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.

Antimicrobial resistance (AMR) is a multifaceted, wicked problem. Evolution of resistant microbes can arise anywhere along agrifood chains, leading to diseases that cannot be treated by currently used medicines. Human, animal, plant and environmental health are interconnected; actions such as antimicrobial use (AMU) in one sector, may influence AMR arising in another. National and global movements of people, animals and goods therefore creates a web of factors that influence AMR, necessitating systems-based approaches to effectively tackle problems. AMR transcends disciplinary boundaries, requiring collaboration amongst human and veterinary healthcare professionals, researchers from multiple disciplines, policymakers, regulators and the agriculture sector. The benefit of the AMAST (AMr in Agrifood Systems Transdisciplinary) Network is that it brings together, for the first time, actors from diverse backgrounds across agrifood systems to co-develop solutions to AMR challenges through collaboration, dialogue and action. Our aims are to CREATE a transdisciplinary community that bridges the range of research expertise, working together and directly with industry and policymakers, to collectively consider complex configurations in agrifood systems. We will HARNESS the collective strength of experience and expertise of our members to fully understand the challenges and opportunities to mitigate AMR in agrifood including across production systems, such as crop, livestock and aquaculture. From this understanding, and the collaborative resolve established amongst the AMAST membership, we will PREPAREnew systems-level frameworks for transdisciplinary research and partnership that acknowledge the dynamic interactions between actors within those agrifood systems. These frameworks will be used to guide understanding on (new) interventions on AMU and other AMR-promoting practices, that will lead to reductions in AMR in targeted agrifood subsystems, whilst minimising unintended consequences in others to achieve holistically beneficial outcomes. AMAST has been initiated by researcher coalition and partners from across the United Kingdom, representing agrifood-related trade and farming associations, agrifood research and innovation institutes, business development consultants, food-sector networks, government-led AMR surveillance initiatives, and other AMR-focussed networks. The formation and progression of AMAST will be guided by an expert panel, sharing their perspectives on AMR and connections related to infectious disease, aquaculture, livestock, food systems, food safety and transdisciplinary research partnering approaches. Core activities encompassed in 11 objectives at the outset of AMAST will be driven by meaningful engagement between industry, policy and academic researchers in a series of directed-events to understand varying perspectives, expertise and accompanying evidence on current food production processes that exacerbate AMR; and the challenges of moving away from current practices to mitigate AMR without compromising yield, quality and welfare. These events will include stakeholder interviews, workshops, and horizon-scanning activities, knowledge synthesis and authentically focused knowledge-exchange outputs such as perspective ('white') papers. These activities will inform subsequent programming to be developed within AMAST, including use of AMAST Flexible Funds supporting collaborative activities such as targeted researcher and industry short-term-scientific-missions, an AMAST Fellowship training that is authentic to AMR challenges, and further knowledge synthesis activities. Visibility of AMAST outputs and capacity building within and outside the network will occur using a tailored communication strategy and creative multimedia.

