Genetic and Phenotypic Intra-Clade Variation in Candida auris Isolated from Critically Ill Patients in a New York City Tertiary Care Center

作者：Marie C. Smithgall, Abdullah Kılıç, Maxwell D. Weidmann, Kenneth Ofori, Yue Gu, Lahari Koganti, Shijun Mi, Hongai Xia, Jun Yi Shi, Jiuhong Pang, Mahesh Mansukhani, Susan J. Hsiao, Fann Wu · 发表于：Clinical Chemistry · 年份：2025 · DOI：10.1093/clinchem/hvae185 · 被引用次数：6 · 研究领域：Antifungal resistance and susceptibility、Fungal Infections and Studies、Parasitic Diseases Research and Treatment

BACKGROUND: 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. METHODS: 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×. 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. RESULTS: 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. CONCLUSIONS: With potential resi...