Quantitative Biology

, Volume 5, Issue 1, pp 42–54 | Cite as

Phage engineering: how advances in molecular biology and synthetic biology are being utilized to enhance the therapeutic potential of bacteriophages

Open Access
Review

Abstract

Background

The therapeutic potential of bacteriophages has been debated since their first isolation and characterisation in the early 20th century. However, a lack of consistency in application and observed efficacy during their early use meant that upon the discovery of antibiotic compounds research in the field of phage therapy quickly slowed. The rise of antibiotic resistance in bacteria and improvements in our abilities to modify and manipulate DNA, especially in the context of small viral genomes, has led to a recent resurgence of interest in utilising phage as antimicrobial therapeutics.

Results

In this article a number of results from the literature that have aimed to address key issues regarding the utility and efficacy of phage as antimicrobial therapeutics utilising molecular biology and synthetic biology approaches will be introduced and discussed, giving a general view of the recent progress in the field.

Conclusions

Advances in molecular biology and synthetic biology have enabled rapid progress in the field of phage engineering, with this article highlighting a number of promising strategies developed to optimise phages for the treatment of bacterial disease. Whilst many of the same issues that have historically limited the use of phages as therapeutics still exist, these modifications, or combinations thereof, may form a basis upon which future advances can be built. A focus on rigorous in vivo testing and investment in clinical trials for promising candidate phages may be required for the field to truly mature, but there is renewed hope that the potential benefits of phage therapy may finally be realised.

Keywords

bacteriophage phage therapy phage engineering synthetic biology 

Notes

Acknowledgments

This work was supported by the Bill and Melinda Gates Foundation under the Grand Challenges Explorations grant (OPP1139488).

