The project ARENA aimed to produce an overview of antibiotic resistance genes (ARGs), pathogenic bacteria (PB), and antibiotic (AB) contamination in fish farms with open (mariculture) and closed (RAS - Recirculating Aquaculture System) settings. The sources and pathways of potential contamination were explored through biomolecular techniques and novel early warning tools in environmental samples (water, sediment, feed, benthic biota) and fish tissues collected during seasonal sampling campaigns.

According to current European regulations, the targeted aquaculture plants are considered AB-free. However, most samples collected from mariculture or RAS plants were contaminated with AB residues.

Common antibiotics such as sulfonamides and macrolides, especially azithromycin and clarithromycin, have been found in fish, sediments, and seawater in mariculture and Recirculating Aquaculture Systems (RAS), posing environmental hazards. Antibiotic resistance genes (AMR) and microbial activity were higher near aquaculture activities; mariculture displayed extensive AMR in the sediments beneath fish cages, while RAS displayed a variety of AMR in internal sites. AMR gene diversity was higher in RAS, according to a metagenomic study. Nanopore sequencing for AMR detection and a biosensor for E. coli demonstrated potential for monitoring environmental and microbial health in aquaculture settings.