Adaptation of Candida glabrata to host-associated niches

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PROJECT SUMMARY Candidiasis was first documented 2,500 years ago and remains a global problem today. In recent decades, the incidence of Non-Candida albicans Candida (NCAC) infections has increased chiefly due to Candida glabrata, an opportunistic fungal pathogen. C. glabrata, which has intrinsic drug resistance, is now second only to Candida albicans in clinical prevalence. While it is well-known that fungi can adapt to many types of environments, we know little about how different regions of the human body enable C. glabrata to establish an infection and whether these different host niches constrain the organism’s subsequent evolutionary trajectory. My overarching goal is to determine the short- and long-term influences of different host niches on C. glabrata biology. Specifically, I will culture C. glabrata in media designed to simulate two common sites of infection: the mouth and the urinary tract, and compare these treatments to two controls: RPMI and synthetic complete (SC) medium, which is routinely used in antifungal drug susceptibility testing. I will pursue three Specific Aims to achieve my overarching goal. First, to better understand how C. glabrata adapts physiologically to different host niches I will establish patterns of growth and global gene expression under all four conditions. Second, to understand the tempo of evolutionary adaptation to each condition, I will experimentally evolve replicate populations founded by the ATCC 2001 strain by serially transferring cultures for 250 generations. For each population, I will determine how population and clone fitness change relative to their common ancestor. Third, to uncover the mechanisms of evolutionary adaptation I will carry out whole-genome, whole-population sequencing (WGWPS) on these populations at 50 generation intervals. De novo mutations in genes that are recurrently mutated in multiple replicates and that rise to high frequency are the mutations that are most likely to contribute to fitness increases. To establish linkage relations among de novo mutations discovered by WGWPS we will sequence a set of random clones from each simulated host niche and each control. We will also evaluate the relative fitness of a subset of these clones and determine the resistance and sensitivity of the most fit to four classes of antifungal drugs. A long-term goal of this research is to discover whether the host niche from which a systemic infection originates selects for mutations that confer increased risk of morbidity and mortality. Completion of these three Specific Aims will provide valuable insight into the physiological changes that occur as an opportunistic pathogen initially adapts to a new host niche and discover subsequent evolutionary changes that occur throughout a chronic infection. Escalating C. glabrata infections are typically fought with higher and higher doses of antifungal drugs, which can result in acute toxicity. Detailed knowledge of physiological and evolutionary adaptations that occur at different infection sites will move us closer towards the development of site-specific treatments that minimize such unwanted side-effects.