{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T17:38:09Z","timestamp":1792690689770,"version":"4.5.0"},"reference-count":42,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,4,19]],"date-time":"2024-04-19T00:00:00Z","timestamp":1713484800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003970","name":"Isfahan University of Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003970","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"\n Introduction<\/jats:title>\n \n Although the existence of\n Candida<\/jats:italic>\n species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of\n Candida<\/jats:italic>\n colonization in immunocompromised or COVID-19 patients. The emergence of\n Candida auris<\/jats:italic>\n as an emerging pathogen further emphasizes the importance of monitoring yeast infection\/colonization, particularly in COVID-19 patients.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n In this study, respiratory samples mainly from COVID-19 patients, primarily those suspected of having a fungal infection, were cultured on Sabouraud dextrose agar plates and the yeast colonies were identified using a two-step multiplex PCR method. The samples suspected of\n C. auris<\/jats:italic>\n underwent specific nested PCR followed by sequence analysis.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n A total of 199 respiratory samples were collected from 73 women and 126 men, ranging in age from 1.6 to 88 years. Among the patients, 141 had COVID-19, 32 had cancer, 5 were hospitalized in ICU, 2 had chronic obstructive pulmonary disease)COPD(, and others were patients with combination diseases. From these samples, a total of 334 yeast strains were identified.\n C. albicans<\/jats:italic>\n (n=132, 39.52%) was the most common species, followed by\n C. tropicalis<\/jats:italic>\n (n=67, 20%),\n C. glabrata<\/jats:italic>\n (n=56, 16.76%),\n C. krusei<\/jats:italic>\n (n=18, 5.4%),\n C. parapsilosis<\/jats:italic>\n (n=17, 5.08%),\n Saccharomyces cerevisiae<\/jats:italic>\n (n=10, 3%),\n C. kefyr<\/jats:italic>\n (n=9, 2.6%),\n C. dubliniensis<\/jats:italic>\n (n=7, 2.1%),\n C. lusitaniae<\/jats:italic>\n (n=5, 1.5%),\n C. auris<\/jats:italic>\n (n=3, 0.9%),\n C. guilliermondii<\/jats:italic>\n (n=2, 0.6%),\n C. rugosa<\/jats:italic>\n (n=1, 0.3%),\n C. intermedia<\/jats:italic>\n (n=1, 0.3%), and\n Trichosporon<\/jats:italic>\n spp. (n=1, 0.3%).\n C. auris<\/jats:italic>\n was detected in a patient in ICU and two COVID-19 patients. While its presence was confirmed through sequence analysis, our extensive efforts to isolate\n C. auris<\/jats:italic>\n were unsuccessful.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n While\n C. albicans<\/jats:italic>\n colonization remains prevalent, our study found no evidence of\n Candida<\/jats:italic>\n lung infection. Since the role of\n Candida<\/jats:italic>\n colonization in airway secretions remains ambiguous due to limited research, further studies are imperative to shed light on this matter.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2024.1295841","type":"journal-article","created":{"date-parts":[[2024,4,19]],"date-time":"2024-04-19T00:34:50Z","timestamp":1713486890000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris"],"prefix":"10.3389","volume":"14","author":[{"given":"Faezeh","family":"Rouhi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajedeh","family":"Soltani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Somayeh","family":"Sadeghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elahe","family":"Nasri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahnaz","family":"Hosseini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Safiyeh","family":"Ghafel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shima","family":"Aboutalebian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamed","family":"Fakhim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hossein","family":"Mirhendi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,4,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1111\/myc.12886","article-title":"Candida auris otomycosis in Iran and review of recent literature","volume":"62","author":"Abastabar","year":"2019","journal-title":"Mycoses."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.644060","article-title":"Direct detection and identification of the most common bacteria and fungi causing otitis externa by a stepwise multiplex PCR","volume":"11","author":"Aboutalebian","year":"2021","journal-title":"Front. Cell. infection Microbiol."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1002\/jcla.24370","article-title":"Multiplex size marker (YEAST PLEX) for rapid and accurate identification of pathogenic yeasts","volume":"36","author":"Aboutalebian","year":"2022","journal-title":"J. Clin. Lab. Analysis."},{"key":"B4","doi-asserted-by":"publisher","first-page":"157","DOI":"10.3390\/pathogens10020157","article-title":"First Candida auris outbreak during a COVID-19 pandemic in a tertiary-care center in Lebanon","volume":"10","author":"Allaw","year":"2021","journal-title":"Pathogens."},{"key":"B5","doi-asserted-by":"publisher","first-page":"100937","DOI":"10.1016\/j.resmer.2022.100937","article-title":"Fungal colonization and infections in patients with COVID-19 in intensive care units: A real-life experience at a tertiary-care hospital","volume":"82","author":"Avkan-O\u011fuz","year":"2022","journal-title":"Respir. Med. Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1378\/chest.129.1.110","article-title":"Candida colonization of the respiratory tract and subsequent pseudomonas ventilator-associated pneumonia","volume":"129","author":"Azoulay","year":"2006","journal-title":"Chest."},{"key":"B7","first-page":"52","article-title":"Candida in pulmonary tuberculosis","volume":"51","author":"Baradkar","year":"2009","journal-title":"Bombay Hosp. J."},{"key":"B8","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1056\/NEJM196007142630204","article-title":"The significance of candida albicans in human sputum","volume":"263","author":"Baum","year":"1960","journal-title":"New Engl. J. Med."},{"key":"B9","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1097\/INF.0b013e31806166d7","article-title":"Candida isolated from vaginal mucosa of mothers and oral mucosa of neonates: occurrence and biotypes concordance","volume":"26","author":"Caramalac","year":"2007","journal-title":"Pediatr. Infect. Dis. J."},{"key":"B10","doi-asserted-by":"publisher","first-page":"2694","DOI":"10.3201\/eid2611.203504","article-title":"Multidrug-resistant Candida auris infections in critically ill coronavirus disease patients, India, April\u2013July 2020","volume":"26","author":"Chowdhary","year":"2020","journal-title":"Emerging Infect. diseases."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1521","DOI":"10.3390\/microorganisms10081521","article-title":"First cases of candida auris in a referral intensive care unit in piedmont region, Italy","volume":"10","author":"Corcione","year":"2022","journal-title":"Microorganisms."},{"key":"B12","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/JCM.00326-20","article-title":"A selective medium for isolation and detection of Candida auris, an emerging pathogen","volume":"59","author":"Das","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.jcrc.2008.01.005","article-title":"The clinical significance of Candida colonization of respiratory tract secretions in critically ill patients","volume":"23","author":"Delisle","year":"2008","journal-title":"J. Crit. Care"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.1007\/s00134-014-3364-y","article-title":"Candida colonization of respiratory tract: to treat or not to treat, will we ever get an answer","volume":"40","author":"De Pascale","year":"2014","journal-title":"Intensive Care Med."},{"key":"B15","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1164\/ajrccm.156.2.9612023","article-title":"Significance of the isolation of Candida species from respiratory samples in critically ill, non-neutropenic patients: an immediate postmortem histologic study","volume":"156","author":"El-Ebiary","year":"1997","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2023.1078970","article-title":"Case report: COVID-19-associated mucormycosis co-infection with Lomentospora prolificans: The first case and review on multiple fungal co-infections during COVID-19 pandemic","volume":"10","author":"Erami","year":"2023","journal-title":"Front. Med."},{"key":"B17","doi-asserted-by":"publisher","first-page":"105520","DOI":"10.1016\/j.micpath.2022.105520","article-title":"Clinical impact of Candida respiratory tract colonization and acute lung infections in critically ill patients with COVID-19 pneumonia","volume":"166","author":"Erami","year":"2022","journal-title":"Microbial Pathogenesis."},{"key":"B18","doi-asserted-by":"publisher","first-page":"463","DOI":"10.3390\/pathogens12030463","article-title":"COVID-19 is a confounder of increased candida airway colonisation","volume":"12","author":"Froidefond","year":"2023","journal-title":"Pathogens."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2020.598037","article-title":"Candida colonization in the respiratory tract: what is the significance","volume":"7","author":"Liu","year":"2021","journal-title":"Front. Med."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2023.1148320","article-title":"Molecular and microscopy detection of Pneumocystis jirovecii in hospitalized patients during the COVID-19 pandemic","volume":"10","author":"Matouri","year":"2023","journal-title":"Front. Med."},{"key":"B21","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s15010-014-0668-3","article-title":"Epidemiology and outcome of systemic infections due to Saprochaete capitata: case report and review of the literature","volume":"43","author":"Mazzocato","year":"2015","journal-title":"Infection."},{"key":"B22","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1111\/myc.13396","article-title":"South Asian (Clade I) Candida auris meningitis in a paediatric patient in Iran with a review of the literature","volume":"65","author":"Mirhendi","year":"2022","journal-title":"Mycoses."},{"key":"B23","doi-asserted-by":"publisher","first-page":"56","DOI":"10.3109\/13693780802716532","article-title":"Persistence of Candida species in the respiratory tract of cystic fibrosis patients","volume":"48","author":"Muthig","year":"2010","journal-title":"Med. Mycology."},{"key":"B24","volume-title":"Epidemiological alert: Candida auris outbreaks in health care services","year":"2016"},{"key":"B25","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/cid\/civ933","article-title":"Clinical practice guideline for the management of candidiasis: 2016 update by the Infectious Diseases Society of America","volume":"62","author":"Pappas","year":"2016","journal-title":"Clin. Infect. Diseases."