Development and Application of a Short Tandem Repeat Multiplex Typing Assay for Candida tropicalis

Bram Spruijtenburg; Merlijn H I van Haren; Anuradha Chowdhary; Jacques F Meis; Theun de Groot

doi:10.1128/spectrum.04618-22

Development and Application of a Short Tandem Repeat Multiplex Typing Assay for Candida tropicalis

Microbiol Spectr. 2023 Jan 30;11(2):e0461822. doi: 10.1128/spectrum.04618-22. Online ahead of print.

Authors

Bram Spruijtenburg^{1

2}, Merlijn H I van Haren¹, Anuradha Chowdhary³, Jacques F Meis^{1

2

4}, Theun de Groot^{1

2}

Affiliations

¹ Department of Medical Microbiology and Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
² Centre of Expertise in Mycology, Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
³ Medical Mycology Unit, Department of Medical Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India.
⁴ Department I of Internal Medicine, University of Cologne, Excellence Center for Medical Mycology, Cologne, Germany.

Abstract

Candida tropicalis is a clinically important yeast that causes candidemia in humans with a high mortality rate. The yeast primarily infects immunocompromised patients, and causes outbreaks in health care facilities. Antifungal resistant isolates have been reported. We developed a short tandem repeat (STR) typing scheme for C. tropicalis to enable fast, cost-effective, and high-resolution genotyping. For the development of the typing scheme, 6 novel STR markers were selected, combined into 2 multiplex PCRs. In total, 117 C. tropicalis isolates were typed, resulting in the identification of 104 different genotypes. Subsequently, the outcome of STR typing of 10 isolates was compared to single nucleotide polymorphism (SNP) calling from whole-genome sequencing (WGS). Isolates with more than 111 SNPs were differentiated by the typing assay. Two isolates, which were identical according to SNP analysis, were separated by STR typing in 1 marker. To test specificity, the STR typing was applied to 15 related yeast species, and we found no amplification of these targets. For reproducibility testing, 2 isolates were independently typed five times, which showed identical results in each experiment. In summary, we developed a reliable and multiplex STR genotyping for C. tropicalis, which was found to correlate well to SNP calling by WGS. WGS analysis from and extensive collection of isolates is required to establish the precise resolution of this STR assay. IMPORTANCE Candida tropicalis frequently causes candidemia in immunocompromised patients. C. tropicalis infections have a high mortality rate, and the yeast is able to cause outbreaks in health care facilities. Further, antifungal resistant isolates are on the rise. Genotyping is necessary to investigate potential outbreaks. Here, we developed and applied a STR genotyping scheme in order to rapidly genotype isolates with a high-resolution. WGS SNP outcomes were highly comparable with STR typing results. Altogether, we developed a rapid, high-resolution, and specific STR genotyping scheme for C. tropicalis.

Keywords: Candida tropicalis; PCR; genotyping; short tandem repeats; whole-genome sequencing.