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


Research Project: 2024-04-01 - 2027-03-31
Total sum awarded: €1 943 836

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.

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  • Bart Fraaije, Wageningen University & Research, Netherlands (Coordinator)
  • Stephen Kildae, Teagasc Environmental Research Centre, Ireland (Partner)
  • Kostya Kanyuka, National Institute of Agricultural Botany, United Kingdom (Partner)
  • Anne-Sophie Walker, INRAE, French National Institute for Agriculture, Food and Environment, France (Partner)
  • Tomasz Kulik, University of Warmia & Mazury in Olsztyn, Poland (Partner)
  • Fran Lopez-Ruiz, Curtin University, Australia (Observer)