Journal
EMERGING MICROBES & INFECTIONS
Volume 10, Issue 1, Pages 1300-1308Publisher
TAYLOR & FRANCIS LTD
DOI: 10.1080/22221751.2021.1944323
Keywords
Candida auris; whole genome sequencing; clades; South Africa; single nucleotide polymorphisms
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Funding
- National Health Laboratory Service Research Trust [94523, 94716]
- National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
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The study identified different clades of C. auris isolates in South Africa, confirming introductions from South Asia followed by local transmission, while also indicating early introductions from other regions.
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.
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