{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T05:09:34Z","timestamp":1788066574643,"version":"build-2784847793"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T00:00:00Z","timestamp":1737331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Epidemiological risk factors such as the demography of a place, environment, food, livestock, and companion animals are known sources of <jats:italic>Klebsiella pneumoniae<\/jats:italic> infection. Whole-genome sequencing (WGS) has become a powerful tool to complement traditional microbiological characterization of foodborne pathogens. Moreover, <jats:italic>K. pneumoniae<\/jats:italic> has several species complexes (KpSC) and is very difficult to differentiate using routine microbiological methods. The present study aims to investigate the prevalence of <jats:italic>K. pneumoniae<\/jats:italic> in fish available in the retail market using WGS.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Isolation of <jats:italic>K. pneumoniae<\/jats:italic>, identification of <jats:italic>K. pneumoniae<\/jats:italic> isolates, and determination of the minimum inhibitory concentration (MIC) were performed. Whole-genome sequencing of <jats:italic>K. pneumoniae<\/jats:italic> genomes and phylogenomic analysis were conducted for visual comparison of the genomes. Furthermore, genomes of non-human origin that were submitted from India to the NCBI database were downloaded and included in the comparative analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The findings showed that many antibiotic-resistant genes (ARGs) are prominent, including <jats:italic>acrD, BaeR, cpxA, mdtB, mdtC, CRP, H-NS, KpnE, KpnF, KpnG, KpnH, acrA, acrB, marA, ramB, oqxA, oqxB, LptD<\/jats:italic>, and <jats:italic>emrR<\/jats:italic>. Four fish-sourced isolates had different blaSHV resistance gene variants. The presence of ARGs for aminoglycosides [aac(3)-IId], fluoroquinolones (oqxA, oqxB), and fosfomycin (fosA5, fosA6) in these <jats:italic>K. pneumoniae<\/jats:italic> isolates from fish sources was found. One of the CIFT-K6 isolates had the uncommon serotype of <jats:italic>K. pneumoniae<\/jats:italic> O3b with the high-risk clone \u201cST37.\u201d The ST515 sequence type was present in two <jats:italic>K. pneumoniae<\/jats:italic> isolates (CIFT-K7 and CIFT-K8), but the O3b serotype and ST192 allele type were present in the CIFT-K10 isolate.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>To the best of our knowledge, this research study represents the first Indian report of <jats:italic>K. pneumoniae<\/jats:italic> linked to fish, specifically the high-risk clone \u2018ST37\u2019 and two other STs, 515 and 192. The most common plasmid type detected in all four isolates was IncFIB, and 75% of the isolates were IncFII and IncHI1B. The prevalence of ARGs linked to efflux pump resistance mechanisms is highlighted by the analysis of genome sequence data.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fcimb.2024.1517125","type":"journal-article","created":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T05:24:30Z","timestamp":1737350670000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis"],"prefix":"10.3389","volume":"14","author":[{"given":"Sivaraman Gopalan","family":"Krishnan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudha","family":"Sajeev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Visnuvinayagam","family":"Sivam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raja Swaminathan","family":"T.","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakshit","family":"Ojha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bibek Ranjan","family":"Shome","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thanigaivel","family":"Sundaram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh","family":"M. 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