---
title: "Genomic characterization of CTX-M-15–producing Klebsiella pneumoniae ST709-KL9 from neonatal bacte"
id: "pubmed-42804020"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42804020"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42804020/"
doi: "10.1007/s11033-026-12841-4"
published_at: "2026-09-28T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Genomic characterization of CTX-M-15–producing Klebsiella pneumoniae ST709-KL9 from neonatal bacte
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42804020
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42804020/)
- **DOI:** [10.1007/s11033-026-12841-4](https://doi.org/10.1007%2Fs11033-026-12841-4)
- **Published At:** 2026-09-28T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- Klebsiella pneumoniae is a WHO critical-priority pathogen and a leading cause of neonatal bacteraemia in India, with high morbidity and mortality. - The study reports genomic and phenotypic characterization of a single blood isolate recovered from a 10-day-old neonate in West Bengal (November 2021). - The isolate was identified as sequence type **ST709** (a single-locus variant of ST15) with capsule type **KL9/O2**. - Whole genome sequencing revealed a 5.47 Mb genome comprising one chromosome (~5.2 Mb) and three plasmid-associated contigs predicted by MOB-suite: **IncFIIK** (59.4 kb), **IncHI1B:IncFIB** (219.7 kb), and **IncR** (13.2 kb). - Phenotypically the strain was multidrug-resistant (MDR): resistant to ceftriaxone, ciprofloxacin, chloramphenicol, and co-trimoxazole; susceptible to meropenem, amikacin, and colistin. - The resistome included blaTEM-1B and **blaCTX-M-15**, qnrS1, strA, strB, catA1, sul1, sul2, dfrA1, dfrA5, fosA6, tetA, and tetD; chromosomal mutations were detected in gyrA (Ser83Tyr, Asp87Ala), parC (Ser80Ile) and ompK37 (Ile70Met, Ile128Met). - The isolate carried virulence-associated features including Type-1 and Type-3 fimbriae, a complete T6SS-I cluster, and KL9 capsule biosynthesis genes, but lacked canonical hypervirulent markers such as iucA, rmpA/A2, iroB, and peg344. - Authors state this is the first report from India of an MDR **blaCTX-M-15**-carrying K. pneumoniae ST709-KL9 from neonatal bacteraemia. - The study emphasizes the need for systematic, large-scale genomic AMR surveillance to track and contain emerging resistant and potentially convergent lineages in India. - Ethical approvals and declarations: informed consent was waived; study approved by Institutional Human Ethical Committee of Vidyasagar University (Ref. VU/IEC/122/2020); authors declared no competing interests.
## Clinical Analysis & Structured Key Points
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Patil International University, Pune, 412101, Maharashtra, India."), [Abhi Mallick](https://pubmed.ncbi.nlm.nih.gov/?term=Mallick+A&cauthor_id=42804020)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#full-view-affiliation-2 "Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India."), [Shravani Mitra](https://pubmed.ncbi.nlm.nih.gov/?term=Mitra+S&cauthor_id=42804020)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#full-view-affiliation-3 "Formerly attached division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, West Bengal, India."), [Soma Sarkar](https://pubmed.ncbi.nlm.nih.gov/?term=Sarkar+S&cauthor_id=42804020)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#full-view-affiliation-4 "Department of Microbiology, Infectious Diseases & Beliaghata General Hospital, Kolkata, 700010, West Bengal, India."), [Surojit Das](https://pubmed.ncbi.nlm.nih.gov/?term=Das+S&cauthor_id=42804020)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#full-view-affiliation-5 "Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. esurojitdas@gmail.com.") Affiliations Expand ### Affiliations * 1 School of Biosciences & Bioengineering, D.Y. Patil International University, Pune, 412101, Maharashtra, India. * 2 Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. * 3 Formerly attached division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, West Bengal, India. * 4 Department of Microbiology, Infectious Diseases & Beliaghata General Hospital, Kolkata, 700010, West Bengal, India. * 5 Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. esurojitdas@gmail.com. * PMID: **42804020** * DOI: [ 10.1007/s11033-026-12841-4 ](https://doi.org/10.1007/s11033-026-12841-4) Item in Clipboard # Genomic characterization of CTX-M-15-producing Klebsiella pneumoniae ST709-KL9 from neonatal bacteraemia in eastern India Sampurna Nivedita Sarkar et al. Mol Biol Rep. 2026. Show details Display options Display options Format Abstract PubMed PMID Mol Biol Rep Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Mol+Biol+Rep%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Mol+Biol+Rep%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) . 