{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T20:09:52Z","timestamp":1780517392555,"version":"3.54.1"},"reference-count":202,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T00:00:00Z","timestamp":1668988800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,21]]},"abstract":"<jats:p>\n                  <jats:bold>Introduction.<\/jats:bold>\n                  <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5535\" xlink:type=\"simple\">Enterococcus faecium<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Hypothesis\/Gap statement.<\/jats:bold> Vancomycin resistance rates persist amongst <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5535\" xlink:type=\"simple\">E. faecium<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Methodology.<\/jats:bold> A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using <jats:italic>in silico<\/jats:italic> methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Results.<\/jats:bold> These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5535\" xlink:type=\"simple\">E. faecium<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> persists in Ireland with acquired resistance arising via plasmid acquisition (<jats:italic>vanA<\/jats:italic>) or, to a lesser extent, chromosomal recombination (<jats:italic>vanB<\/jats:italic>). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between <jats:italic>vanA<\/jats:italic> and <jats:italic>vanB<\/jats:italic> isolates.<\/jats:p>\n               <jats:p>\n                  <jats:bold>Conclusions.<\/jats:bold> These results highlight the evolutionary history of Irish <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5535\" xlink:type=\"simple\">E. faecium<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible <jats:italic>\n                     <jats:named-content content-type=\"species\">\n                        <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/doi.org\/10.1601\/nm.5535\" xlink:type=\"simple\">E. faecium<\/jats:ext-link>\n                     <\/jats:named-content>\n                  <\/jats:italic> should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.<\/jats:p>","DOI":"10.1099\/jmm.0.001590","type":"journal-article","created":{"date-parts":[[2022,10,27]],"date-time":"2022-10-27T16:20:49Z","timestamp":1666887649000},"source":"Crossref","is-referenced-by-count":18,"title":["Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals"],"prefix":"10.1099","volume":"71","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7237-2394","authenticated-orcid":false,"given":"Robert J.","family":"Leigh","sequence":"first","affiliation":[{"name":"Department of Biology, Maynooth University, Mariavilla, Maynooth, Co. 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