{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T20:21:24Z","timestamp":1773865284311,"version":"3.50.1"},"posted":{"date-parts":[[2026,3,16]]},"group-title":"Infectious Diseases (except HIV\/AIDS)","reference-count":76,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Colonization of the gastrointestinal (GI) tract by vancomycin-resistant\n                  <jats:italic>Enterococcus faecium<\/jats:italic>\n                  (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected \u226414 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Impact Statement<\/jats:title>\n                  <jats:p>VREfm bloodstream infection is often seeded from bacteria colonizing the gut. The genetic diversity within gut and blood VREfm populations, and the role of this diversity in bacterial transmission, has been difficult to resolve as genomic surveillance typically relies on sequencing a clonal clinical isolate from each patient. Using culture-enriched metagenomic sequencing of matched GI tract and bloodstream VREfm populations from 35 patients at a single hospital, we found that the GI tract reservoir contained VREfm populations with greater strain and variant diversity than populations collected from the bloodstream. By integrating population sequencing with a large collection of VREfm clinical isolate genomes, we further demonstrate that different strains co-colonizing the GI tract of the same patient can reside in multiple putative transmission clusters, revealing potential transmission links that clone-based approaches are likely to miss. These findings demonstrate the potential utility of culture-enriched metagenomic sequencing for higher-resolution hospital surveillance of bacterial transmission. Applying this approach to other bacterial pathogens could improve our ability to detect and interpret transmission involving heterogeneous microbial populations that colonize and infect hospitalized patients.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Data Summary<\/jats:title>\n                  <jats:p>\n                    Patient demographic data and clinical characteristics can be found in\n                    <jats:bold>Table S1<\/jats:bold>\n                    (online Supplementary Material). All sequencing data generated in this study has been deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969, with sample accession numbers listed in\n                    <jats:bold>Table S2<\/jats:bold>\n                    . Sequences used to construct the local reference strain database are available at NCBI BioProject PRJNA475751, with accession numbers listed in\n                    <jats:bold>Table S3<\/jats:bold>\n                    . Variants identified in single-strain blood and GI populations are listed in\n                    <jats:bold>Table S4<\/jats:bold>\n                    . Accession numbers for clinical isolate genomes included in transmission analyses are listed in\n                    <jats:bold>Table S5<\/jats:bold>\n                    .\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Repositories<\/jats:title>\n                  <jats:p>Sequencing data generated in this study is deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.03.11.26348025","type":"posted-content","created":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T00:55:11Z","timestamp":1773708911000},"source":"Crossref","is-referenced-by-count":0,"title":["Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant\n                  <i>Enterococcus faecium<\/i>"],"prefix":"10.64898","author":[{"given":"Emma G.","family":"Mills","sequence":"first","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-5103-3438","authenticated-orcid":false,"given":"Kirsten M.","family":"Evans","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-8148-8835","authenticated-orcid":false,"given":"Ava J.","family":"Dorazio","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-7818-905X","authenticated-orcid":false,"given":"Kevin M.","family":"Squires","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2439-6287","authenticated-orcid":false,"given":"Alexander J.","family":"Sundermann","sequence":"additional","affiliation":[{"name":"Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"},{"name":"Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1478-5190","authenticated-orcid":false,"given":"Madison E.","family":"Stellfox","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8327-4135","authenticated-orcid":false,"given":"Matthew