Genomic epidemiology links azole-resistant Aspergillus fumigatus hospital bioaerosols to chronic respiratory aspergillosis

Drug-resistant infections caused by spores of the mould Aspergillus fumigatus pose a major challenge in managing chronic respiratory disease. Evidence shows that a substantial burden of aspergillosis is caused by strains that have evolved resistance to azole antifungal chemicals in the environment, however the contribution of local exposures to the colonisation of patients remains unclear. To investigate routes of acquisition, we whole-genome sequenced A. fumigatus isolates from individuals with chronic pulmonary fungal disease (n=182, 15 individuals), their homes (n=101, 10 homes), and hospital environments (n=102). These data were then integrated with retrospective sequence datasets enabling phylogenetic resolution across 912 genomes of UK A. fumigatus. We found high genetic diversity in clinical isolates, frequent mixed colonisation, and azole resistance in [~]25% of infections, particularly in those patients with cystic fibrosis (CF) and chronic pulmonary aspergillosis (CPA). The TR34/L98H cyp51A resistance allele, a well characterised marker of environmental adaptation to azole agricultural fungicides, was present in 25% of clinical azole-resistant strains. While azole-resistant A. fumigatus was detected in 6/10 homes, phylogenomic analysis revealed no clear genetic link between the home environment and clinical fungal lung isolates. A. fumigatus was prevalent in hospital environments, with azole-resistant isolates comprising 4.5% (n=9/202) of air and 3.4% (n=6/178) of soil isolates, predominantly harbouring the TR34/L98H allele. In contrast to homes, phylogenomic and pairwise SNP analysis revealed numerous clinical isolates with >97% genetic identity when compared to those isolated from the hospital environment and randomly chosen pairs of UK isolates. These findings indicate widespread exposure and potential nosocomial acquisition of drug-resistant genotypes of A. fumigatus, supporting the need for targeted environmental surveillance and mitigation of exposures in healthcare settings.