{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:25:48Z","timestamp":1760059548984,"version":"build-2065373602"},"reference-count":42,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T00:00:00Z","timestamp":1750377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>Identification and differentiation of Candida spp. yeasts, especially clinically relevant isolates, is of high importance with respect to their origin, pathogenic potential, colonization pattern, and resistance to antimycotics. Currently, numerous typing methods with varying or unknown discriminatory power are used. This study evaluated the utility of five methods\u2014biotyping using the API system, ITS1 and ITS4 sequence analysis, ITS region polymorphism, multiplex PCR of ITS1, ITS3, and ITS4 regions, and karyotyping\u2014for typing 42 strains differing in origin (24 clinical and 18 food-borne). The highest discriminatory power was obtained for ITS sequencing and karyotyping, both yielding a discrimination index of 1.000. The discrimination indices for other methods ranged from 0.957 for genotyping based on ITS region polymorphism to 0.997 for multiplex PCR-genotyping. Although biotyping showed relatively high discriminatory potential, its use led to misclassification of 64.3% of isolates compared to ITS sequencing. These findings emphasize the importance of applying a typing method with a discrimination index of 1.000 to ensure accurate interpretation of strain-relatedness and origin. Methods with lower indices may reflect methodological limitations rather than actual genetic relatedness. Determining the discrimination index is therefore essential when selecting appropriate tools for yeast typing, particularly in clinical and epidemiological contexts.<\/jats:p>","DOI":"10.3390\/pathogens14070614","type":"journal-article","created":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T06:10:27Z","timestamp":1750399827000},"page":"614","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Discrimination of Clinical and Food-Derived Candida Strains Using Biotyping and Molecular Typing Approaches"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6943-8639","authenticated-orcid":false,"given":"Katarzyna","family":"Rajkowska","sequence":"first","affiliation":[{"name":"Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171\/173, 90-530 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3536-3560","authenticated-orcid":false,"given":"Anna","family":"Otlewska","sequence":"additional","affiliation":[{"name":"Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171\/173, 90-530 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dorota","family":"Simi\u0144ska","sequence":"additional","affiliation":[{"name":"Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171\/173, 90-530 Lodz, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1080\/21505594.2021.2019950","article-title":"Pathogenesis and virulence of Candida albicans","volume":"13","author":"Lopes","year":"2021","journal-title":"Virulence"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"myae045","DOI":"10.1093\/mmy\/myae045","article-title":"Candida albicans\u2014A systematic review to inform the World Health Organization Fungal Priority Pathogens List","volume":"62","author":"Parambath","year":"2024","journal-title":"Med. Mycol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Gaffar, N.R., Valand, N., and Venkatraman Girija, U. (2025). Candidiasis: Insights into virulence factors, complement evasion and antifungal drug resistance. Microorganisms, 13.","DOI":"10.3390\/microorganisms13020272"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.ijantimicag.2017.03.028","article-title":"CD101, a long-acting echinocandin, and comparator antifungal agents tested against a global collection of invasive fungal isolates in the SENTRY 2015 Antifungal Surveillance Program","volume":"50","author":"Pfaller","year":"2017","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1569","DOI":"10.1093\/jac\/dkad139","article-title":"Invasive candidiasis: Current clinical challenges and unmet needs in adult populations","volume":"78","author":"Soriano","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Pinho, S., Miranda, I.M., and Costa-de-Oliveira, S. (2024). Global epidemiology of invasive infections by uncommon Candida species: A systematic review. J. Fungi, 10.","DOI":"10.3390\/jof10080558"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"46","DOI":"10.20411\/pai.v7i2.535","article-title":"Update on the pathogenesis, virulence, and treatment of Candida auris","volume":"7","author":"Watkins","year":"2022","journal-title":"Pathog. Immun."