Candida auris Clinical Isolates Associated with Outbreak in Neonatal Unit of Tertiary Academic Hospital, South Africa

Abstract

Candida auris was first detected at a university-affiliated hospital in Johannesburg, South Africa, in 2009. We used whole-genome sequencing to describe the molecular epidemiology of C. auris in the same hospital during 2016-2020; the neonatal unit had a persistent outbreak beginning in June 2019. Of 287 cases with culture-confirmed C. auris infection identified through laboratory surveillance, 207 (72%) had viable isolates and 188 (66%) were processed for whole-genome sequencing. Clade III (118/188, 63%) and IV (70/188, 37%) isolates co-circulated in the hospital. All 181/188 isolates that had a fluconazole MIC >32 µg/mL had ERG11 mutations; clade III isolates had VF125AL substitutions, and clade IV isolates had K177R/N335S/E343D substitutions. Dominated by clade III, the neonatal unit outbreak accounted for 32% (91/287) of all cases during the study period. The outbreak may have originated through transmission from infected or colonized patients, colonized healthcare workers, or contaminated equipment/environment.

Keywords: Candida auris; South Africa; antifungal resistance; antimicrobial resistance; fungi; genome analysis; population genetics.

Figure 1

Epidemic curve by ward location for 287 laboratory-confirmed cases of Candida auris infection or colonization at an academic tertiary hospital, South Africa, March 2016–July 2020. ICU, intensive care unit.

Figure 2

Phylogenetic tree depicting clade distribution and fluconazole resistance mutations of 188 invasive or colonizing South African Candida auris strains isolated from patients admitted to a large metropolitan hospital in South Africa, 2016–2020. The unrooted maximum-parsimony tree was created using MEGA software (https://www.megasoftware.net) using 287,338 single-nucleotide polymorphisms based on 1,000 bootstrap replicates. Scale bar indicates number of pairwise differences. FCZ, fluconazole.

Figure 3

Clade distribution of 188 South African Candida auris isolates from patients admitted to a large metropolitan hospital classified by the patients’ ward locations, South Africa, 2016–2020. ICU, intensive care unit.

Figure 4

Root-to-tip regression analysis of 67 South African Candida auris outbreak isolates from the neonatal ward of a large metropolitan hospital in South Africa. Genetic distance is plotted against sampling time. Every data point represents a tip on the phylogeny. Black line indicates correlation coefficient for the regression. Green lines represent the evolutionary rate in substitutions/site/day.

Figure 5

Maximum clade credibility tree of 118 South Africa clade III Candida auris isolates from patients at an academic tertiary hospital in South Africa estimated using BEAST strict clock and coalescent model (24). Red tips represent cases from the neonatal ward, blue bars represent 95% highest probability density black dashed line indicates clade III tMRCA, and red dashed line indicates outbreak strain tMRCA. tMRCA, time to most recent common ancestor.