Skip to main content
SpringerLink
Log in

Isolation and characterization of a novel bacteriophage against Mycobacterium avium subspecies paratuberculosis

  • Original Article
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne’s disease, has a doubling time of 24 hours, making rapid detection very difficult. Mycobacteriophages can be used in the detection of disease-causing mycobacteria such as MAP. Isolation and sequencing the genomes of lytic MAP bacteriophages are important preliminary steps towards designing phage-based rapid detection assays for this bacterium. A simple optimized protocol was developed to allow reproducible production of confluent growth of MAP on plates within four to six weeks of incubation at 30 °C. This protocol was applied to the screening of environmental and fecal samples for bacteriophages inhibiting the growth of MAP. As a result, a lytic phage, vB_MapS_FF47, was isolated from bovine feces. FF47 contains a double-stranded DNA genome ~48 kb in length with 73 protein coding sequences. It does not carry temperate or known virulence genes. This phage was shown to be most closely related to Mycobacterium phage Muddy, isolated in South Africa, and Gordonia phage GTE2; however, it could not infect any of the tested Gordonia, Rhodococcus, or Nocardia spp. that GTE2 could. The protocols that were developed for growth and phage isolation have potential applications in a high-throughput screening for compounds inhibiting the growth of MAP. This work describes the first time that a phage was isolated against M. paratuberculosis.

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

Abbreviations

BLAST:

Basic local alignment search tool

Ca.:

circa

CD:

Crohn’s disease

CDS:

Coding sequence

gp:

Gene product

JD:

Johne’s disease

MAP:

Mycobacterium avium subsp. paratuberculosis

MEROPS:

Peptide database

OADC:

Oleic albumin dextrose catalase

References

  1. Harris N, Barletta R (2001) Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine. Clin Microbiol Rev 14:489–512

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  2. Over K, Crandall P, O’Bryan C, Ricke S (2011) Current perspectives on Mycobacterium avium subsp. paratuberculosis, Johne’s disease, and Crohn’s disease: a review. Crit Rev Microbiol 37:141–156

    Article  PubMed  Google Scholar 

  3. Mihajlovic B, Klassen M, Springthorpe S, Couture H, Farber J (2011) Assessment of food as a source of exposure to Mycobacterium avium subspecies paratuberculosis (MAP). J Food Prot 73:1357–1397

    Google Scholar 

  4. Collins M, Manning, E (2010) Johne’s Information Center. http://www.johnes.org/index.shtml. Accessed 26 Feb 2014

  5. McKenna S, Keefe G, Tiwari A, VanLeeuwen J, Barkema H (2006) Johne’s disease in Canada part II: disease impacts, risk factors, and control programs for dairy producers. Can Vet J 47:1089–1099

    PubMed  PubMed Central  Google Scholar 

  6. Kreeger J (1991) Ruminant paratuberculosis—a century of progress and frustration. J Vet Diagn Invest 3:373–383

    Article  PubMed  CAS  Google Scholar 

  7. Timms VJ, Gehringer MM, Mitchell HH, Daskalopoulos G, Neilan BA (2011) How accurately can we detect Mycobacterium avium subsp. paratuberculosis infection? J Microbiol Methods 85:1–8

    Article  PubMed  Google Scholar 

  8. Ratledge C (1982) Lipids: cell composition, fatty acid biosyntheses. In: Ratledge C, Standford JL (eds) The biology of the mycobacteria, 1st edn. Academic Press, London, p 53

    Google Scholar 

  9. De Juan L, Álvarez J, Romero B, Bezos J, Castellanos E, Aranaz A, Mateos A, Dominquez L (2006) Comparison of four different culture media for isolation and growth of type II and type I/III Mycobacterium avium subsp. paratuberculosis strains isolated from cattle and goats. Appl Environ Microbiol 72:5927–5932

    Article  PubMed  PubMed Central  Google Scholar 

  10. Hatfull GF et al (2012) Complete genomes sequences of 138 mycobacteriophages. J Virol 86:2382–2384

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  11. Adams MH (1959) Bacteriophages. Interscience Publishers Inc, New York

    Google Scholar 

  12. Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP (2009) Enumeration of bacteriophages by double agar overlay plaque assay. In: Kropinski AM, Clokie MRJ (eds) Methods in molecular biology, 1st edn. Humana Press, New Jersey, pp 69–76

