{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T05:14:32Z","timestamp":1789708472909,"version":"4.0.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T00:00:00Z","timestamp":1760659200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Candidemias caused by the yeasts formerly encompassed as Candida spp. require expedited identification to decide on the antifungal treatment and reduce mortality. Traditional methods rely on subcultures for diagnosis, with turnaround times of 72\u201396 h, or expensive equipment. Deep learning and convolutional neural networks (CNN) have shown high accuracy for image recognition in microbiology. We compared the accuracy of six CNNs (GoogLeNet, InceptionV3, AlexNet, ResNet18, ResNet50, and DenseNet161) to identify Candida spp. at the species level, with photographs obtained mainly from clinical blood cultures showing yeast structures in the Gram stain, which were identified as Candida spp. in the subculture. Images were obtained from January 2012 to May 2024 and stored in the image databank of two third-level teaching hospitals in Mexico City. We analyzed the five most frequent species from both centers\u2019 clinical samples and included simulated blood culture images from Candida auris (Candidozyma auris) and C. krusei (Pichia kudriavzevii) strains. After processing and segmentation, we loaded the CNNs with 531 whole photographs and 2804 patches. The CNN Densnet161, using a scan-based approach, showed higher accuracy identifying 87%, 99%, 94%, 100%, 89%, and 95% of the images containing C. albicans, C. auris, C. glabrata (Nakaseomyces glabrata), C. krusei (P. kudriavzevii), C. parapsilosis, and C. tropicalis, respectively. These results show that CNN image recognition can identify clinically relevant Candida spp. directly from positive Gram-stained smears, which may help make early decisions for antifungal treatment.<\/jats:p>","DOI":"10.1093\/mmy\/myaf097","type":"journal-article","created":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T12:15:37Z","timestamp":1760703337000},"source":"Crossref","is-referenced-by-count":6,"title":["Deep learning for the identification of\n                    <i>Candida<\/i>\n                    spp. directly from blood culture gram stains from candidemia patients"],"prefix":"10.1093","volume":"63","author":[{"given":"Juan Carlos","family":"Cuevas-Tello","sequence":"first","affiliation":[{"name":"Laboratory of Bioinformatics, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78210, San Luis Potos\u00ed ,","place":["Mexico"]},{"name":"Facultad de Ingenier\u00eda, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78290, San Luis Potos\u00ed ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azael","family":"Monreal-de\u00a0la\u00a0Rosa","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78210, San Luis Potos\u00ed ,","place":["Mexico"]},{"name":"Facultad de Ingenier\u00eda, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78290, San Luis Potos\u00ed ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Luis","family":"Quistian-Navarro","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78210, San Luis Potos\u00ed ,","place":["Mexico"]},{"name":"Facultad de Ingenier\u00eda, Universidad Aut\u00f3noma de San Luis Potos\u00ed , 78290, San Luis Potos\u00ed ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Areli","family":"Martinez-Gamboa","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n Department of Infectious Diseases, , 14080, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Fernanda","family":"Gonz\u00e1lez-Lara","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n Department of Infectious Diseases, , 14080, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norma Irene","family":"L\u00f3pez-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n Department of Infectious Diseases, , 14080, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Rangel-Cordero","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n Department of Infectious Diseases, , 14080, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7387-0937","authenticated-orcid":false,"given":"Luis Esau","family":"L\u00f3pez-Jacome","sequence":"additional","affiliation":[{"name":"Clinical Microbiology Laboratory, Instituto Nacional de Rehabilitaci\u00f3n Luis Guillermo Ibarra Ibarra ,14389, Mexico City ,","place":["Mexico"]},{"name":"Facultad de Qu\u00edmica, Universidad Nacional Aut\u00f3noma de M\u00e9xico Department of Biology, , 04510, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mercedes Isabel","family":"Cervantes-Hernandez","sequence":"additional","affiliation":[{"name":"Clinical Microbiology Laboratory, Instituto Nacional de Rehabilitaci\u00f3n Luis Guillermo Ibarra Ibarra ,14389, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1574-1138","authenticated-orcid":false,"given":"Rafael","family":"Franco-Cendejas","sequence":"additional","affiliation":[{"name":"Clinical Microbiology Laboratory, Instituto Nacional de Rehabilitaci\u00f3n Luis Guillermo Ibarra Ibarra ,14389, Mexico City ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Carlos","family":"Mu\u00f1oz-Escalante","sequence":"additional","affiliation":[{"name":"Laboratory of Infectious Diseases, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed ,78210, San Luis Potos\u00ed ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel E","family":"Noyola","sequence":"additional","affiliation":[{"name":"Laboratory of Infectious Diseases, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed ,78210, San Luis Potos\u00ed ,","place":["Mexico"]},{"name":"Facultad de Medicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed Department of Microbiology, , 78210, San Luis Potos\u00ed ,","place":["Mexico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2944-2721","authenticated-orcid":false,"given":"Pedro","family":"Torres-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Laboratory of Infectious Diseases, Centro de Investigaci\u00f3n en Ciencias de la Salud y Biomedicina, Universidad Aut\u00f3noma de San Luis Potos\u00ed ,78210, San Luis Potos\u00ed ,","place":["Mexico"]},{"name":"Facultad de Medicina, 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