Aquaculture: sector-specific challenges and advances

Summary

Antimicrobial resistance (AMR) represents a growing global health concern with major implications for aquaculture, the farming of aquatic animals and algae, such as fish, crustaceans, molluscs and seaweeds. Misuse and overuse of antibiotics in aquaculture can drive the emergence of resistant bacteria, threatening aquatic animal health and posing risks to human health through the food chain. Aquaculture’s close connection to the aquatic environment makes it particularly vulnerable, as antibiotic residues and pollutants from aquaculture, agriculture and wastewater can enrich the resistome and promote the selection and spread of resistance genes in aquatic ecosystems.

The aquatic environment acts as both a reservoir and a vector for AMR, enabling dissemination not only through food, but also via occupational and recreational water exposure and wildlife contact. Addressing AMR in aquaculture requires a One Health approach that acknowledges the interdependence of human, animal and environmental health.

This article explores the historical emergence of AMR in aquaculture, focusing on the role of mobile genetic elements, such as plasmids, integrons and transposons, in horizontal gene transfer. It assesses trends in phenotypic resistance and presents a comprehensive overview of current surveillance and mitigation strategies aligned with One Health principles. International guidance from the World Health Organization, the Food and Agriculture Organization of the United Nations and the World Organisation for Animal Health is discussed, with emphasis on harmonised antimicrobial use surveillance and improved transparency. Advances in antimicrobial susceptibility testing and molecular diagnostics, including whole genome sequencing, are presented as tools to enhance AMR surveillance. Key recommendations include strengthened, system-appropriate biosecurity and on-farm management to prevent disease introduction and reduce antimicrobial reliance. While vaccination has delivered sustained reductions in antimicrobial use in intensive finfish systems in high-income settings, notably Atlantic salmon, it remains unavailable for many species and production systems in low- and middle-income countries. In crustacean aquaculture, where vaccination is not feasible, there is a need for greater emphasis on affordable, validated non-antibiotic disease control approaches, including immunostimulants, probiotics and phage-based interventions, integrated within broader biosecurity frameworks.

Keywords

Antibiotic use – Antimicrobial resistance – Aquaculture – Mobile genetic elements – One Health – Surveillance.