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Antimicrobial resistance dissemination through the food chain is a priority One Health concern. Structurally complex, repeatedly used food-transport containers in institutional catering may provide protected niches for bacterial persistence. This study characterized 53 Escherichia coli isolates recovered in autumn 2025 from the pressure-relief compartments of 53 independent containers originating from a catering system comprising three central kitchens and 17 recipient institutions.

Phenotypic susceptibility was assessed by broth microdilution MIC testing, followed by whole-genome sequencing using Oxford Nanopore MinION as the sole sequencing platform and integrated genomic analysis of all isolates. Phenotypic resistance was detected only to florfenicol in two isolates (3.8%). Four isolates had cefotaxime MICs above the ECOFF but below the clinical breakpoint. Ten isolates showed an inhibitor-synergy signal in at least one cephalosporin–clavulanate pair, although no classical ESBL gene was identified. The assemblies were of high quality, with 99.1% BUSCO completeness and a mean CheckM completeness of 99.88%. The population contained 11 identifiable sequence types and 15 serotypes, dominated by the ST5295/O71:H12 lineage. Panaroo identified 10,294 gene clusters, of which 67% belonged to the variable genome. CARD screening detected 46 resistance-associated genes, predominantly intrinsic efflux, regulatory and stress-response determinants; no acquired ESBL, carbapenemase, mcr, qnr, tet, sul or floR gene was detected. The virulome was dominated by colonization, biofilm and iron-acquisition modules, with no assigned classical diarrhoeagenic pathotype or Shiga toxin. A mean of 8.8 predicted prophage regions occurred per genome.

Compared descriptively with the previous sampling round, the new population showed a lower phenotypic resistance burden, while genomically diverse E. coli lineages were again recovered from the same type of structurally protected container compartment. Targeted hygiene monitoring and integrated phenotypic–genomic surveillance therefore remain warranted.