ORIGINAL RESEARCH
Novel Klebsiella pneumoniae virulent bacteriophage KPPK108.1 capable of infecting the K108 serotype strains
1 Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
2 Central Research Institute of Epidemiology of Rospotrebnadzor, Moscow, Russia
3 Pirogov Russian National Research Medical University, Moscow, Russia
4 Lomonosov Moscow State University, Moscow, Russia
Correspondence should be addressed: Mikhail M. Shneider
Miklukho-Maklaya, 16/10, Moscow, 117997, Russia; ur.liam@nhs_mm
Funding: the study was funded by the Ministry of Health of the Russian Federation (EGISU R&D № 121052800048-3).
Acknowledgements: the authors wish to thank the Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, for advice on research methods.
Author contribution: Shagin DA — research conceptualization, study management, manuscript writing; Evseev PV, Shelenkov AA — formal analysis of sequencing data, manuscript editing; Shneider MM — methodology, study management; Mikhailova YuV — sequencing, data validation; Yanushevich YuG, Moiseenko AV, Karlova MG — methodology; Sokolova OS — electron microscopy, methodology.
- Paczosa MK, Mecsas J. Klebsiella pneumoniae: Going on the Offense with a Strong Defense. Microbiol Mol Biol Rev. 2016; 80 (3): 629–61.
- Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom. 2016; 2 (12): e000102.
- Colombet J, Robin A, Lavie L, Bettarel Y, Cauchie HM, SimeNgando T. Virioplankton “pegylation”: use of PEG (polyethylene glycol) to concentrate and purify viruses in pelagic ecosystems. J Microbiol Methods. 2007; 71 (3): 212–9.
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19 (5): 455–77.
- Drulis-Kawa Z, Mackiewicz P, Kęsik-Szeloch A, MaciaszczykDziubinska E, Weber-Dąbrowska B, Dorotkiewicz-Jach A, et al. Isolation and characterisation of KP34 — a novel φKMV-like bacteriophage for Klebsiella pneumoniae. Appl Microbiol Biotechnol. 2011; 90 (4): 1333–45.
- Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30 (14): 2068–9.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990; 215 (3): 403–10.
- Gabler F, Nam S-Z, Till S, Mirdita M, Steinegger M, Söding J, et al. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics. 2020; 72 (1): e108.
- Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015; 10 (6): 845–58.
- Geneious. Bioinformatics Software for Sequence Data Analysis. Geneious [cited 2021 Nov 11]. Available from: https://www.geneious.com/
- Home — Genome — NCBI [cited 2021 Nov 11]. Available from: https://www.ncbi.nlm.nih.gov/genome.
- Moraru C, Varsani A, Kropinski AM. VIRIDIC — A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses. Viruses. 2020; 12 (11): 1268.
- Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol. 2016; 66 (2): 1100–3.
- Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30 (9): 1312–3.
- Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008; 25 (7): 1307–20.
- Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research. 2002; 30 (14): 3059–66.
- Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011; 27 (7): 1009–10.
- Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021; 596 (7873): 583–9.
- Evans R, O’Neill M, Pritzel A, Antropova N, Senior A, Green T, et al. Protein complex prediction with AlphaFold-Multimer. 2021 [cited 2021 Dec 6]. 2021.10.04.463034. Available from: https:// www.biorxiv.org/content/10.1101/2021.10.04.463034v1.
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids Research. 2000; 28 (1): 235–42.
- Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, et al. Improvements to the APBS biomolecular solvation software suite. Protein Science. 2018; 27 (1): 112–28.
- Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25 (13): 1605–12.
- Schwarzer D, Buettner FFR, Browning C, Nazarov S, Rabsch W, Bethe A, et al. A Multivalent Adsorption Apparatus Explains the Broad Host Range of Phage phi92: a Comprehensive Genomic and Structural Analysis. Journal of Virology. 2012; 86 (19): 10384–98.
- Evseev PV, Lukianova AA, Shneider MM, Korzhenkov AA, Bugaeva EN, Kabanova AP, et al. Origin and Evolution of Studiervirinae Bacteriophages Infecting Pectobacterium: Horizontal Transfer Assists Adaptation to New Niches. Microorganisms. 2020; 8 (11): 1707.
- Roberts GA, Stephanou AS, Kanwar N, Dawson A, Cooper LP, Chen K, et al. Exploring the DNA mimicry of the Ocr protein of phage T7. Nucleic Acids Res. 2012; 40 (16): 8129–43.
- Zavilgelsky GB, Rastorguev SM. Antirestriction proteins ArdA and Ocr as efficient inhibitors of type I restriction-modification enzymes. Mol Biol. 2009; 43 (2): 241.
- Isaev A, Drobiazko A, Sierro N, Gordeeva J, Yosef I, Qimron U, et al. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence. Nucleic Acids Res. 2020; 48 (10): 5397–406.
- Zampara A, Sørensen MCH, Grimon D, Antenucci F, Vitt AR, Bortolaia V, et al. Exploiting phage receptor binding proteins to enable endolysins to kill Gram-negative bacteria. Sci Rep. 2020; 10 (1): 12087.
- Stevenson G, Andrianopoulos K, Hobbs M, Reeves PR. Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid. J Bacteriol. 1996; 178 (16): 4885–93.
- Kim H, Kim M, Bai J, Lim J-A, Heu S, Ryu S. Colanic Acid Is a Novel Phage Receptor of Pectobacterium carotovorum subsp. carotovorum Phage POP72. Frontiers in Microbiology. 2019; 10: 143.