First Detection of mcr-9.1 in Multidrug-Resistant Salmonella Indiana from Retail Eggs in the United Arab Emirates: Genomic Insights from a One Health Perspective

The global spread of the mobile colistin resistance ( mcr ) genes, which confer resistance to colistin, poses a major challenge to antimicrobial stewardship and food safety. Salmonella enterica is a leading foodborne pathogen within the One Health framework. This study reports the first detection of the mcr-9.1 gene in the United Arab Emirates (UAE) microbial communities, identified during a baseline survey of Salmonella in retail table eggs. A total of 380 consumer egg packs were collected from supermarkets in the emirates of Abu Dhabi and Dubai between November 2024 and January 2025. Salmonella isolation followed ISO 6579-1:2017 protocols, with confirmed isolates underwent antimicrobial susceptibility testing and whole-genome sequencing using Illumina and Oxford Nanopore platforms. Hybrid assemblies were generated and analyzed using genomics workflow for antimicrobial resistance (AMRFinderPlus), plasmid typing (MOB-suite), virulence profiling (VirulenceFinder), and phylogenetic placement (kSNP4, FastTree 2.1.10). Out of 380 egg samples tested, 37 (9.7%; 95% CI 7.2–13.1%) were Salmonella -positive. Of which, two (5.4%) S. Indiana isolates (F-9 and F-32), both sequence type ST17, were identified to carry mcr-9.1 yet remained phenotypically susceptible to colistin (MIC ≤1 mg/L). These isolates displayed multidrug resistance, harboring aminoglycoside, tetracycline, sulfonamide, and quinolone resistance genes alongside mcr-9.1 . Hybrid genome assembly localized mcr-9.1 to a chromosomal contig lacking plasmid replicons, with an adjacent IS3 -family element ( ISSen1 ) suggesting potential mobility. Phylogenetic analysis positioned both isolates within a clade of Asian poultry- and food-origin S. Indiana ST17, differing by only six SNPs from each other. This study documents the first detection of mcr-9.1 -positive Salmonella in the UAE, highlighting its chromosomal integration in multidrug-resistant S . Indiana ST17 isolates from retail eggs. These findings underscore the importance of integrated One Health surveillance to track the silent spread of colistin resistance across human, food, and environmental reservoirs. • First detection of the colistin resistance gene mcr-9.1 in Salmonella enterica from retail eggs in the United Arab Emirates. • mcr-9.1 was chromosomally integrated in S. Indiana ST17, not plasmid-borne. • Both mcr-9.1 -positive isolates showed multidrug resistance but remained colistin-susceptible. • Genomic and phylogenetic analyses linked the UAE isolates to Asian poultry- and food-origin lineages. • Findings highlight silent dissemination of mcr-9.1 and the need for integrated One Health AMR surveillance.