribution and frequent gene transfer events.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15797}, pmid = {36138049}, issn = {2045-2322}, mesh = {Ammonia ; *Asparaginase/genetics ; *Asparagine/genetics ; Aspartic Acid/genetics ; Bacteria/enzymology ; Bacterial Proteins/genetics ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {L-Asparaginases, which convert L-asparagine to L-aspartate and ammonia, come in five types, AI-AV. Some bacterial type AII enzymes are a key element in the treatment of acute lymphoblastic leukemia in children, but new L-asparaginases with better therapeutic properties are urgently needed. Here, we search publicly available bacterial genomes to annotate L-asparaginase proteins belonging to the five known types. We characterize taxonomic, phylogenetic, and genomic patterns of L-asparaginase occurrences pointing to frequent horizontal gene transfer (HGT) events, also occurring multiple times in the same recipient species. We show that the reference AV gene, encoding a protein originally found and structurally studied in Rhizobium etli, was acquired via HGT from Burkholderia. We also describe the sequence variability of the five L-asparaginase types and map the conservation levels on the experimental or predicted structures of the reference enzymes, finding the most conserved residues in the protein core near the active site, and the most variable ones on the protein surface. Additionally, we highlight the most common sequence features of bacterial AII proteins that may aid in selecting therapeutic L-asparaginases. Finally, we point to taxonomic units of bacteria that do not contain recognizable sequences of any of the known L-asparaginase types, implying that those microorganisms most likely contain new, as yet unknown types of L-asparaginases. Such novel enzymes, when properly identified and characterized, could hold promise as antileukemic drugs.}, }
@article {pmid36138004, year = {2022}, author = {Kapteijn, R and Shitut, S and Aschmann, D and Zhang, L and de Beer, M and Daviran, D and Roverts, R and Akiva, A and van Wezel, GP and Kros, A and Claessen, D}, title = {Endocytosis-like DNA uptake by cell wall-deficient bacteria.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5524}, pmid = {36138004}, issn = {2041-1723}, mesh = {*Bacteria/genetics ; Cell Wall/metabolism ; DNA/metabolism ; DNA, Bacterial/genetics ; *Dextrans ; Endocytosis ; Liposomes ; Nanoparticles ; Sodium Azide ; }, abstract = {Horizontal gene transfer in bacteria is widely believed to occur via conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. Here, we report that cell wall-deficient bacteria can engulf DNA and other extracellular material via an endocytosis-like process. Specifically, we show that L-forms of the filamentous actinomycete Kitasatospora viridifaciens can take up plasmid DNA, polysaccharides (dextran) and 150-nm lipid nanoparticles. The process involves invagination of the cytoplasmic membrane, leading to formation of intracellular vesicles that encapsulate extracellular material. DNA uptake is not affected by deletion of genes homologous to comEC and comEA, which are required for natural transformation in other species. However, uptake is inhibited by sodium azide or incubation at 4 °C, suggesting the process is energy-dependent. The encapsulated materials are released into the cytoplasm upon degradation of the vesicle membrane. Given that cell wall-deficient bacteria are considered a model for early life forms, our work reveals a possible mechanism for primordial cells to acquire food or genetic material before invention of the bacterial cell wall.}, }
@article {pmid36130651, year = {2022}, author = {Balbuena-Alonso, MG and Cortés-Cortés, G and Kim, JW and Lozano-Zarain, P and Camps, M and Del Carmen Rocha-Gracia, R}, title = {Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102650}, doi = {10.1016/j.plasmid.2022.102650}, pmid = {36130651}, issn = {1095-9890}, mesh = {Humans ; Plasmids/genetics ; *Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Drug Resistance, Microbial/genetics ; Genomics ; *Escherichia coli Infections ; Gene Transfer, Horizontal ; }, abstract = {The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.}, }
@article {pmid36125448, year = {2022}, author = {Zaman, S and Sledzieski, S and Berger, B and Wu, YC and Bansal, MS}, title = {virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2021.0507}, pmid = {36125448}, issn = {1557-8666}, abstract = {An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. In this study, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.}, }
@article {pmid36125273, year = {2022}, author = {Uppal, S and Metz, JL and Xavier, RKM and Nepal, KK and Xu, D and Wang, G and Kwan, JC}, title = {Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0152422}, pmid = {36125273}, issn = {2150-7511}, support = {R21 CA209189/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics ; Phylogeny ; Symbiosis/genetics ; Acyl Carrier Protein/genetics ; Metagenomics ; *Porifera/microbiology ; Bacteria/genetics ; *Biological Products/pharmacology ; *Antineoplastic Agents ; Acyltransferases/genetics ; }, abstract = {Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.}, }
@article {pmid36124853, year = {2022}, author = {Tanaka, E and Wajima, T and Nakaminami, H and Uchiya, KI}, title = {Alternative quinolone-resistance pathway caused by simultaneous horizontal gene transfer in Haemophilus influenzae.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {12}, pages = {3270-3274}, doi = {10.1093/jac/dkac312}, pmid = {36124853}, issn = {1460-2091}, mesh = {*Haemophilus influenzae/genetics ; *Quinolones/pharmacology ; DNA Topoisomerase IV/genetics ; DNA Gyrase/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Mutation ; Fluoroquinolones ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Quinolone-resistant bacteria are known to emerge via the accumulation of mutations in a stepwise manner. Recent studies reported the emergence of quinolone low-susceptible Haemophilus influenzae ST422 isolates harbouring two relevant mutations, although ST422 isolates harbouring one mutation were never identified.<br><br>OBJECTIVES: To investigate if GyrA and ParC from quinolone low-susceptible isolates can be transferred horizontally and simultaneously to susceptible isolates.<br><br>METHODS: Genomic DNA was extracted from an H. influenzae isolate harbouring amino acid substitutions in both gyrA and parC and mixed with clinical isolates. The emergence of resistant isolates was compared, and WGS analysis was performed.<br><br>RESULTS: By adding the genomic DNA harbouring both mutated gyrA and parC, resistant bacteria exhibiting recombination at gyrA only or both gyrA and parC loci were obtained on nalidixic acid and pipemidic acid plates, and the frequency was found to increase with the amount of DNA. Recombination events in gyrA only and in both gyrA and parC occurred with at least 1 and 1-100&#x2005;ng of DNA, respectively. The genome sequence of a representative strain showed recombination events throughout the genome. The MIC of quinolone for the resulting strains was found to be similar to that of the donor. Although the recombination efficacy was different among the various strains, all strains used in this study obtained multiple genes simultaneously.<br><br>CONCLUSIONS: These findings indicate that H. influenzae can simultaneously obtain more than two mutated genes. This mechanism of horizontal transfer could be an alternative pathway for attaining quinolone resistance.}, }
@article {pmid36123439, year = {2022}, author = {Purtschert-Montenegro, G and Cárcamo-Oyarce, G and Pinto-Carbó, M and Agnoli, K and Bailly, A and Eberl, L}, title = {Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1547-1557}, pmid = {36123439}, issn = {2058-5276}, support = {169307/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Biofilms ; *Solanum lycopersicum/microbiology ; *Pseudomonas putida/genetics ; *Ralstonia solanacearum ; Soil ; }, abstract = {Many bacteria utilize contact-dependent killing machineries to eliminate rivals in their environmental niches. Here we show that the plant root colonizer Pseudomonas putida strain IsoF is able to kill a wide range of soil and plant-associated Gram-negative bacteria with the aid of a type IVB secretion system (T4BSS) that delivers a toxic effector into bacterial competitors in a contact-dependent manner. This extends the range of targets of T4BSSs-so far thought to transfer effectors only into eukaryotic cells-to prokaryotes. Bioinformatic and genetic analyses showed that this killing machine is entirely encoded by the kib gene cluster located within a rare genomic island, which was recently acquired by horizontal gene transfer. P. putida IsoF utilizes this secretion system not only as a defensive weapon to kill bacterial competitors but also as an offensive weapon to invade existing biofilms, allowing the strain to persist in its natural environment. Furthermore, we show that strain IsoF can protect tomato plants against the phytopathogen Ralstonia solanacearum in a T4BSS-dependent manner, suggesting that IsoF can be exploited for pest control and sustainable agriculture.}, }
@article {pmid36121484, year = {2022}, author = {Sheikh, BA and Bhat, BA and Mir, MA}, title = {Antimicrobial resistance: new insights and therapeutic implications.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6427-6440}, pmid = {36121484}, issn = {1432-0614}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; *Drug Resistance, Bacterial ; Humans ; }, abstract = {Antimicrobial resistance has not been a new phenomenon. Still, the number of resistant organisms, the geographic areas affected by emerging drug resistance, and the magnitude of resistance in a single organism are enormous and mounting. Disease and disease-causing agents formerly thought to be contained by antibiotics are now returning in new forms resistant to existing therapies. Antimicrobial resistance is one of the most severe and complicated health issues globally, driven by interrelated dynamics in humans, animals, and environmental health sectors. Coupled with various epidemiological factors and a limited pipeline for new antimicrobials, all these misappropriations allow the transmission of drug-resistant organisms. The problem is likely to worsen soon. Antimicrobial resistance in general and antibiotic resistance in particular is a shared global problem. Actions taken by any single country can adversely or positively affect the other country. Targeted coordination and prevention strategies are critical in stopping the spread of antibiotic-resistant organisms and hence its overall management. This article has provided in-depth knowledge about various methods that can help mitigate the emergence and spread of antimicrobial resistance globally. KEY POINTS: • Overview of antimicrobial resistance as a global challenge and explain various reasons for its rapid progression. • Brief about the intrinsic and acquired resistance to antimicrobials and development of antibiotic resistance in bacteria. • Systematically organized information is provided on different strategies for tackling antimicrobial resistance for the welfare of human health.}, }
@article {pmid36118580, year = {2022}, author = {Philips, JG and Martin-Avila, E and Robold, AV}, title = {Horizontal gene transfer from genetically modified plants - Regulatory considerations.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {971402}, pmid = {36118580}, issn = {2296-4185}, abstract = {Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.}, }
@article {pmid36116192, year = {2022}, author = {Wang, D and Meng, Y and Meng, F}, title = {Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia.}, journal = {Water research}, volume = {224}, number = {}, pages = {119062}, doi = {10.1016/j.watres.2022.119062}, pmid = {36116192}, issn = {1879-2448}, mesh = {Amino Acids ; Anaerobic Ammonia Oxidation ; Animals ; Bacteria/metabolism ; *Bioreactors/microbiology ; Biotin/genetics/metabolism ; Carbohydrates ; Denitrification ; *Gene Transfer, Horizontal ; Metagenomics ; Methionine/genetics/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Swine ; Thiamine/metabolism ; Vitamins/metabolism ; }, abstract = {Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.}, }
@article {pmid36114974, year = {2022}, author = {Azhogina, T and Sazykina, M and Konstantinova, E and Khmelevtsova, L and Minkina, T and Antonenko, E and Sushkova, S and Khammami, M and Mandzhieva, S and Sazykin, I}, title = {Bioaccessible PAH influence on distribution of antibiotic resistance genes and soil toxicity of different types of land use.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36114974}, issn = {1614-7499}, abstract = {For a better understanding of the dissemination of antibiotic resistance genes (ARGs) in natural microbial communities, it is necessary to study the factors influencing it. There are not enough studies showing the connection of some pollutants with the dissemination of ARGs and especially few works on the effect of polycyclic aromatic compounds (PAHs) on the spread of resistance in microbiocenosis. In this respect, the aim of the study was to determine the effect of bioaccessible PAHs on soil resistome. The toxicity and the content of bioaccessible PAHs and ARGs were studied in 64 samples of soils of different types of land use in the Rostov Region of Russia. In most soils, a close positive correlation was demonstrated between different ARGs and bioaccessible PAHs with different content of rings in the structure. Six of the seven studied ARGs correlated with the content of 2-, 3-, 4-, 5- or 6-ring PAHs. The greatest number of close correlations was found between the content of PAHs and ARGs in the soils of protected areas, for agricultural purposes, and in soils of hospitals. The diverse composition of microbial communities in these soils might greatly facilitate this process. A close correlation between various toxic effects identified with a battery of whole-cell bacterial biosensors and bioaccessible PAHs of various compositions was established. This correlation showed possible mechanisms of PAHs' influence on microorganisms (DNA damage, oxidative stress, etc.), which led to a significant increase in horizontal gene transfer and spread of some ARGs in soil microbial communities. All this information, taken together, suggests that bioaccessible PAHs can enhance the spread of antibiotic resistance genes.}, }
@article {pmid36114450, year = {2022}, author = {Zhang, C and Lin, Q and Zhang, J and Huang, Z and Nan, P and Li, L and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Comparing complete organelle genomes of holoparasitic Christisonia kwangtungensis (Orabanchaceae) with its close relatives: how different are they?.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {444}, pmid = {36114450}, issn = {1471-2229}, mesh = {*Genome, Mitochondrial/genetics ; *Genome, Plastid/genetics ; *Orobanchaceae/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Orobanchaceae is the only flowering plant family with species from free-living nonparasite, hemi-parasite to holoparasite, making it an ideal system for studying the evolution of parasitism. However, both plastid and mitochondrial genome have been sequenced in only few parasitic species in Orobanchaceae. Therefore, further comparative study is wanted to investigate the impact of holoparasitism on organelle genomes evolution between close relatives. Here, we sequenced organelle genomes and transcriptome of holoparasitic Christisonia kwangtungensis and compared it with its closely related groups to analyze similarities and differences in adaption strategies to the holoparasitic lifestyle.<br><br>RESULTS: The plastid genome of C. kwangtungensis has undergone extensive pseudogenization and gene loss, but its reduction pattern is different from that of Aeginetia indica, the close relative of C. kwangtungensis. Similarly, the gene expression detected in the photosynthetic pathway of these two genera is different. In Orobanchaceae, holoparasites in Buchnereae have more plastid gene loss than Rhinantheae, which reflects their longer history of holoparasitism. Distinct from severe degradation of the plastome, protein-coding genes in the mitochondrial genome of C. kwangtungensis are relatively conserved. Interestingly, besides intracellularly transferred genes which are still retained in its plastid genome, we also found several horizontally transferred genes of plastid origin from diverse donors other than their current hosts in the mitochondrial genome, which probably indicate historical hosts.<br><br>CONCLUSION: Even though C. kwangtungensis and A. indica are closely related and share severe degradation of plastome, they adapt organelle genomes to the parasitic lifestyle in different ways. The difference between their gene loss and gene expression shows they ultimately lost photosynthetic genes but through different pathways. Our study exemplifies how parasites part company after achieving holoparasitism.}, }
@article {pmid36113785, year = {2023}, author = {Wang, L and Yan, X and Zhu, L and Wang, J and Xing, B and Kim, YM and Wang, J}, title = {Spread and driving factors of antibiotic resistance genes in soil-plant system in long-term manured greenhouse under lead (Pb) stress.}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158756}, doi = {10.1016/j.scitotenv.2022.158756}, pmid = {36113785}, issn = {1879-1026}, mesh = {*Manure/microbiology ; *Soil ; Lead ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Livestock manure is often used as fertilizer in greenhouses, resulting in simultaneous enrichment of heavy metals and antibiotic resistance genes (ARGs) in soils. The soil-plant system is a non-negligible way to spread ARGs; however, the effects of lead (Pb) on the spread of ARGs and their driving factors in the greenhouse soil-plant system remain unclear. In this present study, the occurrence of ARGs in greenhouse soils and their spread into plants under Pb stress were studied. Overall, Pb promoted the accumulation of ARGs in root endophytes at 10, 50, and 100 mg/kg as well as in soils at 10 and 200 mg/kg, but reduced the total relative abundance of ARGs in leaf endophytes. Particularly, Pb increased the mobile genetic elements (MGEs) relative abundance and endophytic bacterial community diversity in roots, consistent with the change in the total relative abundance of ARGs. Network analysis revealed that bacterial community and MGEs may jointly affect the migration of ARGs in the soil-plant system of greenhouses. Overall, this study extended our knowledge of how Pb can promote the transmission of ARGs to plant roots from greenhouse soils receiving long-term manure applications, which must be considered when assessing the risk of ARGs to public health.}, }
@article {pmid36113173, year = {2022}, author = {Gao, Q and Ma, X and Wang, Z and Chen, H and Luo, Y and Wu, B and Qi, S and Lin, M and Tian, J and Qiao, Y and Grossart, HP and Xu, W and Huang, L}, title = {Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China).}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114112}, doi = {10.1016/j.marpolbul.2022.114112}, pmid = {36113173}, issn = {1879-3363}, mesh = {Virulence/genetics ; Seasons ; Hemolysin Proteins ; Bays ; *Vibrio ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; China/epidemiology ; *Vibrio parahaemolyticus/genetics ; }, abstract = {In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL[-1] and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 %, 15.52 %, and 11.30 %) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio isolated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality surveillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies.}, }
@article {pmid36108440, year = {2022}, author = {Oliveira, V and Polónia, ARM and Cleary, DFR and Huang, YM and de Voogd, NJ and Keller-Costa, T and Costa, R and Gomes, NCM}, title = {Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbionts.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127183}, doi = {10.1016/j.micres.2022.127183}, pmid = {36108440}, issn = {1618-0623}, mesh = {Animals ; Bacteria/genetics ; Genomics ; Phylogeny ; Plasmids/genetics ; *Porifera/microbiology ; }, abstract = {Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.}, }
@article {pmid36107279, year = {2022}, author = {Huber, KT and Moulton, V and Scholz, GE}, title = {Forest-Based Networks.}, journal = {Bulletin of mathematical biology}, volume = {84}, number = {10}, pages = {119}, pmid = {36107279}, issn = {1522-9602}, mesh = {Arthrogryposis ; Cholestasis ; Forests ; Humans ; *Mathematical Concepts ; Models, Biological ; *Models, Genetic ; Phylogeny ; Renal Insufficiency ; }, abstract = {In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases, tree-based phylogenetic networks can provide a useful, more refined representation of the species' evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree's edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.}, }
@article {pmid36107214, year = {2022}, author = {Wang, J and Yuan, L and Wu, W and Yan, Y}, title = {Characterization of the phosphotriesterase capable of hydrolyzing aryl-organophosphate flame retardants.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6493-6504}, pmid = {36107214}, issn = {1432-0614}, mesh = {Biphenyl Compounds ; Esters ; *Flame Retardants/metabolism ; Organophosphates/metabolism ; Phosphates ; *Phosphoric Triester Hydrolases/chemistry/genetics/metabolism ; Polymers ; Recombinant Proteins ; Resorcinols ; Sphingomonadaceae ; Transposases ; *Tritolyl Phosphates ; }, abstract = {A related group of phosphotriesters known as organophosphate flame retardants (OPFRs) has become emerging contaminants due to its worldwide use. The lack of an easily hydrolysable bond renders OPFRs inert to the well-known phosphotriesterases capable of hydrolyzing the neurotoxic organophosphates. An OPFRs phosphotriesterase gene stpte was cloned from plasmid pStJH of strain Sphingopyxis terrae subsp. terrae YC-JH3 and was heterologously expressed in Escherichia coli. The recombinant protein St-PTE was purified and analyzed. St-PTE showed the highest catalytic activity at pH 8.5 and 35 °C. The optimal substrate for St-PTE is triphenyl phosphate, with kcat/Km of 5.03 × 10[6] M[-1] s[-1], two orders of magnitude higher than those of tricresyl phosphate (4.17 × 10[4] M[-1] s[-1]), 2-ethylhexyl diphenyl phosphate (2.03 × 10[4] M[-1] s[-1]) and resorcinol bis(diphenyl phosphate) (6.30 × 10[4] M[-1] s[-1]). St-PTE could break the P-O bond of tri-esters and convert aryl-OPFRs into their corresponding di-ester metabolites, including polymers of resorcinol bis(diphenyl phosphate). Mediated by transposase, the gene of OPFRs phosphotriesterase could be transferred horizontally among closely related strains of Sphingomonas, Sphingobium and Sphingopyxis. KEY POINTS: • St-PTE from Sphingopyxis terrae subsp. terrae YC-JH3 could hydrolyze aryl-OPFRs. • Metabolites of RBDPP hydrolyzed by phosphotriesterase were identified. • St-PTE could hydrolyze the P-O cleavage of dimer and trimer of RBDPP. • Phosphotriesterase genes transfer among Sphingomonadaceae mediated by transposase.}, }
@article {pmid36106856, year = {2022}, author = {Bourassa, JS and Jeannotte, G and Lebel-Beaucage, S and Beauregard, PB}, title = {Second-Generation Transfer Mediates Efficient Propagation of ICEBs1 in Biofilms.}, journal = {Journal of bacteriology}, volume = {204}, number = {10}, pages = {e0018122}, pmid = {36106856}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; *Bacillus subtilis/genetics ; Gene Transfer, Horizontal ; Biofilms ; Drug Resistance, Microbial ; }, abstract = {Horizontal gene transfer (HGT) by integrative and conjugative elements (ICEs) is an important mechanism in the spread of antibiotic resistance genes. However, little is known about the spatiotemporal dynamic of ICE propagation in bacterial biofilms, which are multicellular structures ubiquitous in natural and clinical environments. We report here that a high level of biofilm matrix production favors ICEBs1 acquisition. Also, using a fluorescently marked ICEBs1, we observed that conjugation appears restricted to clusters of bacteria in a close neighborhood in which a high level of ICEBs1 transfer occurs. These conjugative clusters are heterogeneously distributed in the biofilm, forming close to the air-biofilm interface. Importantly, we established that transconjugant cells are the main contributors to ICEBs1 propagation in biofilms. Our findings provide a novel spatiotemporal understanding of ICEs propagation in biofilms, which should have an important role in our understanding of horizontal gene transfer in relevant settings. IMPORTANCE The transfer of mobile genetic elements between bacteria is the main cause of the spread of antibiotic resistance genes. While biofilms are the predominant bacterial lifestyle both in the environment and in clinical settings, their impact on the propagation of mobile genetic elements is still poorly understood. In this study, we examined the spatiotemporal propagation of the well-characterized ICEBs1. Using the Gram-positive Bacillus subtilis, we observed that the main actors of ICEBs1 propagation in biofilms are the newly formed transconjugants that allow rapid transfer of ICEBs1 to new recipients. Our study provides a better understanding of the spatiotemporal dynamic of conjugative transfer in biofilms.}, }
@article {pmid36106855, year = {2022}, author = {Payot, S}, title = {Key Role of Transconjugants for Dissemination of the Integrative Conjugative Element ICEBs1 in Biofilms.}, journal = {Journal of bacteriology}, volume = {204}, number = {10}, pages = {e0032722}, pmid = {36106855}, issn = {1098-5530}, mesh = {*Conjugation, Genetic ; *Gene Transfer, Horizontal ; Bacillus subtilis/genetics ; Biofilms ; }, abstract = {In this issue of the Journal of Bacteriology, J.-S. Bourassa, G. Jeannotte, S. Lebel-Beaucage, and P. B. Beauregard (J Bacteriol 204:e00181-22, 2022, https://doi.org/10.1128/jb.00181-22) showed that ICEBs1 propagation in Bacillus subtilis biofilm relies almost exclusively on transconjugants. It appears restricted to clusters of bacteria in a close neighborhood of initial donor cells, which are heterogeneously distributed in the biofilm and expand vertically toward the air-liquid interface.}, }
@article {pmid36104761, year = {2022}, author = {Gheorghe-Barbu, I and Barbu, IC and Popa, LI and Pîrcălăbioru, GG and Popa, M and Măruțescu, L and Niță-Lazar, M and Banciu, A and Stoica, C and Gheorghe, &#x218; and Lucaciu, I and Săndulescu, O and Paraschiv, S and Surleac, M and Talapan, D and Muntean, AA and Preda, M and Muntean, MM and Dragomirescu, CC and Popa, MI and Oțelea, D and Chifiriuc, MC}, title = {Temporo-spatial variations in resistance determinants and clonality of Acinetobacter baumannii and Pseudomonas aeruginosa strains from Romanian hospitals and wastewaters.}, journal = {Antimicrobial resistance and infection control}, volume = {11}, number = {1}, pages = {115}, pmid = {36104761}, issn = {2047-2994}, mesh = {*Acinetobacter baumannii ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Hospitals ; Interleukin-1 Receptor-Like 1 Protein ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/genetics ; Romania/epidemiology ; Wastewater/microbiology ; Wastewater-Based Epidemiological Monitoring ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Romania is one of the European countries reporting very high antimicrobial resistance (AMR) rates and consumption of antimicrobials. We aimed to characterize the AMR profiles and clonality of 304 multi-drug resistant (MDR) Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa) strains isolated during two consecutive years (2018 and 2019) from hospital settings, hospital collecting sewage tanks and the receiving wastewater treatment plants (WWTPs) located in the main geographical regions of Romania.<br><br>METHODS: The strains were isolated on chromogenic media and identified by MALDI-TOF-MS. Antibiotic susceptibility testing and confirmation of ESBL- and CP- producing phenotypes and genotypes were performed. The genetic characterization also included horizontal gene transfer experiments, whole-genome sequencing (WGS), assembling, annotation and characterization.<br><br>RESULTS: Both clinical and aquatic isolates exhibited high MDR rates, especially the Ab strains isolated from nosocomial infections and hospital effluents. The phenotypic resistance profiles and MDR rates have largely varied by sampling point and geographic location. The highest MDR rates in the aquatic isolates were recorded in Gala&#x21b;i WWTP, followed by Bucharest. The Ab strains harbored mostly blaOXA-23, blaOXA-24, blaSHV, blaTEM and blaGES, while Pa strains blaIMP, blaVIM, blaNDM, blaVEB, blaGES and blaTEM, with high variations depending on the geographical zone and the sampling point. The WGS analysis revealed the presence of antibiotic resistance genes (ARGs) to other antibiotic classes, such as aminoglycosides, tetracyclines, sulphonamides, fosfomycin, phenicols, trimethoprim-sulfamethoxazole as well as class 1 integrons. The molecular analyses highlighted: (i) The presence of epidemic clones such as ST2 for Ab and ST233 and ST357 for Pa; (ii) The relatedness between clinical and hospital wastewater strains and (iii) The possible dissemination of clinical Ab belonging to ST2 (also proved in the conjugation assays for blaOXA-23 or blaOXA-72 genes), ST79 and ST492 and of Pa strains belonging to ST357, ST640 and ST621 in the wastewaters.<br><br>CONCLUSION: Our study reveals the presence of CP-producing Ab and Pa in all sampling points and the clonal dissemination of clinical Ab ST2 strains in the wastewaters. The prevalent clones were correlated with the presence of class 1 integrons, suggesting that these isolates could be a significant reservoir of ARGs, being able to persist in the environment.}, }
@article {pmid36100085, year = {2022}, author = {Wang, Q and Olesen, AK and Maccario, L and Madsen, JS}, title = {An easily modifiable conjugative plasmid for studying horizontal gene transfer.}, journal = {Plasmid}, volume = {123-124}, number = {}, pages = {102649}, doi = {10.1016/j.plasmid.2022.102649}, pmid = {36100085}, issn = {1095-9890}, mesh = {*Gene Transfer, Horizontal ; Plasmids/genetics ; *Conjugation, Genetic ; beta-Lactamases/genetics ; Anti-Bacterial Agents ; }, abstract = {Horizontal gene transfer is an important mechanism in bacterial evolution and can occur at striking frequencies when mediated by mobile genetic elements. Conjugative plasmids are mobile genetic elements that are main drivers of horizontal transfer and a major facilitator in the spread of antibiotic resistance genes. However, conjugative plasmid models that readily can be genetically modified with the aim to study horizontal transfer are not currently available. The aim of this study was to develop a conjugative plasmid model where the insertion of gene cassettes such as reporter genes (e.g., fluorescent proteins) or antibiotic resistance genes would be efficient and convenient. Here, we introduced a single attTn7 site into the conjugative broad-host-range IncP-1 plasmid pKJK5 in a non-disruptive manner. Furthermore, a version with lower transfer rate and a non-conjugative version of pKJK5-attTn7 were also constructed. The advantage of having the attTn7 sites is that genes of interest can be introduced in a single step with very high success rate using the Tn7 transposition system. In addition, larger genetic fragments can be inserted. To illustrate the efficacy of the constructed pKJK5 plasmids, they were complemented with sfGFP (a gene encoding superfolder green fluorescent protein) in addition to seven different β-lactamase genes representing the four known classes of β-lactamases.}, }
@article {pmid36098534, year = {2022}, author = {Sherlock, D and Fogg, PCM}, title = {Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {19}, pages = {e0094422}, pmid = {36098534}, issn = {1098-5336}, support = {/WT_/Wellcome Trust/United Kingdom ; 109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biofilms ; Cysteine/metabolism ; DNA/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; Phenotype ; *Rhodobacter capsulatus/genetics ; Serine ; Serine O-Acetyltransferase/genetics/metabolism ; }, abstract = {Biofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment. IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.}, }
@article {pmid36096030, year = {2022}, author = {Shi, X and Xia, Y and Wei, W and Ni, BJ}, title = {Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms.}, journal = {Water research}, volume = {224}, number = {}, pages = {119060}, doi = {10.1016/j.watres.2022.119060}, pmid = {36096030}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Microplastics ; Plastics ; }, abstract = {The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.}, }
@article {pmid36090102, year = {2022}, author = {Zhao, H and Wang, J and Peng, Y and Cai, X and Liu, Y and Huang, W and Huang, H and Nie, Y}, title = {Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928153}, pmid = {36090102}, issn = {1664-302X}, abstract = {BACKGROUND: Paraclostridium bifermentans is the most diverse distributed species of Paraclostridium and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of P. bifermentans HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability.<br><br>RESULTS: The de novo assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as P. bifermentans and reclassified some previously non-P. bifermentans strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and Listeria LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as asrABCH, cat, mccF, macB, entS, albA, bcrA, and tetB, were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the hin gene in the plasmids.<br><br>CONCLUSION: The flexible genomic pool of P. bifermentans encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, P. bifermentans HD0315_2 might infect hosts via a Listeria LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses.}, }
@article {pmid36089145, year = {2022}, author = {Hembach, N and Bierbaum, G and Schreiber, C and Schwartz, T}, title = {Facultative pathogenic bacteria and antibiotic resistance genes in swine livestock manure and clinical wastewater: A molecular biology comparison.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120128}, doi = {10.1016/j.envpol.2022.120128}, pmid = {36089145}, issn = {1873-6424}, mesh = {Animals ; Anti-Bacterial Agents/analysis/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; Escherichia coli ; *Escherichia coli Proteins/genetics ; Genes, Bacterial ; Humans ; Livestock ; *Manure/analysis ; Molecular Biology ; Soil ; Soil Microbiology ; Swine ; Wastewater/analysis ; }, abstract = {Manure contains vast amounts of biological contaminants of veterinary origin. Only few studies analyse clinically critical resistance genes against reserve antibiotics in manure. In general, resistances against these high priority antibiotics involve a high potential health risk. Therefore, their spread in the soil as well as the aquatic environment has to be prevented. Manures of 29 different swine livestock were analysed. Abundances of facultative pathogenic bacteria including representatives of the clinically critical ESKAPE-pathogens (P. aeruginosa, K. pneumoniae, A. baumannii, E. faecium) and E. coli were investigated via qPCR. Antibiotic resistance genes against commonly used veterinary antibiotics (ermB, tetM, sul1) as well as various resistance genes against important (mecA, vanA) and reserve antibiotics (blaNDM, blaKPC3, mcr-1), which are identified by the WHO, were also obtained by qPCR analysis. The manures of all swine livestock contained facultative pathogenic bacteria and commonly known resistance genes against antibiotics used in veterinary therapies, but more important also a significant amount of clinically critical resistance genes against reserve antibiotics for human medicine. To illustrate the impact the occurrence of these clinically critical resistance genes, comparative measurements were taken of the total wastewater of a large tertiary care hospital (n = 8). Both manure as well as raw hospital wastewaters were contaminated with significant abundances of gene markers for facultative pathogens and with critical resistance genes of reserve antibiotics associated with genetic mobile elements for horizontal gene transfer. Hence, both compartments bear an exceptional potential risk for the dissemination of facultative pathogens and critical antibiotic resistance genes.}, }
