Archives of Virology

, Volume 162, Issue 4, pp 1129–1139 | Cite as

Characterization and genome analysis of novel bacteriophages infecting the opportunistic human pathogens Klebsiella oxytoca and K. pneumoniae

  • Eun-Ah Park
  • You-Tae Kim
  • Jae-Hyun Cho
  • Sangryeol Ryu
  • Ju-Hoon LeeEmail author
Annotated Sequence Record


Klebsiella is a genus of well-known opportunistic human pathogens that are associated with diabetes mellitus and chronic pulmonary obstruction; however, this pathogen is often resistant to multiple drugs. To control this pathogen, two Klebsiella-infecting phages, K. oxytoca phage PKO111 and K. pneumoniae phage PKP126, were isolated from a sewage sample. Analysis of their host range revealed that they infect K. pneumoniae and K. oxytoca, suggesting host specificity for members of the genus Klebsiella. Stability tests confirmed that the phages are stable under various temperature (4 to 60 °C) and pH (3 to 11) conditions. A challenge assay showed that PKO111 and PKP126 inhibit growth of their host strains by 2 log and 4 log, respectively. Complete genome sequencing of the phages revealed that their genome sizes are quite different (168,758 bp for PKO111 and 50,934 bp for PKP126). Their genome annotation results showed that they have no human virulence-related genes, an important safety consideration. In addition, no lysogen-formation gene cluster was detected in either phage genome, suggesting that they are both virulent phages in their bacterial hosts. Based on these results, PKO111 and PKP126 may be good candidates for development of biocontrol agents against members of the genus Klebsiella for therapeutic purposes. A comparative analysis of tail-associated gene clusters of PKO111 and PKP126 revealed relatively low homology, suggesting that they might differ in the way they recognize and infect their specific hosts.


Biocontrol Agent Indicator Strain Phage Genome Endolysin Phage Therapy 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the Public Welfare & Safety research program through the National Research Foundation of Korea (NRF), funded by the Ministry of Science, ICT, and Future Planning (NRF-2012M3A2A1051684).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

705_2016_3202_MOESM1_ESM.docx (671 kb)
Supplementary material 1 (DOCX 671 kb)


