{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T00:32:16Z","timestamp":1780619536602,"version":"3.54.1"},"reference-count":33,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,8,27]],"date-time":"2021-08-27T00:00:00Z","timestamp":1630022400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000269","name":"Economic and Social Research Council","doi-asserted-by":"publisher","award":["ES\/P010873\/1"],"award-info":[{"award-number":["ES\/P010873\/1"]}],"id":[{"id":"10.13039\/501100000269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000690","name":"Research Councils UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000690","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016270","name":"Global Challenges Research Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016270","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["4078P0_198363"],"award-info":[{"award-number":["4078P0_198363"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006388","name":"H\u00f4pitaux Universitaires de Gen\u00e8ve","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006388","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_PC_19065"],"award-info":[{"award-number":["MC_PC_19065"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","journalofhospitalinfection.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Hospital Infection"],"published-print":{"date-parts":[[2021,11]]},"DOI":"10.1016\/j.jhin.2021.07.013","type":"journal-article","created":{"date-parts":[[2021,8,27]],"date-time":"2021-08-27T11:05:08Z","timestamp":1630062308000},"page":"124-134","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":34,"special_numbering":"C","title":["Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction"],"prefix":"10.1016","volume":"117","author":[{"given":"M.","family":"Abbas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T.","family":"Robalo Nunes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Cori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Cordey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Laubscher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Baggio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T.","family":"Jombart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Iten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L.","family":"Vieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Teixeira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Perez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Pittet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E.","family":"Frangos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.E.","family":"Graf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W.","family":"Zingg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Harbarth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jhin.2021.07.013_bib1","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1164\/rccm.202004-1037CP","article-title":"Hospital preparedness for COVID-19: a practical guide from a critical care perspective","volume":"201","author":"Griffin","year":"2020","journal-title":"Am J Respir Crit Care Med"},{"key":"10.1016\/j.jhin.2021.07.013_bib2","doi-asserted-by":"crossref","first-page":"651","DOI":"10.15585\/mmwr.mm6921e1","article-title":"Universal and serial laboratory testing for SARS-CoV-2 at a long-term care skilled nursing facility for veterans \u2013 Los Angeles, California, 2020","volume":"69","author":"Dora","year":"2020","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"10.1016\/j.jhin.2021.07.013_bib3","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1056\/NEJMoa2008457","article-title":"Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility","volume":"382","author":"Arons","year":"2020","journal-title":"N\u00a0Engl J Med"},{"key":"10.1016\/j.jhin.2021.07.013_bib4","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1017\/ice.2020.99","article-title":"Rapid nosocomial spread of SARS-CoV-2 in a French geriatric unit","volume":"41","author":"Vanhems","year":"2020","journal-title":"Infect Control Hosp Epidemiol"},{"key":"10.1016\/j.jhin.2021.07.013_bib5","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1001\/jamainternmed.2020.5664","article-title":"Asymptomatic and presymptomatic severe acute respiratory syndrome coronavirus 2 infection rates in a multistate sample of skilled nursing facilities","volume":"180","author":"White","year":"2020","journal-title":"JAMA Intern Med"},{"key":"10.1016\/j.jhin.2021.07.013_bib6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13756-020-00875-7","article-title":"Nosocomial transmission