Aerobiome based genomic surveillance of fungicide resistance to track the development and spread of AMR in plant pathogens and the wider environment

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Antimicrobial resistance (AMR) is a growing threat to global health, and the excessive use of antimicrobials in agriculture is a major contributor to its development. In particular, plant pathogenic fungi pose a significant problem for food safety and quality, and with fewer fungicides available due to stricter regulations, the risk of AMR development is increasing. Current surveillance methods are slow and laborious. This project aims to develop a new approach combining the latest technological advances in sampling fungal spores from air and high-throughput long-read Oxford Nanopore Technology (ONT) sequencing to track the development and spread of AMR in fungal pathogens of cereal crops and the wider environment, which includes the opportunistic human pathogen Aspergillus fumigatus whose spores are widespread in the air we breathe. This new approach for the detection of fungal species from air and detection of the fungicide resistance alleles will be validated with the laboratory based conventional fungicide resistance tests of the fungi isolated from naturally infected plants sampled from the same locations as the air. Early season sampling and diagnosis of the status of AMR at the start of the growing season, will lead to improved better cereal disease management practices based on choice and optimal minimal use of fungicide inputs as part of IPM and reduce the risk for further AMR development in plant pathogens. Ultimately, this project will help to safeguard our food supply while improving human health and sustaining biodiversity in the environment.