{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T13:59:51Z","timestamp":1787061591899,"version":"build-2736575974"},"reference-count":37,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,2,5]],"date-time":"2022-02-05T00:00:00Z","timestamp":1644019200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Consejo Nacional de Ciencia y Tecnolog\u00eda (CONACyT)","award":["216112"],"award-info":[{"award-number":["216112"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Systemic candidiasis is a frequent opportunistic mycosis that can be life-threatening. Its main etiological agent is Candida albicans; however, the isolation of non-albicans Candida species has been increasing. Some of these species exhibit greater resistance to antifungals, so the rapid and specific identification of yeasts is crucial for a timely diagnosis and optimal treatment of patients. Multiple molecular assays have been developed, based mainly on polymerase chain reaction (PCR), showing high specificity and sensitivity to detect and identify Candida spp. Nevertheless, its application in diagnosis has been limited due to specialized infrastructure or methodological complexity. The objective of this study was to develop a PCR assay that detects and identifies some of the most common pathogenic Candida species and evaluate their diagnostic utility in blood samples and bronchial lavage. A pair of oligonucleotides was designed, CandF and CandR, based on sequence analysis of the 18S-ITS1-5.8S-ITS2-28S region of the rDNA of Candida spp., deposited in GenBank. The designed oligonucleotides identified C. albicans, C. glabrata, C. tropicalis, C. parapsilosis, C. krusei\/Pichia kudriazevii, C. guilliermondii\/Meyerozyma guilliermondii, C. lusitaniae\/Clavispora lusitaniae, and C. dubliniensis using simplex PCR based on the amplicon size, showing a detection limit of 10 pg\/\u03bcL of DNA or 103 yeasts\/mL. Based on cultures as the gold standard, it was determined that the sensitivity (73.9%), specificity (96.3%), and the positive (94.4%) and negative (81.2%) predictive values of the PCR assay with the designed oligonucleotides justify their reliable use in diagnosis.<\/jats:p>","DOI":"10.3390\/microorganisms10020374","type":"journal-article","created":{"date-parts":[[2022,2,6]],"date-time":"2022-02-06T20:38:40Z","timestamp":1644179920000},"page":"374","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Detection and Molecular Identification of Eight Candida Species in Clinical Samples by Simplex PCR"],"prefix":"10.3390","volume":"10","author":[{"given":"Eduardo","family":"Garc\u00eda-Salazar","sequence":"first","affiliation":[{"name":"Unidad de Investigaci\u00f3n, Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal M\u00e9xico\u2014Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico"},{"name":"Programa de Maestr\u00eda en Ciencias de la Salud, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 07340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gustavo","family":"Acosta-Altamirano","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n, Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal M\u00e9xico\u2014Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paola","family":"Betancourt-Cisneros","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n en Sistem\u00e1tica Vegetal y Suelo, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3866-9995","authenticated-orcid":false,"given":"Mar\u00eda del Roc\u00edo","family":"Reyes-Montes","sequence":"additional","affiliation":[{"name":"Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Rosas-De-Paz","sequence":"additional","affiliation":[{"name":"Unidad de Microbiolog\u00eda, Universitat Rovira i Virgili, Carrer de l\u2019Escorxador, s\/n, 43003 Tarragona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6315-7860","authenticated-orcid":false,"given":"Esperanza","family":"Duarte-Escalante","sequence":"additional","affiliation":[{"name":"Departamento de Microbiolog\u00eda y Parasitolog\u00eda, Facultad de Medicina, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alma Rosa","family":"S\u00e1nchez-Conejo","sequence":"additional","affiliation":[{"name":"Direcci\u00f3n General, Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal M\u00e9xico\u2014Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Ocharan Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Programa de Maestr\u00eda en Ciencias de la Salud, Escuela Superior de Medicina, Instituto Polit\u00e9cnico Nacional, Mexico City 07340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3160-8698","authenticated-orcid":false,"given":"Mar\u00eda Guadalupe","family":"Fr\u00edas-De-Le\u00f3n","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n, Hospital Regional de Alta Especialidad de Ixtapaluca, Carretera Federal M\u00e9xico\u2014Puebla Km. 34.5, Pueblo de Zoquiapan, Ixtapaluca 56530, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1111\/jam.15032","article-title":"A global view on fungal infections in humans and animals: Opportunistic infections and microsporidioses","volume":"131","author":"Gnat","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.cnc.2016.09.011","article-title":"Opportunistic Fungal infections in critical care units","volume":"29","author":"Garbee","year":"2017","journal-title":"Crit. Care Nurs. Clin. N. Am."