Team:Edinburgh OG/Model:References

PhagED: a molecular toolkit to re-sensitise ESKAPE pathogens

Model: References

During the development of our model we used an extensive list of scientific literature on the topic of bacteria-phage interactions. The list presented below includes nearly all available literature on this topic up until August 2017. We hope this will serve as a good resource for anyone who wants to tap into this fascinating topic.

Aidelberg, G. et al. (2014) ‘Hierarchy of non-glucose sugars in Escherichia coli.’, BMC systems biology. BioMed Central, 8, p. 133. doi: 10.1186/s12918-014-0133-z.

Bikard, D. et al. (2014) ‘Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials’, Nature Biotechnology. Nature Publishing Group, 32(11), pp. 1146–1150. doi: 10.1038/nbt.3043.

Cairns, B. J. et al. (2009) ‘Quantitative models of in vitro bacteriophage-host dynamics and their application to phage therapy’, PLoS Pathogens, 5(1), pp. 1–10. doi: 10.1371/journal.ppat.1000253.

Campbell, A. (1961) ‘Conditions for the Existence of Bacteriophage’, Evolution. Society for the Study of Evolution, 15(2), p. 153. doi: 10.2307/2406076.

Carletti, M. (2002) ‘On the stability properties of a stochastic model for phage-bacteria interaction in open marine environment’, Mathematical Biosciences, 175(2), pp. 117–131. doi: 10.1016/S0025-5564(01)00089-X.

Carletti, M. (2007) ‘Mean-square stability of a stochastic model for bacteriophage infection with time delays’, Mathematical Biosciences, 210(2), pp. 395–414. doi: 10.1016/j.mbs.2007.05.009.

Citorik, R. J., Mimee, M. and Lu, T. K. (2014) ‘Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases’, Nature Biotechnology. Nature Publishing Group, 32(11), pp. 1141–1145. doi: 10.1038/nbt.3011.

Clokie, M. R. et al. (2011) ‘Phages in nature.’, Bacteriophage. Taylor & Francis, 1(1), pp. 31–45. doi: 10.4161/bact.1.1.14942.

Cooper, C. J., Mirzaei, M. K. and Nilsson, A. S. (2016) ‘Adapting drug approval pathways for bacteriophage-based therapeutics’, Frontiers in Microbiology. Frontiers Media SA, p. 1209. doi: 10.3389/fmicb.2016.01209.

Davies, J. and Davies, D. (2010) ‘Origins and evolution of antibiotic resistance.’, Microbiology and molecular biology reviews : MMBR. American Society for Microbiology, 74(3), pp. 417–33. doi: 10.1128/MMBR.00016-10.

Demerec, M. and Fano, U. (1945) ‘Bacteriophage-Resistant Mutants in Escherichia Coli.’, Genetics, 30(2), pp. 119–36. Available at: (Accessed: 17 August 2017).

Deng, L. et al. (2014) ‘Grazing of heterotrophic flagellates on viruses is driven by feeding behaviour’, Environmental Microbiology Reports, 6(4), pp. 325–330. doi: 10.1111/1758-2229.12119.

Droste, R. L. (1998) ‘Endogenous decay and bioenergetics theory for aerobic wastewater treatment’, Water Research, 32(2), pp. 410–418. doi: 10.1016/S0043-1354(97)00281-9.

Edgar, R. et al. (2012) ‘Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes.’, Applied and environmental microbiology. American Society for Microbiology, 78(3), pp. 744–51. doi: 10.1128/AEM.05741-11.

Ellis, E. L., Delbrück, M. and Delbruck, M. (1939) ‘The Growth of Bacteriophage.’, The Journal of general physiology, 22(3), pp. 365–84. doi: 10.1085/jgp.22.3.365.

Gadagkar, R. and Gopinathan, K. P. (1980) ‘Bacteriophage burst size during multiple infections’, Journal of Biosciences, 2(3), pp. 253–259. doi: 10.1007/BF02703251.

Hansen, S. R. and Hubbell, S. P. (1980) ‘Single-Nutrient Microbial Competition: Qualitative Agreement between Experimental and Theoretically Forecast Outcomes’, Science, New Series, 207(4438), pp. 1491–1493. Available at: (Accessed: 3 August 2017).

Howard-Varona, C. et al. (2017) ‘Lysogeny in nature: mechanisms, impact and ecology of temperate phages’, The ISME Journal. Nature Publishing Group, 11(7), pp. 1511–1520. doi: 10.1038/ismej.2017.16.

Hsu, S. B., Hubbell, S. and Waltman, P. (1977) ‘A Mathematical Theory for Single-Nutrient Competition in Continuous Cultures of Micro-Organisms’, SIAM Journal on Applied Mathematics, 32(2), pp. 366–383. doi: 10.1137/0132030.

Jones, D. A. and Smith, H. L. (2011) ‘Bacteriophage and acteria in a flow reactor’, Bulletin of Mathematical Biology. Springer-Verlag, 73(10), pp. 2357–2383. doi: 10.1007/s11538-010-9626-0.

Khairalla, A. S., Wasfi, R. and Ashour, H. M. (2017) ‘Carriage frequency, phenotypic, and genotypic characteristics of methicillin-resistant Staphylococcus aureus isolated from dental health-care personnel, patients, and environment’, Scientific Reports, 7(1), p. 7390. doi: 10.1038/s41598-017-07713-8.

