A novel variant in Salmonella genomic island 1 of multidrug-resistant Salmonella enterica serovar Kentucky ST198

Rattanaporn Intuy, Sirirak Supa-Amornkul, Bharkbhoom Jaemsai, Wuthiwat Ruangchai, Witthawat Wiriyarat, Soraya Chaturongakul, Prasit Palittapongarnpim

Research output: Contribution to journalArticlepeer-review

Abstract

Salmonella enterica serovar Kentucky ST198 is a major health threat due to its resistance to ciprofloxacinand several other drugs, including third-generation cephalosporins. Many drug-resistant genes have been identifiedin the Salmonella genomic island 1 variant K (SGI1-K). In this study, we investigated the antimicrobial resistance (AMR) profileand genotypic relatedness of two isolates of ciprofloxacin-resistant(CIPR) S. Kentucky ST198 from poultry in Northeastern Thailand. We successfully assembled the complete genomes of both isolates, namely SSSE-01 and SSSE-03, using hybrid de novo assembly of both short- and long-read sequence data. The complete genomes revealed their highly similar genomic structures and a novel variant of SGI1-K underlying multidrug-resistant (MDR) patterns, including the presence of blaTEM-1b, which confers resistance to beta-lactams, including cephalosporins and lnu(F) which confers resistance to lincomycin and other lincosamides. In addition, the chromosomal mutations in the quinolone resistance-determining region (QRDR) were found at positions 83 (Ser83Phe) and 87 (Asp87Asn) of GyrA and at positions 57 (Thr57Ser) and 80 (Ser80Ile) of ParC suggesting high resistance to ciprofloxacin.We also compared SSSE-01 and SSSE-03 with publicly available complete genome data and revealed significantvariations in SGI1-K genetic structures and variable relationships to antibiotic resistance. In comparison to the other isolates, SGI1-K of SSSE-01 and SSSE-03 had a relatively large deletion in the backbone, spanning from S011 (traGΔ) to S027 (resG), and the inversion of the IS26-S044Δ-yidY segment. Their MDR region was characterized by the inversion of a large segment, including the mer operon and the relocation of IntI1 and several resistance genes downstream of the IS26-S044Δ-yidY segment. These structural changes were likely mediated by the recombination of IS26. The findingsbroaden our understanding of the possible evolution pathway of SGI1-K in fostering drug resistance, which may provide opportunities to control these MDR strains.

Original languageEnglish
JournalMicrobiology Spectrum
Volume12
Issue number6
DOIs
Publication statusPublished - Jun 2024

Keywords

  • Salmonella Kentucky ST198
  • Salmonella genomic island 1 variant
  • blaTEM-1b
  • chromosomal multiple-drug resistance
  • lnu(F)

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