Transcriptional Convergence and Phenotypic Validation of Chitin-Mediated Cell Wall Remodeling in Echinocandin-Stressed Candida auris

Candida auris is a multidrug-resistant fungal pathogen for which echinocandins are recommended first-line therapy, yet its adaptive responses to this drug class remain incompletely understood. This study defined the genome-wide transcriptional responses of C. auris strain B11244 (Clade IV) to subinhibitory caspofungin, micafungin, and anidulafungin and examined whether shared responses corresponded to cell-wall remodeling. Growth-based broth microdilution indicated susceptibility to all three drugs by MIC (caspofungin, approximately 0.5–1 µg/mL; micafungin, 0.125 µg/mL; anidulafungin, approximately 0.03125 µg/mL), but caspofungin uniquely produced marked paradoxical growth at 4–8 µg/mL, consistent with caspofungin tolerance. RNA sequencing identified 2920, 2130, and 2149 differentially expressed genes following caspofungin, micafungin, and anidulafungin exposure, respectively, including 283 co-upregulated and 157 co-downregulated genes. All three drugs induced a conserved cell-wall integrity program marked by transcriptional induction of Bck1-Mkc1 and Hog1 MAPK pathway components and an 18-gene signature involved in chitin synthesis and cell-wall cross-linking. The response was strongest with caspofungin, and RT-qPCR corroborated representative transcriptional changes. No canonical FKS1 hotspot mutation was detected; an I1572L substitution was predicted to be structurally neutral. Calcofluor White microscopy showed qualitatively enhanced peripheral fluorescence following each treatment, whereas colorimetric glucosamine measurement demonstrated significantly increased bulk chitin only with caspofungin (149% of control); micafungin (120%) and anidulafungin (98%) did not differ significantly from control. Taken together, these findings are consistent with inducible, MAPK-associated cell-wall remodeling as a potential FKS1-independent contributor to echinocandin tolerance, while showing that transcriptional convergence does not imply uniform phenotypic outcomes.