Pan-azole- and multi-fungicide-resistantAspergillus fumigatusis widespread in the United States

Abstract

AbstractAspergillus fumigatusis an important global fungal pathogen of humans. Azole drugs are among the most effective treatments forA. fumigatusinfection. Azoles are also widely used in agriculture as fungicides against fungal pathogens of crops. Azole-resistantA. fumigatushas been increasing in Europe and Asia for two decades where clinical resistance is thought to be driven by agricultural use of azole fungicides. The most prevalent mechanisms of azole resistance inA. fumigatusare tandem repeats (TR) in thecyp51Apromoter coupled with mutations in the coding region which result in resistance to multiple azole drugs (pan-azole resistance). Azole-resistantA. fumigatushas been isolated from patients in the United States (U.S.), but little is known about its environmental distribution. To better understand the distribution of azole-resistantA. fumigatusin the U.S., we collected isolates from agricultural sites in 8 states and tested 202 isolates for sensitivity to azoles. We found azole-resistantA. fumigatusin agricultural environments in 7 states showing that it is widespread in the U.S. We sequenced environmental isolates representing the range of U.S. sample sites and compared them with publicly available environmental worldwide isolates in phylogenetic, principal component, and ADMIXTURE analyses. We found worldwide isolates fell into three clades and that TR-based pan-azole resistance was largely in a single clade that was strongly associated with resistance to multiple agricultural fungicides. We also found high levels of gene flow with clear recombination between two clades highlighting the potential for azole-resistance to continue spreading in the U.S.ImportanceAspergillus fumigatusis a fungal pathogen of humans that causes over 250,000 invasive infections each year. It is found in soils, plant debris and compost. Azoles are the first line of defense antifungal drugs againstA. fumigatus. Azoles are also used as agricultural fungicides to combat other fungi that attack plants. Azole-resistantA. fumigatushas been a problem in Europe and Asia for twenty years and has recently been reported in patients in the U.S. Until this study we didn’t know much about azole-resistantA. fumigatusin agricultural settings in the U.S. In this study we isolated azole-resistantA. fumigatusfrom multiple states and compared it to isolates from around the world. We show thatA. fumigatusthat is resistant to azoles and to other strictly agricultural fungicides is widespread in the U.S.