{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T17:30:35Z","timestamp":1767979835009,"version":"3.49.0"},"reference-count":39,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"crossref","award":["ECS00000017"],"award-info":[{"award-number":["ECS00000017"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"crossref","award":["CUP I53C22000780001"],"award-info":[{"award-number":["CUP I53C22000780001"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>In the context of evolving antifungal resistance and increasing reports of clinical outbreaks of non-albicans Candida spp. invasive infections, the rapid detection of resistant patterns is of the utmost importance. Currently, an azole-resistant Candida parapsilosis clinical outbreak is ongoing at Pisa University Hospital. Resistant isolates bear both Y132F and S862C amino acid substitutions. Based on the data and isolates retrieved during the clinical outbreak, mass spectrometry was used to investigate the differences between fluconazole-resistant and -susceptible clinical strains directly from yeast colonies isolated from agar culture media. A total of 39 isolates, 16 susceptible and 23 resistant, were included. Spectra were processed following a standardized pipeline. Several supervised machine learning classifiers such as Random Forest, Light Gradient Boosting Machine, and Support Vector Machine, with and without principal component analysis were implemented to discriminate resistant from susceptible isolates. Support Vector Machine with principal component analysis showed the highest sensitivity in detecting fluconazole resistance (100%). Despite these promising results, external prospective validation of the algorithm with a higher number of clinical isolates retrieved from multiple clinical centers is required.<\/jats:p>","DOI":"10.3390\/jof12010009","type":"journal-article","created":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T03:06:02Z","timestamp":1766718362000},"page":"9","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Detection of Fluconazole Resistance in Candida parapsilosis Clinical Isolates with MALDI-TOF Analysis: A Proof-of-Concept Preliminary Study"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2525-6216","authenticated-orcid":false,"given":"Iacopo","family":"Franconi","sequence":"first","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy"},{"name":"Mycology Unit, Pisa University Hospital, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benedetta","family":"Tuvo","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy"},{"name":"Mycology Unit, Pisa University Hospital, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenzo","family":"Maltinti","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Falcone","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy"},{"name":"Infectious Diseases, Pisa University Hospital, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luis","family":"Mancera","sequence":"additional","affiliation":[{"name":"Clover Bioanalytical Software, 18016 Granada, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6975-8114","authenticated-orcid":false,"given":"Antonella","family":"Lupetti","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy"},{"name":"Mycology Unit, Pisa University Hospital, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.idc.2021.03.001","article-title":"Recent Trends in the Epidemiology of Fungal Infections","volume":"35","author":"Seagle","year":"2021","journal-title":"Infect. Dis. Clin. N. Am."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e428","DOI":"10.1016\/S1473-3099(23)00692-8","article-title":"Global Incidence and Mortality of Severe Fungal Disease","volume":"24","author":"Denning","year":"2024","journal-title":"Lancet Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Bongomin, F., Gago, S., Oladele, R.O., and Denning, D.W. (2017). Global and Multi-National Prevalence of Fungal Diseases-Estimate Precision. J. Fungi, 3.","DOI":"10.3390\/jof3040057"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"dlaf106","DOI":"10.1093\/jacamr\/dlaf106","article-title":"Understanding the Mechanisms of Resistance to Azole Antifungals in Candida Species","volume":"7","author":"Li","year":"2025","journal-title":"JAC Antimicrob. Resist."