Accelerated Increase in Candida auris Bloodstream Infections during COVID-19 Pandemic, South Africa

The COVID-19 pandemic coincided with rising secondary bloodstream infections (BSIs) from multidrug-resistant organisms, including Candida auris. To assess candidemia trends, we conducted a retrospective analysis of blood culture isolates from public and private laboratories in South Africa taken during January 2019-June 2022. We evaluated weekly aggregated Candida BSI counts and COVID-19 cases using segmented regression within an interrupted time-series framework. In total, 15,393 candidemia cases were identified, 70% from the private sector. C. parapsilosis accounted for 39% of cases, whereas C. auris represented 26%. The proportion of C. auris increased significantly from 17% in 2019 to 31% in 2021 (p<0.01). After the pandemic onset, Candida BSIs rose by 11 cases per week (p = 0.03), largely driven by C. auris (+5 cases/week; p<0.01); peaks coincided with COVID-19 waves. Those results highlight an accelerated shift toward C. auris in Candida BSIs and the urgent need for enhanced surveillance, diagnostics, and infection prevention.