{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T17:46:31Z","timestamp":1791049591656,"version":"4.1.0"},"reference-count":39,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T00:00:00Z","timestamp":1717027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Instituto Polit\u00e9cnico Nacional","award":["SIP20240946"],"award-info":[{"award-number":["SIP20240946"]}]},{"name":"Instituto Polit\u00e9cnico Nacional","award":["SIP20231481"],"award-info":[{"award-number":["SIP20231481"]}]},{"name":"Instituto Polit\u00e9cnico Nacional","award":["SIP20231480"],"award-info":[{"award-number":["SIP20231480"]}]},{"name":"Instituto Polit\u00e9cnico Nacional","award":["SIP20220742"],"award-info":[{"award-number":["SIP20220742"]}]},{"name":"Instituto Polit\u00e9cnico Nacional","award":["SIP20220795"],"award-info":[{"award-number":["SIP20220795"]}]},{"name":"Instituto Polit\u00e9cnico Nacional","award":["283225"],"award-info":[{"award-number":["283225"]}]},{"name":"CONACyT","award":["SIP20240946"],"award-info":[{"award-number":["SIP20240946"]}]},{"name":"CONACyT","award":["SIP20231481"],"award-info":[{"award-number":["SIP20231481"]}]},{"name":"CONACyT","award":["SIP20231480"],"award-info":[{"award-number":["SIP20231480"]}]},{"name":"CONACyT","award":["SIP20220742"],"award-info":[{"award-number":["SIP20220742"]}]},{"name":"CONACyT","award":["SIP20220795"],"award-info":[{"award-number":["SIP20220795"]}]},{"name":"CONACyT","award":["283225"],"award-info":[{"award-number":["283225"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Candida auris is an emerging multidrug-resistant and opportunistic pathogenic yeast. Whole-genome sequencing analysis has defined five major clades, each from a distinct geographic region. The current study aimed to examine the genome of the C. auris 20\u20131498 strain, which is the first isolate of this fungus identified in Mexico. Based on whole-genome sequencing, the draft genome was found to contain 70 contigs. It had a total genome size of 12.86 Mbp, an N50 value of 1.6 Mbp, and an average guanine-cytosine (GC) content of 45.5%. Genome annotation revealed a total of 5432 genes encoding 5515 proteins. According to the genomic analysis, the C. auris 20\u20131498 strain belongs to clade IV (containing strains endemic to South America). Of the two genes (ERG11 and FKS1) associated with drug resistance in C. auris, a mutation was detected in K143R, a gene located in a mutation hotspot of ERG11 (lanosterol 14-\u03b1-demethylase), an antifungal drug target. The focus on whole-genome sequencing and the identification of mutations linked to the drug resistance of fungi could lead to the discovery of new therapeutic targets and new antifungal compounds.<\/jats:p>","DOI":"10.3390\/jof10060392","type":"journal-article","created":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T03:46:49Z","timestamp":1717127209000},"page":"392","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Comparative Genomics of the First Resistant Candida auris Strain Isolated in Mexico: Phylogenomic and Pan-Genomic Analysis and Mutations Associated with Antifungal Resistance"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5419-3173","authenticated-orcid":false,"given":"Arturo","family":"Casimiro-Ramos","sequence":"first","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9134-6610","authenticated-orcid":false,"given":"Celia","family":"Bautista-Crescencio","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8100-3080","authenticated-orcid":false,"given":"Alvaro","family":"Vidal-Montiel","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gloria M.","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Departamento de Microbiolog\u00eda, Facultad de Medicina, Universidad Aut\u00f3noma de Nuevo Le\u00f3n, Hospital Universitario \u201cDr. Jos\u00e9 Eleuterio Gonzalez\u201d, Av. Madero y Calle Dr. Eduardo Aguirre Peque\u00f1o s\/n, Colonia Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Alfredo","family":"Hern\u00e1ndez-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2411-9789","authenticated-orcid":false,"given":"C\u00e9sar","family":"Hern\u00e1ndez-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0055-2991","authenticated-orcid":false,"given":"Lourdes","family":"Villa-Tanaca","sequence":"additional","affiliation":[{"name":"Laboratorio