Microbial Genomics最新文献

{"title":"Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.","authors":"George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J Roach, Bhavya Papudeshi, Lousie M Judd, Anna E Sheppard, Robert A Edwards, Sarah Vreugde","doi":"10.1099/mgen.0.001244","DOIUrl":"10.1099/mgen.0.001244","url":null,"abstract":"<p><p>Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.</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/PMC11165638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876822","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":"Analysis of global <i>Aeromonas caviae</i> genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related.","authors":"Sarah K T Chong, Fang Liu, Christopher Yuwono, Alfred Chin Yen Tay, Michael C Wehrhahn, Stephen M Riordan, Lu Liu, Li Zhang","doi":"10.1099/mgen.0.001258","DOIUrl":"10.1099/mgen.0.001258","url":null,"abstract":"<p><p><i>Aeromonas caviae</i> is an emerging human enteric pathogen. However, the genomic features and virulence genes of <i>A. caviae</i> strains from human gastroenteritis and other sources have not been fully elucidated. Here, we conducted a genomic analysis of 565 global <i>A. caviae</i> strains isolated from different sources, including 261 strains isolated from faecal samples of gastroenteritis patients, of which 18 genomes were sequenced in this study. The presence of bacterial virulence genes and secretion systems in <i>A. caviae</i> strains from different sources was compared, and the phylogenetic relationship of <i>A. caviae</i> strains was assessed based on the core genome. The complete genome of <i>A. caviae</i> strain A20-9 isolated from a gastroenteritis patient was obtained in this study, from which 300 putative virulence factors and a T4SS-encoding plasmid, pAC, were identified. Genes encoding T4SS were also identified in a novel genomic island, ACI-1, from other T4SS-positive strains. The prevalence of T4SS was significantly lower in <i>A. caviae</i> strains from gastroenteritis patients than in environmental strains (3 %, <i>P</i><0.0001 vs 14 %, <i>P</i><0.01). Conversely, the prevalence of T6SS was significantly higher in <i>A. caviae</i> strains isolated from gastroenteritis patients than in environmental strains (25 %, <i>P</i><0.05 vs 13  %, <i>P</i><0.01). Four phylogenetic clusters were formed based on the core genome of 565 <i>A</i>. <i>caviae</i> strains, and strains carrying T6SS often showed close phylogenetic relationships. T3SS, aerolysin and thermostable cytotonic enterotoxin were absent in all 565 <i>A</i>. <i>caviae</i> strains. Our findings provide novel information on the genomic features of <i>A. caviae</i> and suggest that T6SS may play a role in <i>A. caviae</i>-induced human gastroenteritis.</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/PMC11165597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175545","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 characterization of <i>Aeromonas</i> spp. isolates from striped catfish with motile <i>Aeromonas</i> septicemia and human bloodstream infections in Vietnam.","authors":"Nhat Ha Minh Truong, Quynh Nguyen, Phat Vinh Voong, Vinh Chau, Nhi Huynh Thanh Nguyen, Tuan Hoa Minh Nguyen, Phuong Hong Vo, Luan Thanh Nguyen, Trinh Thi Phuong Ha, Lan Phu Huong Nguyen, Phuoc Hong Le, Duy Pham Thanh, Hoang Duc Nguyen","doi":"10.1099/mgen.0.001248","DOIUrl":"10.1099/mgen.0.001248","url":null,"abstract":"<p><p><i>Aeromonas</i> spp. are commonly found in the aquatic environment and have been responsible for motile <i>Aeromonas</i> septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 <i>Aeromonas</i> isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated <i>Aeromonas</i> species while traditional methods such as <i>aerA</i> PCR and MALDI-TOF were unable identify <i>A. dhakensis. A. dhakensis</i> was found to be more prevalent than <i>A. hydrophila</i> in both diseased catfish and human infections. <i>A. dhakensis</i> sequence type (ST) 656 followed by <i>A. hydrophila</i> ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin <i>ast</i> in <i>A. dhakensis</i>), AMR genes (i.e. presence of <i>imiH</i> carbapenemase in <i>A. dhakensis</i>), and accessory gene content. To uncover potential conserved proteins of <i>Aeromonas</i> spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of <i>Aeromonas</i> in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent <i>A. dhakensis</i> strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing <i>Aeromonas</i> diseases in catfish and humans, and the search for potential vaccine candidates could focus on <i>Aeromonas</i> core genes encoded for membrane and secreted proteins.