EVAL-FARMS: Evaluating the Threat of Antimicrobial Resistance in Agricultural Manures and Slurries

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences


Antibiotics are used extensively to fight bacterial infections and have saved millions of lives. However, the bacteria are becoming resistant to antibiotics and some antibiotics have stopped working. We refer to this as antimicrobial resistance - AMR. We don't just use antibiotics for people; similar amounts are given to farm animals. More than 900 million farm animals are reared every year in the UK and antibiotic treatments are vital for their welfare, for farms as businesses, and for us to enjoy affordable food. However, farms may be contributing to the development of AMR. The aim of this project is to improve our understanding of how farm practice, especially the way in which manure is handled, could lead to AMR in animal and human pathogens. This understanding will help farmers and vets find new ways to reduce AMR, without harming their animals or their businesses.

For research purposes, Nottingham University maintains a typical high performance dairy farm - its 200 cows produce a lot of milk and a lot of manure. The waste is stored in a 3 million litre slurry tank, any excess goes into a 7 million litre lagoon. This slurry is applied to fields as organic fertilizer. Cow manure contains many harmless bacteria but some, e.g. E. coli O157, can cause severe infection in people. When cows get sick they are treated with antibiotics. Udder infections are treated by injection of antibiotics into the udder. Since this milk contains antibiotics, it cannot be sold but is discarded into the slurry. Foot infections are treated with an antibacterial footbath, which is also emptied into the slurry tank.

As a result, slurry tanks contain a mixture of bacteria, antibiotics and other antimicrobials that are stored for many months. The bacteria that survive in the presence of antibiotics are more likely to have antibiotic resistance. This resistance is encoded in their genes so passed to the next generation. Worse still, the genes can be passed on to other bacteria in the slurry.

Before we wrote this proposal, we investigated our own farm's slurry tank to see if this might be happening. We tested 160 E. coli strains from the slurry; most carried antibiotic resistance. We also found antibiotics in the tank - including some that bacteria were resistant to. Our mathematical modellers showed that reducing spread of resistance genes in the tank might be more effective in preventing resistance than cutting the use of antibiotics. Conversations with the farm vets revealed that they knew about AMR and had changed some of their antibiotic prescriptions. But these analyses leave us with more questions than answers.

In this project, we want to find out if current farming methods are contributing to the development of harmful antibiotic-resistant bacteria in slurry, bacteria that may then be encountered by humans and animals. To do this, we need to integrate scientific and cultural approaches:

- What bacteria are in the slurry? How many are harmful? What resistance genes do they carry? How do these genes spread?
- How long do antibiotics remain in the tank? Do they degrade?
- What happens to the bacteria and antibiotics after they are spread on fields?
- How do farmers, vets and scientists interpret evidence about AMR? What are their hidden assumptions? Can we improve collaborative decision making on AMR risk management?
- Can we reduce resistance by avoiding mixing together bacteria and antimicrobials in slurry?
- Can we predict the risk of emergence of and exposure to resistant pathogens? Can we predict which interventions are likely to be most effective to reduce AMR, taking into account both human and scientific factors?

Through this research, we will learn what can realistically be done to reduce this risk; not just on this farm, but UK wide. We will work with farmers, vets and policy makers to ensure that our results will make a difference to reducing the risk of harmful AMR bacteria arising in agriculture.

Planned Impact

Antibiotics save millions of lives. However, because bacteria adapt, some antibiotics may stop working. We call this antimicrobial resistance - AMR. Farm animals are given antibiotics as well as humans; we need to understand how manure handling on dairy farms could lead to AMR. EVAL-FARMS will help farmers and vets find ways to reduce AMR without harming their animals or businesses, and policy makers to understand AMR risk in agriculture.

Our impact goals are to produce measurable changes in:

- policy understanding of the role slurry handling and management plays in AMR
- the understanding and practice of dairy farmers and associated industries in relation to AMR and slurry management
- wider awareness of the role AMR plays in human food from 'farm-to-fork'.

Who will benefit from this research?

We have identified two key beneficiary communities:

- policy makers working in the fields of waste management, agriculture and the environment in the UK and the EU
- dairy farmers and related industries e.g. vets, farm services and the waste management industry

We will also work to improve public awareness through the media.

How will stakeholders benefit from this research?

