Microbial Genomics最新文献

{"title":"Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.","authors":"Steven G Sutcliffe, Susanne A Kraemer, Isaac Ellmen, Jennifer J Knapp, Alyssa K Overton, Delaney Nash, Jozef I Nissimov, Trevor C Charles, David Dreifuss, Ivan Topolsky, Pelin I Baykal, Lara Fuhrmann, Kim P Jablonski, Niko Beerenwinkel, Joshua I Levy, Abayomi S Olabode, Devan G Becker, Gopi Gugan, Erin Brintnell, Art F Y Poon, Renan Valieris, Rodrigo D Drummond, Alexandre Defelicibus, Emmanuel Dias-Neto, Rafael A Rosales, Israel Tojal da Silva, Aspasia Orfanou, Fotis Psomopoulos, Nikolaos Pechlivanis, Lenore Pipes, Zihao Chen, Jasmijn A Baaijens, Michael Baym, B Jesse Shapiro","doi":"10.1099/mgen.0.001249","DOIUrl":"10.1099/mgen.0.001249","url":null,"abstract":"<p><p>Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087977","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":"SaLTy: a novel <i>Staphylococcus aureus</i> Lineage Typer.","authors":"Liam Cheney, Michael Payne, Sandeep Kaur, Ruiting Lan","doi":"10.1099/mgen.0.001250","DOIUrl":"10.1099/mgen.0.001250","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 <i>S</i>. <i>aureus</i> was associated with 20 000 deaths in the USA alone. Dividing <i>S. aureus</i> isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of <i>S. aureus</i> genome sequences when describing the fundamental population structure of the species. In this study, we developed <i>Staphylococcus aureus</i> Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (<i>n</i>=21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing <i>mecA</i> (SCC<i>mec</i>) which is carried by methicillin-resistant <i>S. aureus</i> (MRSA). Most lineages had isolates lacking SCC<i>mec</i> and the four largest lineages varied in SCC<i>mec</i> over time. Classifying isolates into SaLTy lineages, which were further SCC<i>mec</i> typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of <i>S. aureus</i> genome data. SaLTy will aid the characterisation of <i>S. aureus</i> populations and ongoing surveillance of sub-groups that threaten human health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912394","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>Actinomycetota</i> bioprospecting from ore-forming environments.","authors":"César Aguilar, Amir Alwali, Madeline Mair, Lorena Rodriguez-Orduña, Haydeé Contreras-Peruyero, Ramya Modi, Carson Roberts, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Elizabeth Ivy Parkinson","doi":"10.1099/mgen.0.001253","DOIUrl":"10.1099/mgen.0.001253","url":null,"abstract":"<p><p>Natural products from <i>Actinomycetota</i> have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922265","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":"Genomics and physiology of <i>Catenibacillus</i>, human gut bacteria capable of polyphenol <i>C</i>-deglycosylation and flavonoid degradation.","authors":"Tobias Goris, Annett Braune","doi":"10.1099/mgen.0.001245","DOIUrl":"10.1099/mgen.0.001245","url":null,"abstract":"<p><p>The genus <i>Catenibacillus</i> (family <i>Lachnospiraceae</i>, phylum <i>Bacillota</i>) includes only one cultivated species so far, <i>Catenibacillus scindens,</i> isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinal <i>Catenibacillus</i> strain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designated <i>Catenibacillus decagia</i>, and showed its ability to deglycosylate <i>C</i>-coupled flavone and xanthone glucosides and <i>O</i>-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome of <i>C. scindens</i> and ten faecal metagenome-assembled genomes assigned to the genus <i>Catenibacillus</i>, we performed a comparative genome analysis and searched for genes encoding potential <i>C</i>-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism of <i>Catenibacillus</i> strains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. Both <i>C. scindens</i> and <i>C. decagia</i> encode a flavonoid <i>O</i>-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoid <i>C</i>-deglycosylation system of <i>Dorea</i> strain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required for <i>C</i>-deglycosylation. The diversity of <i>dgpA</i> and <i>dgpBC</i> gene clusters might explain the broad <i>C</i>-glycoside substrate spectrum of <i>C. scindens</i> and <i>C. decagia</i>. The other <i>Catenibacillus</i> genomes encode only a few potential flavonoid-converting enzymes. Our results indicate that several <i>Catenibacillus</i> species