Skip to main content
SpringerLink
Log in

Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A novel virulent phage, vB_KpnP_IME337, isolated from a hospital sewage in Beijing, China, that infects carbapenem-resistant Klebsiella pneumoniae KN2 capsular type was identified and characterized. Next-generation sequencing and genome analysis revealed that vB_KpnP_IME337 had a linear double-stranded genome with a length of 44,266 base pairs and G+C content of 53.7%. Fifty-two putative open reading frames were identified, and no transfer RNA-encoding genes were detected. BLASTn analysis revealed that phage vB_KpnP_IME337 had the highest sequence similarity with Klebsiella phage phiBO1E, with genome coverage of 79%. Based on morphology, phage vB_KpnP_IME337 was determined to belong to the family Podoviridae of the order Caudovirales. It was shown that phage vB_KpnP_IME337 had an infection duration of ~ 90 min and 10 min latent period, and a highly specific to host strain. In conclusion, phage vB_KpnP_IME337 may be a promising alternative candidate to antibiotic treatment for controlling diseases caused by drug-resistant K. pneumoniae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Renshaw A (2009) Pulmonary pathology, a volume in the foundations in diagnostic pathology series. Adv Anat Pathol 16(1):65

    Google Scholar 

  2. Podschun R, Ullmann U (1998) Klebsiella spp as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11(4):589–603

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Cunningham AA, Daszak P, Wood JLN (2017) One Health, emerging infectious diseases and wildlife: two decades of progress? Philos Trans R Soc Lond Ser B 372(1725):20160167

    Google Scholar 

  4. Zilberberg MD, Shorr AF, Micek ST, Vazquez-Guillamet C, Kollef MHJCC (2014) Multi-drug resistance, inappropriate initial antibiotic therapy and mortality in Gram-negative severe sepsis and septic shock: a retrospective cohort study. Crit Care 18(6):1–13

    Google Scholar 

  5. Souli M, Galani I, Antoniadou A, Papadomichelakis E, Poulakou G, Panagea T, Vourli S, Zerva L, Armaganidis A, Kanellakopoulou K, Giamarellou H (2010) An outbreak of infection due to beta-Lactamase Klebsiella pneumoniae Carbapenemase 2-producing K pneumoniae in a Greek University Hospital: molecular characterization, epidemiology, and outcomes. Clin Infect Dis 50(3):364–373

    CAS  PubMed  Google Scholar 

  6. Stapleton PJ, Murphy M, Mccallion N, Brennan M (2016) Outbreaks of extended spectrum beta-lactamaseproducing Enterobacteriaceae in neonatal intensive care units: a systematic review. Arch Dis Childhood Fetal Neonatal Ed 101(1):403–403

    Google Scholar 

  7. Wisgrill L, Lepuschitz S, Blaschitz M, Rittenschober-Böhm J, Diab-El Schahawi M, Schubert S, Indra A, Berger AJPIDJ (2018) Outbreak of yersiniabactin-producing Klebsiella pneumoniae in a neonatal intensive care unit. Pediatr Infect Dis J 38(6):638–642

    Google Scholar 

  8. Ventola CLJP (2015) The antibiotic resistance crisis: part 1: causes and threats. Pharm Ther 40(4):277–283

    Google Scholar 

  9. Payne RJH, Jansen VAAJCP (2000) Phage therapy: the peculiar kinetics of self-replicating pharmaceuticals. Pharmacol Ther 68(3):225–230

    CAS  Google Scholar 

  10. Nilsson AS (2014) Phage therapy—constraints and possibilities. Upsala J Med Sci 119(2):192–198

    PubMed  PubMed Central  Google Scholar 

  11. Gill JJ, Hollyer T, Sabour PM (2007) Bacteriophages and phage-derived products as antibacterial therapeutics. Expert Opin Ther Patents 17(11):1341–1350

