Microbial Genomics最新文献

{"title":"Genome sequences of the first Autographiviridae phages infecting marine Roseobacter","authors":"Sen Du, Ying Wu, Hanqi Ying, Zuqing Wu, Mingyu Yang, Feng Chen, Jiabing Shao, He Liu, Zefeng Zhang and Yanlin Zhao","doi":"10.1099/mgen.0.001240","DOIUrl":"https://doi.org/10.1099/mgen.0.001240","url":null,"abstract":"The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. <span>Autographiviridae</span> is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of <span>Autographiviridae</span> phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine <span>Roseobacter</span> strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38&#8202;917 to 42&#8202;634&#8201;bp and G+C content of 44.6&#8211;50&#8202;%. Comparative genomics showed that they are similar to known <span>Autographiviridae</span> phages regarding gene content and architecture, thus representing the first <span>Autographiviridae</span> roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the <span>Autographiviridae</span>, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new <span>Autographiviridae</span> phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of <span>Autographiviridae</span> phages and roseophages. We suggest that <span>Autographiviridae</span> phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"9 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140615954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning methods in metagenomics: a review","authors":"Gaspar Roy, Edi Prifti, Eugeni Belda and Jean-Daniel Zucker","doi":"10.1099/mgen.0.001231","DOIUrl":"https://doi.org/10.1099/mgen.0.001231","url":null,"abstract":"The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome&#8217;s key role in our health.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"30 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying the best PCR enzyme for library amplification in NGS","authors":"Michael A. Quail, Craig Corton, James Uphill, Jacqueline Keane and Yong Gu","doi":"10.1099/mgen.0.001228","DOIUrl":"https://doi.org/10.1099/mgen.0.001228","url":null,"abstract":"<span>Background.</span> PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [<span xmlns=\"http://pub2web.metastore.ingenta.com/ns/\">\u00001, 2\u0000</span>]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing.\u0000We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) &#8216;Equinox&#8217; and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated <span>S. cerevisiae</span> DNA of average size 21.6 and 13.4 kb, respectively.\u0000The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) &#8216;Equinox&#8217; and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"164 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco","authors":"Hasnaa Talimi, Othmane Daoui, Giovanni Bussotti, Idris Mhaidi, Anne Boland, Jean-François Deleuze, Rachida Fissoune, Meryem Lemrani and Gerald F. Späth","doi":"10.1099/mgen.0.001230","DOIUrl":"https://doi.org/10.1099/mgen.0.001230","url":null,"abstract":"In Morocco, cutaneous leishmaniasis (CL) caused by <span>Leishmania</span> (<span>L.</span>) <span>tropica</span> is an important health problem. Despite the high incidence of CL in the country, the genomic heterogeneity of these parasites is still incompletely understood. In this study, we sequenced the genomes of 14 Moroccan isolates of <span>L. tropica</span> collected from confirmed cases of CL to investigate their genomic heterogeneity. Comparative genomics analyses were conducted by applying the recently established Genome Instability Pipeline (GIP), which allowed us to conduct phylogenomic and principal components analyses (PCA), and to assess genomic variations at the levels of the karyotype, gene copy number, single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) variants. Read-depth analyses revealed a mostly disomic karyotype, with the exception of the stable tetrasomy of chromosome 31. In contrast, we identified important gene copy number variations across all isolates, which affect known virulence genes and thus were probably selected in the field. SNP-based cluster analysis of the 14 isolates revealed a core group of 12 strains that formed a tight cluster and shared 45.1&#8202;% (87&#8202;751) of SNPs, as well as two strains (M3015, Ltr_16) that clustered separately from each other and the core group, suggesting the circulation of genetically highly diverse strains in Morocco. Phylogenetic analysis, which compared our 14 <span>L. tropica</span> isolates against 40 published genomes of <span>L. tropica</span> from a diverse array of locations, confirmed the genetic difference of our Moroccan isolates from all other isolates examined. In conclusion, our results indicate potential regional variations in SNP profiles that may differentiate Moroccan <span>L. tropica</span> from other <span>L. tropica</span> strains circulating in endemic countries in the Middle East. Our report paves the way for future research with a larger number of strains that will allow correlation of diverse phenotypes (resistance to treatments, virulence) and origins (geography, host species, year of isolation) to defined genomic signals such as gene copy number variations or SNP profiles that may represent interesting biomarker candidates","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"77 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140602849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the impact of insertion sequences and transposons in the genomes of the most significant phytopathogenic bacteria","authors":"Alexia Suellen Fernandes, Kiara França Campos, Jéssica Catarine Silva de Assis, Osiel Silva Gonçalves, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli and Mateus Ferreira Santana","doi":"10.1099/mgen.0.001219","DOIUrl":"https://doi.org/10.1099/mgen.0.001219","url":null,"abstract":"Genetic variability in phytopathogens is one of the main problems encountered for effective plant disease control. This fact may be related to the presence of transposable elements (TEs), but little is known about their role in host genomes. Here, we performed the most comprehensive analysis of insertion sequences (ISs) and transposons (Tns) in the genomes of the most important bacterial plant pathogens. A total of 35&#8201;692 ISs and 71 transposons were identified in 270 complete genomes. The level of pathogen&#8211;host specialization was found to be a significant determinant of the element distribution among the species. Some Tns were identified as carrying virulence factors, such as genes encoding effector proteins of the type III secretion system and resistance genes for the antimicrobial streptomycin. Evidence for IS-mediated ectopic recombination was identified in <span>Xanthomonas</span> genomes. Moreover, we found that IS elements tend to be inserted in regions near virulence and fitness genes, such ISs disrupting avirulence genes in <span>X. oryzae</span> genomes. In addition, transcriptome analysis under different stress conditions revealed differences in the expression of genes encoding transposases in the <span>Ralstonia solanacearum</span>, <span>X. oryzae</span>, and <span>P. syringae</span> species. Lastly, we also investigated the role of Tns in regulation via small noncoding regulatory RNAs and found these elements may target plant-cell transcriptional activators. Taken together, the results indicate that TEs may have a fundamental role in variability and virulence in plant pathogenic bacteria.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"82 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative methylome and transcriptome analysis reveals epigenetic regulation of <i>Fusobacterium nucleatum</i> in laryngeal cancer.","authors":"Xiaohui Yuan, Hui-Ching Lau, Huiying Huang, Chi-Yao Hsueh, Hongli Gong, Liang Zhou","doi":"10.1099/mgen.0.001221","DOIUrl":"10.1099/mgen.0.001221","url":null,"abstract":"<p><p>The aetiological mechanisms of <i>Fusobacterium nucleatum</i> in laryngeal cancer remain unclear. This study aimed to reveal the epigenetic signature induced by <i>F. nucleatum</i> in laryngeal squamous cell carcinoma (LSCC). Combined analysis of methylome and transcriptome data was performed to address the functional role of <i>F. nucleatum</i> in laryngeal cancer. Twenty-nine differentially expressed methylation-driven genes were identified by mapping the methylation levels of significant differential methylation sites to the expression levels of related genes. The combined analysis revealed that <i>F. nucleatum</i> promoted Janus kinase 3 (JAK3) gene expression in LSCC. Further validation found decreased methylation and elevated expression of JAK3 in the <i>F. nucleatum-</i>treated LSCC cell group; <i>F. nucleatum</i> abundance and JAK3 gene expression had a positive correlation in tumour tissues. This analysis provides a novel understanding of the impact of <i>F. nucleatum</i> in the methylome and transcriptome of laryngeal cancer. Identification of these epigenetic regulatory mechanisms opens up new avenues for mechanistic studies to explore novel therapeutic strategies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10995630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of <i>Mycobacterium tuberculosis</i> complex.","authors":"Elena Hailu, Daire Cantillon, Carlos Madrazo, Graham Rose, Paul R Wheeler, Paul Golby, Bethlehem Adnew, Sebastien Gagneux, Abraham Aseffa, Stephen V Gordon, Iñaki Comas, Douglas B Young, Simon J Waddell, Gerald Larrouy-Maumus, Stefan Berg","doi":"10.1099/mgen.0.001226","DOIUrl":"10.1099/mgen.0.001226","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11000246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140306122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Streptococcus pneumoniae</i> serotype 3 population structure in the era of conjugate vaccines, 2001-2018.","authors":"Eleonora Cella, Catherine G Sutcliffe, Lindsay R Grant, Carol Tso, Robert C Weatherholtz, Shea Littlepage, Ladonna Becenti, Mohammad Jubair, Brenna C Simons, Marcella Harker-Jones, Raymond Reid, Del Yazzie, Mathuram Santosham, Katherine L O'Brien, Laura L Hammitt, Taj Azarian","doi":"10.1099/mgen.0.001196","DOIUrl":"10.1099/mgen.0.001196","url":null,"abstract":"<p><p><b>Background.