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

Emerg Microbes Infect. 2021 Dec;10(1):1300-1308. doi: 10.1080/22221751.2021.1944323.

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.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Antifungal Agents / pharmacology
  • Candida / classification*
  • Candida / drug effects
  • Candida / genetics*
  • Candida / isolation & purification
  • Candidemia / epidemiology
  • Candidemia / microbiology
  • Candidiasis / epidemiology*
  • Candidiasis / microbiology*
  • Child
  • Child, Preschool
  • Drug Resistance, Fungal
  • Genome, Fungal
  • Humans
  • Infant
  • Infant, Newborn
  • Male
  • Microbial Sensitivity Tests
  • Middle Aged
  • Phylogeny
  • South Africa / epidemiology
  • Whole Genome Sequencing
  • Young Adult

Substances

  • Antifungal Agents

Grants and funding

This work was supported by the National Health Laboratory Service Research Trust [grant numbers 94523 and 94716] and the National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa.