@article {pmid37271423,
year = {2023},
author = {Feyereisen, R and Urban, JM and Nelson, DR},
title = {Aliens in the CYPome of the black fungus gnat, Bradysia coprophila.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {103965},
doi = {10.1016/j.ibmb.2023.103965},
pmid = {37271423},
issn = {1879-0240},
abstract = {The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.},
}

@article {pmid37270585,
year = {2023},
author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q},
title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37270585},
issn = {1751-7370},
abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.},
}

@article {pmid37270161,
year = {2023},
author = {Sharma, HK and Gupta, P and Nagpal, D and Mukherjee, M and Parmar, VS and Lather, V},
title = {Virtual screening and antimicrobial evaluation for identification of natural compounds as the prospective inhibitors of antibacterial drug resistance targets in Staphylococcus aureus.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {105554},
doi = {10.1016/j.fitote.2023.105554},
pmid = {37270161},
issn = {1873-6971},
abstract = {Infectious diseases have remained a burgeoning cause of death and disability since long. Staphylococcus aureus (S. aureus) is a severe bacterial pathogen causing nosocomial and community infections. It exhibits widespread resistance to antibiotics posing a significant threat to their efficacy. For combating this challenge, different strategies may include modifying existing antibiotics, developing new antibacterial agents, and combining treatments with resistance mechanism inhibitors. Resistance in S. aureus occurs through horizontal gene transfer or chromosomal mutations. Acquisition mechanisms involve enzymatic modification, efflux, target bypass, and drug displacement. Mutations can impact drug targets, activate efflux pumps, or alter cell wall composition to impede drug access. Overcoming S. aureus resistance requires innovative approaches to preserve antibiotic effectiveness. The present study involves the virtual screening of phytochemicals of diverse chemical classes from Zinc database against the antibiotic resistant targets of S. aureus like β-Lactamase, Penicillin Binding Protein 2a (PBP2a), Dihydrofolate reductase (DHFR), DNA gyrase, Multidrug ABC transporter SAV1866, Undecaprenyl diphosphate synthase (UPPS), etc. Thymol, eugenol, gallic acid, l-ascorbic acid, curcumin, berberine and quercetin were identified as potential molecules based on their docking score, binding interactions. These molecules were further analyzed for the ADMET and drug likeness properties using pkCSM, SwissADME and Qikprop tools. Further in vitro evaluation of these molecules against antibiotic-resistant strains of S. aureus, both alone and in combination with antibiotics revealed significant findings. Curcumin demonstrated the lowest MIC values (31.25-62.5 μg/ml) when tested individually. Thymol, berberine, and quercetin displayed MIC values within the range of 125-250 μg/ml, while eugenol and gallic acid exhibited MIC values ranging from 500 to 1000 μg/ml. Notably, thymol exhibited potent synergy with all four antibiotics against clinical isolates of S. aureus, with Fractional inhibitory concentration index (FICI) values consistently below 0.5, highlighting its exceptional antibacterial activity, especially in combination with amoxicillin.},
}

@article {pmid37270129,
year = {2023},
author = {Xu, Y and Liu, Q and Meng, G and Dong, C},
title = {Horizontal gene transfer of Cccyt contributes to virulence of mycoparasite Calcarisporium cordycipiticola by interacting with a host heat shock protein.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {124927},
doi = {10.1016/j.ijbiomac.2023.124927},
pmid = {37270129},
issn = {1879-0003},
abstract = {Horizontal gene transfer (HGT) is an important driving force for virulence evolution of pathogens, however, functions of these transferred genes are still not fully investigated. Here, an HGT effector, CcCYT was reported to contribute to virulence of a mycoparasite, Calcarisporium cordycipiticola to the host Cordyceps militaris, an important mushroom. Cccyt was predicted to be horizontally transferred from Actinobacteria ancestor by phylogenetic, synteny, GC content and codon usage pattern analyses. The transcript of Cccyt was sharply up-regulated at the early stage of infecting C. militaris. This effector was localized to the cell wall and contributed to the virulence of C. cordycipiticola without affecting its morphology, mycelial growth, conidiation, and resistance to abiotic stress. CcCYT can firstly bind the septa, and finally cytoplasm of the deformed hyphal cells of C. militaris. Pull-down assay coupled mass spectrometry revealed that proteins with which CcCYT interacted were related to protein process, folding and degradation. GST-Pull down assay confirmed that C. cordycipiticola effector CcCYT can interact with host protein CmHSP90 to inhibit the immune response of host. The results provided functional evidence that HGT is an important driving force for the virulence evolution and will be helpful for revealing the interaction between mycoparasite and mushroom host.},
}

@article {pmid37269713,
year = {2023},
author = {Dai, X and Zhao, J and Sun, J and Chen, L and Han, P and Wang, X and Huang, J and Wang, L},
title = {ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis.},
journal = {Veterinary microbiology},
volume = {283},
number = {},
pages = {109795},
doi = {10.1016/j.vetmic.2023.109795},
pmid = {37269713},
issn = {1873-2542},
abstract = {Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10[-5]. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.},
}

@article {pmid37268165,
year = {2023},
author = {Kameswaran, S and Ramesh, B},
title = {Quenching and Quorum Sensing in Bacterial Bio-films.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104085},
doi = {10.1016/j.resmic.2023.104085},
pmid = {37268165},
issn = {1769-7123},
abstract = {Quorum sensing (QS) is the ability of bacteria to monitor their population density and adjust gene expression accordingly. QS-regulated processes include host-microbe interactions, horizontal gene transfer, and multicellular behaviours (such as the growth and development of biofilm). The creation, transfer, and perception of bacterial chemicals known as autoinducers or QS signals are necessary for QS signalling (e.g. N-acylhomoserine lactones). Quorum quenching (QQ), another name for the disruption of QS signalling, comprises a wide range of events and mechanisms that are described and analysed in this study. In order to better comprehend the targets of the QQ phenomena that organisms have naturally developed and are currently being actively researched from practical perspectives, we first surveyed the diversity of QS-signals and QS-associated responses. Next, the mechanisms, molecular players, and targets related to QS interference are discussed, with a focus on natural QQ enzymes and compounds that function as QS inhibitors. To illustrate the processes and biological functions of QS inhibition in microbe-microbe and host-microbe interactions, a few QQ paradigms are described in detail. Finally, certain QQ techniques are offered as potential instruments in a variety of industries, including agriculture, medical, aquaculture, crop production, and anti-biofouling areas.},
}

@article {pmid37267763,
year = {2023},
author = {Sun, S and Wang, Q and Wang, N and Yang, S and Qi, H},
title = {High-risk antibiotics positively correlated with antibiotic resistance genes in five typical urban wastewater.},
journal = {Journal of environmental management},
volume = {342},
number = {},
pages = {118296},
doi = {10.1016/j.jenvman.2023.118296},
pmid = {37267763},
issn = {1095-8630},
abstract = {Antibiotic resistance genes (ARGs) and antibiotic amount increased within close proximity to human dominated ecosystems. However, few studies assessed the distribution of antibiotics and ARGs in multiple ecosystems especially the different urban wastewater. In this study, the spatial distribution of ARGs and antibiotics across the urban wastewater included domestic, livestock, hospital, pharmaceutical wastewater, influent of the wastewater treatment plant (WWTP) in Northeast China. The q-PCR results showed that ARGs were most abundant in community wastewater and followed by WWTP influent, livestock wastewater, pharmaceutical wastewater and hospital wastewater. The ARG composition differed among the five ecotypes with qnrS was the dominant ARG subtypes in WWTP influent and community wastewater, while sul2 dominant in livestock, hospital, pharmaceutical wastewater. The concentration of antibiotics was closely related to the antibiotic usage and consumption data. In addition to the high concentration of azithromycin at all sampling points, more than half of the antibiotics in livestock wastewater were veterinary antibiotics. However, antibiotics that closely related to humankind such as roxithromycin and sulfamethoxazole accounted for a higher proportion in hospital wastewater (13.6%) and domestic sewage (33.6%), respectively. The ambiguous correlation between ARGs and their corresponding antibiotics was detected. However, antibiotics that exhibited high ecotoxic effects were closely and positively correlated with ARGs and the class 1 integrons (intI1), which indicated that high ecotoxic compounds might affect antimicrobial resistance of bacteria by mediating horizontal gene transfer of ARGs. The coupling mechanism between the ecological risk of antibiotics and bacterial resistance needed to be further studied, and thereby provided a new insight to study the impact of environmental pollutants on ARGs in various ecotypes.},
}

@article {pmid37267681,
year = {2023},
author = {Carlsen, L and Büttner, H and Christner, M and Cordts, L and Franke, G and Hoffmann, A and Knobling, B and Lütgehetmann, M and Nakel, J and Werner, T and Knobloch, JK},
title = {Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany.},
journal = {Journal of infection and public health},
volume = {16},
number = {8},
pages = {1142-1148},
doi = {10.1016/j.jiph.2023.05.029},
pmid = {37267681},
issn = {1876-035X},
abstract = {BACKGROUND: Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages.

METHODS: In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n = 59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n = 240).

RESULTS: Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum β-lactamases decreased over time.

CONCLUSIONS: This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.},
}

@article {pmid37263036,
year = {2023},
author = {Wu, C and Zhang, G and Zhang, K and Sun, J and Cui, Z and Guo, Y and Liu, H and Xu, W},
title = {Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China.},
journal = {Journal of environmental management},
volume = {342},
number = {},
pages = {118132},
doi = {10.1016/j.jenvman.2023.118132},
pmid = {37263036},
issn = {1095-8630},
abstract = {Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.},
}

@article {pmid37261234,
year = {2023},
author = {Fatima, S and Ishaq, Z and Irfan, M and AlAsmari, AF and Achakzai, JK and Zaheer, T and Ali, A and Akbar, A},
title = {Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1151805},
pmid = {37261234},
issn = {2296-2565},
abstract = {INTRODUCTION: Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden.

METHODS: In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization.

RESULTS AND DISCUSSION: MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.},
}

@article {pmid37258869,
year = {2023},
author = {Abdelrazik, E and El-Hadidi, M},
title = {Tracking Antibiotic Resistance from the Environment to Human Health.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {289-301},
pmid = {37258869},
issn = {1940-6029},
abstract = {Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.},
}

@article {pmid37257204,
year = {2023},
author = {Chen, P and Yu, K and He, Y},
title = {The dynamics and transmission of antibiotic resistance associated with plant microbiomes.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107986},
doi = {10.1016/j.envint.2023.107986},
pmid = {37257204},
issn = {1873-6750},
abstract = {Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.},
}

@article {pmid37256324,
year = {2023},
author = {Oliveira, GS and Lentz, SA and Wink, PL and Martins, AF},
title = {Molecular typing of mcr-1 Escherichia coli isolates from pigs and farm environment based on fumC and fimH alleles.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2022-0173},
pmid = {37256324},
issn = {1746-0921},
abstract = {Background: The dissemination of polymyxin resistance represents a significant threat to public health. Materials & methods: Sequence-based typing was performed by 53 mcr-1 Escherichia coli isolates using fumC/fimH (CH) genes to characterize clones spreading from pig farming. Furthermore, 12 isolates had their whole genome sequenced for phylogenetic study. Results: The isolates were classified into 22 distinct CH types, and two novel CH types (CH41-1578 and CH4-1579) and one sequence type (ST12652) was also described. According to phylogenetic study, both multilocus sequence typing and CH methods grouped the isolates similarly. Conclusion: Our findings suggest that the dissemination of the mcr-1 gene in pig farming has occurred mainly by horizontal gene transfer, and CH typing proved to be a good tool to characterize E. coli clones.},
}

@article {pmid37254648,
year = {2023},
author = {Rana, R and Jaiswal, G and Bansal, K and Patil, PB},
title = {Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.13164},
pmid = {37254648},
issn = {1758-2229},
abstract = {Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.},
}

@article {pmid37252660,
year = {2023},
author = {Tokuda, R and Iwabuchi, N and Kitazawa, Y and Nijo, T and Suzuki, M and Maejima, K and Oshima, K and Namba, S and Yamaji, Y},
title = {Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes.},
journal = {Frontiers in genetics},
volume = {14},
number = {},
pages = {1132432},
pmid = {37252660},
issn = {1664-8021},
abstract = {Phytoplasmas are obligate intracellular plant pathogenic bacteria that can induce phyllody, which is a type of abnormal floral organ development. Phytoplasmas possess phyllogens, which are effector proteins that cause phyllody in plants. Phylogenetic comparisons of phyllogen and 16S rRNA genes have suggested that phyllogen genes undergo horizontal transfer between phytoplasma species and strains. However, the mechanisms and evolutionary implications of this horizontal gene transfer are unclear. Here, we analyzed synteny in phyllogen flanking genomic regions from 17 phytoplasma strains that were related to six 'Candidatus' species, including three strains newly sequenced in this study. Many of the phyllogens were flanked by multicopy genes within potential mobile units (PMUs), which are putative transposable elements found in phytoplasmas. The multicopy genes exhibited two distinct patterns of synteny that correlated with the linked phyllogens. The low level of sequence identities and partial truncations found among these phyllogen flanking genes indicate that the PMU sequences are deteriorating, whereas the highly conserved sequences and functions (e.g., inducing phyllody) of the phyllogens suggest that the latter are important for phytoplasma fitness. Furthermore, although their phyllogens were similar, PMUs in strains related to 'Ca. P. asteris' were often located in different regions of the genome. These findings strongly indicate that PMUs drive the horizontal transfer of phyllogens among phytoplasma species and strains. These insights improve our understanding of how symptom-determinant genes have been shared among phytoplasmas.},
}