</b> Despite use of highly effective conjugate vaccines, invasive pneumococcal disease (IPD) remains a leading cause of morbidity and mortality and disproportionately affects Indigenous populations. Although included in the 13-valent pneumococcal conjugate vaccine (PCV13), which was introduced in 2010, serotype 3 continues to cause disease among Indigenous communities in the Southwest USA. In the Navajo Nation, serotype 3 IPD incidence increased among adults (3.8/100 000 in 2001-2009 and 6.2/100 000 in 2011-2019); in children the disease persisted although the rates dropped from 5.8/100 000 to 2.3/100 000.<b>Methods.</b> We analysed the genomic epidemiology of serotype 3 isolates collected from 129 adults and 63 children with pneumococcal carriage (<i>n</i>=61) or IPD (<i>n</i>=131) from 2001 to 2018 of the Navajo Nation. Using whole-genome sequencing data, we determined clade membership and assessed changes in serotype 3 population structure over time.<b>Results.</b> The serotype 3 population structure was characterized by three dominant subpopulations: <i>clade II</i> (<i>n</i>=90, 46.9 %) and <i>clade Iα</i> (<i>n</i>=59, 30.7 %), which fall into Clonal Complex (CC) 180, and a non-CC180 clade (<i>n</i>=43, 22.4 %). The proportion of <i>clade II</i>-associated IPD cases increased significantly from 2001 to 2010 to 2011-2018 among adults (23.1-71.8 %; <i>P</i><0.001) but not in children (27.3-33.3 %; <i>P</i>=0.84). Over the same period, the proportion of <i>clade II-</i>associated carriage increased; this was statistically significant among children (23.3-52.6 %; <i>P</i>=0.04) but not adults (0-50.0 %, <i>P</i>=0.08).<b>Conclusions.</b> In this setting with persistent serotype 3 IPD and carriage, <i>clade II</i> has increased since 2010. Genomic changes may be contributing to the observed trends in serotype 3 carriage and disease over time.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140158438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions.","authors":"Bianca Rodrigues Jardim, Cherie Gambley, Lucy T T Tran-Nguyen, Craig Webster, Monica Kehoe, Wycliff M Kinoti, Samantha Bond, Richard Davis, Lynne Jones, Nandita Pathania, Murray Sharman, Toni Chapman, Brendan C Rodoni, Fiona E Constable","doi":"10.1099/mgen.0.001213","DOIUrl":"10.1099/mgen.0.001213","url":null,"abstract":"<p><p>In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (<i>n</i>=46) or during collection efforts between January 2015 and June 2022 (<i>n</i>=149). The sampled hosts were classified as crop (<i>n</i>=155), weed (<i>n</i>=24), ornamental (<i>n</i>=7), native plant (<i>n</i>=6), and insect (<i>n</i>=3) species. Most samples came from Queensland (<i>n</i>=78), followed by Western Australia (<i>n</i>=46), the Northern Territory (<i>n</i>=32), New South Wales (<i>n</i>=17), and Victoria (<i>n</i>=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (<i>n</i>=153), followed by strains within the 16SrXXXVIII group ('<i>Ca</i>. Phytoplasma stylosanthis'; <i>n</i>=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and '<i>Ca</i>. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of '<i>Ca</i>. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10999746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virulence genes, resistome and mobilome of <i>Streptococcus suis</i> strains isolated in France.","authors":"Manon Dechêne-Tempier, Claire de Boisséson, Pierrick Lucas, Stéphanie Bougeard, Virginie Libante, Corinne Marois-Créhan, Sophie Payot","doi":"10.1099/mgen.0.001224","DOIUrl":"10.1099/mgen.0.001224","url":null,"abstract":"<p><p><i>Streptococcus suis</i> is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in <i>S. suis</i> worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (<i>n</i>=217) was found in the genomes. Apart from the frequently reported <i>erm</i>(B) and <i>tet</i>(O) genes, more recently described AMR genes were identified [<i>vga</i>(F)/<i>sprA</i>, <i>vat</i>(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 3","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10995628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140293892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}