{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T23:46:57Z","timestamp":1790725617263,"version":"4.1.0"},"reference-count":24,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2024,10,26]],"date-time":"2024-10-26T00:00:00Z","timestamp":1729900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Next Generation EU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases","award":["PE00000007, INF-ACT"],"award-info":[{"award-number":["PE00000007, INF-ACT"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>In 2019, Candida auris became the first fungal pathogen included in the list of the urgent antimicrobial threats by the Centers for Disease Control (CDC). Short tandem repeat (STR) analysis and whole-genome sequencing (WGS) are considered the gold standard, and can be complemented by other molecular methods, for the genomic surveillance and clade classification of this multidrug-resistant yeast. However, these methods can be expensive and require time and expertise that are not always available. The long turnaround time is especially not compatible with the speed needed to manage clonal transmission in healthcare settings. Fourier transform infrared (FTIR) spectroscopy, a biochemical fingerprint approach, has been applied in this study to a set of 74 C. auris isolates belonging to the five clades of C. auris (I-V) in combination with an artificial neural network (ANN) algorithm to create and validate \u201cCLADE-FINDER\u201d, a tool for C. auris clade determination. The CLADE-FINDER classifier allowed us to discriminate the four primary C. auris clades (I-IV) with a correct classification for 96% of the samples in the validation set. This newly developed genotyping scheme can be reasonably applied for the effective epidemiological monitoring and management of C. auris cases in real time.<\/jats:p>","DOI":"10.3390\/microorganisms12112153","type":"journal-article","created":{"date-parts":[[2024,10,28]],"date-time":"2024-10-28T05:07:22Z","timestamp":1730092042000},"page":"2153","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["\u201cCLADE-FINDER\u201d: Candida auris Lineage Analysis Determination by Fourier Transform Infrared Spectroscopy and Artificial Neural Networks"],"prefix":"10.3390","volume":"12","author":[{"given":"Carlotta","family":"Magr\u00ec","sequence":"first","affiliation":[{"name":"Dipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario \u201cA. Gemelli\u201d IRCCS, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4757-7256","authenticated-orcid":false,"given":"Elena","family":"De Carolis","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario \u201cA. Gemelli\u201d IRCCS, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vittorio","family":"Ivagnes","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze di Laboratorio ed Ematologiche, Fondazione Policlinico Universitario \u201cA. Gemelli\u201d IRCCS, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5863-5805","authenticated-orcid":false,"given":"Vincenzo","family":"Di Pilato","sequence":"additional","affiliation":[{"name":"Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy"},{"name":"Microbiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6734-361X","authenticated-orcid":false,"given":"Bram","family":"Spruijtenburg","sequence":"additional","affiliation":[{"name":"Radboudumc-CWZ Center of Expertise for Mycology, 6500 Nijmegen, The Netherlands"},{"name":"Canisius-Wilhelmina Hospital (CWZ)\/Dicoon, 6532 Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Marchese","sequence":"additional","affiliation":[{"name":"Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy"},{"name":"Microbiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0226-024X","authenticated-orcid":false,"given":"Eelco F. 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Gemelli\u201d IRCCS, 00168 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,10,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/j.1348-0421.2008.00083.x","article-title":"Candida auris Sp. Nov., a Novel Ascomycetous Yeast Isolated from the External Ear Canal of an Inpatient in a Japanese Hospital","volume":"53","author":"Satoh","year":"2009","journal-title":"Microbiol. Immunol."},{"key":"ref_2","unstructured":"(2024, September 30). Increasing Threat of Spread of Antimicrobial-Resistant Fungus in Healthcare Facilities. CDC Online Newsroom. 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