    Google Scholar 

  13. White A, Knight V (1958) Effect of tween 80 and serum on the interaction of mycobacteriophage D-29 with certain mycobacterial species. Am Rev Tuberc 77:134–145

    PubMed  CAS  Google Scholar 

  14. Tokunaga T, Nakamura RM (1968) Infection of competent Mycobacterium smegmatis with deoxyribonucleic acid extracted from bacteriophage B1. J Virol 2:110–117

    PubMed  CAS  PubMed Central  Google Scholar 

  15. Gadagkar R, Gopinathan K (1978) Inhibition of DNA injection from myocobacteriophage 13 by tween-80. Virology 91:487–488

    Article  PubMed  CAS  Google Scholar 

  16. Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning: a laboratory manual, vol 3, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  17. Hatfull G et al (unknown date) Isolation: protocols and information. The mycobacteriophage database. http://phagesdb.org/workflow/Isolation/. Accessed 26 Feb 2014

  18. Sambrook P, Fritsch E, Maniatis T (1989) Molecular cloning: a Laboratory Manual, vol 1, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  19. Anany H, Lingohr E, Villegas A, Ackermann H, She Y, Griffiths M, Kropinski A (2011) A Shigella boydii bacteriophage which resembles Salmonella phage ViI. Virol J 19:242

    Article  Google Scholar 

  20. Shine J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342–1346

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Maarek Y, Jacovi M, Shtalhaim M, Ur S, Zernik D, Ben-Shaul I (1997) WebCutter: a system for dynamic and tailorable site mapping. Comput Netw ISDN 29:1269–1279

    Article  Google Scholar 

  22. Grant J, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:181–184

    Article  Google Scholar 

  23. Sonnhammer E, Von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Bio 6:175–182

    CAS  Google Scholar 

  24. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Turner D, Reynolds D, Seto D, Mahadevan P (2013) CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Res Notes 6:140

    Article  PubMed  PubMed Central  Google Scholar 

  26. Pedulla M et al (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113:171–182

    Article  PubMed  CAS  Google Scholar 

  27. Stanley E, Mole R, Smith R, Glenn S, Barer M, McGowan M, Rees C (2007) Development of a new, combined rapid method using phage and PCR for detection and identification of viable Mycobacterium paratuberculosis bacteria within 48 hours. Appl Environ Microbiol 73:1851–1857

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Gwozdz J (2008) Paratuberculosis (Johne’s disease). In: World Organisation for Animal Health (ed) OIE terrestrial manual, pp 276–291

  29. Becton, Dickinson and Company (2013) Herrold’s Egg Yolk Agar. Product catalog. http://catalog.bd.com/bdCat/viewProduct.doCustomer?productNumber=222232. Accessed 26 Feb 2014

  30. Bardarov S, Kriakov J, Carriere C, Yu S, Vaamonde C, McAdam R, Bloom B, Hatfull G, Jacobs W (1997) Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 94:10961–10966

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  31. Shafia F, Thompson T (1964) Calcium ion requirement for proliferation of bacteriophage φμ-4. J Bacteriol 88:293–296

    PubMed  CAS  PubMed Central  Google Scholar 

  32. Ackermann H (2007) 5500 Phages examined in the electron microscope. Arch Virol 152:227–243

    Article  PubMed  CAS  Google Scholar 

  33. Petrovski S, Seviour R, Tillett D (2011) Characterization of the genome of the polyvalent lytic bacteriophage GTE2, which has potential for biocontrol of Gordonia-, Rhodococcus-, and Nocardia-stabilized. Appl Environ Microbiol 77:3923–3929

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  34. Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38(Database issue):D234–D236

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  35. Nunes-Düby SE, Kwon HJ, Tirumalai RS, Ellenberger T, Landy A (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26:391–406

    Article  PubMed  PubMed Central  Google Scholar 

  36. Boyd EF, Brüssow H (2002) Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol 10:521–529

    Article  PubMed  CAS  Google Scholar 

  37. Rawlings ND, Waller M, Barrett AJ, Bateman A (2013) MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 42:D503–D509

    Article  PubMed  PubMed Central  Google Scholar 

  38. Paradis-Bleau C, Cloutier I, Lemieux L, Sanschagrin F, Laroche J, Auger M, Garnier A, Levesque RC (2007) Peptidoglycan lytic activity of the Pseudomonas aeruginosa phage phiKZ gp144 lytic transglycosylase. FEMS Microbiol Lett 266:201–209

