{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T17:40:36Z","timestamp":1792604436853,"version":"4.5.0"},"reference-count":78,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T00:00:00Z","timestamp":1787011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T00:00:00Z","timestamp":1792540800000},"content-version":"vor","delay-in-days":64,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["MOSTMICRO-ITQB R&D Unit (UIDB\/04612\/2020, UIDP\/04612\/2020)"],"award-info":[{"award-number":["MOSTMICRO-ITQB R&D Unit (UIDB\/04612\/2020, UIDP\/04612\/2020)"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Med"],"DOI":"10.1186\/s13073-026-01747-2","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T06:06:50Z","timestamp":1787033210000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Recombination and accessory genome turnover shaped the rise and decline of vanA Enterococcus faecium ST80 in Denmark"],"prefix":"10.1186","volume":"18","author":[{"given":"Opeyemi U.","family":"Lawal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid Maria Cecilia","family":"Rubin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Alfredo Samaniego","family":"Castruita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas Munk","family":"Petersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Mollerup","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin Schou","family":"Pedersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"Camoez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuno A.","family":"Faria","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrik","family":"Westh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mette","family":"Pinholt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Miragaia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,18]]},"reference":[{"key":"1747_CR1","doi-asserted-by":"publisher","unstructured":"Tacconelli E, Carrara E, Savoldi A et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis. 2018. https:\/\/doi.org\/10.1016\/s1473-3099(17)30753-3.","DOI":"10.1016\/s1473-3099(17)30753-3"},{"key":"1747_CR2","unstructured":"CDC. Antibiotic Resistance Threats in the United States, 2019. Atlanta, GA: U.S. Department of Health and Human Services, CDC; 2019."},{"key":"1747_CR3","doi-asserted-by":"publisher","unstructured":"Lebreton F, van Schaik W, McGuire AM et al. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. mBio. 2013;4(4):e00534-13. https:\/\/doi.org\/10.1128\/mbio.00534-13.","DOI":"10.1128\/mbio.00534-13"},{"key":"1747_CR4","doi-asserted-by":"publisher","unstructured":"Willems RJL, Top J, Van Santen M et al. Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex. Emerg Infect Dis. 2005;11(6):821-8. https:\/\/doi.org\/10.3201\/1106.041204.","DOI":"10.3201\/1106.041204"},{"key":"1747_CR5","doi-asserted-by":"publisher","unstructured":"Guzman Prieto AM, van Schaik W, Rogers MRC, Coque TM, Baquero F, Corander J, Willems RJL. Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?. Front. Microbiol. 2016;7:788. https:\/\/doi.org\/10.3389\/fmicb.2016.00788.","DOI":"10.3389\/fmicb.2016.00788"},{"key":"1747_CR6","doi-asserted-by":"publisher","unstructured":"Galloway-Pe\u00f1a J, Roh JH, Latorre M, Qin X, Murray BE. Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium. PLoS One. 2012;7(1):e30187. https:\/\/doi.org\/10.1371\/journal.pone.0030187.","DOI":"10.1371\/journal.pone.0030187"},{"key":"1747_CR7","doi-asserted-by":"publisher","unstructured":"van Hal S, Willems R, Gouliouris T et al.The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysisThe Lancet Microbe. 2022;3:e133-41. https:\/\/doi.org\/10.1016\/s2666-5247(21)00236-6.","DOI":"10.1016\/s2666-5247(21)00236-6"},{"key":"1747_CR8","doi-asserted-by":"crossref","unstructured":"Werner G, Coque TM, Hammerum AM, Hope R, Hryniewicz W, Johnson A, et al. Emergence and spread of vancomycin resistance among enterococci in Europe. Euro Surveill. 2008;13(47):19046.","DOI":"10.2807\/ese.13.47.19046-en"},{"key":"1747_CR9","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.1093\/gbe\/evt111","volume":"5","author":"M De Been","year":"2013","unstructured":"De Been M, Van Schaik W, Cheng L, Corander J, Willems RJ. Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium. Genome Biol Evol. 2013;5:1524\u201335.","journal-title":"Genome Biol Evol"},{"key":"1747_CR10","doi-asserted-by":"publisher","unstructured":"Nallapareddy SR, Singh KV, Okhuysen PC, Murray BE. A functional collagen adhesin gene, acm, in clinical isolates of Enterococcus faecium correlates with the recent success of this emerging nosocomial pathogen. Infect Immun. 2008;76(9):4110-9. https:\/\/doi.org\/10.1128\/iai.00375-08.","DOI":"10.1128\/iai.00375-08"},{"key":"1747_CR11","doi-asserted-by":"publisher","unstructured":"Rice LB, Carias L, Rudin S, Vael C, Goossens H, Konstabel C, et al. A potential virulence gene, hylEfm, predominates in Enterococcus faecium of clinical origin. J Infect Dis. 2003;187(3):508\u201312. https:\/\/doi.org\/10.1086\/367711.","DOI":"10.1086\/367711"},{"key":"1747_CR12","doi-asserted-by":"publisher","unstructured":"Doss Susai Backiam A, Duraisamy S, Karuppaiya P, Balakrishnan S, Chandrasekaran B, Kumarasamy A, Raju A. Antibiotic susceptibility patterns and virulence-associated factors of vancomycin-resistant enterococcal isolates from tertiary care hospitals. Antibiotics (Basel). 2023;12(6):981. https:\/\/doi.org\/10.3390\/antibiotics12060981.","DOI":"10.3390\/antibiotics12060981"},{"key":"1747_CR13","doi-asserted-by":"publisher","unstructured":"Hegstad K, Mikalsen T, Coque TM, Werner G, Sundsfjord A. Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium. Clin Microbiol Infect. 2010;16(6):541\u201354. https:\/\/doi.org\/10.1111\/j.1469-0691.2010.03226.x.","DOI":"10.1111\/j.1469-0691.2010.03226.x"},{"key":"1747_CR14","doi-asserted-by":"crossref","unstructured":"Hammerum AM, Justesen US, Pinholt M et al. Surveillance of vancomycin-resistant enterococci reveals shift in dominating clones and national spread of a vancomycin-variable vanA Enterococcus faecium ST1421-CT1134 clone, Denmark, 2015 to March 2019. Euro Surveill. 2019.","DOI":"10.2807\/1560-7917.ES.2019.24.34.1900503"},{"key":"1747_CR15","doi-asserted-by":"crossref","unstructured":"Pinholt M, Bayliss SC, Gumpert H et al. WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA -containing plasmid and acquisition of a heterogeneous accessory ge. J Antimicrob Chemother. 2019. Available at: https:\/\/academic.oup.com\/jac\/advance-article\/doi\/10.1093\/jac\/dkz118\/5423852.","DOI":"10.1093\/jac\/dkz118"},{"key":"1747_CR16","unstructured":"Toft A, Nordestgaard MM, Holm A, Hammerum AM, Hasman H, Justesen US, Danmap. 2019. Danmap 2019 - Use of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark. 2020."},{"key":"1747_CR17","doi-asserted-by":"publisher","unstructured":"Zhou X, Chlebowicz MA, Bathoorn E, Rosema S, Couto N, Lokate M, et al. Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. J Antimicrob Chemother. 2018;73(12):3259\u201367. https:\/\/doi.org\/10.1093\/jac\/dky349.","DOI":"10.1093\/jac\/dky349"},{"key":"1747_CR18","doi-asserted-by":"publisher","first-page":"3548","DOI":"10.1128\/JCM.40.9.3548-3548.2002-a","volume":"40","author":"WL Homan","year":"2002","unstructured":"Homan WL, Tribe D, Poznanski S, et al. Multilocus Sequence Typing Scheme for Enterococcus faecium. J Clin Microbiol. 2002;40:3548\u20133548.","journal-title":"J Clin Microbiol"},{"key":"1747_CR19","unstructured":"EUCAST, Eucast. 