@article {pmid36085101, year = {2022}, author = {Prasad, A and Chirom, O and Prasad, M}, title = {Horizontal gene transfer and the evolution of land plants.}, journal = {Trends in plant science}, volume = {27}, number = {12}, pages = {1203-1205}, doi = {10.1016/j.tplants.2022.08.020}, pmid = {36085101}, issn = {1878-4372}, mesh = {*Gene Transfer, Horizontal/genetics ; Evolution, Molecular ; *Embryophyta/genetics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is the transfer of genetic material between organisms. It has been known for some time that HGT in eukaryotes is not a rare phenomenon. A recent study by Ma et al. has shown that HGT has played a crucial role in shaping the evolution of land plants.}, }
@article {pmid36084857, year = {2022}, author = {Ribeiro, IDA and Bach, E and Passaglia, LMP}, title = {Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family.}, journal = {Molecular phylogenetics and evolution}, volume = {177}, number = {}, pages = {107624}, doi = {10.1016/j.ympev.2022.107624}, pmid = {36084857}, issn = {1095-9513}, mesh = {Nitrogen Fixation/genetics ; *Nitrogenase/genetics/metabolism ; *Paenibacillus/genetics/metabolism ; Phylogeny ; }, abstract = {Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.}, }
@article {pmid36084285, year = {2022}, author = {Cunliffe, TG and Parker, AL and Jaramillo, A}, title = {Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications.}, journal = {ACS synthetic biology}, volume = {11}, number = {10}, pages = {3207-3215}, pmid = {36084285}, issn = {2161-5063}, support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Host Specificity ; *Bacteriophage P2 ; Lipopolysaccharides ; Proteome ; *Bacteriophages/genetics ; Anti-Bacterial Agents ; }, abstract = {Bacteriophages (phages) represent powerful potential treatments against antibiotic-resistant bacterial infections. Antibiotic-resistant bacteria represent a significant threat to global health, with an estimated 70% of infection-causing bacteria being resistant to one or more antibiotics. Developing novel antibiotics against the limited number of cellular targets is expensive and time-consuming, and bacteria can rapidly develop resistance. While bacterial resistance to phage can evolve, bacterial resistance to phage does not appear to spread through lateral gene transfer, and phage may similarly adapt through mutation to recover infectivity. Phages have been identified for all known bacteria, allowing the strain-selective killing of pathogenic bacteria. Here, we re-engineered the Escherichia coli phage P2 to alter its tropism toward pathogenic bacteria. Chimeric tail fibers formed between P2 and S16 genes were designed and generated through two approaches: homology- and literature-based. By presenting chimeric P2:S16 fibers on the P2 particle, our data suggests that the resultant phages were effectively detargeted from the native P2 cellular target, lipopolysaccharide, and were instead able to infect via the proteinaceous receptor, OmpC, the natural S16 receptor. Our work provides evidence that pseudotyping P2 is feasible and can be used to extend the host range of P2 to alternative receptors. Extension of this work could produce alternative chimeric tail fibers to target pathogenic bacterial threats. Our engineering of P2 allows adsorption through a heterologous outer-membrane protein without culturing in its native host, thus providing a potential means of engineering designer phages against pathogenic bacteria from knowledge of their surface proteome.}, }
@article {pmid36083451, year = {2022}, author = {Bansal, MS}, title = {Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {233-252}, pmid = {36083451}, issn = {1940-6029}, mesh = {Algorithms ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Microbial ; Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.}, }
@article {pmid36083447, year = {2022}, author = {Zhu, Q and Mirarab, S}, title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {137-165}, pmid = {36083447}, issn = {1940-6029}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; }, abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.}, }
@article {pmid36083444, year = {2022}, author = {Davín, AA and Schrempf, D and Williams, TA and Hugenholtz, P and Szöllősi, GJ}, title = {Relative Time Inference Using Lateral Gene Transfers.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {75-94}, pmid = {36083444}, issn = {1940-6029}, mesh = {*Biological Evolution ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; }, abstract = {Many organisms are able to incorporate exogenous DNA into their genomes. This process, called lateral gene transfer (LGT), has the potential to benefit the recipient organism by providing useful coding sequences, such as antibiotic resistance genes or enzymes which expand the organism's metabolic niche. For evolutionary biologists, LGTs have often been considered a nuisance because they complicate the reconstruction of the underlying species tree that many analyses aim to recover. However, LGT events between distinct organisms harbor information on the relative divergence time of the donor and recipient lineages. As a result transfers provide a novel and as yet mostly unexplored source of information to determine the order of divergence of clades, with the potential for absolute dating if linked to the fossil record.}, }
@article {pmid36083443, year = {2022}, author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E}, title = {Standard Candles for Dating Microbial Lineages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {41-74}, pmid = {36083443}, issn = {1940-6029}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; }, abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.}, }
@article {pmid36075475, year = {2022}, author = {Cui, Y and Gao, J and Guo, Y and Li, Z and Wang, Z and Zhao, Y}, title = {Unraveling the impact and mechanism of antipyretic paracetamol on intergenera conjugative plasmid transfer.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114263}, doi = {10.1016/j.envres.2022.114263}, pmid = {36075475}, issn = {1096-0953}, mesh = {Acetaminophen/pharmacology ; *Analgesics, Non-Narcotic ; Anti-Bacterial Agents ; *Antipyretics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Humans ; Plasmids/genetics ; Reactive Oxygen Species ; }, abstract = {Antimicrobial resistance has been considered as a great threat to biosecurity and human health. And the transmission of antibiotic resistance genes (ARGs) by conjugated plasmid is a key factor in the prevalence of antimicrobial resistance. Paracetamol (PRC), one of nonopioid analgesics, is an extensively used antipyretic and mild analgesic worldwide available for numerous prescriptions. It was unclear whether PRC could promote the spread of ARGs. Here, it was demonstrated that PRC promoted intergenera conjugative plasmid transfer in an established conjugation model. Both donor and recipient strains treated by PRC emerged the variations of reactive oxygen species (ROS), SOS response and cell membrane permeability. Correspondingly, transcriptome analysis revealed that the gene expression involved in cell membrane permeability and SOS response was up-regulated significantly after PRC exposure. More directly, PRC also increased the expressions of conjugation related genes of trbG and trbP in donor. This study proved for the first time that PRC could enhance the intergenera conjugative plasmid transfer. Collectively, these findings manifested the potential threat associated with the existence of non-antibiotic substance PRC, which could provide an important insight into antimicrobial resistance spread.}, }
@article {pmid36073816, year = {2022}, author = {Castellani, LG and Luchetti, A and Nilsson, JF and Pérez-Giménez, J and Struck, B and Schlüter, A and Pühler, A and Niehaus, K and Romero, D and Pistorio, M and Torres Tejerizo, G}, title = {RcgA and RcgR, Two Novel Proteins Involved in the Conjugative Transfer of Rhizobial Plasmids.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0194922}, pmid = {36073816}, issn = {2150-7511}, mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Quorum Sensing ; Bacteria/genetics ; Nitrogen ; DNA ; Gene Transfer, Horizontal ; }, abstract = {Rhizobia are Gram-negative bacteria that are able to establish a nitrogen-fixing symbiotic interaction with leguminous plants. Rhizobia genomes usually harbor several plasmids which can be transferred to other organisms by conjugation. Two main mechanisms of the regulation of rhizobial plasmid transfer have been described: quorum sensing (QS) and the rctA/rctB system. Nevertheless, new genes and molecules that modulate conjugative transfer have recently been described, demonstrating that new actors can tightly regulate the process. In this work, by means of bioinformatics tools and molecular biology approaches, two hypothetical genes are identified as playing key roles in conjugative transfer. These genes are located between conjugative genes of plasmid pRfaLPU83a from Rhizobium favelukesii LPU83, a plasmid that shows a conjugative transfer behavior depending on the genomic background. One of the two mentioned genes, rcgA, is essential for conjugation, while the other, rcgR, acts as an inhibitor of the process. In addition to introducing this new regulatory system, we show evidence of the functions of these genes in different genomic backgrounds and confirm that homologous proteins from non-closely related organisms have the same functions. These findings set up the basis for a new regulatory circuit of the conjugative transfer of plasmids. IMPORTANCE Extrachromosomal DNA elements, such as plasmids, allow for the adaptation of bacteria to new environments by conferring new determinants. Via conjugation, plasmids can be transferred between members of the same bacterial species, different species, or even to organisms belonging to a different kingdom. Knowledge about the regulatory systems of plasmid conjugative transfer is key in understanding the dynamics of their dissemination in the environment. As the increasing availability of genomes raises the number of predicted proteins with unknown functions, deeper experimental procedures help to elucidate the roles of these determinants. In this work, two uncharacterized proteins that constitute a new regulatory circuit with a key role in the conjugative transfer of rhizobial plasmids were discovered.}, }
@article {pmid36072670, year = {2022}, author = {Chen, K and Zhuang, Y and Wang, L and Li, H and Lei, T and Li, M and Gao, M and Wei, J and Dang, H and Raza, A and Yang, Q and Sharif, Y and Yang, H and Zhang, C and Zou, H and Zhuang, W}, title = {Comprehensive genome sequence analysis of the devastating tobacco bacterial phytopathogen Ralstonia solanacearum strain FJ1003.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {966092}, pmid = {36072670}, issn = {1664-8021}, abstract = {Due to its high genetic diversity and broad host range, Ralstonia solanacearum, the causative phytopathogen of the bacterial wilt (BW) disease, is considered a "species complex". The R. solanacearum strain FJ1003 belonged to phylotype I, and was isolated from the Fuzhou City in Fujian Province of China. The pathogen show host specificity and infects tobacco, especially in the tropical and subtropical regions. To elucidate the pathogenic mechanisms of FJ1003 infecting tobacco, a complete genome sequencing of FJ1003 using single-molecule real-time (SMRT) sequencing technology was performed. The full genome size of FJ1003 was 5.90 Mb (GC%, 67%), containing the chromosome (3.7 Mb), megaplasmid (2.0 Mb), and small plasmid (0.2 Mb). A total of 5133 coding genes (3446 and 1687 genes for chromosome and megaplasmid, respectively) were predicted. A comparative genomic analysis with other strains having the same and different hosts showed that the FJ1003 strain had 90 specific genes, possibly related to the host range of R. solanacearum. Horizontal gene transfer (HGT) was widespread in the genome. A type Ⅲ effector protein (Rs_T3E_Hyp14) was present on both the prophage and genetic island (GI), suggesting that this gene might have been acquired from other bacteria via HGT. The Rs_T3E_Hyp14 was proved to be a virulence factor in the pathogenic process of R. solanacearum through gene knockout strategy, which affects the pathogenicity and colonization ability of R. solanacearum in the host. Therefore, this study will improve our understanding of the virulence of R. solanacearum and provide a theoretical basis for tobacco disease resistance breeding.}, }
@article {pmid36069678, year = {2022}, author = {Rahman, MJ and Haller, SL and Stoian, AMM and Li, J and Brennan, G and Rothenburg, S}, title = {LINE-1 retrotransposons facilitate horizontal gene transfer into poxviruses.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36069678}, issn = {2050-084X}, support = {R01 AI146915/AI/NIAID NIH HHS/United States ; }, mesh = {Gene Transfer, Horizontal ; Phylogeny ; *Poxviridae/genetics ; Retroelements/genetics ; Vaccinia virus/genetics ; }, abstract = {There is ample phylogenetic evidence that many critical virus functions, like immune evasion, evolved by the acquisition of genes from their hosts through horizontal gene transfer (HGT). However, the lack of an experimental system has prevented a mechanistic understanding of this process. We developed a model to elucidate the mechanisms of HGT into vaccinia virus, the prototypic poxvirus. All identified gene capture events showed signatures of long interspersed nuclear element-1 (LINE-1)-mediated retrotransposition, including spliced-out introns, polyadenylated tails, and target site duplications. In one case, the acquired gene integrated together with a polyadenylated host U2 small nuclear RNA. Integrations occurred across the genome, in some cases knocking out essential viral genes. These essential gene knockouts were rescued through a process of complementation by the parent virus followed by nonhomologous recombination during serial passaging to generate a single, replication-competent virus. This work links multiple evolutionary mechanisms into one adaptive cascade and identifies host retrotransposons as major drivers for virus evolution.}, }
@article {pmid36069526, year = {2022}, author = {Fixsen, SM and Cone, KR and Goldstein, SA and Sasani, TA and Quinlan, AR and Rothenburg, S and Elde, NC}, title = {Poxviruses capture host genes by LINE-1 retrotransposition.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36069526}, issn = {2050-084X}, support = {R01 AI146915/AI/NIAID NIH HHS/United States ; R35 GM134936/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; *Poxviridae/genetics ; RNA, Messenger ; *Viruses/genetics ; Retroelements ; }, abstract = {Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.}, }
@article {pmid36067042, year = {2022}, author = {Laforest, M and Martin, S and Soufiane, B and Bisaillon, K and Maheux, L and Fortin, S and James, T and Miville, D and Marcoux, A and Simard, MJ}, title = {Distribution and genetic characterization of bird rape mustard (Brassica rapa) populations and analysis of glyphosate resistance introgression.}, journal = {Pest management science}, volume = {78}, number = {12}, pages = {5471-5478}, doi = {10.1002/ps.7170}, pmid = {36067042}, issn = {1526-4998}, mesh = {Animals ; *Brassica rapa ; Mustard Plant ; Plants, Genetically Modified/genetics ; *Brassica napus ; Hybridization, Genetic ; Plant Weeds/genetics ; Birds/genetics ; }, abstract = {BACKGROUND: The introgression of a transgene conferring glyphosate resistance from Brassica napus (rapeseed, canola) to Brassica rapa weeds (bird rape) was documented at a single location in 2007. In 2015, several cases of glyphosate resistant mustard were reported by growers in areas where rapeseed was seldom grown.<br><br>RESULTS: Survey result indicated glyphosate resistant bird rape mustard is present in areas where glyphosate tolerant corn and soybean are often grown in rotation. Genetic analyses reveal that hybridization followed by introgression and progressive loss of chromosome is the likely mechanism for the horizontal gene transfer (HGT) of glyphosate resistance.<br><br>CONCLUSION: Introgression of the glyphosate-resistance conferring transgene in the populations studied appears to have occurred several times, consistent with the ease for B. rapa to form hybrids with B. napus. The introduction of a transgene into a crop should therefore take into account the weediness of the species that share a common genome and their ability to form hybrids. We provide here such an example between B. napus and B. rapa, and potentially between B. napus and Raphanistrum raphanistrum. &#xa9; 2022 Her Majesty the Queen in Right of Canada. Pest Management Science &#xa9; 2022 Society of Chemical Industry. Reproduced with the permission of the Minister of Agriculture and Agri-Food Canada.}, }
@article {pmid36063716, year = {2023}, author = {Tang, T and Chen, Y and Du, Y and Yao, B and Liu, M}, title = {Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater.}, journal = {Journal of hazardous materials}, volume = {441}, number = {}, pages = {129870}, doi = {10.1016/j.jhazmat.2022.129870}, pmid = {36063716}, issn = {1873-3336}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Livestock ; *Oxytetracycline/pharmacology ; Reactive Oxygen Species/pharmacology ; Sulfamethoxazole ; Type IV Secretion Systems ; Wastewater/analysis ; }, abstract = {The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.}, }
@article {pmid36060751, year = {2022}, author = {Shen, L and Qiu, T and Guo, Y and Gao, M and Gao, H and Zhao, G and Wang, X}, title = {Enhancing control of multidrug-resistant plasmid and its host community with a prolonged thermophilic phase during composting.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {989085}, pmid = {36060751}, issn = {1664-302X}, abstract = {The plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) among bacteria facilitates the evolution and dissemination of antibiotic resistance. Broad-host-range plasmids can be transferred to different bacterial hosts in soil, plant rhizospheres, and wastewater treatment plants. Although composting is an effective way to convert organic waste into fertilizer and reduce some ARGs, few studies have focused on its effects on the spread of ARG-carrying plasmids and their bacterial host communities during composting. In this study, a fluorescently labeled Pseudomonas putida (P. putida) harboring a broad-host-range plasmid RP4 carrying three ARGs was inoculated into a raw material microcosm and composted with different durations of the thermophilic phase. The fate of the donor and RP4 in composting was investigated. The prolonged thermophilic composting removed 95.1% of dsRed and 98.0% of gfp, and it inhibited the rebound of P. putida and RP4 during the maturation phase. The spread potential of RP4 decreased from 10[-4] to 10[-6] transconjugants per recipient after composting. In addition, we sorted and analyzed the composition of RP4 recipient bacteria using fluorescence-activated cell sorting combined with 16S rRNA gene amplicon sequencing. The recipient bacteria of RP4 belonged to eight phyla, and Firmicutes, accounting for 75.3%-90.1%, was the dominant phylum in the transconjugants. The diversity and richness of the RP4 recipient community were significantly reduced by prolonged thermophilic periods. Overall, these findings provide new insights for assessing the contribution of composting in mitigating the dissemination of plasmid-mediated ARGs, and the prolonged thermophilic phase of composting can limit the transfer of multidrug-resistant plasmids.}, }
@article {pmid36060733, year = {2022}, author = {Yadav, G and Singh, R}, title = {In silico analysis reveals the co-existence of CRISPR-Cas type I-F1 and type I-F2 systems and its association with restricted phage invasion in Acinetobacter baumannii.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909886}, pmid = {36060733}, issn = {1664-302X}, abstract = {INTRODUCTION: Acinetobacter baumannii, an opportunistic pathogen, rapidly acquires antibiotic resistance, thus compelling researchers to develop alternative treatments at utmost priority. Phage-based therapies are of appreciable benefit; however, CRISPR-Cas systems are a major constraint in this approach. Hence for effective implementation and a promising future of phage-based therapies, a multifaceted understanding of the CRISPR-Cas systems is necessary.<br><br>METHODS: This study investigated 4,977 RefSeq genomes of A. baumannii from the NCBI database to comprehend the distribution and association of CRISPR-Cas systems with genomic determinants.<br><br>RESULTS: Approximately 13.84% (n = 689/4,977) isolates were found to carry the CRSIPR-Cas system, and a small fraction of isolates, 1.49% (n = 74/4,977), exhibited degenerated CRISPR-Cas systems. Of these CRISPR-Cas positive (+) isolates, 67.48% (465/689) isolates harbored type I-F1, 28.59% (197/689) had type I-F2, and 3.7% (26/689) had co-existence of both type I-F1 and type I-F2 systems. Co-existing type I-F1 and type I-F2 systems are located distantly (&#x223c;1.733 Mb). We found a strong association of CRISPR-Cas systems within STs for type I-F1 and type I-F2, whereas the type I-F1 + F2 was not confined to any particular ST. Isolates with type I-F1 + F2 exhibited a significantly high number of mean spacers (n = 164.58 &#xb1; 46.41) per isolate as compared to isolates with type I-F2 (n = 82.87 &#xb1; 36.14) and type I-F1 (n = 54.51 &#xb1; 26.27) with majority targeting the phages. Isolates with type I-F1 (p < 0.0001) and type I-F2 (p < 0.0115) displayed significantly larger genome sizes than type I-F1 + F2. A significantly reduced number of integrated phages in isolates with co-existence of type I-F1 + F2 compared with other counterparts was observed (p = 0.0041). In addition, the isolates carrying type I-F1 + F2 did not exhibit reduced resistance and virulence genes compared to CRISPR-Cas(-) and CRISPR-Cas (+) type I-F1 and type I-F2, except for bap, abaI, and abaR.<br><br>CONCLUSION: Our observation suggests that the co-existence of type I-F1 and F2 is more effective in constraining the horizontal gene transfer and phage invasion in A. baumannii than the isolates exhibiting only type I-F1 and only type I-F2 systems.}, }
@article {pmid36059613, year = {2022}, author = {Alshaker, H and Hunter, E and Salter, M and Ramadass, A and Westra, W and Winkler, M and Green, J and Akoulitchev, A and Pchejetski, D}, title = {Monocytes acquire prostate cancer specific chromatin conformations upon indirect co-culture with prostate cancer cells.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {990842}, pmid = {36059613}, issn = {2234-943X}, abstract = {BACKGROUND: Three-dimensional chromosome loop conformations are powerful regulators of gene expression. These chromosome conformations can be detected both in tumour and in circulating cells and have significant disease biomarker potential. We have recently detected specific chromosome conformations in circulating cells of patients with prostate cancer (PCa) which were similar to ones found in their primary tumours, however, the possibility of horizontal transfer of chromosome conformations was not studied previously.<br><br>METHODS: Human monocytes (U937) were co-cultured in Boyden chambers through 0.4 uM membrane with or without PC-3 human PCa cells or their conditioned media and a custom DNA microarray for 900,000 chromosomal loops covering all coding loci and non-coding RNA genes was performed on each part of the co-culture system.<br><br>RESULTS: We have detected 684 PC-3 cell-specific chromosome conformations across the whole genome that were absent in na&#xef;ve monocytes but appeared in monocytes co-cultured with PC-3 cells or with PC-3-conditioned media. Comparing PC3-specific conformations to the ones we have previously detected in systemic circulation of high-risk PCa patients revealed 9 positive loops present in both settings.<br><br>CONCLUSIONS: Our results demonstrate for the first time a proof of concept for horizontal transfer of chromosome conformations without direct cell-cell contact. This carries high clinical relevance as we have previously observed chromatin conformations in circulating cells of patients with melanoma and PCa similar to ones in their primary tumours. These changes can be used as highly specific biomarkers for diagnosis and prognosis. Further studies are required to elucidate the specific mechanism of chromosome conformations transfer and its clinical significance in particular diseases.}, }
@article {pmid36054646, year = {2022}, author = {Ding, P and Lu, J and Wang, Y and Schembri, MA and Guo, J}, title = {Antidepressants promote the spread of antibiotic resistance via horizontally conjugative gene transfer.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5261-5276}, doi = {10.1111/1462-2920.16165}, pmid = {36054646}, issn = {1462-2920}, mesh = {Humans ; *Proteomics ; *Depressive Disorder, Major/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Antidepressive Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Antibiotic resistance is a global concern threatening public health. Horizontal gene transfer (HGT) between bacterial species contributes greatly to the dissemination of antibiotic resistance. Conjugation is one of the major HGT pathways responsible for the spread of antibiotic resistance genes (ARGs). Antidepressant drugs are commonly prescribed antipsychotics for major depressive disorders and are frequently detected in aquatic environments. However, little is known about how antidepressants stress bacteria and whether such effect can promote conjugation. Here, we report that commonly prescribed antidepressants, sertraline, duloxetine, fluoxetine, and bupropion, can promote the conjugative transfer of plasmid-borne multidrug resistance genes carried by environmentally and clinically relevant plasmids. Noteworthy, the transfer of plasmids across bacterial genera is significantly enhanced by antidepressants at clinically relevant concentrations. We also reveal the underlying mechanisms of enhanced conjugative transfer by employing flow cytometric analysis, genome-wide RNA sequencing and proteomic analysis. Antidepressants induce the production of reactive oxygen species and the SOS response, increase cell membrane permeability, and upregulate the expression of conjugation relevant genes. Given the contribution of HGT in the dissemination of ARGs, our findings highlight the importance of prudent prescription of antidepressants and to the potential connection between antidepressants and increasing antibiotic resistance.}, }
@article {pmid36051753, year = {2022}, author = {Chen, CY and Fuqua, C and Jackson, CR and Kadlec, K and Top, EM}, title = {Editorial: Plasmid transfer-mechanisms, ecology, evolution and applications.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {993628}, pmid = {36051753}, issn = {1664-302X}, }
@article {pmid36050562, year = {2022}, author = {Hao, H and Shi, B and Zhang, J and Dai, A and Li, W and Chen, H and Ji, W and Gong, C and Zhang, C and Li, J and Chen, L and Yao, B and Hu, P and Yang, H and Brosius, J and Lai, S and Shi, Q and Deng, C}, title = {The vertebrate- and testis- specific transmembrane protein C11ORF94 plays a critical role in sperm-oocyte membrane binding.}, journal = {Molecular biomedicine}, volume = {3}, number = {1}, pages = {27}, pmid = {36050562}, issn = {2662-8651}, abstract = {Sperm-oocyte membrane fusion is necessary for mammalian fertilization. The factors that determine the fusion of sperm with oocytes are largely unknown. So far, spermatozoon factor IZUMO1 and the IZUMO1 counter-receptor JUNO on the oocyte membrane has been identified as a protein requiring fusion. Some sperm membrane proteins such as FIMP, SPACA6 and TEME95, have been proved not to directly regulate fusion, but their knockout will affect the fusion process of sperm and oocytes. Here, we identified a novel gene C11orf94 encoding a testicular-specific small transmembrane protein that emerges in vertebrates likely acquired via horizontal gene transfer from bacteria and plays an indispensable role in sperm-oocyte binding. We demonstrated that the deletion of C11orf94 dramatically decreased male fertility in mice. Sperm from C11orf94-deficient mice could pass through the zona pellucida, but failed to bind to the oocyte membrane, thus accumulating in the perivitelline space. In consistence, when the sperm of C11orf94-deficient mice were microinjected into the oocyte cytoplasm, fertilized oocytes were obtained and developed normally to blastocysts. Proteomics analysis revealed that C11orf94 influenced the expression of multiple gene products known to be indispensable for sperm-oocyte binding and fusion, including IZUMO1, EQTN and CRISP1. Thus, our study indicated that C11ORF94 is a vertebrate- and testis-specific small transmembrane protein that plays a critical role in sperm binding to the oolemma.}, }
@article {pmid36050493, year = {2022}, author = {Wang, T and Weiss, A and Aqeel, A and Wu, F and Lopatkin, AJ and David, LA and You, L}, title = {Horizontal gene transfer enables programmable gene stability in synthetic microbiota.}, journal = {Nature chemical biology}, volume = {18}, number = {11}, pages = {1245-1252}, pmid = {36050493}, issn = {1552-4469}, support = {R01 AI125604/AI/NIAID NIH HHS/United States ; R01 EB031869/EB/NIBIB NIH HHS/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Plasmids/genetics ; }, abstract = {The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.}, }
@article {pmid36046020, year = {2022}, author = {Jans, C and Wambui, J and Stevens, MJA and Tasara, T}, title = {Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {923080}, pmid = {36046020}, issn = {1664-302X}, abstract = {Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.}, }
@article {pmid36042984, year = {2022}, author = {Rios-Miguel, AB and Smith, GJ and Cremers, G and van Alen, T and Jetten, MSM and Op den Camp, HJM and Welte, CU}, title = {Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100152}, pmid = {36042984}, issn = {2589-9147}, abstract = {Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.}, }
@article {pmid36040324, year = {2022}, author = {Coral-Medina, A and Fenton, DA and Varela, J and Baranov, PV and Camarasa, C and Morrissey, JP}, title = {The evolution and role of the periplasmic asparaginase Asp3 in yeast.}, journal = {FEMS yeast research}, volume = {22}, number = {1}, pages = {}, pmid = {36040324}, issn = {1567-1364}, mesh = {*Asparaginase/genetics/metabolism ; Asparagine ; Fermentation ; Nitrogen/metabolism ; *Saccharomyces cerevisiae/metabolism ; }, abstract = {The study of nitrogen assimilation in yeast is of interest from genetic, evolutionary, and biotechnological perspectives. Over the course of evolution, yeasts have developed sophisticated control mechanisms to regulate nitrogen metabolism, with domesticated lineages sometimes displaying particular specialisation. The focus of this study was on assimilation of asparagine, which is a significant nutritional source for some alcoholic fermentations. We were particularly interested in ASP3, which encodes a periplasmic asparaginase and that was proposed to have been acquired relatively recently in S. cerevisiae by horizontal gene transfer. We examined 1680 S. cerevisiae genome assemblies to evaluate the distribution and evolutionary trajectory of ASP3. Our findings suggest an alternative hypothesis that ASP3 is an ancient Saccharomyces gene that has generally been lost over the course of evolution but has been retained in certain fermentative environments. As asparagine is the major nitrogen source in apple juice, we explored whether the presence of ASP3 would confer a growth advantage. Interestingly, we found that although ASP3 enhances growth when asparagine is the sole nitrogen source, the same effect is not seen in apple juice. These data indicate that growth in pure culture may not reflect the original selective environment for ASP3+ strains and highlight the role that complex regulation may play in optimising nitrogen assimilation in yeasts.}, }
@article {pmid36037921, year = {2022}, author = {Nava, AR and Daneshian, L and Sarma, H}, title = {Antibiotic resistant genes in the environment-exploring surveillance methods and sustainable remediation strategies of antibiotics and ARGs.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114212}, doi = {10.1016/j.envres.2022.114212}, pmid = {36037921}, issn = {1096-0953}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Humans ; Wastewater/analysis ; *Water Pollutants, Chemical ; }, abstract = {Antibiotic Resistant Genes (ARGs) are an emerging environmental health threat due to the potential change in the human microbiome and selection for the emergence of antibiotic resistant bacteria. The rise of antibiotic resistant bacteria has caused a global health burden. The WHO (world health organization) predicts a rise in deaths due to antibiotic resistant infections. Since bacteria can acquire ARGs through horizontal transmission, it is important to assess the dissemination of antibioticresistant genes from anthropogenic sources. There are several sources of antibiotics, antibiotic resistant bacteria and genes in the environment. These include wastewater treatment plants, landfill leachate, agricultural, animal industrial sources and estuaries. The use of antibiotics is a worldwide practice that has resulted in the evolution of resistance to antibiotics. Our review provides a more comprehensive look into multiple sources of ARG's and antibiotics rather than one. Moreover, we focus on effective surveillance methods of ARGs and antibiotics and sustainable abiotic and biotic remediation strategies for removal and reduction of antibiotics and ARGs from both terrestrial and aquatic environments. Further, we consider the impact on public health as this problem cannot be addressed without a global transdisciplinary effort.}, }
@article {pmid36036580, year = {2022}, author = {Jiang, C and Zhang, T and Li, Q and Jiang, H and Mao, X}, title = {A Novel Carrageenan Metabolic Pathway in Flavobacterium algicola.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {18}, pages = {e0110022}, pmid = {36036580}, issn = {1098-5336}, mesh = {Carrageenan/metabolism ; Flavobacterium/genetics/metabolism ; *Galactose ; Galactosidases/metabolism ; *Glycoside Hydrolases/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Polysaccharides ; }, abstract = {Carbohydrate-active enzymes are important components of the polysaccharide metabolism system in marine bacteria. Carrageenase is indispensable for forming carrageenan catalytic pathways. Here, two GH16_13 carrageenases showed likely hydrolysis activities toward different types of carrageenans (e.g., κ-, hybrid β/κ, hybrid α/ι, and hybrid λ), which indicates that a novel pathway is present in the marine bacterium Flavobacterium algicola to use κ-carrageenan (KC), ι-carrageenan (IC), and λ-carrageenan (LC). A comparative study described the different features with another reported pathway based on the specific carrageenans (κ, ι, and λ) and expanded the carrageenan metabolic versatility in F. algicola. A further comparative genomic analysis of carrageenan-degrading bacteria indicated different distributions of carrageenan metabolism-related genes in marine bacteria. The crucial core genes encoding the GH127 α-3,6-anhydro-d-galactosidase (ADAG) and 3,6-anhydro-d-galactose (d-AHG)-utilized cluster have been conserved during evolution. This analysis further revealed the horizontal gene transfer (HGT) phenomenon of the carrageenan polysaccharide utilization loci (CarPUL) from Bacteroidetes to other bacterial phyla, as well as the versatility of carrageenan catalytic activities in marine bacteria through different metabolic pathways. IMPORTANCE Based on the premise that the specific carrageenan-based pathway involved in carrageenan use by Flavobacterium algicola has been identified, another pathway was further analyzed, and it involved two GH16_13 carrageenases. Among all the characterized carrageenases, the members of GH16_13 accounted for only a small portion. Here, the functional analysis of two GH16_13 carrageenases suggested their hydrolysis effects on different types of carrageenans (e.g., κ, hybrid β/κ, hybrid α/ι-, and hybrid λ-), which led to the identification of another pathway. Further exploration enabled us to elucidate the novel pathway that metabolizes KC and IC in F. algicola successfully. The coexistence of these two pathways may provide improved survivability by F. algicola in the marine environment.}, }