@article {pmid37251586,
year = {2023},
author = {Scott, TW and West, SA and Dewar, AE and Wild, G},
title = {Is cooperation favored by horizontal gene transfer?.},
journal = {Evolution letters},
volume = {7},
number = {3},
pages = {113-120},
pmid = {37251586},
issn = {2056-3744},
abstract = {It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.},
}

@article {pmid37250807,
year = {2023},
author = {Mwakyoma, AA and Kidenya, BR and Minja, CA and Mushi, MF and Sandeman, A and Sabiti, W and Holden, MTG and Mshana, SE},
title = {Comparison of Horizontal blaCTX-M Gene Transfer via Conjugation among Extended Spectrum β-Lactamases Producing Escherichia coli Isolates from Patients with Urinary Tract Infection, Their Animals, and Environment.},
journal = {Archives of molecular biology and genetics},
volume = {2},
number = {1},
pages = {1-8},
pmid = {37250807},
issn = {2831-6754},
abstract = {BACKGROUND: The dissemination of the extended spectrum β-lactamases (ESBL) producing E. coli poses a significant public health problem. Understanding the efficiency and frequency of horizontal gene transfer via conjugation of ESBL producing E. coli is imperative towards devising prevention and control measures. This study compared the frequencies and efficiencies of horizontal blaCTX-M gene transfer via conjugation among Escherichia coli isolates from urine and gastrointestinal tract (GIT) of patients with urinary tract infection (UTI), their animals and environment.

METHODS: Horizontal blaCTX-M gene transfer via conjugation by a broth mating experiment was performed using 50 confirmed ESBL producing E. coli isolates as donors and Escherichia coli J53 (F[-], met, pro, Az[r]), as the recipient. The transconjugants were detected and their frequencies and efficiencies of conjugation were measured and compared between ESBL producing E. coli isolates multi-sourced from urine, GIT, animals and environment. Antimicrobial susceptibility testing of all resulting transconjugants was performed. DNA was extracted from all transconjugants to confirm the presence and the acquisition of blaCTX-M gene.

RESULTS: Out of 50 ESBL producing E. coli isolates harboring blaCTX-M gene, 37 (74.0%) successfully exercised horizontal gene transfer through conjugation. All transconjugants were confirmed phenotypically and genotypically by PCR. Of note, all of the isolates from environment 100.0% (7/7) performed conjugation, exhibiting the highest transfer efficiency, followed by isolates from urine and animals, with the conjugation transfer efficiency of 77.8% (14/18) and 76.1% (10/13), respectively. The isolates from the environment conjugated with a significant more efficiency than those from the GIT [Two-sample test of proportions; p-value = 0.0119]. The overall conjugation transfer frequencies ranged from 0.4 × 10[-14] - 5.5 × 10[-11] per donor cells with the highest median conjugation transfer frequency observed among isolates from animal (3.23 × 10[-12] [IQR: 0.70 × 10[-12] - 7.22 × 10[-12]]) followed by that of isolates from the environment (1.60 × 10[-12] [IQR: 0.30 × 10[-12] - 5.0 × 10[-12]]).

CONCLUSION: ESBL producing E. coli from human, animals and environment exercises horizontal blaCTX-M gene transfer efficiently with the highest occurrence among isolates from the environment and animals. The antimicrobial resistance control and prevention strategies should be widened up to explore strategies to prevent horizontal AMR gene transfer.},
}

@article {pmid37246713,
year = {2023},
author = {Jowsey, WJ and Morris, CRP and Hall, DA and Sullivan, JT and Fagerlund, RD and Eto, KY and Solomon, PD and Mackay, JP and Bond, CS and Ramsay, JP and Ronson, CW},
title = {DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad457},
pmid = {37246713},
issn = {1362-4962},
abstract = {Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer.},
}

@article {pmid37246198,
year = {2023},
author = {Shafique, MS and Guo, W and Chen, X and Zhao, K and Liu, Y and Wang, C and Ji, Z},
title = {Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice.},
journal = {Functional & integrative genomics},
volume = {23},
number = {2},
pages = {189},
pmid = {37246198},
issn = {1438-7948},
}

@article {pmid37243281,
year = {2023},
author = {Arnau, V and Díaz-Villanueva, W and Mifsut Benet, J and Villasante, P and Beamud, B and Mompó, P and Sanjuan, R and González-Candelas, F and Domingo-Calap, P and Džunková, M},
title = {Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts.},
journal = {Viruses},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/v15051196},
pmid = {37243281},
issn = {1999-4915},
abstract = {The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.},
}

@article {pmid37239594,
year = {2023},
author = {Tuvo, B and Scarpaci, M and Bracaloni, S and Esposito, E and Costa, AL and Ioppolo, M and Casini, B},
title = {Microplastics and Antibiotic Resistance: The Magnitude of the Problem and the Emerging Role of Hospital Wastewater.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {10},
pages = {},
doi = {10.3390/ijerph20105868},
pmid = {37239594},
issn = {1660-4601},
abstract = {The role of microplastics (MPs) in the spread of antibiotic resistance genes (ARGs) is increasingly attracting global research attention due to their unique ecological and environmental effects. The ubiquitous use of plastics and their release into the environment by anthropic/industrial activities are the main sources for MP contamination, especially of water bodies. Because of their physical and chemical characteristics, MPs represent an ideal substrate for microbial colonization and formation of biofilm, where horizontal gene transfer is facilitated. In addition, the widespread and often injudicious use of antibiotics in various human activities leads to their release into the environment, mainly through wastewater. For these reasons, wastewater treatment plants, in particular hospital plants, are considered hotspots for the selection of ARGs and their diffusion in the environment. As a result, the interaction of MPs with drug-resistant bacteria and ARGs make them vectors for the transport and spread of ARGs and harmful microorganisms. Microplastic-associated antimicrobial resistance is an emerging threat to the environment and consequently for human health. More studies are required to better understand the interaction of these pollutants with the environment as well as to identify effective management systems to reduce the related risk.},
}

@article {pmid37239483,
year = {2023},
author = {Alim, NTB and Koppenhöfer, S and Lang, AS and Beatty, JT},
title = {Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/genes14051124},
pmid = {37239483},
issn = {2073-4425},
abstract = {A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.},
}

@article {pmid37239397,
year = {2023},
author = {Dey, S and Gaur, M and Sykes, EME and Prusty, M and Elangovan, S and Dixit, S and Pati, S and Kumar, A and Subudhi, E},
title = {Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/genes14051037},
pmid = {37239397},
issn = {2073-4425},
abstract = {BACKGROUND: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.

METHODS: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.

RESULTS: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.

CONCLUSIONS: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.},
}

@article {pmid37237011,
year = {2023},
author = {Negeri, AA and Mamo, H and Gahlot, DK and Gurung, JM and Seyoum, ET and Francis, MS},
title = {Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8595},
pmid = {37237011},
issn = {2045-2322},
abstract = {CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.},
}

@article {pmid37236960,
year = {2023},
author = {Wang, WJ and Yu, LM and Shao, MY and Jia, YT and Liu, LQ and Ma, XH and Zheng, Y and Liu, YF and Zhang, YZ and Luo, XX and Li, FM and Zheng, H},
title = {Research review on the pollution of antibiotic resistance genes in livestock and poultry farming environments.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {5},
pages = {1415-1429},
doi = {10.13287/j.1001-9332.202305.032},
pmid = {37236960},
issn = {1001-9332},
abstract = {Increasingly serious pollution of antibiotic resistance genes (ARGs) caused by the abuse of antibiotics in livestock and poultry industry has raised worldwide concerns. ARGs could spread among various farming environmental media through adsorption, desorption, migration, and also could transfer into human gut microbiome by hori-zontal gene transfer (HGT), posing potential threats to public health. However, the comprehensive review on the pollution patterns, environmental behaviors, and control techniques of ARGs in livestock and poultry environments in view of One Health is still inadequate, resulting in the difficulties in effectively assessing ARGs transmission risk and developing the efficient control strategies. Here, we analyzed the pollution characteristics of typical ARGs in various countries, regions, livestock species, and environmental media, reviewed the critical environmental fate and influencing factors, control strategies, and the shortcomings of current researches about ARGs in the livestock and poultry farming industry combined with One Health philosophy. In particular, we addressed the importance and urgency of identifying the distribution characteristics and environmental process mechanisms of ARGs, and developing green and efficient ARG control means in livestock farming environments. We further proposed gaps and prospects for the future research. It would provide theoretical basis for the research on health risk assessment and technology exploitation of alleviating ARG pollution in livestock farming environment.},
}

@article {pmid37236388,
year = {2023},
author = {Song, D and Tang, X and Tariq, A and Pan, K and Li, D},
title = {Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau.},
journal = {Environmental research},
volume = {},
number = {},
pages = {116233},
doi = {10.1016/j.envres.2023.116233},
pmid = {37236388},
issn = {1096-0953},
abstract = {Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 10[5] to 6.22 × 10[7] copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.},
}

@article {pmid37232518,
year = {2023},
author = {Burch, CL and Romanchuk, A and Kelly, M and Wu, Y and Jones, CD},
title = {Empirical evidence that complexity limits horizontal gene transfer.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad089},
pmid = {37232518},
issn = {1759-6653},
abstract = {Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of protein families, and facilitating the evolution of new phenotypes, new metabolic pathways, and new species. Comparative studies of gene gain in bacteria suggest that the frequency with which individual genes successfully undergo HGT varies considerably and may be associated with the number of protein-protein interactions in which the gene participates, i.e., its connectivity. Two non-exclusive hypotheses have emerged to explain why transferability should decrease with connectivity: the Complexity Hypothesis (Jain, Rivera, & Lake, 1999) and the Balance Hypothesis (Papp, Pál, & Hurst, 2003). These hypotheses predict that the functional costs of HGT arise from a failure of divergent homologues to make normal protein-protein interactions or from gene mis-expression, respectively. Here we describe genome-wide assessments of these hypotheses in which we used 74 existing prokaryotic whole genome shotgun libraries to estimate rates of horizontal transfer of genes from taxonomically diverse prokaryotic donors into E. coli. We show that 1) transferability declines as connectivity increases, 2) transferability declines as the divergence between donor and recipient orthologs increases, and that 3) the magnitude of this negative effect of divergence on transferability increases with connectivity. These effects are particularly robust among the translational proteins, which span the widest range of connectivities. Whereas the Complexity Hypotheses explains all three of these observations, the Balance Hypothesis explains only the first one.},
}

@article {pmid37115189,
year = {2023},
author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR},
title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.},
journal = {Microbial genomics},
volume = {9},
number = {4},
pages = {},
pmid = {37115189},
issn = {2057-5858},
support = {U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; },
abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.},
}

*Microbiota/genetics
Metagenome
Biological Evolution

@article {pmid37227565,
year = {2023},
author = {Chettri, U and Nongkhlaw, M and Joshi, SR},
title = {Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.},
journal = {Current microbiology},
volume = {80},
number = {7},
pages = {226},
pmid = {37227565},
issn = {1432-0991},
abstract = {Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to PIB-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of PIB-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.},
}

@article {pmid37227251,
year = {2023},
author = {Tonkin-Hill, G and Corander, J and Parkhill, J},
title = {Challenges in prokaryote pangenomics.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001021},
pmid = {37227251},
issn = {2057-5858},
abstract = {Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.},
}

@article {pmid37223257,
year = {2021},
author = {Liu, J and Soler, N and Gorlas, A and Cvirkaite-Krupovic, V and Krupovic, M and Forterre, P},
title = {Extracellular membrane vesicles and nanotubes in Archaea.},
journal = {microLife},
volume = {2},
number = {},
pages = {uqab007},
pmid = {37223257},
issn = {2633-6693},
abstract = {Membrane-bound extracellular vesicles (EVs) are secreted by cells from all three domains of life and their implication in various biological processes is increasingly recognized. In this review, we summarize the current knowledge on archaeal EVs and nanotubes, and emphasize their biological significance. In archaea, the EVs and nanotubes have been largely studied in representative species from the phyla Crenarchaeota and Euryarchaeota. The archaeal EVs have been linked to several physiological processes such as detoxification, biomineralization and transport of biological molecules, including chromosomal, viral or plasmid DNA, thereby taking part in genome evolution and adaptation through horizontal gene transfer. The biological significance of archaeal nanotubes is yet to be demonstrated, although they could participate in EV biogenesis or exchange of cellular contents. We also discuss the biological mechanisms leading to EV/nanotube biogenesis in Archaea. It has been recently demonstrated that, similar to eukaryotes, EV budding in crenarchaea depends on the ESCRT machinery, whereas the mechanism of EV budding in euryarchaeal lineages, which lack the ESCRT-III homologues, remains unknown.},
}

