Beschreibung:
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<jats:bold>Introduction.</jats:bold>
<jats:italic>
<jats:named-content content-type="species">
<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>
</jats:named-content>
</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>
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<jats:bold>Hypothesis/Gap statement.</jats:bold> Vancomycin resistance rates persist amongst <jats:italic>
<jats:named-content content-type="species">
<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>
</jats:named-content>
</jats:italic> isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.</jats:p>
<jats:p>
<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>
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<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>
<jats:named-content content-type="species">
<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>
</jats:named-content>
</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>
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<jats:bold>Conclusions.</jats:bold> These results highlight the evolutionary history of Irish <jats:italic>
<jats:named-content content-type="species">
<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>
</jats:named-content>
</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>
<jats:named-content content-type="species">
<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>
</jats:named-content>
</jats:italic> should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.</jats:p>