Candida glabrata populations during gastrointestinal tract colonization and abdominal candidiasis

About This Grant

Candida spp. are the leading causes of invasive fungal infections in hospitals globally. Invasive candidiasis (IC) includes bloodstream infections (BSIs) and intra-abdominal candidiasis (IAC), which are associated with mortality rates of 20%-40% despite treatment with echinocandins (ECHs), the frontline antifungal class. IAC pathogenesis is under-studied and poorly understood compared to that of Candida BSIs. Candida glabrata is the 2nd leading cause of IC overall and the leading cause of IAC in patients undergoing abdominal surgery. C. glabrata is notable for its haploid, rather than diploid genome, and its propensity to antifungal resistance. However, most ECH treatment failures of C. glabrata IC are not linked to an ECH-resistant strain. Antifungal heteroresistance (HR, a low-frequency subpopulation of resistant cells co-existing with susceptible cells) and tolerance (some cells grow better than controls in presence of drug without minimum inhibitory concentration changes) are reported among Candida spp., but their clinical relevance is not broadly validated. The long- standing paradigm is that almost all sterile site infections, including IAC, stem from a single, clonal organism that passes through a bottleneck to establish disease. Our preliminary data challenge the “single organism” paradigm by demonstrating that blood cultures from individual patients with C. glabrata BSIs are comprised of mixed populations of genetically and phenotypically diverse strains, including strains exhibiting virulence differences and antifungal-HR or tolerance that was not recognized by the clinical lab. We do not know if this diversity was generated in the blood or during gastrointestinal (GI) tract commensalism. In this study, we will investigate C. glabrata diversity during GI tract colonization and from sites of IAC. We hypothesize that C. glabrata strains at sites of IAC originate from GI tract flora, genetic and phenotypic diversity of C. glabrata strains is present at IAC sites but less than that encountered during GI colonization, certain within-host C. glabrata genetic variants enriched in IAC cultures impact pathogenesis of IAC, and other within-host genetic variants enriched during ECH exposure impact ECH-HR or tolerance. In aim 1, we will identify phenotypic and genetic diversity of C. glabrata colonizing the GI tract and from sites of IAC in individual patients. We will recover C. glabrata strains from stool and IAC cultures in each of 6 patients, including those receiving ECH prophylaxis, and assess virulence- associated phenotypes and ECH resistance, HR and tolerance in vitro. We will perform whole genome sequencing on strains from patients in whom phenotypic differences are identified and prioritize certain genetic variants for validation studies. In aim 2, we will validate that C. glabrata genetic variants contribute to pathogenesis of IAC and/or to ECH HR or tolerance. We will create isogenic mutant C. glabrata strains for prioritized genetic variants. Strains will be tested for impact of genetic variants on phenotypes in vitro and on pathogenesis and ECH responsiveness during C. glabrata IAC of mice. This project will afford original scientific insights and carry potentially important implications for clinical and microbiology lab practices.