In 2023, the fish farming industry in Kenya produced 31,767 metric tons, valued at approximately KSh 10.0 billion. Despite the sector’s value, it is faced with challenges. According to a new study, mass deaths of farmed tilapia have become increasingly common, threatening farmers’ livelihoods and the sustainability of this vital ecosystem.
The research, carried out by Cornell University in collaboration with the Kenya Marine Fisheries Research Institute (KMFRI) and the International Livestock Research Institute (ILRI), is the first of its kind in Lake Victoria to isolate and identify bacterial pathogens from a fish mortality event and to assess their antimicrobial susceptibility.
Several of the detected strains showed varying levels of resistance to commonly used antimicrobials — a troubling trend with implications that stretch far beyond fish farming.
“Antimicrobial resistance is not just a human health concern; it’s also an emerging food systems challenge,” said Ekta Patel, CGIAR scientist at ILRI.
“Aquatic ecosystems are often overlooked as potential reservoirs for resistant bacteria and emerging pathogens. By strengthening surveillance, we can detect emerging threats early and generate evidence to guide timely interventions.”
Lead author Eric Teplitz, a veterinarian and PhD candidate at Cornell University, echoed this concern:
“Environmental stewardship and disease management must go hand in hand across terrestrial and aquatic ecosystems. This integrated view is essential to informing effective public health responses and sustainable aquaculture practices.”
From 2020 to 2023, cage farmers reported more than 80 large-scale fish mortality events, resulting in losses exceeding 1.8 million tilapias. However, only 39% of these events were reported to public institutions, and just 17% of farmers attempted any treatment — often without diagnostic confirmation or veterinary input.
According to Kathryn Fiorella, principal investigator from Cornell University’s Department of Public & Ecosystem Health,
“Aquaculture can provide high-quality jobs and nutrition, but its viability depends on biosecurity.”
Christopher Aura, Director of Freshwater Systems Research at KMFRI and a partner on the study, emphasized the structural gaps that exacerbate the crisis. Stronger systems for data sharing and coordination between farmers, regulators, and research institutions, he said, are urgently needed.
Tailored approaches that reduce the incidence of fish disease require a more detailed understanding of its underlying causes, including water quality and infectious disease, informing the need for data sharing.
Additionally, the study shows that improved biosecurity and management practices — including proper disposal of dead fish, more dispersed siting of cages in deeper waters with better water quality, and reduced use of clogged cage nets that restrict water circulation — are crucial.
Teplitz noted that
“Often these pathogens are opportunistic and secondary to stressors such as poor water quality,” highlighting the everyday risks fish are exposed to in poorly managed systems.
He adds that this underscores the importance of a One Health approach, which recognizes the interconnectedness of human, animal, and environmental health.
The findings present an opportunity to align aquaculture practices with national and regional priorities on AMR in aquaculture and sustainable fisheries development,
“as well as AMR stewardship strategies,” according to Aura.
Read also: How fish farming is a booming industry
