Multilocus sequence typing (MLST) analysis reveals many novel genotypes and a high level of genetic diversity in Candida tropicalis isolates from Italy and Africa

Abstract

Background: Candida tropicalis is a human pathogenic yeast frequently isolated in Latin America and Asian-Pacific regions, although recent studies showed that it is also becoming increasingly widespread throughout several African and south-European countries. Nevertheless, relatively little is known about its global patterns of genetic variation as most of existing multilocus sequence typing (MLST) data come from Asia and there are no genotyped African isolates.

Objectives: We report detailed genotyping data from a large set of C. tropicalis isolates recovered from different clinical sources in Italy, Egypt and Cameroon in order to expand the allele/genotype library of MLST database (https://pubmlst.org/ctropicalis), and to explore the genetic diversity in this species.

Methods: A total of 103 C. tropicalis isolates were genotyped using the MLST scheme developed for this species. All isolates were also tested for in vitro susceptibility to various antifungals to assess whether certain genotypes were associated with drug-resistance.

Results and conclusions: A total of 104 different alleles were detected across the MLST-loci investigated. The allelic diversity found at these loci resulted in 51 unique MLST genotypes of which 36 (70.6%) were novel. Global optimal eBURST analysis identified 18 clonal complexes (CCs) and confirm the existence of a specific Italian-cluster (CC36). Three CCs were also statistically associated with fluconazole resistance, which was elevated in Cameroon and Egypt. Our data show high genetic diversity in our isolates suggesting that the global population structure of C. tropicalis is still poorly understood. Moreover, its clinical impact in Italy, Egypt and Cameroon appears to be relevant and should be carefully considered.

Keywords: Candida tropicalis; fluconazole resistance; genetic diversity; non-albicans Candida species, candidiasis, multilocus sequence typing (MLST); population structure.

Figure 1

Details of the 18 goeBURST clonal complexes detected in this study. For each cluster, the total number of DSTs is shown. Putative founder genotypes (green) are positioned centrally in each cluster, and subgroup founders are shown in olive green. The size of each rectangle, containing the DST code, reflects the number of isolates with that MLST genotype in the whole dataset employed for the analysis. The lengths of lines are not significant. The clonal complex circled in red (CC36) represents the exclusive genetic cluster found in southern Italy

Figure 2

Minimum spanning tree showing the population structure of Candida tropicalis generated using the DSTs obtained in this study, including those of 1269 isolates deposited in the central MLST database. Each coloured circle represents a unique DST with the genotype code inside. The size of the circles reflects the number of isolates with that genotype, which is also shown in square brackets in the legends. The global distribution of the DSTs is displayed by country and by continent