This research partnership involves a two-year programme of work focused on the ways in which rapidly changing cultures of poultry meat consumption and agricultural systems in particular Low and Middle Income Countries (LMICs) shape antibiotic use/misuse in farming, with implications for tackling the global antimicrobial resistance (AMR) health challenge. AMR, or in lay terms drug-resistant infections, is one of the top five priorities for the World Health Organization (WHO). The 2016 O'Neill report into 'Tackling Drug-Resistant Infections Globally' warns that if the challenge is left unaddressed, deaths resulting from AMR on a global scale are predicted within the next three decades to reach some 10 million per year. AMR in agriculture and food systems is a critical area of concern, with increasing cases reported of strains of bacteria such as E.Coli, Campylobacter and Salmonella developing resistance to particular groups of antibiotics. While antibiotics are a necessary tool to maintain health and welfare on the farm, the problem is their inappropriate and disproportionate use in animals, thereby reducing availability for humans and also catalysing resistance. The first aim of the research partnership is to evaluate the relationships between changing urban diets incorporating increased meat consumption, transforming food systems and the use/misuse of antibiotics in agriculture. It will do so through a focus on the poultry sectors of Kenya and Malawi, in particular the urban contexts of Nairobi and Lilongwe, given the rapid rise of poultry production and consumption in both places and the increased and weakly regulated use of antibiotics in production. Moreover, Kenya and Malawi are a Lower Middle Income Country and a Least Developed Country, respectively, on a continent predicted to see the highest mortality rate from AMR by 2050. The second aim is to generate culturally and geographically sensitive approaches to antibiotic reduction and stewardship initiatives in these contexts, in ways that improve implementation of their governments' AMR National Action Plans. The premise of the research is that policies and targets for the reduction of antibiotic misuse in agriculture, whilst shaped by the WHO and a 'One Health' agenda, are most likely to be effective if their implementation is responsive to the specific pressures, constraints and opportunities experienced by farmers in the context of the particular food systems in which they are embedded, and to the cultural values shaping everyday farming practice. The partnership brings together an interdisciplinary team and wider network of researchers and policy-makers across Kenya, Malawi and the UK. The core team represent the African Population and Health Research Center in Nairobi, the University of Malawi, Newcastle University, Southampton University and UCL. Collaboration in the partnership involves dialogue between the disciplines of Geography, History, Epidemiology, Medicine, Anthropology, Microbiology and Art to understand how cultural values and practices are integral to antibiotic use/misuse in the particular food systems and poultry sectors of Kenya and Malawi. The partnership also involves influential AMR policy institutions on its advisory board, including the UK's Food Standards Agency, the UN's Codex Alimentarius, Malawi's Ministry of Health and the International Livestock Research Institute in Kenya as Project Partners. The model for the partnership involves a programme of interwoven scoping research, involving secondary and primary data collection in Kenya and Malawi, and three intensive workshops in London, Nairobi and Lilongwe. Research will develop understanding of the embeddedness of antibiotic use and AMR awareness in everyday cultures and practices of subsistence and commercial farming. From this research, recommendations will be made to Kenyan and Malawian AMR policy-makers regarding culturally-sensitive and effective approaches to antibiotic stewardship.

Humans are riddled with life. Our bodies, homes and cities support myriad microbial biodiversity. These are generally thought of as disease-causing 'germs' that should be eradicated. But recent developments in metagenomics - the sequencing of genetic material taken from the environment - have begun to reveal the ubiquity and functional importance of the 'human microbiome': the microbial life in, on and around us. Metagenomics helps identify extensive changes in these hitherto invisible worlds with possible implications for human health. Some, like allergy, autoimmunity and antibiotic resistance, have been linked to modern hygiene practices. There is a growing popular and policy interest in the microbiome, and the possibilities of more nuanced or 'probiotic' ways of living with germs. To date however there has been limited public engagement with the science and technology of metagenomics and its potentially transformative means of representing the microbiome. This project will address this gap. Through an in-depth investigation of domestic kitchen practices, it will explore the transformative potential of metagenomics for developing new public understandings of domestic hygiene. The project research design will combine ethnographic methods with laboratory techniques, through a year long collaboration with twelve households from an urban neighbourhood. These households will be asked to survey their domestic microbiome once a month for nine months, undertaking nine metaphorical microbial safaris. The focus of these safaris will emerge from a negotiation informed by our participants' interests, relevant academic literatures and the specific concerns and expertise of our project partners. Each month we will collaboratively design a range of safe, 'antibiotic' and 'probiotic' kitchen experiments - for example involving cleaning practices and products, food preparation or sampling possible sources of kitchen microbes (e.g. pets, gardens, groceries or cars). The gathered samples will be sequenced for subsequent participatory analysis and visualisation. The outcomes and implications of each experiment will be discussed at monthly group meetings, facilitated by members of the project team, alongside project partners and invited experts. This project involves a partnership with the Food Standards Agency and aims to explore the implications of public engagements with the domestic microbiome for a range of stakeholders responsible for or interested in the management of domestic hygiene. Our participatory model will be outlined in a user report and through a practitioners' workshop. The project will deliver an extensive public database of biological and qualitative data on kitchen practices and microbiologies. It will present a range of academic outputs exploring the transformative implications of participatory metagenomics for the social and biological sciences. Good germs, bad germs will demonstrate the potential of interdisciplinary research and participatory approaches to transform how publics, policy makers and academics perceive, engage with and seek to govern microbial life. While its substantive findings will be of direct relevance to understanding the domestic microbiome, the participatory model developed through the project has great potential for future transformative research into the microbiomes of further elements of the built environment (e.g. hospitals, schools, money, transport infrastructure) as well as the intimate spaces of the human body, like the gut.

