Revealing the most contaminated stages and spots of foodborne pathogens and antibiotic resistance along the whole fish production chain in Greek aquaculture.

Aquaculture constitutes a significant reservoir for antibiotic-resistant bacteria (ARB) posing substantial risks to seafood consumers and public health. This study aimed to reveal the most contaminated stages and spots of foodborne pathogens, and ARB along the whole fish production chain in Greece. To reach this aim, samples (water, surfaces, fish feed, and fish) were collected from multiple spots (e.g. surfaces, equipment) of all stages of the entire chain, from farming to packaging, and analyzed for their microbiological and antibiotic resistance status through classical and molecular approaches. At population point of view, surfaces from broodstock, larvae and pre-fattening tanks were found to be the most burdened spots in farming stages, recording levels close to 5 log cfu/ml or g or cm2, while the most burdened spots were found to be on working surfaces before and after decontamination, the concrete floor, transport boxes for fish and fish samples in processing. Based on High-Resolution Melting analysis (HRM) followed by Sanger sequencing, the potential pathogenic microbiota, mainly consisting of Enterococcus spp., Serratia spp., Morganella morganii and Klebsiella pneumoniae. at both pre-fattening and processing stages, indicating the possible transfer of these microorganisms along the fish production chain. These potential pathogens, mainly isolated from surfaces and water of weaning and pre-fattening tanks, fish feeds, working surfaces, fish transport boxes, concrete floors and fish especially from transport boxes and harvesting, presented a noteworthy resistance to most antibiotics tested (e.g., Clindamycin, Nalidixic acid, Streptomycin, Sulphonamides, Ceftazidime, Erythromycin, Vancomycin, Penicillin G, and Cefoxitin). The findings underscore the importance of early detection and intervention strategies to mitigate ARB transmission, thereby enhancing the safety and quality of aquaculture products.