New study ties fish disease to drug resistance in Lake Victoria

KENYA – A new study has revealed critical insights into the rising challenge of fish disease and antimicrobial resistance (AMR) in Lake Victoria’s cage aquaculture industry, which is expanding rapidly to meet growing demand for fish across East Africa.

The research, conducted by Cornell University in partnership with the Kenya Marine and Fisheries Research Institute (KMFRI) and the International Livestock Research Institute (ILRI), highlights the urgent need for improved disease management and biosecurity practices to prevent mass tilapia die-offs and protect the livelihoods of smallholder fish farmers.

Between 2020 and 2023, cage fish farmers around Lake Victoria reported more than 80 mass mortality events, resulting in the loss of over 1.8 million tilapia. 

Yet the study found that only 39% of these incidents were formally reported to public institutions, and just 17% of affected farmers attempted any kind of treatment, often without a diagnosis or veterinary guidance.

“This study shows how locally grounded science can inform national biosecurity and best management practices’ enhancement, as well as AMR stewardship strategies,” said Christopher Aura, Director of Freshwater Systems Research at KMFRI.

The researchers combined farmer surveys, active disease surveillance, and laboratory testing to understand the underlying causes of fish mortality and AMR patterns. 

Lead author Eric Teplitz, a veterinarian and PhD candidate at Cornell University, noted that many of the bacterial pathogens identified during investigations were opportunistic, taking advantage of fish already stressed by poor water quality and overcrowded cages.

“We identified a range of bacterial pathogens from a mass tilapia mortality event in Busia County and broader surveillance across the lake,” Teplitz said. 

“Often these pathogens are opportunistic and secondary to stressors such as poor water quality; this underscores the importance of a One Health approach to environmental stewardship and disease management across terrestrial and aquatic ecosystems.”

Biosecurity training and AMR risk

As part of the study, Cornell, KMFRI, and ILRI conducted a series of workshops for fish farmers in western Kenya, promoting practical disease prevention measures. 

These included burying or composting dead fish instead of discarding them into the lake, dispersing cages into deeper waters with better oxygen levels, cleaning clogged cage nets to improve water flow, and encouraging prompt disease reporting.

The study is also the first in Lake Victoria to isolate and identify bacterial pathogens from a tilapia mortality event and assess their resistance to antibiotics. 

Several strains exhibited varying degrees of resistance to commonly used drugs, raising concerns about the future effectiveness of treatment options.

“Antimicrobial resistance is not just a human health concern, it’s also an emerging food systems challenge,” said Ekta Patel, a 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.”

Toward stronger fish health systems

The study’s findings align with broader national and regional goals to combat AMR and develop sustainable fisheries.

According to Kathryn Fiorella, the study’s principal investigator from Cornell’s Department of Public & Ecosystem Health, biosecurity must be treated as a foundation for aquaculture growth.

“Aquaculture has the potential to provide high-quality jobs and nutrition, but its viability depends on biosecurity,” Fiorella said. 

“Disease will always be present in aquatic systems, but understanding and responding to it is critical to supporting aquaculture development and the surrounding aquatic ecosystems.”

The authors stress the importance of policies that support responsible antimicrobial use, early surveillance, farmer engagement, and investment in diagnostic and fish health infrastructure. 

Without such measures, the long-term sustainability of East Africa’s aquaculture sector and the food security it provides remain at risk.

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