References

  1. 1.
    Summers, W. C. (2012) The strange history of phage therapy. Bacteriophage, 2, 130–133CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Twort, F.W. (1915) An investigation on the nature of ultra-microscopic viruses. Lancet, 186, 1241–1243CrossRefGoogle Scholar
  3. 3.
    d’Herelle, F. (1917) On an invisible microbe antagonistic to dysentery bacili. CR Acad. Sci. Paris, 165, 373–375Google Scholar
  4. 4.
    Abedon, S. T., Kuhl, S. J., Blasdel, B. G. and Kutter, E. M. (2011) Phage treatment of human infections. Bacteriophage, 1, 66–85CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Neu, H. C. (1992) The crisis in antibiotic resistance. Science, 257, 1064–1073CrossRefPubMedGoogle Scholar
  6. 6.
    Davies, J. and Davies, D. (2010) Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev., 74, 417–433CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Bradley, R. W., Buck, M. and Wang, B. (2016) Tools and principles for microbial gene circuit engineering. J. Mol. Biol., 428, 862–888CrossRefPubMedGoogle Scholar
  8. 8.
    Wang, B. and Buck, M. (2012) Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol., 20, 376–384CrossRefPubMedGoogle Scholar
  9. 9.
    Wang, B., Kitney, R. I., Joly, N. and Buck, M. (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun., 2, 508CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Wang, B., Barahona, M. and Buck, M. (2013) A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals. Biosens. Bioelectron., 40, 368–376CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Bradley, R. W. and Wang, B. (2015) Designer cell signal processing circuits for biotechnology. N. Biotechnol., 32, 635–643CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Haellman, V. and Fussenegger, M. (2016) Synthetic biology—toward therapeutic solutions. J. Mol. Biol., 428, 945–962CrossRefPubMedGoogle Scholar
  13. 13.
    Smith, H. O., Hutchison, C. A. III, Pfannkoch, C. and Venter, J. C. (2003) Generating a synthetic genome by whole genome assembly: ΦX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA, 100, 15440–15445CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Chan, L.Y., Kosuri, S., and Endy, D. (2005) Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005. 0018CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Lu, T. K. and Koeris, M. S. (2011) The next generation of bacteriophage therapy. Curr. Opin. Microbiol., 14, 524–531CrossRefPubMedGoogle Scholar
  16. 16.
    Pires, D. P., Cleto, S., Sillankorva, S., Azeredo, J. and Lu, T. K. (2016) Genetically engineered phages: a review of advances over the last decade. Microbiol. Mol. Biol. Rev., 80, 523–543CrossRefPubMedGoogle Scholar
  17. 17.
    Rakhuba, D. V., Kolomiets, E. I., Dey, E. S. and Novik, G. I. (2010) Bacteriophage receptors, mechanisms of phage adsorption and penetration into host cell. Pol. J. Microbiol., 59, 145–155PubMedGoogle Scholar
  18. 18.
    Crawford, J. T. and Goldberg, E. B. (1977) The effect of baseplate mutations on the requirement for tail-fiber binding for irreversible adsorption of bacteriophage T4. J. Mol. Biol., 111, 305–313CrossRefPubMedGoogle Scholar
  19. 19.
    Crawford, J. T. and Goldberg, E. B. (1980) The function of tail fibers in triggering baseplate expansion of bacteriophage T4. J. Mol. Biol., 139, 679–690CrossRefPubMedGoogle Scholar
  20. 20.
    Arscott, P. G. and Goldberg, E. B. (1976) Cooperative action of the T4 tail fibers and baseplate in triggering conformational change and in determining host range. Virology, 69, 15–22CrossRefPubMedGoogle Scholar
  21. 21.
    Molineux, I. J. (2001) No syringes please, ejection of phage T7 DNA from the virion is enzyme driven. Mol. Microbiol., 40, 1–8CrossRefPubMedGoogle Scholar
  22. 22.
    Kemp, P., Garcia, L. R. and Molineux, I. J. (2005) Changes in bacteriophage T7 virion structure at the initiation of infection. Virology, 340, 307–317CrossRefPubMedGoogle Scholar
  23. 23.
    Heller, K. and Braun, V. (1979) Accelerated adsorption of bacteriophage T5 to Escherichia coli F, resulting from reversible tail fiberlipopolysaccharide binding. J. Bacteriol., 139, 32–38PubMedPubMedCentralGoogle Scholar
  24. 24.
    Heller, K. and Braun, V. (1982) Polymannose O-antigens of Escherichia coli, the binding sites for the reversible adsorption of bacteriophage T5+ via the L-shaped tail fibers. J. Virol., 41, 222–227PubMedPubMedCentralGoogle Scholar
  25. 25.