To secure a continued supply of safe, tasty, affordable and functional/healthy proteins while supporting Net Zero goals and future-proofing UK food security, a phased-transition towards low-emission alternative proteins (APs) with a reduced reliance on animal agriculture is imperative. However, population-level access to and acceptance of APs is hindered by a highly complex marketplace challenged by taste, cost, health and safety concerns for consumers, and the fear of diminished livelihoods by farmers. Furthermore, complex regulatory pathways and limited access to affordable and accessible scale-up infrastructure impose challenges for industry and SMEs in particular. Synergistic bridging of the UK's trailblazing science and innovation strengths in AP with manufacturing power is key to realising the UK's ambitious growth potential in AP of £6.8B annually and could create 25,000 jobs across multiple sectors. The National Alternative Protein Innovation Centre (NAPIC), a cohesive pan-UK centre, will revolutionise the UK's agri-food sector by harnessing our world-leading science base through a co-created AP strategy across the Discovery?Innovation?Commercialisation pipeline to support the transition to a sustainable, high growth, blended protein bioeconomy using a consumer-driven approach, thereby changing the economics for farmers and other stakeholders throughout the supply chain. Built on four interdisciplinary knowledge pillars, PRODUCE, PROCESS, PERFORM and PEOPLE covering the entire value chain of AP, we will enable an efficacious and safe translation of new transformative technologies unlocking the benefits of APs. Partnering with global industry, regulators, investors, academic partners and policymakers, and engaging in an open dialogue with UK citizens, NAPIC will produce a clear roadmap for the development of a National Protein Strategy for the UK. NAPIC will enable us to PRODUCE tasty, nutritious, safe, and affordable AP foods and feedstocks necessary to safeguard present and future generations, while reducing concerns about ultra-processed foods and assisting a just-transition for producers. Our PROCESS Pillar will catalyse bioprocessing at scale, mainstreaming cultivated meat and precision fermentation, and diversify AP sources across the terrestrial and aquatic kingdoms of life, delivering economies of scale. Delivering a just-transition to an AP-rich future, we will ensure AP PERFORM, both pre-consumption, and post-consumption, safeguarding public health. Finally, NAPIC is all about PEOPLE, guiding a consumers' dietary transition, and identifying new business opportunities for farmers, future-proofing the UK's protein supply against reliance on imports. Working with UK industry, the third sector and academia, NAPIC will create a National Knowledge base for AP addressing the unmet scientific, commercial, technical and regulatory needs of the sector, develop new tools and standards for product quality and safety and simplify knowledge transfer by catalysing collaboration. NAPIC will ease access to existing innovation facilities and hubs, accelerating industrial adoption underpinned by informed regulatory pathways. We will develop the future leaders of this rapidly evolving sector with bespoke technical, entrepreneurial, regulatory and policy training, and promote knowledge exchange through our unrivalled international network of partners across multiple continents including Protein Industries Canada and the UK-Irish Co-Centre, SUREFOOD. NAPIC will provide a robust and sustainable platform of open innovation and responsible data exchange that mitigates risks associated with this emerging sector and addresses concerns of consumers and producers. Our vision is to make "alternative proteins mainstream for a sustainable planet" and our ambition is to deliver a world-leading innovation and knowledge centre to put the UK at the forefront of the fights for population health equity and against climate change.