{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:16:35Z","timestamp":1788225395219,"version":"build-2803163510"},"reference-count":24,"publisher":"American Society for Microbiology","issue":"7","license":[{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,7,7]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Vancomycin-resistant enterococci (VREs) have emerged as an important public health concern and a leading cause of healthcare-associated infections. Accurately distinguishing between closely related VRE strains is imperative for infection control measures in the setting of hospital outbreaks. Although pulsed-field gel electrophoresis (PFGE) is considered the gold standard for VRE strain typing, recent studies have identified whole-genome sequencing (WGS) as a promising alternative with greater resolution. In this study, we report on the validation and utility of a WGS and single-nucleotide polymorphism (SNP) analysis pipeline toward vancomycin-resistant\n                      <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n                      (VREfm) strain typing in a large academic medical center. Using PFGE as the reference method, we identified a conservative threshold of \u226410 SNPs as robustly identifying related VREfm isolates with 98.5% sensitivity and 93.1% specificity. Comparing VREfm infection control surveillance pre- and post-WGS SNP strain typing revealed a proportionally greater number of isolates with related strain types and epidemiological links in the post-WGS SNP group. These findings suggest that WGS SNP analysis can improve the resolution of emerging hospital outbreaks and infection control measures, as compared to PFGE.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Distinguishing between closely related antibiotic-resistant bacteria is an important task toward infection control measures in a hospital environment. This study focused on strains of one particular antibiotic-resistant bacterium (vancomycin-resistant\n                      <jats:italic toggle=\"yes\">Enterococcus faecium<\/jats:italic>\n                      ) and assessed the utility of a whole-genome sequencing analysis pipeline toward distinguishing strain relatedness compared to the gold standard reference method. The results showed that strain typing with whole-genome sequencing identified a proportionally greater number of transmission\/outbreak events compared to the reference method over a similar time period. The findings suggest that a whole-genome sequencing pipeline, when available, can improve hospital infection control measures.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00847-26","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T13:43:43Z","timestamp":1779803023000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Comparing whole-genome sequencing to pulsed-field gel electrophoresis for vancomycin-resistant\n                    <i>Enterococcus faecium<\/i>\n                    hospital surveillance"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0859-2226","authenticated-orcid":true,"given":"Joshua","family":"Mayoral","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02ets8c94","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, Northwestern University Feinberg School of Medicine","place":["Chicago, USA"]},{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Malczynski","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"Ruiz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanda","family":"Polanco","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Fritz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jovanne\u00e9","family":"Nunez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shardul N.","family":"Rathod","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Healthcare Epidemiology and Infection Prevention, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kendall","family":"Kling","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02ets8c94","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, Northwestern University Feinberg School of Medicine","place":["Chicago, USA"]},{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]},{"name":"Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0741-3070","authenticated-orcid":true,"given":"Chao","family":"Qi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02ets8c94","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, Northwestern University Feinberg School of Medicine","place":["Chicago, USA"]},{"id":[{"id":"https:\/\/ror.org\/009543z50","id-type":"ROR","asserted-by":"publisher"}],"name":"Clinical Microbiology Laboratory, Northwestern Memorial Hospital","place":["Chicago, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2023.09.008"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00868-0"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(25)00118-5"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2019.12.007"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1186\/s44263-025-00186-2"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01946-15"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-28156-4"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2017.12.016"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.03385-14"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw872"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00806-7"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.04204-22"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(21)00149-X"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.33.9.2233-2239.1995"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.004948"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.05107-22"},{"key":"e_1_3_4_18_2","volume-title":"R: a language and environment for statistical computing","author":"R Core Team","year":"2023","unstructured":"R Core Team. 2023. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria."},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4"},{"key":"e_1_3_4_20_2","unstructured":"Iannone R. 2025. gt: easily create presentation-ready display tables. Available from: https:\/\/gt.rstudio.com"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.5858\/arpa.2014-0250-CP"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2017.11.003"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-024-01058-6"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00102-19"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1917130117"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00847-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00847-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T01:01:22Z","timestamp":1788224482000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00847-26"}},"subtitle":[],"editor":[{"given":"Victoria L.","family":"Campod\u00f3nico","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,7]]},"references-count":24,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,7,7]]}},"alternative-id":["10.1128\/spectrum.00847-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00847-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,7]]},"assertion":[{"value":"2026-03-09","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-27","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-26","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00847-26"}}