@article {pmid36028018, year = {2022}, author = {Li, W and Zhang, WG and Zhang, MS and Lei, ZF and Li, PF and Ma, Y and Gao, Y}, title = {Environmentally relevant concentrations of mercury facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158272}, doi = {10.1016/j.scitotenv.2022.158272}, pmid = {36028018}, issn = {1879-1026}, mesh = {Conjugation, Genetic ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Genes, Bacterial ; *Mercury/toxicity ; Antioxidants ; Reactive Oxygen Species ; Drug Resistance, Microbial/genetics ; Plasmids ; *Escherichia coli K12 ; Glutathione ; Malondialdehyde ; Gene Transfer, Horizontal ; }, abstract = {Abundant antibiotic resistance genes (ARGs) are typically found in mercury (Hg)-contaminated aquatic environments. This phenomenon is partly attributed to the co-resistance, cross-resistance, and shared regulatory responses to Hg and antibiotics. However, it remains unclear whether and how Hg influences the conjugative transfer of ARGs mediated by mobilizable plasmids. In the present study, we found that Hg[2+] at the environmentally relevant concentrations (0.001-0.5 mg L[-1]) facilitated the conjugative transfer of ARGs through the mobilizable plasmid RP4 from the donor Escherichia coli HB101 to the recipient E. coli K12. Exposure to Hg[2+] significantly increases the formation of reactive oxygen species, malondialdehyde production, antioxidant enzyme activities, and cell membrane permeability, while decreasing the concentration of glutathione. Scanning electron microscopy and transmission electron microscopy showed that the cell membrane suffered from oxidative damage, which is beneficial for conjugative transfer. The expression of global regulatory genes (korA, korB, and trbA) negatively regulating conjugative transfer was restrained by Hg[2+], while promoting the expression of positive regulatory genes involved in the mating pair formation system (trbBp and traF) and the DNA transfer and replication systems (trfAp and traJ). Although a high Hg[2+] concentration (1.0 mg L[-1]) suppressed ARGs conjugative transfer, our results suggest that Hg[2+] facilitates the dissemination of ARGs in aquatic environments at environmentally relevant concentrations. This study improves our understanding of ARGs dissemination in Hg-contaminated aquatic environments.}, }
@article {pmid36026509, year = {2022}, author = {Li, Z and Li, Y and Xue, AZ and Dang, V and Holmes, VR and Johnston, JS and Barrick, JE and Moran, NA}, title = {The Genomic Basis of Evolutionary Novelties in a Leafhopper.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {36026509}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Genomics ; *Hemiptera/genetics ; Proteomics ; Symbiosis/genetics ; }, abstract = {Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.}, }
@article {pmid36015378, year = {2022}, author = {Guo, X and Wang, M and Kang, H and Zhou, Y and Han, F}, title = {Distribution, Polymorphism and Function Characteristics of the GST-Encoding Fhb7 in Triticeae.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {16}, pages = {}, pmid = {36015378}, issn = {2223-7747}, abstract = {Encoding a glutathione S-transferase (GST) and conferring resistance to Fusarium head blight (FHB), Fhb7 was successfully isolated from the newly assembled Thinopyrum elongatum genome by researchers, with blasting searches revealing that Thinopyrum gained Fhb7 through horizontal gene transfer from an endophytic Epichloë species. On the contrary, our molecular evidence reveals that the homologs of Fhb7 are distributed commonly in Triticeae. Other than Thinopyrum, the Fhb7 homologs were also detected in four other genera, Elymus, Leymus, Roegneria and Pseudoroegneria, respectively. Sequence comparisons revealed that the protein sequences were at least 94% identical across all of the Fhb7 homologs in Triticeae plants, which in turn suggested that the horizontal gene transfer of the Fhb7 might have occurred before Triticeae differentiation instead of Thinopyrum. The multiple Fhb7 homologs detected in some Triticeae accessions and wheat-Thinopyrum derivatives might be attributed to the alloploid nature and gene duplication during evolution. In addition, we discovered that some wheat-Thinopyrum derivatives carrying the Fhb7 homologs had a completely different reaction to Fusarium head blight, which made us question the ability of the GST-encoding Fhb7 to resist FHB.}, }
@article {pmid36014979, year = {2022}, author = {Dewing, C and Van der Nest, MA and Santana, QC and Proctor, RH and Wingfield, BD and Steenkamp, ET and De Vos, L}, title = {Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36014979}, issn = {2076-0817}, abstract = {The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.}, }
@article {pmid36014080, year = {2022}, author = {Chen, Y and Shah, S and Dougan, KE and van Oppen, MJH and Bhattacharya, D and Chan, CX}, title = {Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014080}, issn = {2076-2607}, abstract = {Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35-36% have putatively originated via horizontal gene transfer (HGT), predominantly (19-23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10-11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates.}, }
@article {pmid36013391, year = {2022}, author = {Gibert, M and Jiménez, CJ and Comas, J and Zechner, EL and Madrid, C and Balsalobre, C}, title = {In Situ Monitoring and Quantitative Determination of R27 Plasmid Conjugation.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {36013391}, issn = {2075-1729}, abstract = {Horizontal gene transfer (HGT) by plasmid conjugation is a major driving force in the spread of antibiotic resistance among Enterobacteriaceae. Most of the conjugation studies are based on calculation of conjugation ratios (number of transconjugants/number of donors) after viable counting of transconjugant and donor cells. The development of robust, fast and reliable techniques for in situ monitoring and quantification of conjugation ratios might accelerate progress in understanding the impact of this cellular process in the HGT. The IncHI1 plasmids, involved in multiresistance phenotypes of relevant pathogens such as Salmonella and E. coli, are distinguished by the thermosensitivity of their conjugative transfer. Conjugation mediated by IncHI1 plasmids is more efficient at temperatures lower than 30 °C, suggesting that the transfer process takes place during the environmental transit of the bacteria. In this report, we described a methodology to monitor in situ the conjugation process during agar surface matings of the IncHI1 plasmid R27 and its derepressed derivative drR27 at different temperatures. A three-color-labeling strategy was used to visualize the spatial distribution of transconjugants within the heterogeneous environment by epifluorescence and confocal microscopy. Moreover, the fluorescent labelling was also used to quantify conjugation frequencies in liquid media by flow cytometry.}, }
@article {pmid36012061, year = {2022}, author = {Zhang, K and Li, K and Liu, Z and Li, Q and Li, W and Chen, Q and Xia, Y and Hu, F and Yang, F}, title = {The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {16}, pages = {}, pmid = {36012061}, issn = {1660-4601}, mesh = {*Anti-Bacterial Agents/analysis/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Metagenomics/methods ; *Rivers/microbiology ; }, abstract = {The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.}, }
@article {pmid36011312, year = {2022}, author = {Le, NG and van Ulsen, P and van Spanning, R and Brouwer, A and van Straalen, NM and Roelofs, D}, title = {A Functional Carbohydrate Degrading Enzyme Potentially Acquired by Horizontal Gene Transfer in the Genome of the Soil Invertebrate Folsomia candida.}, journal = {Genes}, volume = {13}, number = {8}, pages = {}, pmid = {36011312}, issn = {2073-4425}, mesh = {Animals ; *Arthropods/genetics ; Bacteria/genetics ; Carbohydrates ; Escherichia coli/genetics ; Eukaryota ; *Gene Transfer, Horizontal ; Insecta ; Protein Sorting Signals/genetics ; Soil ; }, abstract = {Horizontal gene transfer (HGT) is defined as the acquisition by an organism of hereditary material from a phylogenetically unrelated organism. This process is mostly observed among bacteria and archaea, and considered less likely between microbes and multicellular eukaryotes. However, recent studies provide compelling evidence of the evolutionary importance of HGT in eukaryotes, driving functional innovation. Here, we study an HGT event in Folsomia candida (Collembola, Hexapoda) of a carbohydrate-active enzyme homologous to glycosyl hydrase group 43 (GH43). The gene encodes an N-terminal signal peptide, targeting the product for excretion, which suggests that it contributes to the diversity of digestive capacities of the detritivore host. The predicted α-L-arabinofuranosidase shows high similarity to genes in two other Collembola, an insect and a tardigrade. The gene was cloned and expressed in Escherichia coli using a cell-free protein expression system. The expressed protein showed activity against p-nitrophenyl-α-L-arabinofuranoside. Our work provides evidence for functional activity of an HGT gene in a soil-living detritivore, most likely from a bacterial donor, with genuine eukaryotic properties, such as a signal peptide. Co-evolution of metazoan GH43 genes with the Panarthropoda phylogeny suggests the HGT event took place early in the evolution of this ecdysozoan lineage.}, }
@article {pmid36009992, year = {2022}, author = {Palm, M and Fransson, A and Hultén, J and Búcaro Stenman, K and Allouche, A and Chiang, OE and Constandse, ML and van Dijk, KJ and Icli, S and Klimesova, B and Korhonen, E and Martínez-Crespo, G and Meggers, D and Naydenova, M and Polychronopoulou, MA and Schuntermann, DB and Unal, H and Wasylkowska, A and Farewell, A}, title = {The Effect of Heavy Metals on Conjugation Efficiency of an F-Plasmid in Escherichia coli.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36009992}, issn = {2079-6382}, abstract = {Conjugation, the process by which conjugative plasmids are transferred between bacteria, is regarded as a major contributor to the spread of antibiotic resistance, in both environmental and clinical settings. Heavy metals are known to co-select for antibiotic resistance, but the impact of the presence of these metals on conjugation itself is not clear. Here, we systematically investigate the impact that five heavy metals (arsenic, cadmium, copper, manganese, and zinc) have on the transfer of an IncF conjugative plasmid in Escherichia coli. Our results show that two of the metals, cadmium and manganese, have no significant impact, while arsenic and zinc both reduce conjugation efficiency by approximately 2-fold. Copper showed the largest impact, with an almost 100-fold decrease in conjugation efficiency. This was not mediated by any change in transcription from the major Py promoter responsible for transcription of the conjugation machinery genes. Further, we show that in order to have this severe impact on the transfer of the plasmid, copper sulfate needs to be present during the mating process, and we suggest explanations for this.}, }
@article {pmid36009937, year = {2022}, author = {Zhai, W and Tian, Y and Shao, D and Zhang, M and Li, J and Song, H and Sun, C and Wang, Y and Liu, D and Zhang, Y}, title = {Fecal Carriage of Escherichia coli Harboring the tet(X4)-IncX1 Plasmid from a Tertiary Class-A Hospital in Beijing, China.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36009937}, issn = {2079-6382}, abstract = {The emergence of the mobile tigecycline-resistance gene, tet(X4), poses a significant threat to public health. To investigate the prevalence and genetic characteristics of the tet(X4)-positive Escherichia coli in humans, 1101 human stool samples were collected from a tertiary class-A hospital in Beijing, China, in 2019. Eight E. coli isolates that were positive for tet(X4) were identified from clinical departments of oncology (n = 3), hepatology (n = 2), nephrology (n = 1), urology (n = 1), and general surgery (n = 1). They exhibited resistance to multiple antibiotics, including tigecycline, but remained susceptible to meropenem and polymyxin B. A phylogenetic analysis revealed that the clonal spread of four tet(X4)-positive E. coli from different periods of time or departments existed in this hospital, and three isolates were phylogenetically close to the tet(X4)-positive E. coli from animals and the environment. All tet(X4)-positive E. coli isolates contained the IncX1-plasmid replicon. Three isolates successfully transferred their tigecycline resistance to the recipient strain, C600, demonstrating that the plasmid-mediated horizontal gene transfer constitutes another critical mechanism for transmitting tet(X4). Notably, all tet(X4)-bearing plasmids identified in this study had a high similarity to several plasmids recovered from animal-derived strains. Our findings revealed the importance of both the clonal spread and horizontal gene transfer in the spread of tet(X4) within human clinics and between different sources.}, }
@article {pmid36007892, year = {2022}, author = {Shi, WT and Zhang, B and Li, ML and Liu, KH and Jiao, J and Tian, CF}, title = {The convergent xenogeneic silencer MucR predisposes α-proteobacteria to integrate AT-rich symbiosis genes.}, journal = {Nucleic acids research}, volume = {50}, number = {15}, pages = {8580-8598}, pmid = {36007892}, issn = {1362-4962}, mesh = {*Alphaproteobacteria/genetics ; Bacterial Proteins/metabolism ; DNA ; Escherichia coli/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; Symbiosis ; }, abstract = {Bacterial adaptation is largely shaped by horizontal gene transfer, xenogeneic silencing mediated by lineage-specific DNA bridgers (H-NS, Lsr2, MvaT and Rok), and various anti-silencing mechanisms. No xenogeneic silencing DNA bridger is known for α-proteobacteria, from which mitochondria evolved. By investigating α-proteobacterium Sinorhizobium fredii, a facultative legume microsymbiont, here we report the conserved zinc-finger bearing MucR as a novel xenogeneic silencing DNA bridger. Self-association mediated by its N-terminal domain (NTD) is required for DNA-MucR-DNA bridging complex formation, maximizing MucR stability, transcriptional silencing, and efficient symbiosis in legume nodules. Essential roles of NTD, CTD (C-terminal DNA-binding domain), or full-length MucR in symbiosis can be replaced by non-homologous NTD, CTD, or full-length protein of H-NS from γ-proteobacterium Escherichia coli, while NTD rather than CTD of Lsr2 from Gram-positive Mycobacterium tuberculosis can replace the corresponding domain of MucR in symbiosis. Chromatin immunoprecipitation sequencing reveals similar recruitment profiles of H-NS, MucR and various functional chimeric xenogeneic silencers across the multipartite genome of S. fredii, i.e. preferring AT-rich genomic islands and symbiosis plasmid with key symbiosis genes as shared targets. Collectively, the convergently evolved DNA bridger MucR predisposed α-proteobacteria to integrate AT-rich foreign DNA including symbiosis genes, horizontal transfer of which is strongly selected in nature.}, }
@article {pmid36003770, year = {2022}, author = {Valcz, G and Újvári, B and Buzás, EI and Krenács, T and Spisák, S and Kittel, &#xc1; and Tulassay, Z and Igaz, P and Takács, I and Molnár, B}, title = {Small extracellular vesicle DNA-mediated horizontal gene transfer as a driving force for tumor evolution: Facts and riddles.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {945376}, pmid = {36003770}, issn = {2234-943X}, abstract = {The basis of the conventional gene-centric view on tumor evolution is that vertically inherited mutations largely define the properties of tumor cells. In recent years, however, accumulating evidence shows that both the tumor cells and their microenvironment may acquire external, non-vertically inherited genetic properties via horizontal gene transfer (HGT), particularly through small extracellular vesicles (sEVs). Many phases of sEV-mediated HGT have been described, such as DNA packaging into small vesicles, their release, uptake by recipient cells, and incorporation of sEV-DNA into the recipient genome to modify the phenotype and properties of cells. Recent techniques in sEV separation, genome sequencing and editing, as well as the identification of new secretion mechanisms, shed light on a number of additional details of this phenomenon. Here, we discuss the key features of this form of gene transfer and make an attempt to draw relevant conclusions on the contribution of HGT to tumor evolution.}, }
@article {pmid36002568, year = {2022}, author = {Ocaña-Pallarès, E and Williams, TA and López-Escardó, D and Arroyo, AS and Pathmanathan, JS and Bapteste, E and Tikhonenkov, DV and Keeling, PJ and Szöllősi, GJ and Ruiz-Trillo, I}, title = {Divergent genomic trajectories predate the origin of animals and fungi.}, journal = {Nature}, volume = {609}, number = {7928}, pages = {747-753}, pmid = {36002568}, issn = {1476-4687}, support = {616960/ERC_/European Research Council/International ; 714774/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; }, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal ; Genes ; *Genome/genetics ; Genome, Fungal/genetics ; *Genomics ; Metabolism/genetics ; *Phylogeny ; }, abstract = {Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta[1,2]. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation[3-5]. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and Fungi.}, }
@article {pmid36000914, year = {2022}, author = {Xu, J and Mei, C and Zhi, Y and Liang, ZX and Zhang, X and Wang, HJ}, title = {Comparative Genomics Analysis and Outer Membrane Vesicle-Mediated Horizontal Antibiotic-Resistance Gene Transfer in Avibacterium paragallinarum.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0137922}, pmid = {36000914}, issn = {2165-0497}, mesh = {Animals ; Chickens/microbiology ; *Poultry Diseases/microbiology ; *Haemophilus Infections/microbiology/veterinary ; *Haemophilus paragallinarum/genetics ; Gram-Negative Bacteria ; Drug Resistance, Microbial ; Tetracycline ; Anti-Bacterial Agents/pharmacology ; Chloramphenicol ; Erythromycin ; Streptomycin ; Genomics ; Deoxyribonucleases ; }, abstract = {Avibacterium paragallinarum is the etiological agent of infectious coryza, an acute respiratory disease of chickens that is globally distributed and causes serious economic losses for chicken production. A. paragallinarum is a Gram-negative bacterium that releases outer membrane vesicles (OMVs). In this study, a comparative genomic analysis of A. paragallinarum isolate P4chr1 and its OMVs was carried out, and the ability to transfer antibiotic resistance genes (ARGs) via the OMVs was studied. Sequencing and data analyses demonstrated that the genomic size of A. paragallinarum P4chr1 was approximately 2.77 Mb with a 25 kb tolerance island that covered six types of antibiotics and 11 ARGs. The genomic size of its OMVs was approximately 2.69 Mb, covering 97% of the genomic length and almost all the gene sequences of P4chr1. Purified and DNase-treated A. paragallinarum P4chr1 OMVs were cocultured with the antibiotic-sensitive A. paragallinarum Modesto strain on an antibiotic (chloramphenicol, erythromycin, tetracycline, or streptomycin)-containing plate, and the corresponding ARGs were detected in the colonies grown on the plates. However, using an antimicrobial susceptibility test, we found that ARGs delivered by OMVs were not persistent but only appeared transiently on the antibiotic-containing plates. Antibiotic resistance and ARGs were lost by the second bacterial passage. IMPORTANCE The functions and roles of OMVs on ARG and virulent gene transfer and dissemination have been reported in numerous Gram-negative bacteria. However, the role of OMVs in mediating antibiotic resistance in A. paragallinarum has not been reported. This study is the first report to compare the genomic characteristics of OMVs with its parent A. paragallinarum strain and to study A. paragallinarum ARG transfer via OMVs. This work has provided useful data for further studies focusing on nonplasmid ARG transfer mediated by A. paragallinarum OMVs.}, }
@article {pmid35994648, year = {2022}, author = {Colnaghi, M and Lane, N and Pomiankowski, A}, title = {Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2205041119}, pmid = {35994648}, issn = {1091-6490}, mesh = {Computer Simulation ; *DNA Repeat Expansion/genetics ; *Eukaryota/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Genome/genetics ; *Meiosis/genetics ; Mutation ; Mutation Accumulation ; Phylogeny ; Prokaryotic Cells ; }, abstract = {The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.}, }
@article {pmid35992716, year = {2022}, author = {Zhang, Y and Guo, Y and Qiu, T and Gao, M and Wang, X}, title = {Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {936267}, pmid = {35992716}, issn = {1664-302X}, abstract = {Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.}, }
@article {pmid35991959, year = {2022}, author = {,  and More, S and Bampidis, V and Benford, D and Bragard, C and Halldorsson, T and Hernández-Jerez, A and Bennekou, SH and Koutsoumanis, K and Lambré, C and Machera, K and Mullins, E and Nielsen, SS and Schlatter, J and Schrenk, D and Turck, D and Younes, M and Herman, L and Pelaez, C and van Loveren, H and Vlak, J and Revez, J and Aguilera, J and Schoonjans, R and Cocconcelli, PS}, title = {Evaluation of existing guidelines for their adequacy for the food and feed risk assessment of microorganisms obtained through synthetic biology.}, journal = {EFSA journal. European Food Safety Authority}, volume = {20}, number = {8}, pages = {e07479}, pmid = {35991959}, issn = {1831-4732}, abstract = {EFSA was asked by the European Commission to evaluate synthetic biology (SynBio) developments for agri-food use in the near future and to determine whether or not they are expected to constitute potential new hazards/risks. Moreover, EFSA was requested to evaluate the adequacy of existing guidelines for risk assessment of SynBio and if updated guidance is needed. The scope of this Opinion covers food and feed risk assessment, the variety of microorganisms that can be used in the food/feed chain and the whole spectrum of techniques used in SynBio. This Opinion complements a previously adopted Opinion with the evaluation of existing guidelines for the microbial characterisation and environmental risk assessment of microorganisms obtained through SynBio. The present Opinion confirms that microbial SynBio applications for food and feed use, with the exception of xenobionts, could be ready in the European Union in the next decade. New hazards were identified related to the use or production of unusual and/or new-to-nature components. Fifteen cases were selected for evaluating the adequacy of existing guidelines. These were generally adequate for assessing the product, the production process, nutritional and toxicological safety, allergenicity, exposure and post-market monitoring. The comparative approach and a safety assessment per se could be applied depending on the degree of familiarity of the SynBio organism/product with the non-genetically modified counterparts. Updated guidance is recommended for: (i) bacteriophages, protists/microalgae, (ii) exposure to plant protection products and biostimulants, (iii) xenobionts and (iv) feed additives for insects as target species. Development of risk assessment tools is recommended for assessing nutritional value of biomasses, influence of microorganisms on the gut microbiome and the gut function, allergenic potential of new-to-nature proteins, impact of horizontal gene transfer and potential risks of living cell intake. A further development towards a strain-driven risk assessment approach is recommended.}, }
@article {pmid35989606, year = {2022}, author = {Haudiquet, M and de Sousa, JM and Touchon, M and Rocha, EPC}, title = {Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1861}, pages = {20210234}, pmid = {35989606}, issn = {1471-2970}, mesh = {Biological Evolution ; *Gene Transfer, Horizontal ; *Interspersed Repetitive Sequences ; }, abstract = {Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell-MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.}, }
@article {pmid35989605, year = {2022}, author = {Huisman, JS and Vaughan, TG and Egli, A and Tschudin-Sutter, S and Stadler, T and Bonhoeffer, S}, title = {The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1861}, pages = {20210245}, pmid = {35989605}, issn = {1471-2970}, mesh = {Animals ; Anti-Bacterial Agents ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; *Genome, Bacterial ; Humans ; Phylogeny ; Plasmids/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The spread of antibiotic resistance genes on plasmids is a threat to human and animal health. Phylogenies of bacteria and their plasmids contain clues regarding the frequency of plasmid transfer events, as well as the co-evolution of plasmids and their hosts. However, whole genome sequencing data from diverse ecological or clinical bacterial samples are rarely used to study plasmid phylogenies and resistance gene transfer. This is partially due to the difficulty of extracting plasmids from short-read sequencing data. Here, we use both short- and long-read sequencing data of 24 clinical extended-spectrum [Formula: see text]-lactamase (ESBL)-producing Escherichia coli to estimate chromosomal and plasmid phylogenies. We compare the impact of different sequencing and assembly methodologies on these phylogenies and on the inference of horizontal gene transfer. We find that chromosomal phylogenies can be estimated robustly with all methods, whereas plasmid phylogenies have more variable topology and branch lengths across the methods used. Specifically, hybrid methods that use long reads to resolve short-read assemblies (HybridSPAdes and Unicycler) perform better than those that started from long reads during assembly graph generation (Canu). By contrast, the inference of plasmid and antibiotic resistance gene transfer using a parsimony-based criterion is mostly robust to the choice of sequencing and assembly method. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.}, }
@article {pmid35986092, year = {2022}, author = {Kikuchi, Y and Matsui, H and Asami, Y and Kuwae, A and Inahashi, Y and Hanaki, H and Abe, A}, title = {Landscape of blaNDM genes in Enterobacteriaceae.}, journal = {The Journal of antibiotics}, volume = {75}, number = {10}, pages = {559-566}, pmid = {35986092}, issn = {1881-1469}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Enterobacteriaceae/genetics ; Gene Transfer, Horizontal ; Microbial Sensitivity Tests ; Plasmids/genetics ; *beta-Lactamases/genetics/metabolism ; }, abstract = {The blaNDM-1 gene encodes a carbapenemase, New Delhi metallo-β-lactamase (NDM-1), and the ability to produce NDM-1 is spread among Enterobacteriaceae via horizontal gene transfer of plasmids. It has been widely accepted that blaNDM-1 is regulated by a hybrid promoter (PISAba125) consisting of a -10 box from the original blaNDM-1 and a -35 box from ISAba125. However, the conservation of this promoter and the vertical transmission of blaNDM genes by chromosomal integration have not been comprehensively analyzed. We retrieved the region containing the ORF of blaNDM-1 (>95% translated protein identity) and a region 120 bp upstream of the blaNDM-1 start codon from the complete sequence data of Enterobacteriaceae plasmids (n = 10,914) and chromosomes (n = 4908) deposited in GenBank, and the 310 extracted blaNDM genes were analyzed by an in-silico approach. The results showed that most blaNDM genes (99.0%) utilized the promoter, PISAba125. Interestingly, two blaNDM-1 genes from the genus Citrobacter utilized the ISCR1-derived outward-oriented promoters POUT (PISCR1). Furthermore, the insertion of ISAba125 and ISCR1 occurred upstream of the CCATATTT sequence, which is located upstream of the -10 box. We also confirmed that most of the blaNDM genes were disseminated by horizontal gene transfer of the plasmid, but 10 cases of the blaNDM genes were integrated into the chromosome via mobile genetic elements such as IS26, IS150, ISCR1, ICE, and Tn7-like elements. Thus, plasmid-mediated transmission of the PISAba125-blaNDM genes is predominant in Enterobacteriaceae. However, the spread of blaNDM genes with new promoters and vertical dissemination via chromosomal integrations may pose additional serious clinical problems.}, }
@article {pmid35985927, year = {2022}, author = {Marcilla, A and Sánchez-López, CM}, title = {Extracellular vesicles as a horizontal gene transfer mechanism in Leishmania.}, journal = {Trends in parasitology}, volume = {38}, number = {10}, pages = {823-825}, doi = {10.1016/j.pt.2022.08.004}, pmid = {35985927}, issn = {1471-5007}, mesh = {Animals ; Drug Resistance ; *Extracellular Vesicles ; Gene Transfer, Horizontal ; *Leishmania/genetics ; *Parasites ; }, abstract = {Douanne et al. recently reported horizontal gene transfer (HGT) mediated by extracellular vesicles (EVs) in Leishmania; this constitutes the first report of this phenomenon in parasites. They showed that EVs facilitate the transmission of drug-resistance genes and increased cell fitness in stressful environments, indicating potential clinical application of these findings.}, }
@article {pmid35985290, year = {2022}, author = {Fillol-Salom, A and Rostøl, JT and Ojiogu, AD and Chen, J and Douce, G and Humphrey, S and Penadés, JR}, title = {Bacteriophages benefit from mobilizing pathogenicity islands encoding immune systems against competitors.}, journal = {Cell}, volume = {185}, number = {17}, pages = {3248-3262.e20}, doi = {10.1016/j.cell.2022.07.014}, pmid = {35985290}, issn = {1097-4172}, support = {201531/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/M003876/1/MRC_/Medical Research Council/United Kingdom ; MR/S00940X/1/MRC_/Medical Research Council/United Kingdom ; MR/V000772/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Gene Transfer, Horizontal ; *Genomic Islands ; Immune System ; Plasmids ; }, abstract = {Bacteria encode sophisticated anti-phage systems that are diverse and versatile and display high genetic mobility. How this variability and mobility occurs remains largely unknown. Here, we demonstrate that a widespread family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs), carry an impressive arsenal of defense mechanisms, which can be disseminated intra- and inter-generically by helper phages. These defense systems provide broad immunity, blocking not only phage reproduction, but also plasmid and non-cognate PICI transfer. Our results demonstrate that phages can mobilize PICI-encoded immunity systems to use them against other mobile genetic elements, which compete with the phages for the same bacterial hosts. Therefore, despite the cost, mobilization of PICIs may be beneficial for phages, PICIs, and bacteria in nature. Our results suggest that PICIs are important players controlling horizontal gene transfer and that PICIs and phages establish mutualistic interactions that drive bacterial ecology and evolution.}, }
@article {pmid35985212, year = {2022}, author = {Peng, S and Zhang, H and Song, D and Chen, H and Lin, X and Wang, Y and Ji, L}, title = {Distribution of antibiotic, heavy metals and antibiotic resistance genes in livestock and poultry feces from different scale of farms in Ningxia, China.}, journal = {Journal of hazardous materials}, volume = {440}, number = {}, pages = {129719}, doi = {10.1016/j.jhazmat.2022.129719}, pmid = {35985212}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Chickens/genetics ; *Chlortetracycline ; Doxycycline ; Drug Resistance, Microbial/genetics ; *Environmental Pollutants ; Farms ; Feces ; Genes, Bacterial ; Livestock ; Manure ; *Metals, Heavy/toxicity ; Poultry/genetics ; Sheep/genetics ; Swine ; }, abstract = {With the rapid development of livestock and poultry breeding industries, pollution problems caused by the discharge of animal feces have become increasingly severe. Nevertheless, there are limited investigations about nutrients and pollutants in animal feces from different scale of farms, especially in Northwest China. Here we investigated nutrients content, 19 antibiotics, 7 heavy metals, 329 antibiotic resistance genes (ARGs) and 35 mobile genetic elements (MGEs) in six main livestock and poultry feces collected from 5 coastal regions of Ningxia. Pig and chicken feces exhibited higher levels of nutrients content, but antibiotics, heavy metals, ARGs and MGEs were also more abundant than those in cattle and sheep feces. Chlortetracycline hydrochloride and doxycycline hyclate were the most commonly used antibiotic, which detected with the highest rate and concentrations, especially in broiler, layer and pig feces. Strong positive correlations were found among different ARGs or between ARGs and MGEs, indicated the risk of horizontal gene transfer of ARGs. Residual antibiotic and heavy metals significantly affect the abundance of ARGs. Feeding mode and the scales of the animal farms served little effect on the distribution of the pollutants (including residual antibiotics, heavy metals, MGEs and ARGs), which were significantly different among animal types. Use of antibiotics and heavy metals should be strictly regulated, especially in chicken and pig farms, in order to control contaminants and reduce potential risks to the environment.}, }
@article {pmid35983328, year = {2022}, author = {Qian, C and Ma, J and Liang, J and Zhang, L and Liang, X}, title = {Comprehensive deciphering prophages in genus Acetobacter on the ecology, genomic features, toxin-antitoxin system, and linkage with CRISPR-Cas system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951030}, pmid = {35983328}, issn = {1664-302X}, abstract = {Acetobacter is the predominant microbe in vinegar production, particularly in those natural fermentations that are achieved by complex microbial communities. Co-evolution of prophages with Acetobacter, including integration, release, and dissemination, heavily affects the genome stability and production performance of industrial strains. However, little has been discussed yet about prophages in Acetobacter. Here, prophage prediction analysis using 148 available genomes from 34 Acetobacter species was carried out. In addition, the type II toxin-antitoxin systems (TAs) and CRISPR-Cas systems encoded by prophages or the chromosome were analyzed. Totally, 12,000 prophage fragments were found, of which 350 putatively active prophages were identified in 86.5% of the selected genomes. Most of the active prophages (83.4%) belonged to the order Caudovirales dominated by the families Siphoviridae and Myroviridae prophages (71.4%). Notably, Acetobacter strains survived in complex environments that frequently carried multiple prophages compared with that in restricted habits. Acetobacter prophages showed high genome diversity and horizontal gene transfer across different bacterial species by genomic feature characterization, average nucleotide identity (ANI), and gene structure visualization analyses. About 31.14% of prophages carry type II TAS, suggesting its important role in addiction, bacterial defense, and growth-associated bioprocesses to prophages and hosts. Intriguingly, the genes coding for Cse1, Cse2, Cse3, Cse4, and Cas5e involved in type I-E and Csy4 involved in type I-F CRISPR arrays were firstly found in two prophages. Type II-C CRISPR-Cas system existed only in Acetobacter aceti, while the other Acetobacter species harbored the intact or eroded type I CRISPR-Cas systems. Totally, the results of this study provide fundamental clues for future studies on the role of prophages in the cell physiology and environmental behavior of Acetobacter.}, }