1. Policy makers: Our policy stakeholders will benefit from our research in three ways. First, through Defra representatives on our EAB, we will improve the quality of understanding of AMR in the policy community, and take up opportunities to directly influence policy-making. Second, we will produce a policy pack to ensure our evidence is embedded at the leading edge of policy thinking in the UK/EU. The research will be presented in usable formats, including policy/ministerial briefings, case studies and slides. Finally, we will work with the James Hutton Institute to inform Scottish Government policy through the co-creation of research outputs.

2. Dairy farmers and associated industries: We will work with a range of partners (NFU, Severn Trent Water, the BCVA and Velcourt Farm Management Services) to share our findings with the farming community. We will have a presence at events in the dairy diary, in periodicals and will run farm demonstrations to explore the implications of our findings. Co-creation and representing a meaningful understanding of the cultural context will make our research accessible and usable. As a result the dairy industry will improve AMR risk management.

3. Public interest: The UoN Press Office will produce a range of PR material for national and international media outlets including broadcast, print and online platforms covering science, environment and agriculture. The team will have access to UoN's media hub. Articles will be produced for sites such as The Conversation, and messages targeted at programmes such as The Archers and Countryfile.

How will we measure impact?

We will measure the reach and significance of our impact using the following metrics:

- EVAL-FARMS research cited in UK/EU policy documentation, conversation and directives. This will be tracked via policy presence on the EAB and document scanning.
- 90% of policy makers working on slurry management/storage understand the importance of AMR to their work.
- Industrial partners report quantifiable changes in design/practices following access to the research. We will track this via follow up phone calls six months after engagement with the project.
- Numbers of vets taking up our CPD offer or farm visits, and reporting changes in practice via evaluation forms.
- Numbers of dairy farmers accessing our research through periodicals, events and call to action pack downloads.
- Numbers of dairy farmers reporting a change in practice on farms, tracked via the Farm Business Survey using telephone and text messages.
- Media impact metrics are those gathered as a matter of routine by UoN and include reach, value, positive/ negative coverage, media type, source (international and national), press release impact.


10 25 50
Description Dairy farmers and vets do not report antimicrobial resistant infections in animals, but this may be because ascribe antibiotic treatment failure to a wide variety of reasons, and in fact antimicrobial resistant infections might be present.

Slurry storage can reduce the concentrations of E. coli and other organisms. We recommend storing isolated slurry (with no fresh input) for at least 40 days prior to spreading on fields to achieve 99% reduction in microbes. This can be achieved with two tanks or a tank and lagoon.

CEssation of use of 3rd/4th generations cephalosporins on dairy farms is appropriate. Reversion to use of these drugs would likely lead to increased levels of resistance to these important medicines.
Exploitation Route We will report this finding to stakeholders in dairy and vet industry, including NFU, AHDB, VMD and BCVA.

WE are preparing an animated video describing slurry storage for dissemination to stakeholders. We will also produce a policy briefing.
Sectors Agriculture, Food and Drink,Environment

URL https://doi.org/10.1057/s41599-019-0220-2
Description Some of our preliminary findings have been presented as evidence to the Defra Antimicrobial Resistance Coordination (DARC) committee on 21st February 2018. These were primarily used to demonstrate the value of transdisciplinary approaches to AMR that include empirical, data and social sciences. We have concluded that storing isolated slurry - with no further input of material - has a mitigatory impact on E. coli and other organisms. Storage for at least 40 days is recommended to reduce relevant microbes by 99% prior to spreading on land. Results have been shared with UK farmers through UK Dairy Day. Further impact activities are planned, including the production of an animation and of a policy briefing.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Environment
Impact Types Societal,Policy & public services

