Analysis of antifungal resistance-specific mutations

Nonsynonymous mutations including SNPs and indels linked to resistance to antifungal drugs and their correlations with antifungal MICs were investigated. We first analyzed the nonsynonymous mutations of all genes among isolates that belonged to the same MLST genotype to eliminate MLST-specific SNPs. Subsequently, we compared these mutations with those in antifungal-susceptible or F-SDD isolates to identify candidate antifungal resistance-specific or FR-specific mutations. For all isolates, mutations in genes associated with resistance to azole drugs (PDR1), echinocandins (FKS1 and FKS2), 5-fluorocytosine (FCY1, FCY2, FPS1, and FPS2), and representative ERG (ERG 1–11, ERG 13, ERG 20, and ERG 25–27) and MSH2 genes were examined (10, 49–51). For FR isolates, nonsynonymous mutations in 182 genes identified previously (10, 52) were examined among the same MLST genotype isolates, and mutations in genes with FR-specific SNPs were analyzed for their associations with azole resistance using information from the Candida Genome Database (http://www.candidagenome.org/). After excluding MLST genotype-specific Pdr1p SNPs, which were present in both F-SDD and FR isolates of the same ST (as shown in Table S2), the remaining Pdr1p SNPs that were exclusively present in FR isolates were categorized as FR-specific SNPs.