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.3389\/fmicb.2018.01351","article-title":"Candida infections and therapeutic strategies: Mechanisms of action for traditional and alternative agents","volume":"9","author":"Vasconcelos","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1111\/myc.13148","article-title":"Breakthrough invasive fungal infections: Who is at risk?","volume":"63","author":"Jenks","year":"2020","journal-title":"Mycoses"},{"key":"ref_5","first-page":"41","article-title":"Growing role of non-Candida albicans species in clinical disorders of human and animals","volume":"53","author":"Pal","year":"2015","journal-title":"J. Mycopathol. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"18026","DOI":"10.1038\/nrdp.2018.26","article-title":"Invasive candidiasis","volume":"4","author":"Pappas","year":"2018","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bassetti, M., Righi, E., Costa, A., Fasce, R., Molinari, M.P., Rosso, R., Pallavicini, F.B., and Viscoli, C. (2006). Epidemiological trends in nosocomial candidemia in intensive care. BMC Infect. Dis., 6.","DOI":"10.1186\/1471-2334-6-21"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1055\/s-0039-1693704","article-title":"Diagnosis and treatment of candidemia in the intensive care unit","volume":"40","author":"Bassetti","year":"2019","journal-title":"Semin. Respir. Crit. Care Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1111\/myc.12206","article-title":"Regional data analysis of Candida non-albicans strains collected in United States medical sites over a 6-year period, 2006\u20132011","volume":"57","author":"Pfaller","year":"2014","journal-title":"Mycoses"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"S79","DOI":"10.1093\/ofid\/ofy358","article-title":"Twenty Years of the SENTRY Antifungal Surveillance Program: Results for Candida Species From 1997\u20132016","volume":"6","author":"Pfaller","year":"2019","journal-title":"Open Forum Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.riam.2017.05.001","article-title":"Current status of the etiology of candidiasis in Mexico","volume":"34","year":"2017","journal-title":"Rev. Iberoam. Micol."},{"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","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.3389\/fmicb.2019.01585","article-title":"Clinical and laboratory development of echinocandin resistance in Candida glabrata: Molecular characterization","volume":"10","author":"Capilla","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.cmi.2019.03.028","article-title":"Resistance of Candida to azoles and echinocandins worldwide","volume":"25","author":"Pristov","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"483","DOI":"10.3109\/13693786.2012.745953","article-title":"Distribution, virulence attributes and antifungal susceptibility patterns of Candida parapsilosis complex strains isolated from clinical samples","volume":"51","author":"Tosun","year":"2013","journal-title":"Med. Mycol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s12929-017-0376-2","article-title":"Virulence factors, antifungal susceptibility and molecular mechanisms of azole resistance among Candida parapsilosis complex isolates recovered from clinical specimens","volume":"24","author":"Neji","year":"2017","journal-title":"J. Biomed. Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2187","DOI":"10.1128\/JCM.00938-16","article-title":"Identification and Antifungal Susceptibility Profile of Candida guilliermondii and Candida fermentati from a Multicenter Study in China","volume":"54","author":"Cheng","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"880","DOI":"10.3389\/fmicb.2017.00880","article-title":"Molecular Epidemiology and Antifungal Susceptibility of Candida glabrata in China (August 2009 to July 2014): A Multi-Center Study","volume":"8","author":"Hou","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1128\/JCM.02417-14","article-title":"Design and evaluation of peptide nucleic acid probes for specific identification of Candida albicans","volume":"53","author":"Kim","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"699","DOI":"10.7754\/Clin.Lab.2016.161101","article-title":"Evaluation of MALDI-TOF-MS for the identification of yeast isolates causing bloodstream infection","volume":"63","author":"Turhan","year":"2017","journal-title":"Clin. Lab."