{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T01:38:42Z","timestamp":1773884322472,"version":"3.50.1"},"reference-count":59,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,9,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              Since 2012, Denmark has seen a significant rise in vancomycin-resistant\n              <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n              (VREfm) cases, mirroring trends in other countries, though exceptions occurred during the coronavirus disease 2019 (COVID-19) lockdown and between 2022 and 2023. This rise has been accompanied by ongoing changes in the endemic VREfm clones, reflecting the species\u2019 high genetic plasticity. VREfm rapidly acquires plasmids and mobile genetic elements, enriching it with putative virulence markers (PVMs), including surface proteins, pili, and factors encoding biofilm production and adhesion. L. Roer, H. Kaya, A.P. Tedim, C. Novias, et al. (Microbiol Spectr 12:e0372423, 2024,\n              <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/doi.org\/10.1128\/spectrum.03724-23\" xlink:type=\"simple\">https:\/\/doi.org\/10.1128\/spectrum.03724-23<\/jats:ext-link>\n              ) released a database of 27 PVMs for\n              <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n              and\n              <jats:italic toggle=\"yes\">Enterococcus lactis<\/jats:italic>\n              . In this study, we examined 516 VREfm bloodstream isolates from 2015 to 2023, identifying eight new putative virulence genes added to the database, bringing the total to 35 PVMs. Using whole-genome sequencing (WGS) and single linkage clustering, we identified six dominant VREfm clusters: ST80-CT14\n              <jats:italic toggle=\"yes\">vanA<\/jats:italic>\n              , ST117-CT24\n              <jats:italic toggle=\"yes\">vanA<\/jats:italic>\n              , ST203-CT859\n              <jats:italic toggle=\"yes\">vanA<\/jats:italic>\n              , ST1421-CT1134\n              <jats:italic toggle=\"yes\">vanA<\/jats:italic>\n              , ST117-CT36\n              <jats:italic toggle=\"yes\">vanB<\/jats:italic>\n              , and ST80-CT2406\n              <jats:italic toggle=\"yes\">vanB<\/jats:italic>\n              . We observed significant differences in the distribution of PVMs, particularly in pilin, gene clusters (PGC-1, PGC-2, and PGC-4), genes involved in carbohydrate metabolism (e.g.,\n              <jats:italic toggle=\"yes\">orf1481<\/jats:italic>\n              ,\n              <jats:italic toggle=\"yes\">ccpA<\/jats:italic>\n              ), and biofilm production (e.g.,\n              <jats:italic toggle=\"yes\">hylEfm<\/jats:italic>\n              ,\n              <jats:italic toggle=\"yes\">capD<\/jats:italic>\n              ,\n              <jats:italic toggle=\"yes\">lysM3<\/jats:italic>\n              ). These differences could explain variability in pathogenicity, metabolism, and adaptation to stress, contributing to shifts in endemic clones.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                The newly developed and now updated database, VirulenceFinder, features 35 potential virulence markers for E.\n                <jats:italic toggle=\"yes\">faecium<\/jats:italic>\n                and E.\n                <jats:italic toggle=\"yes\">lactis<\/jats:italic>\n                , is highly scalable and provides a valuable tool for the in-depth analysis of closely related species using whole-genome sequencing (WGS) data. It holds considerable promise for a range of public health applications, such as hospital outbreak investigations, surveillance, and assessment of pathogenicity of bacterial species.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.01289-25","type":"journal-article","created":{"date-parts":[[2025,7,31]],"date-time":"2025-07-31T14:22:47Z","timestamp":1753971767000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Virulence signature of the endemic vancomycin-resistant\n            <i>Enterococcus faecium<\/i>\n            clones in Denmark, 2015-2023"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6158-2927","authenticated-orcid":true,"given":"Ingrid Maria 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