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Updated: Jun 10, 2026
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Complete nucleotide sequence of KPC-3-encoding plasmid pKpQIL in the epidemic Klebsiella pneumoniae sequence type 258
Azita Leavitt1, Inna Chmelnitsky, Yehuda Carmeli
1Division of Epidemiology, Molecular Epidemiology and Antibiotic Resistance Laboratory, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Abstract:
We have determined the entire DNA sequence of plasmid pKpQIL, the bla(KPC-3)-carrying plasmid harbored by the carbapenem-resistant Klebsiella pneumoniae clone sequence type 258 (ST 258) in Israel. pKpQIL is a 113,637-bp, self-transmissible plasmid that belongs to the incompatibility group IncFII. It consists of a large backbone of a pKPN4-like plasmid and carries the bla(KPC-3)-containing Tn4401a transposon of a pNYC-like plasmid.
Insights
Researchers sequenced the bla(KPC-3) plasmid, pKpQIL, from carbapenem-resistant Klebsiella pneumoniae ST 258. This self-transmissible IncFII plasmid combines a pKPN4-like backbone with a Tn4401a transposon carrying bla(KPC-3).
Area of Science:
- Microbiology
- Genomics
- Molecular Biology
Background:
- Carbapenem resistance in Klebsiella pneumoniae poses a significant global health threat.
- Sequence type 258 (ST 258) is a prevalent clone associated with carbapenem resistance.
- Plasmids are key mobile genetic elements mediating the spread of antibiotic resistance genes.
Purpose of the Study:
- To determine the complete DNA sequence of the pKpQIL plasmid.
- To characterize the genetic elements and structure of a bla(KPC-3)-carrying plasmid in a carbapenem-resistant Klebsiella pneumoniae ST 258 isolate from Israel.
Main Methods:
- Whole-genome sequencing of the plasmid.
- Bioinformatic analysis to identify plasmid backbone, transposons, and resistance genes.
Main Results:
- The complete DNA sequence of the 113,637-bp plasmid pKpQIL was determined.
- pKpQIL was identified as a self-transmissible plasmid belonging to the IncFII incompatibility group.
- The plasmid comprises a pKPN4-like backbone and harbors the Tn4401a transposon carrying the bla(KPC-3) gene, originating from a pNYC-like plasmid.
Conclusions:
- The genetic architecture of pKpQIL provides insights into the evolution and dissemination of carbapenem resistance.
- Understanding plasmid structure is crucial for developing strategies to combat antibiotic resistance spread.
