Aquaculture shapes antibiotic resistance in Mediterranean gilthead sea bream farming: From hatcheries to offshore cages

Intensive farming in crowded cages increases antibiotic treatments, promoting antimicrobial resistance (AMR) in fish-associated bacteria. Combined with environmental pollution, this accelerates AMR emergence, impacting food safety and ecosystems. To better understand AMR dynamics in aquaculture, this study examined antibiotic resistance genes (ARGs) in farmed gilthead sea bream ( Sparus aurata ) and in environmental samples, including seawater, sediments, and feed. Sampling was conducted across the full production cycle in three Mediterranean countries (Italy, Greece, and Spain) with wild S. aurata specimens also collected in Italy and Greece as a comparative baseline. Shotgun metagenomics revealed distinct ARG profiles between farmed fish and their surrounding environment, with notable shifts from land-based phases (eggs to juveniles) to open sea farms (juveniles to adults). Beta-lactam resistance dominated in adult farmed specimens across all sites, underscoring its prevalence in Mediterranean aquaculture. Interestingly, Greek wild fish samples lacked beta-lactamases. This study emphasizes the effectiveness of metagenomics-based approaches for tracking ARGs in fish farming, and underlines its potential to mitigate risks to human health, preserve aquatic ecosystems and make aquaculture more sustainable.