Acquisition of azole resistant aspergillus fumigatus in individuals with chronic respiratory diseases.

Azole resistance in Aspergillus fumigatus presents a significant challenge to effective treatment in chronic respiratory diseases, where prolonged azole antifungal therapy is routinely employed. Individuals with chronic respiratory diseases are disproportionately impacted by the emergence of drug resistance, thought to be driven by strong selective pressures associated with environmental fungicide use and oral azole therapy. The mechanisms driving antifungal resistance acquisition and evolution in individuals with chronic respiratory diseases remain poorly described. This thesis investigates the prevalence, genetic diversity, and transmission dynamics of azole resistant A. fumigatus across clinical and environmental settings in the UK, with a focus on the TR34/L98H resistance mechanism. Utilising whole-genome sequencing (WGS) and high-throughput phenotyping, 912 isolates were characterised to elucidate the genetic basis of resistance and adaptation. Analysis of 210 virulence-associated genes revealed increased frequencies of nonsynonymous SNPs in TR34/L98H isolates, indicating genetic diversification that may support adaptation under antifungal pressures. Phenotypic profiling under 384 growth conditions highlighted metabolic adaptations in TR34/L98H isolates, including shifts in carbon and nitrogen utilisation, osmotic stress tolerance, and reduced reliance on d-trehalose during germination, potentially contributing to persistence in clinical settings. Prospective longitudinal surveillance of 55 individuals with chronic respiratory diseases identified a 25% prevalence of azole resistance, predominantly among those with chronic pulmonary aspergillosis and cystic fibrosis. WGS of clinical and environmental isolates revealed the dominance of TR34/L98H and emerging TR46/Y121F/T289A resistance mechanisms. Integration of environmental and clinical WGS data from hospital settings revealed genetic similarities between isolates, suggesting bidirectional transmission pathways. Additionally, home environments were surveyed through a citizen science approach, identifying resistant isolates in 60% of homes, with soil as a key reservoir. These findings emphasise the role of environmental reservoirs in the persistence and transmission of azole-resistant A. fumigatus, underscoring the need for advanced surveillance strategies.