The antifungal flucytosine (5-fluorocytosine [5FC]) is a prodrug metabolized to its toxic form, 5-fluorouracil (5FU), only by organisms expressing cytosine deaminase. One such organism is Candida glabrata, which has emerged as the second most common agent of bloodstream and mucosal candidiasis. This emergence has been attributed to the high rate at which C. glabrata develops resistance to azole antifungals. As an oral agent, 5FC represents an attractive alternative or complement to azoles; however, the frequency of 5FC resistance mutations and the mechanisms by which these mutations confer resistance have been explored only minimally. On RPMI 1640 medium containing 1 g/ml 5FC (32-fold above the MIC, but less than 1/10 of typical serum levels), resistant mutants occurred at a relatively low frequency (2 ؋ 10 ؊7 ). Three of six mutants characterized were 5FU cross-resistant, suggesting a mutation downstream of the Fcy1 gene (cytosine deaminase), which was confirmed by sequence analysis of the Fur1 gene (uracil phosphoribosyl transferase). The remaining three mutants had Fcy1 mutations. To ascertain the effects of 5FC resistance mutations on enzyme function, mutants were isolated in ura3 strains. Three of seven mutants harbored Fcy1 mutations and failed to grow in uridinefree, cytosine-supplemented medium, consistent with inactive Fcy1. The remainder grew in this medium and had wild-type Fcy1; further analysis revealed these to be mutated in the Fcy2L homolog of S. cerevisiae Fcy2 (purine-cytosine transporter). Based on this analysis, we characterized three 5FC-resistant clinical isolates, and mutations were identified in Fur1 and Fcy1. These data provide a framework for understanding 5FC resistance in C. glabrata and potentially in other fungal pathogens.Candida glabrata has emerged in recent years as the second most common agent of mucosal and invasive candidiasis (16,17,20,25). This emergence can be attributed largely to the intrinsically low susceptibility of C. glabrata to azole antifungals and its high capacity for acquired azole resistance. Azoles such as fluconazole, introduced in 1990, are used widely due to their low toxicity, availability in both oral and intravenous formulations, and excellent activity versus most other yeasts, including Candida albicans. With one exception, the remaining classes of antifungals are deficient in one or more of these properties; specifically, polyenes such as amphotericin B are toxic, echinocandins such as caspofungin can only be administered intravenously, and allylamines such as terbinafine lack anticandidal activity. The exception is the pyrimidine analog flucytosine (5-fluorocytosine [5FC]), which represents an attractive alternative or complement to azoles, with excellent activity against most C. glabrata isolates (MIC 90 of Յ0.12 g/ml) (21) and the capacity for both oral and intravenous administration (although the latter formulations are not currently available in the United States). 5FC is also well tolerated when moderately dosed (e.g., serum level of 25 g/ml) (2...