de Biolog\u00eda Molecular de Bacterias y Levaduras, Departamento de Microbiolog\u00eda, Escuela Nacional de Ciencias Biol\u00f3gicas, Instituto Polit\u00e9cnico Nacional, Prolongaci\u00f3n de Carpio y Plan de Ayala, Casco de Santo Tom\u00e1s, Ciudad de M\u00e9xico 11340, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,5,30]]},"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","first-page":"1","DOI":"10.1093\/mmy\/myy054","article-title":"Candida auris: The recent emergence of a multidrug-resistant fungal pathogen","volume":"57","author":"Forsberg","year":"2019","journal-title":"Med. Mycol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e03364-19","DOI":"10.1128\/mBio.03364-19","article-title":"Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses","volume":"11","author":"Chow","year":"2020","journal-title":"mBio"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1093\/cid\/ciw691","article-title":"Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses","volume":"64","author":"Lockhart","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.3201\/eid2509.190686","article-title":"Potential Fifth Clade of Candida auris, Iran, 2018","volume":"25","author":"Chow","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2405","DOI":"10.1080\/22221751.2022.2125349","article-title":"Confirmation of fifth Candida auris clade by whole genome sequencing","volume":"11","author":"Spruijtenburg","year":"2022","journal-title":"Emerg. Microbes Infect."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Suphavilai, C., Ko, K.K.K., Lim, K.M., Tan, M.G., Boonsimma, P., Keat Chu, J.J., Goh, S.S., Rajandran, P., and Nagarajan, N. (2023). Discovery of the Sixth Candida auris Clade in Singapore.medRxiv. medRxiv.","DOI":"10.1101\/2023.08.01.23293435"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"iyab029","DOI":"10.1093\/genetics\/iyab029","article-title":"Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris","volume":"218","author":"Welsh","year":"2021","journal-title":"Genetics"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1093\/jac\/dkx480","article-title":"A multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009-17) in India: Role of the ERG11 and FKS1 genes in azole and echinocandin resistance","volume":"73","author":"Chowdhary","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1007\/s15010-020-01525-1","article-title":"First case of Candida auris isolated from the bloodstream of a Mexican patient with serious gastrointestinal complications from severe endometriosis","volume":"49","author":"Montoya","year":"2021","journal-title":"Infection"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.ijid.2019.12.037","article-title":"First report of a catheter-related bloodstream infection by Candida haemulonii in a children\u2019s hospital in Mexico City","volume":"92","year":"2020","journal-title":"Int. J. Infect. Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: Algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkw292","article-title":"Companion: A web server for annotation and analysis of parasite genomes","volume":"44","author":"Steinbiss","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the National Center for Biotechnology Information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Emms, D.M., and Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol., 20.","DOI":"10.1186\/s13059-019-1832-y"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"W397","DOI":"10.1093\/nar\/gkad313","article-title":"OrthoVenn3: An integrated platform for exploring and visualizing orthologous data across genomes","volume":"51","author":"Sun","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"6728","DOI":"10.1074\/jbc.M117.778308","article-title":"Structural analyses of Candida albicans sterol 14\u03b1-demethylase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis","volume":"292","author":"Hargrove","year":"2017","journal-title":"J. Biol. Chem."