Nicole L Kavanagh, Peter M Kinnevey, Grainne I Brennan, Brian O'Connell, Richard V Goering, David C Coleman
{"title":"爱尔兰一家医院70%的患者共同携带多种耐万古霉素屎肠球菌st80谱系。","authors":"Nicole L Kavanagh, Peter M Kinnevey, Grainne I Brennan, Brian O'Connell, Richard V Goering, David C Coleman","doi":"10.1093/jacamr/dlaf065","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse <i>vanA</i>-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient VREfm diversity could confound surveillance. This study investigated the intra-host VREfm genetic diversity among colonized Irish hospital patients.</p><p><strong>Methods: </strong>Rectal VREfm (<i>n</i> = 150) from 10 patients (15 isolates each) were investigated by WGS, core-genome MLST and split <i>k-mer</i> (SKA)-SNP analysis. Plasmids and <i>vanA</i>-transposons from 39 VREfm representative of CTs identified were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible <i>E. faecium</i> (VSEfm) from four VREfm-positive patients were also investigated.</p><p><strong>Results: </strong>All isolates were clade A1 and most were ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent of patients (7/10) harboured either two (<i>n</i> = 4), three (<i>n</i> = 2) or four (<i>n</i> = 1) VREfm CTs. Individual patient isolate pairs from different CTs differed significantly (median SKA-SNPs 2933), but differences were minimal between isolate pairs of the same CT (median SKA-SNPs 0). In total, 193 plasmids were identified in 39 VREfm investigated. Near-identical plasmids (≥99.5% average nucleotide identity) were identified in divergent CTs from multiple patients. Most VREfm (28/39, 72%) harboured <i>vanA</i> on closely related transferable, linear plasmids. Divergent CTs within individual patients harboured either indistinguishable <i>vanA</i>-transposons or <i>vanA</i>-transposons with distinct organizational iterations. Four VSEfm from different CTs investigated harboured similar plasmids to VREfm.</p><p><strong>Conclusion: </strong>VREfm within-host diversity is highly prevalent in Irish hospital patients, which complicates surveillance. Linear plasmids play an important role in the emergence of Irish VREfm.</p>","PeriodicalId":14594,"journal":{"name":"JAC-Antimicrobial Resistance","volume":"7 3","pages":"dlaf065"},"PeriodicalIF":3.3000,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12039289/pdf/","citationCount":"0","resultStr":"{\"title\":\"Co-carriage of diverse vancomycin-resistant <i>Enterococcus faecium</i> ST80-lineages by 70% of patients in an Irish hospital.\",\"authors\":\"Nicole L Kavanagh, Peter M Kinnevey, Grainne I Brennan, Brian O'Connell, Richard V Goering, David C Coleman\",\"doi\":\"10.1093/jacamr/dlaf065\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse <i>vanA</i>-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient VREfm diversity could confound surveillance. This study investigated the intra-host VREfm genetic diversity among colonized Irish hospital patients.</p><p><strong>Methods: </strong>Rectal VREfm (<i>n</i> = 150) from 10 patients (15 isolates each) were investigated by WGS, core-genome MLST and split <i>k-mer</i> (SKA)-SNP analysis. Plasmids and <i>vanA</i>-transposons from 39 VREfm representative of CTs identified were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible <i>E. faecium</i> (VSEfm) from four VREfm-positive patients were also investigated.</p><p><strong>Results: </strong>All isolates were clade A1 and most were ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent of patients (7/10) harboured either two (<i>n</i> = 4), three (<i>n</i> = 2) or four (<i>n</i> = 1) VREfm CTs. Individual patient isolate pairs from different CTs differed significantly (median SKA-SNPs 2933), but differences were minimal between isolate pairs of the same CT (median SKA-SNPs 0). In total, 193 plasmids were identified in 39 VREfm investigated. Near-identical plasmids (≥99.5% average nucleotide identity) were identified in divergent CTs from multiple patients. Most VREfm (28/39, 72%) harboured <i>vanA</i> on closely related transferable, linear plasmids. Divergent CTs within individual patients harboured either indistinguishable <i>vanA</i>-transposons or <i>vanA</i>-transposons with distinct organizational iterations. Four VSEfm from different CTs investigated harboured similar plasmids to VREfm.</p><p><strong>Conclusion: </strong>VREfm within-host diversity is highly prevalent in Irish hospital patients, which complicates surveillance. Linear plasmids play an important role in the emergence of Irish VREfm.</p>\",\"PeriodicalId\":14594,\"journal\":{\"name\":\"JAC-Antimicrobial Resistance\",\"volume\":\"7 3\",\"pages\":\"dlaf065\"},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2025-04-29\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12039289/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"JAC-Antimicrobial Resistance\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/jacamr/dlaf065\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/6/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"JAC-Antimicrobial Resistance","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/jacamr/dlaf065","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/6/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital.
Background: Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Irish VREfm comprise diverse vanA-encoding ST80-complex type (CT) lineages. Recent studies indicate that within-patient VREfm diversity could confound surveillance. This study investigated the intra-host VREfm genetic diversity among colonized Irish hospital patients.
Methods: Rectal VREfm (n = 150) from 10 patients (15 isolates each) were investigated by WGS, core-genome MLST and split k-mer (SKA)-SNP analysis. Plasmids and vanA-transposons from 39 VREfm representative of CTs identified were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences. Plasmid relatedness was assessed based on Mash distances. Thirty vancomycin-susceptible E. faecium (VSEfm) from four VREfm-positive patients were also investigated.
Results: All isolates were clade A1 and most were ST80 (VREfm, 147/150; VSEfm, 25/30). Seventy-percent of patients (7/10) harboured either two (n = 4), three (n = 2) or four (n = 1) VREfm CTs. Individual patient isolate pairs from different CTs differed significantly (median SKA-SNPs 2933), but differences were minimal between isolate pairs of the same CT (median SKA-SNPs 0). In total, 193 plasmids were identified in 39 VREfm investigated. Near-identical plasmids (≥99.5% average nucleotide identity) were identified in divergent CTs from multiple patients. Most VREfm (28/39, 72%) harboured vanA on closely related transferable, linear plasmids. Divergent CTs within individual patients harboured either indistinguishable vanA-transposons or vanA-transposons with distinct organizational iterations. Four VSEfm from different CTs investigated harboured similar plasmids to VREfm.
Conclusion: VREfm within-host diversity is highly prevalent in Irish hospital patients, which complicates surveillance. Linear plasmids play an important role in the emergence of Irish VREfm.
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