{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:55:58Z","timestamp":1790916958234,"version":"4.1.0"},"reference-count":35,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Vancomycin-resistant enterococci challenge intensive care. During the interval between organism identification and final phenotypic antimicrobial susceptibility testing, clinicians must balance delayed effective anti-VRE therapy against unnecessary anti-VRE exposure. We aimed to develop and pseudo-temporally validate a model for the vancomycin-resistance phenotype of the index isolate; the model does not determine whether the isolate represents clinically significant infection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      In this retrospective MIMIC-IV cohort, adult ICU admissions with a sterile-site\n                      <jats:italic>Enterococcus<\/jats:italic>\n                      -positive culture obtained more than 48 hours after ICU admission were assigned by de-identified anchor-year group to development (groups labelled 2008\u20132016; n = 552) or pseudo-temporal validation (2017\u20132022; n = 259). Predictors were restricted to information available by specimen collection. Elastic Net with bootstrap stability screening retained 19 of 141 candidates; four tree-based models were comparators.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Among 811 admissions (507 resistant isolates; prevalence, 62.5%), Elastic Net achieved a validation AUROC of 0.835 (95% CI, 0.778\u20130.889) and calibration slope of 0.91 (0.71\u20131.18). Tree-model AUROCs were 0.842\u20130.855; non-significant pairwise DeLong tests were evidence insufficient to detect differences, not evidence of equivalence. Removing both species indicators reduced AUROC to 0.657 (DeLong\n                      <jats:italic>P<\/jats:italic>\n                      \u00a0&amp;lt;\u00a00.001). Development-OOF-fitted Platt scaling improved validation slopes for Random Forest, XGBoost, and CatBoost from 1.41, 2.41, and 1.46 to 0.94, 1.02, and 1.01. At the Youden index threshold, Elastic Net sensitivity was 0.884 and specificity was 0.690. In exploratory decision-curve analysis, its net benefit did not exceed treat-all at thresholds 0.10 or 0.20; the paired difference was 0.044 (95% CI, 0.014\u20130.071) at 0.30.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The model predicts isolate resistance phenotype, not adjudicated infection, and is not a stand-alone treatment rule. These estimates are specific to a single-center cohort with high VRE prevalence. Independent external validation, local recalibration, clinical adjudication, and periodic updating are prerequisites for use.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1935284","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:41:06Z","timestamp":1790916066000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Prediction of vancomycin-resistant phenotype in ICU-onset sterile-site Enterococcus-positive cultures: development and pseudo-temporal validation of a clinical prediction model using MIMIC-IV"],"prefix":"10.3389","volume":"16","author":[{"given":"Wenhao","family":"Sun","sequence":"first","affiliation":[{"name":"School of Information Engineering and Artificial Intelligence, Lanzhou University of Finance and Economics","place":["Lanzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-lan","family":"Gu","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou","place":["Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingmei","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou","place":["Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinxia","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou","place":["Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanbin","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou","place":["Gansu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","year":"2022","journal-title":"Lancet"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00356-21","article-title":"Development and validation of a tool for the prediction of vancomycin-resistant enterococci colonization persistence \u2013 the PREVENT score","volume":"9","author":"Boeing","year":"2021","journal-title":"Microbiol. Spectr."},{"key":"B3","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1017\/ice.2020.12","article-title":"Using VRE screening tests to predict vancomycin resistance in enterococcal bacteremia","volume":"41","author":"Butler-Laporte","year":"2020","journal-title":"Infection Control Hosp. Epidemiol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.00059-22","article-title":"Therapeutics for vancomycin-resistant enterococcal bloodstream infections","volume":"36","author":"Cairns","year":"2023","journal-title":"Clin. Microbiol. Rev."},{"key":"B5","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1007\/s10096-019-03755-0","article-title":"Risk factor analysis for linezolid-associated thrombocytopenia in critically ill patients","volume":"39","author":"Cazavet","year":"2020","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B6","unstructured":"Antibiotic Resistance Threats in the United States, 2019\n          \n          \n          Atlanta, GA\n          U.S. Department of Health and Human Services, CDC\n          \n          2019"},{"key":"B7","unstructured":"Antimicrobial Resistance Threats in the United States, 2021\u20132022\n          \n          \n          Atlanta, GA\n          U.S. Department of Health and Human Services, CDC\n          \n          2024"},{"key":"B8","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1016\/j.jclinepi.2019.02.004","article-title":"A systematic review shows no performance benefit of machine learning over logistic regression for clinical prediction models","volume":"110","author":"Christodoulou","year":"2019","journal-title":"J. Clin. Epidemiol."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-023-01278-0","article-title":"Vancomycin-resistant enterococci (VRE) in hospital settings across European borders: a scoping review comparing the epidemiology in the Netherlands and Germany","volume":"12","author":"Cimen","year":"2023","journal-title":"Antimicrobial Resistance Infection Control"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1136\/bmj-2023-078378","article-title":"TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods","volume":"385","author":"Collins","year":"2024","journal-title":"BMJ"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00181-19","article-title":"Antimicrobial resistance in ESKAPE pathogens","volume":"33","author":"De Oliveira","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1725","DOI":"10.1097\/CCM.0000000000005662","article-title":"Epidemiology of ICU-onset bloodstream infection: prevalence, pathogens, and risk factors among 150,948 ICU patients at 85 U.S. hospitals","volume":"50","author":"Gouel-Cheron","year":"2022","journal-title":"Crit. Care Med."