},{"key":"ref_23","first-page":"5","article-title":"Comparative protein structure modeling using Modeller","volume":"54","author":"Eswar","year":"2006","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"G\u00f3mez-Garc\u00eda, O., Andrade-Pav\u00f3n, D., Campos-Aldrete, E., Ballinas-Indil\u00ed, R., M\u00e9ndez-Tenorio, A., Villa-Tanaca, L., and \u00c1lvarez-Toledano, C. (2018). Synthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo [1,2-a] pyrimidines. Molecules, 23.","DOI":"10.3390\/molecules23030599"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Rodrigues, L.S., Gazara, R.K., Passarelli-Araujo, H., Valengo, A.E., Pontes PV, M., Nunes-da-Fonseca, R., de Souza, R.F., Venancio, T.M., and Dalla-Costa, L.M. (2020). First Genome Sequences of Two Multidrug-Resistant Candida haemulonii var. vulnera Isolates From Pediatric Patients With Candidemia. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01535"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Li, D., Wang, Y., Hu, W., Chen, F., Zhao, J., Chen, X., and Han, L. (2021). Application of Machine Learning Classifier to Candida auris Drug Resistance Analysis. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.742062"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e0005322","DOI":"10.1128\/aac.00053-22","article-title":"Candida auris Pan-Drug-Resistant to Four Classes of Antifungal Agents","volume":"66","author":"Jacobs","year":"2022","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Kiyohara, M., Miyazaki, T., Okamoto, M., Hirayama, T., Makimura, K., Chibana, H., Nakada, N., Ito, Y., Sumiyoshi, M., and Ashizawa, N. (2023). Evaluation of a Novel FKS1 R1354H Mutation Associated with Caspofungin Resistance in Candida auris Using the CRISPR-Cas9 System. J. Fungi, 9.","DOI":"10.3390\/jof9050529"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Reslan, L., Araj, G.F., Finianos, M., El Asmar, R., Hrabak, J., Dbaibo, G., and Bitar, I. (2022). Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.770635"},{"key":"ref_31","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_32","doi-asserted-by":"crossref","first-page":"5346","DOI":"10.1038\/s41467-018-07779-6","article-title":"Genomic insights into multidrug-resistance, mating and virulence in Candida auris and related emerging species","volume":"9","author":"Gade","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_33","unstructured":"Centers for Disease Control and Prevention (2024, May 28). Antifungal Susceptibility Testing and Interpretation|Candida auris|Fungal Diseases|CDC, Available online: https:\/\/www.cdc.gov\/candida-auris\/hcp\/laboratories\/antifungal-susceptibility-testing.html."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e01427-18","DOI":"10.1128\/AAC.01427-18","article-title":"Limited ERG11 Mutations Identified in Isolates of Candida auris Directly Contribute to Reduced Azole Susceptibility","volume":"62","author":"Healey","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e03333-20","DOI":"10.1128\/mBio.03333-20","article-title":"Genome-Wide Analysis of Experimentally Evolved Candida auris Reveals Multiple Novel Mechanisms of Multidrug Resistance","volume":"12","author":"Carolus","year":"2021","journal-title":"mBio"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Li, J., Aubry, L., Brandalise, D., Coste, A.T., Sanglard, D., and Lamoth, F. (2024). Upc2-mediated mechanisms of azole resistance in Candida auris. Microbiol. Spectr., 12.","DOI":"10.1128\/spectrum.03526-23"},{"key":"ref_37","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_38","doi-asserted-by":"crossref","unstructured":"Jackson, B.R., Chow, N., Forsberg, K., Litvintseva, A.P., Lockhart, S.R., Welsh, R., Vallabhaneni, S., and Chiller, T. (2019). On the Origins of a Species: What Might Explain the Rise of Candida auris?. J. Fungi, 5.","DOI":"10.3390\/jof5030058"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.cmi.2020.12.030","article-title":"Outbreak of Candida auris infection in a COVID-19 hospital in Mexico","volume":"27","author":"AlemanBocanegra","year":"2021","journal-title":"Clin. Microbiol. Infect."}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/10\/6\/392\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:51:26Z","timestamp":1760107886000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/10\/6\/392"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,30]]},"references-count":39,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6]]}},"alternative-id":["jof10060392"],"URL":"https:\/\/doi.org\/10.3390\/jof10060392","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,30]]}}}