Isolation and characterization of virulent bacteriophages against Klebsiella pneumoniae of significant capsular types

About authors

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

2 Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia

3 Sklifosovsky Research Institute for Emergency Medicine, Moscow, Russia

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

About paper

Funding: the study was conducted under the State Assignment “Development of a Complex Treatment Regimen for Drug-Resistant Pathogens Causing Infectious Diseases Using Bacteriophages and their Derivatives in Combination with Antimicrobial Drugs” (code: Bacteriophage-2). The Klebsiella pneumoniae strain typing was supported by the Russian Science Foundation grant (№ 22-15-00149, https://rscf.ru/project/22-15-00149/).

Acknowledgements: the whole-genome sequencing data were acquired using the equipment provided by the Core Facility Center “Genomics, Proteomics, Metabolomics” (http://rcpcm.org/?p=2806).

Author contribution: Gorodnichev RB — study plan, data acquisition and processing, manuscript writing; Kornienko MA — study plan, data acquisition and processing; Bespiatykh DA — data processing; Malakhova MV, Krivulia AO — data acquisition; Veselovsky VA, Goloshchapov OV, Chernenkaya TV, Bespyatykh YuA — data acquisition and processing; Shitikov EA — study plan, о data processing, manuscript writing.

Compliance with the ethical standards: experimental procedure was compliant with SanPiN 3.3686-21 “Sanitary Epidemiological Requirements for the Prevention of Infectious Diseases”; SanPiN 2.1.3684-21 “Sanitary and Epidemiological Requirements for the Maintenance of the Territories of Urban and Rural Settlements, for Water Bodies, Drinking Water and Drinking Water Supply, Atmospheric Air, Soils, Residential Premises, Operation of Industrial and Public Premises, Organization and Conduct of Sanitary and Anti-Epidemic (Preventive) Measures”, as well as Federal Clinical Guidelines "Rational Use of Bacteriophages in Clinical and Epidemiological Practice".

Received: 2023-11-01 Accepted: 2023-12-14 Published online: 2023-12-31

The growing proportion of antibiotic-resistant Klebsiella pneumoniae strains raises challenges to the healthcare system and requires the development of alternative treatment options. Bacteriophage therapy is one of such options. The study was aimed to isolate and describe bacteriophages effective against K. pneumoniae strains of clinically significant capsular types. The bacteriophages were isolated from the sewage and river water samples using the enrichment culture technique. The spectrum of lytic activity of the phages was tested on the collection of K. pneumoniae clinical isolates (n = 279). The studied bacteriophages lysed 52.8–100% of K. pneumoniae strains of respective capsular types: phage VKV295 lysed 100% of strains with the capsular type KL1, SAA231 — 52.8 of strains with KL2, NNK-G4 — 100% of strains with KL39, VSG32 — 66.7% of strains with KL41, NKA196 — 87.5% of strains with KL47, Rappa3 — 87.5% of strains with KL57, PEA128 — 95.5% of strains with KL64, and ChM-G5 — 69.6% of strains with KL102. Whole-genome sequencing and subsequent bioinformatic analysis revealed that the phages belong to the Autographiviridae family and are classified into three genera.The lytic spectrum of phages was limited to specific capsular types due to the presence of specific receptor-binding proteins, polysaccharide depolymerases. The isolated bacteriophages were strictly virulent, did not carry harmful genetic determinants, and had a specific host range, making them applicable in therapeutic practice for combating antibiotic-resistant infections caused by K. pneumoniae.