{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T17:57:20Z","timestamp":1783533440603,"version":"3.55.0"},"reference-count":41,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T00:00:00Z","timestamp":1648771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,4,1]],"date-time":"2022-04-01T00:00:00Z","timestamp":1648771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,2,7]],"date-time":"2022-02-07T00:00:00Z","timestamp":1644192000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005969","name":"Alma Mater Studiorum University of Bologna","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005969","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","ijidonline.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal of Infectious Diseases"],"published-print":{"date-parts":[[2022,4]]},"DOI":"10.1016\/j.ijid.2022.02.011","type":"journal-article","created":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T11:53:15Z","timestamp":1644407595000},"page":"233-240","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":27,"special_numbering":"C","title":["Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in patients colonized with Candida spp."],"prefix":"10.1016","volume":"117","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2431-8270","authenticated-orcid":false,"given":"Elisa","family":"Viciani","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3791-8635","authenticated-orcid":false,"given":"Paolo","family":"Gaibani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8131-974X","authenticated-orcid":false,"given":"Andrea","family":"Castagnetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6755-1937","authenticated-orcid":false,"given":"Andrea","family":"Liberatore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Bartoletti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierluigi","family":"Viale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiziana","family":"Lazzarotto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simone","family":"Ambretti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2815-3119","authenticated-orcid":false,"given":"Monica","family":"Cricca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ijid.2022.02.011_bib0001","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1890\/12-2010.1","article-title":"ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?","volume":"83","author":"Anderson","year":"2013","journal-title":"Ecol. Monogr."},{"issue":"4","key":"10.1016\/j.ijid.2022.02.011_bib0002","doi-asserted-by":"crossref","first-page":"211","DOI":"10.3390\/jof6040211","article-title":"COVID-19-Associated Candidiasis (CAC): An Underestimated Complication in the Absence of Immunological Predispositions?","volume":"6","author":"Arastehfar","year":"2020","journal-title":"J Fungi (Basel)"},{"key":"10.1016\/j.ijid.2022.02.011_bib0003","article-title":"Epidemiology of invasive pulmonary aspergillosis among COVID-19 intubated patients: a prospective study","author":"Bartoletti","year":"2020","journal-title":"Clin Infect Dis"},{"issue":"11","key":"10.1016\/j.ijid.2022.02.011_bib0004","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1007\/s00134-020-06219-8","article-title":"Bacterial and fungal superinfections in critically ill patients with COVID-19","volume":"46","author":"Bassetti","year":"2020","journal-title":"Intensive Care Med"},{"key":"10.1016\/j.ijid.2022.02.011_bib0005","unstructured":"Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodr\u00edguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann"},{"issue":"1","key":"10.1016\/j.ijid.2022.02.011_bib0006","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.02136-20","article-title":"COVID-19-Associated Invasive Aspergillosis: Data from the UK National Mycology Reference Laboratory","volume":"59","author":"Borman","year":"2020","journal-title":"J Clin Microbiol"},{"issue":"1","key":"10.1016\/j.ijid.2022.02.011_bib0007","doi-asserted-by":"crossref","first-page":"185","DOI":"10.3390\/microorganisms9010185","article-title":"Detection of SARS-CoV-2 and Other Infectious Agents in Lower Respiratory Tract Samples Belonging to Patients Admitted to Intensive Care Units of a Tertiary-Care Hospital, Located in an Epidemic Area, during the Italian Lockdown","volume":"9","author":"Calderaro","year":"2021","journal-title":"Microorganisms"},{"key":"10.1016\/j.ijid.2022.02.011_bib0008","first-page":"1","article-title":"State-of-the-art review of secondary pulmonary infections in patients with COVID-19 pneumonia","author":"Chong","year":"2021","journal-title":"Infection"},{"key":"10.1016\/j.ijid.2022.02.011_bib0009","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.ijid.2022.02.011_bib0010","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.mib.2021.04.006","article-title":"Invasive pulmonary aspergillosis associated with viral pneumonitis","volume":"62","author":"Dewi","year":"2021","journal-title":"Curr