Salmonella enterica serotype Kentucky (S. Kentucky) is a common cause of salmonellosis, usually associated with consumption of contaminated poultry. Antibiotic resistance to multiple drugs including ciprofloxacin is an emerging problem within this serotype. We used whole genome sequencing to investigate the phylogenetic structure of 50 S. Kentucky from 27 countries, and to examine changes in gene content that are responsible for antibiotic resistance. Sequencing was performed using Illumina HiSeq, and population structure was inferred using phylogenomic analysis of single nucleotide polymorphisms (SNPs). Mutations responsible for ciprofloxacin resistance were detected in thegyrA (DNA gyrase) and parC (DNA topoisomerase) genes of many of the isolates. Whole genomes were compared to one another to look at changes in gene content, with a focus on acquired antibiotic resistance genes.
The results showed the S. Kentucky isolates mostly belong to a single clone that has acquired several substitution mutations in gyrA conferring resistance to ciprofloxacin. A single substitution in the parC gene has also contributed to ciprofloxacin resistance in some isolates. Gene content was very similar across all isolates, with most differences occurring in phage regions and the antimicrobial resistance associated Salmonella genomic island (SGI), located in the S. Kentucky chromosome. Insertion sequences (IS), especially IS26, complicate the assembly of the SGI, hence we developed a novel analytical method to help to reconstruct the individual SGI sequences. Our findings suggest the SGI was acquired by the S. Kentucky clone on multiple occasions, and reveal rapid changes in the genomic island leading to highly diverse multidrug resistance phenotypes within the clone. Phylogeographic analysis also revealed the likely pattern of dissemination of the multidrug resistance S. Kentucky clone, out of Northern Africa into Southern and Western Africa, then to the Middle East and Asia.