Intervention of antimicrobial resistance transfer into the food chain (INART)

Soil and water have been identified as reservoirs of antimicrobial resistance (AMR) and the food chain as the most likely mode of AMR transfer into human and animal pathogens. Manure is reused as soil fertiliser in which food plants grow and is a source of AMR.

Ongoing project

We hypothesise that pre-treatment of manure will reduce and remove the abundance and diversity of AMR genes and pathogenic bacteria of high priority from entering the food chain. Alleviating AMR elements from entering the food chain will reduce the transfer and uptake of mobile AMR genes and pathogens by human and animals.

This project will focus on chicken and pig manure as both have been demonstrated to carry a wide variety and abundance of mobile AMR genes of clinical relevance. Our intervention is to pre-treat the manure in order to reduceor remove the burden of AMR in the manure prior to reuse as fertiliser. The microbiomes of chicken and pig manure differ, but the AMR genes and mobile elements overlap. Our study will investigate if the same pre-treatments will reduce or remove AMR prior to application and if these reductions or removal are maintained on the food plants or grass, and in the soil.

We will also identify the main microbiome changes mediated by the intervention and analyse if these bacterial changes are important in the mitigation of AMR. Reducing or removing thethreat of AMR at the start of the food chain will reduce the potential for selection and transfer of such AMR genes and pathogens further along the food chain. By stopping or reducing the continuous transfer of AMR genes and mobile elements along the food chain we will reduce the burden of AMR in pathogenic bacteria.


Project partners

  • Fiona Walsh, Maynooth University, Ireland (Coordinator)
  • Edward Topp, University of Western Ontario, Canada
  • Magdalena Popowska, University of Warsaw, Poland
  • Eddie Cytryn, Agriculture Research Organisation, Israel
  • David Drissner, Albstadt-Sigmaringen University, Germany
  • Fiona Brennan, Teagasc Environmental Research Centre, Ireland
  • Xavier Sidler, University of Zurich, Switzerland


Project resources

INART project website