Microbiological and genomic surveillance of WHO critical priority pathogens along the oyster supply chain: water quality as a driver of persistence and depuration as a mitigating strategy in a One Health context

Introduction Oysters are widely consumed worldwide, often raw, which raises food safety concerns. These filter-feeding bivalves can accumulate contaminants, including antimicrobial-resistant bacteria (ARB), posing a public health risk. This study aimed to investigate the presence of ARB in the oyster supply chain, evaluating the impact of production, commercialization and depuration processes on ARB contamination. Methods Samples were collected from six oyster farms and commercial establishments supplied by them in the North and South Bays of Florianópolis, Brazil. Seawater, farmed oysters, commercially available oysters, depurated oysters, and larval-stage oysters were analyzed. Results A total of 167 antimicrobial-resistant isolates were identified, with Escherichia coli and Klebsiella pneumoniae being the most prevalent, many of which are classified as WHO critical-priority pathogens. Whole genome sequencing of selected isolates revealed a high diversity of sequence types, including globally distributed lineages, and the presence of shared clones across seawater and oysters, indicating bacterial circulation along the supply chain. Genomic analysis also identified a wide range of resistance genes, including extended-spectrum β-lactamases (ESBL), as well as determinants conferring resistance to quinolones, aminoglycosides, tetracyclines, sulfonamides, and trimethoprim, many of which were associated with plasmids. A similarity was observed between the antimicrobial resistance profiles of oysters collected from the marine environment and those commercially available. Sites with higher ARB contamination in the seawater showed increased resistance levels in oysters sold for human consumption. In some cases, identical resistance profiles and sequence types were detected across different stages of the supply chain, indicating persistence and dissemination along the supply chain. Additionally, the depuration process effectively reduced resistant bacteria and the prevalence of resistance genes in oysters. Discussion These findings demonstrate that contaminated seawater is a key driver of ARB dissemination throughout the oyster supply chain, while depuration is an effective microbiological control measure that reduces resistant bacteria and resistance genes, thereby contributing to improved food safety.