{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T16:28:20Z","timestamp":1784824100153,"version":"3.55.0"},"reference-count":64,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2019,7,4]],"date-time":"2019-07-04T00:00:00Z","timestamp":1562198400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100013281","name":"Joint Programming Initiative on Antimicrobial Resistance","doi-asserted-by":"publisher","award":["JPIAMR2016\u2010AC16\/00039"],"award-info":[{"award-number":["JPIAMR2016\u2010AC16\/00039"]}],"id":[{"id":"10.13039\/100013281","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environmental Microbiology"],"published-print":{"date-parts":[[2019,8]]},"abstract":"<jats:title>Summary<\/jats:title>\n                  <jats:p>\n                    Wild birds have been suggested to be reservoirs of antimicrobial resistant and\/or pathogenic\n                    <jats:italic>Enterococcus faecalis<\/jats:italic>\n                    (\n                    <jats:italic>Efs<\/jats:italic>\n                    ) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97\n                    <jats:italic>Efs<\/jats:italic>\n                    isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone\u2010responsive plasmids predominate in wild bird\n                    <jats:italic>Efs<\/jats:italic>\n                    while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other\n                    <jats:italic>Efs<\/jats:italic>\n                    lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.14702","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T13:15:52Z","timestamp":1559654152000},"page":"3046-3062","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Phylogenomics of\n                    <i>Enterococcus faecalis<\/i>\n                    from wild birds: new insights into host\u2010associated differences in core and accessory genomes of the species"],"prefix":"10.1111","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5317-8310","authenticated-orcid":false,"given":"Ricardo","family":"Le\u00f3n\u2010Sampedro","sequence":"first","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"},{"name":"Biomedical Research Networking Center for Epidemiology and Public Health (CIBER\u2010ESP)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosa","family":"del Campo","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"},{"name":"Spanish Network for Research in Infectious Diseases (REIPI) Health Institute Carlos III  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mercedes","family":"Rodriguez\u2010Ba\u00f1os","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Val F.","family":"Lanza","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"},{"name":"Biomedical Research Networking Center for Epidemiology and Public Health (CIBER\u2010ESP)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda Jos\u00e9","family":"Pozuelo","sequence":"additional","affiliation":[{"name":"Department of Biology, Pharmacy Faculty University San Pablo\u2010CEU  Boadilla del Monte Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4195-054X","authenticated-orcid":false,"given":"Carlos","family":"Franc\u00e9s\u2010Cuesta","sequence":"additional","affiliation":[{"name":"Infection and Public Health Unit FISABIO\/University of Valencia  Spain"},{"name":"Institute for Integrative Systems Biology, I<sup>2<\/sup>SysBio CSIC\u2010University of Valencia  Valencia Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana P.","family":"Tedim","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana R.","family":"Freitas","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty University of Porto  Porto Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carla","family":"Novais","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty University of Porto  Porto Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00edsa","family":"Peixe","sequence":"additional","affiliation":[{"name":"UCIBIO\/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty University of Porto  Porto Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob J. L.","family":"Willems","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology University Medical Center Utrecht  Utrecht the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jukka","family":"Corander","sequence":"additional","affiliation":[{"name":"Department of Biostatistics University of Oslo  Oslo Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Gonz\u00e1lez Candelas","sequence":"additional","affiliation":[{"name":"Biomedical Research Networking Center for Epidemiology and Public Health (CIBER\u2010ESP)  Madrid Spain"},{"name":"Infection and Public Health Unit FISABIO\/University of Valencia  Spain"},{"name":"Institute for Integrative Systems Biology, I<sup>2<\/sup>SysBio CSIC\u2010University of Valencia  Valencia Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Baquero","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"},{"name":"Biomedical Research Networking Center for Epidemiology and Public Health (CIBER\u2010ESP)  Madrid Spain"},{"name":"Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teresa M.","family":"Coque","sequence":"additional","affiliation":[{"name":"Department of Microbiology University Hospital Ram\u00f3n y Cajal, Ram\u00f3n y Cajal Health Research Institute (IRYCIS)  Madrid Spain"},{"name":"Biomedical Research Networking Center for Epidemiology and Public Health (CIBER\u2010ESP)  Madrid Spain"},{"name":"Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC)  Madrid Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,7,4]]},"reference":[{"key":"e_1_2_7_2_1","first-page":"e000220","article-title":"PANINI: Pangenome neighbor identification for bacterial populations","volume":"5","author":"Abudahab K.","year":"2017","journal-title":"Microb Genom"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw493"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1006\/abio.1995.1220"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2015.12.003"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst028"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02763-13"},{"key":"e_1_2_7_9_1","volume-title":"Enterococci: From Commensals to Leading Causes of Drug Resistant Infection","author":"Clewell 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