fmicb-11-01171 June 1, 2020 Time: 18:7 # 7
Pirnay Phage Therapy in 2035
Some parts of the proposed system, such as cell free production
of synthetic phages using a bedside device, have a reasonable
chance of being realized, while other elements, such as
corporate sponsorship, will likely remain limited to the
realm of science fiction. You may say that I’m a dreamer,
so feel free to wake me up in 2035 to confront me
with reality!
AUTHOR CONTRIBUTIONS
J-PP conceived the vision and drafted the manuscript.
FUNDING
Publication costs were covered by “Société Scientifique du
Service Médical Militaire – Wetenschappelijke Vereniging van de
Militaire Medische Dienst”.
ACKNOWLEDGMENTS
The personal vision, or dream, developed in this manuscript
came about as a result of interactions with many fellow
researchers over the past 15 years. It is impossible to name
them all, but it would not be fair to take all the credits alone.
Therefore, I decided to acknowledge some of them here (in
alphabetical order), with the risk—or better, the certainty—
of forgetting some important influencers: Joana Azeredo, Nata
Bakuradze, Bob Blasdel, Dimitri Boeckaerts, Angus Buckling,
Yves Briers, Pieter-Jan Ceyssens, Nina Chanishvili, Laurent
Debarbieux, Sarah Djebara, Dorien Dams, Daniel De Vos,
Quirin Emslander, Alan Fauconnier, Ville Friman, Andrzej
Górski, Téa Glonti, Nino Grdzelishvili, Serge Jennes, Elene
Kakabadze, Betty Kutter, Rob Lavigne, Cédric Lood, Alice
Maestri, Khatuna Makalatia, Maya Merabishvili, Tobi Nagel,
Thomas Rose, Patrick Soentjens, Michiel Stock, Rüdiger Trojok,
An Van den Bossche, Mario Vaneechoutte, Gilbert Verbeken,
and Kilian Vogele.
REFERENCES
American Academy of Microbiology (2016). Applications of Clinical Microbial
Next-Generation Sequencing: Report on an American Academy of Microbiology
Colloquium Held in Washington, DC, in April 2015. Washington, DC: American
Society for Microbiology.
Amgarten, D., Braga, L. P. P., da Silva, A. M., and Setubal, J. C. (2018). MARVEL,
a tool for prediction of bacteriophage sequences in metagenomic bins. Front.
Genet. 9:304. doi: 10.3389/fgene.2018.00304
Ando, H., Lemire, S., Pires, D. P., and Lu, T. K. (2015). Engineering modular
viral scaffolds for targeted bacterial population editing. Cell. Syst. 1, 187–196.
doi: 10.1016/j.cels.2015.08.013
Barbu, E. M., Cady, K. C., and Hubby, B. (2016). Phage therapy in the era of
synthetic biology. Cold Spring Harb. Perspect. Biol. 8:a023879. doi: 10.1101/
cshperspect.a023879
Brown, R., Lengeling, A., and Wang, B. (2017). Phage engineering: how advances
in molecular biology and synthetic biology are being utilized to enhance the
therapeutic potential of bacteriophages. Quant. Biol 5, 42–54.
Buckling, A., and Rainey, P. B. (2002). Antagonistic coevolution between a
bacterium and a bacteriophage. Proc. Biol. Sci. 269, 931–936. doi: 10.1098/rspb.
2001.1945
Cassini, A., Högberg, L. D., Plachouras, D., Quattrocchi, A., Hoxha, A., Simonsen,
G. S., et al. (2019). Attributable deaths and disability-adjusted life-years caused
by infections with antibiotic-resistant bacteria in the EU and the European
Economic Area in 2015: a population-level modelling analysis. Lancet Infect.
Dis. 19, 56–66. doi: 10.1016/S1473-3099(18)30605-4
Dedrick, R. M., Guerrero-Bustamante, C. A., Garlena, R. A., Russell, D. A., Ford,
K., Harris, K., et al. (2019). Engineered bacteriophages for treatment of a patient
with a disseminated drug-resistant Mycobacterium abscessus. Nat. Med. 25,
730–733. doi: 10.1038/s41591-019-0437-z
Dunne, M., Rupf, B., Tala, M., Qabrati, X., Ernst, P., Shen, Y., et al. (2019).
