AMRoots: AMR in small-scale farming communities

Our multidisciplinary framework will generate new data towards holistic understanding of the development and transmission of antimicrobial resistance (AMR) in livestock farming communities that are critical for the future food security of sub Saharan Africa, while integrating scalable and community-led approaches to mitigating AMR in these regions.

Two NPOs and five co-leads with expertise in genomics, antibiotic measurement, public health, social and economic dimensions are chaired by Helen McIlleron, Professor of Clinical Pharmacology, University of Cape Town(UCT)

The ±33 million smallholder farms in Africa are at high risk of AMR which is critical for future food security of expanding urban populations (www.ifad.org). These communities are typically marginalised - lacking access to markets, information, education and health care. Limited access to safe water, poor sanitation, proximity of livestock and humans, and high rates of HIV, increase risks of AMR. Data on antibiotic use, and contamination of water and agricultural produce, are limited, but raise concern about AMR in these settings which will assume increasingly important roles in food supply systems. Local knowledge systems and practices could mitigate the development and/or transmission of AMR. Herding for Health (H4H) approaches supported by environmental NPOs for rangeland regeneration, improved biodiversity and livestock farming efficiency, may reduce AMR through appropriate antibiotic use, and reduced transmission of microbes between livestock and humans. Sustained changes reducing AMR depend on translation into benefits (such as meat market advantages) to encourage community-wide buy-in. We will apply our multidisciplinary framework to understand the human, animal, environmental, social and economic dimensions of AMR, and evaluate the impact of H4H, and other community-developed practices mitigating AMR - thus empowering communities to adapt to the challenges.

Our focus is smallscale farming communities - typically marginalised with limited economic opportunities (in SA, the proportion of rural people living in poverty is twice that in urban areas; food insecurity is a major concern). Poverty is linked to a high burden of infectious diseases, poorly regulated antibiotic use, poor water, sanitation and hygiene, and proximity of livestock and humans, which increase risks of AMR development and zoonotic transmission. In eastern South Africa, rural communities have high burdens of HIV (>40% in women), which is associated with AMR. Understanding the extent and impact of AMR is critical to shaping community-driven mitigation approaches contributing to food security for the wider community. The H4H activities of Meat Naturally are improving rangeland quality, and supporting access to meat markets, but also separating homes from livestock and supporting livestock disease management. The impact of H4H and other community co-developed interventions identified during the project, could potentially mitigate AMR, resulting in safer food production with market advantages, while supporting community resilience. Positive findings on their health benefits for community would promote expanded access to H4H activities. Our focus on empowering community will promote awareness about AMR and how to mitigate AMR.

We envisage open access publication of the findings of this research including papers describing: 

• The spacial distribution of AMR in humans, animals and environment, and the impact of H4H, and other community interventions.
• Homestead level socio-economic and health status as well as access to and use of antibiotics in humans and animals. 
• Antibiotic contamination of water, food and produce. 
• Analysis of AMR risk factors and their spacial distribution in this setting. 
• Social aspects of AMR- knowledge, attitudes, mitigating practices, development of community responses. 
• Food safety and antibiotic contamination comparison of community/H4H-produce and commercial products.
• Socio-economics of AMR in the setting and impact on livelihoods.
• Integrated analysis towards development of holistic interventions

We will share our original data through open data repository.

Conscious and responsive community involvement approaches will focus on understanding community perspectives and understanding of AMR before creating tailored science communication tools that could be useful beyond this project. By closely involving communities, we will ensure that information and solutions are not only available in the academic literature, but begin to permeate communities that may not have high levels of knowledge around AMR and mitigation approaches. The films and AMR communication materials could be reused. 

