{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T08:46:38Z","timestamp":1770972398740,"version":"3.50.1"},"reference-count":25,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,8,31]],"date-time":"2022-08-31T00:00:00Z","timestamp":1661904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013015","name":"Cedars-Sinai Medical Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p><jats:italic>Candida auris<\/jats:italic> continues to be a global threat for infection and transmission in hospitals and long-term care facilities. The emergence of SARS-CoV-2 has rerouted attention and resources away from this silent pandemic to the frontlines of the ongoing COVID-19 disease. Cases of <jats:italic>C. auris<\/jats:italic> continue to rise, and clinical laboratories need a contingency plan to prevent a possible outbreak amid the COVID-19 pandemic. Here, we introduce a two-tier <jats:italic>Candida auris<\/jats:italic> surveillance program that includes, first, a rapid qualitative rt-PCR for the identification of high-risk patients and, second, a method to analyze the isolated <jats:italic>C. auris<\/jats:italic> for strain typing using the Fourier-Transform Infrared spectroscopy. We have performed this two-tier surveillance for over 700 at-risk patients being admitted into our hospital and have identified 28 positive specimens (4%) over a 1-year period. Strain typing analysis by the IR spectrum acquisition typing method, supplemented by whole genome sequencing, has shown grouping of two significant clusters. The majority of our isolates belong to circulating African lineage associated with <jats:italic>C. auris<\/jats:italic> Clade III and an isolated strain grouping differently belonging to South Asian lineage <jats:italic>C. auris<\/jats:italic> Clade I. Low numbers of genomic variation point to local and ongoing transmission within the Los Angeles area not specifically within the hospital setting. Collectively, clinical laboratories having the ability to rapidly screen high-risk patients for <jats:italic>C. auris<\/jats:italic> and to participate in outbreak investigations by offering strain typing will greatly assist in the control of <jats:italic>C. auris<\/jats:italic> transmission within the hospital setting.<\/jats:p>","DOI":"10.3389\/fcimb.2022.887754","type":"journal-article","created":{"date-parts":[[2022,8,31]],"date-time":"2022-08-31T07:18:14Z","timestamp":1661930294000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":16,"title":["Surveillance diagnostic algorithm using real-time PCR assay and strain typing method development to assist with the control of C. auris amid COVID-19 pandemic"],"prefix":"10.3389","volume":"12","author":[{"given":"Deisy A.","family":"Contreras","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margie A.","family":"Morgan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,8,31]]},"reference":[{"key":"B1","volume-title":"Antibiotic resistance threats in the united states","year":"2019"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1016\/S1473-3099(18)30597-8","article-title":"Multiple introductions and subsequent transmission of multidrug-resistant candida auris in the USA: a molecular epidemiological survey","volume":"18","author":"Chow","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"B3","doi-asserted-by":"publisher","first-page":"e03364","DOI":"10.1128\/mBio.03364-19","article-title":"Tracing the evolutionary history and global expansion of candida auris using population genomic analyses","volume":"11","author":"Chow","year":"2020","journal-title":"mBio."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2020.00351","article-title":"Nine things genomics can tell us about Candida auris","volume":"11","author":"Chybowska","year":"2020","journal-title":"Front. Gen."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9040853","article-title":"Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy","author":"Cordovana","year":"2021","journal-title":"Microorganisms"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.692975","article-title":"Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy","author":"Deidda","year":"2021","journal-title":"Front Microbiol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1008921","article-title":"Candida auris: Epidemiology, biology, antifungal resistance, and virulence","volume":"16","author":"Du","year":"2020","journal-title":"PloS Pathog."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1093\/mmy\/myy054","article-title":"Candida auris: The recent emergence of a multidrug-resistant fungal pathogen","volume":"57","author":"Forsberg","year":"2019","journal-title":"Med. Mycol."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1007\/s42770-022-00774-6","article-title":"Fourier transform infrared spectroscopy as a new tool for surveillance in local stewardship antimicrobial program: a retrospective study in a nosocomial Acinetobacter baumannii outbreak","author":"Guerrero-Lozano","year":"2020","journal-title":"Brazil J. Microbiol"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1017\/ice.2022.109","article-title":"Analysis of four carbapenem-resistant Acinetobacter baumannii outbreaks using Fourier-transform infrared spectroscopy","author":"Hadas","year":"2022","journal-title":"Infection Control Hosp Epidemiol"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.13709","article-title":"Evaluation of the IR biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management","author":"Hu","year":"2020","journal-title":"Microb. 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Immunol."},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02055-18","article-title":"Candida auris isolates of the southern Asian and south African lineages exhibit different phenotypic and antifungal susceptibility profiles in vitro","volume":"57","author":"Szekely","year":"2019","journal-title":"J. Clin. Micro."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3390\/jof6030146","article-title":"Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris","volume":"6","author":"Vatanshenassan","year":"2020","journal-title":"J. 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