Vuoso, Valeria (2025) Integrated approach to antimicrobial resistance in bivalve molluscs: phenotypic, genomic and food safety perspectives from the Campania Region. [Tesi di dottorato]

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Abstract

Antimicrobial resistance (AMR) in bivalve molluscs intended for human consumption represents an emerging food safety concern, particularly in regions where regulated, non-compliant and illegal distribution channels coexist. Within an applied food safety perspective, this thesis investigates AMR not only as a laboratory phenomenon but as a dynamic and context-dependent process within real supply networks. Chapter I aimed to characterize the commercial circulation patterns of mussels in the Campania region, focusing on the coexistence of officially regulated markets, semi-compliant outlets and fully illegal street vending. This heterogeneous scenario revealed substantial gaps in traceability and official oversight, showing how bivalves may circulate outside conventional monitoring frameworks and potentially act as silent carriers of microbiological hazards along informal food distribution routes. Chapter II aimed to characterize the phenotypic and genomic AMR profiles of Escherichia coli and Vibrio spp. isolated from mussels collected across these distinct commercial channels. Antimicrobial susceptibility testing revealed a high prevalence of multidrug-resistant strains, including resistance to critically important antimicrobials. Whole-genome sequencing (WGS) provided deeper insight into resistome variability and strain-specific genomic features, suggesting that AMR profiles may be influenced by commercial origin, handling practices and environmental exposure, beyond formal compliance status alone. Chapter III aimed to investigate resistance mechanisms not fully explainable through classical ARG detection, with particular attention to genomic–phenotypic discrepancies observed in E. coli and Vibrio spp. Several isolates exhibited resistance behaviours not attributable to conventional resistance genes, highlighting the presence of non-canonical mechanisms. These findings reinforced the scientific relevance of integrating traditional microbiological testing with advanced WGS-based approaches to achieve a more accurate and mechanistic interpretation of AMR expression and persistence. Chapter IV aimed to assess the functional performance of the depuration process under controlled flow-through conditions, evaluating the real capacity of different bivalve species to reduce E. coli contamination following controlled exposure. The results demonstrated pronounced species-specific variability in clearance kinetics, indicating that depuration efficiency is not uniformly predictable and may depend on biological traits, initial contamination level and environmental compatibility. Overall, this thesis provides a multidimensional and evidence-based interpretation of AMR in bivalve molluscs, supporting the development of more informed, species-aware monitoring and risk interpretation strategies capable of better reflecting the complexity of real-world food systems and anticipating, rather than documenting, the evolving dynamics of antimicrobial resistance.

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