    CAS  Google Scholar 

  12. Matsuzaki S, Rashel M, Uchiyama J, Sakurai S, Ujihara T, Kuroda M, Ikeuchi M, Tani T, Fujieda M (2005) Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother 11(5):211–219

    PubMed  Google Scholar 

  13. Domingo-Calap P, Delgado-Martinez J (2018) Bacteriophages: protagonists of a post-antibiotic era. Antibiotics (Basel, Switzerland) 7(3):66

    CAS  Google Scholar 

  14. Cha K, Oh HK, Jang JY, Jo Y, Kim WK, Ha GU, Ko KS, Myung H (2018) Characterization of two novel bacteriophages infecting multidrug-resistant (MDR) Acinetobacter baumannii and evaluation of their therapeutic efficacy in vivo. Front Microbiol 9:696

    PubMed  PubMed Central  Google Scholar 

  15. Sao-Jose C (2018) Engineering of phage-derived lytic enzymes: improving their potential as antimicrobials. Antibiotics (Basel, Switzerland) 7(2):29

    Google Scholar 

  16. Pallavali RR, Degati VL, Lomada D, Reddy MC, Durbaka VRP (2017) Isolation and in vitro evaluation of bacteriophages against MDR-bacterial isolates from septic wound infections. PLoS ONE 12(7):e0179245

    PubMed  PubMed Central  Google Scholar 

  17. Chadha P, Katare OP, Chhibber S (2017) Liposome loaded phage cocktail: enhanced therapeutic potential in resolving Klebsiella pneumoniae mediated burn wound infections. Burns 43(7):1532–1543

    PubMed  Google Scholar 

  18. Manohar P, Tamhankar AJ, Lundborg CS, Nachimuthu R (2019) Therapeutic characterization and efficacy of bacteriophage cocktails infecting Escherichia coli, Klebsiella pneumoniae, and enterobacter species. Front Microbiol 10:574

    PubMed  PubMed Central  Google Scholar 

  19. Greisen K, Loeffelholz M, Purohit A, Leong D (1994) PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J Clin Microbiol 32(2):335–351

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Pan YJ, Lin TL, Chen YH, Hsu CR, Hsieh PF, Wu MC, Wang JT (2013) Capsular types of Klebsiella pneumoniae revisited by wzc sequencing. PLoS ONE 8(12):e80670

    PubMed  PubMed Central  Google Scholar 

  21. Zhao F, Sun H, Zhou X, Liu G, Li M, Wang C, Liu S, Zhuang Y, Tong Y, Ren H (2019) Characterization and genome analysis of a novel bacteriophage vB_SpuP_Spp16 that infects Salmonella enterica serovar pullorum. Virus Genes 55(4):532–540

    CAS  PubMed  Google Scholar 

  22. Anderson TF (1949) Bacteriophages. 4(4):21

  23. Ackermann HW (2009) Basic phage electron microscopy. Methods Mol Biol (Clifton, NJ) 501:113–126

    CAS  Google Scholar 

  24. Delbrück MJ (1940) The growth of bacteriophage and lysis of the host. J Gen Physiol 23(5):643

    PubMed  PubMed Central  Google Scholar 

  25. Adams MH (1959) Bacteriophage. Interscience Publishers, New York, pp 450–456

    Google Scholar 

  26. Li F, Xing S, Fu K, Zhao S, Liu J, Tong Y, Zhou L (2019) Genomic and biological characterization of the Vibrio alginolyticus-infecting "Podoviridae" bacteriophage, vB_ValP_IME271. Virus Genes 55(2):218–226

    CAS  PubMed  Google Scholar 

  27. Chen Y, Sun E, Song J, Yang L, Wu B (2018) Complete genome sequence of a novel T7-like bacteriophage from a pasteurella multocida capsular type A isolate. Curr Microbiol 75(5):574–579

    CAS  PubMed  Google Scholar 

  28. Yang Y, Cai L, Ma R, Xu Y, Tong Y, Huang Y, Jiao N, Zhang R (2017) A novel roseosiphophage isolated from the oligotrophic South China Sea. Viruses 9(5):109