Reprogramming bacteriophage host range through structure-guided design of
chimeric receptor binding proteins. Cell Rep. 29, 1336.e4–1350.e4. doi: 10.1016/
j.celrep.2019.09.062
Expert round table on acceptance and re-implementation of bacteriophage therapy,
Sybesma, W., Rohde, C., Bardy, P., Pirnay, J.-P., Cooper, I., et al. (2018). Silk
route to the acceptance and re-implementation of bacteriophage therapy-part
II. Antibiotics 7:E35. doi: 10.3390/antibiotics7020035
Fortuna, M. A., Barbour, M. A., Zaman, L., Hall, A. R., Buckling, A., and
Bascompte, J. (2019). Coevolutionary dynamics shape the structure of bacteria-
phage infection networks. Evolution 73, 1001–1011. doi: 10.1111/evo.13731
Friman, V. P., Soanes-Brown, D., Sierocinski, P., Molin, S., Johansen, H. K.,
Merabishvili, M., et al. (2016). Pre-adapting parasitic phages to a pathogen
leads to increased pathogen clearance and lowered resistance evolution with
Pseudomonas aeruginosa cystic fibrosis bacterial isolates. J. Evol. Biol. 29,
188–198. doi: 10.1111/jeb.12774
Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A. III,
and Smith, H. O. (2009). Enzymatic assembly of DNA molecules up to
several hundred kilobases. Nat. Methods 6, 343–345. doi: 10.1038/nmeth.
1318
Hwang, I. Y., Lee, H. L., Huang, J. G., Lim, Y. Y., Yew, W. S., Lee, Y. S., et al. (2018).
Engineering microbes for targeted strikes against human pathogens. Cell Mol.
Life. Sci. 75, 2719–2733. doi: 10.1007/s00018-018-2827-7
Jault, P., Leclerc, T., Jennes, S., Pirnay, J. P., Que, Y.-A., Resch, G., et al. (2019).
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds
infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled,
double-blind phase 1/2 trial. Lancet Infect. Dis. 19, 35–45. doi: 10.1016/S1473-
3099(18)30482-1
Jernberg, C., Löfmark, S., Edlund, C., and Jansson, J. K. (2010). Long-term impacts
of antibiotic exposure on the human intestinal microbiota. Microbiology 156,
3216–3223. doi: 10.1099/mic.0.040618-0
Joñczyk-Matysiak, E., Kłak, M., Weber-Da¸browska, B., Borysowski, J., and Górski,
A. (2014). Possible use of bacteriophages active against Bacillus anthracis and
other B. cereus group members in the face of a bioterrorism threat. Biomed. Res.
Int. 2014:735413. doi: 10.1155/2014/735413
Kilcher, S., Studer, P., Muessner, C., Klumpp, J., and Loessner, M. J. (2018).
Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in
L-form bacteria. Proc. Natl. Acad. Sci. U.S.A. 115, 567–572. doi: 10.1073/pnas.
1714658115
Lemire, S., Yehl, K. M., and Lu, T. K. (2018). Phage-based applications in synthetic
biology. Annu. Rev. Virol. 5, 453–476. doi: 10.1146/annurev-virology-092917-
043544
Luria, S. E., and Delbrück, M. (1943). Mutations of bacteria from virus sensitivity
to virus resistance. Genetics 28, 491–511.
Martorell-Marugán, J., Tabik, S., Benhammou, Y., del Val, C., Zwir, I., Herrera, F.,
et al. (2019). “Deep learning in omics data analysis and precision medicine,”
in Computational Biology, ed. H. Husi (Brisbane: Codon Publications), 37–53.
doi: 10.15586/computationalbiology.2019.ch3
Merabishvili, M., De Vos, D., Verbeken, G., Kropinski, A. M., Vandenheuvel,
D., Lavigne, R., et al. (2012). Selection and characterization of a candidate
therapeutic bacteriophage that lyses the Escherichia coli O104:H4 strain from
the 2011 outbreak in Germany. PLoS One 7:e52709. doi: 10.1371/journal.pone.
0052709
Miêdzybrodzki, R., Borysowski, J., Weber-Da¸browska, B., Fortuna, W., Letkiewicz,
S., Szufnarowski, K., et al. (2012). Clinical aspects of phage therapy. Adv. Virus
Res. 83, 73–121. doi: 10.1016/B978-0-12-394438-2.00003-7
Frontiers in Microbiology | www.frontiersin.org 7 June 2020 | Volume 11 | Article 1171