Antibiotic resistance in aquaculture: Contributions and perspectives of genomics

The global rise of antibiotic resistance (AR) poses a major threat to public health, food security, and environmental sustainability. In aquaculture, the extensive and often unregulated use of antibiotics for disease prevention and growth promotion has driven the emergence and spread of ARB and resistance genes, which may transfer to humans and other ecosystems. Advances in genomic technologies have greatly enhanced our ability to investigate, monitor, and manage AR in aquatic environments. This review synthesizes current knowledge on genomic tools, including whole-genome sequencing (WGS), metagenomics, transcriptomics, proteomics, plasmidomics, CRISPR-Cas systems, and comparative genomics, used to identify resistance determinants, track gene flow, and elucidate the evolution and functional expression of resistance. These approaches improve surveillance accuracy, uncover novel mechanisms, and guide targeted intervention strategies. Despite their promise, genomic applications face challenges related to technical complexity, data interpretation, and accessibility, particularly in low- and middle-income regions. Addressing these barriers through interdisciplinary collaboration and sustainable practices is crucial to mitigate AR in aquaculture. To our knowledge, this review provides the most comprehensive synthesis of genomic approaches applied to AR in aquaculture, integrating recent advancements and their implications within a One Health framework. Ultimately, incorporating genomics into resistance surveillance supports responsible antibiotic use and safeguards antimicrobial efficacy for future generations.