and outbreaks of coronavirus disease 2019: the need to protect both patients and healthcare workers","volume":"10","author":"Abbas","year":"2021","journal-title":"Antimicrob Resist Infect Control"},{"key":"10.1016\/j.jhin.2021.07.013_bib7","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.15585\/mmwr.mm6937a3","article-title":"Serial testing for SARS-CoV-2 and virus whole genome sequencing inform infection risk at two skilled nursing facilities with COVID-19 outbreaks \u2013 Minnesota, April\u2013June 2020","volume":"69","author":"Taylor","year":"2020","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"10.1016\/j.jhin.2021.07.013_bib8","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/S1473-3099(20)30527-2","article-title":"COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study","volume":"20","author":"Sikkema","year":"2020","journal-title":"Lancet Infect Dis"},{"key":"10.1016\/j.jhin.2021.07.013_bib9","doi-asserted-by":"crossref","first-page":"e727","DOI":"10.1093\/cid\/ciaa1433","article-title":"Whole-genome sequencing to track SARS-CoV-2 transmission in nosocomial outbreaks","volume":"72","author":"Lucey","year":"2021","journal-title":"Clin Infect Dis"},{"key":"10.1016\/j.jhin.2021.07.013_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2021.07.034","article-title":"Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals","author":"Lumley","year":"2021","journal-title":"J Infect"},{"key":"10.1016\/j.jhin.2021.07.013_bib11","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.65453.sa2","article-title":"Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission","author":"Ellingford","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.jhin.2021.07.013_bib12","doi-asserted-by":"crossref","DOI":"10.1093\/cid\/ciab281","article-title":"Viral sequencing to investigate sources of SARS-CoV-2 infection in US healthcare personnel","author":"Braun","year":"2021","journal-title":"Clin Infect Dis"},{"key":"10.1016\/j.jhin.2021.07.013_bib13","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/S1473-3099(07)70082-8","article-title":"The ORION statement: guidelines for transparent reporting of outbreak reports and intervention studies of nosocomial infection","volume":"7","author":"Stone","year":"2007","journal-title":"Lancet Infect Dis"},{"key":"10.1016\/j.jhin.2021.07.013_bib14","unstructured":"Swissnoso Prevention and control of healthcare-associated COVID-19 outbreaks. Available at: https:\/\/www.swissnoso.ch\/fileadmin\/swissnoso\/Dokumente\/5_Forschung_und_Entwicklung\/6_Aktuelle_Erreignisse\/200515_Prevention_and_control_of_healthcare-associated_COVID-19_outbreaks_V1.0_ENG.pdf (last accessed September 2021)."},{"key":"10.1016\/j.jhin.2021.07.013_bib15","doi-asserted-by":"crossref","first-page":"w20475","DOI":"10.4414\/smw.2021.20475","article-title":"Cohort profile: SARS-CoV-2\/COVID-19 hospitalised patients in Switzerland","volume":"151","author":"Thiabaud","year":"2021","journal-title":"Swiss Med Wkly"},{"key":"10.1016\/j.jhin.2021.07.013_bib16","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1503\/cmaj.050051","article-title":"A\u00a0global clinical measure of fitness and frailty in elderly people","volume":"173","author":"Rockwood","year":"2005","journal-title":"CMAJ"},{"key":"10.1016\/j.jhin.2021.07.013_bib17","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/jpen.1451","article-title":"Hypoalbuminemia: pathogenesis and clinical significance","volume":"43","author":"Soeters","year":"2019","journal-title":"J\u00a0Parenter Enteral Nutr"},{"key":"10.1016\/j.jhin.2021.07.013_bib18","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/0021-9681(87)90171-8","article-title":"A\u00a0new method of classifying prognostic comorbidity in longitudinal studies: development and validation","volume":"40","author":"Charlson","year":"1987","journal-title":"J\u00a0Chronic Dis"},{"key":"10.1016\/j.jhin.2021.07.013_bib19","doi-asserted-by":"crossref","first-page":"1926","DOI":"10.1111\/j.1532-5415.2008.01935.x","article-title":"A\u00a0manual of guidelines to score the modified cumulative illness rating scale and its validation in acute hospitalized elderly patients","volume":"56","author":"Salvi","year":"2008","journal-title":"J\u00a0Am Geriatr Soc"},{"key":"10.1016\/j.jhin.2021.07.013_bib20","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.jamda.2010.11.011","article-title":"Prospective comparison of 6 comorbidity indices as predictors of 1-year post-hospital discharge institutionalization, readmission, and mortality in elderly individuals","volume":"13","author":"Zekry","year":"2012","journal-title":"J\u00a0Am