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/s41579-023-00861-x","article-title":"The WHO Fungal Priority Pathogens List as a Game-Changer","volume":"21","author":"Fisher","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Franconi, I., Rizzato, C., Poma, N., Tavanti, A., and Lupetti, A. (2023). Candida parapsilosis Sensu Stricto Antifungal Resistance Mechanisms and Associated Epidemiology. J. Fungi, 9.","DOI":"10.3390\/jof9080798"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2300661","DOI":"10.2807\/1560-7917.ES.2024.29.29.2300661","article-title":"Increase in Candidemia Cases and Emergence of Fluconazole-Resistant Candida parapsilosis and C. auris Isolates in a Tertiary Care Academic Hospital during the COVID-19 Pandemic, Greece, 2020 to 2023","volume":"29","author":"Siopi","year":"2024","journal-title":"Eurosurveillance"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1994","DOI":"10.1093\/jac\/dkw091","article-title":"Emergence of Azole-Resistant Candida parapsilosis Causing Bloodstream Infection: Results from Laboratory-Based Sentinel Surveillance in South Africa","volume":"71","author":"Govender","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e0071022","DOI":"10.1128\/aac.00710-22","article-title":"Evidence of Fluconazole-Resistant Candida parapsilosis Genotypes Spreading across Hospitals Located in Madrid, Spain and Harboring the Y132F ERG11p Substitution","volume":"66","author":"Reigadas","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e470","DOI":"10.1016\/S2666-5247(23)00067-8","article-title":"Worldwide Emergence of Fluconazole-Resistant Candida parapsilosis: Current Framework and Future Research Roadmap","volume":"4","author":"Daneshnia","year":"2023","journal-title":"Lancet Microbe"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Yamin, D., Akanmu, M.H., Al Mutair, A., Alhumaid, S., Rabaan, A.A., and Hajissa, K. (2022). Global Prevalence of Antifungal-Resistant Candida parapsilosis: A Systematic Review and Meta-Analysis. Trop. Med. Infect. Dis., 7.","DOI":"10.3390\/tropicalmed7080188"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"i4","DOI":"10.1093\/jac\/dkx444","article-title":"Changes in the Epidemiological Landscape of Invasive Candidiasis","volume":"73","author":"Lamoth","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_13","unstructured":"(2024, December 13). CDC Clinical Overview of Invasive Candidiasis, Available online: https:\/\/www.cdc.gov\/candidiasis\/hcp\/clinical-overview\/index.html."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Bassetti, M., Taramasso, L., Nicco, E., Molinari, M.P., Mussap, M., and Viscoli, C. (2011). Epidemiology, Species Distribution, Antifungal Susceptibility and Outcome of Nosocomial Candidemia in a Tertiary Care Hospital in Italy. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0024198"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1111\/myc.13050","article-title":"Changing Epidemiology of Candidaemia: Increase in Fluconazole-Resistant Candida parapsilosis","volume":"63","author":"Mesini","year":"2020","journal-title":"Mycoses"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Franconi, I., Rizzato, C., Tavanti, A., Falcone, M., and Lupetti, A. (2023). Paradigm Shift: Candida parapsilosis Sensu Stricto as the Most Prevalent Candida Species Isolated from Bloodstream Infections with Increasing Azole-Non-Susceptibility Rates: Trends from 2015\u20132022 Survey. J. Fungi, 9.","DOI":"10.3390\/jof9101012"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"dlaf051","DOI":"10.1093\/jacamr\/dlaf051","article-title":"The S862C Amino Acid Change in CpMrr1 Confers Fluconazole Resistance in Candida parapsilosis","volume":"7","author":"Franconi","year":"2025","journal-title":"JAC Antimicrob. Resist."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Martini, C., Torelli, R., de Groot, T., De Carolis, E., Morandotti, G.A., De Angelis, G., Posteraro, B., Meis, J.F., and Sanguinetti, M. (2020). Prevalence and Clonal Distribution of Azole-Resistant Candida parapsilosis Isolates Causing Bloodstream Infections in a Large Italian Hospital. Front. Cell Infect. Microbiol., 10.","DOI":"10.3389\/fcimb.2020.00232"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Ahmad, S., and Alfouzan, W. (2021). Candida auris: Epidemiology, Diagnosis, Pathogenesis, Antifungal Susceptibility, and Infection Control Measures to Combat the Spread of Infections in Healthcare Facilities. Microorganisms, 9.","DOI":"10.3390\/microorganisms9040807"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Cristina, M.L., Spagnolo, A.M., Sartini, M., Carbone, A., Oliva, M., Schinca, E., Boni, S., and Pontali, E. (2023). An Overview on Candida auris in Healthcare Settings. J. Fungi, 9.","DOI":"10.3390\/jof9090913"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e00289-22","DOI":"10.1128\/aac.00289-22","article-title":"Candida parapsilosis Mdr1B and Cdr1B Are Drivers of Mrr1-Mediated Clinical Fluconazole Resistance","volume":"66","author":"Doorley","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"E248","DOI":"10.1111\/j.1469-0691.2012.03890.x","article-title":"EUCAST Technical Note on Aspergillus and Amphotericin B, Itraconazole, and Posaconazole","volume":"18","author":"Arendrup","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1093\/jac\/dkac373","article-title":"Multicentre Validation of a Modified EUCAST MIC Testing Method and Development of Associated Epidemiologic Cut-off (ECOFF) Values for Rezafungin","volume":"78","author":"Arendrup","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Calvo, M., Scalia, G., Palermo, C.I., Oliveri, S., and