are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087970","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":"Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment.","authors":"Becca L Handley, Oliver Sokana, Kennedy Kwasi Addo, Josef Wagner, María Fookes, Emma Harding-Esch, Michael Marks, Nicholas R Thomson, Ronan M Doyle","doi":"10.1099/mgen.0.001234","DOIUrl":"10.1099/mgen.0.001234","url":null,"abstract":"<p><p>Cutaneous ulcers are common in yaws-endemic areas. Although often attributed to '<i>Treponema pallidum</i> subsp. <i>pertenue'</i> and <i>Haemophilus ducreyi</i>, quantitative PCR has highlighted a significant proportion of these ulcers are negative for both pathogens and are considered idiopathic. This is a retrospective analysis utilising existing 16S rRNA sequencing data from two independent yaws studies that took place in Ghana and the Solomon Islands. We characterized bacterial diversity in 38 samples to identify potential causative agents for idiopathic cutaneous ulcers. We identified a diverse bacterial profile, including <i>Arcanobacterium haemolyticum</i>, <i>Campylobacter concisus</i>, <i>Corynebacterium diphtheriae</i>, <i>Staphylococcus</i> spp<i>.</i> and <i>Streptococcus pyogenes</i>, consistent with findings from previous cutaneous ulcer microbiome studies. No single bacterial species was universally present across all samples. The most prevalent bacterium, <i>Campylobacter ureolyticus</i>, appeared in 42% of samples, suggesting a multifactorial aetiology for cutaneous ulcers in yaws-endemic areas. This study emphasizes the need for a nuanced understanding of potential causative agents. The findings prompt further exploration into the intricate microbial interactions contributing to idiopathic yaw-like ulcers, guiding future research toward comprehensive diagnostic and therapeutic strategies.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912397","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":"Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen.","authors":"Julie Ramírez Martínez, Sonia Guillou, Stéphanie Le Prieur, Pauline Di Vittorio, Florelle Bonal, Demetris Taliadoros, Elise Gueret, Elisabeth Fournier, Eva H Stukenbrock, Romain Valade, Pierre Gladieux","doi":"10.1099/mgen.0.001241","DOIUrl":"10.1099/mgen.0.001241","url":null,"abstract":"<p><p>Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. <i>Pyrenophora teres</i> is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of <i>P. teres</i> remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of <i>P. teres</i> in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11170133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140863238","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":"Presence of phage-plasmids in multiple serovars of <i>Salmonella enterica</i>.","authors":"Satheesh Nair, Clare R Barker, Matthew Bird, David R Greig, Caitlin Collins, Anaïs Painset, Marie Chattaway, Derek Pickard, Lesley Larkin, Saheer Gharbia, Xavier Didelot, Paolo Ribeca","doi":"10.1099/mgen.0.001247","DOIUrl":"10.1099/mgen.0.001247","url":null,"abstract":"<p><p>Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a <i>bla</i> _CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in <i>Salmonella enterica</i> serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in <i>Enterobacterales</i>, in this study we carried out a follow-up retrospective analysis of UK <i>Salmonella</i> isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene <i>repL</i>, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to <i>S</i>. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in <i>Salmonella</i>, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876823","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 analysis of an outbreak of Shiga toxin-producing <i>Escherichia coli</i> O183:H18 in the United Kingdom, 2023.","authors":"David R Greig, Orlagh I Quinn, Ella V Rodwell, Israel Olonade, Craig Swift, Amy Douglas, Sooria Balasegram, Claire Jenkins","doi":"10.1099/mgen.0.001243","DOIUrl":"10.1099/mgen.0.001243","url":null,"abstract":"<p><p>In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing <i>Escherichia coli</i>, STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % cases were aged 0-9 years), distributed across the UK with onset dates range between 22 May 2023 and 4 July 2023. The epidemiological and food chain investigations were inconclusive, although meat products made from beef mince were implicated as a potential vehicle. The