Research

Antifungal Resistance

The treatment of fungal infections is compounded by rising antifungal resistance. A 2019 CDC report on antimicrobial threats included for the first time included a fungal species, Candida auris, among the five most urgent antimicrobial threats. The same report listed with other Candida species as serious threats, and included azole-resistant Aspergillus fumigatus on a watch list. Our goal is to identify genomic changes that confer antifungal resistance across populations of clinical isolates, and to study the impact of these mutations on fitness.

Fungal Evolution of Pathogenesis

Cryptococcus is a major cause of environmentally-acquired fungal infections. Individual Cryptococcus isolates vary in how they interact with the host and cause disease. By comparing fungal genomes from large sets of clinical and environmental isolates, we are identifying variants associated with clinical and in vitro phenotypes, characterizing the global population structure of Cryptococcus, studying how microevolution can reveal genes involved in host adaptation, and cataloging how expression varies across distinct genetic lineages.

Candida albicans is commonly found in the microbiome of healthy individuals, and is a frequent cause of bloodstream infections. We are interested in characterizing 1) how variation between diverse strains is linked to host phenotypes, and 2) the microevolutionary changes that occur when the immune system or antifungal drugs fail to clear a single infecting strain.