@article {pmid37223255,
year = {2021},
author = {Afonina, I and Tien, B and Nair, Z and Matysik, A and Lam, LN and Veleba, M and Jie, AKJ and Rashid, R and Cazenave-Gassiot, A and Wenk, M and Wai, SN and Kline, KA},
title = {The composition and function of Enterococcus faecalis membrane vesicles.},
journal = {microLife},
volume = {2},
number = {},
pages = {uqab002},
pmid = {37223255},
issn = {2633-6693},
abstract = {Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host-pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.},
}

@article {pmid37221009,
year = {2023},
author = {Shaferman, M and Gencel, M and Alon, N and Alasad, K and Rotblat, B and Serohijos, AWR and Alfonta, L and Bershtein, S},
title = {The fitness effects of codon composition of the horizontally transferred antibiotic resistance genes intensify at sub-lethal antibiotic levels.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad123},
pmid = {37221009},
issn = {1537-1719},
abstract = {The rampant variability in codon bias existing between bacterial genomes is expected to interfere with horizontal gene transfer (HGT), a phenomenon that drives bacterial adaptation. However, delineating the constraints imposed by codon bias on functional integration of the transferred genes is complicated by multiple genomic and functional barriers controlling HGT, and by the dependence of the evolutionary outcomes of HGT on the host's environment. Here, we designed an experimental system in which codon composition of the transferred genes is the only variable triggering fitness change of the host. We replaced E. coli's chromosomal folA gene encoding dihydrofolate reductase, an essential enzyme that constitutes a target for trimethoprim, with combinatorial libraries of synonymous codons of folA genes from trimethoprim-sensitive Listeria grayi and trimethoprim-resistant Neisseria sicca. The resulting populations underwent selection at a range of trimethoprim concentrations, and the ensuing changes in variant frequencies were used to infer the fitness effects of the individual combinations of codons. We found that when HGT causes overstabilization of the 5'-end mRNA, the fitness contribution of mRNA folding stability dominates over that of codon optimality. The 5'-end overstabilization can also lead to mRNA accumulation outside of the polysome, thus preventing the decay of the foreign transcripts despite the codon composition-driven reduction in translation efficiency. Importantly, the fitness effects of mRNA stability or codon optimality become apparent only at sub-lethal levels of trimethoprim individually tailored for each library, emphasizing the central role of the host's environment in shaping the codon bias compatibility of horizontally transferred genes.},
}

@article {pmid37219457,
year = {2023},
author = {Murthy, AC and Aleksanyan, N and Morton, GM and Toyoda, HC and Kalashyan, M and Chen, S and Ragucci, AE and Broulidakis, MP and Swerdlow, KJ and Bui, MNN and Muccioli, M and Berkmen, MB},
title = {Characterization of ConE, the VirB4 Homolog of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0003323},
doi = {10.1128/jb.00033-23},
pmid = {37219457},
issn = {1098-5530},
abstract = {Conjugation is a major form of horizontal gene transfer, contributing to bacterial evolution and the acquisition of new traits. During conjugation, a donor cell transfers DNA to a recipient through a specialized DNA translocation channel classified as a type IV secretion system (T4SS). Here, we focused on the T4SS of ICEBs1, an integrative and conjugative element in Bacillus subtilis. ConE, encoded by ICEBs1, is a member of the VirB4 family of ATPases, the most conserved component of T4SSs. ConE is required for conjugation and localizes to the cell membrane, predominantly at the cell poles. In addition to Walker A and B boxes, VirB4 homologs have conserved ATPase motifs C, D, and E. Here, we created alanine substitutions in five conserved residues within or near ATPase motifs in ConE. Mutations in all five residues drastically decreased conjugation frequency but did not affect ConE protein levels or localization, indicating that an intact ATPase domain is critical for DNA transfer. Purified ConE is largely monomeric with some oligomers and lacks enzymatic activity, suggesting that ATP hydrolysis may be regulated or require special solution conditions. Finally, we investigated which ICEBs1 T4SS components interact with ConE using a bacterial two-hybrid assay. ConE interacts with itself, ConB, and ConQ, but these interactions are not required to stabilize ConE protein levels and largely do not depend on conserved residues within the ATPase motifs of ConE. The structure-function characterization of ConE provides more insight into this conserved component shared by all T4SSs. IMPORTANCE Conjugation is a major form of horizontal gene transfer and involves the transfer of DNA from one bacterium to another through the conjugation machinery. Conjugation contributes to bacterial evolution by disseminating genes involved in antibiotic resistance, metabolism, and virulence. Here, we characterized ConE, a protein component of the conjugation machinery of the conjugative element ICEBs1 of the bacterium Bacillus subtilis. We found that mutations in the conserved ATPase motifs of ConE disrupt mating but do not alter ConE localization, self-interaction, or levels. We also explored which conjugation proteins ConE interacts with and whether these interactions contribute to stabilizing ConE. Our work contributes to the understanding of the conjugative machinery of Gram-positive bacteria.},
}

@article {pmid37218693,
year = {2023},
author = {Bejenari, M and Sondergaard, TE and Sørensen, JL},
title = {6-MSA, a secondary metabolite distribution hub with multiple fungal destinations.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxad107},
pmid = {37218693},
issn = {1365-2672},
abstract = {6-methylsalicylic acid is a small, simple polyketide produced by a broad spectrum of fungal species. Since fungi obtained the ability to synthesize 6-MSA from bacteria through a horizontal gene transfer event, it has developed into a multipurpose metabolic hub from where numerous complex compounds are produced. The most relevant metabolite from a human perspective is the small lactone patulin as it is one of the most potent mycotoxins. Other important end products derived from 6-MSA include the small quinone epoxide terreic acid and the prenylated yanuthones. The most advanced modification of 6-MSA is observed in the aculin biosynthetic pathway, which is mediated by a non-ribosomal peptide synthase and a terpene cyclase. In this short review, we summarize for the first time all the possible pathways that takes their onset from 6-MSA and provide a synopsis of the responsible gene clusters and derive the resulting biosynthetic pathways.},
}

@article {pmid37078595,
year = {2023},
author = {Botelho, J},
title = {Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance.},
journal = {Nucleic acids research},
volume = {51},
number = {9},
pages = {4385-4397},
pmid = {37078595},
issn = {1362-4962},
mesh = {*Anti-Bacterial Agents ; Virulence/genetics ; *Conjugation, Genetic ; Gene Transfer, Horizontal ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.},
}

*Anti-Bacterial Agents
Virulence/genetics
*Conjugation, Genetic
Gene Transfer, Horizontal
Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences

@article {pmid37217185,
year = {2023},
author = {Maruyama, M and Kagamoto, T and Matsumot, Y and Onum, R and Miyagishima, SY and Tanifuj, G and Nakazawa, M and Kashiyama, Y},
title = {Horizontally Acquired Nitrate Reductase Realized Kleptoplastic Photoautotrophy of Rapaza viridis.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcad044},
pmid = {37217185},
issn = {1471-9053},
abstract = {While photoautotrophic organisms utilize inorganic nitrogen as the nitrogen source, heterotrophic organisms utilize organic nitrogen and thus do not generally have an inorganic nitrogen assimilation pathway. Here we focused on the nitrogen metabolism of Rapaza viridis, a unicellular eukaryote exhibiting kleptoplasty. Although belonging to the lineage of essentially heterotrophic flagellates, R. viridis exploits the photosynthetic products of the kleptoplasts and was therefore suspected to potentially utilize inorganic nitrogen. From the transcriptome data of R. viridis, we identified the gene RvNaRL, which had sequence similarity to nitrate reductases found in plants. Phylogenetic analysis revealed that RvNaRL was acquired by a horizontal gene transfer event. To verify its function of the protein product RvNaRL, we established a RNAi mediated knockdown and a CRISPR-Cas9-mediated knockout experiments for the first time in R. viridis and applied them to this gene. The RvNaRL knockdown and knockout cells exhibited significant growth only when ammonium was supplied. However, in contrast to the wild-type cells, no substantial growth was observed when nitrate was supplied. Such arrested growth in absence of ammonium was attributed to impaired amino acid synthesis due to the deficiency of nitrogen supply from the nitrate assimilation pathway; this in turn resulted in the accumulation of excess photosynthetic products in the form of cytosolic polysaccharide grains as observed. These results indicate that RvNaRL is certainly involved in nitrate assimilation by R. viridis. Thus, we inferred that R. viridis achieved its advanced kleptoplasty for photoautotrophy, owing to acquisition of the nitrate assimilation by the horizontal gene transfer.},
}

@article {pmid37215039,
year = {2023},
author = {Giengkam, S and Kullapanich, C and Wongsantichon, J and Adcox, HE and Gillespie, JJ and Salje, J},
title = {Orientia tsutsugamushi: analysis of the mobilome of a highly fragmented and repetitive genome reveals ongoing lateral gene transfer in an obligate intracellular bacterium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.05.11.540415},
pmid = {37215039},
abstract = {The rickettsial human pathogen Orientia tsutsugamushi (Ot) is an obligate intracellular Gram-negative bacterium with one of the most highly fragmented and repetitive genomes of any organism. Around 50% of its ∼2.3 Mb genome is comprised of repetitive DNA that is derived from the highly proliferated Rickettsiales amplified genetic element (RAGE). RAGE is an integrative and conjugative element (ICE) that is present in a single Ot genome in up to 92 copies, most of which are partially or heavily degraded. In this report, we analysed RAGEs in eight fully sequenced Ot genomes and manually curated and reannotated all RAGE-associated genes, including those encoding DNA mobilisation proteins, P-type (vir) and F-type (tra) type IV secretion system (T4SS) components, Ankyrin repeat- and tetratricopeptide repeat-containing effectors, and other piggybacking cargo. Originally, the heavily degraded Ot RAGEs led to speculation that they are remnants of historical ICEs that are no longer active. Our analysis, however, identified two Ot genomes harbouring one or more intact RAGEs with complete F-T4SS genes essential for mediating ICE DNA transfer. As similar ICEs have been identified in unrelated rickettsial species, we assert that RAGEs play an ongoing role in lateral gene transfer within the Rickettsiales. Remarkably, we also identified in several Ot genomes remnants of prophages with no similarity to other rickettsial prophages. Together these findings indicate that, despite their obligate intracellular lifestyle and host range restricted to mites, rodents and humans, Ot genomes are highly dynamic and shaped through ongoing invasions by mobile genetic elements and viruses.},
}

@article {pmid37213501,
year = {2023},
author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X},
title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1145315},
pmid = {37213501},
issn = {1664-302X},
abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.},
}

@article {pmid37213168,
year = {2023},
author = {Youngblom, MA and Shockey, AC and Callaghan, MM and Dillard, JP and Pepperell, CS},
title = {The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
doi = {10.1099/mgen.0.000985},
pmid = {37213168},
issn = {2057-5858},
abstract = {The incidence of gonorrhoea is increasing at an alarming pace, and therapeutic options continue to narrow as a result of worsening drug resistance. Neisseria gonorrhoeae is naturally competent, allowing the organism to adapt rapidly to selection pressures including antibiotics. A sub-population of N. gonorrhoeae carries the Gonococcal Genetic Island (GGI), which encodes a type IV secretion system (T4SS) that secretes chromosomal DNA. Previous research has shown that the GGI increases transformation efficiency in vitro, but the extent to which it contributes to horizontal gene transfer (HGT) during infection is unknown. Here we analysed genomic data from clinical isolates of N. gonorrhoeae to better characterize GGI+ and GGI- sub-populations and to delineate patterns of variation at the locus itself. We found the element segregating at an intermediate frequency (61%), and it appears to act as a mobile genetic element with examples of gain, loss, exchange and intra-locus recombination within our sample. We further found evidence suggesting that GGI+ and GGI- sub-populations preferentially inhabit distinct niches with different opportunities for HGT. Previously, GGI+ isolates were reported to be associated with more severe clinical infections, and our results suggest this could be related to metal-ion trafficking and biofilm formation. The co-segregation of GGI+ and GGI- isolates despite mobility of the element suggests that both niches inhabited by N. gonorrhoeae remain important to its overall persistence as has been demonstrated previously for cervical- and urethral-adapted sub-populations. These data emphasize the complex population structure of N. gonorrhoeae and its capacity to adapt to diverse niches.},
}

