Abstract

Filter-feeding bivalves can accumulate fecal bacteria and antimicrobial resistance determinants, yet routine regulatory monitoring relies mainly on quantitative Escherichia coli criteria. This study provides a whole-genome characterization of an ExPEC-like E. coli ST536 (O21) isolate recovered from commercially depurated retail mussels originating from a Class B harvesting area in Portugal. The isolate was phenotypically identified by MicroScan WalkAway Plus and subjected to antimicrobial susceptibility testing and Oxford Nanopore long-read sequencing, followed by genome assembly, annotation, antimicrobial resistance and virulence screening, plasmid and prophage detection, and phylogenomic analysis. Phenotypically, only resistance to tobramycin was detected using the MicroScan WalkAway system. Genomic analysis revealed a complex mobile element-rich architecture, including multiple resistance-associated determinants, 116 virulence-associated loci, prophage regions, and a mobilizable IncY plasmid carrying CTX-like class A β-lactamase-associated hits detected by ABRicate. Despite its ST536 assignment and ExPEC-associated traits, phylogenomic analysis placed the isolate within a phylogroup A/commensal-like background rather than among classical B2 ExPEC lineages, suggesting acquisition of pathoadaptive modules by an atypical environmental lineage. These findings highlight the potential utility of WGS as a complementary tool and suggest that depurated bivalves may serve as sentinels, warranting further investigation.

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