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Characterization and genome analysis of Klebsiella phage P509, with lytic activity against clinical carbapenem-resistant Klebsiella pneumoniae of the KL64 capsular type

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Abstract

The increasing population infected by carbapenem-resistant Klebsiella pneumoniae necessitates the development of alternative therapies. In this study, we isolated, characterized, and sequenced a bacteriophage, P509, which was able to specifically infect and lyse carbapenem-resistant K. pneumoniae of K locus type KL64. A one-step growth curve experiment showed that the latent time period of phage P509 was 5 min, and the burst size was about 85 phage particles/cell. Stability tests confirmed that P509 was stable over a wide range of temperatures (4 to 50 °C) and pH (3 to 11) conditions. Phage P509 was identified as a linear double-stranded DNA phage with a genome of 40,954 bp with 53.2% G + C content, encoding 50 predicted proteins. Genomic and morphological analysis suggested that P509 belonged to the genus Przondovirus, family Autographiviridae, order Caudovirales. Further analysis showed that no virulence-related genes or lysogen-formation gene clusters were detected in the genome, suggesting that P509 is a lytic phage, making it potentially suitable for clinical applications. In vitro, the number of viable cells in three phage-treated groups (MOI = 0.1, 0.01, 0.001) decreased by 3.75 log10 CFU/ml, 3.32 log10 CFU/ml and 3.21 log10 CFU/ml, respectively, after 80 min of incubation, in comparison to that in the untreated group. Based on these characteristics, phage P509 may be a promising candidate for future phage therapy applications.

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The genome sequence of phage P509 was deposited in the GenBank database under accession number MT542697.

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Funding

This study was supported by grants from the National Natural Science Foundation of China (U1803109), National Key R&D Program of China (2018YFC1602500), University-Level Science and Technology Team of Wuhu Institute of Technology (wzykjtd202002), Key Research and Development Project of Jiangsu Provincial Science and Technology Department (BE2017654), Gusu Key Health Talent of Suzhou, Jiangsu Youth Medical Talents Program (QN-867), and the Science and Technology Program of Suzhou (SZS201715).

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Authors and Affiliations

  1. College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China

    Min Li, Yuyi Xiao, Pei Li, Zitong Wang, Weiling Qi, Zitai Qi & Wei Zhang

  2. Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, 210095, China

    Min Li, Yuyi Xiao, Pei Li & Wei Zhang

  3. Joint Laboratory of International Cooperation On Animal Health And Food Safety, Ministry of Education, Nanjing, China

    Min Li, Yuyi Xiao, Pei Li & Wei Zhang

  4. Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, NJ, 07110, USA

    Liang Chen

  5. Hackensack Meridian School of Medicine, Seton Hall University, Nutley, NJ, 07110, USA

    Liang Chen

  6. Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China

    Hong Du

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  1. Min Li
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  9. Wei Zhang
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Contributions

All authors contributed to the conception and design of the study. ML, YX, PL, ZW, WQ and ZQ performed experiments and computational analysis. ML wrote the first draft of the manuscript. All authors read, revised, and approved the final manuscript.

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Correspondence to Wei Zhang.

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Li, M., Xiao, Y., Li, P. et al. Characterization and genome analysis of Klebsiella phage P509, with lytic activity against clinical carbapenem-resistant Klebsiella pneumoniae of the KL64 capsular type. Arch Virol 165, 2799–2806 (2020). https://doi.org/10.1007/s00705-020-04822-0

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