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Fidler, G., Leiter, E., Kocsube, S., Biro, S., and Paholcsek, M. (2018). Validation of a simplex PCR assay enabling reliable identification of clinically relevant Candida species. BMC Infect. Dis., 18.","DOI":"10.1186\/s12879-018-3283-6"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1111\/j.1582-4934.2004.tb00278.x","article-title":"Scanning of beta-globin gene for identification of beta-thalassemia mutation in Romanian population","volume":"8","author":"Talmaci","year":"2004","journal-title":"J. Cell Mol. Med."},{"key":"ref_23","unstructured":"NCBI (2018, February 22). An Online Data Base Currently Coordinated and Supported by National Center for Biothecnology, Available online: http:\/\/ncbi.nlm.nih.gov."},{"key":"ref_24","unstructured":"Clustal \u2126 (2018, April 17). Multiple Sequence Alignment. Available online: http:\/\/www.ebi.ac.uk\/Tools\/msa\/clustalo\/."},{"key":"ref_25","first-page":"95","article-title":"BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT","volume":"41","author":"Hall","year":"1999","journal-title":"Nucl. Acids Symp. Ser."},{"key":"ref_26","first-page":"14","article-title":"GeneDoc: Analysis and Visualization of Genetic Variation","volume":"4","author":"Nicholas","year":"1997","journal-title":"EMBnet.news"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1093\/bioinformatics\/bti134","article-title":"Primaclade a flexible tool to find conserved PCR primers across multiple species","volume":"21","author":"Michael","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1128\/JCM.01344-06","article-title":"Development of novel real-time PCR assays for detection and differentiation of eleven medically important Aspergillus and Candida species in clinical specimens","volume":"45","author":"Selitsch","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Taira, C.L., Okay, T.S., Delgado, A.F., Rivero Ceccon, M.E.J., Gottardo de Almeida, M.G., and Barbaro Del Negro, G.M. (2014). A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients. BMC Infect. Dis., 14.","DOI":"10.1186\/1471-2334-14-406"},{"key":"ref_30","first-page":"288","article-title":"Molecular identification of Candida species isolated from gastro-oesophageal candidiasis in Tehran, Iran","volume":"8","author":"Mohammadi","year":"2015","journal-title":"Gastroenterol. Hepatol. Bed Bench"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3466","DOI":"10.1128\/JCM.39.10.3466-3471.2001","article-title":"Rapid identification of yeasts in positive blood cultures by a Multiplex PCR method","volume":"39","author":"Chang","year":"2001","journal-title":"J. Clin. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.riam.2010.11.003","article-title":"Comparaci\u00f3n entre m\u00e9todos convencionales, ChromAgar Candida y el m\u00e9todo de la PCR para la identificaci\u00f3n de especies de Candida en aislamientos cl\u00ednicos","volume":"28","author":"Flores","year":"2011","journal-title":"Rev. Iberoam. Micol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Merseguel, K., Nishikaku, A., Rodrigues, A., Padovan, A., e Ferreira, R., Salles de Azevedo Melo, A., Ribeiro da Silva Briones, M., and Lopes Colombo, A. (2015). Genetic diversity of medically important and emerging Candida species causing invasive infection. BMC Infect. Dis., 15.","DOI":"10.1186\/s12879-015-0793-3"},{"key":"ref_34","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_35","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1099\/jmm.0.037812-0","article-title":"Prevalence, distribution and antifungal susceptibility profiles of Candida parapsilosis, Candida orthopsilosis and Candida metapsilosis bloodstream isolates","volume":"61","author":"Bonfietti","year":"2012","journal-title":"J. Med. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e00099-17","DOI":"10.1128\/AAC.00099-17","article-title":"Candida guilliermondii Complex Is Characterized by High Antifungal Resistance but Low Mortality in 22 Cases of Candidemia","volume":"61","author":"Escribano","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s12223-018-0655-7","article-title":"Prevalence of human pathogens of the clade Nakaseomyces in a culture collection\u2014Tthe first report on Candida bracarensis in Poland","volume":"64","author":"Mrowiec","year":"2019","journal-title":"Folia Microbiol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/2\/374\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:14:40Z","timestamp":1760134480000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/10\/2\/374"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,5]]},"references-count":37,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["microorganisms10020374"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms10020374","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,5]]}}}