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).