@article {pmid35980276, year = {2022}, author = {Zhang, C and Saad, Z and Zhang, S and Chen, B and He, X and Liu, S}, title = {Effects of voltage and tetracycline on horizontal transfer of ARGs in microbial electrolysis cells.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/09593330.2022.2114860}, pmid = {35980276}, issn = {1479-487X}, abstract = {The abuse of antibiotics leads to the production of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Microbial electrolysis cells (MECs) have been widely applicated in the field of degrading antibiotics. ARGs were increased via horizontal transfer in single and two-chamber MECs. As one of the critical parameters in MECs, voltage has a particular impact on the ARGs transfer via horizontal transfer. However, there have been few studies of ARGs transfer under the exposure of antibiotics and voltage in MECs. In this study, five concentrations of tetracycline (0, 1, 5, 10, 20 mg/L) were selected to explore the conjugative transfer frequency of plasmid-encoded the ARGs from the donor (E. coli RP4) to receptor (E. coli HB101) in MECs, two voltages (1.5 and 2.0 V) were used to explore the conjugative transfer frequency of ARGs in MECs, then, the transfer of ARGs in MECs under the co-effect of tetracycline and voltage was explored. The results showed that the conjugative transfer frequency of ARGs was significantly increased with the increase of tetracycline concentration and voltage, respectively (p < 0.05). Under the pressure of tetracycline and voltage, the conjugative transfer frequency of ARGs is significantly enhanced with the co-effect of tetracycline and voltage (p < 0.05). The oxidative response induced by electrical stimulation promotes the overproduction of reactive oxygen species and the enhancement of cell membrane permeability of donor and recipient bacteria in MECs. These findings provide insights for studying the spread of ARGs in MECs.}, }
@article {pmid35979495, year = {2022}, author = {Uzun, M and Koziaeva, V and Dziuba, M and Leão, P and Krutkina, M and Grouzdev, D}, title = {Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {945734}, pmid = {35979495}, issn = {1664-302X}, abstract = {Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. Magnetotactic bacteria belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.}, }
@article {pmid35977641, year = {2022}, author = {Neethu, CS and Saravanakumar, C and Purvaja, R and Robin, RS and Ramesh, R}, title = {Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {311}, number = {}, pages = {119937}, doi = {10.1016/j.envpol.2022.119937}, pmid = {35977641}, issn = {1873-6424}, mesh = {*Arsenic/pharmacology ; *Betaproteobacteria ; Carbon ; Escherichia coli ; *Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Nitrogen/pharmacology ; Phylogeny ; }, abstract = {Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsB[R]amp[R]) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.}, }
@article {pmid35977623, year = {2022}, author = {Qiu, D and Ke, M and Zhang, Q and Zhang, F and Lu, T and Sun, L and Qian, H}, title = {Response of microbial antibiotic resistance to pesticides: An emerging health threat.}, journal = {The Science of the total environment}, volume = {850}, number = {}, pages = {158057}, doi = {10.1016/j.scitotenv.2022.158057}, pmid = {35977623}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/metabolism/toxicity ; Bacteria/metabolism ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; *Pesticides/metabolism/toxicity ; }, abstract = {The spread of microbial antibiotic resistance has seriously threatened public health globally. Non-antibiotic stressors have significantly contributed to the evolution of bacterial antibiotic resistance. Although numerous studies have been conducted on the potential risk of pesticide pollution for bacterial antibiotic resistance, a systematic review of these concerns is still lacking. In the present study, we elaborate the mechanism underlying the effects of pesticides on bacterial antibiotic resistance acquisition as well as the propagation of antimicrobial resistance. Pesticide stress enhanced the acquisition of antibiotic resistance in bacteria via various mechanisms, including the activation of efflux pumps, inhibition of outer membrane pores for resistance to antibiotics, and gene mutation induction. Horizontal gene transfer is a major mechanism whereby pesticides influence the transmission of antibiotic resistance genes (ARGs) in bacteria. Pesticides promoted the conjugation transfer of ARGs by increasing cell membrane permeability and increased the proportion of bacterial mobile gene elements, which facilitate the spread of ARGs. This review can improve our understanding regarding the pesticide-induced generation and spread of ARGs and antibiotic resistant bacteria. Moreover, it can be applied to reduce the ecological risks of ARGs in the future.}, }
@article {pmid35974915, year = {2022}, author = {Hemamalini, N and Shanmugam, SA and Kathirvelpandian, A and Deepak, A and Kaliyamurthi, V and Suresh, E and Ezhilmathi, S}, title = {Prevalence, Antimicrobial Susceptibility and Resistance Gene Detection in Bacteria Isolated from Goldfish and Tiger Barb from Ornamental Fish Farms of Tamil Nadu.}, journal = {Indian journal of microbiology}, volume = {62}, number = {3}, pages = {441-446}, pmid = {35974915}, issn = {0046-8991}, abstract = {UNLABELLED: This study aims to determine the antimicrobial resistance (AMR) pattern in freshwater ornamental cyprinids, such as Goldfish and Tiger barb. Molecular characterization of bacterial isolates confirmed the presence of 7 bacterial isolates in Goldfish and 6 in Tiger barb. Antimicrobial susceptibility test using 36 antibiotics revealed a higher resistance pattern for bacitracin, rifampicin, trimethoprim, cefalexin, ampicillin, amoxicillin, nalidixic acid and nitrofurantoin. Sulphafurazole, norfloxacin and ciprofloxacin were effective against all the bacterial isolates derived from Goldfish and Tiger barb. Most bacterial isolates exhibited > 0.2 multi-drug resistance index (MDR), indicating the severity of antibiotic use in the culture system. The finding of the present study suggests that ornamental fish may act as the reservoir of MDR bacteria and dissemination of resistance genes to clinical and human commensal bacteria through horizontal gene transfer.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01023-y.}, }
@article {pmid35970720, year = {2022}, author = {González-Villalobos, E and Balcázar, JL}, title = {Does phage-mediated horizontal gene transfer represent an environmental risk?.}, journal = {Trends in microbiology}, volume = {30}, number = {11}, pages = {1022-1024}, doi = {10.1016/j.tim.2022.07.011}, pmid = {35970720}, issn = {1878-4380}, mesh = {Anti-Bacterial Agents ; *Bacteriophages/genetics ; *Gene Transfer, Horizontal ; }, abstract = {A growing number of recent studies suggest that the contribution of phages to antibiotic resistance should not be underestimated. Here we describe their implications for public and environmental health, with a special emphasis on the mechanisms underlying phage-mediated horizontal gene transfer.}, }
@article {pmid35967855, year = {2022}, author = {Chen, H and Tao, S and Li, N and Wang, F and Wang, L and Tang, Y and Liang, W}, title = {Functional comparison of anti-restriction and anti-methylation activities of ArdA, KlcA, and KlcAHS from Klebsiella pneumoniae.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {916547}, pmid = {35967855}, issn = {2235-2988}, mesh = {*Gene Transfer, Horizontal ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; Protein Processing, Post-Translational ; }, abstract = {Anti-restriction proteins are typically encoded by plasmids, conjugative transposons, or phages to improve their chances of entering a new bacterial host with a type I DNA restriction and modification (RM) system. The invading DNA is normally destroyed by the RM system. The anti-restriction proteins ArdA, KlcA, and their homologues are usually encoded on plasmid of carbapenemase-resistant Klebsiella pneumoniae. We found that the plasmid sequence and restriction proteins affected horizontal gene transfer, and confirmed the anti-restriction and anti-methylation activities of ArdA and KlcA during transformation and transduction. Among the three anti-restriction proteins, ArdA shows stronger anti-restriction and anti-methylation effects, and KlcAHS was weaker. KlcA shows anti-methylation only during transformation. Understanding the molecular mechanism underlying the clinical dissemination of K. pneumoniae and other clinically resistant strains from the perspective of restrictive and anti-restrictive systems will provide basic theoretical support for the prevention and control of multidrug-resistant bacteria, and new strategies for delaying or even controlling the clinical dissemination of resistant strains in the future.}, }
@article {pmid35966708, year = {2022}, author = {Entfellner, E and Li, R and Jiang, Y and Ru, J and Blom, J and Deng, L and Kurmayer, R}, title = {Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {901762}, pmid = {35966708}, issn = {1664-302X}, abstract = {It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7-4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4-5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3-6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1-3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.}, }
@article {pmid35963060, year = {2022}, author = {Hou, L and Li, J and Wang, H and Chen, Q and Su, JQ and Gad, M and Ahmed, W and Yu, CP and Hu, A}, title = {Storm promotes the dissemination of antibiotic resistome in an urban lagoon through enhancing bio-interactions.}, journal = {Environment international}, volume = {168}, number = {}, pages = {107457}, doi = {10.1016/j.envint.2022.107457}, pmid = {35963060}, issn = {1873-6750}, abstract = {Antibiotic-resistance genes (ARGs) and resistant bacteria (ARB) are abundant in stormwater that could cause serious infections, posing a potential threat to public health. However, there is no inference about how stormwater contributes to ARG profiles as well as the dynamic interplay between ARGs and bacteria via vertical gene transfer (VGT) or horizontal gene transfer (HGT) in urban water ecosystems. In this study, the distribution of ARGs, their host communities, and the source and community assembly process of ARGs were investigated in Yundang Lagoon (China) via high-throughput quantitative PCR, 16S rRNA gene amplicon sequencing, and application of SourceTracker before, after and recovering from an extreme precipitation event (132.1 mm). The abundance of ARGs and mobile genetic elements (MGEs) was the highest one day after precipitation and then decreased 2 days after precipitation and so on. Based on SourceTracker and NMDS analysis, the ARG and bacterial communities in lagoon surface water from one day after precipitation were mainly contributed by the wastewater treatment plant (WWTP) influent and effluent. However, the contribution of WWTP to ARG communities was minor 11 days after the precipitation, suggesting that the storm promoted the ARG levels by introducing the input of ARGs, MGEs, and ARB from point and non-point sources, such as sewer overflow and land-applied manure. Based on a novel microbial network analysis framework, the contribution of positive biological interactions between ARGs and MGEs or bacteria was the highest one day after precipitation, indicating a promoted VGT and HGT for ARG dissemination. The microbial networks deconstructed 11 days after precipitation, suggesting the stormwater practices (e.g., tide gate opening, diversion channels, and pumping) alleviated the spread of ARGs. These results advanced our understanding of the distribution and transport of ARGs associated with their source in urban stormwater runoff.}, }
@article {pmid35962419, year = {2022}, author = {de Assis, JCS and Gonçalves, OS and Fernandes, AS and de Queiroz, MV and Bazzolli, DMS and Santana, MF}, title = {Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria.}, journal = {Mobile DNA}, volume = {13}, number = {1}, pages = {19}, pmid = {35962419}, issn = {1759-8753}, abstract = {BACKGROUND: ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.<br><br>RESULTS: Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.<br><br>CONCLUSIONS: Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.}, }
@article {pmid35953866, year = {2022}, author = {Wang, Y and Yu, Z and Ding, P and Lu, J and Klümper, U and Murray, AK and Gaze, WH and Guo, J}, title = {Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {124}, pmid = {35953866}, issn = {2049-2618}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Gene Transfer, Horizontal ; Pharmaceutical Preparations ; Plasmids/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Horizontal gene transfer (HGT) plays a critical role in the spread of antibiotic resistance and the evolutionary shaping of bacterial communities. Conjugation is the most well characterized pathway for the spread of antibiotic resistance, compared to transformation and transduction. While antibiotics have been found to induce HGT, it remains unknown whether non-antibiotic pharmaceuticals can facilitate conjugation at a microbial community-wide level.<br><br>RESULTS: In this study, we demonstrate that several commonly consumed non-antibiotic pharmaceuticals (including carbamazepine, ibuprofen, naproxen and propranolol), at environmentally relevant concentrations (0.5&#xa0;mg/L), can promote the conjugative transfer of IncP1-&#x3b1; plasmid-borne antibiotic resistance across entire microbial communities. The over-generation of reactive oxygen species in response to these non-antibiotic pharmaceuticals may contribute to the enhanced conjugation ratios. Cell sorting and 16S rRNA gene amplicon sequencing analyses indicated that non-antibiotic pharmaceuticals modulate transconjugant microbial communities at both phylum and genus levels. Moreover, microbial uptake ability of the IncP1-&#x3b1; plasmid was also upregulated under non-antibiotic pharmaceutical exposure. Several opportunistic pathogens, such as Acinetobacter and Legionella, were more likely to acquire the plasmid conferring multidrug resistance.<br><br>CONCLUSIONS: Considering the high possibility of co-occurrence of pathogenic bacteria, conjugative IncP1-&#x3b1; plasmids and non-antibiotic pharmaceuticals in various environments (e.g., activated sludge systems), our findings illustrate the potential risk associated with increased dissemination of antibiotic resistance promoted by non-antibiotic pharmaceuticals in complex environmental settings. Video abstract.}, }
@article {pmid35949392, year = {2022}, author = {Chase, EE and Desnues, C and Blanc, G}, title = {Integrated viral elements suggest the dual lifestyle of Tetraselmis spp. Polinton-like viruses.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac068}, pmid = {35949392}, issn = {2057-1577}, abstract = {In this study, we aimed at exploring horizontal gene transfer between viruses and Chlorodendraceae green algae (Chlorophyta) using available genomic and transcriptomic sequences for twenty algal strains. We identified a significant number of genes sharing a higher sequence similarity with viral homologues, thus signalling their possible involvement in horizontal gene transfers with viruses. Further characterization showed that many of these genes were clustered in DNA regions of several tens to hundreds of kilobases in size, originally belonging to viruses related to known Tetraselmis spp. viruses (TetV and TsV). In contrast, the remaining candidate HGT genes were randomly dispersed in the algal genomes, were more frequently transcribed, and belonged to large multigene families. The presence of homologues in Viridiplantae suggested that the latter were more likely of algal rather than viral origin. We found a remarkable diversity in polinton-like virus (PLV) elements inserted in Tetraselmis genomes, all of which were most similar to the Tetraselmis striata virus (TsV). The genes of PLV elements are transcriptionally inactive with the notable exception of the homologue of the TVSG_00024 gene of TsV whose function is unknown. We suggest that this gene may be involved in a sentinel process to trigger virus reactivation and excision in response to an environmental stimulus. Altogether, these results provide evidence that TsV-related viruses have a dual lifestyle, alternating between a free viral phase (i.e. virion) and a phase integrated into host genomes.}, }
@article {pmid35947951, year = {2022}, author = {Sherlock, D and Fogg, PCM}, title = {The archetypal gene transfer agent RcGTA is regulated via direct interaction with the enigmatic RNA polymerase omega subunit.}, journal = {Cell reports}, volume = {40}, number = {6}, pages = {111183}, pmid = {35947951}, issn = {2211-1247}, support = {109363/Z/15/A/WT_/Wellcome Trust/United Kingdom ; BB/V016288/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Alphaproteobacteria ; Bacterial Proteins/genetics/metabolism ; DNA/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Gene Expression Regulation, Bacterial ; Gene Transfer, Horizontal ; *Rhodobacter capsulatus/genetics/metabolism ; }, abstract = {Gene transfer agents (GTAs) are small virus-like particles that indiscriminately package and transfer any DNA present in their host cell, with clear implications for bacterial evolution. The first transcriptional regulator that directly controls GTA expression, GafA, was recently discovered, but its mechanism of action has remained elusive. Here, we demonstrate that GafA controls GTA gene expression via direct interaction with the RNA polymerase omega subunit (Rpo-ω) and also positively autoregulates its own expression by an Rpo-ω-independent mechanism. We show that GafA is a modular protein with distinct DNA and protein binding domains. The functional domains we observe in Rhodobacter GafA also correspond to two-gene operons in Hyphomicrobiales pathogens. These data allow us to produce the most complete regulatory model for a GTA and point toward an atypical mechanism for RNA polymerase recruitment and specific transcriptional activation in the Alphaproteobacteria.}, }
@article {pmid35947446, year = {2022}, author = {Swarthout, JM and Chan, EMG and Garcia, D and Nadimpalli, ML and Pickering, AJ}, title = {Human Colonization with Antibiotic-Resistant Bacteria from Nonoccupational Exposure to Domesticated Animals in Low- and Middle-Income Countries: A Critical Review.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {14875-14890}, doi = {10.1021/acs.est.2c01494}, pmid = {35947446}, issn = {1520-5851}, mesh = {Animals ; Humans ; *Developing Countries ; *Animals, Domestic/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Data on community-acquired antibiotic-resistant bacterial infections are particularly sparse in low- and middle-income countries (LMICs). Limited surveillance and oversight of antibiotic use in food-producing animals, inadequate access to safe drinking water, and insufficient sanitation and hygiene infrastructure in LMICs could exacerbate the risk of zoonotic antibiotic resistance transmission. This critical review compiles evidence of zoonotic exchange of antibiotic-resistant bacteria (ARB) or antibiotic resistance genes (ARGs) within households and backyard farms in LMICs, as well as assesses transmission mechanisms, risk factors, and environmental transmission pathways. Overall, substantial evidence exists for exchange of antibiotic resistance between domesticated animals and in-contact humans. Whole bacteria transmission and horizontal gene transfer between humans and animals were demonstrated within and between households and backyard farms. Further, we identified water, soil, and animal food products as environmental transmission pathways for exchange of ARB and ARGs between animals and humans, although directionality of transmission is poorly understood. Herein we propose study designs, methods, and topical considerations for priority incorporation into future One Health research to inform effective interventions and policies to disrupt zoonotic antibiotic resistance exchange in low-income communities.}, }
@article {pmid35946347, year = {2022}, author = {Chen, MY and Teng, WK and Zhao, L and Han, BP and Song, LR and Shu, WS}, title = {Phylogenomics Uncovers Evolutionary Trajectory of Nitrogen Fixation in Cyanobacteria.}, journal = {Molecular biology and evolution}, volume = {39}, number = {9}, pages = {}, pmid = {35946347}, issn = {1537-1719}, mesh = {*Cyanobacteria/genetics ; Gene Transfer, Horizontal ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Photosynthesis/genetics ; Phylogeny ; }, abstract = {Biological nitrogen fixation (BNF) by cyanobacteria is of significant importance for the Earth's biogeochemical nitrogen cycle but is restricted to a few genera that do not form monophyletic group. To explore the evolutionary trajectory of BNF and investigate the driving forces of its evolution, we analyze 650 cyanobacterial genomes and compile the database of diazotrophic cyanobacteria based on the presence of nitrogen fixation gene clusters (NFGCs). We report that 266 of 650 examined genomes are NFGC-carrying members, and these potentially diazotrophic cyanobacteria are unevenly distributed across the phylogeny of Cyanobacteria, that multiple independent losses shaped the scattered distribution. Among the diazotrophic cyanobacteria, two types of NFGC exist, with one being ancestral and abundant, which have descended from diazotrophic ancestors, and the other being anaerobe-like and sparse, possibly being acquired from anaerobic microbes through horizontal gene transfer. Interestingly, we illustrate that the origin of BNF in Cyanobacteria coincide with two major evolutionary events. One is the origin of multicellularity of cyanobacteria, and the other is concurrent genetic innovations with massive gene gains and expansions, implicating their key roles in triggering the evolutionary transition from nondiazotrophic to diazotrophic cyanobacteria. Additionally, we reveal that genes involved in accelerating respiratory electron transport (coxABC), anoxygenic photosynthetic electron transport (sqr), as well as anaerobic metabolisms (pfor, hemN, nrdG, adhE) are enriched in diazotrophic cyanobacteria, representing adaptive genetic signatures that underpin the diazotrophic lifestyle. Collectively, our study suggests that multicellularity, together with concurrent genetic adaptations contribute to the evolution of diazotrophic cyanobacteria.}, }
@article {pmid35944516, year = {2022}, author = {Goldman, AD and Kaçar, B}, title = {Very early evolution from the perspective of microbial ecology.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16144}, pmid = {35944516}, issn = {1462-2920}, support = {/NASA/NASA/United States ; /NASA/NASA/United States ; }, abstract = {The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.}, }
@article {pmid35944241, year = {2022}, author = {Wu, Y and Yan, H and Zhu, X and Liu, C and Chu, C and Zhu, X and Chen, B}, title = {Biochar Effectively Inhibits the Horizontal Transfer of Antibiotic Resistance Genes via Restraining the Energy Supply for Conjugative Plasmid Transfer.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {17}, pages = {12573-12583}, doi = {10.1021/acs.est.2c02701}, pmid = {35944241}, issn = {1520-5851}, mesh = {Adenosine Triphosphate/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Charcoal ; Drug Resistance, Microbial/genetics ; *Escherichia coli/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Plasmids/genetics ; }, abstract = {Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation poses a major threat to global public health. Biochar, a widely used environmental remediation material, has remarkable impacts on the fate of ARGs. However, although biochar was reported being able to inhibit the HGT of ARGs via conjugation and transformation, little is known about the intracellular process that mediates the inhibition effects. On the other hand, as typical natural organic matter, fulvic acid is a common environmental influencer, and how it interferes with the effect of biochar on the HGT of ARGs is unknown. Therefore, this study investigated the effects on the conjugative transfer of ARGs between Escherichia coli MG1655 and E. coli HB101 carrying plasmid RP4, with biochars pyrolyzed at three temperatures and with the corresponding biochars coating with fulvic acid. Results showed that biochar with higher pyrolyzed temperature had a more substantial inhibitory effect on the conjugative transfer of the RP4 plasmid. The inhibitory effect of biochar was mainly attributed to (i) down-regulation of plasmid transfer gene expression, including the formation of conjugative transfer channel and plasmid replication, due to restrained adenosine triphosphate (ATP) energy supply and (ii) decreased cell membrane permeability. Conversely, the fulvic acid coating diminished this inhibition effect of biochar, mainly by providing more ATP and strengthening intracellular reactive oxygen species (ROS) defense. Our findings shed light on the intracellular process that mediates the effects of biochar on the conjugative transfer of ARGs, which would provide support for using biochar to reduce the spread of ARGs.}, }
@article {pmid35942309, year = {2022}, author = {Tao, S and Chen, H and Li, N and Liang, W}, title = {The Application of the CRISPR-Cas System in Antibiotic Resistance.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4155-4168}, pmid = {35942309}, issn = {1178-6973}, abstract = {The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.}, }
@article {pmid35942087, year = {2022}, author = {Gao, C and Liang, Y and Jiang, Y and Paez-Espino, D and Han, M and Gu, C and Wang, M and Yang, Y and Liu, F and Yang, Q and Gong, Z and Zhang, X and Luo, Z and He, H and Guo, C and Shao, H and Zhou, C and Shi, Y and Xin, Y and Xing, J and Tang, X and Qin, Q and Zhang, YZ and He, J and Jiao, N and McMinn, A and Tian, J and Suttle, CA and Wang, M}, title = {Virioplankton assemblages from challenger deep, the deepest place in the oceans.}, journal = {iScience}, volume = {25}, number = {8}, pages = {104680}, pmid = {35942087}, issn = {2589-0042}, abstract = {Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.}, }
@article {pmid35941147, year = {2022}, author = {Stone, J and Edgar, JO and Gould, JA and Telling, J}, title = {Tectonically-driven oxidant production in the hot biosphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4529}, pmid = {35941147}, issn = {2041-1723}, mesh = {Biological Evolution ; Earth, Planet ; *Hydrogen Peroxide ; *Oxidants ; Oxygen ; Photosynthesis/physiology ; }, abstract = {Genomic reconstructions of the common ancestor to all life have identified genes involved in H2O2 and O2 cycling. Commonly dismissed as an artefact of lateral gene transfer after oxygenic photosynthesis evolved, an alternative is a geological source of H2O2 and O2 on the early Earth. Here, we show that under oxygen-free conditions high concentrations of H2O2 can be released from defects on crushed silicate rocks when water is added and heated to temperatures close to boiling point, but little is released at temperatures <80 °C. This temperature window overlaps the growth ranges of evolutionary ancient heat-loving and oxygen-respiring Bacteria and Archaea near the root of the Universal Tree of Life. We propose that the thermal activation of mineral surface defects during geological fault movements and associated stresses in the Earth's crust was a source of oxidants that helped drive the (bio)geochemistry of hot fractures where life first evolved.}, }
@article {pmid35940152, year = {2022}, author = {Zhou, Q and Zhang, J and Zhang, M and Wang, X and Zhang, D and Pan, X}, title = {Persistent versus transient, and conventional plastic versus biodegradable plastic? -Two key questions about microplastic-water exchange of antibiotic resistance genes.}, journal = {Water research}, volume = {222}, number = {}, pages = {118899}, doi = {10.1016/j.watres.2022.118899}, pmid = {35940152}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; *Biodegradable Plastics/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Microplastics ; *Plastics ; Water/pharmacology ; }, abstract = {The ubiquitous microplastics (MPs) in water environment play an important role in the dissemination of antibiotic resistance genes (ARGs) due to their exchange between floating MPs and receiving waters. However, whether the ARG exchange is persistent or transient and what are the differences in ARG exchange between conventional plastics and biodegradable plastics are the two key issues to be addressed. In this study, biodegradable PBAT and non-biodegradable PET MPs were chosen to explore the MP-water ARG exchange after the MPs floated to the receiving waters. The results demonstrated that the active exchange of ARGs between MPs and receiving waters occurred, which, however, were transient for most of ARGs. The relative abundance of ARGs both on the MPs and in the waters rapidly decreased to the initial or lower levels within 4 weeks. Approximately 25-50% (ARG subtype number ratio) of studied ARG subtypes were introduced into the receiving waters by MPs, and 35-65% of studied ARG subtypes went through fluctuation in terms of abundance on MPs and in the receiving water. ARGs tended to converge between MPs and the receiving waters with time. Furthermore, the ARG exchange between MPs and waters facilitated horizontal gene transfer (HGT). IntI1 and tnpA05 played the crucial roles in HGT, which was indicated by their correlated change with most ARGs; in contrast, tnpA04 showed the obvious lagging responses. The biodegradable MP of PBAT generally accumulated higher levels of most ARGs including multidrug resistant genes than the non-biodegradable MP of PET. The transient exchange of most ARGs between MPs and water implies that the on-off hitchhiking of ARGs on MPs in aquatic environment may not exert significant influence on ARG transmission. However, compared with the conventional plastics, the biodegradable MPs might pose much higher ARG dissemination risks due to the higher enrichment of ARGs particularly with people's ever-increasingly usage. Enough attention must be paid to this emerging issue.}, }
@article {pmid35938813, year = {2022}, author = {Wang, Y and Yang, J and Sun, X and Li, M and Zhang, P and Zhu, Z and Jiao, H and Guo, T and Li, G}, title = {CRISPR-Cas in Acinetobacter baumannii Contributes to Antibiotic Susceptibility by Targeting Endogenous AbaI.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0082922}, pmid = {35938813}, issn = {2165-0497}, mesh = {*Acinetobacter baumannii/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism ; Biofilms ; *CRISPR-Associated Proteins/genetics/metabolism ; CRISPR-Cas Systems ; Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Reactive Oxygen Species/metabolism ; }, abstract = {Acinetobacter baumannii is a well-known human opportunistic pathogen in nosocomial infections, and the emergence of multidrug-resistant Acinetobacter baumannii has become a complex problem for clinical anti-infective treatments. The ways this organism obtains multidrug resistance phenotype include horizontal gene transfer and other mechanisms, such as altered targets, decreased permeability, increased enzyme production, overexpression of efflux pumps, metabolic changes, and biofilm formation. A CRISPR-Cas system generally consists of a CRISPR array and one or more operons of cas genes, which can restrict horizontal gene transfer in bacteria. Nevertheless, it is unclear how CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii. Thus, we sought to assess how CRISPR-Cas affects biofilm formation, membrane permeability, efflux pump, reactive oxygen species, and quorum sensing to clarify further the mechanism of CRISPR-Cas regulation of Acinetobacter baumannii antibiotic resistance. In the clinical isolate AB43, which has a complete I-Fb CRISPR-Cas system, we discovered that the Cas3 nuclease of this type I-F CRISPR-Cas system regulates Acinetobacter baumannii quorum sensing and has a unique function in changing drug resistance. As a result of quorum sensing, synthase abaI is reduced, allowing efflux pumps to decrease, biofilm formation to become weaker, reactive oxygen species to generate, and drug resistance to decrease in response to CRISPR-Cas activity. These observations suggest that the CRISPR-Cas system targeting endogenous abaI may boost bacterial antibiotic sensitivity. IMPORTANCE CRISPR-Cas systems are vital for genome editing, bacterial virulence, and antibiotic resistance. How CRISPR-Cas systems regulate antibiotic resistance in Acinetobacter baumannii is almost wholly unknown. In this study, we reveal that the quorum sensing regulator abaI mRNA was a primary target of the I-Fb CRISPR-Cas system and the cleavage activity of Cas3 was the most critical factor in regulating abaI mRNA degradation. These results advance our understanding of how CRISPR-Cas systems inhibit drug resistance. However, the mechanism of endogenous targeting of abaI by CRISPR-Cas needs to be further explored.}, }
@article {pmid35938729, year = {2022}, author = {Du, S and Zhang, Y and Shen, JP and Hu, HW and Zhang, J and Shu, C and He, JZ}, title = {Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0052922}, pmid = {35938729}, issn = {2379-5077}, abstract = {Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.}, }
@article {pmid35934149, year = {2022}, author = {Di Pippo, F and Crognale, S and Levantesi, C and Vitanza, L and Sighicelli, M and Pietrelli, L and Di Vito, S and Amalfitano, S and Rossetti, S}, title = {Plastisphere in lake waters: Microbial diversity, biofilm structure, and potential implications for freshwater ecosystems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {310}, number = {}, pages = {119876}, doi = {10.1016/j.envpol.2022.119876}, pmid = {35934149}, issn = {1873-6424}, mesh = {Biofilms ; Eukaryota ; Lakes ; *Microbiota ; *Plastics ; Spectroscopy, Fourier Transform Infrared ; Water ; }, abstract = {Once dispersed in water, microplastic (MP) particles are rapidly colonised by aquatic microbes, which can adhere and grow onto solid surfaces in the form of biofilms. This study provides new insights on microbial diversity and biofilm structure of plastisphere in lake waters. By combining Fourier Confocal Laser Scanning Microscopy (CLSM), Transform Infrared Spectroscopy (FT-IR) and high-throughput DNA sequencing, we investigated the microbial colonization patterns on floating MPs and, for the first time, the occurrence of eukaryotic core members and their possible relations with biofilm-forming bacterial taxa within the plastisphere of four different lakes. Through PCR-based methods (qPCR, LAMP-PCR), we also evaluated the role of lake plastisphere as long-term dispersal vectors of potentially harmful organisms (including pathogens) and antibiotic resistance genes (ARGs) in freshwater ecosystems. Consistent variation patterns of the microbial community composition occurred between water and among the plastisphere samples of the different lakes. The eukaryotic core microbiome was mainly composed by typical freshwater biofilm colonizers, such as diatoms (Pennales, Bacillariophyceaea) and green algae (Chlorophyceae), which interact with eukaryotic and prokaryotic microbes of different trophic levels. Results also showed that MPs are suitable vectors of biofilm-forming opportunistic pathogens and a hotspot for horizontal gene transfer, likely facilitating antibiotic resistance spread in the environments.}, }
@article {pmid35925827, year = {2023}, author = {Kwak, Y and Argandona, JA and Degnan, PH and Hansen, AK}, title = {Chromosomal-level assembly of Bactericera cockerelli reveals rampant gene family expansions impacting genome structure, function and insect-microbe-plant-interactions.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {233-252}, doi = {10.1111/1755-0998.13693}, pmid = {35925827}, issn = {1755-0998}, mesh = {Animals ; *Hemiptera/genetics ; Symbiosis/genetics ; Genome ; Bacteria/genetics ; Chromosomes ; }, abstract = {Lineage specific expansions and gene duplications are some of the most important sources of evolutionary novelty in eukaryotes. Although not as prevalent in eukaryotes compared to bacteria, horizontal gene transfer events can also result in key adaptations for insects, especially for those involved in insect-microbe interactions. In this study we assemble the first chromosomal assembly of the psyllid Bactericera cockerelli and reveal that the B. cockerelli genome has experienced significantly more gene expansion events compared to other Hemipteran representatives with fully sequenced genomes. We also reveal that B. cockerelli's genome is the largest psyllid genome (567 Mb) sequenced to date and is ~15% larger than the other two psyllid species genomes sequenced (Pachypsylla venusta and Diaphorina citri). Structurally, B. cockerelli appears to have an additional chromosome compared to the distantly related psyllid species P. venusta due to a previous chromosomal fission or fusion event. The increase in genome size and dynamic nature of the B. cockerelli genome may largely be contributed to the widespread expansion of type I and II repeat elements that are rampant across all of B. cockerelli's. chromosomes. These repeat elements are distributed near equally in both euchromatic and heterochromatic regions. Furthermore, significant gene family expansions and gene duplications were uncovered for genes that are expected to be important in its adaptation to insect-plant and microbe interactions, which include transcription factors, proteases, odorant receptors, and horizontally transferred genes that are involved in the nutritional symbioses with their long-term nutritional endosymbiont Carsonella.}, }
