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Updated: Dec 12, 2025
Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance
Published on: May 2, 2018
Identification of plasmids by PCR based replicon typing in bacteremic Klebsiella pneumoniae
Chaitra Shankar1, Dhiviya Prabaa Muthuirulandi Sethuvel1, Ayyan Raj Neeravi1
1Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
Background:
Klebsiella pneumoniae is a notorious pathogen with plasmid mediated resistance to all classes of antibiotics. It is important to determine the plasmid profile coding for resistance genes. Plasmid profile varies among geographical regions and tracking the types helps in determining the MDR and XDR K. pneumoniae spread especially in hospital setting. Aim of the present study was to determine the plasmid profile and types among bacteraemic K. pneumoniae.
Materials And Methods:
Ninety consecutive K. pneumoniae collected over a period of three months from blood cultures were characterised by PCR for plasmid profile. Inc plasmid types were determined by PCR based replicon typing (PBRT) and carbapenemases were determined by multiplex PCR. For a subset of isolates hybrid assemblies were developed by sequencing with Ion Torrent and MinIon.
Results:
Overall, PBRT showed 29% of isolates carried four plasmids including IncHI1B, IncFIA, IncFII(K) and IncR. The most common type of plasmid was IncHI1B (93%) followed by IncFIIK (89%) and IncR (82%). IncFIA was predominant among carbapenem resistant isolates. Almost all plasmids identified in K. pneumoniae were AMR plasmids, except two isolates which had virulence plasmids. IncX3 plasmid observed in this study was previously reported to be self-disseminating. Furthermore, the hybrid genome sequencing revealed complete structural arrangements of plasmids, which would be missed in short-read sequencing. NDM and OXA48-like were co-produced in 59% of the carbapenem resistant isolates. BlaOXA-232 was present on ColKP3; aac(6')-lb3 and rmtF on IncFIB.
Conclusion:
Diverse plasmid profile among the successive K. pneumoniae isolates indicates the transfer of resistance genes through different types of plasmids. IncHI1B, IncFIA, IncFIIK and IncR were the prevalent plasmid types. Hybrid assembly revealed blaOXA-232 was present on ColKP3 unlike global reports of IncL/M. Hybrid assemblies provide better plasmid structure that long and short read assemblies. There was no significant association of β-lactamases with specific Inc groups in this study.
Insights
Diverse plasmid profiles in Klebsiella pneumoniae, including IncHI1B, IncFIA, IncFII(K), and IncR, were identified. Hybrid genome sequencing provided detailed plasmid structures, crucial for understanding antimicrobial resistance spread.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Klebsiella pneumoniae is a significant pathogen known for plasmid-mediated antibiotic resistance.
- Understanding plasmid profiles is crucial for tracking multidrug-resistant (MDR) and extensively drug-resistant (XDR) K. pneumoniae, especially in healthcare settings.
Purpose of the Study:
- To determine the plasmid profiles and types among bacteraemic Klebsiella pneumoniae isolates.
- To characterize the plasmids carrying antimicrobial resistance (AMR) genes.
Main Methods:
- Plasmid profiling of 90 K. pneumoniae isolates using PCR.
- Identification of Inc plasmid types via PCR-based replicon typing (PBRT).
- Detection of carbapenemases using multiplex PCR and hybrid genome sequencing (Ion Torrent, MinIon) for a subset of isolates.
Main Results:
- Prevalence of IncHI1B (93%), IncFII(K) (89%), and IncR (82%) plasmids was observed.
- IncFIA plasmids were predominant in carbapenem-resistant isolates.
- Hybrid sequencing elucidated complete plasmid structures, revealing blaOXA-232 on ColKP3, and co-production of NDM and OXA48-like carbapenemases in 59% of resistant isolates.
Conclusions:
- Diverse plasmid profiles in K. pneumoniae facilitate the transfer of resistance genes.
- Hybrid assembly offers superior plasmid structural analysis compared to short-read sequencing.
- While specific plasmids were identified, no significant association between beta-lactamases and specific Inc groups was found in this study.
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