First detection and genomic analysis of mcr-1-positive Salmonella Infantis isolated from a broiler production system in the United Arab Emirates

This study reports the first detection of <i>mcr-1.1</i>-mediated colistin resistance in <i>Salmonella enterica</i> serovar Infantis from a commercial broiler farm in the United Arab Emirates (UAE). Two <i>S. infantis</i> isolates (SAL_93 and SAL_94) were recovered from caecal droppings and characterized using whole-genome sequencing (WGS). Genomic analysis revealed a single-nucleotide polymorphism (SNP) difference between them, confirming their close epidemiological relationship. Both isolates belonged to multilocus sequence type 32 and exhibited multidrug resistance (MDR), including resistance to colistin (MIC = 4 mg/L) and ciprofloxacin (MIC = 0.5 mg/L). Notably, the <i>mcr-1.1</i> gene was detected on a conjugative IncX4 plasmid. Additionally, the isolates harbored a large (275,043 bp) conjugative IncFIB plasmid carrying multiple AMR genes, including <i>aadA1</i>, <i>sul1</i>, <i>tet(A)</i>, <i>qacEdelta1</i>. Bioinformatic analysis showed a high identity for globally reported <i>mcr-1.1</i>-carrying IncX4 plasmids. The investigation of virulence-associated factors in the studied isolates identified 162 potential virulence-related genes. These included genes linked to the type 3 secretion system, specifically those encoded by pathogenicity island-1 (SPI-1). However, multiple genes linked to the second type 3 secretion system, encoded by SPI-2, were absent in all isolates. These findings suggest a potential risk of horizontal gene transfer in poultry production. Given these risks, the UAE's recent ban on colistin in veterinary medicine marks a crucial step in mitigating AMR transmission within a One Health framework.