Fungal Genomics and Antagonistic Community Interactions

Fungal pathogens within the Candida genus, including C. albicans, C. parapsilosis and C. auris, represent a growing public health concern on a global scale. Resistance to key antifungal drugs, particularly azoles and echinocandins, is on the rise. Increased virulence or resistance is driven by multiple factors including the dual use of antifungals, but our understanding of these drivers is incomplete. The implementation and utility of genomics in Candida epidemiology significantly lags behind its use for bacterial pathogens, and there is little data on the transmission dynamics of these species between clinical and non-clinical (One Health) environments. Moreover, we lack a detailed understanding of how competitive interactions with co-colonising bacterial species impact the survival and spread of pathogenic fungi. This proposal synergises expertise in genomic epidemiology, bioinformatics and microbiome ecology. We will combine existing genomic data with novel genome and metagenome data from clinical and non-clinical settings from Europe and Australia. We will also characterise extensive wastewater and environmental samples from the UK and NL. We will examine hospital transmission dynamics, and link this with the identification of commensal bacteria that are inhibitory to high-risk Candida strains. This data will inform novel intervention strategies to mitigate Candida transmission.