    Article  PubMed  CAS  Google Scholar 

  39. Miroshnikov KA, Faizullina NM, Sykilinda NN, Mesyanzhinov VV (2006) Properties of the endolytic transglycosylase encoded by gene 144 of Pseudomonas aeruginosa bacteriophage phiKZ. Biochemistry (Mosc) 71:300–305

    Article  CAS  Google Scholar 

  40. Käll L, Krogh A, Sonnhammer ELL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338:1027–1036

    Article  PubMed  Google Scholar 

  41. Omasits U, Ahrens CH, Müller S, Wollscheid B (2013) Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics. doi:10.1093/bioinformatics/btt607

  42. Catalão MJ, Gil F, Moniz-Pereira J, São-José C, Pimentel M (2013) Diversity in bacterial lysis systems: bacteriophages show the way. FEMS Microbiol Rev 37:554–571

    Article  PubMed  Google Scholar 

  43. Nelson DC, Schmelcher M, Rodriguez-Rubio L, Klumpp J, Pritchard DG, Dong S, Donovan DM (2012) Endolysins as antimicrobials. Adv Virus Res 83:299–365

    Article  PubMed  CAS  Google Scholar 

  44. Schmelcher M, Donovan DM, Loessner MJ (2012) Bacteriophage endolysins as novel antimicrobials. Future Microbiol 7:1147–1171

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  45. Hatfull G, Cresawn S, Hendrix R (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res Microbiol 159:332–339

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  46. Froman S, Will D, Bogen E (1954) Bacteriophage active against virulent Mycobacterium tuberculosis—I. Isolation and activity. Am J Public Health Nations Health 44:1326–1333

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  47. Foley-Thomas E, Whipple D, Bermudez L, Barletta R (1995) Phage infection, transfection and transformation of Mycobacterium avium complex and Mycobacterium paratuberculosis. Microbiology 141:1173–1181

    Article  PubMed  CAS  Google Scholar 

  48. Loessner MJ, Busse M (1990) Bacteriophage typing of Listeria species. Appl Environ Microbiol 56:1912–1918

    PubMed  CAS  PubMed Central  Google Scholar 

  49. Carlton RM, Noordman WH, Biswas B, de Meester ED, Loessner MJ (2005) Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application. Regul Toxicol Pharmacol 43:301–312

    Article  PubMed  CAS  Google Scholar 

  50. Lavigne R, Seto D, Mahadevan P, Ackermann H-W, Kropinski AM (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159:406–414

    Article  PubMed  CAS  Google Scholar 

  51. Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann HW, Kropinski AM (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 9:224

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge the financial support from SENTINEL Bioactive Paper Network and Beef Cattle Research Council (BCRC). The authors wish to thank Dr. Junghoan Kim for his assistance with this work, and Dr. Herman Barkema and Dr. Jeroen De Buck at the University of Calgary for sending freshly collected fecal samples of suspect JD cows and MAP strains and offering their time and suggestions for the research. The authors also wish to thank Bob Harris and Dr. Hans-Wolfgang Ackermann for assistance with TEM, Dr. Lucy Mutharia for providing bacterial strains and offering time to discuss the research, and finally Teagan Brown of Dr. Daniel Tillett’s group for conducting the Gordonia, Rhodococcus, and Nocardia host range study for us. Finally, the authors wish to thank Ms. Debbie Jacobs-Sera for her time answering questions over email, and the rest of the Dr. Graham Hatfull group for providing us with D29.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, N1G 2W1, Canada

    Simone Basra, Hany Anany, Lioubov Brovko & Mansel W. Griffiths

  2. Department of Microbiology, Ain Shams University, Khalifa El-Maamon St., Cairo Governorate, 11566, Egypt

    Hany Anany

  3. Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, N1G 3W4, Canada

    Andrew M. Kropinski

  4. Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada

    Andrew M. Kropinski

Authors
  1. Simone Basra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hany Anany
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lioubov Brovko
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrew M. Kropinski
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mansel W. Griffiths
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Hany Anany or Andrew M. Kropinski.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 12 kb)

Supplementary material 2 (DOCX 11 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Basra, S., Anany, H., Brovko, L. et al. Isolation and characterization of a novel bacteriophage against Mycobacterium avium subspecies paratuberculosis . Arch Virol 159, 2659–2674 (2014). https://doi.org/10.1007/s00705-014-2122-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-014-2122-3

Keywords

Search

Navigation