Genomic analysis of Klebsiella pneumoniae strains virulence and antibiotic resistance

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Recently, Klebsiella pneumoniae strains have become widespread both in community-acquired infectious processes and in nosocomial infections. There are two pathotypes of K. pneumoniae: classical (cKp) and hypervirulent (hvKp). Representatives of any pathotype are prone to acquire and further transmit genetic factors of antibiotic resistance and virulence. This combination accounts for severity of the infectious process. Therefore, information about whether the strain belongs to either pathotype can help in prescribing proper therapy. Since there is no consensus upon hypervirulence marker, we attempted to find the most significant combinations of genetic markers of virulence and antibiotic resistance in K. pneumoniae strains. The study was aimed to conduct a genomic analysis of virulence and antibiotic resistance of K. pneumoniae clinical isolates. Materials and methods. There were examined 85 strains of K. pneumoniae isolated from diverse clinical material samples from patients in large St. Petersburg hospitals. In our work, we used classical bacteriological methods, including determination of the hypermucoviscous type using the “string test”, the mass spectrometric method (MALDI-ToF MS) for identifying bacteria, molecular methods for studying markers of virulence and antibiotic resistance (multilocus sequence typing, genome sequencing of K. pneumoniae strains). Results. Among the studied K. pneumoniae strains, the most common carbapenemase genes were OXA-48 (18.7%) and NDM-1 genes — 17.3% of strains; in 6.7% of strains, NDM-1 and OXA-48 genes were found simultaneously. The percentage of strains with β-lactamase genes CTX-M-15 was 54.7%, OXA-1 — 17.3%, TEM-1D — 13.3%, and in 17.3% of cases the OXA-1 and TEM-1D genes were simultaneously present in bacterial strains. Quinolone resistance genes were found in 68.4% of strains. The most common genes were qnrS1 (40% of strains) and qnrB1 (22.7%). Phenotypic antimicrobial susceptibility testing showed that 23.5% and 64.7% strains were resistant to colistin and carbapenems, respectively. 32.9% K. pneumoniae strains, isolated in patients with phlegmon, pneumonia, sepsis, and peritonitis, had a hypermucoid phenotype. The most common sequence types were: ST395 (24.3%), ST23 (17.6%) and ST512 (9.5%). 8% and 25.3% of strains belonged to capsule types K1 and K2, respectively. The polyketide synthesis locus ybt, which characterizes virulent strains, was detected in 69.3% isolates, and the clb locus was present in 10.7% of strains. In 73.3% and 14.7% strains, the plasmid-associated virulence loci iuc and iro were identified, which encode the biosynthesis of the siderophores aerobactin and salmochelin. We described 44 cases (58.7% of strains) of genotypic convergence of virulence and antibiotic resistance, as shown by simultaneously detected the aerobactin (iuc) locus and β-lactamase or carbapenemase genes. Thus, identification of hypervirulence may provide valuable information for the clinical management of patients with hvKp infections. Therefore, it is is obviously necessary to develop comprehensive diagnostic test for simultaneous screening of multidrug-resistant hypervirulent K. pneumoniae strains.

作者简介

A. Samoilova

St. Petersburg Pasteur Institute

编辑信件的主要联系方式.
Email: samoilova@pasteurorg.ru

Junior Researcher, Laboratory of Biological Products

俄罗斯联邦, St. Petersburg

L. Kraeva

St. Petersburg Pasteur Institute; Military Medical Academy named after S.M. Kirov

Email: samoilova@pasteurorg.ru

DSc (Medicine), Head of the Laboratory of Medical Bacteriology; Professor of the Department of Microbiology

俄罗斯联邦, St. Petersburg; St. Petersburg

N. Mikhailov

St. Petersburg Pasteur Institute; V.A. Almazov National Medical Research Centre

Email: samoilova@pasteurorg.ru

PhD (Medicine), Senior Researcher, Laboratory of Biological Products; Associate Professor, Department of Microbiology and Virology, Institute of Medical Education

俄罗斯联邦, St. Petersburg; St. Petersburg

A. Saitova

St. Petersburg Pasteur Institute

Email: samoilova@pasteurorg.ru

Laboratory Assistant-Researcher, Metagenomic Research Group

俄罗斯联邦, St. Petersburg

D. Polev

St. Petersburg Pasteur Institute

Email: samoilova@pasteurorg.ru

PhD (Biology), Senior Researcher, Head of the Metagenomic Research Group

俄罗斯联邦, St. Petersburg

M. Vashukova

Clinical Infectious Diseases Hospital named after S.P. Botkin, Ministry of Health of the Russian Federation

Email: samoilova@pasteurorg.ru

PhD (Medicine), Deputy Chief Physician for Medical Care Development

俄罗斯联邦, St. Petersburg

S. Gordeeva

Clinical Infectious Diseases Hospital named after S.P. Botkin, Ministry of Health of the Russian Federation

Email: samoilova@pasteurorg.ru

Bacteriologist, Head of the Centralized Bacteriological Laboratory

俄罗斯联邦, St. Petersburg

E. Smirnova

Hygiene and Epidemiology Centre in St. Petersburg of Rospotrebnadzor

Email: samoilova@pasteurorg.ru

Bacteriologist, Head of the Bacteriological Laboratory

俄罗斯联邦, St. Petersburg

L. Beljatich

St. Petersburg State Hospital No. 14, Ministry of Health of the Russian Federation

Email: samoilova@pasteurorg.ru

Bacteriologist, Head of the Bacteriological Laboratory

俄罗斯联邦, St. Petersburg

A. Dolgova

St. Petersburg Pasteur Institute

Email: samoilova@pasteurorg.ru

PhD (Biology), Head of the Laboratory of Molecular Genetics of Pathogenic Microorganisms

俄罗斯联邦, St. Petersburg

A. Shabalina

St. Petersburg Pasteur Institute

Email: samoilova@pasteurorg.ru

Junior Researcher, Laboratory of Molecular Genetics of Pathogenic Microorganisms

俄罗斯联邦, St. Petersburg

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