Microbiological safety of aquaponic systems: pathogen risks, challenges, and food safety interventions for Africa

Abstract

Aquaponics, an integrated food production system combining aquaculture and hydroponics in a closed recirculating system, holds significant potential for addressing food insecurity in Africa, where foodborne diseases account for an estimated 91 million illnesses and 137,000 deaths annually. Despite the increasing adoption of aquaponics across Sub-Saharan Africa, there is no comprehensive microbiological safety review focused on the safety of aquaponic systems and products, particularly in areas characterised by weak regulatory frameworks and limited surveillance infrastructure This narrative review fills this gap by examining the microbiological safety challenges in aquaponic systems within Africa, focusing on pathogen sources, contamination pathways, detection methods, and preventive control strategies. Key microbial hazards identified include pathogenic bacteria such as Salmonella spp., Aeromonas hydrophila, and Escherichia coli, toxigenic fungi, and enteric viruses. The spread of antimicrobial resistance genes within aquaponic microbial communities is identified as a critical emerging public health concern requiring integration into One Health surveillance frameworks. Barriers to aquaponics adoption in Africa are assessed across economic, technological, environmental, and regulatory dimensions. Targeted preventive controls, including water quality management, biosecurity, disinfection, and good agricultural practices, are discussed within resource-appropriate frameworks. Future directions including smart monitoring, AI-driven decision support, and probiotic biocontrol are examined. We conclude that evidence-based microbiological safety strategies based on regulatory realities are indispensable for the safe and sustainable expansion of aquaponics as a food security tool in Africa.