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Peer-reviewedCC BY-NCInfection and drug resistance

Functional Characterization and Genomic Insights into Klebsiella Virulomes, Resistomes, and Mobilome Signatures.

  • Jie Li1,2,3
  • Taif Shah4
  • Mei Yang2
  • Zahir Shah5
  • Weihong Qin2
5 affiliations
  1. 1Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
  2. 2Kunming Customs Port Outpatient Department, Yunnan International Travel Health Care Center, Kunming, Yunnan, 650200, People's Republic of China.
  3. 3Yunnan Key Laboratory of Cross-Border Infectious Disease Control and Prevention and Novel Drug Development, Kunming Medical University, Kunming, Yunnan, 650500, People's Republic of China.
  4. 4Yunnan Provincial Key Laboratory of Public Health and Biosafety, School of Public Health, Kunming Medical University, Kunming, 650500, People's Republic of China.
  5. 5College of Veterinary Sciences, The University of Agriculture, Peshawar, KP, 25130, Pakistan.
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Abstract

Introduction

Klebsiella is an emerging human pathogen that can cause severe infections, including bloodstream infections, pneumonia, urinary tract infections, and meningitis. Klebsiella spp. are becoming resistant to multiple antibiotics, including carbapenems, making them difficult to treat.Methods

This study analyzed the complete genome sequence of some closely related Klebsiella spp. including one newly sequenced multidrug resistance (MDR) K. pneumoniae subspecies pneumoniae, and the remaining K. variicola, K. pneumoniae HS11286, K. quasipneumoniae, K. quasivariicola, K. oxytoca, K. africana, K. aerogenes, and K. grimontii retrieved from the publicly available NCBI database for comparative analysis.Results

PubMLST Klebsiella profiling corresponded to these species for various sequence types (STs). Taxonomic and phylogenomic frameworks highlight the genetic diversity and evolutionary coherence of the K. pneumoniae complex and its close relatives. Additionally, complete genome annotation has revealed AMR phenotypes across the Klebsiella isolates. Moreover, these pathogens harbor several potential virulence factors involved in adherence, invasion, immune modulation, biofilm formation, enterobactin, yersiniabactin, aerobactin, and exotoxins, demonstrating their diverse pathogenic strategies. We also compared the diverse plasmid types among these Klebsiella isolates; K. pneumoniae HS11286 comprised five plasmids carrying multiple AMR genes. Moreover, the identification of distinct prophages, CAZymes, and KEGG annotations revealed functionally dense elements in the Klebsiella genomes. A minimum inhibitory concentration (MIC) assay revealed that K. pneumoniae was resistant to several key AMR drugs.Discussion

The findings of this study help us to better understand the genomic landscapes of clinically important Klebsiella spp. paving the way for antimicrobial stewardship strategies to combat these pathogens.

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Cite

BibTeXRIS
BibTeX
@article{li2026functional,
  title = {{Functional Characterization and Genomic Insights into Klebsiella Virulomes, Resistomes, and Mobilome Signatures.}},
  author = {Jie Li and Taif Shah and Mei Yang and Zahir Shah and Weihong Qin},
  journal = {Infection and drug resistance},
  year = {2026},
  month = oct,
  doi = {10.2147/idr.s600552},
  url = {https://europepmc.org/article/MED/42974478},
  note = {CC BY-NC},
}
RIS
TY  - JOUR
TI  - Functional Characterization and Genomic Insights into Klebsiella Virulomes, Resistomes, and Mobilome Signatures.
AU  - Jie Li
AU  - Taif Shah
AU  - Mei Yang
AU  - Zahir Shah
AU  - Weihong Qin
PY  - 2026
DA  - 2026/10/29
JO  - Infection and drug resistance
DO  - 10.2147/idr.s600552
UR  - https://europepmc.org/article/MED/42974478
AB  - Introduction  Klebsiella is an emerging human pathogen that can cause severe infections, including bloodstream infections, pneumonia, urinary tract infections, and meningitis. Klebsiella spp. are becoming resistant to multiple antibiotics, including carbapenems, making them difficult to treat.Methods  This study analyzed the complete genome sequence of some closely related Klebsiella spp. including one newly sequenced multidrug resistance (MDR) K. pneumoniae subspecies pneumoniae, and the remaining K. variicola, K. pneumoniae HS11286, K. quasipneumoniae, K. quasivariicola, K. oxytoca, K. africana, K. aerogenes, and K. grimontii retrieved from the publicly available NCBI database for comparative analysis.Results  PubMLST Klebsiella profiling corresponded to these species for various sequence types (STs). Taxonomic and phylogenomic frameworks highlight the genetic diversity and evolutionary coherence of the K. pneumoniae complex and its close relatives. Additionally, complete genome annotation has revealed AMR phenotypes across the Klebsiella isolates. Moreover, these pathogens harbor several potential virulence factors involved in adherence, invasion, immune modulation, biofilm formation, enterobactin, yersiniabactin, aerobactin, and exotoxins, demonstrating their diverse pathogenic strategies. We also compared the diverse plasmid types among these Klebsiella isolates; K. pneumoniae HS11286 comprised five plasmids carrying multiple AMR genes. Moreover, the identification of distinct prophages, CAZymes, and KEGG annotations revealed functionally dense elements in the Klebsiella genomes. A minimum inhibitory concentration (MIC) assay revealed that K. pneumoniae was resistant to several key AMR drugs.Discussion  The findings of this study help us to better understand the genomic landscapes of clinically important Klebsiella spp. paving the way for antimicrobial stewardship strategies to combat these pathogens.
SN  - 1178-6973
ER  -