Microbial Genomics最新文献

{"title":"16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces","authors":"Angelika B. Kiepas, Paul A. Hoskisson and Leighton Pritchard","doi":"10.1099/mgen.0.001287","DOIUrl":"https://doi.org/10.1099/mgen.0.001287","url":null,"abstract":"<span>Streptomyces</span> is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of <span>Streptomyces</span> would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based <span>Streptomyces</span> classifications using 2276 publicly available <span>Streptomyces</span> genome assemblies and 48&#8201;981 publicly available full-length 16S rRNA <span>Streptomyces</span> sequences from <span>silva</span>, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14&#8201;239 distinct <span>Streptomyces</span> sequences that resolves three major lineages of <span>Streptomyces</span>, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for <span>Streptomyces</span>, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate <span>Streptomyces</span> species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as <span>Streptomyces</span> taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the <span>Streptomyces</span> community.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193262","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":"Genetic heterogeneity in the Salmonella Typhi Vi capsule locus: a population genomic study from Fiji","authors":"Aneley Getahun Strobel, Andrew J. Hayes, Wytamma Wirth, Mikaele Mua, Tiko Saumalua, Orisi Cabenatabua, Vika Soqo, Varanisese Rosa, Nancy Wang, Jake A. Lacey, Dianna Hocking, Mary Valcanis, Adam Jenney, Benjamin P. Howden, Sebastian Duchene, Kim Mulholland, Richard A. Strugnell and Mark R. Davies","doi":"10.1099/mgen.0.001288","DOIUrl":"https://doi.org/10.1099/mgen.0.001288","url":null,"abstract":"Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji implemented a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology of <span>Salmonella</span> Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (<span>n</span>=419) of the total cases from the Northern and Central Divisions of Fiji that occurred in the period 2017&#8211;2019. We found elevated rates of nucleotide polymorphisms in the <span>tviD</span> and <span>tviE</span> genes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemic <span>S</span>. Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12&#8202;382 <span>S</span>. Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the same <span>tviE</span> mutations across the <span>S</span>. Typhi population, indicating that <span>tvi</span> selection has occurred both independently and globally. The functional impact of <span>tvi</span> mutations on the Vi-capsular structure and other phenotypic characteristics are not fully elucidated, yet commonly occurring <span>tviE</span> polymorphisms localize adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide in <span>S</span>. Typhi biology and vaccination, further integrated epidemiological, genomic and phenotypic surveillance is required to determine the spread and functional implications of these mutations.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193261","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":"Evaluation of <i>Klebsiella pneumoniae</i> pathogenicity through holistic gene content analysis.","authors":"Miyu Isogai, Kumiko Kawamura, Tetsuya Yagi, Shizuo Kayama, Motoyuki Sugai, Yohei Doi, Masahiro Suzuki","doi":"10.1099/mgen.0.001295","DOIUrl":"https://doi.org/10.1099/mgen.0.001295","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of <i>K. pneumoniae</i> is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical <i>K. pneumoniae</i> strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of <i>K. pneumoniae</i> strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (<i>rmpA</i>, <i>iucA</i>, <i>iutA</i>, <i>irp2</i>, <i>fyuA</i>, <i>ybtS</i>, <i>iroN</i>, <i>allS</i> and <i>clbA</i>) compared to the major group. Pathogenicity was assessed using <i>Galleria mellonella</i> larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the <i>G. mellonella</i> infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142290819","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":"Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.","authors":"Laura Glendinning, Zhiguang Wu, Lonneke Vervelde, Mick Watson, Adam Balic","doi":"10.1099/mgen.0.001289","DOIUrl":"10.1099/mgen.0.001289","url":null,"abstract":"<p><p>The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109157","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":"Genomic study substantiates the intensive care unit as a reservoir for carbapenem-resistant <i>Klebsiella pneumoniae</i> in a teaching hospital in China.","authors":"Shuo Jiang, Zheng Ma, Huiluo Cao, Li Mo, Jinlan Jin, Bohai Yu, Kankan Chu, Jihua Hu","doi":"10.1099/mgen.0.001299","DOIUrl":"10.1099/mgen.0.001299","url":null,"abstract":"<p><p>Carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP) has recently emerged as a notable public health concern, while the underlying drivers of CRKP transmission among patients across different healthcare facilities have not been fully elucidated. To explore the transmission dynamics of CRKP, 45 isolates were collected from both the intensive care unit (ICU) and non-ICU facilities in a teaching hospital in Guangdong, China, from March 2020 to August 2023. The collection of clinical data and antimicrobial resistance phenotypes was conducted, followed by genomic data analysis for these isolates. The mean age of the patients was 75.2 years, with 18 patients (40.0%) admitted to the ICU. The predominant strain in hospital-acquired CRKP was sequence type 11 (ST11), with k-locus type 64 and serotype O1/O2v1 (KL64:O1/O2v1), accounting