A novel variant in
Salmonella
genomic island 1 of multidrug-resistant
Salmonella enterica
serovar Kentucky ST198
Authors: Intuy Rattanaporn , Supa-Amornkul Sirirak , Jaemsai Bharkbhoom , Ruangchai Wuthiwat , Wiriyarat Witthawat , Chaturongakul Soraya , Palittapongarnpim Prasit 
Published: April 2024

Salmonella enterica
serovar Kentucky ST198 is a major health threat due to its resistance to ciprofloxacin and several other drugs, including third-generation cephalosporins. Many drug-resistant genes have been identified in the
Salmonella
genomic island 1 variant K (SGI1-K). In this study, we investigated the antimicrobial resistance (AMR) profile and genotypic relatedness of two isolates of ciprofloxacin-resistant (CIP
R
)
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

bla
TEM-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 significant variations 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
(
traG∆
) to
S027 (res
G), and the inversion of the IS
26-S044∆-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 IS
26-S044∆-yidY
segment. These structural changes were likely mediated by the recombination of IS
26
. The findings broaden our understanding of the possible evolution pathway of SGI1-K in fostering drug resistance, which may provide opportunities to control these MDR strains.

IMPORTANCE

The emergence of ciprofloxacin-resistant (CIP
R
)
Salmonella
Kentucky ST198 globally has raised significant concerns. This study focuses on two poultry isolates from Thailand, revealing a distinct
Salmonella
genomic island 1 variant K (SGI1-K) genetic structure. Remarkably, multiple antibiotic resistance genes (ARGs) were identified within the SGI1-K as well as other locations in the chromosome, but not in plasmids. Comparing the SGI1-K genetic structures among global and even within-country isolates unveiled substantial variations. Intriguingly, certain isolates lacked ARGs within the SGI1-K, while others had ARGs relocated outside. The presence of chromosomal extended-spectrum
β
-lactamase (ESBL) genes and lincosamide resistance,
lnu
(F), gene, could potentially inform the choices of the treatment of CIP
R
S
. Kentucky ST198 infections in humans. This study highlights the importance of understanding the diverse genetic structures of SGI1-K and emphasizes the role of animals and humans in the emergence of antimicrobial resistance.