2026 Sep 28;53(1):1655. doi: 10.1007/s11033-026-12841-4. ### Authors [Sampurna Nivedita Sarkar](https://pubmed.ncbi.nlm.nih.gov/?term=Sarkar+SN&cauthor_id=42804020)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#short-view-affiliation-1 "School of Biosciences & Bioengineering, D.Y. Patil International University, Pune, 412101, Maharashtra, India."), [Abhi Mallick](https://pubmed.ncbi.nlm.nih.gov/?term=Mallick+A&cauthor_id=42804020)[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#short-view-affiliation-2 "Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India."), [Shravani Mitra](https://pubmed.ncbi.nlm.nih.gov/?term=Mitra+S&cauthor_id=42804020)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#short-view-affiliation-3 "Formerly attached division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, West Bengal, India."), [Soma Sarkar](https://pubmed.ncbi.nlm.nih.gov/?term=Sarkar+S&cauthor_id=42804020)[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#short-view-affiliation-4 "Department of Microbiology, Infectious Diseases & Beliaghata General Hospital, Kolkata, 700010, West Bengal, India."), [Surojit Das](https://pubmed.ncbi.nlm.nih.gov/?term=Das+S&cauthor_id=42804020)[ 5 ](https://pubmed.ncbi.nlm.nih.gov/42804020/#short-view-affiliation-5 "Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. esurojitdas@gmail.com.") ### Affiliations * 1 School of Biosciences & Bioengineering, D.Y. Patil International University, Pune, 412101, Maharashtra, India. * 2 Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. * 3 Formerly attached division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, 700010, West Bengal, India. * 4 Department of Microbiology, Infectious Diseases & Beliaghata General Hospital, Kolkata, 700010, West Bengal, India. * 5 Department of Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, 721102, West Bengal, India. esurojitdas@gmail.com. * PMID: **42804020** * DOI: [ 10.1007/s11033-026-12841-4 ](https://doi.org/10.1007/s11033-026-12841-4) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID Linked Discoveries ## Abstract **Background:** Klebsiella pneumoniae, a WHO-designated critical-priority pathogen, is a predominant cause of neonatal bacteraemia in India, associated with high morbidity and mortality. The global emergence and spread of high-risk clones, combined with convergence of antimicrobial resistance (AMR) and virulence traits, underscores the need for close genomic surveillance. This study presents AMR and virulence traits of K. pneumoniae ST709-KL9 strain isolated from neonatal blood in West Bengal, India. **Methods and results:** The blood isolate from a 10-day-old neonate (November 2021) underwent identification, antimicrobial susceptibility testing, hypermucoviscosity assessment, and whole genome sequence analysis. The 5.47 Mb genome comprised one chromosome (5.2 Mb) and three MOB-suite-predicted plasmid-associated contigs [IncFIIK (59.4 kb), IncHI1B: IncFIB (219.7 kb), IncR (13.2 kb)]. Core findings included ST709 (single-locus variant of ST15), KL9/O2 capsular-type, and multidrug-resistant (MDR) phenotype (CeftriaxoneR-CiprofloxacinR-ChloramphenicolR-Co-trimoxazoleR) The strain was treatable with meropenem, amikacin, and colistin. Resistome analysis revealed resistance genes (blaTEM-1B-blaCTX-M-15-qnrS1-strA-strB-catA1-sul1-sul2-dfrA1-dfrA5-fosA6-tetA-tetD) and chromosomal point-mutations (gyrA: Ser83Tyr, Asp87Ala; parC: Ser80Ile; ompK37: Ile70Met, Ile128Met). Virulome included Type-1/3 fimbriae, complete T6SS-I cluster, KL9 capsule biosynthesis, enterobactin siderophore-lacking canonical hvKp markers (iucA-ybt-rmpA/A2-iroB-peg344). **Conclusions:** This single-isolate genomic study is the first report of blaCTX-M-15-caryying MDR K. pneumoniae ST709-KL9 in India. Systematic and strategic large-scale genomic AMR surveillance is essential to understand the trafficking and contain the transmission of emerging pathogens in India. **Keywords:** Klebsiella pneumoniae; Antimicrobial resistance; Bacteraemia; ST709; Virulence. © 2026. The Author(s), under exclusive licence to Springer Nature B.V. [PubMed Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) ## Conflict of interest statement Declarations. Competing interests: The authors declare no competing interests. Consent to participate: Informed consent was waived because this study, with an observational nature, focused mainly on bacteria and involved no interventions with patients. Consent to publish: Not applicable. Ethics approval: This study was approved by the Institutional Human Ethical Committee of Vidyasagar University (Ref. VU/IEC/122/2020). ## References 1. 