@article {pmid37213139,
year = {2023},
author = {C Silva-de-Jesus, A and Rossi, CC and Pereira-Ribeiro, PM and Guaraldi, AL and Giambiagi-deMarval, M},
title = {Unusual carriage of virulence genes sasX/sesI/shsA by nosocomial Staphylococcus haemolyticus from Brazil.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2022-0225},
pmid = {37213139},
issn = {1746-0921},
abstract = {Background: Staphylococcus haemolyticus is an emerging threat in the nosocomial environment but only some virulence factors are known. Materials & methods: The frequency of the sasX gene (or orthologues sesI/shsA), encoding an invasiveness-related surface-associated protein, in S. haemolyticus was detected in different hospitals in Rio de Janeiro. Results: 9.4% of strains were sasX/sesI/shsA-positive, some were in the context of the ΦSPβ-like prophage and devoid of CRISPR systems, indicating potential transferability of their virulence genes. Gene sequencing evidenced that Brazilian S. haemolyticus harbored sesI, instead of the usual sasX, while S. epidermidis had sasX instead of sesI, suggesting horizontal acquisition. Conclusion: The contexts of Brazilian sasX/sesI/shsA favor transfer, which is alarming given the difficulty in treating infections caused by S. haemolyticus.},
}

@article {pmid37210032,
year = {2023},
author = {Yin, Y and Lou, T and Song, W and Wang, C and Wang, J},
title = {Production of medium chain fatty acids from antibiotic fermentation residuals pretreated by ionizing radiation: Elimination of antibiotic resistance genes.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {129180},
doi = {10.1016/j.biortech.2023.129180},
pmid = {37210032},
issn = {1873-2976},
abstract = {The propagation of antibiotic resistance genes (ARGs) restricts the application of antibiotic fermentation residues (AFRs). This study investigated medium chain fatty acids (MCFA) production from AFRs, focusing on the effect of ionizing radiation pretreatment on the fates of ARGs. The results indicated that ionizing radiation pretreatment not only stimulated the MCFA production, but also inhibited the proliferation of ARGs. Radiation at 10-50 kGy decreased ARGs abundances by 0.6-21.1% at the end of fermentation process. Mobile genetic elements (MGEs) exhibited higher resistance to ionizing radiation, radiation over 30 kGy was required to suppress the proliferation of MGEs. Radiation at 50 kGy achieved an adequate inhibition to MGEs, and the degradation efficiency was 17.8-74.5% for different kinds of MGEs. This work suggested that ionizing radiation pretreatment could be a good option to ensure the safer application of AFRs by eliminating the ARGs and preventing the horizontal gene transfer of ARGs.},
}

@article {pmid37209559,
year = {2023},
author = {Yuan, B and Zhang, Y and Zhang, Z and Lin, Z and Ma, Y and Sun, Y},
title = {Fluorescent tag reveals the potential mechanism of how indigenous soil bacteria affect the transfer of the wild fecal antibiotic resistance plasmid pKANJ7 in different habitat soils.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131659},
doi = {10.1016/j.jhazmat.2023.131659},
pmid = {37209559},
issn = {1873-3336},
abstract = {Plasmids have increasingly become a point of concern since they act as a vital medium for the dissemination of antibiotic resistance genes (ARGs). Although indigenous soil bacteria are critical hosts for these plasmids, the mechanisms driving the transfer of antibiotic resistance plasmids (ARPs) have not been well researched. In this study, we tracked and visualized the colonization of the wild fecal antibiotic resistance plasmid pKANJ7 in indigenous bacteria of different habitat soils (unfertilized soil (UFS), chemical fertilized soil (CFS), and manure fertilized soil (MFS)). The results showed that plasmid pKANJ7 mainly transferred to the dominant genera in the soil and genera that were highly related to the donor. More importantly, plasmid pKANJ7 also transferred to intermediate hosts which aid in the survival and persistence of these plasmids in soil. Nitrogen levels also raised the plasmid transfer rate (14th day: UFS: 0.09%, CFS: 1.21%, MFS: 4.57%). Lastly, our structural equation model (SEM) showed that dominant bacteria shifts caused by nitrogen and loam were the major driver shaping the difference in the transfer of plasmid pKANJ7. Overall, our findings enhance the mechanistic understanding of indigenous soil bacteria's role in plasmid transfer and inform potential methods to prevent the transmission of plasmid-borne resistance in the environment.},
}

@article {pmid37204585,
year = {2023},
author = {Lü, W and Ren, H and Ding, W and Li, H and Yao, X and Jiang, X},
title = {Rapid shifts in pond sediment microbiota in response to high ambient temperature in a water-sediment microcosm.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-023-26823-7},
pmid = {37204585},
issn = {1614-7499},
abstract = {Unlike the extensive research on the response of soil microorganisms to high ambient temperature (HTA), the response of sediment microorganisms to HTA remains unclear. Understanding the response of sediment microorganisms to HTA is important to forecast their impacts on ecosystems and climate warming under projected climate change scenarios. Against the background of climate warming and frequent high ambient temperatures in summer, we conducted a laboratory incubation experiment to clarify the unique assembly characteristics of pond sediment bacterial communities at different temperatures (4, 10, 15, 25, 30 and 35 °C). The results showed that the structure and function of the microbial community in pond sediments at 35 °C were different from those under other temperatures; the microbial community structure at 35 °C had the most large modules and an average module size. Temperature and dissolved oxygen influenced the microbial community network modularity. The CO2 emission rates of pond sediments at 35 °C were significantly higher than those at other temperatures. At 35 °C, heterogeneous selection was the most important assembly process. Additionally, warming altered the microbial network structure and ecosystem functioning but not the microbial diversity or community composition, which may be related to horizontal gene transfer. Revealing the rapid response of pond sediment microorganisms to HTA is important for identifying their role in nutrient cycling and assessing the ecological impacts of climate warming and high ambient temperatures on inland water sediments.},
}

@article {pmid37201375,
year = {2023},
author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC},
title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.},
journal = {Water research},
volume = {239},
number = {},
pages = {120061},
doi = {10.1016/j.watres.2023.120061},
pmid = {37201375},
issn = {1879-2448},
abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.},
}

@article {pmid37196739,
year = {2023},
author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y},
title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {129190},
doi = {10.1016/j.biortech.2023.129190},
pmid = {37196739},
issn = {1873-2976},
abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.},
}

@article {pmid37191574,
year = {2023},
author = {Zhu, Q and Gao, S and Xiao, B and He, Z and Hu, S},
title = {Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0464522},
doi = {10.1128/spectrum.04645-22},
pmid = {37191574},
issn = {2165-0497},
abstract = {Identification of plasmids in bacterial genomes is critical for many factors, including horizontal gene transfer, antibiotic resistance genes, host-microbe interactions, cloning vectors, and industrial production. There are several in silico methods to predict plasmid sequences in assembled genomes. However, existing methods have evident shortcomings, such as unbalance in sensitivity and specificity, dependency on species-specific models, and performance reduction in sequences shorter than 10 kb, which has limited their scope of applicability. In this work, we proposed Plasmer, a novel plasmid predictor based on machine-learning of shared k-mers and genomic features. Unlike existing k-mer or genomic-feature based methods, Plasmer employs the random forest algorithm to make predictions using the percent of shared k-mers with plasmid and chromosome databases combined with other genomic features, including alignment E value and replicon distribution scores (RDS). Plasmer can predict on multiple species and has achieved an average the area under the curve (AUC) of 0.996 with accuracy of 98.4%. Compared to existing methods, tests of both sliding sequences and simulated and de novo assemblies have consistently shown that Plasmer has outperforming accuracy and stable performance across long and short contigs above 500 bp, demonstrating its applicability for fragmented assemblies. Plasmer also has excellent and balanced performance on both sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which has eliminated the bias on sensitivity or specificity that was common in existing methods. Plasmer also provides taxonomy classification to help identify the origin of plasmids. IMPORTANCE In this study, we proposed a novel plasmid prediction tool named Plasmer. Technically, unlike existing k-mer or genomic features-based methods, Plasmer is the first tool to combine the advantages of the percent of shared k-mers and the alignment score of genomic features. This has given Plasmer (i) evident improvement in performance compared to other methods, with the best F1-score and accuracy on sliding sequences, simulated contigs, and de novo assemblies; (ii) applicability for contigs above 500 bp with highest accuracy, enabling plasmid prediction in fragmented short-read assemblies; (iii) excellent and balanced performance between sensitivity and specificity (both >0.95 above 500 bp) with the highest F1-score, which eliminated the bias on sensitivity or specificity that commonly existed in other methods; and (iv) no dependency of species-specific training models. We believe that Plasmer provides a more reliable alternative for plasmid prediction in bacterial genome assemblies.},
}

@article {pmid37187278,
year = {2023},
author = {Zhou, Q and Zhang, J and Fang, Q and Zhang, M and Wang, X and Zhang, D and Pan, X},
title = {Microplastic biodegradability dependent responses of plastisphere antibiotic resistance to simulated freshwater-seawater shift in onshore marine aquaculture zones.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {121828},
doi = {10.1016/j.envpol.2023.121828},
pmid = {37187278},
issn = {1873-6424},
abstract = {MPs carrying ARGs can travel between freshwater and seawater due to intensive land-sea interaction in onshore marine aquaculture zones (OMAZ). However, the response of ARGs in plastisphere with different biodegradability to freshwater-seawater shift is still unknown. In this study, ARG dynamics and associated microbiota on biodegradable poly (butyleneadipate-co-terephthalate) (PBAT) and non-biodegradable polyethylene terephthalate (PET) MPs were investigated through a simulated freshwater-seawater shift. The results exhibited that freshwater-seawater shift significantly influenced ARG abundance in plastisphere. The relative abundance of most studied ARGs decreased rapidly in plastisphere after they entered seawater from freshwater but increased on PBAT after MPs entered freshwater from seawater. Besides, the high relative abundance of multi-drug resistance (MDR) genes occurred in plastisphere, and the co-change between most ARGs and mobile genetic elements indicated the role of horizontal gene transfer on ARG regulation. Proteobacteria was dominant phylum in plastisphere and the dominant genera, such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Afipia, Gemmobacter and Enhydrobacter, were significantly associated with qnrS, tet and MDR genes in plastisphere. Moreover, after MPs entered new water environment, the ARGs and microbiota genera in plastisphere changed significantly and tended to converge with those in receiving water. These results indicated that MP biodegradability and freshwater-seawater interaction influenced potential hosts and distributions of ARGs, of which biodegradable PBAT posed a high risk in ARG dissemination. This study would be helpful for understanding the impact of biodegradable MP pollution on spread of antibiotic resistance in OMAZ.},
}

@article {pmid37185344,
year = {2023},
author = {Riccardi, C and Koper, P and Innocenti, G and diCenzo, GC and Fondi, M and Mengoni, A and Perrin, E},
title = {Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria.},
journal = {Microbial genomics},
volume = {9},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001025},
pmid = {37185344},
issn = {2057-5858},
abstract = {Multipartite genomes, consisting of more than one replicon, have been found in approximately 10 % of bacteria, many of which belong to the phylum Proteobacteria. Many aspects of their origin and evolution, and the possible advantages related to this type of genome structure, remain to be elucidated. Here, we performed a systematic analysis of the presence and distribution of multipartite genomes in the class Gammaproteobacteria, which includes several genera with diverse lifestyles. Within this class, multipartite genomes are mainly found in the order Alteromonadales (mostly in the genus Pseudoalteromonas) and in the family Vibrionaceae. Our data suggest that the emergence of secondary replicons in Gammaproteobacteria is rare and that they derive from plasmids. Despite their multiple origins, we highlighted the presence of evolutionary trends such as the inverse proportionality of the genome to chromosome size ratio, which appears to be a general feature of bacteria with multipartite genomes irrespective of taxonomic group. We also highlighted some functional trends. The core gene set of the secondary replicons is extremely small, probably limited to essential genes or genes that favour their maintenance in the genome, while the other genes are less conserved. This hypothesis agrees with the idea that the primary advantage of secondary replicons could be to facilitate gene acquisition through horizontal gene transfer, resulting in replicons enriched in genes associated with adaptation to different ecological niches. Indeed, secondary replicons are enriched both in genes that could promote adaptation to harsh environments, such as those involved in antibiotic, biocide and metal resistance, and in functional categories related to the exploitation of environmental resources (e.g. carbohydrates), which can complement chromosomal functions.},
}