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.12659\/MSM.939088","article-title":"Editorial: the world health organization (WHO) fungal priority pathogens list in response to emerging fungal pathogens during the COVID-19 pandemic","volume":"28","author":"Parums","year":"2022","journal-title":"Med. Sci. Monit."},{"key":"B27","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1097\/CPM.0000000000000279","article-title":"Respiratory tract colonization by candida species portends worse outcomes in immunocompromised patients","volume":"25","author":"Pendleton","year":"2018","journal-title":"Clin. Pulm Med."},{"key":"B28","doi-asserted-by":"publisher","first-page":"ftx029","DOI":"10.1093\/femspd\/ftx029","article-title":"The significance of Candida in the human respiratory tract: our evolving understanding","volume":"75","author":"Pendleton","year":"2017","journal-title":"Pathog. Dis."},{"key":"B29","doi-asserted-by":"publisher","first-page":"422","DOI":"10.3201\/eid2902.221523","article-title":"Candida auris discovery through community wastewater surveillance during healthcare outbreak, Nevada, USA, 2022","volume":"29","author":"Rossi","year":"2023","journal-title":"Emerging Infect. Diseases."},{"key":"B30","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1007\/s11046-021-00605-6","article-title":"A chronic autochthonous fifth clade case of Candida auris otomycosis in Iran","volume":"187","author":"Safari","year":"2022","journal-title":"Mycopathologia."},{"key":"B31","doi-asserted-by":"publisher","first-page":"34","DOI":"10.18502\/cmm.7.2.7034","article-title":"Differentiation of Candida albicans complex species isolated from invasive and non-invasive infections using HWP1 gene size polymorphism","volume":"7","author":"Salehipour","year":"2021","journal-title":"Curr. Med. Mycol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1590\/S1516-89132012000200020","article-title":"Rapid yeast DNA extraction by boiling and freeze-thawing without using chemical reagents and DNA purification","volume":"55","author":"Silva","year":"2012","journal-title":"Braz. Arch. Biol. technology."},{"key":"B33","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/s11908-019-0675-8","article-title":"The epidemiology and prevention of candida auris","volume":"21","author":"Snyder","year":"2019","journal-title":"Curr. Infect. Dis. Rep."},{"key":"B34","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1093\/mmy\/myv075","article-title":"Emergence of Magnusiomyces capitatus infections in Western Nepal","volume":"54","author":"Subramanya Supram","year":"2015","journal-title":"Sabouraudia."},{"key":"B35","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1017\/S0950268817002643","article-title":"Blastoschizomyces capitatus pulmonary infections in immunocompetent patients: case report, case series and literature review","volume":"146","author":"Tanabe","year":"2018","journal-title":"Epidemiol. Infection."},{"key":"B36","doi-asserted-by":"publisher","first-page":"94.e1","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. Infection."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.1006375","article-title":"Molecular identification, antifungal susceptibility, and resistance mechanisms of pathogenic yeasts from the China antifungal resistance surveillance trial (CARST-fungi) study","volume":"13","author":"Wang","year":"2022","journal-title":"Front. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1016\/B978-0-12-372180-8.50042-1","article-title":"Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics","volume":"18","author":"White","year":"1990","journal-title":"PCR protocols: guide to Methods applications."},{"key":"B39","doi-asserted-by":"publisher","first-page":"4737321","DOI":"10.1155\/2016\/4737321","article-title":"Candida glabrata pneumonia in a patient with chronic obstructive pulmonary disease","volume":"2016","author":"Yazici","year":"2016","journal-title":"Case Rep. Infect. Diseases."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.988734","article-title":"The research progress in the interaction between Candida albicans and cancers","volume":"13","author":"Yu","year":"2022","journal-title":"Front. Microbiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1016\/j.funbio.2011.04.007","article-title":"Dishwashers\u2013a man-made ecological niche accommodating human opportunistic fungal pathogens","volume":"115","author":"Zalar","year":"2011","journal-title":"Fungal Biol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1080\/21501203.2021.2000059","article-title":"Invasive infections due to Magnusiomyces capitatus: case report and review of its prevalence in China","volume":"13","author":"Zhu","year":"2022","journal-title":"Mycology."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1295841\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,19]],"date-time":"2024-04-19T00:34:54Z","timestamp":1713486894000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2024.1295841\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,19]]},"references-count":42,"alternative-id":["10.3389\/fcimb.2024.1295841"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2024.1295841","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,19]]},"article-number":"1295841"}}