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

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.

Antimicrobials are essential to control pests and diseases in agriculture, but their excessive use has a negative impact on human health and the environment due to the effect on non-target species. Antimicrobial resistance (AMR) has developed in plant pathogenic fungi and Aspergillus fumigatus, an opportunistic human pathogen present in the environment. With fewer fungicides available due to stricter EU legislation, the risk of AMR development is increasing for difficult-to-control diseases. It is urgent to monitor the level of AMR in fungal populations to reduce the risk for fungicide resistance development. However, current surveillance methods are slow and laborious. We aim to develop an innovative approach for tracking the development and spread of AMR in fungal pathogens of the main arable crops, wheat and barley. The project will use long-read Nanopore sequencing to identify the distribution and abundance of fungal species in bioaerosols collected using air samplers, as well as to detect fungicide resistance alleles in cereal pathogen populations and in A. fumigatus. We will establish and operate a bioaerosol collection network in 6 countries and validate the aerobiome fungicide resistance genomic surveillance system by carrying out a conventional field fungicide sensitivity surveys. The project will advance our understanding of AMR in plant pathogens and inform optimization of disease control programs based on a rational use of fungicides as part of IPM, thus reducing the risk of AMR development. Data will be shared, stored and analysed using FAIR principles.