Krysiak-Baltyn, K. et al. (2016) ‘Computational models of populations of bacteria and lytic phage’, Critical Reviews in Microbiology, 42(6), pp. 942–968. doi: 10.3109/1040841X.2015.1114466.

Kumada, K., Koike, K. and Fujiwara, K. (1985) ‘The Survival of Bacteria under Starvation Conditions: a Mathematical Expression of Microbial Death’, Journal of General Microbiology. Microbiology Society, 131(9), pp. 2309–2312. doi: 10.1099/00221287-131-9-2309.

Laxminarayan, R. et al. (2016) ‘Antibiotic Resistance in India: Drivers and Opportunities for Action’, PLOS Medicine. Public Health Foundation of India, 13(3), p. e1001974. doi: 10.1371/journal.pmed.1001974.

Lenski, R. E. and Levin, B. R. (1985) ‘Constraints on the Coevolution of Bacteria and Virulent Phage : A Model , Some Experiments , and Predictions for Natural Communities’, The American Naturalist, 125(4), pp. 585–602.

Levin, B. R., Stewart, F. M. and Chao, L. (1977) ‘Resource-Limited Growth, Competition, and Predation: A Model and Experimental Studies with Bacteria and Bacteriophage’, The American Naturalist. University of Chicago Press, 111(977), pp. 3–24. doi: 10.1086/283134.

Ling, L. L. et al. (2015) ‘A new antibiotic kills pathogens without detectable resistance’, Nature, 520(7547), pp. 388–388. doi: 10.1038/nature14303.

Maffioli, S. I. et al. (2017) ‘Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase’, Cell, 169(7), p. 1240–1248.e23. doi: 10.1016/j.cell.2017.05.042.

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Mazel, D. and Davies, J. (1999) ‘Antibiotic resistance in microbes’, CMLS, Cell. Mol. Life Sci, 56, pp. 742–754. Available at: (Accessed: 11 July 2017).

Meyenburg, K. Von (1971) ‘Transport-Limited Growth Rates in a Mutant of Escherichia coli’, Journal of Bacteriology, 107(3), pp. 878–888. Available at: (Accessed: 7 August 2017).

Monod, J. (1949) ‘The Growth of Bacterial Cultures’, Annual Review of Microbiology.  Annual Reviews  4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA  , 3(1), pp. 371–394. doi: 10.1146/annurev.mi.03.100149.002103.

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Nguyen, H. M. and Kang, C. (2014) ‘Lysis delay and burst shrinkage of coliphage T7 by deletion of terminator Tφ reversed by deletion of early genes.’, Journal of virology. American Society for Microbiology (ASM), 88(4), pp. 2107–15. doi: 10.1128/JVI.03274-13.

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Poccia, M. E., Beccaria, A. J. and Dondo, R. G. (2014) ‘Modeling the microbial growth of two escherichia coli strains in a multi-substrate environment’, Brazilian Journal of Chemical Engineering. Associação Brasileira de Engenharia Química, 31(2), pp. 347–354. doi: 10.1590/0104-6632.20140312s00002587.

Qiu, Z. (2007) ‘The analysis and regulation for the dynamics of a temperate bacteriophage model’, Mathematical Biosciences, 209(2), pp. 417–450. doi: 10.1016/j.mbs.2007.02.005.

Rastogi, R. P. et al. (2010) ‘Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair.’, Journal of nucleic acids. Hindawi, 2010, p. 592980. doi: 10.4061/2010/592980.

Reardon, S. (2015) ‘Antibiotic alternatives rev up bacterial arms race’, Nature, 521(7553), pp. 402–403. doi: 10.1038/521402a.

Robledo, I. E., Aquino, E. E. and Vázquez, G. J. (2011) ‘Detection of the KPC gene in Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii during a PCR-based nosocomial surveillance study in Puerto Rico’, Antimicrobial Agents and Chemotherapy. American Society for Microbiology, 55(6), pp. 2968–2970. doi: 10.1128/AAC.01633-10.

Shao, Y. and Wang, I. N. (2009) ‘Effect of late promoter activity on bacteriophage lambda fitness’, Genetics, 181(4), pp. 1467–1475. doi: 10.1534/genetics.108.098624.

Smith, H. L. and Thieme, H. R. (2012) ‘Mathematical Biology Persistence of bacteria and phages in a chemostat’, J. Math. Biol, 64, pp. 951–979. doi: 10.1007/s00285-011-0434-4.

Smith, H. L. and Trevino, R. T. (2009) ‘Bacteriophage Infection Dynamics: Multiple Host Binding Sites’, Mathematical Modelling of Natural Phenomena. EDP Sciences, 4(6), pp. 109–134. doi: 10.1051/mmnp/20094604.

Stokes, H. W., Elbourne, L. D. H. and Hall, R. M. (2007) ‘Tn1403, a multiple-antibiotic resistance transposon made up of three distinct transposons.’, Antimicrobial agents and chemotherapy. American Society for Microbiology (ASM), 51(5), pp. 1827–9. doi: 10.1128/AAC.01279-06.

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Wang, I.-N., Dykhuizen, D. E. and Slobodkin, L. B. (1996) ‘The evolution of phage lysis timing’, Evolutionary Ecology. Kluwer Academic Publishers, 10(5), pp. 545–558. doi: 10.1007/BF01237884.

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Yosef, I. et al. (2015) ‘Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria’, Proceedings of the National Academy of Sciences, 112(23), pp. 7267–7272. doi: 10.1073/pnas.1500107112.