{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T02:39:09Z","timestamp":1778035149875,"version":"3.51.4"},"reference-count":38,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T00:00:00Z","timestamp":1709596800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,3,5]],"date-time":"2024-03-05T00:00:00Z","timestamp":1709596800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["CEECIND\/02268\/2017"],"award-info":[{"award-number":["CEECIND\/02268\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDP\/04378\/2020, UIDB\/04378\/2020, LA\/P\/0140\/2020, EXPL\/SAU-INF\/0261\/2021"],"award-info":[{"award-number":["UIDP\/04378\/2020, UIDB\/04378\/2020, LA\/P\/0140\/2020, EXPL\/SAU-INF\/0261\/2021"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,3,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              <jats:italic>Enterococcus faecium<\/jats:italic>\n              (\n              <jats:italic>Efm<\/jats:italic>\n              ) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the\n              <jats:italic>Efm<\/jats:italic>\n              clade B was assigned as\n              <jats:italic>Enterococcus lactis<\/jats:italic>\n              (\n              <jats:italic>Elts<\/jats:italic>\n              ), which usually lack HA-\n              <jats:italic>Efm<\/jats:italic>\n              infection markers. Available databases for extracting PVM are incomplete and\/or present an intermix of genes from\n              <jats:italic>Efm<\/jats:italic>\n              and\n              <jats:italic>Enterococcus faecalis<\/jats:italic>\n              , with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [\n              <jats:italic>acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20<\/jats:italic>\n              (pili gene cluster 1, PGC-1),\n              <jats:italic>fms14-fms17-fms13<\/jats:italic>\n              (PGC-2),\n              <jats:italic>empA-empB-empC<\/jats:italic>\n              (PGC-3),\n              <jats:italic>fms11-fms19-fms16<\/jats:italic>\n              (PGC-4),\n              <jats:italic>ccpA, bepA, gls20-glsB1,<\/jats:italic>\n              and\n              <jats:italic>gls33-glsB<\/jats:italic>\n              ] from nine reference genomes (seven\n              <jats:italic>Efm<\/jats:italic>\n              + two\n              <jats:italic>Elts<\/jats:italic>\n              ). The database was validated against these reference genomes and further evaluated using a collection of well-characterized\n              <jats:italic>Efm<\/jats:italic>\n              (\n              <jats:italic>n<\/jats:italic>\n              = 43) and\n              <jats:italic>Elts<\/jats:italic>\n              (\n              <jats:italic>n<\/jats:italic>\n              = 7) control strains, by assessing PVM presence\/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and\n              <jats:italic>in silico<\/jats:italic>\n              findings of the PVM, with\n              <jats:italic>Elts<\/jats:italic>\n              clustering separately and mostly carrying\n              <jats:italic>Elts-<\/jats:italic>\n              specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of\n              <jats:italic>Efm<\/jats:italic>\n              and\n              <jats:italic>Elts<\/jats:italic>\n              based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>The newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.<\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.03724-23","type":"journal-article","created":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T14:00:25Z","timestamp":1707400825000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":27,"title":["VirulenceFinder for\n            <i>Enterococcus faecium<\/i>\n            and\n            <i>Enterococcus lactis<\/i>\n            : an enhanced database for detection of putative virulence markers by using whole-genome sequencing data"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6892-913X","authenticated-orcid":false,"given":"Louise","family":"Roer","sequence":"first","affiliation":[{"name":"Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark"}]},{"given":"H\u00fclya","family":"Kaya","sequence":"additional","affiliation":[{"name":"Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1016-7173","authenticated-orcid":false,"given":"Ana P.","family":"Tedim","sequence":"additional","affiliation":[{"name":"Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca, Salamanca, Spain"},{"name":"Grupo de Investigaci\u00f3n Biom\u00e9dica en Sepsis-BioSepsis, Hospital Universitario R\u00edo Hortega, Instituto de Investigaci\u00f3n Biom\u00e9dica de Salamanca (IBSAL), Valladollid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3826-6731","authenticated-orcid":false,"given":"Carla","family":"Novais","sequence":"additional","affiliation":[{"name":"UCIBIO, Departamento de Ci\u00eancias Biol\u00f3gicas, Laborat\u00f3rio de Microbiologia, Faculdade de Farm\u00e1cia, Universidade do Porto, Porto, Portugal"},{"name":"Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8228-3491","authenticated-orcid":false,"given":"Teresa M.","family":"Coque","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Ram\u00f3n y Cajal University Hospital and Ram\u00f3n y Cajal Health Research Institute (IRYCIS), Madrid, Spain"},{"name":"Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7116-2723","authenticated-orcid":false,"given":"Frank M.","family":"Aarestrup","sequence":"additional","affiliation":[{"name":"Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, 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