Abstract
Echinocandins, which target the fungal β-1,3-glucan synthase (Fks), are essential for treating invasive fungal infections, yet resistance is increasingly reported. While resistance typically arises through mutations in Fks hotspots, emerging evidence suggests a contributing role of changes in membrane sterol composition due to ERG3 mutations. Here, we present a clinical case of Nakaseomyces glabratus (Candida glabrata) in which combined mutations in ERG3 and FKS2, but not FKS2 alone, appear to confer echinocandin resistance. Integrated analyses reveal a recurrent association between Erg3 loss-of-function and echinocandin resistance mediated by Fks variation across Candida species, but exclude Erg3 loss-of-function as an independent resistance mechanism. Advances in Fks structural biology and insights into echinocandin-Fks interactions support a model of epistatic cross-talk between membrane sterols and Fks function. Understanding this interaction is crucial, as it may underlie not only acquired echinocandin resistance but also the broader development of multidrug resistance across major antifungal drug classes.IMPORTANCEA clinical case in which the combination of variation in a β‑1,3‑glucan synthase-encoding gene (FKS2) and the sterol desaturase-encoding gene ERG3 seems to underlie echinocandin resistance, prompted us to hypothesize that membrane sterol changes may modulate, rather than independently cause, Fks‑linked resistance. We were able to explore this hypothesis due to recent developments in the field, such as the release of the FungAMR database, which enables global co‑occurrence analyses; AI‑driven variant effect predictors such as Evolutionary Scale Modeling (ESM) that can explore the impact of thousands of ERG3 alleles; the cryo‑EM resolution of the Fks1 protein; and the first mechanistic model of echinocandin‑Fks1 binding. Together, these advances provide the structural and computational framework needed to delineate our hypothesis that specific sterol variants might influence β‑1,3‑glucan synthase function and drug binding. Further surveillance of this potentially epistatic interaction can be of significant clinical importance amid rising multidrug‑resistant infections, as overlooking such interactions could lead to under‑calling resistance and misguided therapy.