Microbial Genomics最新文献

{"title":"Towards quantifying plasmid similarity","authors":"William Matlock, Liam P. Shaw, Samuel K. Sheppard and Edward Feil","doi":"10.1099/mgen.0.001290","DOIUrl":"https://doi.org/10.1099/mgen.0.001290","url":null,"abstract":"Plasmids are extrachromosomal replicons which can quickly spread resistance and virulence genes between clinical pathogens. From the tens of thousands of currently available plasmid sequences we know that overall plasmid diversity is structured, with related plasmids sharing a largely conserved ‘backbone’ of genes while being able to carry very different genetic cargo. Moreover, plasmid genomes can be structurally plastic and undergo frequent rearrangements. So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193191","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":"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":"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":"","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":"","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}

{"title":"Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome.","authors":"Yuka Adachi Katayama, Ryoma Kamikawa, Takashi Yoshida","doi":"10.1099/mgen.0.001285","DOIUrl":"10.1099/mgen.0.001285","url":null,"abstract":"<p><p>Although the production of carbon monoxide (CO) within the human body has been detected, only two CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut. Therefore, the phylogenetic diversity of the human gut CO-utilizing prokaryotes remains unclear. Here, we unveiled more than a thousand representative genomes containing genes for putative nickel-containing CO dehydrogenase (pCODH), an essential enzyme for CO utilization. The taxonomy of genomes encoding pCODH was expanded to include 8 phyla, comprising 82 genera and 248 species. In contrast, putative molybdenum-containing CODH genes were not detected in the human gut microbial genomes. pCODH transcripts were detected in 97.3 % (<i>n</i>=110) of public metatranscriptome datasets derived from healthy human faeces, suggesting the ubiquitous presence of prokaryotes bearing transcriptionally active pCODH genes in the human gut. More than half of the pCODH-encoding genomes contain a set of genes for the autotrophic Wood-Ljungdahl pathway (WLP). However, 79 % of these genomes commonly lack a key gene for the WLP, which encodes the enzyme that synthesizes formate from CO₂, suggesting that potential human gut CO-utilizing prokaryotes share a degenerated gene set for WLP. In the other half of the pCODH-encoding genomes, seven genes, including putative genes for flavin adenine dinucleotide-dependent NAD(P) oxidoreductase (FNOR), ABC transporter and Fe-hydrogenase, were found adjacent to the pCODH gene. None of the putative genes associated with CO-oxidizing respiratory machinery, such as energy-converting hydrogenase genes, were found in pCODH-encoding genomes. This suggests that the human gut CO utilization is not for CO removal, but potentially for fixation and/or biosynthesis, consistent with the harmless yet continuous production of CO in the human gut. Our findings reveal the diversity and distribution of prokaryotes with pCODH in the human gut microbiome, suggesting their potential contribution to microbial ecosystems in human gut environments.</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/PMC11338639/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142017965","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":"Whole-genome sequencing of Western Canadian <i>Borrelia</i> spp. collected from diverse tick and animal hosts reveals short-lived local genotypes interspersed with longer-lived continental genotypes.","authors":"Jennifer N Russell, Min-Kuang Lee, Miguel I Uyaguari-Diaz, Ashton N Sies, Danae M Suchan, William Hsiao, Erin Fraser, Muhammad G Morshed, Andrew D S Cameron","doi":"10.1099/mgen.0.001276","DOIUrl":"10.1099/mgen.0.001276","url":null,"abstract":"<p><p>Changing climates are allowing the geographic expansion of ticks and their animal hosts, increasing the risk of <i>Borrelia</i>-caused zoonoses in Canada. However, little is known about the genomic diversity of <i>Borrelia</i> from the west of the Canadian Rockies and from the tick vectors <i>Ixodes pacificus</i>, <i>Ixodes auritulus</i> and <i>Ixodes angustus</i>. Here, we report the whole-genome shotgun sequences of 51 <i>Borrelia</i> isolates from multiple tick species collected on a range of animal hosts between 1993 and 2016, located primarily in coastal British Columbia. The bacterial isolates represented three different species from the Lyme disease-causing <i>Borrelia burgdorferi sensu lato</i> genospecies complex [<i>Borrelia burgdorferi sensu stricto</i> (<i>n</i>=47), <i>Borrelia americana</i> (<i>n</i>=3) and <i>Borrelia bissettiae</i> (<i>n</i>=1)]. The traditional eight-gene multi-locus sequence typing (MLST) strategy was applied to facilitate comparisons across studies. This identified 13 known <i>Borrelia</i> sequence types (STs), established 6 new STs, and assigned 5 novel types to the nearest sequence types. <i>B. burgdorferi</i> s. s. isolates were further differentiated into ten <i>ospC</i> types, plus one novel <i>ospC</i> with less than 92 % nucleotide identity to all previously defined <i>ospC</i> types. The MLST types resampled over extended time periods belonged to previously described STs that are distributed across North America. The most geographically widespread ST, ST.12, was isolated from all three tick species. Conversely, new <i>B. burgdorferi</i> s. s. STs from Vancouver Island and the Vancouver region were only detected for short periods, revealing a surprising transience in space, time and host tick species, possibly due to displacement by longer-lived genotypes that expanded across North America.This article contains data hosted by Microreact.</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/PMC11296321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875283","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}