Characterization of genetic diversity of the Klebsiella pneumoniae strains in a Moscow tertiary care center using next-generation sequencing

Clinical Microbiology and Antimicrobial Chemotherapy. 2019; 21(1):69-74

Journal article


To study genetic diversity of Klebsiella pneumoniae strains obtained in the National Medical and Surgical Center named after N.I. Pirogov (Moscow) using next-generation sequencing.

Materials and Methods.

A total of 19 isolates of K. pneumoniae were included in the study (18 – from patients and 1 – from nosocomial environment). The strains were isolated from January 30 to October 9, 2017 and phenotypically showed multi-drug resistance. DNA sequencing of the strains was performed on the Illumina HiSeq1500 instrument using the Illumina HiSeq PE Rapid Cluster Kit v2 and Illumina HiSeq Rapid SBS Kit v2 kits.


A total of 9 different sequence types were found. One strain had a novel allelic profile. There was one hypervirulent strain of K. pneumoniae carrying a carbapenemase gene. The genes of beta-lactamase SHV were detected in each strain. The proportion of strains carrying CTX-M, OXA or TEM beta-lactamase genes was 63.2%, 68.4% and 57.9%, respectively. NDM-1 beta-lactamase genes were found in two strains. Nearly all strains had several types of beta-lactamase genes simultaneously. Plasmid-associated determinants of resistance to fluoroquinolones and the fosA gene providing resistance to fosfomycin were determined in 100% of strains.


There was a high genetic diversity of K. pneumoniae strains isolated in the Moscow tertiary care center. No prevalence of any sequence type has been identified. Hypervirulent ST23 clones and high-risk resistant ST11 and ST147 clones were detected. Two hypervirulent strains ST23 had blaSHV-1, blaCTX-M-55, blaOXA-1 and blaSHV-1, blaOXA-48, respectively. The main mechanism of multiple antimicrobial resistance was β-lactamase production. Colistin was the only drug to which all K. pneumoniae strains were susceptible.

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