{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T01:04:30Z","timestamp":1790298270779,"version":"4.1.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Candida auris is an emerging multidrug-resistant pathogen. Interpretation of susceptibility testing can be difficult since minimum inhibitory concentration (MIC) breakpoints have not been fully established.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>All C. auris isolates from unique patients identified at a large urban hospital between 2020 and 2024 (n = 66) underwent whole-genome sequencing (WGS). Genomic DNA was extracted from pure culture isolates and underwent PCR-free library preparation. WGS was performed on an Illumina platform (NextSeq2000) with an average coverage of 50\u00d7. Genomic analysis was conducted via an adapted GATK-based pipeline using the B11205 strain as the reference genome based on the CDC (MycoSNP) protocol. All isolates underwent FKS1 gene Sanger sequencing for confirmation of WGS results. Genotypic results were correlated with antifungal susceptibility testing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>All clinical isolates were part of Clade I and carried azole resistance mutations in ERG11, TAC1b, and CDR1, consistent with 100% phenotypic fluconazole resistance. Across all isolates, 5 distinct missense variants in FKS1 were identified: one case with p.Ser639Tyr, one case with both a p.Arg1354Ser and a p.Asp642His, 7 cases with p.Met690Ile, and 9 cases with p.Val1818Ile. Isolates with known echinocandin resistance conferring mutations p.Ser639Tyr and p.Arg1354Ser were resistant to micafungin and anidulafungin. Two isolates with Met690Ile were resistant to caspofungin alone.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>With potential resistance to all 3 major antifungal classes of drugs, C. auris is an emerging public health threat. Early detection of echinocandin resistance by molecular methods could impact treatment course to include novel antifungal agents. Further study of the FKS1 Met690Ile variant is warranted.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/clinchem\/hvae185","type":"journal-article","created":{"date-parts":[[2025,1,3]],"date-time":"2025-01-03T09:50:12Z","timestamp":1735897812000},"page":"185-191","source":"Crossref","is-referenced-by-count":9,"title":["Genetic and Phenotypic Intra-Clade Variation in <i>Candida auris<\/i> Isolated from Critically Ill Patients in a New York City Tertiary Care Center"],"prefix":"10.1093","volume":"71","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6706-0700","authenticated-orcid":false,"given":"Marie C","family":"Smithgall","sequence":"first","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdullah","family":"Kilic","sequence":"additional","affiliation":[{"name":"Department of Pathology, Wake Forest University School of Medicine , Winston Salem, NC ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell","family":"Weidmann","sequence":"additional","affiliation":[{"name":"Department of Population Medicine, State University of New York at Albany , Albany, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4422-2882","authenticated-orcid":false,"given":"Kenneth","family":"Ofori","sequence":"additional","affiliation":[{"name":"Department of Pathology, Indiana University School of Medicine , Indianapolis, IN ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Gu","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lahari","family":"Koganti","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijun","family":"Mi","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongai","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiuhong","family":"Pang","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahesh","family":"Mansukhani","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Hsiao","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fann","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Pathology and Cell Biology, Columbia University Irving Medical Center , New York, NY ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,3]]},"reference":[{"key":"2025010523234777000_hvae185-B1","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":"2025010523234777000_hvae185-B2","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 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multidrug resistance: defining the new normal","volume":"131","author":"Lockhart","year":"2019","journal-title":"Fungal Genet Biol"},{"key":"2025010523234777000_hvae185-B12","doi-asserted-by":"crossref","first-page":"2788","DOI":"10.3389\/fmicb.2019.02788","article-title":"Review on antifungal resistance mechanisms in the emerging pathogen Candida auris","volume":"10","author":"Chaabane","year":"2019","journal-title":"Front Microbiol"},{"key":"2025010523234777000_hvae185-B13","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1146\/annurev-micro-032521-015858","article-title":"Candida auris genetics and emergence","volume":"77","author":"Chowdhary","year":"2023","journal-title":"Annu Rev Microbiol"},{"key":"2025010523234777000_hvae185-B14","doi-asserted-by":"crossref","first-page":"489","DOI":"10.7326\/M22-3469","article-title":"Worsening spread of Candida auris in the United States, 2019 to 2021","volume":"176","author":"Lyman","year":"2023","journal-title":"Ann Intern 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