</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/PMC11165649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912332","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":"Development of a sequence-based <i>in silico</i> OspA typing method for <i>Borrelia burgdorferi sensu lato</i>.","authors":"Jonathan T Lee, Zhenghui Li, Lorna D Nunez, Daniel Katzel, B Scott Perrin, Varun Raghuraman, Urvi Rajyaguru, Katrina E Llamera, Lubomira Andrew, Annaliesa S Anderson, Joppe W Hovius, Paul A Liberator, Raphael Simon, Li Hao","doi":"10.1099/mgen.0.001252","DOIUrl":"10.1099/mgen.0.001252","url":null,"abstract":"<p><p>Lyme disease (LD), caused by spirochete bacteria of the genus <i>Borrelia burgdorferi sensu lato</i>, remains the most common vector-borne disease in the northern hemisphere. <i>Borrelia</i> outer surface protein A (OspA) is an integral surface protein expressed during the tick cycle, and a validated vaccine target. There are at least 20 recognized <i>Borrelia</i> genospecies, that vary in OspA serotype. This study presents a new <i>in silico</i> sequence-based method for OspA typing using next-generation sequence data. Using a compiled database of over 400 <i>Borrelia</i> genomes encompassing the 4 most common disease-causing genospecies, we characterized OspA diversity in a manner that can accommodate existing and new OspA types and then defined boundaries for classification and assignment of OspA types based on the sequence similarity. To accommodate potential novel OspA types, we have developed a new nomenclature: OspA <i>in silico</i> type (IST). Beyond the ISTs that corresponded to existing OspA serotypes 1-8, we identified nine additional ISTs that cover new OspA variants in <i>B. bavariensis</i> (IST9-10), <i>B. garinii</i> (IST11-12), and other <i>Borrelia</i> genospecies (IST13-17). The IST typing scheme and associated OspA variants are available as part of the PubMLST <i>Borrelia</i> spp. database. Compared to traditional OspA serotyping methods, this new computational pipeline provides a more comprehensive and broadly applicable approach for characterization of OspA type and <i>Borrelia</i> genospecies to support vaccine development.</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/PMC11165634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088031","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":"Nanopore and Illumina sequencing reveal different viral populations from human gut samples","authors":"Ryan Cook, Andrea Telatin, Shen-Yuan Hsieh, Fiona Newberry, Mohammad A. Tariq, Dave J. Baker, Simon R. Carding and Evelien M. Adriaenssens","doi":"10.1099/mgen.0.001236","DOIUrl":"https://doi.org/10.1099/mgen.0.001236","url":null,"abstract":"The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"34 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140842512","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":"Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)","authors":"Jack Pilgrim","doi":"10.1099/mgen.0.001242","DOIUrl":"https://doi.org/10.1099/mgen.0.001242","url":null,"abstract":"<span>Erwinia</span> (Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe <span>Candidatus</span> Erwinia impunctatus (Erwimp) associated with the Highland midge <span>Culicoides impunctatus</span> (Diptera: Ceratopogonidae), an abundant biting pest in the Scottish Highlands. The genome of this new <span>Erwinia</span> species was assembled using hybrid long and short read techniques, and a comparative analysis was undertaken with other members of the genus to understand its potential ecological niche and impact. Genome composition analysis revealed that Erwimp is similar to other endophytic and ectophytic species in the genus and is unlikely to be restricted to its insect host. Evidence for an additional plant host includes the presence of a carotenoid synthesis operon implicated as a virulence factor in plant-associated members in the sister genus <span>Pantoea</span>. Unique features of Erwimp include several copies of intimin-like proteins which, along with signs of genome pseudogenization and a loss of certain metabolic pathways, suggests an element of host restriction seen elsewhere in the genus. Furthermore, a screening of individuals over two field seasons revealed the absence of the bacteria in <span>Culicoides impunctatus</span> during the second year indicating this microbe-insect interaction is likely to be transient. These data suggest that <span>Culicoides impunctatus</span> may have an important role to play beyond a biting nuisance, as an insect vector transmitting Erwimp alongside any conferred impacts to surrounding biota.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"113 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616009","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":"Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts","authors":"Kyle Schutz, Tina Melie, Stacey D. Smith and C. Alisha Quandt","doi":"10.1099/mgen.0.001233","DOIUrl":"https://doi.org/10.1099/mgen.0.001233","url":null,"abstract":"Fungal pathogens commonly originate from benign or non-pathogenic strains living in the natural environment. The recently emerged human pathogen, <span>Candida auris,</span> is one example of a fungus believed to have originated in the environment and recently transitioned into a clinical setting. To date, however, there is limited evidence about the origins of this species in the natural environment and when it began associating with humans. One approach to overcome this gap is to reconstruct phylogenetic relationships between (1) strains isolated from clinical and non-clinical environments and (2) between species known to cause disease in humans and benign environmental saprobes. <span>C. auris</span> belongs to the <span>Candida/Clavispora</span> clade, a diverse group of 45 yeast species including human pathogens and environmental saprobes. We present a phylogenomic analysis of the <span>Candida/Clavispora</span> clade aimed at understanding the ecological breadth and evolutionary relationships between an expanded sample of environmentally and clinically isolated yeasts. To build a robust framework for investigating these relationships, we developed a whole-genome sequence dataset of 108 isolates representing 18 species, including four newly sequenced species and 18 environmentally isolated strains. Our phylogeny, based on 619 orthologous genes, shows environmentally isolated species and strains interspersed with clinically isolated counterparts, suggesting that there have been many transitions between humans and the natural environment in this clade. Our findings highlight the breadth of environments these yeasts inhabit and imply that many clinically isolated yeasts in this clade could just as easily live outside the human body in diverse natural environments and vice versa.