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.2807\/1560-7917.ES.2024.29.23.2300633","article-title":"Surveillance of vancomycin-resistant enterococci reveals shift in dominating clusters from vanA to vanB Enterococcus faecium clusters, Denmark 2015 to 2022","volume":"29","author":"Hammerum","year":"2024","journal-title":"Eurosurveillance"},{"key":"B14","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/s13756-024-01430-4","article-title":"Development and validation of machine learning models to predict MDRO colonization or infection on ICU admission by using electronic health record data","volume":"13","author":"Li","year":"2024","journal-title":"Antimicrobial Resistance Infection Control"},{"key":"B15","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s10096-023-04708-4","article-title":"Risk exploration and prediction model construction for linezolid-resistant Enterococcus faecalis based on big data in a province in southern China","volume":"43","author":"Liu","year":"2024","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/sur.2016.261","article-title":"The Surgical Infection Society revised guidelines on the management of intra-abdominal infection","volume":"18","author":"Mazuski","year":"2017","journal-title":"Surg. Infections"},{"key":"B17","doi-asserted-by":"publisher","first-page":"3453","DOI":"10.1093\/jac\/dkw319","article-title":"Longitudinal, (2001\u20132014) analysis of enterococci and VRE causing invasive infections in European and US hospitals, including a contemporary, (2010\u20132013) analysis of oritavancin in vitro potency","volume":"71","author":"Mendes","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001055","article-title":"Emergence of linezolid-resistant Enterococcus faecium in a tertiary hospital in Copenhagen","volume":"9","author":"Misiakou","year":"2023","journal-title":"Microb. Genomics"},{"key":"B19","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1145\/1102351.1102430","article-title":"Predicting good probabilities with supervised learning","volume-title":"Proceedings of the 22nd International Conference on Machine Learning (ICML \u201805)","author":"Niculescu-Mizil","year":"2005"},{"key":"B20","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1093\/jac\/dkaf225","article-title":"Impact of empiric anti-VRE therapy on survival in vancomycin-resistant enterococcal bloodstream infection","volume":"80","author":"Ou","year":"2025","journal-title":"J. Antimicrob. Chemother."},{"key":"B21","doi-asserted-by":"publisher","first-page":"201","DOI":"10.7326\/0003-4819-144-3-200602070-00009","article-title":"Translating clinical research into clinical practice: impact of using prediction rules to make decisions","volume":"144","author":"Reilly","year":"2006","journal-title":"Ann. Internal Med."},{"key":"B22","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1086\/502196","article-title":"Effect of nosocomial vancomycin-resistant enterococcal bacteremia on mortality, length of stay, and costs","volume":"24","author":"Song","year":"2003","journal-title":"Infection Control Hosp. Epidemiol."},{"key":"B23","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-030-16399-0","volume-title":"Clinical Prediction Models: A Practical Approach to Development, Validation, and Updating","author":"Steyerberg","year":"2019"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2026.1789841","article-title":"Rapid prediction of vancomycin-resistant Enterococcus faecium using MALDI-TOF mass spectrometry and machine learning","volume":"17","author":"Sun","year":"2026","journal-title":"Front. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1111\/j.1469-0691.2010.03392.x","article-title":"Mortality in enterococcal bloodstream infections increases with inappropriate antimicrobial therapy","volume":"17","author":"Suppli","year":"2011","journal-title":"Clin. Microbiol. Infection"},{"key":"B26","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1111\/j.1574-695X.2008.00383.x","article-title":"Emergence of CC17 Enterococcus faecium: from commensal to hospital-adapted pathogen","volume":"52","author":"Top","year":"2008","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1038\/s41586-024-08095-4","article-title":"Rifaximin prophylaxis causes resistance to the last-resort antibiotic daptomycin","volume":"635","author":"Turner","year":"2024","journal-title":"Nature"},{"key":"B28","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1186\/s12916-019-1466-7","article-title":"Calibration: the Achilles heel of predictive analytics","volume":"17","author":"Van Calster","year":"2019","journal-title":"BMC Med."},{"key":"B29","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.jclinepi.2015.12.005","article-title":"A calibration hierarchy for risk models was defined: from utopia to empirical data","volume":"74","author":"Van Calster","year":"2016","journal-title":"J. Clin. Epidemiol."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00308","article-title":"Modern tools for rapid diagnostics of antimicrobial resistance","volume":"10","author":"Vasala","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1186\/s40560-023-00695-y","article-title":"A deep learning model for predicting multidrug-resistant organism infection in critically ill patients","volume":"11","author":"Wang","year":"2023","journal-title":"J. Intensive Care"},{"key":"B32","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1093\/cid\/cix232","article-title":"Prediction of bloodstream infection due to vancomycin-resistant Enterococcus in patients undergoing leukemia induction or hematopoietic stem-cell transplantation","volume":"64","author":"Webb","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"B33","doi-asserted-by":"publisher","first-page":"821","DOI":"10.3201\/eid1106.041204","article-title":"Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex","volume":"11","author":"Willems","year":"2005","journal-title":"Emerging Infect. Dis."},{"key":"B34","doi-asserted-by":"publisher","first-page":"2963","DOI":"10.1093\/jac\/dks321","article-title":"Clinical prediction rule for identifying patients with vancomycin-resistant enterococci (VRE) at the time of admission to the intensive care unit in a low VRE prevalence setting","volume":"67","author":"Yoon","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1186\/s12879-025-11900-8","article-title":"Evaluating antimicrobial resistance and clinical outcomes in surgical ICU using a machine learning perspective: a retrospective observational study","volume":"25","author":"Ziaian","year":"2025","journal-title":"BMC Infect. Dis."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1935284\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:41:19Z","timestamp":1790916079000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2026.1935284\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,2]]},"references-count":35,"alternative-id":["10.3389\/fcimb.2026.1935284"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2026.1935284","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,2]]},"article-number":"1935284"}}