In South Africa’s Rural Eastern Cape, a Tiny Lab Tackles a Global Health Crisis

Deep in South Africa’s Eastern Cape, where winding dirt roads and patchy phone signals make connection a daily challenge, a new kind of laboratory is taking root.

Inside a small room in a homestead granted by a local Chief, scientists, youth volunteers, and community leaders are gathering to take on one of the world’s biggest and growing threats: antimicrobial resistance (AMR).

This small, community-powered project led by Trinity Challenge winners AMRoots, is led by University of Cape Town researcher Helen McIlleron and supported by local NGO Meat Naturally, community-based environmental organisation CEET, and the acclaimed science engagement initiative Eh!woza. AMRoots investigates antibiotics, how they are accessed, used and disposed of and how they are impacting rural communities and what this means for resistant bacteria in humans, animals, and the environment.

Why Here, Why Now?

Despite a growing national population, South Africa’s rural areas – especially in provinces like the Eastern Cape are shrinking. Young people leave for the cities and small-scale farmers are cut off from formal markets due to poor infrastructure, limited internet, and a lack of support.

“Farmers here are often neglected,” Helen explains. “They’re locked out of markets and have limited basic services, but they are needed for future food security, and are key to rural economies.”

Antibiotics are widely used in livestock across the Global South, sometimes without adequate oversight. When they are not used responsibly in animals or people, resistant strains of bacteria can spread undetected, especially in regions with limited health data or surveillance.

AMRoots is a proof-of-concept project aiming to map AMR across a sample of 25 homesteads in one community. It’s using a “One Health” approach-integrating environmental, animal, and human health data to paint a picture of how antibiotics circulate through the rural food and health system.

Hair and meat from livestock, water samples, and human health data are all being analysed on site. “We’re extracting and sequencing right here in the community,” says Helen. “We want the science to happen in the same place as the people it affects. We also want to inspire the next generation of scientists in rural areas like the Eastern Cape.”

Beyond the Lab: Education, Empowerment and new markets

Beyond the scientific study, AMRoots is implementing community engagement and education workshops. Partnering with Eh!Woza, workshops are being run explaining what AMR is, how antibiotics work, and why overuse can pose a danger not just to animals, but to entire communities.

Tasha Koch, a scientist and educator from Eh!Woza has experience in DNA sequencing and other academic practices. “We’re bringing that same energy here. It’s not just about gathering data, it’s about making the science visible, real, and local.”

Nine young community members will be selected to participate in a film-making workshop. They will make documentaries about their/the community’s experience and interpretation of AMR. The documentaries will be screened in the community and discussions held around them. The project will employ two young people from the area to support the research activities with translation and data collection.

If the study finds that local livestock are free of antibiotic residues, there is a potential economic upside. “There’s growing demand for antibiotic-free, ethically raised meat,” Helen notes. “If we can prove it, we might be able to connect these farmers to new markets.”

Scaling Up a Small Start

The current project is small, but it’s a vital test run. “Holistic data (across humans, animals and the environment) is new for this kind of setting,” Helen says. “What we learn here will tell us where to focus next and how to scale such research efficiently.”