@article {pmid37178001,
year = {2023},
author = {Vesel, N and Iseli, C and Guex, N and Lemopoulos, A and Blokesch, M},
title = {DNA modifications impact natural transformation of Acinetobacter baumannii.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad377},
pmid = {37178001},
issn = {1362-4962},
support = {407240_167061/SNSF_/Swiss National Science Foundation/Switzerland ; 55008726/HHMI/Howard Hughes Medical Institute/United States ; },
abstract = {Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes of horizontal gene transfer (HGT), is thought to contribute to ARG acquisition and has therefore been intensively studied. However, knowledge regarding the potential role of epigenetic DNA modification(s) on this process remains lacking. Here, we demonstrate that the methylome pattern of diverse A. baumannii strains differs substantially and that these epigenetic marks influence the fate of transforming DNA. Specifically, we describe a methylome-dependent phenomenon that impacts intra- and inter-species DNA exchange by the competent A. baumannii strain A118. We go on to identify and characterize an A118-specific restriction-modification (RM) system that impairs transformation when the incoming DNA lacks a specific methylation signature. Collectively, our work contributes towards a more holistic understanding of HGT in this organism and may also aid future endeavors towards tackling the spread of novel ARGs. In particular, our results suggest that DNA exchanges between bacteria that share similar epigenomes are favored and could therefore guide future research into identifying the reservoir(s) of dangerous genetic traits for this multi-drug resistant pathogen.},
}

@article {pmid37177929,
year = {2023},
author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F},
title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {44},
number = {5},
pages = {2551-2561},
doi = {10.13227/j.hjkx.202206267},
pmid = {37177929},
issn = {0250-3301},
abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.},
}

@article {pmid37173437,
year = {2023},
author = {Feng, SY and Hauck, Y and Morgene, F and Mohammedi, R and Mirouze, N},
title = {The complex regulation of competence in Staphylococcus aureus under microaerobic conditions.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {512},
pmid = {37173437},
issn = {2399-3642},
abstract = {To perform natural transformation, one of the three main Horizontal Gene Transfer mechanisms, bacteria need to enter a physiological differentiated state called genetic competence. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus.Here, we show an optimized protocol, based on planktonic cells cultures, leading to a large percentage of the population activating the development of competence and a significant improvement of S. aureus natural transformation efficiencies. Taking advantage of these conditions, we perform transcriptomics analyses to characterize the regulon of each central competence regulator. SigH and ComK1 are both found essential for activating natural transformation genes but also important for activation or repression of peripheral functions. Even though ComK2 is not found important for the control of transformation genes, its regulon shows an important overlap with that of SigH and ComK1. Finally, we propose that microaerobic conditions, sensed by the SrrAB two-component system, are key to activate competence in S. aureus.},
}

@article {pmid37173063,
year = {2023},
author = {Ayllón, MA and Vainio, EJ},
title = {Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle.},
journal = {Advances in virus research},
volume = {115},
number = {},
pages = {1-86},
doi = {10.1016/bs.aivir.2023.02.002},
pmid = {37173063},
issn = {1557-8399},
abstract = {Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.},
}

@article {pmid37172383,
year = {2023},
author = {Liu, YJ and Li, ZH and He, YT and Yuan, L and Sheng, GP},
title = {Antibiotic resistomes in face-mask biofilm along an urban river: Multiple drivers and co-occurrence with human opportunistic pathogens.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131587},
doi = {10.1016/j.jhazmat.2023.131587},
pmid = {37172383},
issn = {1873-3336},
abstract = {Discarded face masks from the global COVID-19 pandemic have contributed significantly to plastic pollution in surface water, whereas their potential as a reservoir for aquatic pollutants is not well understood. Herein, we conducted a field experiment along a human-impacted urban river, investigating the variations of antibiotic resistance genes (ARGs), pathogens, and water-borne contaminants in commonly-used face masks. Results showed that high-biomass biofilms formed on face masks selectively enriched more ARGs than stone biofilm (0.08-0.22 vs 0.07-0.15 copies/16 S rRNA gene copies) from bulk water, which mainly due to unique microbial communities, enhanced horizontal gene transfer, and selective pressure of accumulated contaminants based on redundancy analysis and variation partitioning analysis. Several human opportunistic pathogens (e.g., Acinetobacter, Escherichia-Shigella, Bacillus, and Klebsiella), which are considered potential ARG carriers, were also greatly concentrated in face-mask biofilms, imposing a potential threat to aquatic ecological environment and human health. Moreover, wastewater treatment plant effluents, as an important source of pollutants to urban rivers, further aggravated the abundances of ARGs and opportunistic pathogens in face-mask biofilms. Our findings demonstrated that discarded face masks provide a hotspot for the proliferation and spread of ARGs and pathogens in urban water, highlighting the urgent requirement for implementing stricter regulations in face mask disposal.},
}

@article {pmid37172034,
year = {2023},
author = {Green, VE and Klancher, CA and Yamamoto, S and Dalia, AB},
title = {The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae.},
journal = {PLoS genetics},
volume = {19},
number = {5},
pages = {e1010767},
doi = {10.1371/journal.pgen.1010767},
pmid = {37172034},
issn = {1553-7404},
abstract = {Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. In this niche, V. cholerae commonly interacts with the chitinous shells of crustacean zooplankton. As a chitinolytic microbe, V. cholerae degrades insoluble chitin into soluble oligosaccharides. Chitin oligosaccharides serve as both a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae. Namely, these oligosaccharides induce the chitin sensor, ChiS, to activate the genes required for chitin utilization and horizontal gene transfer by natural transformation. Thus, interactions with chitin impact the survival of V. cholerae in marine environments. Chitin is a complex carbon source for V. cholerae to degrade and consume, and the presence of more energetically favorable carbon sources can inhibit chitin utilization. This phenomenon, known as carbon catabolite repression (CCR), is mediated by the glucose-specific Enzyme IIA (EIIAGlc) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS). In the presence of glucose, EIIAGlc becomes dephosphorylated, which inhibits ChiS transcriptional activity by an unknown mechanism. Here, we show that dephosphorylated EIIAGlc interacts with ChiS. We also isolate ChiS suppressor mutants that evade EIIAGlc-dependent repression and demonstrate that these alleles no longer interact with EIIAGlc. These findings suggest that EIIAGlc must interact with ChiS to exert its repressive effect. Importantly, the ChiS suppressor mutations we isolated also relieve repression of chitin utilization and natural transformation by EIIAGlc, suggesting that CCR of these behaviors is primarily regulated through ChiS. Together, our results reveal how nutrient conditions impact the fitness of an important human pathogen in its environmental reservoir.},
}

@article {pmid37168121,
year = {2023},
author = {Tao, S and Zhou, D and Chen, H and Li, N and Zheng, L and Fang, Y and Xu, Y and Jiang, Q and Liang, W},
title = {Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1177841},
doi = {10.3389/fmicb.2023.1177841},
pmid = {37168121},
issn = {1664-302X},
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign mobile genetic elements, such as plasmids and phages. This study aims to analyze the gene structure and to explore the function of the CRISPR system in the Enterococcus genome, especially with regard to drug resistance. The whole genome information of 110 enterococci was downloaded from the NCBI database to analyze the distribution and the structure of the CRISPR-Cas system including the Cas gene, repeat sequences, and spacer sequence of the CRISPR-Cas system by bioinformatics methods, and to find drug resistance-related genes and analyze the relationship between them and the CRISPR-Cas system. Multilocus sequence typing (MLST) of enterococci was performed against the reference MLST database. Information on the drug resistance of Enterococcus was retrieved from the CARD database, and its relationship to the presence or absence of CRISPR was statistically analyzed. Among the 110 Enterococcus strains, 39 strains (35.45%) contained a complete CRISPR-Cas system, 87 CRISPR arrays were identified, and 62 strains contained Cas gene clusters. The CRISPR system in the Enterococcus genome was mainly type II-A (59.68%), followed by type II-C (33.87%). The phylogenetic analysis of the cas1 gene sequence was basically consistent with the typing of the CRISPR-Cas system. Of the 74 strains included in the study for MLST typing, only 19 (25.68%) were related to CRISPR-Cas typing, while the majority of the strains (74.32%) of MLST typing were associated with the untyped CRISPR system. Additionally, the CRISPR-Cas system may only be related to the carrying rate of some drug-resistant genes and the drug-resistant phenotype. In conclusion, the distribution of the enterococcus CRISPR-Cas system varies greatly among different species and the presence of CRISPR loci reduces the horizontal transfer of some drug resistance genes.},
}

@article {pmid37167868,
year = {2023},
author = {Cai, P and Chen, Q and Du, W and Yang, S and Li, J and Cai, H and Zhao, X and Sun, W and Xu, N and Wang, J},
title = {Deciphering the dynamics of metal and antibiotic resistome profiles under different metal(loid) contamination levels.},
journal = {Journal of hazardous materials},
volume = {455},
number = {},
pages = {131567},
doi = {10.1016/j.jhazmat.2023.131567},
pmid = {37167868},
issn = {1873-3336},
abstract = {Metal(loid) contaminations pose considerable threats to ecological security and public health, yet little is known about the dynamics of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) under different metal(loid) contamination levels. Here, we provided a systematic investigation of MRGs and ARGs in three zones (Zones I, II, and III) with different metal(loid) contamination levels across an abandoned sewage reservoir. More diverse MRGs and ARGs were detected from the high-contaminated Zone I and the moderate-contaminated Zone II, while the abundant MGEs (mobile genetic elements) potentially enhanced the horizontal gene transfer potential and the resistome diversity in Zone I. Particularly, resistome hosts represented by Thiobacillus, Ramlibacter, and Dyella were prevalent in Zone II, promoting the vertical gene transfer of MRGs and ARGs. The highest health risk of ARGs was predicted for Zone I (about 7.58% and 0.48% of ARGs classified into Rank I and Rank II, respectively), followed by Zone II (2.11% and 0%) and Zone III (0% and 0%). However, the ARGs co-occurring with MRGs might exhibit low proportions and low health risks (all were Rank IV) in the three zones. Overall, these findings uncovered the dynamic responses of resistomes and their hosts to different metal(loid) contamination levels, contributing to formulating accurate management and bioremediation countermeasures for various metal(loid) contaminated environments.},
}

@article {pmid37166501,
year = {2023},
author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A},
title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37166501},
issn = {1432-184X},
abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.},
}

@article {pmid37164096,
year = {2023},
author = {Gao, Y and Luo, W and Zhang, H and Chen, Y and Li, Z and Wei, G and Chen, W},
title = {Enrichment of antibiotic resistance genes in roots is related to specific bacterial hosts and soil properties in two soil-plant systems.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163933},
doi = {10.1016/j.scitotenv.2023.163933},
pmid = {37164096},
issn = {1879-1026},
abstract = {Soil microorganisms carrying antibiotic resistance genes (ARGs) can colonize plants as endophytes, posing a huge risk to human health. However, the distribution and transmission patterns of ARGs in different soil-plant systems are unclear. Here, we investigated the distribution of ARGs and the microbial communities in the soil-wheat and soil-cucumber systems by quantitative PCR (qPCR) and 16S rRNA gene sequencing. The results showed that the relative abundances of seven ARGs and intI1 in roots were higher than those of other samples in both soil-plant systems. Pseudomonas, Enterobacteriaceae, Rhizobiales and Gammaproteobacteria were dominant potential bacterial hosts of endophytic ARGs, with enrichment patterns similar to that of ARGs in roots. In addition, more ARGs were significantly positively correlated with intI1 in roots, indicating that ARGs may be more prone to horizontal gene transfer (HGT). Variation partitioning analysis (VPA) and structural equation models (SEM) revealed that the variations of ARGs were mainly directly affected by the HGT of intI1 and indirectly affected by soil properties in roots. These results demonstrated that root could have a strong proliferative effect on ARGs entering host plant endophytes. Overall, our findings enhanced the understanding distribution patterns of ARGs in different soil-plant systems, and provided an effective basis for developing measures to minimize the spread of ARGs.},
}

@article {pmid37158891,
year = {2023},
author = {Tapia, SM and Macías, LG and Pérez-Torrado, R and Daroqui, N and Manzanares, P and Querol, A and Barrio, E},
title = {A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {102},
pmid = {37158891},
issn = {1741-7007},
abstract = {BACKGROUND: Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.

RESULTS: Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.