@article {pmid35919999, year = {2022}, author = {Malaka De Silva, P and Stenhouse, GE and Blackwell, GA and Bengtsson, RJ and Jenkins, C and Hall, JPJ and Baker, KS}, title = {A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1980}, pages = {20220581}, pmid = {35919999}, issn = {1471-2954}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/R020787/1/MRC_/Medical Research Council/United Kingdom ; 106690/A/14/Z/WT_/Wellcome Trust/United Kingdom ; MR/N013840/1/MRC_/Medical Research Council/United Kingdom ; BB/V009184/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Phenotype ; Plasmids ; *Shigella/genetics ; }, abstract = {Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid-associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.}, }
@article {pmid35917316, year = {2022}, author = {Nonaka, L and Masuda, M and Yano, H}, title = {Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271627}, pmid = {35917316}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; Plasmids/genetics ; *Vibrio/genetics ; }, abstract = {The exchange of antimicrobial resistance (AMR) genes between aquaculture and terrestrial microbial populations has emerged as a serious public health concern. However, the nature of the mobile genetic elements in marine bacteria is poorly documented. To gain insight into the genetic mechanisms underlying AMR gene transfer from marine bacteria, we mated a multidrug-resistant Vibrio alfacsensis strain with an Escherichia coli strain, and then determined the complete genome sequences of the donor and the transconjugant strains. Sequence analysis revealed a conjugative multidrug resistance plasmid in the donor strain, which was integrated into the chromosome of the recipient. The plasmid backbone in the transconjugant chromosome was flanked by two copies of a 7.1 kb unclassifiable integrative element harboring a β-lactamase gene. The 7.1 kb element and the previously reported element Tn6283 share four coding sequences, two of which encode the catalytic R-H-R-Y motif of tyrosine recombinases. Polymerase chain reaction and sequencing experiments revealed that these elements generate a circular copy of one specific strand without leaving an empty site on the donor molecule, in contrast to the movement of integron gene cassettes or ICE/IMEs discovered to date. These elements are termed SEs (strand-biased circularizing integrative elements): SE-6945 (the 7.1 kb element) and SE-6283 (Tn6283). The copy number and location of SE-6945 in the chromosome affected the antibiotic resistance levels of the transconjugants. SEs were identified in the genomes of other Vibrio species. Overall, these results suggest that SEs are involved in the spread of AMR genes among marine bacteria.}, }
@article {pmid35916503, year = {2022}, author = {Singh, A and Bansal, K and Kumar, S and Patil, PB}, title = {Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0055022}, pmid = {35916503}, issn = {1098-5336}, mesh = {Genome, Bacterial ; Lipopolysaccharides ; Metagenomics ; *Oryza/microbiology ; Plant Diseases/microbiology ; *Saccharum/genetics ; *Xanthomonas/genetics ; }, abstract = {The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.}, }
@article {pmid35916502, year = {2022}, author = {Liang, J and Liu, J and Wang, X and Sun, H and Zhang, Y and Ju, F and Thompson, F and Zhang, XH}, title = {Genomic Analysis Reveals Adaptation of Vibrio campbellii to the Hadal Ocean.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0057522}, pmid = {35916502}, issn = {1098-5336}, mesh = {Genomics ; Oceans and Seas ; Phylogeny ; *Vibrio/genetics ; Water ; }, abstract = {The genus Vibrio is characterized by high metabolic flexibility and genome plasticity and is widely distributed in the ocean from euphotic layers to deep-sea environments. The relationship between genome features and environmental adaptation strategies of Vibrio has been extensively investigated in coastal environments, yet very little is known about their survival strategies in oligotrophic deep-sea. In this study, we compared genomes of five Vibrio campbellii strains isolated from the Mariana and Yap Trenches at different water depths, including two epipelagic strains and three hadopelagic strains, to identify genomic characteristics that facilitate survival in the deep sea. Genome streamlining is found in pelagic strains, such as smaller genome sizes, lower G+C contents, and higher gene densities, which might be caused by long-term residence in an oligotrophic environment. Phylogenetic results showed that these five Vibrio strains are clustered into two clades according to their collection depth. Indeed, hadopelagic isolates harbor more genes involved in amino acid metabolism and transport, cell wall/membrane/envelope biogenesis, and inorganic ion transport and metabolism through comparative genomics analysis. Specific macrolide export gene and more tellurite resistance genes present in hadopelagic strains by the annotation of antibiotic and metal resistance genes. In addition, several genes related to substrate degradation are enriched in hadopelagic strains, such as chitinase genes, neopullulanase genes, and biopolymer transporter genes. In contrast, epipelagic strains are unique in their capacity for assimilatory nitrate reduction. The genomic characteristics investigated here provide insights into how Vibrio adapts to the deep-sea environment through genomic evolution. IMPORTANCE With the development of deep-sea sampling technology, an increasing number of deep-sea Vibrio strains have been isolated, but the adaptation mechanism of these eutrophic Vibrio strains to the deep-sea environment is unclear. Here, our results show that the genome of pelagic Vibrio is streamlined to adapt to a long-term oligotrophic environment. Through a phylogenomic analysis, we find that genomic changes in marine Vibrio campbellii strains are related to water depth. Our data suggest that an increase in genes related to antibiotic resistance, degradation of macromolecular and refractory substrates, and utilization of rare ions is related to the adaptation of V. campbellii strains to adapt to hadal environments, and most of the increased genes were acquired by horizontal gene transfer. These findings may deepen our understanding of adaptation strategies of marine bacteria to the extreme environment in hadal zones.}, }
@article {pmid35913911, year = {2022}, author = {Ward, LM and Shih, PM}, title = {Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0270187}, pmid = {35913911}, issn = {1932-6203}, mesh = {Carbon Cycle ; *Chlorobi/genetics ; Iron/metabolism ; Oxygen/metabolism ; Photosynthesis ; Phototrophic Processes ; Phylogeny ; }, abstract = {While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, for much of Earth history it is thought that anoxygenic photosynthesis-using compounds like ferrous iron or sulfide as electron donors-drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere during late Archean and early Paleoproterozoic time before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.}, }
@article {pmid35909963, year = {2022}, author = {Soontrapa, P and Jitmuang, A and Ruenchit, P and Tiewcharoen, S and Sarasombath, PT and Rattanabannakit, C}, title = {The First Molecular Genotyping of Naegleria fowleri Causing Primary Amebic Meningoencephalitis in Thailand With Epidemiology and Clinical Case Reviews.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {931546}, pmid = {35909963}, issn = {2235-2988}, mesh = {*Central Nervous System Protozoal Infections/epidemiology ; Genotype ; Humans ; *Naegleria fowleri/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Retrospective Studies ; Thailand/epidemiology ; }, abstract = {Primary amebic meningoencephalitis (PAM) is a rare and fatal central nervous system infection caused by Naegleria fowleri, a free-living amoeba found in the environment. To date, eight pathogenic N. fowleri genotypes have been reported worldwide. We aimed to explore the genotypes of N. fowleri that cause primary amebic meningoencephalitis in Thailand. In 2021, the 17th PAM case was reported, and a retrospective literature search of PAM cases in Thailand from 1982 through April 2021 was performed. Phylogenetic and genotyping analyses of the two mitochondrial (12S rRNA and 16S rRNA) and nuclear (ITS1 and 5.8s rRNA) genes of N. fowleri were performed on four available clinical isolates. Based on the mitochondrial and nuclear genes, N. fowleri genotype T3 was found to cause PAM in three out of four cases. However, disagreement between the genotype based on the mitochondrial and nuclear genes was found in one of the PAM cases, in which the 12S rRNA locus suggested the causative genotype as T1, while the ITS1 implied genotype T4. The discrepancy between the mitochondrial and nuclear genome was previously observed, which suggests the possible horizontal gene transfer among N. fowleri species. Based on the ITS1 gene, two N. fowleri genotypes, T3 and T4, were found to be the genotypes causing PAM in this study. In addition, N. fowleri genotype T2 was previously reported in a traveler who was infected in Thailand. Thus, at least three genotypes (T2, T3, and T4) of N. fowleri are found to be associated with PAM in Thailand.}, }
@article {pmid35909620, year = {2022}, author = {Kasagaki, S and Hashimoto, M and Maeda, S}, title = {Subminimal inhibitory concentrations of ampicillin and mechanical stimuli cooperatively promote cell-to-cell plasmid transformation in Escherichia coli.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100130}, pmid = {35909620}, issn = {2666-5174}, abstract = {Horizontal gene transfer (HGT) is a bacterial evolution tool for improved survival. Although several environmental stimuli induce or promote HGT, the diversity and complexity of the environmental factors have not been sufficiently elucidated. In this study, we showed that the biofilm culture of Escherichia coli at the air-solid interface in the presence of a subminimal inhibitory concentration (sub-MIC) of ampicillin (∼0.5-4 µg/mL) and subsequent mechanical stimulation (rolling small glass balls, ø = 5-8 mm) cooperatively promoted horizontal plasmid transfer without the usual competence-inducing conditions. Either of the two treatments promoted plasmid transfer at a lower frequency than when the treatments were combined. The effect of several parameters on the two treatments was tested and then optimized, achieving a high frequency of plasmid transfer (up to 10[-6] per cell) under optimal conditions. Plasmid transfer was DNase-sensitive for both treatments, demonstrating its mechanism of transformation. Plasmid transfer occurred using various E. coli strains, plasmids, ball materials, shaking conditions, and even the mechanical stimulation of brushing the biofilm with a toothbrush, indicating the conditional flexibility of this phenomenon. This is the first demonstration of the promoting effect of the combination of a sub-MIC antibiotic and mechanical stimulation on horizontal plasmid transfer between E. coli cells via transformation. Regarding environmental bacterial physiology, the aggregations or biofilms of bacterial cells may encounter both sub-MIC antibiotics and mechanical stimuli in some specific environments, therefore, this type of HGT could also occur naturally.}, }
@article {pmid35909010, year = {2022}, author = {Macquet, J and Mounichetty, S and Raffaele, S}, title = {Genetic co-option into plant-filamentous pathogen interactions.}, journal = {Trends in plant science}, volume = {27}, number = {11}, pages = {1144-1158}, doi = {10.1016/j.tplants.2022.06.011}, pmid = {35909010}, issn = {1878-4372}, mesh = {Biological Evolution ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Host-Pathogen Interactions/genetics ; *Plant Diseases/genetics ; *Plants/genetics/metabolism ; Virulence/genetics ; }, abstract = {Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.}, }
@article {pmid35906926, year = {2022}, author = {Leducq, JB and Sneddon, D and Santos, M and Condrain-Morel, D and Bourret, G and Martinez-Gomez, NC and Lee, JA and Foster, JA and Stolyar, S and Shapiro, BJ and Kembel, SW and Sullivan, JM and Marx, CJ}, title = {Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.}, journal = {Genome biology and evolution}, volume = {14}, number = {8}, pages = {}, pmid = {35906926}, issn = {1759-6653}, mesh = {Ecosystem ; *Methylobacterium ; Phylogeny ; Plant Leaves ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.}, }
@article {pmid35904761, year = {2022}, author = {Liu, C and Kenney, T and Beiko, RG and Gu, H}, title = {The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes based on Phylogenetic Profiles.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syac052}, pmid = {35904761}, issn = {1076-836X}, abstract = {Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration. Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes. A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.}, }
@article {pmid35900180, year = {2022}, author = {Galindo, LJ and Torruella, G and López-García, P and Ciobanu, M and Gutiérrez-Preciado, A and Karpov, SA and Moreira, D}, title = {Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syac054}, pmid = {35900180}, issn = {1076-836X}, abstract = {The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the 'Opisthosporidia hypothesis'). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the 'Aphelida+Fungi hypothesis'). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.}, }
@article {pmid35900091, year = {2022}, author = {Hansen, AK and Sanchez, AN and Kwak, Y}, title = {Divergent Host-Microbe Interaction and Pathogenesis Proteins Detected in Recently Identified Liberibacter Species.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0209122}, pmid = {35900091}, issn = {2165-0497}, mesh = {Fimbriae, Bacterial ; Host Microbial Interactions ; *Liberibacter ; Plant Diseases/microbiology ; Plants ; *Rhizobiaceae/genetics ; Sequence Analysis, DNA ; }, abstract = {Candidatus (Ca.) Liberibacter taxa are economically important bacterial plant pathogens that are not culturable; however, genome-enabled insights can help us develop a deeper understanding of their host-microbe interactions and evolution. The draft genome of a recently identified Liberibacter taxa, Ca. Liberibacter capsica, was curated and annotated here with a total draft genome size of 1.1 MB with 1,036 proteins, which is comparable to other Liberibacter species with complete genomes. A total of 459 orthologous clusters were identified among Ca. L. capsica, Ca. L. asiaticus, Ca. L. psyllaurous, Ca. L. americanus, Ca. L. africanus, and L. crescens, and these genes within these clusters consisted of housekeeping and environmental response functions. We estimated the rates of molecular evolution for each of the 443 one-to-one ortholog clusters and found that all Ca. L. capsica orthologous pairs were under purifying selection when the synonymous substitutions per synonymous site (dS) were not saturated. These results suggest that these genes are largely maintaining their conserved functions. We also identified the most divergent single-copy orthologous proteins in Ca. L. capsica by analyzing the ortholog pairs that represented the highest nonsynonymous substitutions per nonsynonymous site (dN) values for each pairwise comparison. From these analyses, we found that 21 proteins which are known to be involved in pathogenesis and host-microbe interactions, including the Tad pilus complex, were consistently divergent between Ca. L. capsica and the majority of other Liberibacter species. These results further our understanding of the evolutionary genetics of Ca. L. capsica and, more broadly, the evolution of Liberibacter. IMPORTANCE "Candidatus" (Ca.) Liberibacter taxa are economically important plant pathogens vectored by insects; however, these host-dependent bacterial taxa are extremely difficult to study because they are unculturable. Recently, we identified a new Ca. Liberibacter lineage (Ca. Liberibacter capsica) from a rare insect metagenomic sample. In this current study, we report that the draft genome of Ca. Liberibacter capsica is similar in genome size and protein content compared to the other Ca. Liberibacter taxa. We provide evidence that many of their shared genes, which encode housekeeping and environmental response functions, are evolving under purifying selection, suggesting that these genes are maintaining similar functions. Our study also identifies 21 proteins that are rapidly evolving amino acid changes in Ca. Liberibacter capsica compared to the majority of other Liberibacter taxa. Many of these proteins represent key genes involved in Liberibacter-host interactions and pathogenesis and are valuable candidate genes for future studies.}, }
@article {pmid35900090, year = {2022}, author = {Li, X and Zhang, J and Yang, C and Li, J and Wang, J and Huang, W and Zeng, L and Liang, X and Long, W and Zhang, X}, title = {Increased Expression and Amplification of blaKPC-2 Contributes to Resistance to Ceftazidime/Avibactam in a Sequence Type 11 Carbapenem-Resistant Klebsiella pneumoniae Strain.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0095522}, pmid = {35900090}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azabicyclo Compounds ; Bacterial Proteins/genetics/metabolism ; Carbapenems/pharmacology/therapeutic use ; *Ceftazidime/pharmacology/therapeutic use ; Humans ; *Klebsiella Infections/drug therapy ; Klebsiella pneumoniae/genetics ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; }, abstract = {Ceftazidime/avibactam (CAZ/AVI) is regarded as an effective alternative antibiotic for the clinical treatment of Klebsiella pneumoniae carbapenemase (KPC)-producing isolates. As resistance has been reported in some strains, it is critical to understand the key mechanisms contributing to the acquired resistance to CAZ/AVI. From January 2018 to April 2020, 127 KPC-producing carbapenem-resistant Klebsiella pneumoniae strains (CRKPs) were isolated at a university hospital in Chongqing, China, and 25 strains showed reduced susceptibility to CAZ/AVI. All reduced-susceptibility CRKPs were deficient in Ompk35 and Ompk36 porins, and 24 strains had a premature termination at amino acid position 63 in Ompk35 and 134 to 135 glycine and aspartic acid (GD) insertion in OmpK36, while the blaKPC-2 expression level showed no significant difference compared to that of strain BAA-1705. Four reduced-susceptibility strains evolved resistance under selective pressure of CAZ/AVI with the blaKPC-2 expression level increased, and two of these strains had mutations in the Ω-loop. The study found a strain of CRKP55 with changes in the resistance phenotype during conjugation, evolving from reduced sensitivity to high-level resistance to CAZ/AVI. Through plasmid sequencing and reverse transcription-quantitative PCR, it was speculated that insertion sequence (IS)26-mediated blaKPC-2 gene amplification caused the MIC value change in the conjugant JKP55. Our findings illustrated the potential of CAZ/AVI resistance under antibiotic stress and demonstrated that IS26 may mediate blaKPC-2 replication transposition, leading to high-level resistance during horizontal gene transfer. Investigation of CAZ/AVI resistance mechanisms may offer a unique opportunity to study the horizontal evolutionary trajectories of K. pneumoniae high-risk clones. IMPORTANCE Klebsiella pneumoniae carbapenemase (KPC) production is the most common mechanism of K. pneumoniae resistance to carbapenems in China. Currently, CAZ/AVI is considered a potential alternative therapeutic option for infections caused by these isolates. However, there have been increasing reports of resistant or reduced-sensitivity strains since the approval of this agent. In this study, resistance to CAZ/AVI was induced under drug-selective pressure and was caused by blaKPC-2 overexpression and/or substitutions in the Ω-loop of KPC. Additionally, it was demonstrated that a conjugative plasmid carrying blaKPC-2 could transfer horizontally between species, and perhaps, IS26-derived tandem amplification of blaKPC-2 during this period led to high-level resistance to CAZ/AVI. Our research suggests that IS26-mediated resistance evolution may have important implications in guiding clinical antibiotic use.}, }
@article {pmid35899254, year = {2022}, author = {Zhang, L and Fu, Y and Zhang, L and Xu, Q and Yang, Y and He, J and Leptihn, S and Loh, B and Moran, RA and van Schaik, W and Toleman, MA and Chen, Q and Liu, L and Yu, Y and Hua, X}, title = {Co-evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase-encoding plasmid during carbapenem exposure.}, journal = {Evolutionary applications}, volume = {15}, number = {7}, pages = {1045-1061}, pmid = {35899254}, issn = {1752-4571}, support = {MR/S013660/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {OXA-23 is the predominant carbapenemase in carbapenem-resistant Acinetobacter baumannii. The co-evolutionary dynamics of A. baumannii and OXA-23-encoding plasmids are poorly understood. Here, we transformed A. baumannii ATCC 17978 with pAZJ221, a bla OXA-23-containing plasmid from clinical A. baumannii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub-inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of bla OXA-23 in pAZJ221, interfering allele dynamics, and chromosomal locus-level parallelism were observed. To characterize genotype-to-phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3' → 5') GMP-metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the effects of these mutations on fitness costs and plasmid kinetics, and the evolved plasmid containing two copies of bla OXA-23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of bla OXA-23 increased host fitness under carbapenem pressure but imposed a burden on the host in antibiotic-free media relative to the ancestral pAZJ221. Overall, our study provides a framework for the co-evolution of A. baumannii and a clinical bla OXA-23-containing plasmid in the presence of imipenem, involving early bla OXA-23 duplication followed by chromosomal adaptations that improved the fitness of plasmid-carrying cells.}, }
@article {pmid35898691, year = {2022}, author = {Tao, S and Chen, H and Li, N and Wang, T and Liang, W}, title = {The Spread of Antibiotic Resistance Genes In Vivo Model.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {3348695}, pmid = {35898691}, issn = {1712-9532}, abstract = {Infections caused by antibiotic-resistant bacteria are a major public health threat. The emergence and spread of antibiotic resistance genes (ARGs) in the environment or clinical setting pose a serious threat to human and animal health worldwide. Horizontal gene transfer (HGT) of ARGs is one of the main reasons for the dissemination of antibiotic resistance in vitro and in vivo environments. There is a consensus on the role of mobile genetic elements (MGEs) in the spread of bacterial resistance. Most drug resistance genes are located on plasmids, and the spread of drug resistance genes among microorganisms through plasmid-mediated conjugation transfer is the most common and effective way for the spread of multidrug resistance. Experimental studies of the processes driving the spread of antibiotic resistance have focused on simple in vitro model systems, but the current in vitro protocols might not correctly reflect the HGT of antibiotic resistance genes in realistic conditions. This calls for better models of how resistance genes transfer and disseminate in vivo. The in vivo model can better mimic the situation that occurs in patients, helping study the situation in more detail. This is crucial to develop innovative strategies to curtail the spread of antibiotic resistance genes in the future. This review aims to give an overview of the mechanisms of the spread of antibiotic resistance genes and then demonstrate the spread of antibiotic resistance genes in the in vivo model. Finally, we discuss the challenges in controlling the spread of antibiotic resistance genes and their potential solutions.}, }
@article {pmid35897639, year = {2022}, author = {Lipszyc, A and Szuplewska, M and Bartosik, D}, title = {How Do Transposable Elements Activate Expression of Transcriptionally Silent Antibiotic Resistance Genes?.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35897639}, issn = {1422-0067}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *DNA Transposable Elements/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Integrons ; }, abstract = {The rapidly emerging phenomenon of antibiotic resistance threatens to substantially reduce the efficacy of available antibacterial therapies. Dissemination of resistance, even between phylogenetically distant bacterial species, is mediated mainly by mobile genetic elements, considered to be natural vectors of horizontal gene transfer. Transposable elements (TEs) play a major role in this process-due to their highly recombinogenic nature they can mobilize adjacent genes and can introduce them into the pool of mobile DNA. Studies investigating this phenomenon usually focus on the genetic load of transposons and the molecular basis of their mobility. However, genes introduced into evolutionarily distant hosts are not necessarily expressed. As a result, bacterial genomes contain a reservoir of transcriptionally silent genetic information that can be activated by various transposon-related recombination events. The TEs themselves along with processes associated with their transposition can introduce promoters into random genomic locations. Thus, similarly to integrons, they have the potential to convert dormant genes into fully functional antibiotic resistance determinants. In this review, we describe the genetic basis of such events and by extension the mechanisms promoting the emergence of new drug-resistant bacterial strains.}, }
@article {pmid35896060, year = {2022}, author = {Macedo, G and Olesen, AK and Maccario, L and Hernandez Leal, L and V D Maas, P and Heederik, D and Mevius, D and Sørensen, SJ and Schmitt, H}, title = {Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {16}, pages = {11398-11408}, pmid = {35896060}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Escherichia coli/genetics ; Gene Transfer, Horizontal ; *Manure/microbiology ; Plasmids/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; }, abstract = {The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10[-5] and 10[-4] transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.}, }
@article {pmid35895240, year = {2022}, author = {Hossain, M and Ibne Momen, AM and Rahman, A and Biswas, J and Yasmin, M and Nessa, J and Ahsan, CR}, title = {Draft-genome analysis provides insights into the virulence properties and genome plasticity of Vibrio fluvialis organisms isolated from shrimp farms and Turag river in Bangladesh.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {527}, pmid = {35895240}, issn = {1432-072X}, mesh = {Aquaculture ; Bangladesh ; Rivers ; Seafood ; *Vibrio/genetics ; *Vibrio cholerae ; Virulence/genetics ; }, abstract = {Vibrio fluvialis is an opportunistic waterborne and seafood-borne enteric pathogen capable of causing severe diarrhea leading to death. This pathogen is endemic to Bangladesh, a country which is a major producer of cultured shrimp and wild-caught prawns. In this study, we carried out whole-genome sequencing of three V. fluvialis organisms isolated from shrimp farm and river sediment showing strong pathogenic characteristics in vivo and in vitro and compared their genomes against other V. fluvialis and related pathogenic species to glean insights into their potential as pathogens. Numerous virulence-associated genes including hemolysins, cytolysins, three separate Type IV pili, Types II and VI secretion systems, biofilm, and the V. cholerae pathogenesis regulating gene, toxR, were identified. Moreover, we found strain S-10 to have the propensity to acquire antibiotic resistance genes through horizontal gene transfer. These findings indicate that shrimp farms and rivers could be potential sources of V. fluvialis organisms which are an infection threat of public health concern.}, }
@article {pmid35890320, year = {2022}, author = {Chen, Q and Dharmaraj, T and Cai, PC and Burgener, EB and Haddock, NL and Spakowitz, AJ and Bollyky, PL}, title = {Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics.}, journal = {Pharmaceutics}, volume = {14}, number = {7}, pages = {}, pmid = {35890320}, issn = {1999-4923}, abstract = {Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.}, }
@article {pmid35889177, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Jacquet, S and Ogorzaly, L}, title = {Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889177}, issn = {2076-2607}, abstract = {Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.}, }
@article {pmid35889093, year = {2022}, author = {Yamamoto, H and Uesaka, K and Tsuzuki, Y and Yamakawa, H and Itoh, S and Fujita, Y}, title = {Comparative Genomic Analysis of the Marine Cyanobacterium Acaryochloris&amp;nbsp;marina MBIC10699 Reveals the Impact of Phycobiliprotein Reacquisition and the Diversity of Acaryochloris Plasmids.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889093}, issn = {2076-2607}, abstract = {Acaryochloris is a marine cyanobacterium that synthesizes chlorophyll d, a unique chlorophyll that absorbs far-red lights. Acaryochloris is also characterized by the loss of phycobiliprotein (PBP), a photosynthetic antenna specific to cyanobacteria; however, only the type-strain A. marina MBIC11017 retains PBP, suggesting that PBP-related genes were reacquired through horizontal gene transfer (HGT). Acaryochloris is thought to have adapted to various environments through its huge genome size and the genes acquired through HGT; however, genomic information on Acaryochloris is limited. In this study, we report the complete genome sequence of A.&amp;nbsp;marina MBIC10699, which was isolated from the same area of ocean as A. marina MBIC11017 as a PBP-less strain. The genome of A.marina MBIC10699 consists of a 6.4 Mb chromosome and four large plasmids totaling about 7.6 Mb, and the phylogenic analysis shows that A.marina MBIC10699 is the most closely related to A. marina MBIC11017 among the Acaryochloris species reported so far. Compared with A. marina MBIC11017, the chromosomal genes are highly conserved between them, while the genes encoded in the plasmids are significantly diverse. Comparing these genomes provides clues as to how the genes for PBPs were reacquired and what changes occurred in the genes for photosystems during evolution.}, }
@article {pmid35889069, year = {2022}, author = {Bukhari, SAR and Irfan, M and Ahmad, I and Chen, L}, title = {Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889069}, issn = {2076-2607}, abstract = {Akkermanisia muciniphila imparts important health benefits and is considered a next-generation probiotic. It is imperative to understand the genomic diversity and metabolic potential of the species for safer applications as probiotics. As it resides with both health-promoting and pathogenic bacteria, understanding the evolutionary patterns are crucial, but this area remains largely unexplored. Moreover, pan-genome has previously been established based on only a limited number of strains and without careful strain selection. The pan-genomics have become very important for understanding species diversity and evolution. In the current study, a systematic approach was used to find a refined pan-genome profile of A. muciniphila by excluding too-diverse strains based on average nucleotide identity-based species demarcation. The strains were divided into four phylogroups using a variety of clustering techniques. Horizontal gene transfer and recombination patterns were also elucidated. Evolutionary patterns revealed that different phylogroups were expanding differently. Furthermore, a comparative evaluation of the metabolic potential of the pan-genome and its subsections was performed. Lastly, the study combines functional annotation, persistent genome, and essential genes to devise an approach to determine a minimal genome that can systematically remove unwanted genes, including virulent factors. The selection of one strain to be used as a chassis for the prediction of a reduced genome was very carefully performed by analyzing several genomic parameters, including the number of unique genes and the resistance and pathogenic potential of the strains. The strategy could be applied to other microbes, including human-associated microbiota, towards a common goal of predicting a minimal or a reduced genome.}, }
@article {pmid35889010, year = {2022}, author = {Levi, G and Lurie-Weinberger, M and Keren-Paz, A and Andremont, AO and Schwartz, D and Carmeli, Y}, title = {Unraveling the Diversity of Co-Colonization by CPE.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889010}, issn = {2076-2607}, abstract = {Antibiotic-resistant bacteria, and more specifically, carbapenem-producing Enterobacterales (CPE) strains, are increasing worldwide. Despite their growing prevalence, in most high-income countries, the detection of CPE is still considered a low-frequency event. Sporadically, patients co-colonized with distinct CPE strains and/or different carbapenemase enzymes are detected. In this paper, we present three cases that illustrate the underlying mechanisms of co-colonization, focusing on horizontal gene transfer (HGT) and patient-to-patient transmission. We also demonstrate the diversity of CPE species and discuss the potential consequences of co-colonization.}, }
@article {pmid35884226, year = {2022}, author = {Costa, M and Meirinhos, C and Cunha, E and Gomes, D and Pereira, M and Dias, R and Tavares, L and Oliveira, M}, title = {Nisin Mutant Prevention Concentration and the Role of Subinhibitory Concentrations on Resistance Development by Diabetic Foot Staphylococci.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884226}, issn = {2079-6382}, abstract = {The most prevalent microorganism in diabetic foot infections (DFI) is Staphylococcus aureus, an important multidrug-resistant pathogen. The antimicrobial peptide nisin is a promising compound for DFI treatment, being effective against S. aureus. However, to avoid the selection of resistant mutants, correct drug therapeutic doses must be established, being also important to understand if nisin subinhibitory concentrations (subMIC) can potentiate resistant genes transfer between clinical isolates or mutations in genes associated with nisin resistance. The mutant selection window (MSW) of nisin was determined for 23 DFI S. aureus isolates; a protocol aiming to prompt vanA horizontal transfer between enterococci to clinical S. aureus was performed; and nisin subMIC effect on resistance evolution was assessed through whole-genome sequencing (WGS) applied to isolates subjected to a MEGA-plate assay. MSW ranged from 5-360 μg/mL for two isolates, from 5-540 μg/mL for three isolates, and from 5-720 μg/mL for one isolate. In the presence of nisin subMIC values, no transconjugants were obtained, indicating that nisin does not seem to promote vanA transfer. Finally, WGS analysis showed that incubation in the presence of nisin subMIC did not promote the occurrence of significant mutations in genes related to nisin resistance, supporting nisin application to DFI treatment.}, }
