Genomic and Epidemiological Analyses of Candida auris: Unraveling Insights into a Critical Human Fungal Pathogen

Abstract

Fungi are vital microbes present throughout the biosphere. Many species are essential decomposers in the ecosystem, breaking down organic materials and nourishing other lives. Moreover, some have directly influenced human civilization by providing beneficial products, such as edible mushrooms, brewer's yeast, baker's yeast, and antibiotics. However, it's important to note that this group of organisms can also have a "dark side". Each year, fungal pathogens cause approximately 150 million severe infections and 1.7 million deaths. The high rate of infection is compounded by the limited availability of antifungal drugs and the increasing prevalence of antifungal resistance. In response to the global burden of fungal diseases, the World Health Organization published a list of priority fungal pathogens in 2022 and highlighted strategies such as surveillance, sustainable research investments, and public health interventions to combat the increasing fungal threats. My PhD research has focused on surveillance and genomic analyses of several human fungal pathogens, particularly Candida auris. Candida auris is an emerging multidrug-resistant yeast that causes systemic infections with high mortality rates. While initially recognized as a nosocomial pathogen, our genomic analyses of strains isolated from clinical environments, tropical wetlands, fruit surfaces, and dog ears revealed potential transmission routes between diverse environments and patients, including a potential driver for the prevalence of antifungal resistance. Furthermore, our research indicated limited genetic exchange within and between lineages of Candida auris. Through genome-wide association analyses of global Candida auris strains, several known and novel genomic variants were identified associated with susceptibility to azoles, echinocandins, and amphotericin B. Overall, our studies underscore the importance of continuous surveillance to understand potential routes of Candida auris transmission and the urgent need for innovative approaches to treat multidrug-resistant Candida auris infections.