Survival of the unfittest: clinical emergence of hyper-multidrug-resistant Nakaseomyces glabratus with rare nonfunctional Erg3 and Erg11 and severely impaired fitness.

Carolus, H.; Biriukov, V.; Vreys, J.; Lobo Romero, C.; Paolo Herrera, J.; Vergauwen, R.; Sofras, D.; Vanreppelen, G.; Vinken, L.; Britto Xavier, B.; Gabaldon, T.; Lagrou, K.; Naesens, R.; Van Dijck, P.

doi:10.1101/2025.02.05.636719

bioRxiv · 10.1101/2025.02.05.636719

Survival of the unfittest: clinical emergence of hyper-multidrug-resistant Nakaseomyces glabratus with rare nonfunctional Erg3 and Erg11 and severely impaired fitness.

Carolus, H.·Biriukov, V.·Vreys, J.·Lobo Romero, C.·Paolo Herrera, J.·Vergauwen, R.·Sofras, D.·Vanreppelen, G.·Vinken, L.·Britto Xavier, B.·Gabaldon, T.·Lagrou, K.·Naesens, R.·Van Dijck, P.

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Abstract

BackgroundNakaseomyces glabratus (Candida gabrata) poses a significant clinical challenge due to common drug resistance. We report a case of a complicated urinary tract infection (UTI) progressing to prostatitis and urosepsis, with the emergence of a hyper-multidrug-resistant isolate with low stress tolerance, slow growth and a short life span. This study elucidates the genetic mechanisms and phenotypic characteristics underlying antifungal hyper-resistance with strong fitness trade-offs, and explores potential alternative therapies for resistant UTIs. MethodsWhole-genome sequencing was performed to identify resistance-associated mutations and gene knock-out strains were generated to assess the relative impact of putative loss-of-function (LoF) mutations on antifungal resistance, fitness and membrane sterol composition. Drug susceptibility testing of the antibiotic nitroxoline and related compounds was conducted to evaluate it as a therapeutic alternative and study the mechanism of action. FindingsLoss-of-function mutations in ERG3 and ERG11 were identified and linked to the accumulation of 4,14-dimethylzymosterol and lanosterol instead of ergosterol. Engineered ERG3{Delta}+ERG11{Delta} strains recapitulated the clinical isolates hyper-multidrug resistance and associated fitness deficits. While ERG3{Delta} strains showed no resistance but enhanced thermotolerance, ERG11{Delta} and ERG3{Delta}+ERG11{Delta} strains exhibited multidrug resistance with severe fitness trade-offs. Interestingly, ERG3{Delta}+ERG11{Delta} strains showed mild resistance to flucytosine, but an additional FUR1 mutation in the clinical isolate most probably underlies hyper-resistance to flucytosine. The UTI antibiotic nitroxoline demonstrated high antifungal activity against all strains, and the LoF of ERG3 and/or ERG11 induced collateral sensitivity to this drug. Testing of related compounds suggest a mode of action beyond iron chelation. InterpretationThis case demonstrates that hyper-resistant strains of N. glabratus can emerge despite significant fitness costs and persist under prolonged antifungal therapy in specific clinical settings. These findings underscore the importance of vigilant antifungal resistance monitoring and highlight nitroxoline as a promising alternative treatment for complicated fungal UTIs. These results challenge the notion that strains with fitness deficits are clinically irrelevant and emphasize the need for novel therapeutic strategies including repurposed agents.

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Carolus, H., Biriukov, V., Vreys, J., Lobo Romero, C., Paolo Herrera, J., Vergauwen, R., Sofras, D., Vanreppelen, G., Vinken, L., Britto Xavier, B., Gabaldon, T., Lagrou, K., Naesens, R., Van Dijck, P.. 2025-02-05. Survival of the unfittest: clinical emergence of hyper-multidrug-resistant Nakaseomyces glabratus with rare nonfunctional Erg3 and Erg11 and severely impaired fitness.. https://doi.org/10.1101/2025.02.05.636719

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