Description Co-authorship of Food Standards Agency report: Antimicrobial resistance in the food chain; research questions and potential approaches
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
URL https://acmsf.food.gov.uk/sites/default/files/amrtaskandfinish2.pdf
Description Co-authorship of international white paper: Initiatives for Addressing Antimicrobial Resistance in the Environment: Current Situation and Challenges. 2018
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
URL https://wellcome.ac.uk/sites/default/files/antimicrobial-resistance-environment-report.pdf
Description European Commission consultation on the risks of pharmaceuticals in the environment, including the impact on AMR (society response)
Geographic Reach Europe 
Policy Influence Type Participation in a national consultation
Impact Both legislative and regulatory. At UK level, impact to multi million UK Water Inudstry investment in the chemical investigation programmes. Pharmaceutical manufacturers impact.
URL https://ec.europa.eu/info/consultations/public-consultation-pharmaceuticals-environment_en
Description FSA Task and Finish Group
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Description Science and Innovation Network
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Description Veterinary Medicines Directorate
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Description AMR in Argentine Broiler Poultry Systems: Risks and Mitigation
Amount £979,404 (GBP)
Funding ID BB/T004681/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2019 
End 05/2022
Description FARM WATCH: Fight AbR with Machine learning and a Wide Array of sensing TeCHnologies
Amount £743,205 (GBP)
Funding ID 104986 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2021
Description Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research
Amount £4,000,000 (GBP)
Organisation Medical Research Council (MRC) 
Department Medical Research Foundation
Sector Charity/Non Profit
Country United Kingdom
Start 09/2017 
End 09/2023
Description NERC-NBAF
Amount £5,118 (GBP)
Funding ID NBAF1115 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2018 
Title LITSoN database of innovation relevant to the UK Water Sector 
Description The need for innovation in the water sector to meet societal needs is widely accepted. The UK Water Partnership LITSoN pilot (Linking Innovation To Societal Needs) provides an overview of innovation in UK water utilities, demonstrating benefits in terms of increased innovation alignment, better market information and opportunities for capability development, ultimately contributing to economic growth. Outcomes form the 4 invited workshops with industry and academia is to produce a database of innovation relevant to the UK water sector which will be accessible to all UKWIR members - and participants. This will feed into the ISCF including EOI and funding under water. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact ISCF wave EOI 
Description MOOC AMR in the Food Chain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Invited to deliver a perspective on pharmaceutical and steroid pollutants in the environment based on the BIOTRANS project. Highlighted the need to consider chemical pollutants when considering AMR, in addition to the microorganism perspective. Need for data on pollutant fate and biotransformations, which currently unknown how inform on AMR development and spread. University of Nottingham media delivered short video for the MOOC AMR in the Food Chain. The MOOC has been nominated and shortlisted for the British Universities Film and Video Council's "Learning on Screen" awards, March 2017.
Year(s) Of Engagement Activity 2016,2017
URL https://www.futurelearn.com/courses/antimicrobial-resistance-food-chain
Description Panel at Lord Jim O'Neill Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Lord Jim O'Neill gave a public talk about AMR as part of the University of Nottingham Chancellor's Lectures. I was one of four members on the panel who took questions after the talk. It was attended by ~200 members of the general public.
Year(s) Of Engagement Activity 2017
URL http://www.nottingham.ac.uk/alumni/newseventsandfeatures/news/news-items/alt/drug-resistant-infectio...
Description Presenting results to dairy farmers at UK Dairy Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact We held a stand at UK Dairy Day 2019 to present research results on slurry storage to UK dairy farmers and other associated industries. We held conversations with ~30 dairy farmers and provided information leaflets to ~150 participants. Many dairy farmers, especially those of the larger farms, were receptive to our message.
Year(s) Of Engagement Activity 2019
Description UK Water Partnership LITSoN Industry / Academia Workshop on research and innovation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Invited to share overview of current research and innovation projects and where and how it applies to the water sector, and rating its potential impact against UKWIR's Big Questions (also represented selected projects to showcase University of Nottingham research). To feed into the UK Water Partnership (UKWP) reviewing research and innovation activity in the UK water sector to understand how it aligns with societal needs in a project called LITSoN. An initial pilot project in 2017 identified a number of opportunities for collaboration, currently being actively pursued by multiple water companies who are funding this follow-on work to collect more detailed information. Showcase my and UoN capabilities to water companies and across the sector, as well as receiving access to the whole national database.Series of workshops to collect data on current water research and innovation projects and stimulate collaboration. Key findings and recommendations will be shared with all participants and UKWP members in April to help inform future activities and identify collaboration opportunities. Details of individual projects will be shared amongst those organisations that release them.

• Opportunities to improve impact scores through industry collaboration ahead of REF2021
• Understand future funding opportunities through the Industrial Strategy Challenge Fund
• Showcase research for potential collaboration with water companies
• Gain insight into current research and innovation in the UK water sector to identify gaps and future priorities
Year(s) Of Engagement Activity 2016,2018
URL https://www.theukwaterpartnership.org/litson-review-of-innovation-in-uk-water-utilities/