CONCLUSIONS: The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.},
}

@article {pmid37156983,
year = {2023},
author = {Calderón-Franco, D and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG},
title = {Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing.},
journal = {Antonie van Leeuwenhoek},
volume = {},
number = {},
pages = {},
pmid = {37156983},
issn = {1572-9699},
abstract = {The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L[-1]). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L[-1]). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.},
}

@article {pmid37156401,
year = {2023},
author = {Gartzonika, K and Politi, L and Mavroidi, A and Tsantes, AG and Spanakis, N and Priavali, E and Vrioni, G and Tsakris, A},
title = {High prevalence of clonally-related ST182 NDM-1-producing Enterobacter cloacae complex clinical isolates in Greece.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {106837},
doi = {10.1016/j.ijantimicag.2023.106837},
pmid = {37156401},
issn = {1872-7913},
abstract = {NDM-type metallo-β-lactamase (MBL)-producing Enterobacterales remain uncommon in the European region, especially among species other than Klebsiella pneumoniae and Escherichia coli. The aim of this study was to describe epidemiological and molecular characteristics of a widespread NDM-1-producing Enterobacter cloacae complex outbreak in Greece. Over a 6-year period (March 2016-March 2022), a retrospective study was conducted in a tertiary care Greek hospital. Ninety single-patient carbapenem-non-susceptible E. cloacae complex clinical isolates were consecutively recovered. The isolates were subjected to further investigation, including antimicrobial susceptibility testing and combined-disk tests for carbapenemase production, PCR and sequencing for resistance genes, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments, genotyping by multilocus sequence typing, whole genome sequencing and phylogenetic analysis. Phenotypic and molecular testing confirmed the presence of blaNDM-1 in 47 (52.2%) of the E. cloacae complex isolates. MLST analysis clustered all but four of the NDM-1 producers into a single MLST ST (ST182), whereas single isolates belonged to different STs (ST190, ST269, ST443, ST743). PFGE analysis has revealed that ST182 isolates were clustered into a single clonal type, with three subtypes, which differed from the clonal types detected among the remaining carbapenem non-susceptible E. cloacae complex isolates of the study period. All ST182 blaNDM-1-carrying isolates also harbored the blaACT-16 AmpC gene, while blaESBL, blaOXA-1 and blaTEM-1 genes were detected in most of the cases. In all clonal isolates the blaNDM-1 gene was located on an IncA/C-type plasmid and flanked upstream by an ISAba125 element and downstream by bleMBL. Conjugation experiments failed to produce carbapenem resistant transconjugants, indicating a low dynamic for horizontal gene transfer. Application of enforced infection control measures led to the absence of new NDM-positive cases for periods of time during the survey. Our study represents the largest clonal outbreak of NDM-producing E. cloacae complex in Europe.},
}

@article {pmid37156383,
year = {2023},
author = {Tyrrell, C and Do, TT and Leigh, RJ and Burgess, CM and Brennan, FP and Walsh, F},
title = {Differential impact of swine, bovine and poultry manure on the microbiome and resistome of agricultural grassland.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163926},
doi = {10.1016/j.scitotenv.2023.163926},
pmid = {37156383},
issn = {1879-1026},
abstract = {Land spreading of animal manure is an essential process in agriculture. Despite the importance of grassland in global food security the potential of the grass phyllosphere as a reservoir of antimicrobial resistance (AMR) is unknown. Additionally, the comparative risk associated with different manure sources is unclear. Due to the One Health nature of AMR there is an urgent need to fully understand the risk associated with AMR at the agriculture - environmental nexus. We performed a grassland field study to assess and compare the relative and temporal impact of bovine, swine and poultry manure application on the grass phyllosphere and soil microbiome and resistome over a period of four months, using 16S rRNA amplicon sequencing and high-throughput quantitative PCR (HT-qPCR). The soil and grass phyllosphere contained a diverse range of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). Manure treatment was found to introduce ARGs belonging to clinically important antimicrobial classes, such as aminoglycoside and sulphonamide into grass and soil. Temporal analysis of ARGs and MGEs associated with manure treatment indicated ARGs patterns were similar across the different manure types in the manure treated soil and grass phyllosphere. Manure treatment resulted in the enrichment in members of the indigenous microbiota and the introduction of manure associated bacteria, with this impact extending past the recommended six-week exclusion period. However, these bacteria were in low relative abundance and manure treatment was not found to significantly impact the overall composition of the microbiome or resistome. This provides evidence that the current guidelines facilitate reduction of biological risk to livestock. Additionally, in soil and grass samples MGEs correlated with ARGs from clinically important antimicrobial classes, indicating the key role MGEs play in horizontal gene transfer in agricultural grassland. These results demonstrate the role of the grass phyllosphere as an under-studied sink of AMR.},
}

@article {pmid37155884,
year = {2023},
author = {Kinsella, CM and van der Hoek, L},
title = {Vertebrate-tropism of a cressdnavirus lineage implicated by poxvirus gene capture.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {20},
pages = {e2303844120},
doi = {10.1073/pnas.2303844120},
pmid = {37155884},
issn = {1091-6490},
abstract = {Among cressdnaviruses, only the family Circoviridae is recognized to infect vertebrates, while many others have unknown hosts. Detection of virus-to-host horizontal gene transfer is useful for solving such virus-host relationships. Here, we extend this utility to an unusual case of virus-to-virus horizontal transfer, showing multiple ancient captures of cressdnavirus Rep genes by avipoxviruses-large dsDNA pathogens of birds and other saurians. As gene transfers must have occurred during virus coinfections, saurian hosts were implied for the cressdnavirus donor lineage. Surprisingly, phylogenetic analysis revealed that donors were not members of the vertebrate-infecting Circoviridae, instead belonging to a previously unclassified family that we name Draupnirviridae. While draupnirviruses still circulate today, we show that those in the genus Krikovirus infected saurian vertebrates at least 114 Mya, leaving endogenous viral elements inside snake, lizard, and turtle genomes throughout the Cretaceous Period. Endogenous krikovirus elements in some insect genomes and frequent detection in mosquitoes imply that spillover to vertebrates was arthropod mediated, while ancestral draupnirviruses likely infected protists before their emergence in animals. A modern krikovirus sampled from an avipoxvirus-induced lesion shows that their interaction with poxviruses is ongoing. Captured Rep genes in poxvirus genomes often have inactivated catalytic motifs, yet near-total presence across the Avipoxvirus genus, and evidence of both expression and purifying selection on them suggests currently unknown functions.},
}

@article {pmid37155541,
year = {2023},
author = {Jiang, Y and Zhao, L and Li, JD and Sun, J and Miao, R and Shao, B and Wu, P},
title = {The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer.},
journal = {Journal of advanced veterinary and animal research},
volume = {10},
number = {1},
pages = {103-112},
doi = {10.5455/javar.2023.j658},
pmid = {37155541},
issn = {2311-7710},
abstract = {OBJECTIVES: This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts.

MATERIALS AND METHODS: Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed.

RESULTS: The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs.

CONCLUSIONS: The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.},
}

@article {pmid37154532,
year = {2023},
author = {Cai, L},
title = {Rethinking convergence in plant parasitism through the lens of molecular and population genetic processes.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e16174},
doi = {10.1002/ajb2.16174},
pmid = {37154532},
issn = {1537-2197},
abstract = {The autotrophic lifestyle of photosynthetic plants has profoundly shaped their body plan, physiology, and gene repertoire. Shifts to parasitism and heterotrophy have evolved at least 12 times in more than 4000 species, and this transition has consequently left major evolutionary footprints among these parasitic lineages. Features that are otherwise rare at the molecular level and beyond have evolved repetitively, including reduced vegetative bodies, carrion-mimicking during reproduction, and the incorporation of alien genetic material. Here, I propose an integrated conceptual model, referred to as the funnel model, to define the general evolutionary trajectory of parasitic plants and provide a mechanistic explanation for their convergent evolution. This model connects our empirical understanding of gene regulatory networks in flowering plants with classical theories of molecular and population genetics. It emphasizes that the cascading effects brought about by the loss of photosynthesis may be a major force constraining the physiological capacity of parasitic plants and shaping their genomic landscapes. Here I review recent studies on the anatomy, physiology, and genetics of parasitic plants that lend support to this photosynthesis-centered funnel model. Focusing on nonphotosynthetic holoparasites, I elucidate how they may inevitably reach an evolutionary terminal status (i.e., extinction) and highlight the utility of a general, explicitly described and falsifiable model for future studies of parasitic plants.},
}

@article {pmid37152757,
year = {2023},
author = {Nie, Z and Tang, K and Wang, W and Wang, P and Guo, Y and Wang, Y and Kao, SJ and Yin, J and Wang, X},
title = {Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1138751},
pmid = {37152757},
issn = {1664-302X},
abstract = {Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO2 hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb 3-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.},
}

@article {pmid37071810,
year = {2023},
author = {Paulat, NS and Storer, JM and Moreno-Santillán, DD and Osmanski, AB and Sullivan, KAM and Grimshaw, JR and Korstian, J and Halsey, M and Garcia, CJ and Crookshanks, C and Roberts, J and Smit, AFA and Hubley, R and Rosen, J and Teeling, EC and Vernes, SC and Myers, E and Pippel, M and Brown, T and Hiller, M and , and Rojas, D and Dávalos, LM and Lindblad-Toh, K and Karlsson, EK and Ray, DA},
title = {Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.},
journal = {Molecular biology and evolution},
volume = {40},
number = {5},
pages = {},
pmid = {37071810},
issn = {1537-1719},
mesh = {Animals ; *DNA Transposable Elements/genetics ; *Chiroptera/genetics ; Gene Transfer, Horizontal ; Evolution, Molecular ; Mammals/genetics ; Phylogeny ; },
abstract = {Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.},
}

Animals
*DNA Transposable Elements/genetics
*Chiroptera/genetics
Gene Transfer, Horizontal
Evolution, Molecular
Mammals/genetics
Phylogeny

@article {pmid37149187,
year = {2023},
author = {Li, LG and Zhang, T},
title = {Plasmid-mediated antibiotic resistance gene transfer under environmental stresses: Insights from laboratory-based studies.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163870},
doi = {10.1016/j.scitotenv.2023.163870},
pmid = {37149187},
issn = {1879-1026},
abstract = {Although clinical settings play a major role in the current global dissemination of antibiotic resistance, once antibiotic resistance bacteria and genes are released into the environment, their fate will be subject to complex ecological processes. One of the processes prevalent in microbial communities - horizontal gene transfer - can largely facilitate the dissemination of antibiotic resistance genes (ARGs) across phylogenetic and ecological boundaries. Especially, plasmid transfer has aroused increasing concern as it has been proved a significant role in promoting ARG dissemination. As a multi-step process, plasmid transfer can be influenced by various factors, among which those stresses caused by environmental pollutants are important elements affecting the plasmid mediated ARG transfer in the environment. In fact, diverse traditional and emerging pollutants are continuously entering the environment nowadays, as evidenced by the global occurrence of pollutants like metals and pharmaceuticals in aquatic and terrestrial systems. It is therefore imperative to understand to what extent and in which way the plasmid mediated ARG dissemination can be influenced by these stresses. Over the past decades, numerous research endeavours have been made to understand the plasmid mediated ARG transfer under various environmental relevant pressures. In this review, progress and challenges of studies on environmental stress regulating plasmid mediated ARG dissemination will be discussed, with specific focus on emerging pollutants like antibiotics and non-antibiotic pharmaceuticals, metals and their nanoparticles, disinfectants and disinfection by-products, as well as the emerging particulate matter like microplastics. Despite the previous efforts, we are still lacking insights into the in situ plasmid transfer under environmental stresses, which can be addressed by future studies considering environmental relevant pollution status and multi-species microbial communities. We believe that future development of standardized high-throughput screening platforms will assist in rapidly identifying which pollutants enhance plasmid transfer and also which ones may block such gene transfer processes.},
}

@article {pmid37148762,
year = {2023},
author = {Jiang, H and Zhang, L and Wang, X and Gu, J and Song, Z and Wei, S and Guo, H and Xu, L and Qian, X},
title = {Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements.},
journal = {Journal of environmental management},
volume = {341},
number = {},
pages = {118071},
doi = {10.1016/j.jenvman.2023.118071},
pmid = {37148762},
issn = {1095-8630},
abstract = {Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO2 nanoparticles (SiO2NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO2NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO2NPs to reduce the propagation of ARGs.},
}

@article {pmid37146969,
year = {2023},
author = {Takada, H and Katoh, T and Sakanaka, M and Odamaki, T and Katayama, T},
title = {GH20 and GH84 β-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {104781},
doi = {10.1016/j.jbc.2023.104781},
pmid = {37146969},
issn = {1083-351X},
abstract = {Intestinal mucus layers mediate symbiosis and dysbiosis of host-microbe interactions. These interactions are influenced by the mucin O-glycan degrading ability of several gut microbes. The identities and prevalence of many glycoside hydrolyses (GHs) involved in microbial mucin O-glycan breakdown have been previously reported; however, the exact mechanisms and extent to which these GHs are dedicated to mucin O-glycan degradation pathways warrant further research. Here, using Bifidobacterium bifidum as a model mucinolytic bacterium, we revealed that two β-N-acetylglucosaminidases belonging to the GH20 (BbhI) and GH84 (BbhIV) families play important roles in mucin O-glycan degradation. Using substrate specificity analysis of natural oligosaccharides and O-glycomic analysis of porcine gastric mucin (PGM) incubated with purified enzymes or B. bifidum carrying bbhI and/or bbhIV mutations, we showed that BbhI and BbhIV are highly specific for β-(1→3)- and β-(1→6)-GlcNAc linkages of mucin core structures, respectively. Interestingly, we found that efficient hydrolysis of the β-(1→3)-linkage by BbhI of the mucin core 4 structure [GlcNAcβ1-3(GlcNAcβ1-6)GalNAcα-O-Thr] required prior removal of the β-(1→6)-GlcNAc linkage by BbhIV. Consistent with this, inactivation of bbhIV markedly decreased the ability of B. bifidum to release GlcNAc from PGM. When combined with a bbhI mutation, we observed that the growth of the strain on PGM was reduced. Finally, phylogenetic analysis suggests that GH84 members may have gained diversified functions through microbe-microbe and host-microbe horizontal gene transfer events. Taken together, these data strongly suggest GH84 family members in host glycan breakdown.},
}