1. Denissen J, Reyneke B, Waso-Reyneke M et al (2022) Prevalence of ESKAPE pathogens in the environment: Antibiotic resistance status, community-acquired infection and risk to human health. Int J Hyg Environ Health 244:114006. - [DOI](https://doi.org/10.1016/j.ijheh.2022.114006) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/35841823/) 2. 1. Al Ismail D, Campos-Madueno EI, Donà V et al (2025) Hypervirulent Klebsiella pneumoniae (hvKp): overview, epidemiology, and laboratory detection. Pathog Immun 10:80–119. - [DOI](https://doi.org/10.20411/pai.v10i1.777) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/39911145/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/11792540/) 3. 1. Lee MY, Ko KS, Kang CI et al (2011) High prevalence of CTX-M-15-producing Klebsiella pneumoniae isolates in Asian countries: diverse clones and clonal dissemination. Int J Antimicrob Agents 38:160–163. - [DOI](https://doi.org/10.1016/j.ijantimicag.2011.03.020) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/21605960/) 4. 1. Attia Hussein Mahmoud H, Parekh R, Dhandibhotla S et al (2023) Insight into neonatal sepsis: an overview. Cureus 15:e45530. - [DOI](https://doi.org/10.7759/cureus.45530) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/37868444/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/10585949/) 5. 1. Fleischmann C, Reichert F, Cassini A et al (2021) Global incidence and mortality of neonatal sepsis: a systematic review and meta-analysis. Arch Dis Child 106:745–752. - [DOI](https://doi.org/10.1136/archdischild-2020-320217) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/33483376/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/8311109/) Show all 27 references ## MeSH terms * Anti-Bacterial Agents / pharmacology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Anti-Bacterial+Agents%2Fpharmacology%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Anti-Bacterial+Agents) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Bacteremia* / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Bacteremia%2Fgenetics%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Bacteremia) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Bacteremia* / microbiology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Bacteremia%2Fmicrobiology%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Bacteremia) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Drug Resistance, Multiple, Bacterial / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Drug+Resistance%2C+Multiple%2C+Bacterial%2Fgenetics%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Drug+Resistance%2C+Multiple%2C+Bacterial) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Genome, Bacterial Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Genome%2C+Bacterial%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Genome%2C+Bacterial) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Humans Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Humans%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Humans) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * India Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22India%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=India) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Infant, Newborn Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Infant%2C+Newborn%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Infant%2C+Newborn) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Klebsiella Infections* / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Klebsiella+Infections%2Fgenetics%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Klebsiella+Infections) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Klebsiella Infections* / microbiology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Klebsiella+Infections%2Fmicrobiology%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Klebsiella+Infections) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Klebsiella pneumoniae* / drug effects Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Klebsiella+pneumoniae%2Fdrug+effects%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Klebsiella+pneumoniae) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Klebsiella pneumoniae* / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Klebsiella+pneumoniae%2Fgenetics%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Klebsiella+pneumoniae) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42804020/) * Klebsiella pneumoniae* / isolation & purification Actions
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