The first report on genome sequence of high-level ciprofloxacin-resistant Salmonella enterica serovar Indiana ST17 in Korean livestock

Objectives: Salmonella enterica Indiana ST17 strain (K16SI097), exclusively found in China, was first isolated in 2016 in Korea from a chicken carcass. This strain contains multidrug-resistant genes, and is particularly resistant to ciprofloxacin (64 μg/mL). In this study, we aimed to elucidate the genomic relationship and compare antimicrobial resistance factors between Korean chicken-derived and Chinese clones of S. Indiana ST17. Methods: The genomic DNA of S. enterica Indiana K16SI097 was sequenced via the combined analysis of 20-kb PacBio SMRTbell library and PacBio RS II. Antimicrobial resistance genes were analysed by the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/). Chromosomal and plasmid DNA of the Korean and Chinese strains were compared. Results: The K16SI097 genome comprises two contiguous sequences (contigs) amounting to 4 731 335 base pairs with a 51.85% GC content. In total, 4574 protein-coding regions, 84 tRNA genes, and 22 rRNA genes were detected. Among the annotated contigs, 14 antimicrobial resistance genes were detected; DNA gyrase and topoisomerase IV contained mutations. Moreover, chromosomal DNA of K16SI097 and of the published Chinese strain displayed 99.9% similarity. Furthermore, plasmids displayed similar sizes, sequences, and structures. Conclusions: This is the first report on the complete genome sequence of the high-level ciprofloxacin-resistant S. enterica Indiana ST17 strain isolated in Korea. This genome sequence will help us understand the ST17 strain lineage and its features such as antimicrobial resistance.