    Riede, I., Degen, M. and Henning, U. (1985) The receptor specificity of bacteriophages can be determined by a tail fiber modifying protein. EMBO J., 4, 2343–2346PubMedPubMedCentralGoogle Scholar
  26. 26.
    Montag, D., Riede, I., Eschbach, M.-L., Degen, M. and Henning, U. (1987) Receptor-recognizing proteins of T-even type bacteriophages: constant and hypervariable regions and an unusual case of evolution. J. Mol. Biol., 196, 165–174CrossRefPubMedGoogle Scholar
  27. 27.
    Moody, M. F. (1973) Sheath of bacteriophage T4: III. contraction mechanism deduced from partially contracted sheaths. J. Mol. Biol., 80, 613–635CrossRefPubMedGoogle Scholar
  28. 28.
    Wright, A., Hawkins, C. H., Änggård, E. E. and Harper, D. R. (2009) A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy. Clin. Otolaryngol., 34, 349–357CrossRefPubMedGoogle Scholar
  29. 29.
    Gu, J., Liu, X., Li, Y., Han, W., Lei, L., Yang, Y., Zhao, H., Gao, Y., Song, J., Lu, R., et al. (2012) A method for generation phage cocktail with great therapeutic potential. PLoS One, 7, e31698CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Oliveira, A., Sereno, R. and Azeredo, J. (2010) In vivo efficiency evaluation of a phage cocktail in controlling severe colibacillosis in confined conditions and experimental poultry houses. Vet. Microbiol., 146, 303–308CrossRefPubMedGoogle Scholar
  31. 31.
    Jaiswal, A., Koley, H., Ghosh, A., Palit, A. and Sarkar, B. (2013) Efficacy of cocktail phage therapy in treating Vibrio cholerae infection in rabbit model. Microbes Infect., 15, 152–156CrossRefPubMedGoogle Scholar
  32. 32.
    Chan, B. K. and Abedon, S. T. (2012). Chapter 1–Phage therapy pharmacology: phage cocktails. In Advances in Applied Microbiology, Laskin, A.I., Sariaslani, S. and Gadd, G.M. ed. 1–23. Massachusetts: Academic PressGoogle Scholar
  33. 33.
    Chan, B. K., Abedon, S. T. and Loc-Carrillo, C. (2013) Phage cocktails and the future of phage therapy. Future Microbiol., 8, 769–783CrossRefPubMedGoogle Scholar
  34. 34.
    Gill, J. J. and Hyman, P. (2010) Phage choice, isolation, and preparation for phage therapy. Curr. Pharm. Biotechnol., 11, 2–14CrossRefPubMedGoogle Scholar
  35. 35.
    Merabishvili, M., Pirnay, J.-P., Verbeken, G., Chanishvili, N., Tediashvili, M., Lashkhi, N., Glonti, T., Krylov, V., Mast, J., Van Parys, L., et al. (2009) Quality-controlled small-scale production of a well-defined bacteriophage cocktail for use in human clinical trials. PLoS One, 4, e4944CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Kutter, E., De Vos, D., Gvasalia, G., Alavidze, Z., Gogokhia, L., Kuhl, S. and Abedon, S. T. (2010) Phage therapy in clinical practice: treatment of human infections. Curr. Pharm. Biotechnol., 11, 69–86CrossRefPubMedGoogle Scholar
  37. 37.
    Mahichi, F., Synnott, A. J., Yamamichi, K., Osada, T. and Tanji, Y. (2009) Site-specific recombination of T2 phage using IP008 long tail fiber genes provides a targeted method for expanding host range while retaining lytic activity. FEMS Microbiol. Lett., 295, 211–217CrossRefPubMedGoogle Scholar
  38. 38.
    Yoichi, M., Abe, M., Miyanaga, K., Unno, H. and Tanji, Y. (2005) Alteration of tail fiber protein gp38 enables T2 phage to infect Escherichia coli O157:H7. J. Biotechnol., 115, 101–107CrossRefPubMedGoogle Scholar
  39. 39.
    Pouillot, F., Blois, H. and Iris, F. (2010) Genetically engineered virulent phage banks in the detection and control of emergent pathogenic bacteria. Biosecur. Bioterror., 8, 155–169CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Krüger, D. H. and Schroeder, C. (1981) Bacteriophage T3 and bacteriophage T7 virus-host cell interactions. Microbiol. Rev., 45, 9–51PubMedPubMedCentralGoogle Scholar
  41. 41.
    Lin, T.-Y., Lo, Y.-H., Tseng, P.-W., Chang, S.-F., Lin, Y.-T. and Chen, T.-S. (2012) A T3 and T7 recombinant phage acquires efficient adsorption and a broader host range. PLoS One, 7, e30954CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Ando, H., Lemire, S., Pires, D. P. and Lu, T. K. (2015) Engineering modular viral scaffolds for targeted bacterial population editing. Cell Syst., 1, 187–196CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Friedman, D. I. (1992) Interaction between bacteriophage l and its Escherichia coli host. Curr. Opin. Genet. Dev., 2, 727–738CrossRefPubMedGoogle Scholar
  44. 44.
