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A systems understanding of the flow of Antimicrobial Resistance from livestock production to the environment and humans: informing risk analyses

A systems understanding of the flow of Antimicrobial Resistance from livestock production to the environment and humans: informing risk analyses

  • Diet & Food Safety
  • 2022-2027
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Antimicrobial Resistance (AMR) is a global, immediate, and ongoing concern to human health. AMR occurs when microbes become resistant to clinical or veterinary drugs used to treat disease, and this has major consequences on how microbial diseases are managed, and therefore how antimicrobial compounds are used.

Shiga toxigenic Escherichia coli (STEC) is transmitted from the primary reservoir of ruminants (principally cattle) directly into the food chain, or indirectly via environmental compartments. STEC is also transmitted directly via contact, such as farm workers, petting zoos, or from contaminated soil. Furthermore, STEC, like other foodborne pathogens is characterised by its ability to adapt to a wide variety of environments with the result that it can survive, and in some cases thrive along every step of the food chain.


Bacterials risks and hazards in the Scottish food chain

Although meat and dairy products are attributed to STEC transmission, other foodstuffs including fruits and vegetables also account for a significant proportion of illness, up to 35 % in the European Union. Ready-to-eat fresh produce is a particular hazard as it is often consumed raw or minimally processed. Fresh produce normally becomes contaminated with STEC from manure-contaminated irrigation water, or via direct contact on the plant or in the soil from manure.

Scotland has a small horticultural sector, but some ready-to-eat produce is home-grown, and we import produce from countries that have STEC incidence. As such, reported cases of STEC associated with fresh produce within Scotland and the wider UK is from a mixture of home-grown and imported sources. Scotland also has a record of STEC cases from environmental direct contact. Food source attribution data for AMR is less certain, but all food groups have some association with AMR bacteria, indicating that the same hazards exist.

Transmission via fresh produce incorporates both components of the environment (water, soil) and the food chain, hence quantification of the risk of transmission of hazards via this pathway addresses more than one area. Under some conditions of environmental stress, STEC (and other E. coli) enters a quiescent physiological state and may only be present in very low numbers, making detection extremely challenging, yet it still poses a risk to human health because of the low infectious dose.  Furthermore, there is a knowledge gap for STEC survival and persistence in water, with the result that quantitative risk modelling for this pathway is incomplete or incorporates many uncertainties. Therefore, there is a need to obtain robust data for STEC transmission from environmental sources, for which we propose that (contaminated) water is a central source.


  • What are the sources and epidemiology of foodborne disease in Scotland and what interventions can be introduced to reduce foodborne disease?
  • What new methods can be developed to assist with identifying and tackling emerging microbiological, chemical, and nutrient risks in food for Scottish consumers and businesses?


The aim of this project is to characterise and quantify the flow of AMR genes within and from livestock holdings to the wider environment and human population, to inform antimicrobial stewardship and optimal use, and human risk via the food chain.


Characterising and quantifying the AMR gene flow from livestock to the environment and humans

We take a bottom-up systems approach and use Easter Howgate farm as a case study. We are characterising and quantifying the flow of AMR genes through co-located pig and beef production units, and linked environments (soil, wildlife, farm workers, water courses) by quantifying the copy number of specific AMR genes. The AMR gene counts quantified complement the AMR gene profiles (AMR gene presence, richness, diversity) in the microbiomes and E.coli isolates of the livestock and linked environments from the same system in a complementary project.


Quantifying the risk of illness of bacterial and AMR hazards in the Scottish food chain

In previous work, we produced risk frameworks for the risk to human health from STEC O157:H7 in leafy greens (lettuce or spinach), and ongoing projects are assessing the risk of microbial hazards in produce grown in vertical farms, with a focus on irrigation water. Quantification of the risk can inform intervention and control strategies, relevant to the argri-food industry and to public health. Therefore, we build on our data for STEC in this transmission route. The work also allows us to assess the risks of other foodborne hazards transmitted via the same pathway, including AMR E. coli.

To understand the hazard of foodborne illness caused by STEC and AMR in fresh produce, either produced or sold in Scotland, we quantify the risk of illness using quantitative microbial risk assessment (QMRA) modelling. This is helping us understand the hazard of foodborne illness caused by STEC and AMR in fresh produce, either produced or sold in Scotland.

The ultimate aim of this applied project into AMR is to limit AMR development and spread, and to increase  the longevity of antimicrobial efficiency. Our systems approach delivers a range of outputs from the more fundamental biology of AMR gene population dynamics and spread to the current national distribution of phenotypic resistance in bacteria from livestock entering the food chain. 


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