{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T23:56:40Z","timestamp":1787702200752,"version":"build-2784847793"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T00:00:00Z","timestamp":1745884800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"the Irish Health Research Board","award":["ILP-POR-2019-010"],"award-info":[{"award-number":["ILP-POR-2019-010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,4,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Rectal VREfm (n\u200a=\u200a150) 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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\u200a=\u200a4), three (n\u200a=\u200a2) or four (n\u200a=\u200a1) 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 (\u226599.5% 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jacamr\/dlaf065","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T15:10:22Z","timestamp":1745939422000},"source":"Crossref","is-referenced-by-count":5,"title":["Co-carriage of diverse vancomycin-resistant <i>Enterococcus faecium<\/i> ST80-lineages by 70% of patients in an Irish hospital"],"prefix":"10.1093","volume":"7","author":[{"given":"Nicole L","family":"Kavanagh","sequence":"first","affiliation":[{"name":"Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin , Lincoln Place, Dublin D02 F859 ,","place":["Ireland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7334-5745","authenticated-orcid":false,"given":"Peter 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