Antimicrobial Resistance and Genomic Characterization of Four mcr-1-Harbouring Foodborne Salmonella Isolates Recovered from Poultry in Saudi Arabia

Background/Objectives: The emergence of colistin resistance mediated by the mcr-1 gene in Salmonella enterica poses a significant public health concern. In 2022, mcr-1 was identified for the first time in Salmonella isolates recovered from chicken meat in Saudi Arabia, prompting the need for further genomic investigation. Methods: Four Salmonella enterica isolates—two serovar Minnesota and two serovar Infantis—underwent antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and bioinformatics analyses including antimicrobial resistance genes (ARGs), virulence factors, plasmid replicons, and mcr-1 locations. Results: All isolates exhibited resistance to colistin, polymyxin B, and multiple first-line antibiotics. All four isolates were classified as multidrug-resistant (MDR). The mcr-1 gene was plasmid-borne in all isolates, located on IncI1_1_Alpha plasmids in S. Minnesota and IncFIB(K)_1_Kpn3 plasmids in S. Infantis. Additional antimicrobial resistance genes (ARGs) were detected, including blaCTX-M-65, qnrB5, ermB, and aminoglycoside-modifying enzymes, alongside multiple efflux pump genes. Virulence gene profiles showed minor differences between serovars, including the presence of the cdtB toxin gene in S. Infantis isolates. Phylogenetic analysis indicated that the isolates clustered within a distinct clade, suggesting a potential common local source or clonal expansion. Conclusions: This study provides the first detailed genomic insight into mcr-1-positive Salmonella isolates from food in Saudi Arabia. The co-existence of resistance and virulence determinants, together with mobile plasmids carrying the mcr-1 gene, emphasizes the risk of dissemination through the food chain. These findings highlight the urgent need for integrated genomic surveillance and strengthened antimicrobial stewardship within a One Health framework.