2018. European committee on antimicrobial susceptibility testing. 2018."},{"key":"1747_CR20","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1093\/jac\/dkw360","volume":"72","author":"M Pinholt","year":"2017","unstructured":"Pinholt M, Gumpert H, Bayliss S, et al. Genomic analysis of 495 vancomycin-resistant Enterococcus faecium reveals broad dissemination of a vanA plasmid in more than 19 clones from Copenhagen, Denmark. J Antimicrob Chemother. 2017;72:40\u20137.","journal-title":"J Antimicrob Chemother"},{"key":"1747_CR21","doi-asserted-by":"publisher","first-page":"2474","DOI":"10.1093\/jac\/dkv142","volume":"70","author":"M Pinholt","year":"2015","unstructured":"Pinholt M, Larner-Svensson H, Littauer P, et al. Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012\u201313, investigated by WGS, MLST and PFGE. J Antimicrob Chemother. 2015;70:2474\u201382.","journal-title":"J Antimicrob Chemother"},{"key":"1747_CR22","doi-asserted-by":"crossref","unstructured":"Bolger AM, Lohse M, Usadel B, Trimmomatic. A flexible trimmer for Illumina sequence data. Bioinformatics. 2014.","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"1747_CR23","doi-asserted-by":"publisher","unstructured":"Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020;70(1):e102. https:\/\/doi.org\/10.1002\/cpbi.102.","DOI":"10.1002\/cpbi.102"},{"key":"1747_CR24","doi-asserted-by":"publisher","unstructured":"Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-5. https:\/\/doi.org\/10.1093\/bioinformatics\/btt086.","DOI":"10.1093\/bioinformatics\/btt086"},{"key":"1747_CR25","doi-asserted-by":"publisher","unstructured":"Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods. 2023;20(8):1203-1212. Epub 27 Jul 2023. Erratum in: Nat Methods. 2024;21(4):735. https:\/\/doi.org\/10.1038\/s41592-024-02248-z.","DOI":"10.1038\/s41592-024-02248-z"},{"key":"1747_CR26","doi-asserted-by":"publisher","first-page":"3788","DOI":"10.1128\/JCM.01946-15","volume":"53","author":"M De Been","year":"2015","unstructured":"De Been M, Pinholt M, Top J, et al. Core genome multilocus sequence typing scheme for high-resolution typing of enterococcus faecium. J Clin Microbiol. 2015;53:3788\u201397.","journal-title":"J Clin Microbiol"},{"key":"1747_CR27","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1093\/molbev\/msx066","volume":"34","author":"R Mostowy","year":"2017","unstructured":"Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P. Efficient inference of recent and ancestral recombination within bacterial populations. Mol Biol Evol. 2017;34:1167\u201382.","journal-title":"Mol Biol Evol"},{"key":"1747_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gku1196","volume":"43","author":"NJ Croucher","year":"2015","unstructured":"Croucher NJ, Page AJ, Connor TR, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43:1\u201313.","journal-title":"Nucleic Acids Res"},{"key":"1747_CR29","doi-asserted-by":"publisher","unstructured":"Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. https:\/\/doi.org\/10.1371\/journal.pone.0009490.","DOI":"10.1371\/journal.pone.0009490"},{"key":"1747_CR30","doi-asserted-by":"publisher","unstructured":"Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2(1):vew007. https:\/\/doi.org\/10.1093\/ve\/vew007.","DOI":"10.1093\/ve\/vew007"},{"key":"1747_CR31","first-page":"1","volume":"2","author":"S Argim\u00f3n","year":"2016","unstructured":"Argim\u00f3n S, Abudahab K, Goater RJE, et al. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom. 2016;2:1\u201311.","journal-title":"Microb Genom"},{"key":"1747_CR32","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","volume":"30","author":"T Seemann","year":"2014","unstructured":"Seemann T, Prokka. Rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068\u20139.","journal-title":"Bioinformatics"},{"key":"1747_CR33","doi-asserted-by":"publisher","unstructured":"Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btv421.","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"1747_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-016-1108-8","volume":"17","author":"O Brynildsrud","year":"2016","unstructured":"Brynildsrud O, Bohlin J, Scheffer L, Eldholm V. Erratum to: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary [Genome Biol (2016), 17, 238]. Genome Biol. 2016;17:1\u20139. https:\/\/doi.org\/10.1186\/s13059-016-1108-8.","journal-title":"Genome Biol"},{"key":"1747_CR35","doi-asserted-by":"publisher","unstructured":"Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. https:\/\/doi.org\/10.1371\/journal.pcbi.1005595.","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"1747_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-9-75","volume":"9","author":"RK Aziz","year":"2008","unstructured":"Aziz RK, Bartels D, Best A, et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genomics. 2008;9:1\u201315.","journal-title":"BMC Genomics"},{"key":"1747_CR37","doi-asserted-by":"publisher","unstructured":"Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394\u2013403. https:\/\/doi.org\/10.1101\/gr.2289704.","DOI":"10.1101\/gr.2289704"},{"key":"1747_CR38","doi-asserted-by":"publisher","unstructured":"Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. https:\/\/doi.org\/10.1186\/1471-2164-12-402.","DOI":"10.1186\/1471-2164-12-402"},{"key":"1747_CR39","doi-asserted-by":"publisher","unstructured":"Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640\u20134. https:\/\/doi.org\/10.1093\/jac\/dks261.","DOI":"10.1093\/jac\/dks261"},{"key":"1747_CR40","doi-asserted-by":"publisher","unstructured":"Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501\u201310. https:\/\/doi.org\/10.1128\/jcm.03617-13.","DOI":"10.1128\/jcm.03617-13"},{"key":"1747_CR41","doi-asserted-by":"publisher","unstructured":"Malberg Tetzschner AM, Johnson JR, Johnston BD, Lund O, Scheutz F. In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2020;58(10):e01269\u201320. https:\/\/doi.org\/10.1128\/jcm.01269-20.","DOI":"10.1128\/jcm.01269-20"},{"key":"1747_CR42","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.","journal-title":"BMC Bioinformatics"},{"key":"1747_CR43","doi-asserted-by":"publisher","unstructured":"Carattoli A, Hasman H. PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Methods Mol Biol. 2020;2075:285\u201394. https:\/\/doi.org\/10.1007\/978-1-4939-9877-7_20.","DOI":"10.1007\/978-1-4939-9877-7_20"},{"key":"1747_CR44","doi-asserted-by":"publisher","unstructured":"Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom. 2018;4(8):e000206. https:\/\/doi.org\/10.1099\/mgen.0.000206.","DOI":"10.1099\/mgen.0.000206"},{"key":"1747_CR45","doi-asserted-by":"publisher","first-page":"W16","DOI":"10.1093\/nar\/gkw387","volume":"44","author":"D Arndt","year":"2016","unstructured":"Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16\u201321.","journal-title":"Nucleic Acids Res"},{"key":"1747_CR46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-62371-7","volume":"10","author":"R Rios","year":"2020","unstructured":"Rios R, Reyes J, Carvajal LP, et al. Genomic Epidemiology of Vancomycin-Resistant Enterococcus faecium (VREfm) in Latin America: Revisiting The Global VRE Population Structure. Sci Rep. 2020;10:1\u201312.","journal-title":"Sci Rep"},{"key":"1747_CR47","doi-asserted-by":"publisher","unstructured":"Buultjens AH, Lam MM, Ballard S, Monk IR, Mahony AA, Grabsch EA, et al. Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium. PeerJ. 