outbreak strain belonged to sequence type (ST) 657 and harboured a Shiga toxin (<i>stx</i>) subtype <i>stx2a</i> located on a prophage that was unique in the UKHSA <i>stx</i>-encoding bacteriophage database. Plasmid encoded, putative virulence genes <i>subA</i>, <i>ehxA</i>, <i>saa, iha</i>, <i>lpfA</i> and <i>iss</i> were detected, however, the established STEC virulence genes involved in attachment to the gut mucosa (<i>eae</i> and <i>aggR</i>) were absent. The acquisition of <i>stx</i> across the global population structure of ST657 appeared to correspond with the presence of <i>subA</i>, <i>ehxA</i>, <i>saa, iha</i>, <i>lpfA</i> and <i>iss</i>. During the outbreak investigation, we used long read sequencing to characterise the plasmid and prophage content of this atypical STEC, to look for evidence to explain its recent emergence. Although we were unable to determine source and transmission route of the outbreak strain, the genomic analysis revealed potential clues as to how novel strains for STEC evolve. With the implementation of PCR capable of detecting all STEC, and genome sequencing for typing and virulence profiling, we have the tools to enable us to monitor the changing landscape of STEC. Improvements in the standardised collection of epidemiological data and trace-back strategies within the food industry, will ensure we have a surveillance system capable of alerting us to emerging threats to public health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070052","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":"Putative genome contamination has minimal impact on the GTDB taxonomy.","authors":"Aaron J Mussig, Pierre-Alain Chaumeil, Maria Chuvochina, Christian Rinke, Donovan H Parks, Philip Hugenholtz","doi":"10.1099/mgen.0.001256","DOIUrl":"10.1099/mgen.0.001256","url":null,"abstract":"<p><p>The Genome Taxonomy Database (GTDB) provides a species to domain classification of publicly available genomes based on average nucleotide identity (ANI) (for species) and a concatenated gene phylogeny normalized by evolutionary rates (for genus to phylum), which has been widely adopted by the scientific community. Here, we use the Genome UNClutterer (GUNC) software to identify putatively contaminated genomes in GTDB release 07-RS207. We found that GUNC reported 35,723 genomes as putatively contaminated, comprising 11.25 % of the 317,542 genomes in GTDB release 07-RS207. To assess the impact of this high level of inferred contamination on the delineation of taxa, we created 'clean' versions of the 34,846 putatively contaminated bacterial genomes by removing the most contaminated half. For each clean half, we re-calculated the ANI and concatenated gene phylogeny and found that only 77 (0.22 %) of the genomes were not consistent with their original classification. We conclude that the delineation of taxa in GTDB is robust to the putative contamination detected by GUNC.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11261887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175550","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":"Defining the phylogenetics and resistome of the major <i>Clostridioides difficile</i> ribotypes circulating in Australia.","authors":"Keeley O'Grady, Stacey Hong, Papanin Putsathit, Narelle George, Christine Hemphill, Peter G Huntington, Tony M Korman, Despina Kotsanas, Monica Lahra, Rodney McDougall, Andrew McGlinchey, Avram Levy, Casey V Moore, Graeme Nimmo, Louise Prendergast, Jennifer Robson, David J Speers, Lynette Waring, Michael C Wehrhahn, Gerhard F Weldhagen, Richard M Wilson, Thomas V Riley, Daniel R Knight","doi":"10.1099/mgen.0.001232","DOIUrl":"10.1099/mgen.0.001232","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of <i>C. difficile</i> ribotypes (RTs) 014/020 (<i>n</i>=169), 002 (<i>n</i>=77) and 056 (<i>n</i>=36), the three most prominent <i>C. difficile</i> strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLS_B agents <i>in vitro</i>, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, <i>n</i>=36) to 115.6 (RT002, ST8, <i>n</i>=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, <i>n</i>=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, <i>n</i>=14; RT002, <i>n</i>=3; RT056, <i>n</i>=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse <i>C. difficile</i> strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"10 5","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876821","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}