Recent European origin of azole resistance in the critical priority fungal pathogen Aspergillus fumigatus

Resistance to azole antifungals in Aspergillus fumigatus, a WHO Critical Priority fungal pathogen, is rising worldwide and threatens the efficacy of frontline therapies for invasive aspergillosis. This resistance has emerged largely through environmental selection driven by the extensive use of azole fungicides in agriculture and horticulture, yet its evolutionary origins remain obscure. Here, we analysed whole-genome sequences from 1,220 isolates collected over a century from 34 countries, revealing five distinct but interfertile genetic clusters spanning the global population. Azole resistance alleles were highly concentrated within particular clusters and were associated with mutator genotypes carrying defects in DNA repair, known to accelerate the accumulation of adaptive mutations. Two clusters exhibited resistance to multiple fungicide classes, including azoles, benzimidazoles, strobilurins and succinate dehydrogenase inhibitors, indicating the emergence of stacked multidrug resistance with no measurable fitness cost in vitro or in murine models. Molecular dating situates the expansion of resistant lineages in the latter half of the twentieth century, coinciding with the introduction and intensification of modern fungicide use. Phylogeographic reconstruction points to Western Europe—particularly intensive horticultural systems and the international bulb trade—as a major source of globally disseminated azole-resistant A. fumigatus, underscoring the urgent need for coordinated One Health surveillance and intervention.