Widely dispersed clonal expansion of multi-fungicide-resistant Aspergillus fumigatus limits genomic epidemiology prospects
Aspergillus fumigatus is a ubiquitous fungus that causes a range of diseases in animals, including humans. The most lethal manifestation is invasive aspergillosis for which treatment relies on triazoles. The efficacy of medical triazoles is threatened by the emergence of resistance in A. fumigatus and exposure to triazole fungicides in the environment has proven to be the main route of resistance selection. Triazole-resistant A. fumigatus can be recovered from decaying plant material and so-called hotspots containing triazole fungicide residues. Although observations support a strong link between environmental-based resistance genotypes and clinical samples, a direct link between environmental isolates and triazole-resistant invasive aspergillosis has not yet been demonstrated. To understand transmission routes, we used a genomic epidemiology approach with 157 Dutch A. fumigatus isolates, based on whole genome sequencing. Isolates were obtained from three well-characterized agricultural hotspots, potable water samples, and two Dutch hospitals between 2016 and 2019. In the Dutch dataset, A. fumigatus isolates from six patients showed near-identical genomes compared to environmental isolates. One environmental isolate matched three proven/probable cases of triazole-resistant invasive aspergillosis, including one fatal case. Patient isolates were recovered up to 34 months later than culturing of matching environmental isolates. Comparison with a global data set showed hundreds of clonal groups, with nearly identical genomes spread across three continents. The variants associated with resistance to non-triazole fungicides, such as benzimidazole (MBC) and quinone outside inhibitor (QoI) classes, which strongly suggests an agricultural fungicide exposure history. Environmental hotspots represent highly selective habitats for multi-fungicide-resistant A. fumigatus, which can be directly linked to clinical disease. However, widely dispersed clonal expansion of A. fumigatus limits the utility of genomic epidemiology. Furthermore, when reducing a single class of fungicides in agriculture, this may not effectively reduce resistance selection when other classes are still in use.