{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T05:33:08Z","timestamp":1775280788723,"version":"3.50.1"},"reference-count":58,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2024,6,4]],"date-time":"2024-06-04T00:00:00Z","timestamp":1717459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,6,4]],"date-time":"2024-06-04T00:00:00Z","timestamp":1717459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2024,6,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:sec>\n            <jats:title\/>\n            <jats:p>\n              <jats:italic>Salmonella enterica<\/jats:italic>\n              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\n              <jats:italic>Salmonella<\/jats:italic>\n              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\n              <jats:sup>R<\/jats:sup>\n              )\n              <jats:italic>S<\/jats:italic>\n              . Kentucky ST198 from poultry in Northeastern Thailand. We successfully assembled the complete genomes of both isolates, namely SSSE-01 and SSSE-03, using hybrid\n              <jats:italic>de novo<\/jats:italic>\n              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\n              <jats:italic>\n                bla\n                <jats:sub>TEM-1b<\/jats:sub>\n              <\/jats:italic>\n              , which confers resistance to beta-lactams, including cephalosporins and\n              <jats:italic>lnu<\/jats:italic>\n              (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\n              <jats:italic>S011<\/jats:italic>\n              (\n              <jats:italic>traG\u2206<\/jats:italic>\n              ) to\n              <jats:italic>S027 (res<\/jats:italic>\n              G), and the inversion of the IS\n              <jats:italic>26-S044\u2206-yidY<\/jats:italic>\n              segment. Their MDR region was characterized by the inversion of a large segment, including the\n              <jats:italic>mer<\/jats:italic>\n              operon and the relocation of\n              <jats:italic>IntI1<\/jats:italic>\n              and several resistance genes downstream of the IS\n              <jats:italic>26-S044\u2206-yidY<\/jats:italic>\n              segment. These structural changes were likely mediated by the recombination of IS\n              <jats:italic>26<\/jats:italic>\n              . 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.\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                The emergence of ciprofloxacin-resistant (CIP\n                <jats:sup>R<\/jats:sup>\n                )\n                <jats:italic>Salmonella<\/jats:italic>\n                Kentucky ST198 globally has raised significant concerns. This study focuses on two poultry isolates from Thailand, revealing a distinct\n                <jats:italic>Salmonella<\/jats:italic>\n                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\n                <jats:italic>\u03b2<\/jats:italic>\n                -lactamase (ESBL) genes and lincosamide resistance,\n                <jats:italic>lnu<\/jats:italic>\n                (F), gene, could potentially inform the choices of the treatment of CIP\n                <jats:sup>R<\/jats:sup>\n                <jats:italic>S<\/jats:italic>\n                . 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.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/spectrum.03994-23","type":"journal-article","created":{"date-parts":[[2024,4,30]],"date-time":"2024-04-30T13:02:26Z","timestamp":1714482146000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":6,"title":["A novel variant in\n            <i>Salmonella<\/i>\n            genomic island 1 of multidrug-resistant\n            <i>Salmonella enterica<\/i>\n            serovar Kentucky ST198"],"prefix":"10.1128","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6669-2140","authenticated-orcid":false,"given":"Rattanaporn","family":"Intuy","sequence":"first","affiliation":[{"name":"Professor Pornchai Matangkasombut Center for Microbial 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Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wuthiwat","family":"Ruangchai","sequence":"additional","affiliation":[{"name":"Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Witthawat","family":"Wiriyarat","sequence":"additional","affiliation":[{"name":"Department of Pre-Clinical and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Bangkok, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Soraya","family":"Chaturongakul","sequence":"additional","affiliation":[{"name":"Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand"},{"name":"Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, 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