Med Dir Assoc"},{"key":"10.1016\/j.jhin.2021.07.013_bib21","doi-asserted-by":"crossref","first-page":"2000045","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","article-title":"Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR","volume":"25","author":"Corman","year":"2020","journal-title":"Eurosurveillance"},{"key":"10.1016\/j.jhin.2021.07.013_bib22","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: molecular evolutionary genetics analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol Biol Evol"},{"key":"10.1016\/j.jhin.2021.07.013_bib23","first-page":"678","article-title":"Estimation of the number of nucleotide substitutions when there are strong transition\u2013transversion and G+C-content biases","volume":"9","author":"Tamura","year":"1992","journal-title":"Mol Biol Evol"},{"key":"10.1016\/j.jhin.2021.07.013_bib24","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A\u00a0new look at the statistical model identification","volume":"19","author":"Akaike","year":"1974","journal-title":"IEEE Trans Automat Contr"},{"key":"10.1016\/j.jhin.2021.07.013_bib25","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/aje\/kwt133","article-title":"A\u00a0new framework and software to estimate time-varying reproduction numbers during epidemics","volume":"178","author":"Cori","year":"2013","journal-title":"Am J Epidemiol"},{"key":"10.1016\/j.jhin.2021.07.013_bib26","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003457","article-title":"Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data","volume":"10","author":"Jombart","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"Suppl. 11","key":"10.1016\/j.jhin.2021.07.013_bib27","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1186\/s12859-018-2330-z","article-title":"outbreaker2: a modular platform for outbreak reconstruction","volume":"19","author":"Campbell","year":"2018","journal-title":"BMC Bioinform"},{"key":"10.1016\/j.jhin.2021.07.013_bib28","doi-asserted-by":"crossref","first-page":"794","DOI":"10.7326\/M20-7567","article-title":"A\u00a0SARS-CoV-2 cluster in an acute care hospital","volume":"174","author":"Klompas","year":"2021","journal-title":"Ann Intern Med"},{"key":"10.1016\/j.jhin.2021.07.013_bib29","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.cell.2020.11.020","article-title":"Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity","volume":"184","author":"Volz","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.jhin.2021.07.013_bib30","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/S0140-6736(21)00257-9","article-title":"Genomic sequencing in pandemics","volume":"397","year":"2021","journal-title":"Lancet"},{"key":"10.1016\/j.jhin.2021.07.013_bib31","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/s12916-020-01665-z","article-title":"COVID-19: a retrospective cohort study with focus on the over-80s and hospital-onset disease","volume":"18","author":"Brill","year":"2020","journal-title":"BMC Med"},{"key":"10.1016\/j.jhin.2021.07.013_bib32","doi-asserted-by":"crossref","DOI":"10.1016\/j.jamda.2020.09.014","article-title":"Predictors of in-hospital mortality in older patients with COVID-19: the COVIDAge study","volume":"21","author":"Mendes","year":"2020","journal-title":"J\u00a0Am Med Dir Assoc"},{"key":"10.1016\/j.jhin.2021.07.013_bib33","first-page":"1","article-title":"Can long-term care facilities remain a coronavirus disease 2019 (COVID-19)-free bubble? An outbreak report","volume":"11","author":"Robalo Nunes","year":"2021","journal-title":"Infect Control Hosp Epidemiol"}],"container-title":["Journal of Hospital Infection"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S019567012100308X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S019567012100308X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T04:20:14Z","timestamp":1759292414000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S019567012100308X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11]]},"references-count":33,"alternative-id":["S019567012100308X"],"URL":"https:\/\/doi.org\/10.1016\/j.jhin.2021.07.013","relation":{},"ISSN":["0195-6701"],"issn-type":[{"value":"0195-6701","type":"print"}],"subject":[],"published":{"date-parts":[[2021,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction","name":"articletitle","label":"Article Title"},{"value":"Journal of Hospital Infection","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jhin.2021.07.013","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Authors. Published by Elsevier Ltd on behalf of The Healthcare Infection Society.","name":"copyright","label":"Copyright"}]}}