    PubMed Central  Google Scholar 

  29. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 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

    PubMed  PubMed Central  Google Scholar 

  31. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580

    CAS  PubMed  Google Scholar 

  32. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics (Oxford, England) 27(7):1009–1010

    CAS  Google Scholar 

  34. Underwood AP, Mulder A, Gharbia S, Green J (2005) Virulence searcher: a tool for searching raw genome sequences from bacterial genomes for putative virulence factors. Clin Microbiol Infect 11(9):770–772

    CAS  PubMed  Google Scholar 

  35. Kleinheinz KA, Joensen KG, Larsen MV (2014) Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. Bacteriophage 4(1):e27943

    PubMed  PubMed Central  Google Scholar 

  36. Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J (2018) Taxonomy of prokaryotic viruses: 2017 update from the ICTV bacterial and archaeal viruses subcommittee. Adv Virol 163(4):1125–1129

    CAS  Google Scholar 

  37. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 60. Mol Biol Evol 30(12):2725–2729

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Zhang X, Wang Y, Li S, An X, Pei G, Huang Y, Fan H, Mi Z, Zhang Z, Wang W, Chen Y, Tong Y (2015) A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini. BMC Genomics 16:414

    PubMed  PubMed Central  Google Scholar 

  39. Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34:D169–D172

    CAS  PubMed  Google Scholar 

  40. Shi Y, Yan Y, Ji W, Du B, Meng X, Wang H, Sun JJVJ (2012) Characterization and determination of holin protein of Streptococcus suis bacteriophage SMP in heterologous host. Virol J 9(1):70–70

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Sun S, Rao VB, Biol MGRJCOS (2010) Genome packaging in viruses. Curr Opin Struct Biol 20(1):114–120

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Guilliam TA, Keen BA, Brissett NC, Doherty AJJ (2015) Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes. Nucleic Acids Res 43(14):6651–6664

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Tu J, Park T, Morado DR, Hughes KT, Molineux IJ, Liu JJV (2017) Dual host specificity of phage SP6 is facilitated by tailspike rotation. Virology 507:206–215

    CAS  PubMed  Google Scholar 

  44. Hambly E, Tetart F, Desplats C, Wilson WH, Krisch HM (2001) A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc Natl Acad Sci 98(20):11411–11416

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The work was supported by the Capital Characteristic Clinic Project of Beijing (Z161100000516181) and the National Key Research and Development Program of China (2016YFC1202705, AWS16J020, and AWS15J006) and the National Science and Technology Major Project (2018ZX10201001).

Author information

Author notes

  1. Mingming Gao and Can Wang contribute equally to this work.

Authors and Affiliations

  1. Department of Graduate, Hebei North University, Zhangjiakou, 075000, China

    Mingming Gao & Changqing Bai

  2. Department of Respiratory and Critical Care Diseases, The Fifth Medical Center, Chinese General Hospital of the PLA, Beijing, 100071, China

    Can Wang, Huiying Liu, Puyuan Li & Changqing Bai

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

    Xin Qiang, Guangqian Pei, Xianglilan Zhang, Zhiqiang Mi, Yong Huang & Yigang Tong

  4. Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China

    Yigang Tong

  5. Shenzhen University General Hospital, Shenzhen, 518055, China

    Changqing Bai

Authors
  1. Mingming Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Can Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xin Qiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Huiying Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Puyuan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guangqian Pei
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xianglilan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Zhiqiang Mi
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yong Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Yigang Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Changqing Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yigang Tong or Changqing Bai.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 39 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gao, M., Wang, C., Qiang, X. et al. Isolation and Characterization of a Novel Bacteriophage Infecting Carbapenem-Resistant Klebsiella pneumoniae. Curr Microbiol 77, 722–729 (2020). https://doi.org/10.1007/s00284-019-01849-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-019-01849-8

Search

Navigation