Detection of Antifungal Resistance and Identification of Factors Contributing to Resistance in Agricultural Environments

The goal of the proposed research is to better understand the development of azole resistance of A. fumigatus in agricultural environments so that efficient and targeted strategies aimed at mitigating antimicrobial resistance can be developed, and azoles can be preserved for use in treating human, animal and plant diseases caused by fungi. Antimicrobial resistance in Aspergillus fumigatus, the cause of life-threatening aspergillosis in humans, to azole drugs has become a major public health concern worldwide. Studies have linked clinical resistance to increased agricultural use of azole fungicides to combat plant pathogens. Azoles are the first line of defense in patients with aspergillosis; however, mortality in patients with azole-resistant infections is dismal at 88%. Preliminary studies by the Co-PI's have shown that azole-resistant strains of A. fumigatus are present at frequencies of 28% in agricultural environments in the U.S. where azole fungicides are used. There is a clear need for azole resistance monitoring of A. fumigatus in agricultural environments. We need to improve molecular detection methods and identify problematic environmental azole applications that lead to resistance development in A. fumigatus. This will help us formulate strategies to slow the development of azole resistance.To accomplish the goal of the proposed research, our specific objectives are to:Develop assays for the rapid detection of azole-resistant strains of A. fumigatus in the environment, including soil, plant matter, and air. 1A) Develop and validate an assay for rapid detection of cyp51A-based resistance in environmental samples. 1B) Identify non-cyp51A-based azole resistance mechanisms in A. fumigatus in order to develop a rapid detection assay for these strains.Investigate agricultural environments conducive to azole resistance development and exposure of resistant A. fumigatus. 2A) Quantify abundance and frequency of azole-resistant strains in different agricultural environments and at different sampling times during the year. 2B) Determine if high frequencies of azole-resistance are correlated with azole fungicide concentrations in soil and plant matter. 2C) Determine if azole-resistant strains are present on food items produced in environments where a high frequency of azole-resistance has been detected.Determine if there is a fitness to cost to azole resistance in strains of A. fumigatus from agricultural environments. 3A) Compare fitness parameters of susceptible strains and strains with diverse resistance phenotypes and genotypes under different growth conditions. 3B) Conduct competition assays among resistant and sensitive strains of A. fumigatus.