{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T03:20:57Z","timestamp":1784604057070,"version":"3.55.0"},"reference-count":31,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases","award":["PE00000007"],"award-info":[{"award-number":["PE00000007"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Recently Candida auris has emerged as a multi-resistant fungal pathogen, with a significant clinical impact, and is able to persist for a long time on human skin and hospital environments. It is a critical issue on the WHO fungal priority list and therefore it is fundamental to reinforce hospital surveillance protocols to limit nosocomial outbreaks. The purpose of this study was to apply Fourier transform infrared spectroscopy (FT-IR) to investigate the phylogenetic relationships among isolated strains from a C. auris outbreak at the University Intensive Care Unit of a Tertiary University hospital in Turin (Italy). To calculate a clustering cut-off, intra- and inter-isolate, distance values were analysed. The data showed the presence of a major Alfa cluster and a minor Beta cluster with a defined C. auris clustering cut-off. The results were validated by an external C. auris strain and Principal Component and Linear Discriminant Analyses. The application of FT-IR technology allowed to obtain important information about the phylogenetic relationships between the analysed strains, defining for the first time a \u201cnot WGS-based\u201d clustering cut-off with a statistical\u2013mathematical approach. FT-IR could represent a valid alternative to molecular methods for the rapid and cost-saving typing of C. auris strains with important clinical implications.<\/jats:p>","DOI":"10.3390\/microorganisms12071312","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T08:57:50Z","timestamp":1719478670000},"page":"1312","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Fourier Transform Infrared Spectroscopy Application for Candida auris Outbreak Typing in a Referral Intensive Care Unit: Phylogenetic Analysis and Clustering Cut-Off Definition"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8101-4196","authenticated-orcid":false,"given":"Antonio","family":"Curtoni","sequence":"first","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Microbiology and Virology Unit, Department of Laboratory Medicine, University Hospital Citt\u00e0 della Salute e della Scienza di Torino, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Pastrone","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Cordovana","sequence":"additional","affiliation":[{"name":"Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1979-3229","authenticated-orcid":false,"given":"Alessandro","family":"Bondi","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Microbiology and Virology Unit, Department of Laboratory Medicine, University Hospital Citt\u00e0 della Salute e della Scienza di Torino, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6800-5522","authenticated-orcid":false,"given":"Giorgia","family":"Piccinini","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"},{"name":"PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mattia","family":"Genco","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6337-5729","authenticated-orcid":false,"given":"Paolo","family":"Bottino","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlotta","family":"Polizzi","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8701-8486","authenticated-orcid":false,"given":"Lorenza","family":"Cavallo","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2949-4556","authenticated-orcid":false,"given":"Narcisa","family":"Mandras","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Corcione","sequence":"additional","affiliation":[{"name":"Infectious Diseases, Department of Medical Sciences, University of Turin, 10126 Turin, Italy"},{"name":"School of Medicine, Tufts University, Boston, MA 02111, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9341-965X","authenticated-orcid":false,"given":"Giorgia","family":"Montrucchio","sequence":"additional","affiliation":[{"name":"Department of Surgical Sciences, University of Turin, 10126 Turin, Italy"},{"name":"Intensive Care and Emergency, Department of Anaesthesia, University Hospital Citt\u00e0 della Salute e della Scienza di Torino, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7059-0622","authenticated-orcid":false,"given":"Luca","family":"Brazzi","sequence":"additional","affiliation":[{"name":"Department of Surgical Sciences, University of Turin, 10126 Turin, Italy"},{"name":"Intensive Care and Emergency, Department of Anaesthesia, University Hospital Citt\u00e0 della Salute e della Scienza di Torino, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6549-4553","authenticated-orcid":false,"given":"Cristina","family":"Costa","sequence":"additional","affiliation":[{"name":"Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Microbiology and Virology Unit, Department of Laboratory Medicine, University Hospital Citt\u00e0 della Salute e della Scienza di Torino, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,27]]},"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","doi-asserted-by":"crossref","unstructured":"Vatanshenassan, M., Boekhout, T., Mauder, N., Robert, V., Maier, T., Meis, J.F., Berman, J., Then, E., Kostrzewa, M., and Hagen, F. (2020). Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida Auris. J. Fungi, 6.","DOI":"10.3390\/jof6030146"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Du, H., Bing, J., Hu, T., Ennis, C.L., Nobile, C.J., and Huang, G. (2020). Candida auris: Epidemiology, Biology, Antifungal Resistance, and Virulence. PLoS Pathog., 16.","DOI":"10.1371\/journal.ppat.1008921"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Fasciana, T., Cortegiani, A., Ippolito, M., Giarratano, A., Di Quattro, O., Lipari, D., Graceffa, D., and Giammanco, A. (2020). Candida auris: An Overview of How to Screen, Detect, Test and Control This Emerging Pathogen. Antibiotics, 9.","DOI":"10.3390\/antibiotics9110778"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1007\/s12281-021-00420-y","article-title":"Candida auris: Diagnostic Challenges and Emerging Opportunities for the Clinical Microbiology Laboratory","volume":"15","author":"Keighley","year":"2021","journal-title":"Curr. Fungal Infect. Rep."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Chakrabarti, A., and Sood, P. (2021). On the Emergence, Spread and Resistance of Candida auris: Host, Pathogen and Environmental Tipping Points. J. Med. Microbiol., 70.","DOI":"10.1099\/jmm.0.001318"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/mmy\/myw147","article-title":"Isolates of the Emerging Pathogen Candida auris Present in the UK Have Several Geographic Origins","volume":"55","author":"Borman","year":"2017","journal-title":"Med. Mycol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2200846","DOI":"10.2807\/1560-7917.ES.2022.27.46.2200846","article-title":"Candida auris survey collaborative group includes the following national experts Increasing Number of Cases and Outbreaks Caused by Candida Auris in the EU\/EEA, 2020 to 2021","volume":"27","author":"Kohlenberg","year":"2022","journal-title":"Euro Surveill"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1900549","DOI":"10.2807\/1560-7917.ES.2019.24.37.1900549","article-title":"Isolation of Candida auris from Invasive and Non-Invasive Samples of a Patient Suffering from Vascular Disease, Italy, July 2019","volume":"24","author":"Crea","year":"2019","journal-title":"Euro Surveill"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Sticchi, C., Raso, R., Ferrara, L., Vecchi, E., Ferrero, L., Filippi, D., Finotto, G., Frassinelli, E., Silvestre, C., and Zozzoli, S. (2023). Increasing Number of Cases Due to Candida auris in North Italy, July 2019\u2013December 2022. J. Clin. Med., 12.","DOI":"10.3390\/jcm12051912"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Corcione, S., Montrucchio, G., Shbaklo, N., De Benedetto, I., Sales, G., Cedrone, M., Vita, D., Costa, C., Zozzoli, S., and Zaccaria, T. (2022). First Cases of Candida auris in a Referral Intensive Care Unit in Piedmont Region, Italy. Microorganisms, 10.","DOI":"10.3390\/microorganisms10081521"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/s12281-023-00451-7","article-title":"Strategies to Prevent Transmission of Candida auris in Healthcare Settings","volume":"17","author":"Ahmad","year":"2023","journal-title":"Curr. Fungal Infect. Rep."},{"key":"ref_13","unstructured":"(2023, November 18). USEPA List P: Antimicrobial Products Registered with EPA for Claims against C. Auris, Available online: https:\/\/www.Epa.Gov\/Pesticide-Registration\/List-p-Antimicrobial-Products-Registered-Epa-Claims-against-Candida-Auris."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"7179","DOI":"10.1007\/s00216-022-04270-6","article-title":"Comparison of Fast Fourier Transform Infrared Spectroscopy Biotyping with Whole Genome Sequencing-Based Genotyping in Common Nosocomial Pathogens","volume":"414","author":"Teng","year":"2022","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Curtoni, A., Cordovana, M., Bondi, A., Scaiola, F., Criscione, G., Ghibaudo, D., Pastrone, L., Zanotto, E., Camaggi, A., and Caroppo, M.S. (2023). Application of FT-IR Spectroscopy for Mycobacterium Abscessus Complex Subspecies Differentiation. J. Microbiol. Methods, 212.","DOI":"10.1016\/j.mimet.2023.106792"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Bisognin, F., Messina, F., Butera, O., Nisii, C., Mazzarelli, A., Cristino, S., Pascale, M.R., Lombardi, G., Cannas, A., and Dal Monte, P. (2022). Investigating the Origin of Mycobacterium Chimaera Contamination in Heater-Cooler Units: Integrated Analysis with Fourier Transform Infrared Spectroscopy and Whole-Genome Sequencing. Microbiol. Spectr., 10.","DOI":"10.1128\/spectrum.02893-22"},{"key":"ref_17","unstructured":"(2024, June 20). CDC Infection Prevention and Control for C. auris. Fungal Diseases, CDC, Available online: https:\/\/www.cdc.gov\/candida-auris\/hcp\/infection-control\/?CDC_AAref_Val=https:\/\/www.cdc.gov\/fungal\/candida-auris\/c-auris-infection-control.html."