@article {pmid37144438,
year = {2023},
author = {Hu, X and Xu, Y and Liu, S and Gudda, FO and Ling, W and Qin, C and Gao, Y},
title = {Graphene Quantum Dots Nonmonotonically Influence the Horizontal Transfer of Extracellular Antibiotic Resistance Genes via Bacterial Transformation.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2301177},
doi = {10.1002/smll.202301177},
pmid = {37144438},
issn = {1613-6829},
abstract = {Graphene quantum dots (GQDs) coexist with antibiotic resistance genes (ARGs) in the environment. Whether GQDs influence ARG spread needs investigation, since the resulting development of multidrug-resistant pathogens would threaten human health. This study investigates the effect of GQDs on the horizontal transfer of extracellular ARGs (i.e., transformation, a pivotal way that ARGs spread) mediated by plasmids into competent Escherichia coli cells. GQDs enhance ARG transfer at lower concentrations, which are close to their environmental residual concentrations. However, with further increases in concentration (closer to working concentrations needed for wastewater remediation), the effects of enhancement weaken or even become inhibitory. At lower concentrations, GQDs promote the gene expression related to pore-forming outer membrane proteins and the generation of intracellular reactive oxygen species, thus inducing pore formation and enhancing membrane permeability. GQDs may also act as carriers to transport ARGs into cells. These factors result in enhanced ARG transfer. At higher concentrations, GQD aggregation occurs, and aggregates attach to the cell surface, reducing the effective contact area of recipients for external plasmids. GQDs also form large agglomerates with plasmids and thus hindering ARG entrance. This study could promote the understanding of the GQD-caused ecological risks and benefit their safe application.},
}

@article {pmid36933870,
year = {2023},
author = {Yang, Q and Zhu, Y and Schwarz, S and Wang, L and Liu, W and Yang, W and Liu, S and Zhang, W},
title = {Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E.},
journal = {International journal of antimicrobial agents},
volume = {61},
number = {5},
pages = {106793},
doi = {10.1016/j.ijantimicag.2023.106793},
pmid = {36933870},
issn = {1872-7913},
mesh = {*Conjugation, Genetic ; Plasmids/genetics ; *Streptococcus/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; },
abstract = {Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.},
}

*Conjugation, Genetic
Plasmids/genetics
*Streptococcus/genetics
Drug Resistance, Microbial
Gene Transfer, Horizontal

@article {pmid37143068,
year = {2023},
author = {Valach, M and Moreira, S and Petitjean, C and Benz, C and Butenko, A and Flegontova, O and Nenarokova, A and Prokopchuk, G and Batstone, T and Lapébie, P and Lemogo, L and Sarrasin, M and Stretenowich, P and Tripathi, P and Yazaki, E and Nara, T and Henrissat, B and Lang, BF and Gray, MW and Williams, TA and Lukeš, J and Burger, G},
title = {Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {99},
pmid = {37143068},
issn = {1741-7007},
support = {BB/R016437/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.

RESULTS: We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.

CONCLUSIONS: Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.},
}

@article {pmid37138596,
year = {2023},
author = {Zhao, Y and Wei, HM and Yuan, JL and Xu, L and Sun, JQ},
title = {A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1177951},
pmid = {37138596},
issn = {1664-302X},
abstract = {Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.},
}

@article {pmid37137974,
year = {2023},
author = {Ikhimiukor, OO and Souza, SSR and Marcovici, MM and Nye, GJ and Gibson, R and Andam, CP},
title = {Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {482},
pmid = {37137974},
issn = {2399-3642},
abstract = {Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.},
}

@article {pmid37133439,
year = {2023},
author = {Tran, NN and Morrisette, T and Jorgensen, SCJ and Orench-Benvenutti, JM and Kebriaei, R},
title = {Current therapies and challenges for the treatment of Staphylococcus aureus biofilm-related infections.},
journal = {Pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1002/phar.2806},
pmid = {37133439},
issn = {1875-9114},
abstract = {Staphylococcus aureus is a major cause of nosocomial and community-acquired infections and contributes to significant increase in morbidity and mortality especially when associated with medical devices and in biofilm form. Biofilm structure provides a pathway for enrichment of resistant and persistent phenotypes of S. aureus leading to relapse and recurrence of infection. Minimal diffusion of antibiotics inside biofilm structure leads to heterogeneity and distinct physiological activity. Additionally, horizontal gene transfer between cells in proximity adds to the challenges associated with eradication of biofilms. This narrative review focuses on biofilm-associated infections caused by S. aureus, the impact of environmental conditions on biofilm formation, interactions inside biofilm communities, and the clinical challenges that they present. Conclusively, potential solutions, novel treatment strategies, combination therapies and reported alternatives are discussed.},
}

@article {pmid37126651,
year = {2023},
author = {Akmal, M and Akatsuka, M and Nishiki, I and Yoshida, T},
title = {Resistance and genomic characterization of a plasmid pkh2101 harbouring erm(B) isolated from emerging fish pathogen Lactococcus garvieae serotype II in Japan.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfd.13793},
pmid = {37126651},
issn = {1365-2761},
abstract = {The emergence of antibiotic-resistant pathogenic strains of Lactococcus garvieae serotype II isolated from fish in Japan has become a growing concern in recent years. The data on drug susceptibility and its associated resistance mechanism are limited. Therefore, the present study was conducted to determine the minimum inhibitory concentrations (MICs) of chemotherapeutic agents against 98 pathogenic strains of emerging Lactococcus garvieae serotype II isolated from fish from six different prefectures in Japan from 2018 to 2021. The tested strains were resistant to erythromycin, lincomycin and tiamulin. PCR amplification revealed the presence of erm(B) in all erythromycin-resistant strains, while a conjugation experiment confirmed that these strains carried erm(B) that could be transferred to recipient Enterococcus faecalis OG1RF with frequencies from 10[-4] to 10[-6] per donor cells. Nucleotide sequencing of the representative isolated plasmid pkh2101 from an erythromycin-resistant strain showed that it was a 26,850 bp molecule with an average GC content of 33.49%, comprising 31 CDSs, 13 of which remained without any functional annotation. Comparative genomic analysis suggested that pkh2101 shared the highest similarity (97.57% identity) with the plasmid pAMbeta1, which was previously isolated clinically from Enterococcus faecalis DS-5. This study provides potential evidence that the plasmid harbouring erm(B) could be a source of antibiotic resistance transmission in emerging L. garvieae infection in aquaculture.},
}

@article {pmid37125932,
year = {2023},
author = {Quan, J and Hu, H and Zhang, H and Meng, Y and Liao, W and Zhou, J and Han, X and Shi, Q and Zhao, D and Wang, Q and Jiang, Y and Yu, Y},
title = {Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0355422},
doi = {10.1128/spectrum.03554-22},
pmid = {37125932},
issn = {2165-0497},
abstract = {The coinfection process producing multiple species of pathogens provides a specific ecological niche for the exchange of genetic materials between pathogens, in which plasmids play a vital role in horizontal gene transfer, especially for drug resistance, but the underlying transfer pathway remains unclear. Interspecies communication of the plasmids associated with the transfer of third-generation cephalosporins, quinolones, and colistin resistance has been observed in simultaneously isolated Escherichia coli and Klebsiella pneumoniae from abdominal drainage following surgery. The MICs of antimicrobial agents were determined by the broth microdilution method. The complete chromosome and plasmid sequences were obtained by combining Illumina paired-end short reads and MinION long reads. S1-PFGE, southern blot analysis and conjugation assay confirmed the transferability of the mcr-1-harboring plasmid. Both the E. coli isolate EC15255 and K. pneumoniae isolate KP15255 from the same specimen presented multidrug resistance. Each of them harbored one chromosome and three plasmids, and two plasmids and their mediated resistance could be transferred to the recipient by conjugation. Comparison of their genome sequences suggested that several genetic communication events occurred between species, especially among their plasmids, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion. Exchange of plasmids or the genetic elements they harbor plays a critical role in antimicrobial resistance gene transmission and poses a substantial threat to nosocomial infection control, necessitating the continued surveillance of multidrug resistant pathogens, especially during coinfection. IMPORTANCE The genome sequence of bacterial pathogens commonly provides a detailed clue of genetic communication among clones or even distinct species. The intestinal microecological environment is a representative ecological niche for genetic communication. However, it is still difficult to describe the details of horizontal gene transfer or other genetic events within them because the evidence in the genome sequence is incomplete and limited. In this study, the simultaneously isolated Escherichia coli and Klebsiella pneumoniae from a coinfection process provided an excellent example for observation of interspecies communication between the two genomes and the plasmids they harbor. A complete genome sequence acquired by combining the Illumina and MinION sequencing platforms facilitated the understanding of genetic communication events, such as whole-plasmid transfer, insertion, deletion, amplification, or inversion, which contribute to antimicrobial resistance gene transmission and are a substantial threat to nosocomial infection control.},
}

@article {pmid37125466,
year = {2023},
author = {Castanheira, M and Mendes, RE and Gales, AC},
title = {Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {76},
number = {Supplement_2},
pages = {S166-S178},
doi = {10.1093/cid/ciad109},
pmid = {37125466},
issn = {1537-6591},
abstract = {Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.},
}

@article {pmid37121291,
year = {2023},
author = {Kosterlitz, O and Huisman, JS},
title = {Guidelines for the estimation and reporting of plasmid conjugation rates.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102685},
doi = {10.1016/j.plasmid.2023.102685},
pmid = {37121291},
issn = {1095-9890},
abstract = {Conjugation is a central characteristic of plasmid biology and an important mechanism of horizontal gene transfer in bacteria. However, there is little consensus on how to accurately estimate and report plasmid conjugation rates, in part due to the wide range of available methods. Given the similarity between approaches, we propose general reporting guidelines for plasmid conjugation experiments. These constitute best practices based on recent literature about plasmid conjugation and methods to measure conjugation rates. In addition to the general guidelines, we discuss common theoretical assumptions underlying existing methods to estimate conjugation rates and provide recommendations on how to avoid violating these assumptions. We hope this will aid the implementation and evaluation of conjugation rate measurements, and initiate a broader discussion regarding the practice of quantifying plasmid conjugation rates.},
}

@article {pmid37120693,
year = {2023},
author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K},
title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {42},
pmid = {37120693},
issn = {2730-6151},
abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.},
}

@article {pmid37120212,
year = {2023},
author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P},
title = {Lebanese fermented goat milk products: From tradition to meta-omics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {168},
number = {},
pages = {112762},
doi = {10.1016/j.foodres.2023.112762},
pmid = {37120212},
issn = {1873-7145},
abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.},
}

@article {pmid37120023,
year = {2023},
author = {Adomako, MO and Yu, FH},
title = {Potential effects of micro- and nanoplastics on phyllosphere microorganisms and their evolutionary and ecological responses.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163760},
doi = {10.1016/j.scitotenv.2023.163760},
pmid = {37120023},
issn = {1879-1026},
abstract = {Plastic pollution is among the most urgent environmental and social challenges of the 21st century, and their influxes in the environment have altered critical growth drivers in all biomes, attracting global concerns. In particular, the consequences of microplastics on plants and their associated soil microorganisms have gained a large audience. On the contrary, how microplastics and nanoplastics (M/NPs) may influence the plant-associated microorganisms in the phyllosphere (i.e., the aboveground portion of plants) is nearly unknown. We, therefore, summarize evidence that may potentially connect M/NPs, plants, and phyllosphere microorganisms based on studies on other analogous contaminants such as heavy metals, pesticides, and nanoparticles. We show seven pathways that may link M/NPs into the phyllosphere environment, and provide a conceptual framework explaining the direct and indirect (soil legacy) effects of M/NPs on phyllosphere microbial communities. We also discuss the adaptive evolutionary and ecological responses, such as acquiring novel resistance genes via horizontal gene transfer and microbial degradation of plastics of the phyllosphere microbial communities, to M/NPs-induced threats. Finally, we highlight the global consequences (e.g., disruption of ecosystem biogeochemical cycling and impaired host-pathogen defense chemistry that can lead to reduced agricultural productivity) of altered plant-microbiome interactions in the phyllosphere in the context of a predicted surge of plastic production and conclude with pending questions for future research priorities. In conclusion, M/NPs are very likely to produce significant effects on phyllosphere microorganisms and mediate their evolutionary and ecological responses.},
}

