Genomic characterization and comparative analysis of multidrug-resistant Salmonella Indiana sequence type 17 carrying...

The occurrence and genomic context of the mobile colistin resistance gene mcr-9.1 in the United Arab Emirates (UAE) food chain remain poorly characterized, with no previous reports identified from retail food products based on the available literature and public genomic databases. Salmonella enterica is a leading foodborne zoonotic pathogen within the One Health framework. This study reports, to the best of our knowledge, the first detection of the mcr-9.1 gene in the UAE, 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 on a non-replicon-bearing large contig likely associated with the chromosome, 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. To the best of our knowledge, this study documents the first detection of mcr-9.1-positive Salmonella in the UAE, highlighting its putative chromosomal integration in multidrug-resistant S. Indiana ST17 isolates from retail eggs. These findings support targeted AMR surveillance of retail egg products and food-associated Salmonella in the UAE, including routine screening for mcr genes and WGS of multidrug-resistant isolates. Linking genomic data with product origin and distribution metadata would improve the ability to monitor the emergence, persistence, and possible dissemination routes of colistin resistance determinants in the food chain.