Flows of antimicrobial resistance and pathogens through environment to food chain

Challenges

Farm animals are a major source of key zoonotic pathogens of humans, including enteric disease-causing Campylobacter spp., Salmonella spp., enterotoxigenic Escherichia coli and Clostridioides difficile. There are around 2.4 million cases of foodborne pathogen infections annually in Scotland, with a financial burden of £9 billion Importantly, many gut bacteria carry antimicrobial resistance (AMR) genes, some of which are located on mobile genetic elements with the potential to transfer to other bacteria (commensal or pathogenic). It is predicted that by 2050, deaths caused by AMR will exceed those caused by cancer and diabetes. Reducing the carriage of zoonotic pathogens within the gastrointestinal tract of farm animals has clear potential to reduce the incidence of human foodborne disease and the spread of AMR - both of which are real health crises.  

Despite a significant body of research globally on AMR in the environment, there are still many unknowns about transmission from the environment to humans. We need to improve our understanding of the routes of transmission of resistance including the impact of the environment and food. There is a lack of understanding of how differences in farming practices can drive antimicrobial resistance and pathogen transmission combined with a paucity of data quantifying antimicrobial gene load onto food crops. There are also challenges around identifying increased risk to farmers due to their proximity to antimicrobials and animals. There is also a limited understanding of how farmers perceive the link between antimicrobial use and antimicrobial resistance, and how this may influence behaviours. Lastly, there is a lack of a unifying model to predict future scenarios of hazards to food.

Questions

Solutions

The aim of this project is to quantify the flow of antimicrobial resistance (AMR) genes and pathogens from the environment to the food chain and directly to humans in the farm environment. We are integrating social science work to understand the perceptions farmers have of the link between antimicrobial use and antimicrobial resistance. Both quantitative and qualitative data is being used to develop a risk assessment model based on the source-pathway-receptor principle.

Understanding the flow of bacterial antimicrobial resistance genes and pathogenic E. coli through soils, animals, and humans

We are better understanding the flow of bacterial antimicrobial resistance genes and pathogenic E. coli through soils, animals, and humans. To quantify antibiotics in soils, we are developing new methods to track the transmission of ARG from sources through the environment to the food chain under different farming practices. Soils and manures are known sources of ARG, with water sources acting as conduits between environments, but little is known about how farming practices may influence the transmission of ARG from these sources to the food chain.

Next, we are quantifying ARG loading onto food crops grown under traditional vs integrated crop management, and ARG carriage in farm workers compared to the animals they handle. We are determining farmer perceptions of the link between antimicrobial use and AMR. Social sciences work has focused on attitudes and behaviours related to antimicrobial use on-farm, but little is known about how farm workers conceptualise and deal with the link between antimicrobial use and AMR regarding their health, animal health and environmental AMR. Lastly, we are addressing the flow of pathogenic and non-pathogenic E. coli from source to receptor. Similarly, this activity is identifying the drivers of pathogen flows from the environment to the food chain.

This project links to the work done in the Emerging Water Futures project on antibiotic and ARG quantification methods in soils, manures and crops and some shared aspects of Bayesian Belief Network modelling.

Developing models to support quantitative risk assessments on hazards that affect the Scottish food chain

We are developing models to support quantitative risk assessments on hazards that affect the Scottish food chain. To do this, we are building a risk assessment model to assess the impact of different farm management approaches on ARG and pathogen flows and inform where management interventions can be implemented in the food chain system to reduce foodborne risks.

Understanding how current farming practices contribute to AMR and pathogen dissemination allows for better-targeted interventions. Therefore, this work is helping inform policy and industry governance on farming practices (including antimicrobial use) to reduce the transmission of antimicrobials, AMR, and pathogens to the food chain. Ultimately, this is impacting and benefiting public health through the reduction of human exposure to food hazards and reducing pressure on public health services.