Azole resistance in Candida glabrata clinical isolates from global surveillance is associated with efflux overexpression

•Fluconazole resistance rates were as high as 8% in North America and almost 6% in Europe.•Resistance to azoles in Candida glabrata can arise during therapy due to induction of overexpression of efflux pumps.•Overexpression of CgCDR1 and CgCDR2 individually or in combination was detected in C. glabrata clinical isolates.•The PDR1 GoF mutations may also play a role in azole-resistance in C. glabrata.•No mutations in ERG11 were observed. We evaluated the azole resistance mechanisms and epidemiology of fluconazole-resistant Candida glabrata from a global survey. A total of 2992 Candida spp. isolates collected during 2018–2019 were susceptibility tested by the broth microdilution reference method following CLSI guidelines. Fluconazole-resistant C. glabrata isolates were submitted to whole genome sequencing and gene expression assays using qRT-PCR. Among 561 CGLA isolates tested, 34 (6.1%) were fluconazole resistant. These isolates were collected from 11 countries and mainly recovered from bloodstream infections (79.4%). All fluconazole-resistant C. glabrata isolates were non-wild type for voriconazole, 24/34 were non-wild type for posaconazole, but only 2/34 were non-wild type for itraconazole. Isavuconazole MIC values ranged from 0.25 to >4 mg/L. Fluconazole-resistant C. glabrata isolates belonged to 14 different sequence types (ST). None of the isolates exhibited alterations in ERG3 or ERG11, the target of azoles. All but two fluconazole-resistant isolates displayed overexpression of CgCDR1 (22/34; 64.7%) and/or CgCDR2 (26/34; 76.5%), while 16 isolates had both genes overexpressed. Overexpression of CgSNQ2 or ERG11 was not observed. Gain of function (GoF) alterations in the transcription factor CgPDR1 were noted in 14 isolates. Four (11.8%) isolates that were nonsusceptible to one or more echinocandins had FKS2 HS1 alterations (2 S663P and 2 F659Y/deletion). Fluconazole-resistant C. glabrata was driven by overexpression of CgCDR1 and/or CgCDR2. GoF alterations in PDR1 that have been associated with increased virulence were observed. Susceptibility results and surveillance data are needed to guide treatment for these isolates.