Tracing patterns of evolution and acquisition of drug resistant Aspergillus fumigatus infection from the environment using population genomics

Rhodes, Johanna; Abdolrasouli, Alireza; Dunne, Katie; Sewell, Thomas R.; Zhang, Yuyi; Ballard, Eloise; Brackin, Amelie P.; van Rhijn, Norman; Tsitsopoulou, Alexandra; Posso, Raquel B.; Chotirmall, Sanjay H; McElvaney, Noel G; Murphy, Philip G; Talento, Alida Fe; Renwick, Julie; Dyer, Paul S.; Szekely, Adrien; Bromley, Michael J.; Johnson, Elizabeth M.; White, P. Lewis; Warris, Adilia; Barton, Richard C.; Schelenz, Silke; Rogers, Thomas R.; Armstrong-James, Darius; Fisher, Matthew C.

Infections caused by opportunistic fungal pathogens are increasingly resistant to first-line azole antifungal drugs. However, despite its clinical importance, little is known about the extent to which susceptible patients acquire infection from drug resistant genotypes in the environment. Here, we present a population genomic analysis of the mould Aspergillus fumigatus from across the United Kingdom and Republic of Ireland. First, we show occurrences where azole resistant isolates of near identical genotypes were obtained from both environmental and clinical sources, indicating with high confidence the infection of patients with resistant isolates transmitted from the environment. Second, we find that the fungus is structured into two clades (‘A’ and ‘B’) with little interclade recombination and the majority of environmental azole resistance genetically clustered inside Clade A. Genome-scans show the impact of selective sweeps across multiple regions of the genome. These signatures of positive selection are seen in regions containing canonical genes encoding fungicide resistance in the ergosterol biosynthetic pathway, whilst other regions under selection have no defined function. Phenotyping identified genes in these regions that could act as modifiers of resistance showing the utility of reverse genetic approaches to dissect the complex genomic architecture of fungal drug resistance. Understanding the environmental drivers and genetic basis of evolving fungal drug resistance needs urgent attention, especially in light of increasing numbers of patients with severe viral respiratory tract infections who are susceptible to opportunistic fungal superinfections.