    Casjens, S. R., Gilcrease, E. B., Winn-Stapley, D. A., Schicklmaier, P., Schmieger, H., Pedulla, M. L., Ford, M. E., Houtz, J. M., Hatfull, G. F. and Hendrix, R. W. (2005) The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol., 187, 1091–1104CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol., 49, 277–300CrossRefPubMedGoogle Scholar
  46. 46.
    Esvelt, K. M., Carlson, J. C. and Liu, D. R. (2011) A system for the continuous directed evolution of biomolecules. Nature, 472, 499–503CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Bassalo, M. C., Liu, R. and Gill, R. T. (2016) Directed evolution and synthetic biology applications to microbial systems. Curr. Opin. Biotechnol., 39, 126–133CrossRefPubMedGoogle Scholar
  48. 48.
    Prins, J. M., van Deventer, S. J., Kuijper, E. J. and Speelman, P. (1994) Clinical relevance of antibiotic-induced endotoxin release. Antimicrob. Agents Chemother., 38, 1211–1218CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Slopek, S., Durlakowa, I., Weber-Dabrowska, B., Kucharewicz-Krukowska, A., Dabrowski, M. and Bisikiewicz, R. (1983) Results of bacteriophage treatment of suppurative bacterial infections. I. General evaluation of the results. Arch. Immunol. Ther. Exp. (Warsz.), 31, 267–291Google Scholar
  50. 50.
    Gamage, S. D., Patton, A. K., Hanson, J. F. and Weiss, A. A. (2004) Diversity and host range of Shiga toxin-encoding phage. Infect. Immun., 72, 7131–7139CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Krylov, V. N. (2001) Phagotherapy in terms of bacteriophage genetics: hopes, perspectives, safety, limitations. Genetika, 37, 869–887PubMedGoogle Scholar
  52. 52.
    Jerne, N. K. and Avegno, P. (1956) The development of the phageinactivating properties of serum during the course of specific immunization of an animal: reversible and irreversible inactivation. J. Immunol., 76, 200–208PubMedGoogle Scholar
  53. 53.
    Hodyra-Stefaniak, K., Miernikiewicz, P., Drapała, J., Drab, M., Jończyk-Matysiak, E., Lecion, D., Kaźmierczak, Z., Beta, W., Majewska, J., Harhala, M., et al. (2015) Mammalian Host-Versus-Phage immune response determines phage fate in vivo. Sci. Rep., 5, 14802CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    Sokoloff, A. V., Zhang, G., Sebestyén, M. G. and Wolff, J. A. (2000) The interactions of peptides with the innate immune system studied with use of T7 phage peptide display. Mol. Ther., 2, 131–139CrossRefPubMedGoogle Scholar
  55. 55.
    Merril, C. R., Biswas, B., Carlton, R., Jensen, N. C., Creed, G. J., Zullo, S. and Adhya, S. (1996) Long-circulating bacteriophage as antibacterial agents. Proc. Natl. Acad. Sci. USA, 93, 3188–3192CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Vitiello, C. L., Merril, C. R. and Adhya, S. (2005) An amino acid substitution in a capsid protein enhances phage survival in mouse circulatory system more than a 1000-fold. Virus Res., 114, 101–103CrossRefPubMedGoogle Scholar
  57. 57.
    Capparelli, R., Ventimiglia, I., Roperto, S., Fenizia, D. and Iannelli, D. (2006) Selection of an Escherichia coli O157:H7 bacteriophage for persistence in the circulatory system of mice infected experimentally. Clin. Microbiol. Infect., 12, 248–253CrossRefPubMedGoogle Scholar
  58. 58.
    Capparelli, R., Parlato, M., Borriello, G., Salvatore, P. and Iannelli, D. (2007) Experimental phage therapy against Staphylococcus aureus in mice. Antimicrob. Agents Chemother., 51, 2765–2773CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Łusiak-Szelachowska, M., Żaczek, M., Weber-Dąbrowska, B., Międzybrodzki, R., Kłak, M., Fortuna, W., Letkiewicz, S., Rogóż, P., Szufnarowski, K., Jończyk-Matysiak, E., et al. (2014) Phage neutralization by sera of patients receiving phage therapy. Viral Immunol., 27, 295–304CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Loc-Carrillo, C. and Abedon, S. T. (2011) Pros and cons of phage therapy. Bacteriophage, 1, 111–114CrossRefPubMedPubMedCentralGoogle Scholar
  61. 61.
    Hagens, S. and Bläsi, U. (2003) Genetically modified filamentous phage as bactericidal agents: a pilot study. Lett. Appl. Microbiol., 37, 318–323CrossRefPubMedGoogle Scholar
  62. 62.
    Hagens, S., Habel, A., von Ahsen, U., von Gabain, A. and Bläsi, U. (2004) Therapy of experimental pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob. Agents Chemother., 48, 3817–3822CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Matsuda, T., Freeman, T. A., Hilbert, D. W., Duff, M., Fuortes, M., Stapleton, P. P. and Daly, J. M. (2005) Lysis-deficient bacteriophage therapy decreases endotoxin and inflammatory mediator release and improves survival in a murine peritonitis model. Surgery, 137, 639–646CrossRefPubMedGoogle Scholar
