Molecular epidemiology of Candida auris in Qatar using whole genome sequence data

Abstract

Candida auris is an emerging, multidrug resistant fungal pathogen that has become a public health threat worldwide. Candida auris spreads easily among patients within and between hospitals, and the incidence of infections has increased substantially in the last decade. Multiple C. auris outbreaks have been reported worldwide including India, USA and United Kingdom. Infections and outbreaks caused by C. auris have also been reported in the Middle East region including Kuwait, Oman, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. This study uses whole genome sequencing (WGS) data to determine the epidemiology and the drug resistance mutations from C. auris in Qatar. Forty samples isolated from the patients and the hospital environment were sequenced by Illumina Nextseq. Core genome SNPs revealed that all isolates belonged to the Indian lineage, which could be originated from the expatriate labour from South Asia. The genetic variability among the isolates was low but comprised of more than one genetic cluster. The environmental isolates were identical to the clinical isolates, and the isolates from patients of different hospitals/outbreaks clustered together, suggesting the transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Mutations associated with azole and echinocandin resistance were discussed.