Genomic diversity and analysis of resistance determinants of Salmonella enterica subspecies enterica serotype Kentucky isolated in Russia

Abstract

Introduction. Salmonella Kentucky sequence type ST198 is one of the epidemiologically significant non-typhoidal Salmonella clones worldwide and is characterized by the presence of highly resistant strains and the ability to adapt to different animal hosts and environmental conditions. The aim of this study was to analyze S. Kentucky strains isolated from various sources in Russia in terms of their phylogenetic position within the global diversity of the pathogen and their genetic characteristics. Materials and methods. We examined 55 strains of S. Kentucky by whole-genome sequencing, which were isolated from 2010 to 2022 from various sources (clinical strains, food, as well as from farm animals, feed and environmental samples). Whole genome sequencing was performed using Illumina platforms. Phylogenetic analysis based on nucleotide variation analysis included an additional 390 S. Kentucky strains. Results. Most of the Russian strains (n = 50) belonged to the ST198 sequence type, four strains were ST314 and one strain was ST152. Of the 50 Russian sequence-type ST198 strains, 44 belonged to the international monophyletic MDR lineage S. Kentucky ST198, and belonged to four separate sublineages, six strains occupying a basal position in relation to the MDR lineage. A total of 320 genes and mutations responsible for resistance to antimicrobial agents were identified. The most common were point mutations in the QRDR region. In most cases, Russian strains were characterized by the presence of variants of the SGI1-K genomic island. Moreover, the putative structure of SGI1 was correlated with the phylogenetic clustering of S. Kentucky sublineages. Conclusions. The results of the study made it possible to assess the population structure of Russian S. Kentucky ST198 strains on a global scale and determine the genetic determinants of antibiotic resistance, including the structure of the SGI1 genomic island.