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Fr\u00edas-De-Le\u00f3n, M.G., Hern\u00e1ndez-Castro, R., Conde-Cuevas, E., Garc\u00eda-Coronel, I.H., V\u00e1zquez-Aceituno, V.A., Soriano-Urs\u00faa, M.A., Farf\u00e1n-Garc\u00eda, E.D., Ochar\u00e1n-Hern\u00e1ndez, E., Rodr\u00edguez-Cerdeira, C., and Arenas, R. (2021). Candida glabrata antifungal resistance and virulence factors, a perfect pathogenic combination. Pharmaceutics, 13.","DOI":"10.3390\/pharmaceutics13101529"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.fbr.2017.06.001","article-title":"Biotechnological use of Candida yeasts in the food industry: A review","volume":"31","author":"Kieliszek","year":"2017","journal-title":"Fungal Biol. Rev."},{"key":"ref_10","unstructured":"Kurtzman, C.P., Fell, J.W., and Boekhout, T. (2011). Yeast biotechnology. The Yeasts, a Taxonomic Study, Elsevier. [5th ed.]."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Querol, A., and Fleet, G.H. (2006). The public health and probiotic significance of yeasts in foods and beverages. Yeasts in Food and Beverages, Springer. [1st ed.].","DOI":"10.1007\/978-3-540-28398-0"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"5775","DOI":"10.1016\/j.cell.2024.07.039","article-title":"Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome","volume":"187","author":"Carlino","year":"2024","journal-title":"Cell"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1093\/clinids\/21.4.881","article-title":"Candida-associated diarrhea: A syndrome in search of credibility","volume":"21","author":"Levine","year":"1995","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1007\/BF00446998","article-title":"Fungal diarrhoea: Association of different fungi and seasonal variation and their incidence","volume":"110","author":"Talwar","year":"1990","journal-title":"Mycopathologia"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"196","DOI":"10.3109\/00365529208999948","article-title":"The effect of dietary yeast on the activity of stable chronic Crohn\u2019s disease","volume":"27","author":"Barclay","year":"1992","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.ijfoodmicro.2018.05.002","article-title":"Typing and virulence factors of food-borne Candida spp. isolates","volume":"279","author":"Rajkowska","year":"2018","journal-title":"Int. J. Food Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1007\/s43994-023-00049-2","article-title":"Candida diagnostic techniques: A review","volume":"9","author":"Arafa","year":"2023","journal-title":"J. Umm Al-Qura Univ. Appll. Sci."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1590\/S0036-46652013000600003","article-title":"Molecular typing of Candida albicans isolates from hospitalized patients","volume":"55","author":"Fiorini","year":"2013","journal-title":"Rev. Inst. Med. Trop. Sao Paulo"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.33425\/2639-9458.1165","article-title":"RAPD typing, antibiotic resistance profiling and genetic diversity of Candida isolates","volume":"6","author":"Jha","year":"2022","journal-title":"Microbiol. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1128\/JCM.41.1.414-420.2003","article-title":"Identification of Candida spp. by randomly amplified polymorphic DNA analysis and differentiation between Candida albicans and Candida dubliniensis by direct PCR methods","volume":"41","author":"Boldo","year":"2003","journal-title":"J. Clin. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1016\/j.riam.2016.03.005","article-title":"Molecular characterization of Candida isolates from intensive care unit patients, Krakow, Poland","volume":"34","author":"Paluchowska","year":"2017","journal-title":"Rev. Iberoam. Micol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Makled, A.F., Ali, S.A.M., Labeeb, A.Z., Salman, S.S., Shebl, D.Z.M., Hegazy, S.G., and Sabal, M.S. (2024). Characterization of Candida species isolated from clinical specimens: Insights into virulence traits, antifungal resistance and molecular profiles. BMC Microbiol., 24.","DOI":"10.1186\/s12866-024-03515-x"},{"key":"ref_23","unstructured":"Innis, M.A., Gelfand, D.H., Shinsky, J.J., and White, T.J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications, Academic Press."