Molecular Analysis of Phenotypic Diversity in Human Fungal Pathogens

Abstract Fungal pathogens are a leading cause of human mortality, in part due to their ability to thwart therapeutic regimens by rapidly evolving resistance to antifungal drugs, and their ability to readily adapt to the hostile conditions experienced in a mammalian host. Candida species can colonize various niches in the human body making them common commensals of the mucosal microbiota, where the maintenance of a stable host-fungus relationship is presumably critical for avoiding disease. However, the importance of fungi is only beginning to be appreciated in context of the human microbiome. My doctoral research focuses on two aspects of how Candida species influence human health and disease. First, I characterized fungal communities of 28 cystic fibrosis patients by coupling high-throughput ITS1 sequencing with phenotypic analyses of fungal isolates from sputum samples. Fungal communities were not determined by clinical characteristics, but considerable phenotypic variation in traits such as antifungal resistance and morphogenesis was identified within Candida species. Notably, filamentation in the absence of inducing cues was observed in 28 Candida isolates from six patients, with most isolates harboring mutations in a transcriptional repressor of filamentation, NRG1. These mutants were resistant to the filament inhibitory effects of Pseudomonas aeruginosa, implicating interkingdom interactions as the driver of adaptation. Second, I characterized the role of the molecular chaperone Hsp90 in drug resistance and morphogenesis in an emerging fungal pathogen, Candida auris. I showed that fluconazole resistance of C. auris was independent of HSP90 expression, but in part mediated by the ABC transporter CDR1. Further, I showed that C. auris is capable of filamentous growth in response to Hsp90 depletion or inhibition. Transcriptomic analysis upon HSP90 depletion showed that filamentous growth is associated with upregulation of putative cell wall associated genes. Overall, my research provides key insights into mechanisms governing phenotypic diversity in human fungal pathogens.