Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis
BackgroundEpidemiological risk factors such as the demography of a place, environment, food, livestock, and companion animals are known sources of Klebsiella pneumoniae infection. Whole-genome sequencing (WGS) has become a powerful tool to complement traditional microbiological characterization of f...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| author | Sivaraman Gopalan Krishnan Sudha Sajeev Visnuvinayagam Sivam Raja Swaminathan T. Rakshit Ojha Bibek Ranjan Shome Mark Holmes Thanigaivel Sundaram Ramesh M. D. Saranya Vinayagam Suseela Meesala Tabarak Malik Tabarak Malik Pavan Kumar Dara |
| author_facet | Sivaraman Gopalan Krishnan Sudha Sajeev Visnuvinayagam Sivam Raja Swaminathan T. Rakshit Ojha Bibek Ranjan Shome Mark Holmes Thanigaivel Sundaram Ramesh M. D. Saranya Vinayagam Suseela Meesala Tabarak Malik Tabarak Malik Pavan Kumar Dara |
| author_sort | Sivaraman Gopalan Krishnan |
| collection | DOAJ |
| description | BackgroundEpidemiological risk factors such as the demography of a place, environment, food, livestock, and companion animals are known sources of Klebsiella pneumoniae infection. Whole-genome sequencing (WGS) has become a powerful tool to complement traditional microbiological characterization of foodborne pathogens. Moreover, K. pneumoniae has several species complexes (KpSC) and is very difficult to differentiate using routine microbiological methods. The present study aims to investigate the prevalence of K. pneumoniae in fish available in the retail market using WGS.MethodsIsolation of K. pneumoniae, identification of K. pneumoniae isolates, and determination of the minimum inhibitory concentration (MIC) were performed. Whole-genome sequencing of K. pneumoniae 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.ResultsThe findings showed that many antibiotic-resistant genes (ARGs) are prominent, including acrD, BaeR, cpxA, mdtB, mdtC, CRP, H-NS, KpnE, KpnF, KpnG, KpnH, acrA, acrB, marA, ramB, oqxA, oqxB, LptD, and emrR. 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 K. pneumoniae isolates from fish sources was found. One of the CIFT-K6 isolates had the uncommon serotype of K. pneumoniae O3b with the high-risk clone “ST37.” The ST515 sequence type was present in two K. pneumoniae isolates (CIFT-K7 and CIFT-K8), but the O3b serotype and ST192 allele type were present in the CIFT-K10 isolate.ConclusionTo the best of our knowledge, this research study represents the first Indian report of K. pneumoniae linked to fish, specifically the high-risk clone ‘ST37’ 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. |
| format | Article |
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| publishDate | 2025-01-01 |
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| spelling | doaj-art-e33106f37b3a46adb4e0e6db4b4e18f32025-01-20T05:23:51ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-01-011410.3389/fcimb.2024.15171251517125Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysisSivaraman Gopalan Krishnan0Sudha Sajeev1Visnuvinayagam Sivam2Raja Swaminathan T.3Rakshit Ojha4Bibek Ranjan Shome5Mark Holmes6Thanigaivel Sundaram7Ramesh M. D.8Saranya Vinayagam9Suseela Meesala10Tabarak Malik11Tabarak Malik12Pavan Kumar Dara13Microbiology Fermentation and Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, Kerala, IndiaMicrobiology Fermentation and Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Institute of Fisheries Technology, Kochi, Kerala, IndiaDepartment of Disease Investigation, Indian Council of Agricultural Research (ICAR)-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, Karnataka, IndiaDepartment of Disease Investigation, Indian Council of Agricultural Research (ICAR)-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, Karnataka, IndiaDepartment of Veterinary Medicine, University of Cambridge, Cambridge, United KingdomDepartment of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology (SRMIST), Tamil Nadu, Kattankulathur, IndiaInstituto de Alta Investigación, Universidad de Tarapacá, Arica, ChileDepartment of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, IndiaDepartment of Zoology, Vikrama Simhapuri University, Kavali, Andhra Pradesh, IndiaDepartment of Biomedical Sciences, Jimma University, Jimma, EthiopiaDivision of Research & Development, Lovely Professional University, Phagwara, Punjab, IndiaDepartment of Biotechnology, Faculty of Science and Humanities, SRM Institute of Science and Technology (SRMIST), Tamil Nadu, Kattankulathur, IndiaBackgroundEpidemiological risk factors such as the demography of a place, environment, food, livestock, and companion animals are known sources of Klebsiella pneumoniae infection. Whole-genome sequencing (WGS) has become a powerful tool to complement traditional microbiological characterization of foodborne pathogens. Moreover, K. pneumoniae has several species complexes (KpSC) and is very difficult to differentiate using routine microbiological methods. The present study aims to investigate the prevalence of K. pneumoniae in fish available in the retail market using WGS.MethodsIsolation of K. pneumoniae, identification of K. pneumoniae isolates, and determination of the minimum inhibitory concentration (MIC) were performed. Whole-genome sequencing of K. pneumoniae 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.ResultsThe findings showed that many antibiotic-resistant genes (ARGs) are prominent, including acrD, BaeR, cpxA, mdtB, mdtC, CRP, H-NS, KpnE, KpnF, KpnG, KpnH, acrA, acrB, marA, ramB, oqxA, oqxB, LptD, and emrR. 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 K. pneumoniae isolates from fish sources was found. One of the CIFT-K6 isolates had the uncommon serotype of K. pneumoniae O3b with the high-risk clone “ST37.” The ST515 sequence type was present in two K. pneumoniae isolates (CIFT-K7 and CIFT-K8), but the O3b serotype and ST192 allele type were present in the CIFT-K10 isolate.ConclusionTo the best of our knowledge, this research study represents the first Indian report of K. pneumoniae linked to fish, specifically the high-risk clone ‘ST37’ 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.https://www.frontiersin.org/articles/10.3389/fcimb.2024.1517125/fullK. pneumoniaeantibiotic resistant geneswhole genome sequencingserotypehigh-risk clone |
| spellingShingle | Sivaraman Gopalan Krishnan Sudha Sajeev Visnuvinayagam Sivam Raja Swaminathan T. Rakshit Ojha Bibek Ranjan Shome Mark Holmes Thanigaivel Sundaram Ramesh M. D. Saranya Vinayagam Suseela Meesala Tabarak Malik Tabarak Malik Pavan Kumar Dara Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis Frontiers in Cellular and Infection Microbiology K. pneumoniae antibiotic resistant genes whole genome sequencing serotype high-risk clone |
| title | Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis |
| title_full | Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis |
| title_fullStr | Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis |
| title_full_unstemmed | Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis |
| title_short | Identification of serotype O3b and high-risk clone ST37 of Klebsiella pneumoniae revealed by comparative genomic analysis |
| title_sort | identification of serotype o3b and high risk clone st37 of klebsiella pneumoniae revealed by comparative genomic analysis |
| topic | K. pneumoniae antibiotic resistant genes whole genome sequencing serotype high-risk clone |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2024.1517125/full |
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