},{"key":"ref_18","unstructured":"European Centre for Disease Prevention and Control (2018). C. auris in Healthcare Settings\u2014Europe\u2014First Update, ECDC."},{"key":"ref_19","unstructured":"Bishop, L., Cummins, M., Guy, R., Hoffman, P., Jeffery, K., Jefferey-Smith, A., Johnson, E., Lamagni, T., Manuel, R., and Mohamed-Klein, R. (2017). Guidance for the Laboratory Investigation, Management and Infection Prevention and Control for Cases of C. auris, Public Health England."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"w20297","DOI":"10.4414\/smw.2020.20297","article-title":"Candida auris\u2014Recommendations on Infection Prevention and Control Measures in Switzerland","volume":"150","author":"Sommerstein","year":"2020","journal-title":"Swiss Med. Wkly."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1111\/imj.14612","article-title":"Diagnosis, Management and Prevention of Candida auris in Hospitals: Position Statement of the Australasian Society for Infectious Diseases","volume":"49","author":"Ong","year":"2019","journal-title":"Intern. Med. J."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Kordalewska, M., and Perlin, D.S. (2019). Molecular Diagnostics in the Times of Surveillance for Candida auris. JoF, 5.","DOI":"10.3390\/jof5030077"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Bandara, H.M.H.N., and Samaranayake, L.P. (2022). Emerging Strategies for Environmental Decontamination of the Nosocomial Fungal Pathogen Candida auris. J. Med. Microbiol.","DOI":"10.1099\/jmm.0.001548"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Lockhart, S.R., Lyman, M.M., and Sexton, D.J. (2022). Tools for Detecting a \u201cSuperbug\u201d: Updates on Candida auris Testing. J. Clin. Microbiol., 60.","DOI":"10.1128\/jcm.00808-21"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e00098-20","DOI":"10.1128\/JCM.00098-20","article-title":"Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: A Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella Pneumoniae Outbreak in a Neonatal Intensive Care Unit","volume":"58","author":"Rakovitsky","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Contreras, D.A., and Morgan, M.A. (2022). 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. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.887754"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"De Carolis, E., Posteraro, B., Falasca, B., Spruijtenburg, B., Meis, J.F., and Sanguinetti, M. (2023). The Fourier-Transform Infrared Spectroscopy-Based Method as a New Typing Tool for Candida Parapsilosis Clinical Isolates. Microbiol. Spectr., 11.","DOI":"10.1128\/spectrum.02388-23"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Deidda, F., Bozzi Cionci, N., Cordovana, M., Campedelli, I., Fracchetti, F., Di Gioia, D., Ambretti, S., and Pane, M. (2021). Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.692975"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.2217\/fmb-2020-0276","article-title":"Application of Fourier Transform Infrared Spectroscopy for Real-Time Typing of Acinetobacter Baumannii Outbreak in Intensive Care Unit","volume":"16","author":"Lombardo","year":"2021","journal-title":"Future Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1349","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","volume":"53","year":"2022","journal-title":"Braz. J. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Kaprou, G.D., Berg\u0161pica, I., Alexa, E.A., Alvarez-Ord\u00f3\u00f1ez, A., and Prieto, M. (2021). Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics, 10.","DOI":"10.3390\/antibiotics10020209"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/7\/1312\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:06:19Z","timestamp":1760108779000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/7\/1312"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,27]]},"references-count":31,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7]]}},"alternative-id":["microorganisms12071312"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms12071312","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,27]]}}}