Opin Microbiol"},{"issue":"7","key":"10.1016\/j.ijid.2022.02.011_bib0011","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004923","article-title":"The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease","volume":"11","author":"Dickson","year":"2015","journal-title":"PLoS Pathog"},{"issue":"10","key":"10.1016\/j.ijid.2022.02.011_bib0012","doi-asserted-by":"crossref","first-page":"L1047","DOI":"10.1152\/ajplung.00279.2015","article-title":"Homeostasis and its disruption in the lung microbiome","volume":"309","author":"Dickson","year":"2015","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"10.1016\/j.ijid.2022.02.011_bib0013","doi-asserted-by":"crossref","DOI":"10.1016\/j.ebiom.2020.102995","article-title":"Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome","volume":"60","author":"Fern\u00e1ndez-Barat","year":"2020","journal-title":"EBioMedicine"},{"issue":"3","key":"10.1016\/j.ijid.2022.02.011_bib0014","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1007\/s00134-020-06338-2","article-title":"Respiratory microbiome in mechanically ventilated patients: a narrative review","volume":"47","author":"Fromentin","year":"2021","journal-title":"Intensive Care Med"},{"issue":"1","key":"10.1016\/j.ijid.2022.02.011_bib0015","doi-asserted-by":"crossref","first-page":"10103","DOI":"10.1038\/s41598-021-89516-6","article-title":"The lower respiratory tract microbiome of critically ill patients with COVID-19","volume":"11","author":"Gaibani","year":"2021","journal-title":"Sci Rep"},{"key":"10.1016\/j.ijid.2022.02.011_bib0016","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/978-1-4939-8728-3_8","article-title":"16S rRNA Gene Analysis with QIIME2","volume":"1849","author":"Hall","year":"2018","journal-title":"Methods Mol Biol"},{"issue":"10","key":"10.1016\/j.ijid.2022.02.011_bib0017","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nri.2017.55","article-title":"Fungal dysbiosis: immunity and interactions at mucosal barriers","volume":"17","author":"Iliev","year":"2017","journal-title":"Nat Rev Immunol"},{"key":"10.1016\/j.ijid.2022.02.011_bib0018","article-title":"Defining and managing COVID-19-associated pulmonary aspergillosis: the 2020 ECMM\/ISHAM consensus criteria for research and clinical guidance [published online ahead of print, 2020 Dec 14]","author":"Koehler","year":"2020","journal-title":"Lancet Infect Dis"},{"issue":"10","key":"10.1016\/j.ijid.2022.02.011_bib0019","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1016\/j.cmi.2019.04.024","article-title":"Morbidity and mortality of candidaemia in Europe: an epidemiologic meta-analysis","volume":"25","author":"Koehler","year":"2019","journal-title":"Clin Microbiol Infect"},{"issue":"5","key":"10.1016\/j.ijid.2022.02.011_bib0020","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0155033","article-title":"Zollner-Schwetz I. Characterisation of Candida within the Mycobiome\/Microbiome of the Lower Respiratory Tract of ICU Patients","volume":"11","author":"Krause","year":"2016","journal-title":"PLoS One"},{"issue":"2","key":"10.1016\/j.ijid.2022.02.011_bib0021","doi-asserted-by":"crossref","first-page":"70","DOI":"10.3390\/pathogens8020070","article-title":"Fungal-Bacterial Interactions in Health and Disease","volume":"8","author":"Kr\u00fcger","year":"2019","journal-title":"Pathogens"},{"issue":"15","key":"10.1016\/j.ijid.2022.02.011_bib0022","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1056\/NEJMra1315399","article-title":"Invasive Candidiasis","volume":"373","author":"Kullberg","year":"2015","journal-title":"N Engl J Med"},{"issue":"2","key":"10.1016\/j.ijid.2022.02.011_bib0023","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.jinf.2020.05.046","article-title":"Co-infections in people with COVID-19: a systematic review and meta-analysis","volume":"81","author":"Lansbury","year":"2020","journal-title":"J Infect"},{"issue":"3","key":"10.1016\/j.ijid.2022.02.011_bib0024","doi-asserted-by":"crossref","first-page":"492","DOI":"10.3390\/microorganisms9030492","article-title":"The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study","volume":"9","author":"Linnane","year":"2021","journal-title":"Microorganisms"},{"issue":"2","key":"10.1016\/j.ijid.2022.02.011_bib0025","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1111\/myc.13213","article-title":"COVID-19 Study Group. Invasive pulmonary aspergillosis in the COVID-19 era: An expected new entity","volume":"64","author":"Machado","year":"2021","journal-title":"Mycoses"},{"issue":"5","key":"10.1016\/j.ijid.2022.02.011_bib0026","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1128\/JCM.00376-11","article-title":"Brazilian SCOPE Study Group. Nosocomial bloodstream infections in Brazilian hospitals: analysis of 2,563 cases from a prospective nationwide surveillance study","volume":"49","author":"Marra","year":"2011","journal-title":"J Clin