  1. 1.
    Abbasifar R, Kropinski AM, Sabour PM, Ackermann HW, Lingohr EJ, Griffiths MW (2012) Complete genome sequence of Cronobacter sakazakii bacteriophage vB_CsaM_GAP161. J Virol 86:13806–13807CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Adams MH (1959) Enumeration of bacteriophage particles. Bacteriophages. Interscience Publishers, New York, pp 27–30Google Scholar
  3. 3.
    Altermann E, Klaenhammer TR (2003) GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes. OMICS 7:161–169CrossRefPubMedGoogle Scholar
  4. 4.
    Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Bouza E, Cercenado E (2002) Klebsiella and Enterobacter: antibiotic resistance and treatment implications. Semin Resp Infect 17:215–230CrossRefGoogle Scholar
  7. 7.
    Cao F, Wang X, Wang L, Li Z, Che J, Wang L, Li X, Cao Z, Zhang J, Jin L (2015) Evaluation of the efficacy of a bacteriophage in the treatment of pneumonia induced by multidrug resistance Klebsiella pneumoniae in mice. Biomed Res Int 2015:752930PubMedPubMedCentralGoogle Scholar
  8. 8.
    Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J (2005) ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423CrossRefPubMedGoogle Scholar
  9. 9.
    Demirdag K, Hosoglu S (2010) Epidemiology and risk factors for ESBL-producing Klebsiella pneumoniae: a case control study. J Infect Dev Ctries 4:717–722PubMedGoogle Scholar
  10. 10.
    Deresinski S (2009) Bacteriophage therapy: exploiting smaller fleas. Clin Infect Dis 48:1096–1101CrossRefPubMedGoogle Scholar
  11. 11.
    Duckworth DH, Gulig PA (2002) Bacteriophages: potential treatment for bacterial infections. BioDrugs 16:57–62CrossRefPubMedGoogle Scholar
  12. 12.
    Failla ML, Benedict C, Weinberg E (1975) Bacterial and fungal growth in total parenteral nutrition solutions. Antonie Van Leeuwenhoek 41:319–328CrossRefPubMedGoogle Scholar
  13. 13.
    Gyles C (2007) Shiga toxin-producing Escherichia coli: an overview. J Anim Sci 85:E45–E62CrossRefPubMedGoogle Scholar
  14. 14.
    Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol 2(2006):0007PubMedGoogle Scholar
  15. 15.
    Hendrix RW (2003) Bacteriophage genomics. Curr Opin Microbiol 6:506–511CrossRefPubMedGoogle Scholar
  16. 16.
    Hirsch EB, Tam VH (2010) Detection and treatment options for Klebsiella pneumoniae carbapenemases (KPCs): an emerging cause of multidrug-resistant infection. J Antimicrobe Chemother 65:1119–1125CrossRefGoogle Scholar
  17. 17.
    Kumari S, Harjai K, Chhirbber S (2010) Topical treatment of Klebsiella pneumoniae B5055 induced burn wound infection in mice using natural products. J Infect Dev Ctries 4:367–377CrossRefPubMedGoogle Scholar
  18. 18.
    Lang LH (2006) FDA approves use of bacteriophages to be added to meat and poultry product. Gastroenterology 131:1370PubMedGoogle Scholar
  19. 19.
    Maal KB, Delfan AS, Salmanizadeh S (2014) Isolation and identification of Klebsiella pneumonia and Klebsiella oxytoca bacteriophages and their application in wastewater treatment and coliforrn’s phage therapy. Res J Environ Sci 8:123–138CrossRefGoogle Scholar
  20. 20.
    Maki DG (1976) Growth properties of microorganisms in infusion fluid and methods of detection. In: Phillips I, Meers PD, D’Arcy PF (eds) Microbiological hazards of infusion therapy. Microbiological hazards of infusion therapy. MTP Press, Lancaster, pp 13–47CrossRefGoogle Scholar
  21. 21.
    McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852–856CrossRefPubMedGoogle Scholar
  22. 22.
    McNair K, Bailey BA, Edwards RA (2012) PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28:614–618CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Park K-H, Kurokawa K, Zheng L, Jung D-J, Tateishi K, Jin J-O, Ha N-C, Kang HJ, Matsushita M, Kwak J-Y (2010) Human serum mannose-binding lectin senses wall teichoic acid Glycopolymer of Staphylococcus aureus, which is restricted in infancy. J Biol Chem 285:27167–27175CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Park M, Lee J-H, Shin H, Kim M, Choi J, Kang D-H, Heu S, Ryu S (2012) Characterization and comparative genomic analysis of a novel bacteriophage, SFP10, simultaneously inhibiting both Salmonella enterica and Escherichia coli O157:H7. Appl Environ Microbiol 78:58–69CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Podschun R, Ullmann U (1998) Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11:589–603PubMedPubMedCentralGoogle Scholar
  26. 26.
    Pomakova D, Hsiao C, Beanan J, Olson R, MacDonald U, Keynan Y, Russo T (2012) Clinical and phenotypic differences between classic and hypervirulent Klebsiella pneumonia: an emerging and under-recognized pathogenic variant. Eur J Clin Microbiol Infect Dis 31:981–989CrossRefPubMedGoogle Scholar
  27. 27.
    Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Ribot EM, Wierzba RK, Angulo FJ, Barrett TJ (2002) Salmonella enterica serotype Typhimurium DT104 isolated from humans, United States, 1985, 1990, and 1995. Emerg Infect Dis 8:387–391CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944–945CrossRefPubMedGoogle Scholar
  30. 30.
    Shen Y-J, Jiang H, Jin J-P, Zhang Z-B, Xi B, He Y-Y, Wang G, Wang C, Qian L, Li X (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Shoma S, Kamruzzaman M, Ginn AN, Iredell JR, Partridge SR (2014) Characterization of multidrug-resistant Klebsiella pneumoniae from Australia carrying blaNDM-1. Diagn Microbiol Infect Dis 78:93–97CrossRefPubMedGoogle Scholar
  32. 32.
    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Struve C, Krogfelt KA (2004) Pathogenic potential of environmental Klebsiella pneumoniae isolates. Environ Microbiol 6:584–590CrossRefPubMedGoogle Scholar
  34. 34.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Tatusova TA, Madden TL (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250CrossRefPubMedGoogle Scholar
  36. 36.
    Unerwood 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 11:770–772CrossRefGoogle Scholar
  37. 37.
    Verma V, Harjai K, Chhibber S (2009) Characterization of a T7-like lytic bacteriophage of Klebsiella pneumoniae B5055: a potential therapeutic agent. Curr Microbiol 59:274–281CrossRefPubMedGoogle Scholar
  38. 38.
    Wilcox S, Toder R, Foster J (1996) Rapid isolation of recombinant lambda phage DNA for use in fluorescence in situ hybridization. Chromosome Res 4:397–404CrossRefPubMedGoogle Scholar
  39. 39.
    Wu L-T, Chang S-Y, Yen M-R, Yang T-C, Tseng Y-H (2007) Characterization of extended-host-range pseudo-T-even bacteriophage Kpp95 isolated on Klebsiella pneumoniae. Appl Environ Microbiol 73:2532–2540CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Zhu J, Jiang R, Kong H, Zhang R, Lü H, Sun C, Huang Z (2013) Emergence of novel variants of gyrA, parC, qnrS genes in multi-drug resistant Klebsiella caused pneumonia. Zhonghua Liu Xing Bing Xue Za Zhi 34:61–66PubMedGoogle Scholar

Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Eun-Ah Park
    • 1
  • You-Tae Kim
    • 1
  • Jae-Hyun Cho
    • 1
  • Sangryeol Ryu
    • 2
  • Ju-Hoon Lee
    • 1
    Email author
  1. 1.Department of Food Science and Biotechnology, Institute of Life Sciences and ResourcesKyung Hee UniversityYonginKorea
  2. 2.Department of Food and Animal Biotechnology, Department of Agriculture Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and BioconvergenceSeoul National UniversitySeoulKorea

Personalised recommendations