Trovato, L. (2023). Comparison between EUCAST Broth Microdilution and MIC Strip Test in Defining Isavuconazole In Vitro Susceptibility against Candida and Rare Yeast Clinical Isolates. Antibiotics, 12.","DOI":"10.3390\/antibiotics12020251"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Agnetti, J., B\u00fcchler, A.C., Osthoff, M., Helfenstein, F., Weisser, M., Siegemund, M., Bassetti, S., Bingisser, R., Schaefer, D.J., and Clauss, M. (2023). Identification of Microorganisms by a Rapid PCR Panel from Positive Blood Cultures Leads to Faster Optimal Antimicrobial Therapy\u2014A before-after Study. BMC Infect. Dis., 23.","DOI":"10.1186\/s12879-023-08732-9"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Leena Sankari, S., Mahalakshmi, K., and Naveen Kumar, V. (2019). Chromogenic Medium versus PCR-RFLP in the Speciation of Candida: A Comparative Study. BMC Res. Notes, 12.","DOI":"10.1186\/s13104-019-4710-5"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1099\/jmm.0.000804","article-title":"Multicenter Assessment of the Rapid Unyvero Blood Culture Molecular Assay","volume":"67","author":"Personne","year":"2018","journal-title":"J. Med. Microbiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"831","DOI":"10.7754\/Clin.Lab.2023.231133","article-title":"Pitfalls of a Multiplex PCR Panel for Identification of Bloodstream Pathogens","volume":"70","author":"Park","year":"2024","journal-title":"Clin. Lab."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1111\/j.1574-6976.2011.00298.x","article-title":"Applications of MALDI-TOF Mass Spectrometry in Clinical Diagnostic Microbiology","volume":"36","author":"Croxatto","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1016\/j.cll.2013.03.001","article-title":"Maldi-Tof Mass Spectrometry for Microorganism Identification","volume":"33","author":"Dingle","year":"2013","journal-title":"Clin. Lab. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1007\/s00216-008-2288-1","article-title":"MALDI-TOF Mass Signatures for Differentiation of Yeast Species, Strain Grouping and Monitoring of Morphogenesis Markers","volume":"392","author":"Qian","year":"2008","journal-title":"Anal. Bioanal. Chem."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Maenchantrarath, C., Khumdee, P., Samosornsuk, S., Mungkornkaew, N., and Samosornsuk, W. (2022). Investigation of Fluconazole Susceptibility to Candida albicans by MALDI-TOF MS and Real-Time PCR for CDR1, CDR2, MDR1 and ERG11. BMC Microbiol., 22.","DOI":"10.1186\/s12866-022-02564-4"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1007\/s11046-014-9757-1","article-title":"MALDI-TOF Mass Spectrometry: Any Use for Aspergilli?","volume":"178","author":"Sanguinetti","year":"2014","journal-title":"Mycopathologia"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4627","DOI":"10.1002\/pmic.200900152","article-title":"MALDI-TOF MS-Based Drug Susceptibility Testing of Pathogens: The Example of Candida albicans and Fluconazole","volume":"9","author":"Marinach","year":"2009","journal-title":"Proteomics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1128\/JCM.00224-12","article-title":"Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Caspofungin Susceptibility Testing of Candida and Aspergillus Species","volume":"50","author":"Vella","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e00420-18","DOI":"10.1128\/JCM.00420-18","article-title":"Proof of Concept for MBT ASTRA, a Rapid Matrix-Assisted Laser Desorption Ionization\u2013Time of Flight Mass Spectrometry (MALDI-TOF MS)-Based Method to Detect Caspofungin Resistance in Candida albicans and Candida glabrata","volume":"56","author":"Vatanshenassan","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Vecchione, A., Florio, W., Celandroni, F., Barnini, S., Lupetti, A., and Ghelardi, E. (2018). A Rapid Procedure for Identification and Antifungal Susceptibility Testing of Yeasts From Positive Blood Cultures. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.02400"},{"key":"ref_38","unstructured":"Arendrup, M.C., Meletiadis, J., Mouton, J.W., Lagrou, K., Hamal, P., and Guinea, J. (EUCAST DEFINITIVE DOCUMENT E.DEF, 2020). EUCAST DEFINITIVE DOCUMENT E.DEF, Method for the Determination of Broth Dilution Minimum Inhibitory Concentrations of Antifungal Agents for Yeasts."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: A Unified Bioinformatics Toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/1\/9\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T05:12:58Z","timestamp":1766725978000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/1\/9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,23]]},"references-count":39,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["jof12010009"],"URL":"https:\/\/doi.org\/10.3390\/jof12010009","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,23]]}}}