Abstract Antimicrobial resistance (AMR) has emerged as a major global challenge in aquaculture, largely driven by the widespread and frequently unregulated use of antibiotics in finfish, shrimp, and shellfish production systems. Intensive farming practices characterized by high stocking densities, suboptimal biosecurity, and limited disease diagnostics increase infection pressure and encourage prophylactic and metaphylactic antimicrobial use. Consequently, antibiotic residues accumulate in water, sediments, and aquatic organisms, imposing strong selective pressure that promotes the emergence and persistence of antimicrobial-resistant bacteria and accelerates the horizontal transfer of antimicrobial resistance genes (ARGs) within aquatic ecosystems through horizontal gene transfer (HGT) mechanisms such as conjugation, transformation, and transduction. Increasing evidence indicates that aquaculture systems function as critical hotspots for AMR development, facilitating the dissemination of resistant pathogens and ARGs to wild aquatic biota, terrestrial environments, livestock systems, and humans through direct exposure, environmental pathways, and the consumption of aquaculture products. This review synthesizes current knowledge on regional patterns of antimicrobial use in aquaculture. It examines the molecular and ecological mechanisms driving antimicrobial resistance, including antibiotic persistence in water and sediments and the resulting selection pressure on microbial communities. The review also highlights the spread of ARGs through HGT, which contributes to the emergence and dissemination of resistance. Furthermore, it discusses the environmental and public health implications of AMR, particularly the transmission of resistant bacteria and ARGs through aquatic environments and seafood. These pathways may increase the risk of human infections and reduce the effectiveness of antibiotic treatments. It further examines the prevalence and diversity of antimicrobial-resistant pathogens in cultured finfish, shellfish, and ornamental species, identifying integrated farming systems as key amplifiers of resistance dissemination. Finally, the review highlights critical gaps in surveillance and governance and emphasizes the urgent need for strengthened regulatory frameworks, comprehensive AMR monitoring, and the adoption of sustainable disease management alternatives, including vaccination, probiotics, immunostimulants, bacteriophage therapy, and phytotherapeutics. Advancing One Health–oriented strategies is essential to mitigate AMR risks, safeguard aquatic animal health, preserve environmental integrity, and ensure global food safety. Highlights <UnorderedList Mark="Bullet"> <ItemContent> Widespread and often unregulated antibiotic use in aquaculture is a major driver of AMR. </ItemContent> <ItemContent> Intensive farming practices increase disease pressure and promote prophylactic and metaphylactic antimicrobial use. </ItemContent> <ItemContent> Antibiotic residues in water, sediments, and aquatic organisms create selective pressure that accelerates the spread of resistant bacteria and resistance genes. </ItemContent> <ItemContent> Aquaculture systems act as hotspots for AMR dissemination to wild aquatic species, terrestrial environments, livestock, and humans. </ItemContent> <ItemContent> Strengthened regulations, improved AMR surveillance, and sustainable alternatives such as vaccines, probiotics, and phage therapy are essential for effective AMR management. </ItemContent> </UnorderedList> Graphical Abstract

Addressing the escalating threat of antimicrobial resistance (AMR) in fisheries and aquaculture

期刊论文
发表日期：

2026年4月25日

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Mutum Deepti,
Nitesh Kumar Yadav,
Naresh Raj Keer,
Dushyant Mahavadiya,
Parvind Kumar,
Madhulika,
Dharmendra Kumar Meena

摘要

Abstract

Antimicrobial resistance (AMR) has emerged as a major global challenge in aquaculture, largely driven by the widespread and frequently unregulated use of antibiotics in finfish, shrimp, and shellfish production systems. Intensive farming practices characterized by high stocking densities, suboptimal biosecurity, and limited disease diagnostics increase infection pressure and encourage prophylactic and metaphylactic antimicrobial use. Consequently, antibiotic residues accumulate in water, sediments, and aquatic organisms, imposing strong selective pressure that promotes the emergence and persistence of antimicrobial-resistant bacteria and accelerates the horizontal transfer of antimicrobial resistance genes (ARGs) within aquatic ecosystems through horizontal gene transfer (HGT) mechanisms such as conjugation, transformation, and transduction. Increasing evidence indicates that aquaculture systems function as critical hotspots for AMR development, facilitating the dissemination of resistant pathogens and ARGs to wild aquatic biota, terrestrial environments, livestock systems, and humans through direct exposure, environmental pathways, and the consumption of aquaculture products. This review synthesizes current knowledge on regional patterns of antimicrobial use in aquaculture. It examines the molecular and ecological mechanisms driving antimicrobial resistance, including antibiotic persistence in water and sediments and the resulting selection pressure on microbial communities. The review also highlights the spread of ARGs through HGT, which contributes to the emergence and dissemination of resistance. Furthermore, it discusses the environmental and public health implications of AMR, particularly the transmission of resistant bacteria and ARGs through aquatic environments and seafood. These pathways may increase the risk of human infections and reduce the effectiveness of antibiotic treatments. It further examines the prevalence and diversity of antimicrobial-resistant pathogens in cultured finfish, shellfish, and ornamental species, identifying integrated farming systems as key amplifiers of resistance dissemination. Finally, the review highlights critical gaps in surveillance and governance and emphasizes the urgent need for strengthened regulatory frameworks, comprehensive AMR monitoring, and the adoption of sustainable disease management alternatives, including vaccination, probiotics, immunostimulants, bacteriophage therapy, and phytotherapeutics. Advancing One Health–oriented strategies is essential to mitigate AMR risks, safeguard aquatic animal health, preserve environmental integrity, and ensure global food safety.

Highlights

Widespread and often unregulated antibiotic use in aquaculture is a major driver of AMR.

Intensive farming practices increase disease pressure and promote prophylactic and metaphylactic antimicrobial use.

Antibiotic residues in water, sediments, and aquatic organisms create selective pressure that accelerates the spread of resistant bacteria and resistance genes.

Aquaculture systems act as hotspots for AMR dissemination to wild aquatic species, terrestrial environments, livestock, and humans.

Strengthened regulations, improved AMR surveillance, and sustainable alternatives such as vaccines, probiotics, and phage therapy are essential for effective AMR management.

Graphical Abstract