Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses

Abstract

Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. aurisIMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

Keywords: Candida auris; antifungal resistance; emerging species; genome analysis; population genetics.

FIG 1

Global distribution of Candida auris clades. (a) Phylogenetic tree of 304 C. auris whole-genome sequences clustering into four major clades. Maximum likelihood phylogeny using 222,619 SNPs based on 1,000 bootstrap replicates. (b) Map detailing C. auris clade distribution by country (n = 19). (c) Phylogenetic tree of clades I to IV. The countries are indicated by color.

FIG 2

Dating the emergence of Candida auris. (a) Distribution of collection dates for source specimens and environmental samples by clade. (b) Maximum clade credibility phylogenetic tree of C. auris estimated using BEAST (strict clock and coalescent model). Purple bars indicate 95% highest probability density around a node. (c) Marginal posterior distributions for the date of the most recent common ancestor (TMRCA) of Candida auris clades I, II, III, and IV. The Bayesian coalescent analysis was performed with BEAST.

FIG 3

Population structure and genetic differentiation in Candida auris. (a and b) PCA analysis (a) and phylogenetic tree (b) of 304 C. auris isolates depicting genome-wide population genetic metrics of nucleotide diversity (π) and Tajima’s D (TD) (td in panel b) for each clade. (c) Genome-wide distribution of TD for each clade. (d) Average of genome-wide (5-kb windows) variation in fixation index (F_ST), for pairwise comparisons in each clade as designated in the first vertical and horizontal row. (e) Genome-wide (5-kb windows) pairwise F_ST and pairwise nucleotide diversity (D_XY) between clade I versus clade III and clade I versus clade II are shown across the 10 largest scaffolds of the B8441 reference genome. All pairwise comparisons of π, TD, F_ST, and D_XY are shown in Fig. S2 in the supplemental material.

FIG 4

Antifungal susceptibility and point mutations in drug targets in Candida auris. (a) Phylogenetic tree detailing clade, susceptibility to fluconazole (FCZ), amphotericin B (AMB), and micafungin (MCF), and point mutations in lanosterol 14-alpha-demethylase ERG11 (Y132F, K143R, and F126L) and beta-1,3-d-glucan synthase FKS1 (S639Y/P/F) associated with resistance. (b) Bar plot describing frequency (as a percentage) (y axis) of Y132F, K143R, and F126L point mutations in ERG11 for each clade.