Eggshell-associated Escherichia coli from United Arab Emirates retail eggs exhibits diverse antimicrobial resistance phenotypes, resistome profiles, and genomic backgrounds

Background Antimicrobial-resistant bacteria associated with foods of animal origin are an increasing food-safety concern; however, data on the hygienic indicator Escherichia coli from retail eggs in the Middle East remain scarce. This study investigated the occurrence, antimicrobial resistance, virulence determinants, and genomic diversity of E. coli recovered from retail table eggs in the United Arab Emirates. Methods A total of 200 retail egg packs, comprising 2,400 individual eggs, were collected from supermarkets in three major cities between October 2024 and June 2025. Eggshells and egg contents from each pack were analyzed separately. Phenotypic antimicrobial susceptibility testing was performed on 50 isolates, and 20 selected isolates underwent whole-genome sequencing. Results E. coli was recovered from 50 of 200 eggshell pools (25.0%; 95% confidence interval: 19.2–31.6%) but was not detected from any of the 200 egg-content pools under the analytical conditions used. An unadjusted pack-level analysis showed an association between the labeled production system and E. coli detection, with higher recovery in cage-laid packs (Fisher’s exact test, P = 0.011). Non-wild-type phenotypes were frequently observed for ciprofloxacin (76.0%), nalidixic acid (60.0%), tetracycline (48.0%), ampicillin (46.0%), and chloramphenicol (40.0%). Multiclass resistance (i.e., resistance to three or more antimicrobial classes) was detected in 26 isolates (52.0%), whereas all isolates retained wild-type phenotypes to colistin, meropenem, and tigecycline. Twenty isolates were sequenced; one was excluded after quality control, leaving 19 isolates for genomic analysis. Whole-genome sequencing identified a diverse resistome dominated by quinolone-resistance determinants, including gyrA mutations and qnrS1 , alongside tet(A) , bla TEM-1, cmlA1 , and floR . One isolate carried the extended-spectrum β-lactamase gene bla CTX-M-55 . The sequenced isolates subset represented 12 sequence types and were assigned predominantly to phylogroups B1 and A, demonstrating a heterogeneous population without a dominant clone. Virulence-associated genes involved in adhesion, iron acquisition, serum survival, toxin production, and stress adaptation were widely distributed. Conclusion To our knowledge, this study establishes the first integrated phenotypic and genomic baseline for eggshell-associated generic E. coli in UAE retail eggs. The findings support targeted antimicrobial-resistance surveillance and emphasize the importance of improved eggshell hygiene and consumer handling practices to minimize cross-contamination during egg preparation.