Short Tandem Repeat Genotyping and Antifungal Susceptibility Testing of Latin American Candida tropicalis Isolates

Abstract

Candida tropicalis is emerging as one of the most common Candida species causing opportunistic infections in Latin America. Outbreak events caused by C. tropicalis were reported, and antifungal resistant isolates are on the rise. In order to investigate population genomics and look into antifungal resistance, we applied a short tandem repeat (STR) genotyping scheme and antifungal susceptibility testing (AFST) to 230 clinical and environmental C. tropicalis isolates from Latin American countries. STR genotyping identified 164 genotypes, including 11 clusters comprised of three to seven isolates, indicating outbreak events. AFST identified one isolate as anidulafungin-resistant and harboring a FKS1 S659P substitution. Moreover, we identified 24 clinical and environmental isolates with intermediate susceptibility or resistance to one or more azoles. ERG11 sequencing revealed each of these isolates harboring a Y132F and/or Y257H/N substitution. All of these isolates, except one, were clustered together in two groups of closely related STR genotypes, with each group harboring distinct ERG11 substitutions. The ancestral C. tropicalis strain of these isolates likely acquired the azole resistance-associated substitutions and subsequently spread across vast distances within Brazil. Altogether, this STR genotyping scheme for C. tropicalis proved to be useful for identifying unrecognized outbreak events and better understanding population genomics, including the spread of antifungal-resistant isolates.

Keywords: Candida tropicalis; PCR; antifungal susceptibility; genotyping; short tandem repeat.

Figure 1

Minimum-spanning tree of 230 C. tropicalis isolates. Branch lengths indicate the similarity between isolates with thick solid lines (variation in one allele), thin solid lines (variation in two alleles), and thin dotted lines (variation in three or more alleles). Azole-intermediate and azole-resistant isolates are demarcated in dotted black lines and solid black lines, respectively. On the left (A), the number of isolates per city are shown in the color key; on the right (B), isolates with ERG11 substitutions and reduced azole susceptibility are shown as in the color key. LATAM, Latin American.