Candida tropicalis WGS

Candida tropicalis is a clinically relevant yeast which 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. Here, 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 six novel STR markers were selected, combined into two multiplex PCRs. In total, 117 C. tropicalis isolates were typed, including 12 azole resistant isolates, resulting in the identification of 104 different genotypes. The outcome of STR typing of ten isolates was then compared to single nucleotide polymorphism (SNP) calling from whole genome sequencing (WGS). Isolates with >111 SNPs were differentiated by the typing assay. Two isolates which were identical according to SNP analysis were separated by STR typing in one 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, two isolates were typed independently five times, which showed identical results in each experiment. ERG11 mutation screening on azole resistant isolates revealed no mutations except for one isolate, which harbored a novel Y257N mutation. In summary, we developed a reliable, rapid, and high resolution STR genotyping for C. tropicalis, which was found to correlate well to SNP calling by WGS.