Microbiol"},{"key":"10.1016\/j.ijid.2022.02.011_bib0027","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.ijid.2022.02.011_bib0028","unstructured":"Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., O'Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H. and Wagner, H. (2014) Vegan: Community Ecology Package. R Package Version 2.2-0. http:\/\/CRAN.Rproject.org\/package=vegan"},{"issue":"10","key":"10.1016\/j.ijid.2022.02.011_bib0029","doi-asserted-by":"crossref","first-page":"1409","DOI":"10.1007\/s10482-019-01271-x","article-title":"Candida spp. and phagocytosis: multiple evasion mechanisms","volume":"112","author":"Oliver","year":"2019","journal-title":"Antonie Van Leeuwenhoek"},{"issue":"3","key":"10.1016\/j.ijid.2022.02.011_bib0030","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1053\/jhin.2000.0897","article-title":"Candida colonization in mechanically ventilated patients","volume":"47","author":"Palabiyiko\u011flu","year":"2001","journal-title":"J Hosp Infect"},{"issue":"6","key":"10.1016\/j.ijid.2022.02.011_bib0031","doi-asserted-by":"crossref","first-page":"7745","DOI":"10.18632\/aging.202742","article-title":"Fungal co-infection in COVID-19 patients: evidence from a systematic review and meta-analysis","volume":"13","author":"Peng","year":"2021","journal-title":"Aging (Albany NY)"},{"key":"10.1016\/j.ijid.2022.02.011_bib0032","article-title":"COVID-19 Associated Pulmonary Aspergillosis in Mechanically Ventilated Patients","author":"Permpalung","year":"2021","journal-title":"Clin Infect Dis"},{"issue":"3","key":"10.1016\/j.ijid.2022.02.011_bib0033","doi-asserted-by":"crossref","first-page":"163","DOI":"10.3390\/jof6030163","article-title":"Pan-Echinocandin-Resistant Candida glabrata Bloodstream Infection Complicating COVID-19: A Fatal Case Report","volume":"6","author":"Posteraro","year":"2020","journal-title":"J Fungi (Basel)"},{"key":"10.1016\/j.ijid.2022.02.011_bib0034","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: A versatile open source tool for metagenomics","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"issue":"6","key":"10.1016\/j.ijid.2022.02.011_bib0035","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic Biomarker Discovery and Explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biology"},{"key":"10.1016\/j.ijid.2022.02.011_bib0036","doi-asserted-by":"crossref","DOI":"10.1155\/2021\/6670798","article-title":"The Role of Bacterial and Fungal Human Respiratory Microbiota in COVID-19 Patients","volume":"2021","author":"Soltani","year":"2021","journal-title":"Biomed Res Int"},{"issue":"4","key":"10.1016\/j.ijid.2022.02.011_bib0037","doi-asserted-by":"crossref","first-page":"279","DOI":"10.3390\/jof6040279","article-title":"Fungal Infections Complicating COVID-19: With the Rain Comes the Spores","volume":"6","author":"Talento","year":"2020","journal-title":"J Fungi (Basel)"},{"issue":"1","key":"10.1016\/j.ijid.2022.02.011_bib0038","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.cmi.2015.09.002","article-title":"Impact of Candida spp. isolation in the respiratory tract in patients with intensive care unit-acquired pneumonia","volume":"22","author":"Terraneo","year":"2016","journal-title":"Clin Microbiol Infect"},{"key":"10.1016\/j.ijid.2022.02.011_bib0039","series-title":"PCR Protocols. A Guide to Methods and Applications","first-page":"315","article-title":"Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics","author":"White","year":"1990"},{"key":"10.1016\/j.ijid.2022.02.011_bib0040","series-title":"ggplot2: elegant graphics for data analysis","author":"Wickham","year":"2016"},{"issue":"7","key":"10.1016\/j.ijid.2022.02.011_bib0041","doi-asserted-by":"crossref","DOI":"10.1136\/bmjopen-2019-036452","article-title":"Risk of invasive candidiasis with prolonged duration of ICU stay: a systematic review and meta-analysis","volume":"10","author":"Zhang","year":"2020","journal-title":"BMJ Open"}],"container-title":["International Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971222000881?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1201971222000881?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T08:07:41Z","timestamp":1761120461000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1201971222000881"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4]]},"references-count":41,"alternative-id":["S1201971222000881"],"URL":"https:\/\/doi.org\/10.1016\/j.ijid.2022.02.011","relation":{},"ISSN":["1201-9712"],"issn-type":[{"value":"1201-9712","type":"print"}],"subject":[],"published":{"date-parts":[[2022,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in patients colonized with Candida spp.","name":"articletitle","label":"Article Title"},{"value":"International Journal of Infectious Diseases","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijid.2022.02.011","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases.","name":"copyright","label":"Copyright"}]}}