Antifungal susceptibility testing identifies the abdominal cavity as a source of Candida glabrata resistant isolates.

To identify unrecognized niches of resistant Candida isolates and compartmentalization we retrospectively studied the antifungal susceptibility of 1,103 Candida spp. isolates from blood cultures, non-blood sterile samples, and non-sterile samples. Antifungal susceptibility was assessed by EUCAST E.Def 7.3.2; sequencing and genotyping of the FKS1-2 and ERG11 genes were carried out for non-wild type isolates. Resistance compartmentalization (presence of resistant and susceptible isogenic isolates in different anatomical sites of a given patient) was studied. Clinical charts of patients carrying non-wild type isolates were reviewed. Most isolates (63%) were Candida albicans, regardless the clinical source; Candida glabrata (27%) was the second most frequently found species in abdominal cavity samples. Fluconazole and echinocandin resistance rates were 1.5% and 1.3%, respectively, and highest in C. glabrata. We found 22 genotypes among non-wild type isolates, none of them widespread across the hospital. Fluconazole/echinocandin resistance rates of isolates from abdominal cavity (3.2%/3.2%) were significantly higher than those from blood cultures (0.7%/1.3%) (P<0.05). Overall, fifteen patients with different forms of candidiasis were infected by resistant isolates, 80% of whom had received antifungals before or at the time of isolate collection; resistance compartmentalization was found in six patients, mainly due to C. glabrata. The highest antifungal resistance rate was detected in isolates from the abdominal cavity, mostly C. glabrata. Resistance was not caused by the spread of resistant clones, but because of antifungal treatment. Resistance compartmentalization illustrates how resistance might be overlooked if susceptibility testing is restricted to bloodstream isolates.