ORIGINAL RESEARCH

Molecular genetic characterization of three new Klebsiella pneumoniae bacteriophages suitable for phage therapy

About authors

Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia

Correspondence should be addressed: Roman B. Gorodnichev
Malaya Pirogovskaya, 1а, Moscow, 119435; moc.liamg@b.r.vehcindorog

About paper

Funding: the study was carried out within the framework of the State Assignment "Development of a Personalized Approach to the Therapy of Infections Using Virulent Bacteriophages" (CODE: Bacteriophage).

Acknowledgements: the authors thank the Center for Precision Genome Editing and Genetic Technologies for Biomedicine, the Federal Research and Clinical Center of Physical-Chemical Medicine of the Russian Federal Medical Biological Agency, for their help with bacteriophage genome sequencing.

Author contribution: Gorodnichev RB, Kornienko MA, Shitikov EA — study plan, data processing, manuscript writing; Kuptsov NS — data acquisition and processing, manuscript writing; Malakhova MV, Veselovsky VA — data acquisition; Bespiatykh DA — data processing, Ilina EN — study plan, manuscript writing.

Compliance with ethical standards: experimental work was carried out in strict compliance with the guidelines SP 1.3.2322-08 "Safety of Working With Microorganisms of III–IV Groups of Pathogenicity (Danger) and Causative Agents of Parasitic Diseases"; guidelines SP 1.3.2518-09 “Additions and Amendments № 1 to the guidelines SP 1.3.2322-08 "Safety of Working With Microorganisms of III–IV Groups of Pathogenicity (Danger) and Causative Agents of Parasitic Diseases"; guidelines "Sanitary and Epidemiologic Requirements for the Handling of Medical Waste" (SanPiN 2.1.7.2790-10), and Federal Clinical Guidelines "Rational Use of Bacteriophages in Clinical and Epidemiological Practice".

Received: 2021-07-21 Accepted: 2021-08-26 Published online: 2021-09-29
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The Klebsiella pneumoniae bacterium is capable of causing the broad range of human nosocomial infections associated with antibiotic resistance and high mortality. Virulent bacteriophage therapy is one of the promising alternatives to antibiotic treatment of such infections. The study was aimed to isolate virulent bacteriophages effective against the relevant clinical K. pneumoniae strains, and to perform the molecular genetic characterization of these phages. Bacteriophages were isolated from the river water samples using the enrichment method. The whole-genome sequencing was performed on the MiSeq platform (Illumina). Three novel K. pneumoniae bacteriophages belonging to families Autographiviridae (vB_KpnP_NER40, GenBank MZ602146) and Myoviridae (vB_KpnM_VIK251, GenBank MZ602147; vB_KpnM_FRZ284, GenBank MZ602148) have been isolated and characterized. On the collection of 105 K. pneumoniae clinical strains, it has been found that bacteriophages vB_KpnP_NER40 and vB_KpnM_VIK251 have a narrow lytic spectrum (22% and 11%), which is limited to strains of the capsular types К2 and К20 respectively. In contrast, bacteriophage vB_KpnM_FRZ284 has a broad lytic spectrum (37%), causing the lysis of strains with different types of capsular polysaccharide. The phages are strictly virulent and have no genes encoding integrases, toxins or pathogenicity factors in their genomes. Genes of depolymerases, encoding the potential receptor binding proteins, have been found in the genomes of the capsular-specific bacteriophages vB_KpnP_NER40 and vB_KpnM_VIK251. The cocktail of three bacteriophages has lysed about 65% of the studied collection of K. рneumoniae strain and is potentially applicable for therapeutic purposes.

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