Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates

Abstract

In South Africa, Candida auris was the third most common cause of candidemia in 2016-2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hospitals and a colonization study during a neonatal unit outbreak. The first known South African C. auris strain from 2009 clustered in clade IV. Overall, 98 strains clustered within clade III (85%), 14 within clade I (12%) and three within clade IV (3%). All environmental and colonizing strains clustered in clade III. We also identified known clade-specific resistance mutations in the ERG11 and FKS1 genes. Identification of clade I strains between 2016 and 2018 suggests introductions from South Asia followed by local transmission. SNP analysis characterized most C. auris strains into clade III, the clade first reported from South Africa, but the presence of clades I and IV strains also suggest early introductions from other regions.

Keywords: Candida auris; South Africa; clades; single nucleotide polymorphisms; whole genome sequencing.

Figure 1.

WGS SNP and resistance gene mutation analysis of 115 invasive, environmental and colonizing South African Candida auris strains collected between 2009 and 2018 during national laboratory-based candidemia and Candida auris surveillance, an environmental survey and a neonatal unit outbreak. There were 211 626 SNPs in total with a coverage breadth of 62% and this is an unrooted maximum parsimony tree with 500 bootstrap replicates. The consistency index was 0.89 and the number of phylogenetic sites were 211 626. Circles represent invasive isolates, red squares represent colonizing strains and the green square represents the one isolate from urine in 2018. The red triangles represent the environmental strains and the light blue star represents the first C. auris strain isolated in 2009.

Figure 2.

Epidemic curve of cases of Candida auris bloodstream infection by clade (I – green, III – red, IV – blue and not sequenced – grey) and collection date (2016–2017).

Figure 3.

Epidemic curve of cases of Candida auris bloodstream infection by clade (I – green, III – red, IV – blue and not sequenced – grey) and acute-care hospital facility (collection dates: 2016–2017).