Antimicrobial resistance in Kenya isn’t confined to hospital wards. Experts say it travels through wastewater, rivers, fish and the ocean, exposing gaps in One Health surveillance and financing that leave environmental threats and coastal livelihoods poorly monitored.
For a fisherman working in Kenya’s coast, antimicrobial resistance sounds like a problem for hospitals, doctors and pharmacies, something that happens far from the water where he earns his living. Scientists and environmental officials studying the issue say it may just as easily travel a different route, through wastewater, rivers, fish and even the open ocean.
These are some of the questions raised at the AMR Governance and Financing Summit 2026, a two-day gathering held on 9 and 10 September, under the theme “Sustainable Governance and Financing for AMR Containment” which drew researchers, government officials and county representatives from across Kenya’s One Health sectors to debate how resistance is spreading, and how the country intends to pay for containing it.
According to experts, antimicrobials used to treat people, animals and crops do not simply disappear once they have done their job. Residues can wash into wastewater, rivers and other parts of the environment, turning a problem people often think of as purely medical into a One Health crisis that hospitals cannot solve alone.
One Health is the principle that human, animal and environmental health are interconnected, meaning resistant bacteria that emerge in one part of the system can just as easily surface in another.
Speaking at the summit, Dr John Mumbo, assistant director at the National Environment Management Authority (NEMA), said medicines and their residues reach the environment through several routes, among them human waste, expired or unused medicines discarded improperly, farm manure and slaughterhouse waste.
“Inadequate treatment of effluent can allow antimicrobial residues and resistant organisms into the environment, while existing treatment systems may not be designed to deal effectively with many antimicrobial compounds,” he explained.
Waste from households, hospitals and industry enters the same water systems that people depend on for food and livelihoods
Dr Sophie Uyoga, a research scientist and deputy director at the Kenya Medical Research Institute’s (KEMRI) Centre for Geographic Medicine Research Coast in Kilifi, said environmental contamination matters because what enters oceans, rivers and other water systems can return to people through the food chain.
For coastal communities, she said, the question is not simply whether a patient takes an antibiotic correctly. Waste from households, hospitals and industry enters the same water systems that people depend on for food and livelihoods; therefore, fish, sanitation, waste management and how seafood is handled all become part of the wider AMR conversation.
“Fishermen could be a potential source because even though they fished properly, the handling, sanitation, and waste management were done poorly,” she added.
Experts noted that fisheries and aquaculture add another layer to the risk, as fish kept in cages may be exposed to antibiotics or vaccines, while other sources of contamination can enter lakes and the waters around them. For communities whose livelihoods depend on those waters, the implications reach beyond any single farm or cage.
Kenya has built relatively strong systems for tracking resistance in hospitals and communities, but environmental surveillance is still developing. Without data from water, wastewater, livestock, fisheries and other environments, large parts of the country’s One Health picture could remain invisible.
NEMA has already piloted environmental AMR detection in Nairobi and built environmental surveillance into its strategic plans, Mumbo said. The authority is now seeking dedicated funding to expand that work and use its findings to shape policy and resource allocation.
Patients with drug-resistant infections faced a 44 per cent higher risk of death and stayed in hospital for about five additional days
That data gap carries a real cost, one already visible in Kenya’s hospitals. A study from a tertiary Kenyan hospital found that patients with drug-resistant infections faced a 44 per cent higher risk of death, stayed in hospital for about five additional days and incurred almost 60 per cent higher costs, partly because treatment had to move to more expensive second- or third-line medicines, the costlier drugs doctors turn to once frontline antibiotics stop working.
For Kenya, failing to finance prevention could ultimately prove more expensive than financing it. That interdependence between sectors is why stakeholders are coming together under the One Health banner, said Dr Edna Mutua, a researcher at the KEMRI-Wellcome Trust Research Programme.
The approach brings together human health, animals, crops, fisheries and aquaculture, wildlife and the environment, sectors she described as too interconnected to tackle separately. She also pointed to persistent challenges such as over-the-counter access to antibiotics and the role community pharmacies play as many patients’ first point of contact.
Money is emerging as one of the biggest obstacles to Kenya’s AMR response. The country’s National Action Plan on Prevention and Containment of AMR for 2023 to 2027 costs about Ksh2 billion over five years, said Dr Emmanuel Tanui, the National AMR Focal Point at the Kenya National Public Health Institute.
Dr Tanui said when broken down, it comes to around Ksh600 million per annum to implement amid a rapidly shifting financing landscape.
Tanui said the end of support from the Fleming Fund, which had financed a significant share of Kenya’s AMR activities, has exposed the need for the country to increasingly finance its own response through national and county resources, a moment he believes Kenya should treat as a chance to make AMR a national health priority.
The private sector should be treated not simply as an industry to regulate but as a critical steward in the AMR response
Dr Mutua said the Mombasa summit aimed partly to bring counties, national policymakers, researchers and partners together to rethink governance and build a stronger case for financing AMR control.
AMR spending does not always sit under a budget line marked “AMR,” however. Dr Gregory Ganda, Kisumu County’s health executive, argued that counties need to stop asking where the AMR budget is and start identifying what their existing spending already contributes to preventing resistance.
A toilet, he said, may appear in a water, sanitation and hygiene budget rather than an AMR one, yet improving sanitation helps prevent infections and reduces the need for antibiotics. He said the distinction matters practically because a county need not wait for a dedicated AMR line to make progress if it can recognise and better coordinate the resistance-relevant work it is already funding.
“When you reduce the number of infections, you are actually reducing the number of microbes that are being used,” he explained.
The financing debate also raised the question of who should carry responsibility. Dr Anne Musuva, acting CEO of the Kenya Health Federation, argued that the private sector should be treated not simply as an industry to regulate but as a critical steward in the AMR response.
She called for private-sector participation in governance, better alignment of incentives, investment in diagnostics, stronger accountability and shared data systems, the sort of infrastructure that could begin closing the environmental data gaps NEMA and KEMRI researchers describe.
According to her, wider recognition of AMR-relevant spending already built into county budgets could stretch existing money further, while a private sector treated as a partner in governance, rather than only a target of regulation, could bring resources the public purse does not have.
