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Many antibiotic resistance traits, in particular, vancomycin resistance, can be encoded in autonomous and extrachromosomal elements called plasmids. These sequences can be disseminated to other isolates by horizontal gene transfer and confer novel mechanisms to source specificity. In our study, we elucidated the total plasmid content, referred to as the plasmidome, of 1,644\n                    <jats:named-content content-type=\"genus-species\">E. faecium<\/jats:named-content>\n                    isolates by using short- and long-read whole-genome technologies with the combination of a machine-learning classifier. This was fundamental to investigate the full collection of plasmid sequences present in our collection (pan-plasmidome) and to observe the potential transfer of plasmid sequences between\n                    <jats:named-content content-type=\"genus-species\">E. faecium<\/jats:named-content>\n                    hosts. We observed that\n                    <jats:named-content content-type=\"genus-species\">E. faecium<\/jats:named-content>\n                    isolates from hospitalized patients carried a larger number of plasmid sequences compared to that from other sources, and they elucidated different configurations of plasmidome populations in the hospital environment. We assessed the contribution of different genomic components and observed that plasmid sequences have the highest contribution to source specificity. Our study suggests that\n                    <jats:named-content content-type=\"genus-species\">E. faecium<\/jats:named-content>\n                    plasmids are regulated by complex ecological constraints rather than physical interaction between hosts.\n                  <\/jats:p>","DOI":"10.1128\/mbio.03284-19","type":"journal-article","created":{"date-parts":[[2020,2,10]],"date-time":"2020-02-10T06:45:37Z","timestamp":1581317137000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":135,"title":["Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium"],"prefix":"10.1128","volume":"11","author":[{"given":"S.","family":"Arredondo-Alonso","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"Top","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"McNally","sequence":"additional","affiliation":[{"name":"Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Puranen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Aalto University, Espoo, Finland"},{"name":"Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Pesonen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Aalto University, Espoo, Finland"},{"name":"Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"Pensar","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Marttinen","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), University of Helsinki, Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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