@article {pmid35884138, year = {2022}, author = {Thacharodi, A and Lamont, IL}, title = {Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884138}, issn = {2079-6382}, abstract = {Aminoglycosides are widely used to treat infections of Pseudomonas aeruginosa. Genes encoding aminoglycoside-modifying enzymes (AMEs), acquired by horizontal gene transfer, are commonly associated with aminoglycoside resistance, but their effects have not been quantified. The aim of this research was to determine the extent to which AMEs increase the antibiotic tolerance of P. aeruginosa. Bioinformatics analysis identified AME-encoding genes in 48 out of 619 clinical isolates of P. aeruginosa, with ant(2')-Ia and aac(6')-Ib3, which are associated with tobramcyin and gentamicin resistance, being the most common. These genes and aph(3')-VIa (amikacin resistance) were deleted from antibiotic-resistant strains. Antibiotic minimum inhibitory concentrations (MICs) were reduced by up to 64-fold, making the mutated bacteria antibiotic-sensitive in several cases. Introduction of the same genes into four antibiotic-susceptible P. aeruginosa strains increased the MIC by up to 128-fold, making the bacteria antibiotic-resistant in all cases. The cloned genes also increased the MIC in mutants lacking the MexXY-OprM efflux pump, which is an important contributor to aminoglycoside resistance, demonstrating that AMEs and this efflux pump act independently in determining levels of aminoglycoside tolerance. Quantification of the effects of AMEs on antibiotic susceptibility demonstrates the large effect that these enzymes have on antibiotic resistance.}, }
@article {pmid35882476, year = {2022}, author = {Deekshit, VK and Srikumar, S}, title = {'To be, or not to be'-The dilemma of 'silent' antimicrobial resistance genes in bacteria.}, journal = {Journal of applied microbiology}, volume = {133}, number = {5}, pages = {2902-2914}, doi = {10.1111/jam.15738}, pmid = {35882476}, issn = {1365-2672}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/metabolism ; Drug Resistance, Bacterial/genetics ; Bacteria/metabolism ; Gene Transfer, Horizontal ; *Bacterial Infections/drug therapy ; }, abstract = {Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harbouring silent antimicrobial resistance genes-genes whose presence is not associated with a corresponding resistant phenotype do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance and mechanism of silent antibiotic resistance genes in bacterial pathogens are very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance and their importance in public health.}, }
@article {pmid35879957, year = {2022}, author = {Nakazato, G and Bello-Toledo, HM and Zhang, A and Stehling, EG}, title = {Editorial: Molecular Characterization of Clinically Important Gram-Negative Bacteria Recovered From the Environment: Antimicrobial Resistance, Virulence and Epidemiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {962840}, doi = {10.3389/fmicb.2022.962840}, pmid = {35879957}, issn = {1664-302X}, }
@article {pmid35879588, year = {2022}, author = {Rahman, Z and Dandekar, MP}, title = {Implication of Paraprobiotics in Age-Associated Gut Dysbiosis and Neurodegenerative Diseases.}, journal = {Neuromolecular medicine}, volume = {}, number = {}, pages = {}, pmid = {35879588}, issn = {1559-1174}, abstract = {Neurodegenerative diseases, including Alzheimer's and Parkinson's disease, are major age-related concerns in elderly people. Since no drug fully addresses the progression of neurodegenerative diseases, advance treatment strategies are urgently needed. Several studies have noted the senescence of immune system and the perturbation of gut microbiota in the aged population. In recent years, the role of gut microbiota has been increasingly studied in the manifestation of age-related CNS disorders. In this context, prebiotics, probiotics, and paraprobiotics are reported to improve the behavioural and neurobiological abnormalities in elderly patients. As live microbiota, prescribed in the form of probiotics, shows some adverse effects like sepsis, translocation, and horizontal gene transfer, paraprobiotics could be a possible alternative strategy in designing microbiome-based therapeutics. This review describes the health-beneficial effects of paraprobiotics in age-associated neurodegenerative diseases.}, }
@article {pmid35877768, year = {2022}, author = {Gibson, PS and Bexkens, E and Zuber, S and Cowley, LA and Veening, JW}, title = {The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci.}, journal = {PLoS pathogens}, volume = {18}, number = {7}, pages = {e1010727}, pmid = {35877768}, issn = {1553-7374}, mesh = {*Amoxicillin/metabolism/pharmacology ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacterial Proteins/genetics/metabolism ; Gene Transfer, Horizontal ; Humans ; Microbial Sensitivity Tests ; Penicillin Resistance/genetics ; Penicillin-Binding Proteins/genetics ; *Streptococcus pneumoniae/metabolism ; }, abstract = {Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.}, }
@article {pmid35876510, year = {2022}, author = {Nusrin, S and Asad, A and Hayat, S and Islam, B and Begum, R and Nabila, FH and Islam, Z}, title = {Multiple Mechanisms Confer Resistance to Azithromycin in Shigella in Bangladesh: a Comprehensive Whole Genome-Based Approach.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0074122}, pmid = {35876510}, issn = {2165-0497}, support = {K43 TW011447/TW/FIC NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Azithromycin/pharmacology ; Bangladesh ; Drug Resistance, Bacterial/genetics ; *Dysentery, Bacillary/drug therapy ; Humans ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; *Shigella/genetics ; }, abstract = {Shigella is the second leading cause of diarrheal deaths worldwide. Azithromycin (AZM) is a potential treatment option for Shigella infection; however, the recent emergence of AZM resistance in Shigella threatens the current treatment strategy. Therefore, we conducted a comprehensive whole genome-based approach to identify the mechanism(s) of AZM resistance in Shigella. We performed antimicrobial susceptibility tests, polymerase chain reaction (PCR), Sanger (amplicon) sequencing, and whole genome-based bioinformatics approaches to conduct the study. Fifty-seven (38%) of the Shigella isolates examined were AZM resistant; Shigella sonnei exhibited the highest rate of resistance against AZM (80%). PCR amplification for 15 macrolide resistance genes (MRGs) followed by whole-genome analysis of 13 representative Shigella isolates identified two AZM-modifying genes, mph(A) (in all Shigella isolates resistant to AZM) and mph(E) (in 2 AZM-resistant Shigella isolates), as well as one 23S rRNA-methylating gene, erm(B) (41% of AZM-resistant Shigella isolates) and one efflux pump mediator gene, msr(E) [in the same two Shigella isolates that harbored the mph(E) gene]. This is the first report of msr(E) and mph(E) genes in Shigella. Moreover, we found that an IncFII-type plasmid predominates and can possess all four MRGs. We also detected two plasmid-borne resistance gene clusters: IS26-mph(A)-mrx(A)-mph(R)(A)-IS6100, which is linked to global dissemination of MRGs, and mph(E)-msr(E)-IS482-IS6, which is reported for the first time in Shigella. In conclusion, this study demonstrates that MRGs in association with pathogenic IS6 family insertion sequences generate resistance gene clusters that propagate through horizontal gene transfer (HGT) in Shigella. IMPORTANCE Shigella can frequently transform into a superbug due to uncontrolled and rogue administration of antibiotics and the emergence of HGT of antimicrobial resistance factors. The advent of AZM resistance in Shigella has become a serious concern in the treatment of shigellosis. However, there is an obvious scarcity of clinical data and research on genetic mechanisms that induce AZM resistance in Shigella, particularly in low- and middle-income countries. Therefore, this study is an approach to raise the alarm for the next lifeline. We show that two key MRGs [mph(A) and erm(B)] and the newly identified MRGs [mph(E) and msr(E)], with their origination in plasmid-borne pathogenic islands, are fundamental mechanisms of AZM resistance in Shigella in Bangladesh. Overall, this study predicts an abrupt decrease in the effectiveness of AZM against Shigella in the very near future and suggests prompt focus on seeking a more effective treatment alternative to AZM for shigellosis.}, }
@article {pmid35876475, year = {2022}, author = {Yong, M and Chen, Y and Oo, G and Chang, KC and Chu, WHW and Teo, J and Venkatachalam, I and Thevasagayam, NM and Sridatta, PSR and Koh, V and Marcoleta, AE and Chen, H and Nagarajan, N and Kalisvar, M and Ng, OT and Gan, YH}, title = {Dominant Carbapenemase-Encoding Plasmids in Clinical Enterobacterales Isolates and Hypervirulent Klebsiella pneumoniae, Singapore.}, journal = {Emerging infectious diseases}, volume = {28}, number = {8}, pages = {1578-1588}, pmid = {35876475}, issn = {1080-6059}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins/genetics ; Humans ; *Klebsiella Infections/epidemiology/microbiology ; *Klebsiella pneumoniae ; Plasmids/genetics ; Singapore/epidemiology ; beta-Lactamases/genetics ; }, abstract = {Dissemination of carbapenemase-encoding plasmids by horizontal gene transfer in multidrug-resistant bacteria is the major driver of rising carbapenem-resistance, but the conjugative mechanics and evolution of clinically relevant plasmids are not yet clear. We performed whole-genome sequencing on 1,215 clinical Enterobacterales isolates collected in Singapore during 2010-2015. We identified 1,126 carbapenemase-encoding plasmids and discovered pKPC2 is becoming the dominant plasmid in Singapore, overtaking an earlier dominant plasmid, pNDM1. pKPC2 frequently conjugates with many Enterobacterales species, including hypervirulent Klebsiella pneumoniae, and maintains stability in vitro without selection pressure and minimal adaptive sequence changes. Furthermore, capsule and decreasing taxonomic relatedness between donor and recipient pairs are greater conjugation barriers for pNDM1 than pKPC2. The low fitness costs pKPC2 exerts in Enterobacterales species indicate previously undetected carriage selection in other ecological settings. The ease of conjugation and stability of pKPC2 in hypervirulent K. pneumoniae could fuel spread into the community.}, }
@article {pmid35870604, year = {2022}, author = {Darphorn, TS and Brul, S and Ter Kuile, BH}, title = {Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer.}, journal = {Plasmid}, volume = {122}, number = {}, pages = {102640}, doi = {10.1016/j.plasmid.2022.102640}, pmid = {35870604}, issn = {1095-9890}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; *Escherichia coli/genetics ; *Escherichia coli Infections ; Gene Transfer, Horizontal ; Humans ; Meat ; Plasmids/genetics ; }, abstract = {Resistance plasmids mediate the rapid spread of antimicrobial resistance, which poses a threat to veterinary and human healthcare. This study addresses the question whether resistance plasmids from Escherichia coli isolated from foodstuffs always transfer unchanged to recipient E. coli cells, or that genetic editing can occur. Strains containing between one and five different plasmids were co-incubated with a standard recipient strain. Plasmids isolated from transconjugant strains were sequenced using short and long read technologies and compared to the original plasmids from the donor strains. After one hour of co-incubation only a single plasmid was transferred from donor to recipient strains. If the donor possessed several plasmids, longer co-incubation resulted in multiple plasmids being transferred. Transferred plasmids showed mutations, mostly in mobile genetic elements, in the conjugative transfer gene pilV and in genes involved in plasmid maintenance. In one transconjugant, a resistance cluster encoding tetracycline resistance was acquired by the IncI1 plasmid from the IncX1 plasmid that was also present in the donor strain, but that was not transferred. A single plasmid transferred twelve times back and forth between E. coli strains resulted in a fully conserved plasmid with no mutations, apart from repetitive rearrangements of pilV from and back to its original conformation in the donor strain. The overall outcome suggests that some genetic mutations and rearrangements can occur during plasmid transfer. The possibility of such mutations should be taken into consideration in epidemiological research aimed at attribution of resistance to specific sources.}, }
@article {pmid35865929, year = {2022}, author = {Li, Y and Wang, Y and Liu, J}, title = {Genomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {939406}, pmid = {35865929}, issn = {1664-302X}, abstract = {Bacterial vaginosis (BV) is a common vaginal infection and has been associated with increased risk for a wide array of health issues. BV is linked with a variety of heterogeneous pathogenic anaerobic bacteria, among which Mobiluncus is strongly associated with BV diagnosis. However, their genetic features, pathogenicity, interspecific diversity, and evolutionary characters have not been illustrated at genomic level. The current study performed phylogenomic and comparative genomic analyses of Mobiluncus. Phylogenomic analyses revealed remarkable phylogenetic distinctions among different species. Compared with M. curtisii, M. mulieris had a larger genome and pangenome size with more insertion sequences but less CRISPR-Cas systems. In addition, these two species were diverse in profile of virulence factors, but harbored similar antibiotic resistance genes. Statistically different functional genome profiles between strains from the two species were determined, as well as correlations of some functional genes/pathways with putative pathogenicity. We also showed that high levels of horizontal gene transfer might be an important strategy for species diversification and pathogenicity. Collectively, this study provides the first genome sequence level description of Mobiluncus, and may shed light on its virulence/pathogenicity, functional diversification, and evolutionary dynamics. Our study could facilitate the further investigations of this important pathogen, and might improve the future treatment of BV.}, }
@article {pmid35862819, year = {2022}, author = {Nies, F and Springstein, BL and Hanke, DM and Dagan, T}, title = {Natural Competence in the Filamentous, Heterocystous Cyanobacterium Chlorogloeopsis fritschii PCC 6912.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0099721}, pmid = {35862819}, issn = {2379-5042}, mesh = {*Cyanobacteria/genetics/metabolism ; Gene Transfer, Horizontal ; Photosynthesis ; }, abstract = {Lateral gene transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA transfer via natural transformation depends on the ability of recipient cells to actively transport DNA from the environment into the cytoplasm, termed natural competence, which relies on the presence of type IV pili and other competence proteins. Natural competence has been described in cyanobacteria for several organisms, including unicellular and filamentous species. However, natural competence in cyanobacteria that differentiate specialized cells for N2-fixation (heterocysts) and form branching or multiseriate cell filaments (termed subsection V) remains unknown. Here, we show that genes essential for natural competence are conserved in subsection V cyanobacteria. Furthermore, using the replicating plasmid pRL25C, we experimentally demonstrate natural competence in a subsection V organism: Chlorogloeopsis fritschii PCC 6912. Our results suggest that natural competence is a common trait in cyanobacteria forming complex cell filament morphologies. IMPORTANCE Cyanobacteria are crucial players in the global biogeochemical cycles, where they contribute to CO2- and N2-fixation. Their main ecological significance is the primary biomass production owing to oxygenic photosynthesis. Cyanobacteria are a diverse phylum, in which the most complex species differentiate specialized cell types and form true-branching or multiseriate cell filament structures (termed subsection V cyanobacteria). These bacteria are considered a peak in the evolution of prokaryotic multicellularity. Among others, species in that group inhabit fresh and marine water habitats, soil, and extreme habitats such as thermal springs. Here, we show that the core genes required for natural competence are frequent in subsection V cyanobacteria and demonstrate for the first time natural transformation in a member of subsection V. The prevalence of natural competence has implications for the role of DNA acquisition in the genome evolution of cyanobacteria. Furthermore, the presence of mechanisms for natural transformation opens up new possibilities for the genetic modification of subsection V cyanobacteria.}, }
@article {pmid35862683, year = {2022}, author = {Baseggio, L and Silayeva, O and Engelstädter, J and Barnes, AC}, title = {The Evolution of a Specialized, Highly Virulent Fish Pathogen through Gene Loss and Acquisition of Host-Specific Survival Mechanisms.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0022222}, pmid = {35862683}, issn = {1098-5336}, mesh = {Animals ; *Fish Diseases/microbiology ; Fishes/microbiology ; *Gram-Negative Bacterial Infections/microbiology ; Photobacterium/metabolism ; Phylogeny ; }, abstract = {Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. piscicida, that contrast remarkably despite their taxonomic relationship. The former is opportunistic and free-living but can cause disease in compromised individuals from a broad diversity of taxa, while the latter is a highly specialized, primary fish pathogen. Here, we employ new closed curated genome assemblies from Australia to estimate the global phylogenetic structure of the species P. damselae. We identify genes responsible for the shift from an opportunist to a host-adapted fish pathogen, potentially via an arthropod vector as fish-to-fish transmission was not achieved in repeated cohabitation challenges despite high virulence for Seriola lalandi. Acquisition of ShdA adhesin and of thiol peroxidase may have allowed the environmental, generalist ancestor to colonize zooplankton and to occasionally enter in fish host sentinel cells. As dependence on the host has increased, P. damselae has lost nonessential genes, such as those related to nitrite and sulfite reduction, urea degradation, a type 6 secretion system (T6SS) and several toxin-antitoxin (TA) systems. Similar to the evolution of Yersinia pestis, the loss of urease may be the crucial event that allowed the pathogen to stably colonize zooplankton vectors. Acquisition of host-specific genes, such as those required to form a sialic acid capsule, was likely necessary for the emergent P. damselae subsp. piscicida to become a highly specialized, facultative intracellular fish pathogen. Processes that have shaped P. damselae subsp. piscicida from subsp. damselae are similar to those underlying evolution of Yersinia pestis from Y. pseudotuberculosis. IMPORTANCE Photobacterium damselae subsp. damselae is a ubiquitous marine bacterium and opportunistic pathogen of compromised hosts of diverse taxa. In contrast, its sister subspecies P. damselae subsp. piscicida (Pdp) is highly virulent in fish. Pdp has evolved from a single subclade of Pdd through gene loss and acquisition. We show that fish-to-fish transmission does not occur in repeated infection models in the primary host, Seriola lalandi, and present genomic evidence for vector-borne transmission, potentially via zooplankton. The broad genomic changes from generalist Pdd to specialist Pdp parallel those of the environmental opportunist Yersinia pseudotuberculosis to vector-borne plague bacterium Y. pestis and demonstrate that evolutionary processes in bacterial pathogens are universal between the terrestrial and marine biosphere.}, }
@article {pmid35861439, year = {2022}, author = {Zangishei, Z and Annacondia, ML and Gundlach, H and Didriksen, A and Bruckmüller, J and Salari, H and Krause, K and Martinez, G}, title = {Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.}, journal = {Plant physiology}, volume = {190}, number = {2}, pages = {1242-1259}, pmid = {35861439}, issn = {1532-2548}, mesh = {Animals ; *Cuscuta/genetics ; *MicroRNAs/genetics ; *Orobanche/genetics ; *Parasites ; RNA, Plant/genetics ; }, abstract = {Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.}, }
@article {pmid35858561, year = {2022}, author = {Douanne, N and Dong, G and Amin, A and Bernardo, L and Blanchette, M and Langlais, D and Olivier, M and Fernandez-Prada, C}, title = {Leishmania parasites exchange drug-resistance genes through extracellular vesicles.}, journal = {Cell reports}, volume = {40}, number = {3}, pages = {111121}, doi = {10.1016/j.celrep.2022.111121}, pmid = {35858561}, issn = {2211-1247}, support = {173450//CIHR/Canada ; 168959//CIHR/Canada ; }, mesh = {Animals ; Drug Resistance/genetics ; Eukaryota ; *Extracellular Vesicles/metabolism ; *Leishmania/genetics/metabolism ; *Parasites ; }, abstract = {Leishmania are eukaryotic parasites that have retained the ability to produce extracellular vesicles (EVs) through evolution. To date, it has been unclear if different DNA entities could be associated with Leishmania EVs and whether these could constitute a mechanism of horizontal gene transfer (HGT). Herein, we investigate the DNA content of EVs derived from drug-resistant parasites, as well as the EVs' potential to act as shuttles for DNA transfer. Next-generation sequencing and PCR assays confirm the enrichment of amplicons carrying drug-resistance genes associated with EVs. Transfer assays of drug-resistant EVs highlight a significant impact on the phenotype of recipient parasites induced by the expression of the transferred DNA. Recipient parasites display an enhanced growth and better control of oxidative stress. We provide evidence that eukaryotic EVs function as efficient mediators in HGT, thereby facilitating the transmission of drug-resistance genes and increasing the fitness of cells when encountering stressful environments.}, }
@article {pmid35856561, year = {2022}, author = {Munke, A and Kimura, K and Tomaru, Y and Wang, H and Yoshida, K and Mito, S and Hongo, Y and Okamoto, K}, title = {Primordial Capsid and Spooled ssDNA Genome Structures Unravel Ancestral Events of Eukaryotic Viruses.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0015622}, pmid = {35856561}, issn = {2150-7511}, mesh = {*Capsid/metabolism ; Capsid Proteins/genetics/metabolism ; Cryoelectron Microscopy ; DNA Viruses/genetics ; DNA, Single-Stranded/genetics ; Ecosystem ; Eukaryota/genetics ; Genome, Viral ; Phylogeny ; *Viruses/genetics ; }, abstract = {Marine algae viruses are important for controlling microorganism communities in the marine ecosystem and played fundamental roles during the early events of viral evolution. Here, we have focused on one major group of marine algae viruses, the single-stranded DNA (ssDNA) viruses from the Bacilladnaviridae family. We present the capsid structure of the bacilladnavirus Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II), determined at 2.4-Å resolution. A structure-based phylogenetic analysis supported the previous theory that bacilladnaviruses have acquired their capsid protein via horizontal gene transfer from a ssRNA virus. The capsid protein contains the widespread virus jelly-roll fold but has additional unique features; a third β-sheet and a long C-terminal tail. Furthermore, a low-resolution reconstruction of the CtenDNAV-II genome revealed a partially spooled structure, an arrangement previously only described for dsRNA and dsDNA viruses. Together, these results exemplify the importance of genetic recombination for the emergence and evolution of ssDNA viruses and provide important insights into the underlying mechanisms that dictate genome organization. IMPORTANCE Single-stranded DNA (ssDNA) viruses are an extremely widespread group of viruses that infect diverse hosts from all three domains of life, consequently having great economic, medical, and ecological importance. In particular, bacilladnaviruses are highly abundant in marine sediments and greatly influence the dynamic appearance and disappearance of certain algae species. Despite the importance of ssDNA viruses and the last couple of years' advancements in cryo-electron microscopy, structural information on the genomes of ssDNA viruses remains limited. This paper describes two important achievements: (i) the first atomic structure of a bacilladnavirus capsid, which revealed that the capsid protein gene presumably was acquired from a ssRNA virus in early evolutionary events; and (ii) the structural organization of a ssDNA genome, which retains a spooled arrangement that previously only been observed for double-stranded viruses.}, }
@article {pmid35854227, year = {2022}, author = {Athanasouli, M and Rödelsperger, C}, title = {Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {523}, pmid = {35854227}, issn = {1471-2164}, mesh = {Animals ; *DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genomics ; Retroelements/genetics ; *Rhabditida/genetics ; }, abstract = {BACKGROUND: Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reservoir for molecular innovation. In this study, we aim to add repetitive elements to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation.<br><br>RESULTS: Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences. While retroelements are more frequently found at the chromosome arms, DNA transposons are distributed more evenly. We found multiple DNA transposons, as well as LTR and LINE elements with abundant evidence of expression as single-exon transcripts. When testing whether transposons disproportionately contribute towards new gene formation, we found that roughly 10-20% of genes across all age classes overlap transposable elements with the strongest trend being an enrichment of low complexity regions among the oldest genes. Finally, we characterized a horizontal gene transfer of Zisupton elements into diplogastrid nematodes. These DNA transposons invaded nematodes from eukaryotic donor species and experienced a recent burst of activity in the P. pacificus lineage.<br><br>CONCLUSIONS: The comprehensive annotation of repetitive elements in the P. pacificus genome builds a resource for future functional genomic analyses as well as for more detailed investigations of molecular innovations.}, }
@article {pmid35853593, year = {2022}, author = {Lu, T and Zhang, J and Su, T and Liang, X and Wei, Y and He, T}, title = {Coupled mechanism of enhanced and inhibitory effects of nanoscale zero-valent iron on methane production and antibiotic resistance genes in anaerobic digestion of swine manure.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127635}, doi = {10.1016/j.biortech.2022.127635}, pmid = {35853593}, issn = {1873-2976}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Iron/pharmacology ; *Manure ; Methane ; Swine ; }, abstract = {In this study, the turning point for nanoscale zero-valent iron's (NZVI) promotion and inhibition effects of methane production coupled with the reduction of antibiotic resistance genes (ARGs) was investigated. Adding 150 mmol/L NZVI increased methane production by maximum of 23.8 %, which was due to the chemical reaction producing H2 and enhancement of direct interspecies electron transfer (DIET) by NZVI. NZVI350 dramatically repressed methane generation by 48.0 %, which might be associated with the large quantity of reactive oxygen species (ROS) and excessive H2 inhibiting the functioning of microorganisms. The fate of ARGs was significantly related to daily methane production, indicating that the more methane production finally generated, the less the abundance of ARGs at last left. The reduction of ARGs was enhanced by maximum of 61.0 %, which was attributed to the inhibition of vertical gene transfer (VGT) and horizontal gene transfer (HGT) caused by steric hindrance associated with NZVI corrosion.}, }
@article {pmid35853453, year = {2022}, author = {Li, Y and Liu, Z and Liu, C and Shi, Z and Pang, L and Chen, C and Chen, Y and Pan, R and Zhou, W and Chen, XX and Rokas, A and Huang, J and Shen, XX}, title = {HGT is widespread in insects and contributes to male courtship in lepidopterans.}, journal = {Cell}, volume = {185}, number = {16}, pages = {2975-2987.e10}, pmid = {35853453}, issn = {1097-4172}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; R56 AI146096/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Butterflies/genetics ; Courtship ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Male ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and eukaryotic genomes. HGT-acquired genes have been sporadically reported in insects, a lineage containing >50% of animals. We systematically examined HGT in 218 high-quality genomes of diverse insects and found that they acquired 1,410 genes exhibiting diverse functions, including many not previously reported, via 741 distinct transfers from non-metazoan donors. Lepidopterans had the highest average number of HGT-acquired genes. HGT-acquired genes containing introns exhibited substantially higher expression levels than genes lacking introns, suggesting that intron gains were likely involved in HGT adaptation. Lastly, we used the CRISPR-Cas9 system to edit the prevalent unreported gene LOC105383139, which was transferred into the last common ancestor of moths and butterflies. In diamondback moths, males lacking LOC105383139 courted females significantly less. We conclude that HGT has been a major contributor to insect adaptation.}, }
@article {pmid35853206, year = {2022}, author = {Chowdhury, NN and Hicks, E and Wiesner, MR}, title = {Investigating and Modeling the Regulation of Extracellular Antibiotic Resistance Gene Bioavailability by Naturally Occurring Nanoparticles.}, journal = {Environmental science &amp; technology}, volume = {56}, number = {21}, pages = {15044-15053}, doi = {10.1021/acs.est.2c02878}, pmid = {35853206}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Biological Availability ; Drug Resistance, Microbial/genetics ; Bacteria ; *Nanoparticles ; Deoxyribonuclease I ; }, abstract = {Extracellular antibiotic resistance genes (eARGs) are widespread in the environment and can genetically transform bacteria. This work examined the role of environmentally relevant nanoparticles (NPs) in regulating eARG bioavailability. eARGs extracted from antibiotic-resistant B. subtilis were incubated with nonresistant recipient B. subtilis cells. In the mixture, particle type (either humic acid coated nanoparticles (HASNPs) or their micron-sized counterpart (HASPs)), DNase I concentration, and eARG type were systematically varied. Transformants were counted on selective media. Particles decreased bacterial growth and eARG bioavailability in systems without nuclease. When DNase I was present (≥5 μg/mL), particles increased transformation via chromosomal (but not plasmid-borne) eARGs. HASNPs increased transformation more than HASPs, indicating that the smaller nanoparticle with greater surface area per volume is more effective in increasing eARG bioavailability. These results were also modeled via particle aggregation theory, which represented eARG-bacteria interactions as transport leading to collision, followed by attachment. Using attachment efficiency as a fitting factor, the model predicted transformant concentrations within 35% of experimental data. These results confirm the ability of NPs to increase eARG bioavailability and suggest that particle aggregation theory may be a simplified and suitable framework to broadly predict eARG uptake.}, }
@article {pmid35849537, year = {2022}, author = {Dimitriu, T}, title = {Evolution of horizontal transmission in antimicrobial resistance plasmids.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001214}, pmid = {35849537}, issn = {1465-2080}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; *Gene Transfer, Horizontal ; Plasmids/genetics ; }, abstract = {Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.}, }
@article {pmid35849532, year = {2022}, author = {Zaayman, M and Wheatley, RM}, title = {Fitness costs of CRISPR-Cas systems in bacteria.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001209}, pmid = {35849532}, issn = {1465-2080}, mesh = {*Bacteria/genetics ; *CRISPR-Cas Systems ; Genome, Bacterial/genetics ; }, abstract = {CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.}, }
@article {pmid35849337, year = {2022}, author = {Laroussi, H and Aoudache, Y and Robert, E and Libante, V and Thiriet, L and Mias-Lucquin, D and Douzi, B and Roussel, Y and Chauvot de Beauchêne, I and Soler, N and Leblond-Bourget, N}, title = {Exploration of DNA processing features unravels novel properties of ICE conjugation in Gram-positive bacteria.}, journal = {Nucleic acids research}, volume = {50}, number = {14}, pages = {8127-8142}, pmid = {35849337}, issn = {1362-4962}, mesh = {*Bacterial Proteins/genetics/metabolism ; Binding Sites ; *Conjugation, Genetic ; *DNA Nucleotidyltransferases/genetics/metabolism ; DNA, Bacterial/genetics ; Gene Transfer, Horizontal ; *Gram-Positive Bacteria/genetics ; *Interspersed Repetitive Sequences ; Plasmids/genetics ; }, abstract = {Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 superfamily, which is widespread among Firmicutes, encodes uncanonical relaxases belonging to a recently identified family called MOBT. This family is related to the rolling circle replication initiators of the Rep_trans family. The nic site of these MOBT relaxases is conserved but their DNA binding site is still unknown. Here, we identified the bind site of RelSt3, the MOBT relaxase from ICESt3. Unexpectedly, we found this bind site distantly located from the nic site. We revealed that the binding of the RelSt3 N-terminal HTH domain is required for efficient nicking activity. We also deciphered the role of RelSt3 in the initial and final stages of DNA processing during conjugation. Especially, we demonstrated a strand transfer activity, and the formation of covalent DNA-relaxase intermediate for a MOBT relaxase.}, }
@article {pmid35847067, year = {2022}, author = {Ott, LC and Mellata, M}, title = {Models for Gut-Mediated Horizontal Gene Transfer by Bacterial Plasmid Conjugation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891548}, pmid = {35847067}, issn = {1664-302X}, abstract = {The emergence of new antimicrobial resistant and virulent bacterial strains may pose a threat to human and animal health. Bacterial plasmid conjugation is a significant contributor to rapid microbial evolutions that results in the emergence and spread of antimicrobial resistance (AR). The gut of animals is believed to be a potent reservoir for the spread of AR and virulence genes through the horizontal exchange of mobile genetic elements such as plasmids. The study of the plasmid transfer process in the complex gut environment is limited due to the confounding factors that affect colonization, persistence, and plasmid conjugation. Furthermore, study of plasmid transfer in the gut of humans is limited to observational studies, leading to the need to identify alternate models that provide insight into the factors regulating conjugation in the gut. This review discusses key studies on the current models for in silico, in vitro, and in vivo modeling of bacterial conjugation, and their ability to reflect the gut of animals. We particularly emphasize the use of computational and in vitro models that may approximate aspects of the gut, as well as animal models that represent in vivo conditions to a greater extent. Directions on future research studies in the field are provided.}, }
@article {pmid35841879, year = {2022}, author = {Gonçalves, P and Gonçalves, C}, title = {Horizontal gene transfer in yeasts.}, journal = {Current opinion in genetics &amp; development}, volume = {76}, number = {}, pages = {101950}, doi = {10.1016/j.gde.2022.101950}, pmid = {35841879}, issn = {1879-0380}, mesh = {*Bacteria/genetics ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; }, abstract = {Horizontal gene transfer (HGT), defined as the exchange of genetic material other than from parent to progeny, is very common in bacteria and appears to constitute the most important mechanism contributing to enlarge a species gene pool. However, in eukaryotes, HGT is certainly much less common and some early insufficiently consubstantiated cases involving bacterial donors led some to consider that it was unlikely to occur in eukaryotes outside the host/endosymbiont relationship. More recently, plenty of reports of interdomain HGT have seen the light based on the strictest criteria, many concerning filamentous fungi and yeasts. Here, we attempt to summarize the most prominent instances of HGT reported in yeasts as well as what we have been able to learn so far concerning frequency and distribution, mechanisms, barriers, function of horizontally acquired genes, and the role of HGT in domestication.}, }
