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Genomic analysis of K47-type Klebsiella pneumoniae phage IME305, a newly isolated member of the genus Teetrevirus

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Abstract

We isolated a K47-type Klebsiella pneumoniae phage from untreated hospital sewage: vB_KpnP_IME305 (GenBank no. OK149215). Next-generation sequencing (NGS) demonstrated that IME305 has a double-stranded DNA genome of 38,641 bp with 50.9% GC content. According to BLASTn comparisons, the IME305 genome sequence shares similarity with that of Klebsiella phage 6998 (97.37% identity and 95% coverage). IME305 contains 45 open reading frames (ORFs) and no rRNA, tRNA, or virulence-related gene sequences. Bioinformatic analysis showed that IME305 belongs to the phage subfamily Studiervirinae and genus Teetrevirus.

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References

  1. (2022) Genomic analysis of Acinetobacter phage BUCT629, a newly isolated member of the genus Obolenskvirus. Arch Virol 167:1197–1199

  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  3. Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinf -OXFORD- 27:p1009–1010

    Article  Google Scholar 

  4. Domingo-Calap P, Beamud B, Vienne J, González-Candelas F, Sanjuán R (2020) Isolation of Four Lytic Phages Infecting Klebsiella pneumoniae K22 Clinical Isolates from Spain. Multidisciplinary Digital Publishing Institute

  5. Duffy C, Feiss M (2002) The large subunit of bacteriophage lambda’s terminase plays a role in DNA translocation and packaging termination. J Mol Biol 316:547–561

    Article  CAS  PubMed  Google Scholar 

  6. Gao M, Wang C, Qiang X, Liu H, Bai C (2020) Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae. Curr Microbiol 77

  7. Hatfull GF, Dedrick RM, Schooley RT (2022) Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annu Rev Med 73:197–211

    Article  PubMed  Google Scholar 

  8. Jin X, Chen Q, Shen F, Jiang Y, Yu Y (2021) Resistance Evolution of Hypervirulent Carbapenem-resistant Klebsiella pneumoniae ST11 during Treatment with Tigecycline and Polymyxin. Emerg Microbes Infections :1–29

  9. Khan Mirzaei M, Nilsson AS (2015) Isolation of phages for phage therapy: a comparison of spot tests and efficiency of plating analyses for determination of host range and efficacy. PLoS ONE 10:e0118557

    Article  PubMed  PubMed Central  Google Scholar 

  10. Lee CR, Lee JH, Park KS, Kim YB, Jeong BC, Lee SH (2016) Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods. Front Microbiol 7:895

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lefkowitz EJ, Dempsey DM, Curtis HR, Orton RJ, Siddell SG, Smith DB (2018) Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Research:D708-D717

  12. Liu Y, Leung S, Huang Y, Guo Y, Gao Z (2020) Identification of Two Depolymerases From Phage IME205 and Their Antivirulent Functions on K47 Capsule of Klebsiella pneumoniae. Frontiers in Microbiology 11

  13. Liu Z, Gu Y, Li X, Liu Y, Ye Y, Guan S, Li J (2019) Identification and Characterization of NDM-1-producing Hypervirulent (Hypermucoviscous) Klebsiella pneumoniae in China. Annals of laboratory medicine 39:167–175

    Article  CAS  PubMed  Google Scholar 

  14. Mi L, Liu Y, Wang C, He T, Gao S, Xing S, Huang Y, Fan H, Zhang X, Yu W (2019) Identification of a lytic Pseudomonas aeruginosa phage depolymerase and its anti-biofilm effect and bactericidal contribution to serum. Virus Genes

  15. Mount DW (2007) Using the Basic Local Alignment Search Tool (BLAST). CSH protocols 2007:pdbtop17

    Google Scholar 

  16. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–214

    Article  CAS  PubMed  Google Scholar 

  17. Qi Y, Wei Z, Ji S, Du X, Shen P, Yu Y (2011) ST11, the dominant clone of KPC-producing Klebsiella pneumoniae in China. J Antimicrob Chemother 66:307–312

    Article  CAS  PubMed  Google Scholar 

  18. Tomás M (2021) Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13. Viruses 14

  19. Wang C, Li P, Niu W, Yuan X, Liu H, Huang Y, An X, Fan H, Zhangxiang L, Mi L (2019) Protective and therapeutic application of the depolymerase derived from a novel KN1 genotype of Klebsiella pneumoniae bacteriophage in mice. Research in Microbiology

  20. Wang C, Li P, Zhu Y, Huang Y, Bai C (2020) Identification of a Novel Acinetobacter baumannii Phage-Derived Depolymerase and Its Therapeutic Application in Mice. Frontiers in Microbiology 11

  21. Wang Z, Cai R, Wang G, Guo Z, Liu X, Guan Y, Ji Y, Zhang H, Xi H, Zhao R (2021) Combination Therapy of Phage vB_KpnM_P-KP2 and Gentamicin Combats Acute Pneumonia Caused by K47 Serotype Klebsiella pneumoniae. Front Microbiol 12:674068

    Article  PubMed  PubMed Central  Google Scholar 

  22. Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V (2018) A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol 430:2237–2243

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by the Anhui Natural Science Foundation Youth Program (2108085QH310), the Scientific Research Project of Anhui Health Committee (AHWJ2021b057), and the Research Fund Project of Anhui Medical University (2020xkj060).

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Authors and Affiliations

  1. Department of Respiratory Medicine, Fuyang Hospital of Anhui Medical University, No.99 Huang Shan road, Yingzhou District Anhui province, 236000, Fuyang city, China

    Can Wang, Qiang Wang & Lei Zhao

  2. Department of Respiratory and Critical Care Diseases, the fifth Medical Center, Chinese PLA General Hospital (Former 307th Hospital of PLA), No. 8 Dongda Street, Fengtai District, 100071, Beijing, China

    Changqing Bai

  3. State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China

    Zhiqiang Mi & Lei Zhao

  4. Department of Respiratory and Critical Care Diseases, General Hospital of Shenzhen University, 518060, Guangdong province, China

    Changqing Bai

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  1. Can Wang
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  2. Qiang Wang
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  3. Zhiqiang Mi
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  4. Lei Zhao
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Correspondence to Lei Zhao or Changqing Bai.

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All of the authors declare that they have no competing interests.

Nucleotide sequence accession number

The complete genome sequence of phage vB_KpnP_IME305 with annotations was submitted to the GenBank database under accession number OK149215.

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Communicated by Johannes Wittmann

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Wang, C., Wang, Q., Mi, Z. et al. Genomic analysis of K47-type Klebsiella pneumoniae phage IME305, a newly isolated member of the genus Teetrevirus. Arch Virol 168, 280 (2023). https://doi.org/10.1007/s00705-023-05900-9

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