  64. 64.
    Westwater, C., Kasman, L. M., Schofield, D. A., Werner, P. A., Dolan, J. W., Schmidt, M. G. and Norris, J. S. (2003) Use of genetically engineered phage to deliver antimicrobial agents to bacteria: an alternative therapy for treatment of bacterial infections. Antimicrob. Agents Chemother., 47, 1301–1307CrossRefPubMedPubMedCentralGoogle Scholar
  65. 65.
    Moradpour, Z., Sepehrizadeh, Z., Rahbarizadeh, F., Ghasemian, A., Yazdi, M. T. and Shahverdi, A. R. (2009) Genetically engineered phage harbouring the lethal catabolite gene activator protein gene with an inducer-independent promoter for biocontrol of Escherichia coli. FEMS Microbiol. Lett., 296, 67–71CrossRefPubMedGoogle Scholar
  66. 66.
    Kasman, L. M., Kasman, A., Westwater, C., Dolan, J., Schmidt, M. G. and Norris, J. S. (2002) Overcoming the phage replication threshold: a mathematical model with implications for phage therapy. J. Virol., 76, 5557–5564CrossRefPubMedPubMedCentralGoogle Scholar
  67. 67.
    Krom, R. J., Bhargava, P., Lobritz, M. A. and Collins, J. J. (2015) Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Lett., 15, 4808–4813CrossRefPubMedGoogle Scholar
  68. 68.
    Tamma, P. D., Cosgrove, S. E. and Maragakis, L. L. (2012) Combination therapy for treatment of infections with gram-negative bacteria. Clin. Microbiol. Rev., 25, 450–470CrossRefPubMedPubMedCentralGoogle Scholar
  69. 69.
    Gaj, T., Gersbach, C. A. and Barbas, C. F. III (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol., 31, 397–405CrossRefPubMedPubMedCentralGoogle Scholar
  70. 70.
    Citorik, R. J., Mimee, M. and Lu, T. K. (2014) Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat. Biotechnol., 32, 1141–1145CrossRefPubMedPubMedCentralGoogle Scholar
  71. 71.
    Bikard, D., Euler, C., Jiang, W., Nussenzweig, P. M., Goldberg, G. W., Duportet, X., Fischetti, V. A. and Marraffini, L. A. (2014) Development of sequence-specific antimicrobials based on programmable CRISPRCas nucleases. Nat. Biotechnol., 32, 1146–1150CrossRefPubMedPubMedCentralGoogle Scholar
  72. 72.
    Yosef, I., Manor, M., Kiro, R. and Qimron, U. (2015) Temperate and lytic bacteriophages programmed to sensitize and kill antibioticresistant bacteria. Proc. Natl. Acad. Sci. USA, 112, 7267–7272CrossRefPubMedPubMedCentralGoogle Scholar
  73. 73.
    Yacoby, I., Bar, H. and Benhar, I. (2007) Targeted drug-carrying bacteriophages as antibacterial nanomedicines. Antimicrob. Agents Chemother., 51, 2156–2163CrossRefPubMedPubMedCentralGoogle Scholar
  74. 74.
    Lu, T. K. and Collins, J. J. (2009) Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. USA, 106, 4629–4634CrossRefPubMedPubMedCentralGoogle Scholar
  75. 75.
    Edgar, R., Friedman, N., Molshanski-Mor, S. and Qimron, U. (2012) Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl. Environ. Microbiol., 78, 744–751CrossRefPubMedPubMedCentralGoogle Scholar
  76. 76.
    Libis, V. K., Bernheim, A. G., Basier, C., Jaramillo-Riveri, S., Deyell, M., Aghoghogbe, I., Atanaskovic, I., Bencherif, A. C., Benony, M., Koutsoubelis, N., et al. (2014) Silencing of antibiotic resistance in E. coli with engineered phage bearing small regulatory RNAs. ACS Synth. Biol., 3, 1003–1006CrossRefPubMedGoogle Scholar
  77. 77.
    Bárdy, P., Pantůček, R., Benešík, M. and Doškař, J. (2016) Genetically modified bacteriophages in applied microbiology. J. Appl. Microbiol., 121, 618–633CrossRefPubMedGoogle Scholar
  78. 78.
    Frey, J. (2007) Biological safety concepts of genetically modified live bacterial vaccines. Vaccine, 25, 5598–5605CrossRefPubMedGoogle Scholar
  79. 79.
    http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm293952.htmGoogle Scholar
  80. 80.
    http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Public_assessment_report/human/002617/WC500158413.pdfGoogle Scholar

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OPEN ACCESS This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • Russell Brown
    • 1
    • 2
  • Andreas Lengeling
    • 3
  • Baojun Wang
    • 1
    • 2
  1. 1.School of Biological SciencesUniversity of EdinburghEdinburghUK
  2. 2.Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
  3. 3.Infection and Immunity Division, The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK

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