for 95.6% (43/45) of the cases. The CRKP ST11 isolates from the ICU exhibited a low single nucleotide polymorphism (SNP) distance when compared to isolates from other departments. Genome-wide association studies identified 17 genes strongly associated with SNPs that distinguish CRKP ST11 isolates from those in the ICU and other departments. Temporal transmission analysis revealed that all CRKP isolates from other departments were genetically very close to those from the ICU, with fewer than 16 SNP differences. To further elucidate the transmission routes among departments within the hospital, we reconstructed detailed patient-to-patient transmission pathways using hybrid methods that combine TransPhylo with an SNP-based algorithm. A clear transmission route, along with mutations in potential key genes, was deduced from genomic data coupled with clinical information in this study, providing insights into CRKP transmission dynamics in healthcare settings.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349687","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":"Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.","authors":"Daniel G Barber, Christian A Davies, Iain P Hartley, Richard K Tennant","doi":"10.1099/mgen.0.001298","DOIUrl":"https://doi.org/10.1099/mgen.0.001298","url":null,"abstract":"<p><p>Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11412367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142290820","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":"pQEB1: a hospital outbreak plasmid lineage carrying <i>bla</i> _KPC-2.","authors":"Robert A Moran, Mahboobeh Behruznia, Elisabeth Holden, Mark I Garvey, Alan McNally","doi":"10.1099/mgen.0.001291","DOIUrl":"10.1099/mgen.0.001291","url":null,"abstract":"<p><p>While conducting genomic surveillance of carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene <i>bla</i> _KPC-2. The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of <i>Citrobacter freundii</i>, two STs of <i>Enterobacter cloacae</i>, and three species of <i>Klebsiella</i>. Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an <i>Enterobacter hormaechei</i> isolated from a blood sample at the QE in 2016 and a <i>Klebsiella pneumoniae</i> isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS<i>26</i>-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109158","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>Vibrio cholerae</i> serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965.","authors":"Caroline Rouard, Elisabeth Njamkepo, Marie-Laure Quilici, Scott Nguyen, Victoria Knight-Connoni, Renáta Šafránková, Francois-Xavier Weill","doi":"10.1099/mgen.0.001282","DOIUrl":"10.1099/mgen.0.001282","url":null,"abstract":"<p><p>Several authors have attributed the explosive outbreak of gastroenteritis that occurred in Czechoslovakia in 1965 to a toxigenic strain of <i>Vibrio cholerae</i> serogroup O37 based on unverified metadata associated with three particular strains from the American Type Culture Collection. Here, by sequencing the original strain preserved at the Czech National Collection of Type Cultures since 1966, we show that the strain responsible for this outbreak was actually a <i>V. cholerae</i> O5 that lacks the genes encoding the cholera toxin, the toxin-coregulated pilus protein and <i>Vibrio</i> pathogenicity islands present in <i>V. cholerae</i> O37 strains.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133123","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":"Development and implementation of a core genome multilocus sequence typing scheme for <i>Haemophilus influenzae</i>.","authors":"Made Ananda Krisna, Keith A Jolley, William Monteith, Alexandra Boubour, Raph L Hamers, Angela B Brueggemann, Odile B Harrison, Martin C J Maiden","doi":"10.1099/mgen.0.001281","DOIUrl":"10.1099/mgen.0.001281","url":null,"abstract":"<p><p><i>Haemophilus influenzae</i> is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in <i>H. influenzae</i> necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for <i>H. influenzae</i> using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (<i>N</i> = 14) and high-quality draft <i>H. influenzae</i> genomes (<i>N</i> = 2297). The draft genome dataset was divided into a development dataset (<i>N</i> = 921) and a validation dataset (<i>N</i> = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (<i>R</i> ² = 0.945). We used this cgMLST scheme to define a high-resolution population structure for <i>H. influenzae</i>, which enhances the genomic analysis of this clinically relevant human pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907045","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":"Comparative genomic analysis identifies potential adaptive variation in <i>Mycoplasma ovipneumoniae</i>.","authors":"Kimberly R Andrews, Thomas E Besser, Thibault Stalder, Eva M Top, Katherine N Baker, Matthew W Fagnan, Daniel D New, G Maria Schneider, Alexandra Gal, Rebecca Andrews-Dickert, Samuel S Hunter, Kimberlee B Beckmen, Lauren Christensen, Anne Justice-Allen, Denise Konetchy, Chadwick P Lehman, Kezia Manlove, Hollie Miyasaki, Todd Nordeen, Annette Roug, E Frances Cassirer","doi":"10.1099/mgen.0.001279","DOIUrl":"https://doi.org/10.1099/mgen.0.001279","url":null,"abstract":"<p><p><i>Mycoplasma ovipneumoniae</i> is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared <i>M. ovipneumoniae</i> genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of <i>M. ovipneumoniae</i> assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three <i>M. ovipneumoniae</i> genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of <i>M. ovipneumoniae</i> has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109156","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}