@article {pmid35841790, year = {2022}, author = {Ji, H and Cai, Y and Wang, Z and Li, G and An, T}, title = {Sub-lethal photocatalysis promotes horizontal transfer of antibiotic resistance genes by conjugation and transformability.}, journal = {Water research}, volume = {221}, number = {}, pages = {118808}, doi = {10.1016/j.watres.2022.118808}, pmid = {35841790}, issn = {1879-2448}, mesh = {*Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Water ; }, abstract = {The spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in water is increasingly becoming a worldwide problem due to frequent recent major public health events. Herein, the horizontal ARG transfer mechanisms were studied under sub-lethal photocatalysis. The results show that ARGs had at most a 3- to 6-fold increase in the conjugative transfer frequency when only donor bacteria were induced with sub-lethal photocatalysis, while the frequency exhibited a trend toward inhibition when only the recipient bacteria were induced. However, when the donor or recipient bacteria were induced beforehand for a specific time, the frequency increased by a maximum of 10- to 22-fold. Moreover, the horizontal transfer frequency and its mechanism were related to the oxidative stress systems, ATP systems and the expression of related genes. Furthermore, the transformability of extracellular plasmids of the ARB and the contribution in horizontal transfer were also studied. Results show that the transformation frequency accounted for up to 50% of the total number of transconjugants, indicating that transformation might be a primary mode of horizontal ARG transfer by ARB in water. All of the above results demonstrate that sub-lethal photocatalysis will increase the frequency of horizontal gene transfer of ARGs through both conjugative transfer and the transformation pathway, which increases the risk of ARB in aquatic environments.}, }
@article {pmid35841431, year = {2022}, author = {Mitra, A and Acharya, K and Bhattacharya, A}, title = {Evolutionary analysis of globin domains from kinetoplastids.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {493}, pmid = {35841431}, issn = {1432-072X}, mesh = {Amino Acid Sequence ; Codon ; *Gene Transfer, Horizontal ; *Globins/chemistry/genetics/metabolism ; Heme/chemistry/metabolism ; Phylogeny ; }, abstract = {Globin (Gb) domains function in sensing gaseous ligands like oxygen and nitric oxide. In recent years, Gb domain containing heme binding adenylate cyclases (OsAC or GbAC) emerged as significant modulator of Leishmania response to hypoxia and oxidative stress. During progression of life cycle stages, kinetoplastids experience altered condition in insect vectors or other hosts. Moreover, marked diversity in life style has been accounted among kinetoplastids. Distribution and abundance of Gb-domains vary between different groups of kinetoplastids. While in bodonoids, Gbs are not combined with any other functional domains, in trypanosomatids it is either fused with adenylate cyclase (AC) or oxidoreductase (OxR) domains. In salivarian trypanosomatids and Leishmania (Viannia) subtypes, no gene product featuring Gbs can be identified. In this context, evolution of Gb-domains in kinetoplastids was explored. GbOxR derived Gbs clustered with bacterial flavohemoglobins (fHb) including one fHb from Advenella, an endosymbiont of monoxeneous trypanosomatids. Codon adaptation and other evolutionary analysis suggested that OsAC (LmjF.28.0090), the solitary Gb-domain featuring gene product in Leishmania, was acquired via possible horizontal gene transfer. Substantial functional divergence was estimated between orthologues of genes encoding GbAC or GbOxR; an observation also reflected in structural alignment and heme-binding residue predictions. Orthologue-paralogue and synteny analysis indicated genomic reduction in GbOxR and GbAC loci for dixeneous trypanosomatids.}, }
@article {pmid35833268, year = {2022}, author = {Chouhan, B and Tak, N and Bissa, G and Adhikari, D and Barik, SK and Sprent, JI and James, EK and Jha, S and Gehlot, HS}, title = {Evolution of novel strains of Ensifer nodulating the invasive legume Leucaena leucocephala (Lam.) de Wit in different climatic regions of India through lateral gene transfer.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {9}, pages = {}, doi = {10.1093/femsec/fiac086}, pmid = {35833268}, issn = {1574-6941}, mesh = {DNA, Bacterial ; *Fabaceae ; Gene Transfer, Horizontal ; *Mesorhizobium ; Phylogeny ; RNA, Ribosomal, 16S ; *Rhizobiaceae ; *Rhizobium ; Root Nodules, Plant ; Soil ; Symbiosis ; }, abstract = {More than 200 root-nodule bacterial strains were isolated from Leucaena leucocephala growing at 42 sampling sites across 12 states and three union territories of India. Genetic diversity was observed among 114 strains from various climatic zones; based on recA, these were identified as strains of Ensifer, Mesorhizobium, Rhizobium, and Bradyrhizobium. In multilocus sequence analysis (MLSA) strains clustered into several novel clades and lineages. Ensifer were predominant nodulating genotype isolated from majority of alkaline soils, while Mesorhizobium and Rhizobium strains were isolated from a limited sampling in North-Eastern states with acidic soils. Positive nodulation assays of selected Ensifer representing different genetic combinations of housekeeping and sym genes suggested their broad host range within the closely related mimosoid genera Vachellia, Senegalia, Mimosa, and Prosopis. Leucaena selected diverse strains of Ensifer and Mesorhizobium as symbionts depending on available soil pH, climatic, and other edaphic conditions in India. Lateral gene transfer seems to play a major role in genetic diversification of Ensifer exhibited in terms of Old World vs. Neotropical genetic make-up and mixed populations at several sites. Although Neotropical Ensifer strains were most symbiotically effective on Leucaena, the native Ensifer are promiscuous and particularly well-adapted to a wide range of sampling sites with varied climates and edaphic factors.}, }
@article {pmid35817106, year = {2022}, author = {Zhai, H and Guo, Y and Zhang, L and Miao, Y and Wang, J}, title = {Presence of bromide and iodide promotes the horizontal transfer of antibiotic resistance genes during chlorination: A preliminary study.}, journal = {The Science of the total environment}, volume = {846}, number = {}, pages = {157250}, doi = {10.1016/j.scitotenv.2022.157250}, pmid = {35817106}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/pharmacology ; Bromides ; Bromine ; Chlorine ; Drug Resistance, Microbial/genetics ; Escherichia coli/genetics ; *Escherichia coli K12 ; Gene Transfer, Horizontal ; Genes, Bacterial ; Halogenation ; Humans ; Iodides ; *Iodine ; Oxidants ; Plasmids ; }, abstract = {Chlorination was reported to have a great potential to increase horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs), which poses a great threat to global human health. Bromide (Br[-]) and iodide (I[-]) ions are widely spread ions in water and wastewater. In chlorination, Br[-] and I[-] can be oxidized to active bromine and iodine species. The influence of the co-existing different halogen oxidants (chlorine + bromine or iodine species) on HGT of ARGs were rarely investigated. In this study, the conjugative transfer of ARGs between a donor strain E. coli K12 and a recipient strain E. coli HB101 was investigated in chlorination without/with the presence of Br[-] or I[-]. Immediately after the addition of sodium hypochlorite, 53-88 % of the dosed chlorine was rapidly consumed, 10 %-42 % fast transformed into organic combined chloramines, and only low levels of free chlorine (0.02-0.8 mg/L as Cl2) left in the diluted cultural medium. Conjugative transfer mediated by the RP4 plasmid was not significantly enhanced in chlorination without the presence of Br[-] or I[-]. With the presence of Br[-] (0.5-5.0 mg/L) or I[-] (0.05-0.5 mg/L) in chlorination, the co-existing free halogen oxidants and their organic combined ones up-regulated the mRNA expression of the oxidative stress-regulatory gene (rpoS), outer membrane protein gene (ompC), and conjugation-relevant genes (trbBp and trfAp), and caused more damage to cell entirety. As a result, the co-existing reactive halogen oxidants enhanced the HGT of ARGs probably via conjugative transfer and transformation. This study showed that the presence of Br[-] and I[-] of common levels in aquatic environment promoted HGT of ARGs in chlorination, thus accelerating the transmission and prevalence of ARGs.}, }
@article {pmid35815847, year = {2022}, author = {Tanwar, N and Arya, SS and Rookes, JE and Cahill, DM and Lenka, SK and Bansal, KC}, title = {Prospects of chloroplast metabolic engineering for developing nutrient-dense food crops.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/07388551.2022.2092717}, pmid = {35815847}, issn = {1549-7801}, abstract = {Addressing nutritional deficiencies in food crops through biofortification is a sustainable approach to tackling malnutrition. Biofortification is continuously being attempted through conventional breeding as well as through various plant biotechnological interventions, ranging from molecular breeding to genetic engineering and genome editing for enriching crops with various health-promoting metabolites. Genetic engineering is used for the rational incorporation of desired nutritional traits in food crops and predominantly operates through nuclear and chloroplast genome engineering. In the recent past, chloroplast engineering has been deployed as a strategic tool to develop model plants with enhanced nutritional traits due to the various advantages it offers over nuclear genome engineering. However, this approach needs to be extended for the nutritional enhancement of major food crops. Further, this platform could be combined with strategies, such as synthetic biology, chloroplast editing, nanoparticle-mediated rapid chloroplast transformation, and horizontal gene transfer through grafting for targeting endogenous metabolic pathways for overproducing native nutraceuticals, production of biopharmaceuticals, and biosynthesis of designer nutritional compounds. This review focuses on exploring various features of chloroplast genome engineering for nutritional enhancement of food crops by enhancing the levels of existing metabolites, restoring the metabolites lost during crop domestication, and introducing novel metabolites and phytonutrients needed for a healthy daily diet.}, }
@article {pmid35814695, year = {2022}, author = {Belloso Daza, MV and Milani, G and Cortimiglia, C and Pietta, E and Bassi, D and Cocconcelli, PS}, title = {Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {894241}, pmid = {35814695}, issn = {1664-302X}, abstract = {The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.}, }
@article {pmid35811376, year = {2022}, author = {Villain, P and Catchpole, R and Forterre, P and Oberto, J and da Cunha, V and Basta, T}, title = {Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35811376}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; Bacteria/genetics ; *DNA Gyrase/genetics ; DNA Topoisomerases, Type I/genetics ; Gene Transfer, Horizontal ; }, abstract = {DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaea-specific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labor in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naive archaeon and the associated adaptations in the management of topological constraints.}, }
@article {pmid35811169, year = {2022}, author = {Dickinson, A}, title = {Neck of the woods: Microbes, memory, and resistance.}, journal = {Endeavour}, volume = {46}, number = {1-2}, pages = {100821}, doi = {10.1016/j.endeavour.2022.100821}, pmid = {35811169}, issn = {1873-1929}, mesh = {*Bacteria/genetics ; DNA, Bacterial ; Drug Resistance, Microbial/genetics ; *Gene Transfer, Horizontal ; Humans ; }, abstract = {Horizontal Gene Transfer (HGT) is a key mechanism allowing bacteria to enact genetic changes in response to shifting environmental conditions. The swift lateral movement of genes makes possible antibiotic resistance, which is an increasing medical and ultimately cultural problem. There is evidence that HGT also takes place between species. Bacterial DNA appears in the human mitochondrial genome of acute myeloid leukemia (AML) samples. Responding to a recent diagnosis of AML, this creative piece imagines a literary form of HGT. Adjacency is intrinsic to the conceptual and formal concerns of the text. Moving back and forth between essay and poem, between the personal and the planetary, between the real and the imagined, and between the right and left margins of the page, this piece unfolds beside itself, exploring the lateral movement of memory and family history through concerns with antibiotic resistance, illness, writing, and science. While there are no embedded citations or footnotes, a glossary of terms (Appendix 1) follows the main text, and a brief bibliographic essay (Appendix 2) at the end identifies cited sources that correspond to a list of references.}, }
@article {pmid35801640, year = {2022}, author = {Brahim Belhaouari, D and Pires De Souza, GA and Lamb, DC and Kelly, SL and Goldstone, JV and Stegeman, JJ and Colson, P and La Scola, B and Aherfi, S}, title = {Metabolic arsenal of giant viruses: Host hijack or self-use?.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35801640}, issn = {2050-084X}, support = {P01 ES021923/ES/NIEHS NIH HHS/United States ; }, mesh = {*Amoeba ; DNA Viruses/genetics ; Genome, Viral ; *Giant Viruses/genetics ; Phylogeny ; *Viruses/genetics ; }, abstract = {Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date.}, }
@article {pmid35799218, year = {2022}, author = {Hassler, HB and Probert, B and Moore, C and Lawson, E and Jackson, RW and Russell, BT and Richards, VP}, title = {Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {104}, pmid = {35799218}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Genes, rRNA ; Humans ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].<br><br>RESULTS: At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690&#x2009;&#xb1;&#x2009;110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).<br><br>CONCLUSIONS: Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example,&#xa0;with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.}, }
@article {pmid35798684, year = {2022}, author = {Tahiri, N and Veriga, A and Koshkarov, A and Morozov, B}, title = {Invariant transformers of Robinson and Foulds distance matrices for Convolutional Neural Network.}, journal = {Journal of bioinformatics and computational biology}, volume = {20}, number = {4}, pages = {2250012}, doi = {10.1142/S0219720022500123}, pmid = {35798684}, issn = {1757-6334}, mesh = {*Algorithms ; Gene Transfer, Horizontal ; *Neural Networks, Computer ; Phylogeny ; Software ; }, abstract = {The evolutionary histories of genes are susceptible of differing greatly from each other which could be explained by evolutionary variations in horizontal gene transfers or biological recombinations. A phylogenetic tree would therefore represent the evolutionary history of each gene, which may present different patterns from the species tree that defines the main evolutionary patterns. In addition, phylogenetic trees of closely related species should be merged, thus minimizing the topological conflicts they present and obtaining consensus trees (in the case of homogeneous data) or supertrees (in the case of heterogeneous data). The traditional approaches are consensus tree inference (if the set of trees contains the same set of species) or supertrees (if the set of trees contains different, but overlapping sets of species). Consensus trees and supertrees are constructed to produce unique trees. However, these methods lose precision with respect to different evolutionary variability. Other approaches have been implemented to preserve this variability using the [Formula: see text]-means algorithm or the [Formula: see text]-medoids algorithm. Using a new method, we determine all possible consensus trees and supertrees that best represent the most significant evolutionary models in a set of phylogenetic trees, thereby increasing the precision of the results and decreasing the time required. Results: This paper presents in detail a new method for predicting the number of clusters in a Robinson and Foulds (RF) distance matrix using a convolutional neural network (CNN). We developed a new CNN approach (called CNNTrees) for multiple tree classification. This new strategy returns a number of clusters of the input phylogenetic trees for different-size sets of trees, which makes the new approach more stable and more robust. The paper provides an in-depth analysis of the relevant, but very difficult, problem of constructing alternative supertrees using phylogenies with different but overlapping sets of taxa. This new model will play an important role in the inference of Trees of Life (ToL). Availability and implementation: CNNTrees is available through a web server at https://tahirinadia.github.io/. The source code, data and information about installation procedures are also available at https://github.com/TahiriNadia/CNNTrees. Supplementary information: Supplementary data are available on GitHub platform. The evolutionary history of species is not unique, but is specific to sets of genes. Indeed, each gene has its own evolutionary history that differs considerably from one gene to another. For example, some individual genes or operons may be affected by specific horizontal gene transfer and recombination events. Thus, the evolutionary history of each gene must be represented by its own phylogenetic tree, which may exhibit different evolutionary patterns than the species tree that accounts for the major vertical descent patterns. The result of traditional consensus tree or supertree inference methods is a single consensus tree or supertree. In this paper, we present in detail a new method for predicting the number of clusters in a Robinson and Foulds (RF) distance matrix using a convolutional neural network (CNN). We developed a new CNN approach (CNNTrees) to construct multiple tree classification. This new strategy returns a number of clusters in the order of the input trees, which allows this new approach to be more stable and also more robust.}, }
@article {pmid35798255, year = {2022}, author = {Sengeruan, LP and van Zwetselaar, M and Kumburu, H and Aarestrup, FM and Kreppel, K and Sauli, E and Sonda, T}, title = {Plasmid characterization in bacterial isolates of public health relevance in a tertiary healthcare facility in Kilimanjaro region, Tanzania.}, journal = {Journal of global antimicrobial resistance}, volume = {30}, number = {}, pages = {384-389}, doi = {10.1016/j.jgar.2022.06.030}, pmid = {35798255}, issn = {2213-7173}, mesh = {Escherichia coli/genetics ; *Klebsiella pneumoniae/genetics ; Plasmids/genetics ; *Public Health ; Tanzania/epidemiology ; Tertiary Healthcare ; }, abstract = {OBJECTIVES: Plasmids are infectious double stranded DNA molecules that are found within bacteria. Horizontal gene transfer promotes successful spread of different types of plasmids within or among bacteria species, making their detection an important task for guiding clinical treatment. We used whole genome sequenced data to determine the prevalence of plasmid replicon types in clinical bacterial isolates, the presence of resistance and virulence genes in plasmid replicon types, and the relationship between resistance and virulence genes within each plasmid replicon.<br><br>METHODS: All bacterial sequences were de novo assembled using Unicycler before extraction of plasmids. Assembly graphs were submitted to Gplas+plasflow for plasmid contigs prediction. The predicted plasmid contigs were validated using PlasmidFinder.<br><br>RESULTS: A total of 159 (56.2%) out of 283 bacterial isolates were found to carry plasmid replicons, with Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus being the most prevalent plasmid carriers. A total of 26 (86.7%) multiple-replicon types were found to carry both resistance and virulence genes compared to 4 (13.3%) single plasmid replicons. No statistically significant correlation was found between the number of antibiotic resistance and virulence genes in multiple-replicon types (r&#xa0;=&#xa0;- 0.14, P > 0.05).<br><br>CONCLUSION: Our findings show a relatively high proportion of plasmid replicon-carrying isolates suggesting selection pressure due to antibiotic use in the hospital. Co-occurrence of antibiotic resistance and virulence genes in clinical isolates is a public health problem warranting attention.}, }
@article {pmid35796971, year = {2022}, author = {Palatini, U and Pischedda, E and Bonizzoni, M}, title = {Computational Methods for the Discovery and Annotation of Viral Integrations.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2509}, number = {}, pages = {293-313}, pmid = {35796971}, issn = {1940-6029}, mesh = {DNA Viruses/genetics ; *RNA Viruses/genetics ; RNA, Small Interfering/genetics ; Virus Integration ; *Viruses/genetics ; }, abstract = {The transfer of genetic material between viruses and eukaryotic cells is pervasive. Somatic integrations of DNA viruses and retroviruses have been linked to persistent viral infection and genotoxic effects. Integrations into germline cells, referred to as Endogenous Viral Elements (EVEs), can be co-opted for host functions. Besides DNA viruses and retroviruses, EVEs can also derive from nonretroviral RNA viruses, which have often been observed in piRNA clusters. Here, we describe a bioinformatic framework to annotate EVEs in a genome assembly, study their widespread occurrence and polymorphism and identify sample-specific viral integrations using whole genome sequencing data.}, }
@article {pmid35790381, year = {2022}, author = {Stadnichuk, IN and Tropin, IV}, title = {Cyanidiales as Polyextreme Eukaryotes.}, journal = {Biochemistry. Biokhimiia}, volume = {87}, number = {5}, pages = {472-487}, doi = {10.1134/S000629792205008X}, pmid = {35790381}, issn = {1608-3040}, mesh = {Archaea/genetics ; Biological Evolution ; *Eukaryota/genetics ; *Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Cyanidiales were named enigmatic microalgae due to their unique polyextreme properties, considered for a very long time unattainable for eukaryotes. Cyanidiales mainly inhabit hot sulfuric springs with high acidity (pH 0-4), temperatures up to 56°C, and ability to survive in the presence of dissolved heavy metals. Owing to the minimal for eukaryotes genome size, Cyanidiales have become one of the most important research objects in plant cell physiology, biochemistry, molecular biology, phylogenomics, and evolutionary biology. They play an important role in studying many aspects of oxygenic photosynthesis and chloroplasts origin. The ability to survive in stressful habitats and the corresponding metabolic pathways were acquired by Cyanidiales from archaea and bacteria via horizontal gene transfer (HGT). Thus, the possibility of gene transfer from prokaryotes to eukaryotes was discovered, which was a new step in understanding of the origin of eukaryotic cell.}, }
@article {pmid35789842, year = {2022}, author = {Job, V and Gomez-Valero, L and Renier, A and Rusniok, C and Bouillot, S and Chenal-Francisque, V and Gueguen, E and Adrait, A and Robert-Genthon, M and Jeannot, K and Panchev, P and Elsen, S and Fauvarque, MO and Couté, Y and Buchrieser, C and Attrée, I}, title = {Genomic erosion and horizontal gene transfer shape functional differences of the ExlA toxin in Pseudomonas spp.}, journal = {iScience}, volume = {25}, number = {7}, pages = {104596}, pmid = {35789842}, issn = {2589-0042}, abstract = {Two-partner secretion (TPS) is widespread in the bacterial world. The pore-forming TPS toxin ExlA of Pseudomonas aeruginosa is conserved in pathogenic and environmental Pseudomonas. While P. chlororaphis and P. entomophila displayed ExlA-dependent killing, P. putida did not cause damage to eukaryotic cells. ExlA proteins interacted with epithelial cell membranes; however, only ExlA [Pch] induced the cleavage of the adhesive molecule E-cadherin. ExlA proteins participated in insecticidal activity toward the larvae of Galleria mellonella and the fly Drosophila melanogaster. Evolutionary analyses demonstrated that the differences in the C-terminal domains are partly due to horizontal movements of the operon within the genus Pseudomonas. Reconstruction of the evolutionary history revealed the complex horizontal acquisitions. Together, our results provide evidence that conserved TPS toxins in environmental Pseudomonas play a role in bacteria-insect interactions and discrete differences in CTDs may determine their specificity and mode of action toward eukaryotic cells.}, }
@article {pmid35781905, year = {2022}, author = {Wu, D and Hu, Y and Akashi, S and Nojiri, H and Guo, L and Ye, CY and Zhu, QH and Okada, K and Fan, L}, title = {Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {5}, pages = {1354-1367}, pmid = {35781905}, issn = {1365-313X}, mesh = {*Diterpenes/metabolism ; *Echinochloa/genetics/metabolism ; Multigene Family ; *Oryza/metabolism ; Plants/metabolism ; Poaceae/genetics/metabolism ; }, abstract = {Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.}, }
@article {pmid35780898, year = {2022}, author = {Zhang, J and Lu, T and Xin, Y and Wei, Y}, title = {Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion.}, journal = {The Science of the total environment}, volume = {844}, number = {}, pages = {157054}, doi = {10.1016/j.scitotenv.2022.157054}, pmid = {35780898}, issn = {1879-1026}, mesh = {Anaerobiosis ; Animals ; *Anti-Bacterial Agents/pharmacology ; Chlorides ; Drug Resistance, Microbial/genetics ; Ferric Compounds ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Manure ; Swine ; }, abstract = {The role of ferric chloride (FC) on the reduction of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) system was investigated from the perspective of vertical (VGT) and horizontal gene transfer (HGT) network through the high-throughput qPCR (HT-qPCR). Although FC showed limited impacts on methane production in AD of swine manure, the tetracycline and MLSB resistance genes were specifically reduced at the end, where tetQ of antibiotic target protection and ermF of antibiotic target alteration contributed the most to the reduction. Both VGT and HGT network were divided into three modules, and the complexity of HGT network was largely reduced along with AD, where the HGT connection was reduced from 683 (Module III) to 172 (Module I), and FC addition could further reduce the relative abundance of ARG hosts in Module I. The contribution of VGT and HGT to the changes of ARGs in AD was further deciphered, and although the VGT reflected by the changes of microbial community contributed the most to the dynamics of ARGs (68.0 %), the HGT contribution could further be reduced by the FC addition. This study provided a new perspective on the fate of ARGs response to the FC addition in the AD system.}, }
@article {pmid35779456, year = {2022}, author = {Ye, C and Feng, M and Chen, Y and Zhang, Y and Chen, Q and Yu, X}, title = {Dormancy induced by oxidative damage during disinfection facilitates conjugation of ARGs through enhancing efflux and oxidative stress: A lagging response.}, journal = {Water research}, volume = {221}, number = {}, pages = {118798}, doi = {10.1016/j.watres.2022.118798}, pmid = {35779456}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Chlorine/pharmacology ; *Disinfection/methods ; Gene Transfer, Horizontal ; Genes, Bacterial ; Oxidative Stress ; Water/pharmacology ; }, abstract = {Disinfection is known to greatly alter bacterial characteristics in water, and high horizontal gene transfer (HGT) frequency occurs in eutrophic conditions. Interestingly, these two seemingly irrelevant phenomena were closely linked by a lagging response of the increased conjugation frequency probably via daily water disinfection in this study. Three disinfection methods (UV, chlorine, and UV/chlorine) were selected to investigate the increased frequency of conjugation of ARGs during the stage of continuing culture after disinfection. The results showed that the conjugative transfer frequency was inhibited for all disinfection treatments after 24 h of co-incubation. Unexpectedly, after 3-7 days of co-cultivation, the HGT frequencies were increased by 2.71-5.61-fold and 5.46-13.96-fold in chlorine (30 min) and UV/chlorine (1 min) groups compared to the control, but not in UV-irradiated groups. A neglected lagging response was found for the first time, i.e., oxidative disinfection-induced dormancy promotes conjugative transfer of ARGs. Furthermore, mechanistic insights were gained from (1) membrane permeability, (2) conjugation-regulated system, (3) efflux pump system, and (4) oxidative stress system, suggesting the critical role of enhancing efflux and oxidative stress in the propagation of ARGs. Finally, the known instantaneous effect of oxidation disinfection was compared to address the controversial debate in this research field, proposing that the dormancy level of donor bacteria is the key to evaluating whether it can promote the HGT process. This study has important environmental implications for elucidating the transmission of ARGs after oxidation disinfection.}, }
@article {pmid35770172, year = {2022}, author = {Venhorst, J and van der Vossen, JMBM and Agamennone, V}, title = {Battling Enteropathogenic Clostridia: Phage Therapy for Clostridioides difficile and Clostridium perfringens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891790}, pmid = {35770172}, issn = {1664-302X}, abstract = {The pathogenic Clostridioides difficile and Clostridium perfringens are responsible for many health care-associated infections as well as systemic and enteric diseases. Therefore, they represent a major health threat to both humans and animals. Concerns regarding increasing antibiotic resistance (related to C. difficile and C. perfringens) have caused a surge in the pursual of novel strategies that effectively combat pathogenic infections, including those caused by both pathogenic species. The ban on antibiotic growth promoters in the poultry industry has added to the urgency of finding novel antimicrobial therapeutics for C. perfringens. These efforts have resulted in various therapeutics, of which bacteriophages (in short, phages) show much promise, as evidenced by the Eliava Phage Therapy Center in Tbilisi, Georgia (https://eptc.ge/). Bacteriophages are a type of virus that infect bacteria. In this review, the (clinical) impact of clostridium infections in intestinal diseases is recapitulated, followed by an analysis of the current knowledge and applicability of bacteriophages and phage-derived endolysins in this disease indication. Limitations of phage and phage endolysin therapy were identified and require considerations. These include phage stability in the gastrointestinal tract, influence on gut microbiota structure/function, phage resistance development, limited host range for specific pathogenic strains, phage involvement in horizontal gene transfer, and-for phage endolysins-endolysin resistance, -safety, and -immunogenicity. Methods to optimize features of these therapeutic modalities, such as mutagenesis and fusion proteins, are also addressed. The future success of phage and endolysin therapies require reliable clinical trial data for phage(-derived) products. Meanwhile, additional research efforts are essential to expand the potential of exploiting phages and their endolysins for mitigating the severe diseases caused by C. difficile and C. perfringens.}, }
@article {pmid35769590, year = {2022}, author = {Xia, ZQ and Wei, ZY and Shen, H and Shu, JP and Wang, T and Gu, YF and Jaisi, A and Yan, YH}, title = {Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae: Insights into the polyploidization of Phlegmariurus.}, journal = {Plant diversity}, volume = {44}, number = {3}, pages = {262-270}, pmid = {35769590}, issn = {2468-2659}, abstract = {Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds. They are an excellent study system for examining whole-genome duplications (WGDs), or polyploidization, in spore-dispersed vascular plants. However, a lack of genome sequence data limits the reliable detection of very ancient WGDs, small-scale duplications (SSDs), and recent WGDs. Here, we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites (Ks) of the transcriptomes of 13 species of lycophytes to identify, locate, and date multiple WGDs in the lycophyte family Lycopodiaceae. Additionally, we examined the genus Phlegmariurus for signs of genetic discordance, which can provide valuable insight into the underlying causes of such conflict (e.g., hybridization, incomplete lineage sorting, or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae, with one occurring in the common ancestor of extant Phlegmariurus (Lycopodiaceae) approximately 22-23 million years ago (Mya) and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya. Interestingly, we found significant genetic discordance in the genus Phlegmariurus, indicating that the genus has a complex evolutionary history. This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.}, }
@article {pmid35769291, year = {2022}, author = {Kim, JI and Jo, BY and Park, MG and Yoo, YD and Shin, W and Archibald, JM}, title = {Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {896138}, pmid = {35769291}, issn = {1664-462X}, abstract = {The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.}, }
@article {pmid35765180, year = {2022}, author = {Pandey, SD and Biswas, I}, title = {Clp ATPases differentially affect natural competence development in Streptococcus mutans.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1288}, pmid = {35765180}, issn = {2045-8827}, mesh = {*Adenosine Triphosphatases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Endopeptidases/genetics ; Gene Expression Regulation, Bacterial ; *Streptococcus mutans ; }, abstract = {In naturally competent bacteria, DNA transformation through horizontal gene transfer is an evolutionary mechanism to receive extracellular DNA. Bacteria need to maintain a state of competence to accept foreign DNA, and this is an energy-driven phenomenon that is tightly controlled. In Streptococcus, competence development is a complex process that is not fully understood. In this study, we used Streptococcus mutans, an oral bacterium, to determine how cell density affects competence development. We found that in S. mutans the transformation efficiency is maximum when the transforming DNA was added at low cell density and incubated for 2.5 h before selecting for transformants. We also found that S. mutans cells remain competent until the mid-logarithmic phase, after which the competence decreases drastically. Surprisingly, we observed that individual components of Clp proteolytic complexes differentially regulate competence. If the transformation is carried out at the early growth phase, both ClpP protease and ClpX ATPase are needed for competence. In contrast, we found that both ClpC and ClpE negatively affect competence. We also found that if the transformation is carried out at the mid-logarithmic growth phase ClpX is still required for competence, but ClpP negatively affects competence. While the exact reason for this differential effect of ClpP and ClpX on transformation is currently unknown, we found that both ClpC and ClpE have a negative effect on transformation, which was not reported before.}, }
@article {pmid35764672, year = {2022}, author = {Jenkins, HL and Graham, R and Porter, JS and Vieira, LM and de Almeida, ACS and Hall, A and O'Dea, A and Coppard, SE and Waeschenbach, A}, title = {Unprecedented frequency of mitochondrial introns in colonial bilaterians.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10889}, pmid = {35764672}, issn = {2045-2322}, mesh = {Animals ; *Gene Transfer, Horizontal ; Introns/genetics ; *Mitochondria/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.}, }