Citizen science activities including development of scaleable science communication tools will promote awareness of AMR and empower communities to develop responses to AMR ( e.g. identification of high risk situations/practices for bacterial transmission and development of citizen-driven mitigating solutions). Community engagement about responsible and appropriate antibiotic and chemical use and disposal will reduce the development of AMR which is of wider societal benefit. Food safety and antibiotic contamination studies will enable farmers to develop mitigating interventions and to take advantage of market advantages for meat produced using sustainable antibiotic-wise approaches. Training and employment opportunities in the community (translation, and sample and data collection) with exposure to research technology. Evidence of the AMR and health impacts of H4H activities will support the carbon credit H4H activities of NPOs and communities. Investigation of local disease control systems including use of plant-based medicines for humans and livestock will be mindful of the the communities’ ownership, and benefit-sharing in case of commodification. While every community will be different, the research approach has application to endemic zoonoses affecting health and livelihoods, and the community involvement models with community-driven solutions have potential for impact and scaleability. We will share our stories on www.

From year 2, we hope to start expanding research activities on AMR, in small scale livestock farming community settings, at additional sites as guided by our findings and contingent on future funding. We also plan to expand our multidisciplinary research model to endemic zoonoses and other pathogens impacting on livelihoods in these settings  - and we will aim to develop a mNGS tool/sample processing method that can be used to screen a setting for a broad range of pathogens/resistance mutations -  combining screening for multiple types of pathogens and resistance mutations. 

Meat Naturally has over 100 villages in Southern Africa where it supports H4H activities and it is expanding rapidly, and it has its own extension teams into communities. From the second year, we will seek to roll out successful activities in these communities as our findings of AMR in this setting emerge e.g. Successful community involvement models, and films and other materials generated by Eh!woza with the community could be screened by Sunshine Cinema. We also hope that other organisations working with communal farmers will support these AMR research and mitigating activities. 

• Comparison of citizen-implemented community survey results (of AMR knowledge and perspectives, and antibiotic use) - at beginning and end of the project. 
• Evaluation of changes over time to homestead survey results on use of and access to antibiotics and other chemicals.
• Community participation in AMRoots activities and involvement in development of  community-driven solutions.
• AMR and antibiotic contamination will be measured 3 times, at the same time each year, and the results over time compared.
• Track iterative refinements to research framework and tools (partners, surveys, questionnaires, community involvement, training, sample collection and processing).
• Uptake of AMR and other ROOTS health-topic research activities by H4H implementing organisations and additional communities.
• Publications.
• Engagement with other stakeholders including government and policy makers.

We are engaged in ongoing grant applications and sponsorship seeking to move beyond proof-of-concept phase (expanding to additional sites to study endemic zoonoses involving data collection and mNGS analyses which can readily include AMR).

Community involvement is critical. Recent community visits are encouraging. Detailed discussions with Meat Naturally, community leaders, and H4H farming associations will precede committing to a research site. We will be mindful to schedule activities avoiding community distractions such as natural disasters or political events. Meat Naturally has >100 operational sites many of which would be suitable. Research fatigue will be mitigated by varied community involvement formats. Regular meetings with community leaders, Meat Naturally representatives are planned, and the community will be represented at Scientific and Steering Committee meetings.

Department of Agriculture, Land Reform and Rural Development (who grant Section 20 approval) and the ethics committees of the participating institutions, may not be familiar with the multidisciplinarity - spanning social, medical and veterinary sciences, and community involvement. We will develop submission dossiers early, detailing ethical and regulatory aspects, and offer to meet with regulators. 

We will specifically engage national and local government agencies of agriculture, conservation and health - whose policy interests closely intersect with this work.

In seeking funding for our multidisciplinary one health approach to improving health and livelihoods in marginalised settings, funder recognition of the importance of community involvement is key. We sought support of innovation - a funder embracing the multidisciplinary space, who supports access to technology in the most left-behind communities. AMR is a critical to health and livelihoods in this setting, and sustainable solutions need to empower community to innovate, organise, respond to opportunity and create change with a flexible evidence-responsive approach. 

The current project will allow streamlining of our solution for upscaling as well as adaptation to additional challenges affecting the health and livelihoods of small-scale farming communities (people, animals and environment) of sub Saharan African. As an academic-NPO-community partnership, we need technical advice and expertise, and sponsorship, to do this. We hope our project speaks to the Sustainability position statements of many of Trinity Challenge’s collaborators. Discovery Health would have specific expertise and interests relevant to southern African contexts. In extending our project with a larger and more complex data sources, we would value collaboration with academic institutions with expertise in analysis and modelling of the multidimensional data.