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1128\/JCM.39.10.3617-3622.2001","article-title":"Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains","volume":"39","author":"Fujita","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1007\/s11274-011-0994-x","article-title":"Phenotypic and genotypic diversity of wine yeasts used for acidic musts","volume":"28","author":"Rajkowska","year":"2012","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Heras, J., Dom\u00ednguez, C., Mata, E., and Pascual, V. (2015). GelJ\u2014A tool for analyzing DNA fingerprint gel images. BMC Bioinform., 16.","DOI":"10.1186\/s12859-015-0703-0"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Kumar, S., Stecher, G., Suleski, M., Sanderford, M., Sharma, S., and Tamura, K. (2024). Molecular evolutionary genetics analysis version 12 for adaptive and green computing. Mol. Biol. Evol., 41.","DOI":"10.1093\/molbev\/msae263"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1128\/jcm.26.11.2465-2466.1988","article-title":"Numerical index of the discriminatory ability of typing systems: An application of Simpson\u2019s index of diversity","volume":"26","author":"Hunter","year":"1988","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1128\/JCM.39.11.4066-4075.2001","article-title":"PCR fingerprinting of Candida albicans associated with chronic hyperplastic candidosis and other oral conditions","volume":"39","author":"Bartie","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1590\/S0074-02762005000500007","article-title":"Value of morphotyping for the characterization of Candida albicans clinical isolates","volume":"100","author":"Giammanco","year":"2005","journal-title":"Mem. Inst. Oswaldo Cruz."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1080\/13102818.2009.10818477","article-title":"Genomic approaches to yeast taxonomy","volume":"23","author":"Gouliamova","year":"2009","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5121","DOI":"10.2147\/IDR.S383785","article-title":"Candida lusitaniae: Biology, pathogenicity, virulence factors, diagnosis, and treatment","volume":"15","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1128\/JCM.02061-06","article-title":"Molecular identification of unusual pathogenic yeast isolates by large ribosomal subunit gene sequencing: 2 years of experience at the United Kingdom mycology reference laboratory","volume":"45","author":"Linton","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Ioannou, P., Baliou, S., and Kofteridis, D.P. (2024). Fungemia by Wickerhamomyces anomalus\u2014A narrative review. Pathogens, 13.","DOI":"10.3390\/pathogens13030269"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Douglass, A.P., Offei, B., Braun-Galleani, S., Coughlan, A.Y., Martos, A.A.R., Ortiz-Merino, R.A., Byrne, K.P., and Wolfe, K.H. (2018). Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names. PLoS Pathog., 14.","DOI":"10.1371\/journal.ppat.1007138"},{"key":"ref_36","first-page":"719","article-title":"Antibiotics sensitivity of Candida clinical and food-borne isolates","volume":"60","author":"Rajkowska","year":"2013","journal-title":"Acta Biochim. Pol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Mackenzie, J.S., and Jeggo, M. (2019). The One Health approach-why is it so important?. Trop. Med. Infect. Dis., 4.","DOI":"10.3390\/tropicalmed4020088"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Metcalf, R., Akinbobola, A., Woodford, L., and Quilliam, R.S. (2025). Thermotolerance, virulence, and drug resistance of human pathogenic Candida species colonising plastic pollution in aquatic ecosystems. Environ. Sci. Pollut. Res.","DOI":"10.1007\/s11356-025-36558-2"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1021\/acs.est.8b07287","article-title":"Is plastic pollution in aquatic and terrestrial environments a driver for the transmission of pathogens and the evolution of antibiotic resistance?","volume":"53","author":"Parthasarathy","year":"2019","journal-title":"Environ. Sci. Technol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Gkoutselis, G., Rohrbach, S., Harjes, J., Obst, M., Brachmann, A., Horn, M.A., and Rambold, G. (2021). Microplastics accumulate fungal pathogens in terrestrial ecosystems. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-92405-7"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Akinbobola, A.B., Kean, R., Hanifi, S.M.A., and Quilliam, R.S. (2023). Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1011268"},{"key":"ref_42","first-page":"161","article-title":"Qualitative and quantitative changes of potentially pathogenic fungi in a hydrophyte wastewater treatment plant","volume":"18","author":"Biedunkiewicz","year":"2009","journal-title":"Pol. J. Environ. Stud."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/7\/614\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:55:34Z","timestamp":1760032534000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/14\/7\/614"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,20]]},"references-count":42,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["pathogens14070614"],"URL":"https:\/\/doi.org\/10.3390\/pathogens14070614","relation":{},"ISSN":["2076-0817"],"issn-type":[{"type":"electronic","value":"2076-0817"}],"subject":[],"published":{"date-parts":[[2025,6,20]]}}}