Occurrence, antimicrobial resistance, and whole-genome characterization of Salmonella in retail eggs in the United Arab Emirates: Evidence of a clonal dominance of serovar Braenderup

Salmonella contamination of table eggs remains a significant food safety concern globally; however, data from the Middle East are limited. This study provides the first baseline assessment of the occurrence, antimicrobial resistance, and genomic characteristics of Salmonella recovered from retail table eggs in the United Arab Emirates (UAE). A total of 380 retail egg packs (12 eggs per pack; 4,560 eggs) were collected from supermarkets in three major cities. From each pack, pooled eggshells and egg contents were analyzed separately for Salmonella detection. Salmonella was detected in 37 of 380 eggshell pools (9.7%; 95% CI: 6.9–13.2%), whereas no Salmonella was recovered from egg contents. All positive samples originated from cage-laid production systems, with contamination detected in 37 of 320 cage-laid egg packs (11.6%; 95% CI: 8.3–15.6%), while none of the 60 cage-free (barn or free-range) packs were positive (0%; 95% CI: 0–6.0%). Of the 37 positive sample units, 33 were locally produced in the UAE and four were imported from Oman. Of the recovered isolates, 35 were subjected to whole-genome sequencing (WGS) and antimicrobial susceptibility analysis. WGS identified 14 serovars, with Salmonella enterica serovar Braenderup predominating (13/35; 37.1%). All S. Braenderup isolates belonged to sequence type ST22 and formed a tight single-nucleotide polymorphism-based cluster, despite originating from multiple local producers, suggesting clonal dissemination within the domestic egg production system. S. Enteritidis was the second most frequent (4/35; 11.4%) serovar. Ciprofloxacin showed the highest frequency of phenotypically non-wild-type, observed in 25/37 isolates (67.5%). Correspondingly, plasmid-mediated qnr genes, particularly qnrB19 , were detected in 20/35 isolates (57.1%). Multidrug resistance was limited to four isolates (11.4%), all belonging to S. Indiana and S. Minnesota. Overall, these findings provide a foundational genomic and phenotypic reference for Salmonella in retail eggs in the UAE and help fill a major data gap in the Middle East, reinforcing the value of WGS-based surveillance for regional food safety risk assessment and One Health-oriented monitoring programs. • Salmonella contamination (9.7%) of retail eggs in the UAE was confined to eggshells, with no detection in egg contents • WGS identified S erovar Braenderup (ST22) as the dominant (37.1%) lineage, circulating across multiple local producers • High frequencies (71.4%) of quinolone non-wild-type phenotypes were primarily associated with plasmid-mediated qnr genes • Multidrug resistance was limited and restricted to S. Indiana and S. Minnesota serovars • WGS provided the first genomic baseline on virulence and stress resistance genes in egg-associated Salmonella in the UAE and the Middle East