Cracking the Shell: Genomic Insights into Antimicrobial-Resistant Escherichia coli on Retail Eggs in the United Arab Emirates

Background:
Antimicrobial-resistant bacteria associated with foods of animal origin are an increasing food safety concern. However, data on generic Escherichia coli from retail eggs in the Middle East remain scarce.

Objective:
This study provides baseline evidence on the occurrence, antimicrobial resistance, virulence determinants, and genomic diversity of generic Escherichia coli recovered from retail table eggs in the United Arab Emirates.

Methods:
A total of 200 retail egg packs, representing 2,400 individual eggs, were collected from supermarkets in three major United Arab Emirates 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 whole-genome sequencing was conducted on 20 selected isolates to characterize resistance genes, virulence determinants, phylogroups, sequence types, and genomic backgrounds.

Results:
Escherichia coli was recovered from 50 of 200 eggshell pools, corresponding to 25.0% prevalence with a 95% confidence interval of 19.2–31.6%. No isolates were detected in egg contents, indicating contamination restricted to the external shell surface. Recovery was significantly higher from cage-laid eggs than cage-free eggs. Phenotypic testing revealed frequent non-wild-type profiles to ciprofloxacin, nalidixic acid, tetracycline, ampicillin, and chloramphenicol. Multi-class resistance was detected in 52.0% of isolates, while all remained wild type to colistin, meropenem, and tigecycline. Genome analysis revealed a diverse resistome dominated by quinolone-associated determinants, including gyrA mutations and qnrS1, alongside tet(A), blaTEM-1, cmlA1, floR, and one blaCTX-M-55-positive isolate. Isolates belonged to 12 sequence types, mainly phylogroups B1 and A, indicating heterogeneous genomic backgrounds. Virulence-associated genes related to adhesion, iron acquisition, serum survival, toxins, and stress adaptation were widely detected.

Conclusion:
These findings establish the first integrated phenotypic and genomic baseline for eggshell-associated generic Escherichia coli in United Arab Emirates retail eggs and support targeted surveillance, improved eggshell hygiene, and consumer practices that reduce cross-contamination.