Genomic analysis of Candida parapsilosis and other yeast species

Candida parapsilosis is a human commensal fungal pathogen that is quickly emerging as a global threat to human life. Acquired resistance to commonly used antifungal drugs is increasingly common and has been associated with multiple outbreak events. In this thesis, genomic variants associated with virulence factors such as nitrogen utilisation and antimicrobial resistance were identified. In Chapter 2, I used coverage analysis of a broad sample set of 170 clinical and environmental C. parapsilosis isolates to identify independent recurrent copy number variants (CNVs) covering the genes ARR3 and RTA3. Increased copy number of RTA3 is associated with resistance to the anti-leishmaniasis drug miltefosine. In a laboratory evolution experiment, miltefosine-susceptible C. parapsilosis strains acquired miltefosine resistance by loss-of-function mutations in genes with opposite action to RTA3. In Chapter 3, a genome-wide association study (GWAS) was used to study resistance to fluconazole, an azole drug commonly used to treat Candida spp. infections by inhibiting the ergosterol biosynthesis pathway, in a set of 42 clinical C. parapsilosis isolates. Here, CNVs in the ergosterol gene ERG11 and the drug efflux pump CDR1B were found. Comparative genomics highlighted that C. parapsilosis is primed to undergo duplication of CDR1B due to a gene conversion event. Chapter 4 details a large-scale phenotype assay, testing 382 C. parapsilosis isolates for their growth on 24 different nitrogen sources. Two contrasting GWAS tools were used to identify significant genotype-phenotype associations in this clonally propagating organism. In a departure, Chapter 5 concerns the identification of the first European isolates of Saccharomyces eubayanus, one parent of the hybrid lager yeast Saccharomyces pastorianus. Whole-genome sequencing was used to study the relationship between the three S. pastorianus populations and the two S. pastorianus lineages to determine the likely parenthood of the hybrid.