2017;5:e2916. https:\/\/doi.org\/10.7717\/peerj.2916.","DOI":"10.7717\/peerj.2916"},{"key":"1747_CR48","doi-asserted-by":"publisher","unstructured":"Koskella B, Brockhurst MA. Bacteria-phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38(5):916\u201331. https:\/\/doi.org\/10.1111\/1574-6976.12072.","DOI":"10.1111\/1574-6976.12072"},{"key":"1747_CR49","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1016\/j.cmi.2017.12.016","volume":"24","author":"AC Sch\u00fcrch","year":"2018","unstructured":"Sch\u00fcrch AC, Arredondo-Alonso S, Willems RJL, Goering RV. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene\u2013based approaches. Clin Microbiol Infect. 2018;24:350\u20134.","journal-title":"Clin Microbiol Infect"},{"key":"1747_CR50","doi-asserted-by":"publisher","first-page":"4332","DOI":"10.1172\/JCI43918","volume":"120","author":"C Ubeda","year":"2010","unstructured":"Ubeda C, Taur Y, Jenq RR, et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest. 2010;120:4332\u201341.","journal-title":"J Clin Invest"},{"key":"1747_CR51","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/ofid\/ofw246","volume":"4","author":"M Alevizakos","year":"2017","unstructured":"Alevizakos M, Gaitanidis A, Nasioudis D, Tori K, Flokas ME, Mylonakis E. Colonization with vancomycin-resistant enterococci and risk for bloodstream infection among patients with malignancy: A systematic review and meta-analysis. Open Forum Infect Dis. 2017;4:1\u201310.","journal-title":"Open Forum Infect Dis"},{"key":"1747_CR52","doi-asserted-by":"publisher","unstructured":"Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012;55(7):905\u201314. https:\/\/doi.org\/10.1093\/cid\/cis580.","DOI":"10.1093\/cid\/cis580"},{"key":"1747_CR53","doi-asserted-by":"publisher","unstructured":"Bayjanov JR, Baan J, Rogers MRC, Troelstra A, Willems RJL, van Schaik W. Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization. Microb Genom. 2019;5(7):e000277. https:\/\/doi.org\/10.1099\/mgen.0.000277.","DOI":"10.1099\/mgen.0.000277"},{"key":"1747_CR54","doi-asserted-by":"publisher","unstructured":"Moradigaravand D, Gouliouris T, Blane B, Naydenova P, Ludden C, Crawley C, et al. Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients. Genome Med. 2017;9(1):119. https:\/\/doi.org\/10.1186\/s13073-017-0507-0.","DOI":"10.1186\/s13073-017-0507-0"},{"key":"1747_CR55","doi-asserted-by":"publisher","unstructured":"Blaschke V, Rauschenberger V, Claus H, Kampmeier S. Comparative analysis of vancomycin-resistant enterococci in colonization and infection-a longitudinal study. Microbiol Spectr. 2025;13(11):e0175025. https:\/\/doi.org\/10.1128\/spectrum.01750-25.","DOI":"10.1128\/spectrum.01750-25"},{"key":"1747_CR56","doi-asserted-by":"publisher","unstructured":"Gao W, Howden BP, Stinear TP. Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen. Curr Opin Microbiol. 2018;41:76\u201382. https:\/\/doi.org\/10.1016\/j.mib.2017.11.030.","DOI":"10.1016\/j.mib.2017.11.030"},{"key":"1747_CR57","doi-asserted-by":"publisher","unstructured":"Gouliouris T, Warne B, Cartwright EJP, Bedford L, Weerasuriya CK, Raven KE, et al. Duration of exposure to multiple antibiotics is associated with increased risk of VRE bacteraemia: a nested case-control study. J Antimicrob Chemother. 2018;73(6):1692-1699. https:\/\/doi.org\/10.1093\/jac\/dky075.","DOI":"10.1093\/jac\/dky075"},{"key":"1747_CR58","doi-asserted-by":"publisher","unstructured":"Lee RS, Gon\u00e7alves da Silva A, Baines SL, Strachan J, Ballard S, Carter GP, et al. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. J Antimicrob Chemother. 2018;73(12):3268\u201378. https:\/\/doi.org\/10.1093\/jac\/dky331.","DOI":"10.1093\/jac\/dky331"},{"key":"1747_CR59","doi-asserted-by":"publisher","unstructured":"Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel). 