Development and Validation of Taqman Chemistry Probe-Based Rapid Assay for the Detection of Echinocandin-Resistance in Candida Auris

Authors

YanChun Zhu, Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
Kelli M. Hager, Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
Swati R. Manjari, Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
Nilesh K. Banavali, Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
Vishnu Chaturvedi, Westchester Medical Center, New York Medical College, Valhalla, New York, USA.
Sudha Chaturvedi, Mycology Laboratory, Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA.

Author Type(s)

Faculty

DOI

10.1128/jcm.01767-22

Journal Title

Journal of Clinical Microbiology

First Page

e0176722

Document Type

Article

Publication Date

4-20-2023

Department

Pathology, Microbiology and Immunology

Abstract

Candida auris is a multidrug-resistant yeast pathogen causing outbreaks in health care facilities worldwide, and the emergence of echinocandin-resistant C. auris is a concern. Currently used Clinical and Laboratory Standards Institute (CLSI) and commercial antifungal susceptibility tests (AFST) are phenotype-based, slow, and not scalable, limiting their effectiveness in the surveillance of echinocandin-resistant C. auris. The urgent need for accurate and rapid methods of assessment of echinocandin resistance cannot be overstated, as this class of antifungal drugs is preferred for patient management. We report the development and validation of a TaqMan chemistry probe-based fluorescence melt curve analysis (FMCA) following asymmetric polymerase chain reaction (PCR) to assess mutations within the hot spot one (HS1) region of the gene responsible for encoding 1,3-β-d-glucan synthase that is a target for echinocandins. The assay correctly identified F635C, F635Y, F635del, F635S, S639F or S639Y, S639P, and D642H/R645T mutations. Of these mutations, F635S and D642H/R645T were not involved in echinocandin resistance, while the rest were, as confirmed by AFST. Of 31 clinical cases, the predominant mutation conferring echinocandin resistance was S639F/Y (20 cases) followed by S639P (4 cases), F635del (4 cases), F635Y (2 cases), and F635C (1 case). The FMCA assay was highly specific and did not cross-react with closely and distantly related and other yeast and mold species. Structural modeling of the Fks1 protein, its mutants, and docked conformations of three echinocandin drugs suggest a plausible Fks1 binding orientation for echinocandins. These findings lay the groundwork for future evaluations of additional mutations and their impact on the development of drug resistance. The TaqMan chemistry probe-based FMCA would allow rapid, high throughput, and accurate detection of mutations conferring echinocandin resistance in C. auris.

Recommended Citation

Zhu, Y., Hager, K. M., Manjari, S. R., Banavali, N. K., Chaturvedi, V., & Chaturvedi, S. (2023). Development and Validation of Taqman Chemistry Probe-Based Rapid Assay for the Detection of Echinocandin-Resistance in Candida Auris. Journal of Clinical Microbiology, 61 (4), e0176722. https://doi.org/10.1128/jcm.01767-22