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.

In Vitro Antifungal Activity of Manogepix and Other Antifungal Agents against South African Candida auris Isolates from Bloodstream Infections

“…Laboratories were requested to submit all Candida species isolated from blood cultures to the National Institute for Communicable Diseases (NICD) in Johannesburg and to provide the corresponding patient demographic details and Candida species identification obtained by the submitting laboratory. The isolate data in this study were published previously ( 16 , 30 ).…”

“…We used the sequenced genomes of 84 C. auris isolates to perform a phylogenetic and resistance mutation analysis, as described previously ( 16 , 30 ). Of these 84 isolates, 62 were resistant to fluconazole alone, 19 were multidrug resistant (i.e., resistant to fluconazole and amphotericin B), 2 were pandrug resistant (i.e., resistant to fluconazole, amphotericin B, and micafungin), and 1 was resistant to amphotericin B alone.…”

“…We included reference genome strains representing clade I (PEKT02), clade II (PYFR01), clade IV (PYGM01), and clade V ( SRR9007776 ), which we obtained from NCBI BLAST. Single nucleotide polymorphism variants were called using the Northern Arizona Single Nucleotide Polymorphism (NASP) pipeline, which is publicly available, as described previously ( 30 ). Phylogenetic analysis was performed using MEGA software.…”

ClaID: a Rapid Method of Clade-Level Identification of the Multidrug Resistant Human Fungal Pathogen Candida auris

“…However, subsequent reports suggest dissemination of strains - isolates obtained in Russia clustered with South Asian clade strains and isolates from the UK were of multiple geographical origins ( 21 , 22 ). Strains belonging to clades 1, 2 and 4 were obtained in Singapore, while clades 2, 3 and 4 strains were isolated in South Africa ( 23 , 24 ), suggesting mixing of clades in different geographical zones. These reports also hint that the area of isolation will soon cease to be a reliable basis of clade-typing.…”

Emergence of Candida auris in intensive care units in Algeria

“…Since its emergence, C. auris has been identified in invasive infections and nosocomial outbreaks reported from various countries across six continents 5 . Whole‐genome sequencing has divided C. auris isolates in five distinct clonal lineages, commonly referred to as clade I (South Asian), clade II (East Asian), clade III (African), clade IV (South American) and clade V (Iranian) 16 . Clades I and III are the most widespread, with numerous reported cases and a broad geographic distribution 17 .…”