2023;12(7):1140. https:\/\/doi.org\/10.3390\/antibiotics12071140.","DOI":"10.3390\/antibiotics12071140"},{"key":"1747_CR60","doi-asserted-by":"publisher","unstructured":"van Hal SJ, Ip CLC, Ansari MA, Wilson DJ, Espedido BA, Jensen SO, Bowden R. Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. Microb Genom. 2016;2(1):e000048. https:\/\/doi.org\/10.1099\/mgen.0.000048.","DOI":"10.1099\/mgen.0.000048"},{"key":"1747_CR61","doi-asserted-by":"publisher","unstructured":"Pinholt M, Larner-Svensson H, Littauer P, Moser CE, Pedersen M, Lemming LE, et al. Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012-13, investigated by WGS, MLST and PFGE. J Antimicrob Chemother. 2015;70(9):2474\u201382. https:\/\/doi.org\/10.1093\/jac\/dkv142.","DOI":"10.1093\/jac\/dkv142"},{"key":"1747_CR62","doi-asserted-by":"publisher","unstructured":"Didelot X, Maiden MC. Impact of recombination on bacterial evolution. Trends Microbiol. 2010;18(7):315\u201322. https:\/\/doi.org\/10.1016\/j.tim.2010.04.002.","DOI":"10.1016\/j.tim.2010.04.002"},{"key":"1747_CR63","doi-asserted-by":"publisher","unstructured":"van Hal SJ, Willems RJL, Gouliouris T, Ballard SA, Coque TM, Hammerum AM, et al. The global dissemination of hospital clones of Enterococcus faecium. Genome Med. 2021;13(1):52. https:\/\/doi.org\/10.1186\/s13073-021-00868-0.","DOI":"10.1186\/s13073-021-00868-0"},{"key":"1747_CR64","doi-asserted-by":"publisher","unstructured":"Doubravsk\u00e1 L, Htoutou Sedl\u00e1kov\u00e1 M, Fi\u0161erov\u00e1 K, Pudov\u00e1 V, Urb\u00e1nek K, Petr\u017eelov\u00e1 J, et al. Bacterial Resistance to Antibiotics and Clonal Spread in COVID-19-Positive Patients on a Tertiary Hospital Intensive Care Unit, Czech Republic. Antibiotics (Basel). 2022;11(6):783. https:\/\/doi.org\/10.3390\/antibiotics11060783.","DOI":"10.3390\/antibiotics11060783"},{"key":"1747_CR65","unstructured":"Anon. DANMAP 2021 - Use of antimicrobial agents and occurence of antimicrobial resistance in bacteria from food animals, food and humans in Denmark. ISSN. 1600\u20132032."},{"key":"1747_CR66","doi-asserted-by":"publisher","unstructured":"Lee T, Pang S, Abraham S, Coombs GW. Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future. J Glob Antimicrob Resist. 2019;16:36\u201347. https:\/\/doi.org\/10.1016\/j.jgar.2018.08.016.","DOI":"10.1016\/j.jgar.2018.08.016"},{"key":"1747_CR67","doi-asserted-by":"publisher","unstructured":"Kommineni S, Bretl DJ, Lam V, Chakraborty R, Hayward M, Simpson P, et al. Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. Nature. 2015;526(7575):719\u201322. https:\/\/doi.org\/10.1038\/nature15524.","DOI":"10.1038\/nature15524"},{"key":"1747_CR68","doi-asserted-by":"publisher","unstructured":"Mills EG, Hewlett K, Smith AB, Griffith MP, Pless L, Sundermann AJ, et al. Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium. Nat Microbiol. 2025;10(4):871\u201381. https:\/\/doi.org\/10.1038\/s41564-025-01958-0.","DOI":"10.1038\/s41564-025-01958-0"},{"key":"1747_CR69","doi-asserted-by":"publisher","unstructured":"Freitas AR, Novais C, Tedim AP, Francia MV, Baquero F, Peixe L, Coque TM. Microevolutionary events involving narrow host plasmids influences local fixation of vancomycin-resistance in Enterococcus populations. PLoS One. 2013;8(3):e60589. https:\/\/doi.org\/10.1371\/journal.pone.0060589.","DOI":"10.1371\/journal.pone.0060589"},{"key":"1747_CR70","doi-asserted-by":"publisher","unstructured":"Freitas AR, Tedim AP, Francia MV, Jensen LB, Novais C, Peixe L, et al. Multilevel population genetic analysis of vanA and vanB Enterococcus faecium causing nosocomial outbreaks in 27 countries (1986-2012). J Antimicrob Chemother. 2016;71(12):3351\u201366. https:\/\/doi.org\/10.1093\/jac\/dkw312.","DOI":"10.1093\/jac\/dkw312"},{"key":"1747_CR71","doi-asserted-by":"publisher","unstructured":"Zhu W, Murray PR, Huskins WC, Jernigan JA, McDonald LC, Clark NC, et al. Dissemination of an Enterococcus Inc18-Like vanA plasmid associated with vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 2010;54(10):4314\u201320. https:\/\/doi.org\/10.1128\/aac.00185-10.","DOI":"10.1128\/aac.00185-10"},{"key":"1747_CR72","doi-asserted-by":"publisher","unstructured":"Kohler V, Vaishampayan A, Grohmann E. Broad-host-range Inc18 plasmids: Occurrence, spread and transfer mechanisms. Plasmid. 2018;99:11\u201321. https:\/\/doi.org\/10.1016\/j.plasmid.2018.06.001.","DOI":"10.1016\/j.plasmid.2018.06.001"},{"key":"1747_CR73","doi-asserted-by":"publisher","unstructured":"Lam MM, Seemann T, Tobias NJ, Chen H, Haring V, Moore RJ, et al. Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium. BMC Genomics. 2013;14:595. https:\/\/doi.org\/10.1186\/1471-2164-14-595.","DOI":"10.1186\/1471-2164-14-595"},{"key":"1747_CR74","doi-asserted-by":"publisher","first-page":"2474","DOI":"10.1093\/jac\/dkv142","volume":"70","author":"M Pinholt","year":"2015","unstructured":"Pinholt M, Larner-Svensson H, Littauer P, et al. Multiple hospital outbreaks of vanA Enterococcus faecium in Denmark, 2012-13, investigated by WGS, MLST and PFGE. J Antimicrob Chemother. 2015;70:2474\u201382.","journal-title":"J Antimicrob Chemother"},{"key":"1747_CR75","doi-asserted-by":"crossref","unstructured":"Janice J, Wagner TM, Olsen K, Hegstad J, Hegstad K. Emergence of vancomycin-resistant enterococci from vancomycin-susceptible enterococci in hospitalized patients under antimicrobial therapy. J Glob Antimicrob Resist. 2024;36.","DOI":"10.1016\/j.jgar.2023.12.010"},{"key":"1747_CR76","unstructured":"R Core Team R. A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. 2024. https:\/\/www.R-project.org\/."},{"key":"1747_CR77","doi-asserted-by":"crossref","unstructured":"Heikens E, Bonten MJM, Willems RJL. Enterococcal Surface Protein Esp Is Important for Biofilm Formation of Enterococcus faecium E1162. J ofBacteriol. 2007;189(22):8233\u201340.","DOI":"10.1128\/JB.01205-07"},{"key":"1747_CR78","doi-asserted-by":"publisher","unstructured":"Theilacker C, Sava I, Sanchez-Carballo P, Bao Y, Kropec A, Grohmann E, et al. Deletion of the glycosyltransferase bgsB of Enterococcus faecalisleads to a complete loss of glycolipids from the cell membrane and to impaired biofilm formation. BMC Microbiol. 2011;11:67. https:\/\/doi.org\/10.1186\/1471-2180-11-67.","DOI":"10.1186\/1471-2180-11-67"}],"container-title":["Genome Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13073-026-01747-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-026-01747-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13073-026-01747-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T17:11:50Z","timestamp":1792602710000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13073-026-01747-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,18]]},"references-count":78,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1747"],"URL":"https:\/\/doi.org\/10.1186\/s13073-026-01747-2","relation":{},"ISSN":["1756-994X"],"issn-type":[{"value":"1756-994X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,18]]},"assertion":[{"value":"21 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The trial has been approved by the Danish Data Protection Agency (AHH-2015-047, 03894). Data was collected for internal departmental purposes and an IRB was not required. This study was conducted according to the principles of the Helsinki Declaration.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"162"}}