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"16 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140615952","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":"Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats","authors":"Manuela Montoya-Giraldo, Kathryn R. Piper, Odion O. Ikhimiukor, Cooper J. Park, Nicole A. Caimi, Debbie C. Buecher, Ernest W. Valdez, Diana E. Northup and Cheryl P. Andam","doi":"10.1099/mgen.0.001238","DOIUrl":"https://doi.org/10.1099/mgen.0.001238","url":null,"abstract":"<span>Streptomyces</span> are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of <span>Streptomyces</span> bacteria. We analysed draft genomes of 132 <span>Streptomyces</span> isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. <span>Streptomyces</span> isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with <span>Streptomyces</span> from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the <span>Streptomyces</span> that carry them. Each genome carried between 19&#8211;65 BGCs (median=42.5) and varied even among members of the same <span>Streptomyces</span> species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, <span>Streptomyces</span> genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding <span>Streptomyces</span>-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"75 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140615950","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":"Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis","authors":"Patrick A. da Roza, Héloïse Muller, Geraldine J. Sullivan, Roy S. K. Walker, Hugh D. Goold, Robert D. Willows, Brian Palenik and Ian T. Paulsen","doi":"10.1099/mgen.0.001223","DOIUrl":"https://doi.org/10.1099/mgen.0.001223","url":null,"abstract":"Genome sequencing and assembly of the photosynthetic picoeukaryotic <span>Picochlorum</span> sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C<span>4</span> photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed <span>Ulva</span>, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"75 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616015","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":"Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions","authors":"Beth Blane, Kathy E. Raven, Nicholas M. Brown, Ewan M. Harrison, Francesc Coll, Rachel Thaxter, David A. Enoch, Theodore Gouliouris, Danielle Leek, Sophia T. Girgis, Asha Akram, Marta Matuszewska, Paul Rhodes, Julian Parkhill and Sharon J. Peacock","doi":"10.1099/mgen.0.001235","DOIUrl":"https://doi.org/10.1099/mgen.0.001235","url":null,"abstract":"Genomic epidemiology enhances the ability to detect and refute methicillin-resistant <span>Staphylococcus aureus</span> (MRSA) outbreaks in healthcare settings, but its routine introduction requires further evidence of benefits for patients and resource utilization. We performed a 12&#8201;month prospective study at Cambridge University Hospitals NHS Foundation Trust in the UK to capture its impact on hospital infection prevention and control (IPC) decisions. MRSA-positive samples were identified via the hospital microbiology laboratory between November 2018 and November 2019. We included samples from in-patients, clinic out-patients, people reviewed in the Emergency Department and healthcare workers screened by Occupational Health. We sequenced the first MRSA isolate from 823 consecutive individuals, defined their pairwise genetic relatedness, and sought epidemiological links in the hospital and community. Genomic analysis of 823 MRSA isolates identified 72 genetic clusters of two or more isolates containing 339/823 (41&#8202;%) of the cases. Epidemiological links were identified between two or more cases for 190 (23&#8202;%) individuals in 34/72 clusters. Weekly genomic epidemiology updates were shared with the IPC team, culminating in 49 face-to-face meetings and 21 written communications. Seventeen clusters were identified that were consistent with hospital MRSA transmission, discussion of which led to additional IPC actions in 14 of these. Two outbreaks were also identified where transmission had occurred in the community prior to hospital presentation; these were escalated to relevant IPC teams. We identified 38 instances where two or more in-patients shared a ward location on overlapping dates but carried unrelated MRSA isolates (pseudo-outbreaks); research data led to de-escalation of investigations in six of these. Our findings provide further support for the routine use of genomic epidemiology to enhance and target IPC resources.","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"41 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140616007","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}