@article {pmid37119017,
year = {2023},
author = {Shin, NR and Okamura, Y and Kirsch, R and Pauchet, Y},
title = {Genome sequencing provides insights into the evolution of gene families encoding plant cell wall-degrading enzymes in longhorned beetles.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12844},
pmid = {37119017},
issn = {1365-2583},
abstract = {With more than 36,000 species, the longhorned beetles (family Cerambycidae) are a mega-diverse lineage of mostly xylophagous insects, all of which are represented by the sole sequenced genome of the Asian longhorned beetle (Anoplophora glabripennis; Lamiinae). Their successful radiation has been linked to their ability to degrade plant cell wall components using a range of so-called plant cell wall-degrading enzymes (PCWDEs). Our previous analysis of larval gut transcriptomes demonstrated that cerambycid beetles horizontally acquired genes encoding PCWDEs from various microbial donors; these genes evolved through multiple duplication events to form gene families. To gain further insights into the evolution of these gene families during the Cerambycidae radiation, we assembled draft genomes for four beetle species belonging to three subfamilies using long-read nanopore sequencing. All the PCWDE-encoding genes we annotated from the corresponding larval gut transcriptomes were present in these draft genomes. We confirmed that the newly discovered horizontally acquired glycoside hydrolase family 7 (GH7), subfamily 26 of GH43 (GH43_26), and GH53 (all of which are absent from the A. glabripennis genome) were indeed encoded by these beetles' genome. Most of the PCWDE-encoding genes of bacterial origin gained introns after their transfer into the beetle genome. Altogether, we show that draft genome assemblies generated from nanopore long-reads offer meaningful information to the study of the evolution of gene families in insects. We anticipate that our data will support studies aiming to better understand the biology of the Cerambycidae and other beetles in general.},
}

@article {pmid37116631,
year = {2023},
author = {Garcillán-Barcia, MP and Redondo-Salvo, S and de la Cruz, F},
title = {Plasmid classifications.},
journal = {Plasmid},
volume = {},
number = {},
pages = {102684},
doi = {10.1016/j.plasmid.2023.102684},
pmid = {37116631},
issn = {1095-9890},
abstract = {Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).},
}

@article {pmid37110299,
year = {2023},
author = {Qi, Q and Kamruzzaman, M and Iredell, JR},
title = {A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/microorganisms11040878},
pmid = {37110299},
issn = {2076-2607},
abstract = {Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.},
}

@article {pmid37110264,
year = {2023},
author = {Vittorakis, E and Vică, ML and Zervaki, CO and Vittorakis, E and Maraki, S and Mavromanolaki, VE and Schürger, ME and Neculicioiu, VS and Papadomanolaki, E and Sinanis, T and Giannoulaki, G and Xydaki, E and Kastanakis, SG and Junie, LM},
title = {Examining the Prevalence and Antibiotic Susceptibility of S. aureus Strains in Hospitals: An Analysis of the pvl Gene and Its Co-Occurrence with Other Virulence Factors.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/microorganisms11040841},
pmid = {37110264},
issn = {2076-2607},
abstract = {S. aureus is a pathogenic bacterium that causesinfections. Its virulence is due to surface components, proteins, virulence genes, SCCmec, pvl, agr, and SEs, which are low molecular weight superantigens. SEs are usually encoded by mobile genetic elements, and horizontal gene transfer accounts for their widespread presence in S. aureus. This study analyzed the prevalence of MRSA and MSSA strains of S. aureus in two hospitals in Greece between 2020-2022 and their susceptibility to antibiotics. Specimens collected were tested using the VITEK 2 system and the PCR technique to detect SCCmec types, agr types, pvl genes, and sem and seg genes. Antibiotics from various classes were also tested. This study examined the prevalence and resistance of S. aureus strains in hospitals. It found a high prevalence of MRSA and that the MRSA strains were more resistant to antibiotics. The study also identified the genotypes of the S. aureus isolates and the associated antibiotic resistances. This highlights the need for continued surveillance and effective strategies to combat the spread of MRSA in hospitals. This study examined the prevalence of the pvl gene and its co-occurrence with other genes in S. aureus strains, as well as their antibiotic susceptibility. The results showed that 19.15% of the isolates were pvl-positive and 80.85% were pvl-negative. The pvl gene co-existed with other genes, such as the agr and enterotoxin genes. The results could inform treatment strategies for S. aureus infections.},
}

@article {pmid37110261,
year = {2023},
author = {Karnachuk, OV and Beletsky, AV and Rakitin, AL and Ikkert, OP and Avakyan, MR and Zyusman, VS and Napilov, A and Mardanov, AV and Ravin, NV},
title = {Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming.},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/microorganisms11040838},
pmid = {37110261},
issn = {2076-2607},
abstract = {Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.},
}

@article {pmid37107701,
year = {2023},
author = {Wu, L and Fan, P and Zhou, J and Li, Y and Xu, Z and Lin, Y and Wang, Y and Song, J and Yao, H},
title = {Gene Losses and Homology of the Chloroplast Genomes of Taxillus and Phacellaria Species.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/genes14040943},
pmid = {37107701},
issn = {2073-4425},
abstract = {Research on the chloroplast genome of parasitic plants is limited. In particular, the homology between the chloroplast genomes of parasitic and hyperparasitic plants has not been reported yet. In this study, three chloroplast genomes of Taxillus (Taxillus chinensis, Taxillus delavayi, and Taxillus thibetensis) and one chloroplast genome of Phacellaria (Phacellaria rigidula) were sequenced and analyzed, among which T. chinensis is the host of P. rigidula. The chloroplast genomes of the four species were 119,941-138,492 bp in length. Compared with the chloroplast genome of the autotrophic plant Nicotiana tabacum, all of the ndh genes, three ribosomal protein genes, three tRNA genes and the infA gene were lost in the three Taxillus species. Meanwhile, in P. rigidula, the trnV-UAC gene and the ycf15 gene were lost, and only one ndh gene (ndhB) existed. The results of homology analysis showed that the homology between P. rigidula and its host T. chinensis was low, indicating that P. rigidula grows on its host T. chinensis but they do not share the chloroplast genome. In addition, horizontal gene transfer was not found between P. rigidula and its host T. chinensis. Several candidate highly variable regions in the chloroplast genomes of Taxillus and Phacellaria species were selected for species identification study. Phylogenetic analysis revealed that the species of Taxillus and Scurrula were closely related and supported that Scurrula and Taxillus should be treated as congeneric, while species in Phacellaria had a close relationship with that in Viscum.},
}

@article {pmid37104544,
year = {2023},
author = {Brual, T and Effantin, G and Baltenneck, J and Attaiech, L and Grosbois, C and Royer, M and Cigna, J and Faure, D and Hugouvieux-Cotte-Pattat, N and Gueguen, E},
title = {A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria.},
journal = {PLoS genetics},
volume = {19},
number = {4},
pages = {e1010725},
doi = {10.1371/journal.pgen.1010725},
pmid = {37104544},
issn = {1553-7404},
abstract = {The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.},
}

@article {pmid37102089,
year = {2023},
author = {Shao, M and Liu, L and Liu, B and Zheng, H and Meng, W and Liu, Y and Zhang, X and Ma, X and Sun, C and Luo, X and Li, F and Xing, B},
title = {Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus.},
journal = {ACS environmental Au},
volume = {3},
number = {2},
pages = {105-120},
pmid = {37102089},
issn = {2694-2518},
abstract = {Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.},
}

@article {pmid37099912,
year = {2023},
author = {Sun, X and Kong, T and Huang, D and Chen, Z and Kolton, M and Yang, J and Huang, Y and Cao, Y and Gao, P and Yang, N and Li, B and Liu, H and Sun, W},
title = {Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots.},
journal = {Journal of hazardous materials},
volume = {454},
number = {},
pages = {131458},
doi = {10.1016/j.jhazmat.2023.131458},
pmid = {37099912},
issn = {1873-3336},
abstract = {Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.},
}

@article {pmid37095096,
year = {2023},
author = {Ahmad, M and Prensky, H and Balestrieri, J and ElNaggar, S and Gomez-Simmonds, A and Uhlemann, AC and Traxler, B and Singh, A and Lopatkin, AJ},
title = {Tradeoff between lag time and growth rate drives the plasmid acquisition cost.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2343},
pmid = {37095096},
issn = {2041-1723},
mesh = {Plasmids ; *Bacteria/genetics ; *Gene Transfer, Horizontal ; },
abstract = {Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.},
}

Plasmids
*Bacteria/genetics
*Gene Transfer, Horizontal

@article {pmid37062264,
year = {2023},
author = {Jin, C and Cao, J and Zhang, K and Zhang, X and Cao, Z and Zou, W},
title = {Promotion effects and mechanisms of molybdenum disulfide on the propagation of antibiotic resistance genes in soil.},
journal = {Ecotoxicology and environmental safety},
volume = {256},
number = {},
pages = {114913},
doi = {10.1016/j.ecoenv.2023.114913},
pmid = {37062264},
issn = {1090-2414},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Molybdenum/pharmacology ; Genes, Bacterial ; Soil ; Gene Transfer, Horizontal ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Plasmids ; },
abstract = {The rapid development of nanotechnology has aroused considerable attentions toward understanding the effects of engineered nanomaterials (ENMs) on the propagation of antibiotic resistance. Molybdenum disulfide (MoS2) is an extensively used ENM and poses potential risks associated with environmental exposure; nevertheless, the role of MoS2 toward antibiotic resistance genes (ARGs) transfer remains largely unknown. Herein, it was discovered that MoS2 nanosheets accelerated the horizontal transfer of RP4 plasmid across Escherichia coli in a dose-dependent manner (0.5-10 mg/L), with the maximum transfer frequency 2.07-fold higher than that of the control. Integration of physiological, transcriptomics, and metabolomics analyses demonstrated that SOS response in bacteria was activated by MoS2 due to the elevation of oxidative damage, accompanied by cell membrane permeabilization. MoS2 promoted bacterial adhesion and intercellular contact via stimulating the secretion of extracellular polysaccharides. The ATP levels were maximally increased by 305.7 % upon exposure to MoS2, and the expression of plasmid transfer genes was up-regulated, contributing to the accelerated plasmid conjugation and increased ARG abundance in soil. Our findings highlight the roles of emerging ENMs (e.g., MoS2) in ARGs dissemination, which is significant for the safe applications and risk management of ENMs under the development scenarios of nanotechnology.},
}

*Anti-Bacterial Agents/pharmacology
*Molybdenum/pharmacology
Genes, Bacterial
Soil
Gene Transfer, Horizontal
Drug Resistance, Microbial/genetics
Escherichia coli
Plasmids

@article {pmid37098416,
year = {2023},
author = {Gong, H and Huang, X and Zhu, W and Chen, J and Huang, Y and Zhao, Z and Weng, J and Che, Y and Wang, J and Wang, X},
title = {Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster.},
journal = {Food microbiology},
volume = {113},
number = {},
pages = {104249},
doi = {10.1016/j.fm.2023.104249},
pmid = {37098416},
issn = {1095-9998},
abstract = {Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.},
}

@article {pmid37098287,
year = {2023},
author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J},
title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.},
journal = {Water research},
volume = {237},
number = {},
pages = {119986},
doi = {10.1016/j.watres.2023.119986},
pmid = {37098287},
issn = {1879-2448},
abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.},
}

@article {pmid37097444,
year = {2023},
author = {Bibi, S and Weis, K and Kaur, A and Bhandari, R and Goss, EM and Jones, JB and Potnis, N},
title = {A Brief Evaluation of Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen, Xanthomonas euvesicatoria pv. perforans.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-23-0077-SC},
pmid = {37097444},
issn = {0031-949X},
abstract = {Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple Xanthomonas euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility including both phage related genes and transposase. Among copper tolerant strains of Xanthomonas euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid borne resistance.},
}

@article {pmid37097343,
year = {2023},
author = {Francis, A and Steel, M},
title = {Labellable Phylogenetic Networks.},
journal = {Bulletin of mathematical biology},
volume = {85},
number = {6},
pages = {46},
pmid = {37097343},
issn = {1522-9602},
abstract = {Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations) and non-tree-like 'reticulate' processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper, we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of 'expanding covers' of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.},
}

@article {pmid36778249,
year = {2023},
author = {Zhou, W and Karan, KR and Gu, W and Klein, HU and Sturm, G and De Jager, PL and Bennett, DA and Hirano, M and Picard, M and Mills, RE},
title = {Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36778249},
support = {P30 AG072975/AG/NIA NIH HHS/United States ; U01 AG046152/AG/NIA NIH HHS/United States ; R01 AG066828/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R21 HG011493/HG/NHGRI NIH HHS/United States ; R01 AG015819/AG/NIA NIH HHS/United States ; },
abstract = {The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species and recently demonstrated to occur in rare instances from one human generation to the next. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeatedmeasures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous 2 numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.},
}