Genomic Epidemiology of Candida auris in Qatar Reveals Hospital Transmission Dynamics and a South Asian Origin.

Husam Salah,Clement K M Tsui,Sarah Salameh,Lamya Dalil,Walid Al-Wali,Sathyavathi Sundararaju,Fatma Ben Abid,Patrick Tang

doi:10.3390/jof7030240

Abstract

Candida auris is an emerging, multidrug-resistant fungal pathogen that has become a public health threat with an increasing incidence of infections worldwide. Candida auris spreads easily among patients within and between hospitals. Infections and outbreaks caused by C. auris have been reported in the Middle East region including Oman, Kuwait, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. Pathogen whole genome sequencing (WGS) was used to determine the epidemiology and drug resistance mutations of C. auris in Qatar. Forty-four samples isolated from patients in three hospitals and the hospital environment were sequenced by Illumina NextSeq. Core genome single nucleotide polymorphisms (SNPs) revealed that all isolates belonged to the South Asian lineage with genetic heterogeneity that suggests previous acquisition from foreign healthcare. The genetic variability among the outbreak isolates in the two hospitals (A and B) was low. Four environmental isolates clustered with the related clinical isolates, and epidemiologically linked isolates clustered together, suggesting that the ongoing transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Prominent mutations Y132F and K143R in ERG11 linked to increased fluconazole resistance were detected.

Highlights

Invasive candidiasis is of major public health importance because it is associated with increased mortality, higher healthcare costs, and longer hospital stays compared with other healthcare-associated infections [1]
Candida auris has become an emerging opportunistic pathogen, which was first reported in 2009 as an isolate from the external ear of an inpatient at a hospital in Japan [3]. It has since been identified as a cause of nosocomial bloodstream infections (BSI) in numerous countries in East Asia, the Middle East, Africa, the United States, and Europe [4,5,6,7,8,9]
We sequenced a total of 44 Candida auris genomes, of which 40 were from humans and four were from the hospital environment

Summary

Introduction

Invasive candidiasis is of major public health importance because it is associated with increased mortality, higher healthcare costs, and longer hospital stays compared with other healthcare-associated infections [1] This problem is compounded by the progressive increase in antifungal resistance among clinically relevant Candida spp. such as C. albicans, C. parapsilosis, C. glabrata, C. auris, and C. tropicalis driven by the widespread use of antifungal drugs in human healthcare [1,2]. Candida auris has become an emerging opportunistic pathogen, which was first reported in 2009 as an isolate from the external ear of an inpatient at a hospital in Japan [3] It has since been identified as a cause of nosocomial bloodstream infections (BSI) in numerous countries in East Asia, the Middle East, Africa, the United States, and Europe [4,5,6,7,8,9]. Mutations related to reduced susceptibility to azoles, amphotericin B, and echinocandins were characterized from the genomes

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Conclusion