ER stress selects for Candida auris survivors with acquired fluconazole resistance and caspofungin tolerance

Exposure to endoplasmic reticulum (ER) stress can drive the emergence of antifungal resistance in pathogenic fungi, but the underlying mechanisms remain poorly understood. Here, we show that treatment of Candida auris B12037 (clade 3) with the ER stressor tunicamycin selects for survivors with acquired resistance to fluconazole and, in a subset, tolerance to caspofungin. Pharmacological inhibition revealed that caspofungin tolerance, but not fluconazole resistance, requires the Hsp90-calcineurin axis. RNA-seq analysis of the parental strain exposed to tunicamycin uncovered a coordinated stress response characterized by up-regulation of cell wall biosynthesis, transmembrane transport, and autophagy, alongside global repression of translation and energy metabolism. In the resistant survivors, fluconazole resistance correlated with up-regulation of the efflux pump MDR1, with isolate #10 additionally exhibiting ERG11 overexpression. Caspofungin tolerance in isolate #10 was associated with up-regulation of multiple chitin synthase genes (CHS1, CHS3, CHS5), suggesting chitin-mediated cell wall remodeling. Isolate #19 displayed a distinct pattern, indicating alternative mechanisms of caspofungin tolerance. These findings reveal that ER stress selects for C. auris survivors with divergent antifungal resistance profiles through distinct molecular pathways, highlighting the potential for stress-induced evolution of multidrug resistance in this critical pathogen.