J.","family":"Culyba","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"},{"name":"Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9794-5665","authenticated-orcid":false,"given":"Ryan K.","family":"Shields","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7284-0103","authenticated-orcid":false,"given":"Daria","family":"Van Tyne","sequence":"additional","affiliation":[{"name":"Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"},{"name":"Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2026031805500582000_2026.03.11.26348025v1.1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-micro-091213-113003"},{"key":"2026031805500582000_2026.03.11.26348025v1.2","doi-asserted-by":"crossref","unstructured":"Dubin K , Pamer EG . Enterococci and Their Interactions with the Intestinal Microbiome. Microbiol Spectr. 5(6):10.1128\/microbiolspec.bad-0014\u20132016.","DOI":"10.1128\/microbiolspec.BAD-0014-2016"},{"key":"2026031805500582000_2026.03.11.26348025v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2761"},{"key":"2026031805500582000_2026.03.11.26348025v1.4","doi-asserted-by":"publisher","DOI":"10.1172\/JCI43918"},{"issue":"4","key":"2026031805500582000_2026.03.11.26348025v1.5","first-page":"e00670","article-title":"Last Bacteria Standing: VREfm Persistence in the Hospitalized Gut","volume":"13","year":"2022","journal-title":"mBio"},{"key":"2026031805500582000_2026.03.11.26348025v1.6","doi-asserted-by":"publisher","DOI":"10.7326\/0003-4819-139-6-200309160-00011"},{"issue":"11","key":"2026031805500582000_2026.03.11.26348025v1.7","first-page":"e01750","article-title":"Comparative analysis of vancomycin-resistant enterococci in colonization and infection\u2014a longitudinal study","volume":"13","year":"2025","journal-title":"Microbiology Spectrum"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.8","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s13073-017-0507-0","article-title":"Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients","volume":"9","year":"2017","journal-title":"Genome Medicine"},{"issue":"7","key":"2026031805500582000_2026.03.11.26348025v1.9","first-page":"e000277","article-title":"Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization","volume":"5","year":"2019","journal-title":"Microb Genom"},{"key":"2026031805500582000_2026.03.11.26348025v1.10","doi-asserted-by":"crossref","unstructured":"Kavanagh NL , Kinnevey PM , Brennan GI , O\u2019Connell B , Goering RV , Coleman DC . Co-carriage of diverse vancomycin-resistant Enterococcus faecium ST80-lineages by 70% of patients in an Irish hospital. JAC Antimicrob Resist. 2025 Apr 29;7(3):dlaf065.","DOI":"10.1093\/jacamr\/dlaf065"},{"key":"2026031805500582000_2026.03.11.26348025v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jiv597"},{"issue":"7","key":"2026031805500582000_2026.03.11.26348025v1.12","first-page":"e00102","article-title":"Diversification and Evolution of Vancomycin-Resistant Enterococcus faecium during Intestinal Domination","volume":"87","year":"2019","journal-title":"Infect Immun"},{"key":"2026031805500582000_2026.03.11.26348025v1.13","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkae023"},{"issue":"3","key":"2026031805500582000_2026.03.11.26348025v1.14","first-page":"e01520","article-title":"Genome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection","volume":"56","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2026031805500582000_2026.03.11.26348025v1.15","doi-asserted-by":"crossref","unstructured":"Messina JA , Sinha R , Starr K , Arshad M , Alexander BD , Chao NJ , et al. Clinical and Genomic Characterization of Recurrent Enterococcal Bloodstream Infection in Patients With Acute Leukemia. Open Forum Infect Dis. 2018 May 5;5(6):ofy107.","DOI":"10.1093\/ofid\/ofy107"},{"key":"2026031805500582000_2026.03.11.26348025v1.16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.12.6908"},{"issue":"10","key":"2026031805500582000_2026.03.11.26348025v1.17","doi-asserted-by":"crossref","first-page":"400","DOI":"10.3390\/microorganisms7100400","article-title":"Risk Factors for Long-Term Vancomycin-Resistant Enterococci Persistence\u2014A Prospective Longitudinal Study","volume":"7","year":"2019","journal-title":"Microorganisms"},{"key":"2026031805500582000_2026.03.11.26348025v1.18","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01316-06"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.19","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s44263-025-00186-2","article-title":"Genomic sequencing surveillance of patients colonized with vancomycin-resistant enterococci improves detection of healthcare-associated transmission","volume":"3","year":"2025","journal-title":"BMC Glob Public Health"},{"key":"2026031805500582000_2026.03.11.26348025v1.20","doi-asserted-by":"crossref","unstructured":"Sundermann AJ , Kumar P , Griffith MP , Waggle KD , Rangachar Srinivasa V , Raabe N , et al. Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact. Clin Infect Dis. 2025 Apr 30;ciaf216.","DOI":"10.1093\/cid\/ciaf216"},{"key":"2026031805500582000_2026.03.11.26348025v1.21","doi-asserted-by":"crossref","unstructured":"Thorpe HA , Pesonen M , Corbella M , Pesonen H , Gaiarsa S , Boinett CJ , et al. Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. The Lancet Microbe [Internet]. 2024 Oct 1 [cited 2026 Feb 15];5(10). Available from: https:\/\/www.thelancet.com\/journals\/lanmic\/article\/PIIS2666-5247(24)00113-7\/fulltext","DOI":"10.1016\/S2666-5247(24)00113-7"},{"issue":"11","key":"2026031805500582000_2026.03.11.26348025v1.22","first-page":"001111","article-title":"Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures","volume":"9","year":"2023","journal-title":"Microb Genom"},{"key":"2026031805500582000_2026.03.11.26348025v1.23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp344"},{"issue":"23","key":"2026031805500582000_2026.03.11.26348025v1.24","doi-asserted-by":"crossref","first-page":"e2424797122","DOI":"10.1073\/pnas.2424797122","article-title":"Population sequencing for phylogenetic diversity and transmission analyses","volume":"122","year":"2025","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2026031805500582000_2026.03.11.26348025v1.25","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1917130117"},{"key":"2026031805500582000_2026.03.11.26348025v1.26","unstructured":"nanoporetech\/dorado [Internet]. Oxford Nanopore Technologies; 2024 [cited 2024 Oct 2]. Available from: https:\/\/github.com\/nanoporetech\/dorado"},{"issue":"6","key":"2026031805500582000_2026.03.11.26348025v1.27","doi-asserted-by":"crossref","first-page":"e1005595","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","year":"2017","journal-title":"PLOS Computational Biology"},{"issue":"8","key":"2026031805500582000_2026.03.11.26348025v1.28","first-page":"e000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","year":"2018","journal-title":"Microb Genom"},{"key":"2026031805500582000_2026.03.11.26348025v1.29","doi-asserted-by":"crossref","unstructured":"Harris SR. SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology [Internet]. bioRxiv; 2018 [cited 2024 Apr 13]. p. 453142. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/453142v1","DOI":"10.1101\/453142"},{"key":"2026031805500582000_2026.03.11.26348025v1.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0686-2"},{"key":"2026031805500582000_2026.03.11.26348025v1.31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0"},{"key":"2026031805500582000_2026.03.11.26348025v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-022-00738-y"},{"key":"2026031805500582000_2026.03.11.26348025v1.33","doi-asserted-by":"crossref","unstructured":"Tonkin-Hill G , Shao Y , Zarebski AE , Mallawaarachchi S , Xie O , M\u00e4klin T , et al. Enhanced metagenomics-enabled transmission inference with TRACS [Internet]. bioRxiv; 2024 [cited 2025 Mar 12]. p. 2024.08.19.608527. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.19.608527v1","DOI":"10.1101\/2024.08.19.608527"},{"key":"2026031805500582000_2026.03.11.26348025v1.34","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"2026031805500582000_2026.03.11.26348025v1.35","doi-asserted-by":"publisher","DOI":"10.1002\/CPBI.102"},{"key":"2026031805500582000_2026.03.11.26348025v1.36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"2026031805500582000_2026.03.11.26348025v1.37","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0554-6_12"},{"key":"2026031805500582000_2026.03.11.26348025v1.38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1085"},{"key":"2026031805500582000_2026.03.11.26348025v1.39","doi-asserted-by":"crossref","unstructured":"Cantalapiedra CP , Hern\u00e1ndez-Plaza A , Letunic I , Bork P , Huerta-Cepas J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale [Internet]. bioRxiv; 2021 [cited 2025 Nov 16]. p. 2021.06.03.446934. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/2021.06.03.446934v2","DOI":"10.1101\/2021.06.03.446934"},{"key":"2026031805500582000_2026.03.11.26348025v1.40","doi-asserted-by":"publisher","DOI":"10.1038\/ng.997"},{"key":"2026031805500582000_2026.03.11.26348025v1.41","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"2026031805500582000_2026.03.11.26348025v1.42","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"2026031805500582000_2026.03.11.26348025v1.43","doi-asserted-by":"publisher","DOI":"10.1111\/j.1742-4658.2005.04945.x"},{"key":"2026031805500582000_2026.03.11.26348025v1.44","doi-asserted-by":"crossref","unstructured":"Jolley KA , Bray JE , Maiden MCJ . Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124.","DOI":"10.12688\/wellcomeopenres.14826.1"},{"key":"2026031805500582000_2026.03.11.26348025v1.45","unstructured":"tseemann\/mlst: :id: Scan contig files against PubMLST typing schemes [Internet]. [cited 2024 Apr 13]. Available from: https:\/\/github.com\/tseemann\/mlst"},{"key":"2026031805500582000_2026.03.11.26348025v1.46","doi-asserted-by":"publisher","DOI":"10.1609\/icwsm.v3i1.13937"},{"issue":"7","key":"2026031805500582000_2026.03.11.26348025v1.47","first-page":"e00052","article-title":"Risk factors for vancomycin resistance in patients with Enterococcus faecium bloodstream infections: an analysis of the Munich Multicentric Enterococci Cohort","volume":"13","year":"2025","journal-title":"Microbiology Spectrum"},{"issue":"3","key":"2026031805500582000_2026.03.11.26348025v1.48","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1093\/cid\/ciab946","article-title":"Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection","volume":"75","year":"2022","journal-title":"Clin Infect Dis"},{"issue":"4","key":"2026031805500582000_2026.03.11.26348025v1.49","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/s41564-025-01958-0","article-title":"Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium","volume":"10","year":"2025","journal-title":"Nat Microbiol"},{"key":"2026031805500582000_2026.03.11.26348025v1.50","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis580"},{"key":"2026031805500582000_2026.03.11.26348025v1.51","doi-asserted-by":"crossref","unstructured":"Li W , Hu J , Li L , Zhang M , Cui Q , Ma Y , et al. New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain. Front Microbiol. 2022 Jun 21;13:896916.","DOI":"10.3389\/fmicb.2022.896916"},{"key":"2026031805500582000_2026.03.11.26348025v1.52","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.6.1879-1889.2004"},{"key":"2026031805500582000_2026.03.11.26348025v1.53","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2219540120"},{"key":"2026031805500582000_2026.03.11.26348025v1.54","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3552"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.55","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/emph\/eoac035","article-title":"An orally administered drug prevents selection for antibiotic-resistant bacteria in the gut during daptomycin therapy","volume":"10","year":"2022","journal-title":"Evol Med Public Health"},{"key":"2026031805500582000_2026.03.11.26348025v1.56","doi-asserted-by":"crossref","unstructured":"Zeng W , Feng L , Qian C , Chen T , Wang S , Zhang Y , et al. Acquisition of Daptomycin Resistance by Enterococcus faecium Confers Collateral Sensitivity to Glycopeptides. Front Microbiol. 2022 Apr 12;13:815600.","DOI":"10.3389\/fmicb.2022.815600"},{"issue":"11","key":"2026031805500582000_2026.03.11.26348025v1.57","doi-asserted-by":"crossref","first-page":"2336","DOI":"10.1093\/cid\/ciz666","article-title":"Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance","volume":"70","year":"2020","journal-title":"Clin Infect Dis"},{"issue":"2","key":"2026031805500582000_2026.03.11.26348025v1.58","first-page":"320","article-title":"Genomic analysis of 600 vancomycin-resistant Enterococcus faecium reveals a high prevalence of ST80 and spread of similar vanA regions via IS1216E and plasmid transfer in diverse genetic lineages in Ireland","volume":"77","year":"2021","journal-title":"J Antimicrob Chemother"},{"key":"2026031805500582000_2026.03.11.26348025v1.59","doi-asserted-by":"crossref","unstructured":"Lisotto P , Couto N , Rosema S , Lokate M , Zhou X , Bathoorn E , et al. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117\/CT24 Causing Hospital Outbreaks. Frontiers in Microbiology [Internet]. 2021 [cited 2023 May 27];12. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.728356","DOI":"10.3389\/fmicb.2021.728356"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.60","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s13756-019-0573-8","article-title":"Near-ubiquitous presence of a vancomycin-resistant Enterococcus faecium ST117\/CT71\/vanB \u2013clone in the Rhine-Main metropolitan area of Germany","volume":"8","year":"2019","journal-title":"Antimicrobial Resistance & Infection Control"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.61","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1017\/ice.2022.7","article-title":"Vancomycin-resistant Enterococcus sequence type 1478 spread across hospitals participating in the Canadian Nosocomial Infection Surveillance Program from 2013 to 2018","volume":"44","year":"2023","journal-title":"Infection Control & Hospital Epidemiology"},{"key":"2026031805500582000_2026.03.11.26348025v1.62","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2022.106561"},{"key":"2026031805500582000_2026.03.11.26348025v1.63","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkw539"},{"key":"2026031805500582000_2026.03.11.26348025v1.64","doi-asserted-by":"crossref","unstructured":"Cassone M , Zhu Z , Mantey J , Gibson KE , Perri MB , Zervos MJ , et al. Interplay Between Patient Colonization and Environmental Contamination With Vancomycin-Resistant Enterococci and Their Association With Patient Health Outcomes in Postacute Care. Open Forum Infect Dis. 2019 Dec 11;7(1):ofz519.","DOI":"10.1093\/ofid\/ofz519"},{"issue":"6","key":"2026031805500582000_2026.03.11.26348025v1.65","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1017\/ice.2018.29","article-title":"Defining the Role of the Environment in the Emergence and Persistence of vanA Vancomycin-Resistant Enterococcus (VRE) in an Intensive Care Unit: A Molecular Epidemiological Study","volume":"39","year":"2018","journal-title":"Infection Control & Hospital Epidemiology"},{"issue":"7","key":"2026031805500582000_2026.03.11.26348025v1.66","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1086\/676861","article-title":"A Comparison of Environmental Contamination by Patients Infected or Colonized with Methicillin-Resistant Staphylococcus aureus or Vancomycin-Resistant Enterococci: A Multicenter Study","volume":"35","year":"2014","journal-title":"Infect Control Hosp Epidemiol"},{"key":"2026031805500582000_2026.03.11.26348025v1.67","doi-asserted-by":"publisher","DOI":"10.1086\/527394"},{"key":"2026031805500582000_2026.03.11.26348025v1.68","unstructured":"Votintseva AA , Miller RR , Fung R , Knox K , Godwin H , Peto TEA , et al. Multiple-Strain Colonization in Nasal Carriers of Staphylococcus aureus. Journal of Clinical Microbiology [Internet]. 2014 Apr [cited 2026 Jan 13]; Available from: https:\/\/journals.asm.org\/doi\/10.1128\/jcm.03254-13"},{"key":"2026031805500582000_2026.03.11.26348025v1.69","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.jhin.2024.01.009","article-title":"Whole-genome sequencing reveals two prolonged simultaneous outbreaks involving Pseudomonas aeruginosa high-risk strains ST111 and ST235 with resistance to quaternary ammonium compounds","volume":"145","year":"2024","journal-title":"Journal of Hospital Infection"},{"key":"2026031805500582000_2026.03.11.26348025v1.70","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-39416-2"},{"issue":"1","key":"2026031805500582000_2026.03.11.26348025v1.71","doi-asserted-by":"crossref","first-page":"e82","DOI":"10.1017\/ash.2025.54","article-title":"A persistent sink reservoir as a potential source of Pseudomonas aeruginosa infections in pediatric oncology patients","volume":"5","year":"2025","journal-title":"Antimicrob Steward Healthc Epidemiol"},{"key":"2026031805500582000_2026.03.11.26348025v1.72","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02630-0"},{"key":"2026031805500582000_2026.03.11.26348025v1.73","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evt111"},{"key":"2026031805500582000_2026.03.11.26348025v1.74","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359"},{"key":"2026031805500582000_2026.03.11.26348025v1.75","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3103"},{"key":"2026031805500582000_2026.03.11.26348025v1.76","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01688-w"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.03.11.26348025","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T12:50:35Z","timestamp":1773838235000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.64898\/2026.03.11.26348025"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,16]]},"references-count":76,"URL":"https:\/\/doi.org\/10.64898\/2026.03.11.26348025","relation":{},"subject":[],"published":{"date-parts":[[2026,3,16]]},"subtype":"preprint"}}