Surveillance of Antimicrobial Resistance in the Asian Seabass (Lates calcarifer) Supply Chain Using Nanopore Sequencing

Intensive fish farming worldwide has increased reliance on antibiotics to control bacterial pathogens, raising concerns about antimicrobial resistance (AMR) in aquaculture. These resistant bacteria can persist and pass through the food supply chain, from farms to consumers. Despite this risk, antimicrobial resistance genes (ARGs) in aquaculture environments and fish products have not been elucidated. This study aimed to detect ARGs found in the Asian seabass (<i>Lates calcarifer</i>), an economically important fish in Thailand, collected from farms, fish container vehicles, and markets, using Nanopore metagenomic sequencing. We detected multiple ARGs in all sample types. Water samples harbored the <i>rpsL</i> gene conferring streptomycin resistance. Container samples exhibited the highest diversity of ARGs, including multiple beta-lactamases and the <i>rsmA</i> gene, conferring resistance to fluoroquinolones, diaminopyrimidines, and phenicol antibiotics. Fish samples generally lacked ARGs, except for one sample harboring <i>rsmA</i>. Non-metric multidimensional scaling revealed distinct microbial communities in water, compared with those found in container and fish samples, indicating potential cross-contamination during handling or storage. Our findings emphasize that containers could be critical control points for minimizing AMR spread. Overall, this study highlights the interconnection between environmental, fish, and human health, highlighting the importance of integrated AMR surveillance and management in aquaculture systems.