@article {pmid35763818, year = {2022}, author = {Shin, NR and Doucet, D and Pauchet, Y}, title = {Duplication of horizontally acquired GH5_2 enzymes played a central role in the evolution of longhorned beetles.}, journal = {Molecular biology and evolution}, volume = {39}, number = {6}, pages = {}, pmid = {35763818}, issn = {1537-1719}, abstract = {The rise of functional diversity through gene duplication contributed to the adaption of organisms to various environments. Here we investigate the evolution of putative cellulases of the subfamily 2 of glycoside hydrolase family 5 (GH5_2) in the Cerambycidae (longhorned beetles), a megadiverse assemblage of mostly xylophagous beetles. Cerambycidae originally acquired GH5_2 from a bacterial donor through horizontal gene transfer (HGT), and extant species harbor multiple copies that arose from gene duplication. We ask how these digestive enzymes contributed to the ability of these beetles to feed on wood. We analyzed 113 GH5_2, including the functional characterization of 52 of them, derived from 25 species covering most subfamilies of Cerambycidae. Ancestral gene duplications led to five well-defined groups with distinct substrate specificity, allowing these beetles to break down, in addition to cellulose, polysaccharides that are abundant in plant cell walls (PCWs), namely, xyloglucan, xylan, and mannans. Resurrecting the ancestral enzyme originally acquired by HGT, we show it was a cellulase that was able to break down glucomannan and xylan. Finally, recent gene duplications further expanded the catalytic repertoire of cerambycid GH5_2, giving rise to enzymes that favor transglycosylation over hydrolysis. We suggest that HGT and gene duplication, which shaped the evolution of GH5_2, played a central role in the ability of cerambycid beetles to use a PCW-rich diet and may have contributed to their successful radiation.}, }
@article {pmid35763548, year = {2022}, author = {Sulser, S and Vucicevic, A and Bellini, V and Moritz, R and Delavat, F and Sentchilo, V and Carraro, N and van der Meer, JR}, title = {A bistable prokaryotic differentiation system underlying development of conjugative transfer competence.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010286}, pmid = {35763548}, issn = {1553-7404}, mesh = {*Conjugation, Genetic/genetics ; *Gene Transfer, Horizontal/genetics ; Prokaryotic Cells ; Promoter Regions, Genetic ; Pseudomonas/genetics ; }, abstract = {The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7-4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.}, }
@article {pmid35762208, year = {2022}, author = {Matuszewska, M and Murray, GGR and Ba, X and Wood, R and Holmes, MA and Weinert, LA}, title = {Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35762208}, issn = {2050-084X}, support = {/MRC_/Medical Research Council/United Kingdom ; BB/L018934/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109385/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Humans ; Livestock/microbiology ; *Methicillin-Resistant Staphylococcus aureus/genetics ; *Staphylococcal Infections/microbiology ; }, abstract = {Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.}, }
@article {pmid35760883, year = {2022}, author = {Wang, P and Zhao, Y and Wang, W and Lin, S and Tang, K and Liu, T and Wood, TK and Wang, X}, title = {Mobile genetic elements used by competing coral microbial populations increase genomic plasticity.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2220-2229}, pmid = {35760883}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/genetics ; Conjugation, Genetic ; DNA Transposable Elements ; Gene Transfer, Horizontal ; Genomic Islands ; Genomics ; *Pseudoalteromonas/genetics ; *Vibrio/genetics ; }, abstract = {Intraspecies diversification and niche adaptation by members of the Vibrio genus, one of the most diverse bacterial genera, is thought to be driven by horizontal gene transfer. However, the intrinsic driving force of Vibrio species diversification is much less explored. Here, by studying two dominant and competing cohabitants of the gastric cavity of corals, we found that a phenotype influencing island (named VPII) in Vibrio alginolyticus was eliminated upon coculturing with Pseudoalteromonas. The loss of VPII reduced the biofilm formation and phage resistance, but activated motility, which may allow V. alginolyticus to expand to other niches. Mechanistically, we discovered that the excision of this island is mediated by the cooperation of two unrelated mobile genetic elements harbored in Pseudoalteromonas spp., an integrative and conjugative element (ICE) and a mobilizable genomic island (MGI). More importantly, these mobile genetic elements are widespread in cohabitating Gram-negative bacteria. Altogether, we discovered a new strategy by which the mobilome is employed by competitors to increase the genomic plasticity of rivals.}, }
@article {pmid35757882, year = {2022}, author = {de Lorenzo, V}, title = {Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1857}, pages = {20210395}, pmid = {35757882}, issn = {1471-2970}, mesh = {Biodegradation, Environmental ; Biotechnology ; Gene Transfer, Horizontal ; *Microbiota ; *Synthetic Biology/methods ; }, abstract = {Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.}, }
@article {pmid35745530, year = {2022}, author = {Jungkhun, N and Gomes de Farias, AR and Watcharachaiyakup, J and Kositcharoenkul, N and Ham, JH and Patarapuwadol, S}, title = {Phylogenetic Characterization and Genome Sequence Analysis of Burkholderia glumae Strains Isolated in Thailand as the Causal Agent of Rice Bacterial Panicle Blight.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {35745530}, issn = {2076-0817}, abstract = {Burkholderia glumae is one of the most critical rice-pathogenic bacteria, and it causes bacterial panicle blight (BPB) in rice plants. In 2017, BPB symptoms were observed from rice fields in Chiang Rai, Northern Thailand. Sixty-one isolates obtained from the symptomatic panicles of rice were initially identified as B. glumae by polymerase chain reaction (PCR) using species-specific primers. Among them, six selected strains isolated from the susceptible japonica rice cultivar DOA2 were characterized in terms of morpho-physiology, pathology, phylogenetics, and genomics. Our genome sequence analysis of the six selected strains revealed the presence of multiple prophages, which may reflect the high level of diversity in this bacterial species through dynamic horizontal gene transfer processes, including phage infection. This notion was supported by the results of phylogenetic and phylogenomic analyses, which showed the formation of several subgroups not related to the years of isolation or the geographical origins. This study reports the isolation of B. glumae as the causal pathogen of BPB disease in japonica rice in Thailand and provides genomic resources to better understand the biology and diversity of this plant pathogenic bacterium. Further studies with a vast collection of B. glumae strains from various rice-growing regions around the world are needed to elucidate the evolution, variability, and lifestyle of the pathogen.}, }
@article {pmid35741357, year = {2022}, author = {Merkevičienė, L and Butrimaitė-Ambrozevičienė, &#x10c; and Paškevičius, G and Pikūnienė, A and Virgailis, M and Dailidavičienė, J and Daukšienė, A and Šiugždinienė, R and Ruzauskas, M}, title = {Serological Variety and Antimicrobial Resistance in Salmonella Isolated from Reptiles.}, journal = {Biology}, volume = {11}, number = {6}, pages = {}, pmid = {35741357}, issn = {2079-7737}, abstract = {Salmonella&amp;nbsp;enterica is one of the best adapted bacterial pathogens causing infections in a wide variety of vertebrate species. The aim of this study was to investigate the prevalence of Salmonella in different reptile species and to evaluate their serological variety and patterns of antimicrobial resistance. In total, 97 samples from 25 wild and domesticated reptile species were investigated in Lithuania. Serological variety, as well as phenotypical and genotypical resistance to antimicrobials, were investigated. Fifty isolates of Salmonella were obtained from the ninety-seven tested samples (51.5%; 95% CI 41.2-61.2). A significantly higher prevalence of Salmonella was detected in domesticated individuals (61.3%; 95% CI 50.0-71.5) compared with wild ones (18.2%; 95% CI 7.3-38.5). All isolates belonged to a single species, Salmonella enterica. Results demonstrated that reptiles carry a large variety of Salmonella serovars. Thirty-four isolates (68%) of Salmonella were resistant to at least one antimicrobial drug. The most frequent resistance of the isolates was to streptomycin (26%), cefoxitin, gentamicin, tetracycline and chloramphenicol (16%). Genes encoding resistance to tetracyclines, aminoglycosides, sulphonamides and trimethoprim were detected. No integrons that are associated with horizontal gene transfer were found. Data obtained provided knowledge about the adaptation of Salmonella in reptiles. Healthy individuals, irrespective of their origin, often carry Salmonella, including multi-resistant strains. Due to its large serological diversity, zoonotic potential and antimicrobial resistance, Salmonella in reptiles poses a risk to other animals and humans.}, }
@article {pmid35738252, year = {2022}, author = {George, EE and Tashyreva, D and Kwong, WK and Okamoto, N and Horák, A and Husnik, F and Lukeš, J and Keeling, PJ}, title = {Gene Transfer Agents in Bacterial Endosymbionts of Microbial Eukaryotes.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35738252}, issn = {1759-6653}, mesh = {Bacteria/genetics ; *Eukaryota/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Symbiosis/genetics ; *Viruses ; }, abstract = {Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found to be present in several highly reduced alphaproteobacterial endosymbionts of diplonemid protists (Rickettsiales and Rhodospirillales). Evidence of GTA expression was found in polyA-enriched metatranscriptomes of the diplonemid hosts and their endosymbionts, but due to biases in the polyA-enrichment methods, levels of GTA expression could not be determined. Examining the genomes of closely related bacteria revealed that the pattern of retained GTA head/capsid complexes with missing tail components was common across Rickettsiales and Holosporaceae (Rhodospirillales), all obligate symbionts with a wide variety of eukaryotic hosts. A dN/dS analysis of Rickettsiales and Holosporaceae symbionts revealed that purifying selection is likely the main driver of GTA evolution in symbionts, suggesting they remain functional, but the ecological function of GTAs in bacterial symbionts is unknown. In particular, it is unclear how increasing horizontal gene transfer in small, largely clonal endosymbiont populations can explain GTA retention, and, therefore, the structures may have been repurposed in endosymbionts for host interactions. Either way, their widespread retention and conservation in endosymbionts of diverse eukaryotes suggests an important role in symbiosis.}, }
@article {pmid35736713, year = {2022}, author = {Velasco-Amo, MP and Arias-Giraldo, LF and Olivares-García, C and Denancé, N and Jacques, MA and Landa, BB}, title = {Use of traC Gene to Type the Incidence and Distribution of pXFAS_5235 Plasmid-Bearing Strains of Xylella fastidiosa subsp. fastidiosa ST1 in Spain.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {35736713}, issn = {2223-7747}, abstract = {Xylella fastidiosa (Xf) is a phytopathogenic bacterium with a repertoire of self-replicating genetic elements, including plasmids, pathogenicity islands, and prophages. These elements provide potential avenues for horizontal gene transfer both within and between species and have the ability to confer new virulence traits, including the ability to colonize new host plants. However, they can also serve as a 'footprint' to type plasmid-bearing strains. Genome sequencing of several strains of Xf subsp. fastidiosa sequence type (ST) 1 from Mallorca Island, Spain, revealed the presence of a 38 kb plasmid (pXFAS_5235). In this study, we developed a PCR-based typing approach using primers targeting the traC gene to determine the presence of pXFAS_5235 plasmid or other plasmids carrying this gene in a world-wide collection of 65 strains X. fastidiosa from different subspecies and STs or in 226 plant samples naturally infected by the bacterium obtained from the different outbreaks of Xf in Spain. The traC gene was amplified only in the plant samples obtained from Mallorca Island infected by Xf subsp. fastidiosa ST1 and from all Spanish strains belonging to this ST. Maximum-likelihood phylogenetic tree of traC revealed a close relatedness among Spanish and Californian strains carrying similar plasmids. Our results confirm previous studies, which suggested that a single introduction event of Xf subsp. fastidiosa ST1 occurred in the Balearic Islands. Further studies on the presence and role of plasmids in Xf strains belonging to the same or different subspecies and STs can provide important information in studies of epidemiology, ecology, and evolution of this plant pathogen.}, }
@article {pmid35731940, year = {2022}, author = {Romero Picazo, D and Werner, A and Dagan, T and Kupczok, A}, title = {Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35731940}, issn = {1759-6653}, mesh = {Animals ; Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Methane ; *Mytilidae/genetics/microbiology ; Phylogeny ; Sulfur ; Symbiosis/genetics ; }, abstract = {Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.}, }
@article {pmid35731825, year = {2022}, author = {Cote-L'Heureux, A and Maurer-Alcalá, XX and Katz, LA}, title = {Old genes in new places: A taxon-rich analysis of interdomain lateral gene transfer events.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010239}, pmid = {35731825}, issn = {1553-7404}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Eukaryota/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; *Gene Transfer, Horizontal/genetics ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Vertical inheritance is foundational to Darwinian evolution, but fails to explain major innovations such as the rapid spread of antibiotic resistance among bacteria and the origin of photosynthesis in eukaryotes. While lateral gene transfer (LGT) is recognized as an evolutionary force in prokaryotes, the role of LGT in eukaryotic evolution is less clear. With the exception of the transfer of genes from organelles to the nucleus, a process termed endosymbiotic gene transfer (EGT), the extent of interdomain transfer from prokaryotes to eukaryotes is highly debated. A common critique of studies of interdomain LGT is the reliance on the topology of single-gene trees that attempt to estimate more than one billion years of evolution. We take a more conservative approach by identifying cases in which a single clade of eukaryotes is found in an otherwise prokaryotic gene tree (i.e. exclusive presence). Starting with a taxon-rich dataset of over 13,600 gene families and passing data through several rounds of curation, we identify and categorize the function of 306 interdomain LGT events into diverse eukaryotes, including 189 putative EGTs, 52 LGTs into Opisthokonta (i.e. animals, fungi and their microbial relatives), and 42 LGTs nearly exclusive to anaerobic eukaryotes. To assess differential gene loss as an explanation for exclusive presence, we compare branch lengths within each LGT tree to a set of vertically-inherited genes subsampled to mimic gene loss (i.e. with the same taxonomic sampling) and consistently find shorter relative distance between eukaryotes and prokaryotes in LGT trees, a pattern inconsistent with gene loss. Our methods provide a framework for future studies of interdomain LGT and move the field closer to an understanding of how best to model the evolutionary history of eukaryotes.}, }
@article {pmid35731345, year = {2022}, author = {Da Silva, WM and Larzabal, M and Aburjaile, FF and Riviere, N and Martorelli, L and Bono, J and Amadio, A and Cataldi, A}, title = {Whole-genome sequencing analysis of Shiga toxin-producing Escherichia coli O22:H8 isolated from cattle prediction pathogenesis and colonization factors and position in STEC universe phylogeny.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {7}, pages = {689-704}, pmid = {35731345}, issn = {1976-3794}, mesh = {Animals ; Cattle ; *Escherichia coli Infections/microbiology/veterinary ; *Escherichia coli Proteins/genetics ; Phylogeny ; Shiga Toxin/genetics ; *Shiga-Toxigenic Escherichia coli/genetics ; Virulence Factors/genetics/metabolism ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen capable of causing illness in humans. In a previous study, our group showed that a STEC isolate belonging to O22:H8 serotype (strain 154) can interfere with STEC O157:H7 colonization both in vitro and in vivo. Using whole-genome sequencing and genomic comparative, we predicted a subset of genes acquired by O22:H8 strain 154 through horizontal gene transfer that might be responsible for the phenotype previously described by our group. Among them were identified genes related to the pathogenesis of non-LEE (locus of enterocyte effacement) STEC, specific metabolic processes, antibiotic resistance and genes encoding for the T6SS-1 that is related to inter-bacterial competition. In addition, we showed that this strain carries stx1c and stx2dact, a mucus-inducible variant. The results obtained in this study provide insights into STEC genomic plasticity and the importance of genomic islands in the adaptation and pathogenesis of this pathogen.}, }
@article {pmid35729152, year = {2022}, author = {Li, XT and Huang, ZS and Tang, YQ and Lin, CQ and Wang, CM}, title = {[Generation mechanism and control methods of antibiotic and heavy metal resistance genes in poultry waste: A review].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {33}, number = {6}, pages = {1719-1728}, doi = {10.13287/j.1001-9332.202210.029}, pmid = {35729152}, issn = {1001-9332}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metals, Heavy ; Poultry/genetics ; }, abstract = {As antibiotics and heavy metals are often mixed in animal feed, their excretion through animal feces would cause bacteria to produce antibiotic resistance genes and heavy metal resistance genes. The pollution of antibiotics resistance gene and heavy metal resistance gene has become a major threat to human health and ecological environment. From the perspective of bacterial evolution, we proposed the importance of bacterial long-term evolution experiments about antibiotics and heavy metals. There is a complex co-selection resistance between antibiotic resistance genes and heavy metal resistance genes, which interact with each other and collectively determine the environmental behavior of bacteria. Horizontal transfer of resistance gene increases its variability in the environment. Mobile genetic elements play an important role in horizontal transfer of resistance gene. As for resistance gene pollution control, advanced oxidation technology has a good resistance gene removal effect. The UV/TiO2 oxidation technology can reduce the abundance of antibiotic resistance genes of 4.7-5.8 log, with an efficiency of >99.99%. Other control strategies, such as the use of Macleaya cordata extract and the combination of bacteriophage and antibiotics, are also of significance for controlling resistance genes.}, }
@article {pmid35728321, year = {2022}, author = {Song, L and Jiang, G and Wang, C and Ma, J and Chen, H}, title = {Effects of antibiotics consumption on the behavior of airborne antibiotic resistance genes in chicken farms.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129288}, doi = {10.1016/j.jhazmat.2022.129288}, pmid = {35728321}, issn = {1873-3336}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Chickens/genetics ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; }, abstract = {The antibiotics and antibiotic resistance genes (ARGs) have caused pollution of livestock farm environments. There are limited investigations about airborne ARGs and what role the antibiotics play remains largely unclear. The dynamics of various antibiotics were compared between feces samples from chicken fed a diet with and without antibiotics. In contrast to the farm with no antibiotics drugs, the hazard quotients (HQs) of OTC (24.8-205.4) and CTC (18.0-317.0) are particularly high in the farm with in-feed antibiotics drugs. The high ecological risks of antibiotics in chicken feces with in-feed antibiotic drugs were 100 % as determined. We quantified mobile genetic elements (MGEs) and ARGs and investigated bacterial communities in feces and air samples. The concentration of airborne ARG/MGE subtypes with in-feed antibiotic drugs is about two orders of magnitude higher than those without drugs. This study reveals that the indoor air of chicken farms is a reservoir of ARGs in the environment. Continuous feeding of antibiotics can change the intestinal microbial community structure of the chicken. The possibility of horizontal gene transfer of ARGs in air and feces samples might be increased by in-feed antibiotic drugs. The enrichment of ARGs in the chicken farm can be reduced by minimizing antibiotic use.}, }
@article {pmid35719354, year = {2022}, author = {Lindemann, PC and Mylvaganam, H and Oppegaard, O and Anthonisen, IL and Zecic, N and Skaare, D}, title = {Case Report: Whole-Genome Sequencing of Serially Collected Haemophilus influenzae From a Patient With Common Variable Immunodeficiency Reveals Within-Host Evolution of Resistance to Trimethoprim-Sulfamethoxazole and Azithromycin After Prolonged Treatment With These Antibiotics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896823}, pmid = {35719354}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology/therapeutic use ; Azithromycin/pharmacology/therapeutic use ; *Common Variable Immunodeficiency ; Dihydropteroate Synthase/genetics/metabolism ; *Haemophilus Infections/drug therapy/microbiology ; Haemophilus influenzae ; Humans ; Microbial Sensitivity Tests ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology/therapeutic use ; }, abstract = {We report within-host evolution of antibiotic resistance to trimethoprim-sulfamethoxazole and azithromycin in a nontypeable Haemophilus influenzae strain from a patient with common variable immunodeficiency (CVID), who received repeated or prolonged treatment with these antibiotics for recurrent respiratory tract infections. Whole-genome sequencing of three longitudinally collected sputum isolates during the period April 2016 to January 2018 revealed persistence of a strain of sequence type 2386. Reduced susceptibility to trimethoprim-sulfamethoxazole in the first two isolates was associated with mutations in genes encoding dihydrofolate reductase (folA) and its promotor region, dihydropteroate synthase (folP), and thymidylate synthase (thyA), while subsequent substitution of a single amino acid in dihydropteroate synthase (G225A) rendered high-level resistance in the third isolate from 2018. Azithromycin co-resistance in this isolate was associated with amino acid substitutions in 50S ribosomal proteins L4 (W59R) and L22 (G91D), possibly aided by a substitution in AcrB (A604E) of the AcrAB efflux pump. All three isolates were resistant to aminopenicillins and cefotaxime due to TEM-1B beta-lactamase and identical alterations in penicillin-binding protein 3. Further resistance development to trimethoprim-sulfamethoxazole and azithromycin resulted in a multidrug-resistant phenotype. Evolution of multidrug resistance due to horizontal gene transfer and/or spontaneous mutations, along with selection of resistant subpopulations is a particular risk in CVID and other patients requiring repeated and prolonged antibiotic treatment or prophylaxis. Such challenging situations call for careful antibiotic stewardship together with supportive and supplementary treatment. We describe the clinical and microbiological course of events in this case report and address the challenges encountered.}, }
@article {pmid35714926, year = {2022}, author = {Aslan, E and Arslanyolu, M}, title = {Discovery of deoxyribonuclease II-like proteins in bacteria.}, journal = {Molecular phylogenetics and evolution}, volume = {174}, number = {}, pages = {107554}, doi = {10.1016/j.ympev.2022.107554}, pmid = {35714926}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; *Endodeoxyribonucleases/chemistry/genetics/metabolism ; *Eukaryota/genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {Deoxyribonuclease II (DNase II) is one of the earliest enzymes discovered in the history of biochemistry. Its role in apoptosis and development has been documented with great detail in eukaryotes. Prior in silico analyses showed its complete absence in bacterial genomes, with the exception of single bacterial genus: Burkholderia. It is therefore considered to be a eukaryotic enzyme. Here we show that the presence of DNase II is not limited to Burkholderia, as we find over one hundred DNase II-like sequences spanning 90 bacteria species belonging to 54 different genera and seven phyla. The majority of the significant hits (85%) come from Bacteroidetes and Proteobacteria phyla. Sequence analyses reveal that bacterial DNase II-like proteins possess a signature catalytic motif of eukaryotic DNase II. In phylogenetic analyses, we find that bacterial DNase II-like proteins are divided into two distinct clades. Our structural analyses reveal high levels of similarity between experimentally determined crystal structures of recombinant Burkholderia thailandensis DNase II and candidate bacterial DNase II-like proteins. We also biochemically show that Chromobacterium violaceum cell lysate possesses acidic DNase II-like activities. Collectively, our results indicate that DNase II has deeper evolutionary roots than previously thought. We argue that either some prokaryotic lineages have undergone losses of DNase II genes, resulting in rare conservation, or some lineages have acquired DNase II genes from eukaryotes through lateral gene transfer. We also discuss the possible involvement of DNase II as a part of an anti-phage defense system in bacteria.}, }
@article {pmid35714537, year = {2022}, author = {Schmidt, SBI and Rodríguez-Rojas, A and Rolff, J and Schreiber, F}, title = {Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129280}, doi = {10.1016/j.jhazmat.2022.129280}, pmid = {35714537}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacillus subtilis ; *Disinfectants/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Gene Transfer, Horizontal ; Mutation ; Permethrin ; }, abstract = {Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.}, }
@article {pmid35709577, year = {2022}, author = {Akram, F and Haq, IU and Shah, FI and Aqeel, A and Ahmed, Z and Mir, AS and Qureshi, SS and Raja, SI}, title = {Genus Thermotoga: A valuable home of multifunctional glycoside hydrolases (GHs) for industrial sustainability.}, journal = {Bioorganic chemistry}, volume = {127}, number = {}, pages = {105942}, doi = {10.1016/j.bioorg.2022.105942}, pmid = {35709577}, issn = {1090-2120}, mesh = {*Bacteria/genetics ; *Glycoside Hydrolases/genetics ; Thermotoga ; }, abstract = {Nature is a dexterous and prolific chemist for cataloging a number of hostile niches that are the ideal residence of various thermophiles. Apart from having other species, these subsurface environments are considered a throne of bacterial genus Thermotoga. The genome sequence of Thermotogales encodes complex and incongruent clusters of glycoside hydrolases (GHs), which are superior to their mesophilic counterparts and play a prominent role in various applications due to their extreme intrinsic stability. They have a tremendous capacity to use a wide variety of simple and multifaceted carbohydrates through GHs, formulate fermentative hydrogen and bioethanol at extraordinary yield, and catalyze high-temperature reactions for various biotechnological applications. Nevertheless, no stringent rules exist for the thermo-stabilization of biocatalysts present in the genus Thermotoga. These enzymes endure immense attraction in fundamental aspects of how these polypeptides attain and stabilize their distinctive three-dimensional (3D) structures to accomplish their physiological roles. Moreover, numerous genome sequences from Thermotoga species have revealed a significant fraction of genes most closely related to those of archaeal species, thus firming a staunch belief of lateral gene transfer mechanism. However, the question of its magnitude is still in its infancy. In addition to GHs, this genus is a paragon of encapsulins which carry pharmacological and industrial significance in the field of life sciences. This review highlights an intricate balance between the genomic organizations, factors inducing the thermostability, and pharmacological and industrial applications of GHs isolated from genus Thermotoga.}, }
@article {pmid35709500, year = {2022}, author = {Pepperell, CS}, title = {Evolution of Tuberculosis Pathogenesis.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {661-680}, doi = {10.1146/annurev-micro-121321-093031}, pmid = {35709500}, issn = {1545-3251}, support = {R01 AI113287/AI/NIAID NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Humans ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis/microbiology ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made.}, }
@article {pmid35709325, year = {2022}, author = {Kotsaridis, K and Tsakiri, D and Sarris, PF}, title = {Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/1040841X.2022.2083939}, pmid = {35709325}, issn = {1549-7828}, abstract = {Plant-pathogens interaction is an ongoing confrontation leading to the emergence of new diseases. The majority of the invading microorganisms inject effector proteins into the host cell, to bypass the sophisticated defense system of the host. However, the effectors could also have other specialized functions, which can disrupt various biological pathways of the host cell. Pathogens can enrich their effectors arsenal to increase infection success or expand their host range. This usually is accomplished by the horizontal gene transfer. Nowadays, the development of specialized software that can predict proteins structure, has changed the experimental designing in effectors' function research. Different effectors of distinct plant pathogens tend to fold alike and have the same function and focussed structural studies on microbial effectors can help to uncover their catalytic/functional activities, while the structural similarity can enable cataloguing the great number of pathogens' effectors. In this review, we collectively present phytopathogens' effectors with known enzymatic functions and proteins structure, originated from all the kingdoms of microbial plant pathogens. Presentation of their common domains and motifs is also included. We believe that the in-depth understanding of the enemy's weapons will help the development of new strategies to prevent newly emerging or re-emerging plant pathogens.}, }
@article {pmid35706928, year = {2022}, author = {Chen, H and Mai, H and Lopes, B and Wen, F and Patil, S}, title = {Novel Pseudomonas aeruginosa Strains Co-Harbouring bla NDM-1 Metallo β-Lactamase and mcr-1 Isolated from Immunocompromised Paediatric Patients.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {2929-2936}, pmid = {35706928}, issn = {1178-6973}, abstract = {BACKGROUND: The rising resistance to carbapenems in Gram-negative bacteria worldwide poses a major clinical and public health risk. This study aimed to characterise carbapenem- and colistin-resistance genes, bla NDM-1 and mcr-1 located on IncX4 plasmid in MDR Pseudomonas aeruginosa, isolated from paediatric patients undergoing chemotherapy as a result of leukaemia.<br><br>METHODS: In this study, six carbapenem-resistant strains of P. aeruginosa were isolated from two paediatric patients under chemotherapy treatment (1.8 years old female and 2.1 years male) from the Shenzhen Hospital, China, in the year 2019. Isolates were screened for conventional antibiotics such as tobramycin, cefepime, imipenem, and ciprofloxacin in additional colistin by using the broth dilution method. Furthermore, resistance determinants: mcr-1, bla NDM-1, bla KPC-1, and bla GES were screened using PCR and sequencing followed by multi-locus sequence typing. The horizontal gene transfer and location of mcr-1 and bla NDM-1 were determined by a liquid mating assay. In addition, Incompatibility type (Inc), PCR-based replicon type, and subgroup (MOB) of plasmid were studied.<br><br>RESULTS: The screening for conventional antibiotics isolates showed 100% resistance to all the tested antibiotics except tobramycin. All isolates harboured carbapenemase encoding bla NDM-1, of which three also had mcr-1 located on a single IncX4 transferable plasmid. MLST typing revealed that four strains had a novel (new) STs type, while two belonged to ST1966.<br><br>CONCLUSION: This study identified for the first time colistin- and carbapenem-resistant MDR P. aeruginosa in paediatric patients with leukaemia in Shenzhen, China. It highlights the need for continuous surveillance in high-risk clones of MDR P. aeruginosa. Prudent use of antibiotics based on local antimicrobial susceptibility and clinical characteristics can help in reducing mortality in immunocompromised patients.}, }
@article {pmid35706021, year = {2022}, author = {Wu, B and Hao, W and Cox, MP}, title = {Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {144}, pmid = {35706021}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Plants/genetics ; }, abstract = {BACKGROUND: Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom's evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown.<br><br>RESULTS: By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways.<br><br>CONCLUSIONS: The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.}, }
@article {pmid35705132, year = {2022}, author = {Hoang, HTT and Higashi, A and Yamaguchi, T and Kawahara, R and Calvopina, M and Bastidas-Caldés, A and Yamamoto, M and Yamamoto, Y}, title = {Fusion plasmid carrying the colistin resistance gene mcr of Escherichia coli isolated from healthy residents.}, journal = {Journal of global antimicrobial resistance}, volume = {30}, number = {}, pages = {152-154}, doi = {10.1016/j.jgar.2022.06.007}, pmid = {35705132}, issn = {2213-7173}, mesh = {Colistin/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Escherichia coli Proteins/genetics ; Humans ; Plasmids/genetics ; }, abstract = {OBJECTIVES: The extensive spread of colistin resistance represents an enormous concern to infectious disease treatment, because colistin is one of the few effective antibiotics against multidrug-resistant bacterial infections, including carbapenem-resistant bacteria. This dissemination can be caused by plasmid transfer containing the colistin resistance gene mcr. Therefore, the plasmid host range affects horizontal gene transfer. This study reports a fusion plasmid of different incompatibility types, which could easily expand the plasmid host range, allowing widespread mcr prevalence in the microbial community.<br><br>METHODS: Genome sequences of colistin-resistant Escherichia coli isolates from stool specimens of healthy human residents in Ecuador were determined using the DNBSEQ and MinION platforms. Hybrid genome assembly was performed using Unicycler, and the genomes were annotated using DFAST. Genome analysis was performed using the Geneious Prime software.<br><br>RESULTS: Two colistin-resistant E. coli strains isolated separately from different residents presented mcr-carrying plasmids with fused different incompatibility types, IncFIA, IncHIIA, and IncHIIB. The phylogenies of these host bacteria were different. The sizes of the mcr-carrying fusion plasmids pLR-06 and pLR-50 with the full Tn6330 mcr-transposon were 260 Kbp and 198 Kbp, respectively. Both fusion plasmids possessed other resistance genes, including tet(B), tet(M), blaTEM-1b, sul3, cmlA1, aadA1, aadA2, fosA3, and dfrA12.<br><br>CONCLUSION: This is the first report of a fusion plasmid comprising different incompatibility types with mcr from colistin-resistant E. coli strains isolated from community residents. The mcr fusion plasmid may play a crucial role in achieving horizontal mcr transmission and the evolution of the multidrug resistance plasmid among hosts.}, }
@article {pmid35703039, year = {2022}, author = {Kurushima, J and Tomita, H}, title = {Advances of genetic engineering in streptococci and enterococci.}, journal = {Microbiology and immunology}, volume = {66}, number = {9}, pages = {411-417}, doi = {10.1111/1348-0421.13015}, pmid = {35703039}, issn = {1348-0421}, mesh = {CRISPR-Cas Systems ; *Enterococcus/genetics ; *Gene Editing/methods ; Genetic Engineering/methods ; Streptococcus/genetics ; }, abstract = {In the post-genome era, reverse genetic engineering is an indispensable methodology for experimental molecular biology to provide a deeper understanding of the principal relationship between genomic features and biological phenotypes. Technically, genetic engineering is carried out through allele replacement of a target genomic locus with a designed nucleotide sequence, so called site-directed mutagenesis. To art