Modeling antibiotic resistance in bacterial colonies using agent-based approach

Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology

Volumn , Issue , 2011, Pages 131-154

  Murphy, James T ^a   Walshe, Ray ^a  

^a DUBLIN CITY UNIVERSITY   (Ireland)

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[No Author keywords available]

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EID: 84866846493     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-7964-3_7     Document Type: Chapter

References (47)

1. E. P. Abraham and E. Chain. An enzyme from bacteria able to destroy penicillin. Nature, 146:837, 1940
2. P. G. Ambrose, S.M. Bhavnani, C.M. Rubino, A. Louie, T. Gumbo, A. Forrest, and G. L. Drusano. Pharmacokinetics-pharmacodynamics of antimicrobial therapy: its not just for mice anymore. Clinical Infectious Diseases, 44(1):79-86, 2007
3. E. Ben-Jacob, O. Schochet, A. Tenenbaum, I. Cohen, A. Czirok, and T. Vicsek. Generic modeling of cooperative growth patterns in bacterial colonies. Nature, 368(6466):46-49, 1994
4. A. Bondi and C. C. Dietz. Penicillin resistant staphylococci. Proceedings of the Society for Experimental Biology and Medicine, 60(1):55-58, 1945
5. E. Chain, H. W. Florey, M. B. Adelaide, A. D. Gardner, N. G. Heatley, M. A. Jennings, J. Orr- Ewing, and A. G. Sanders. Penicillin as a chemotherapeutic agent. 1940. Clinical Orthopaedics and Related Research, 295:3-7, 1993
6. H. F. Chambers, M. J. Sachdeva, and C. J. Hackbarth. Kinetics of penicillin binding to penicillinbinding proteins of Staphylococcus aureus. The Biochemical Journal, 301(Pt 1):139-144, 1994
7. D. A. Devine. Cationic antimicrobial peptides in regulation of commensal and pathogenic microbial populations. Mammalian Host Defense Peptides, pages 9-39, 2004
8. A. Elfwing, Y. LeMarc, J. Baranyi, and A. Ballagi. Observing growth and division of large numbers of individual bacteria by image analysis. Applied and Environmental Microbiology, 70(2): 675-678, 2004
9. M. Ender, N. McCallum, R. Adhikari, and B. Berger-Bachi. Fitness cost of sccmec and methicillin resistance levels in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 48(6): 2295-2297, 2004
10. K. R. Eriksen. Celbenin-resistant staphylococci. Ugeskrift for laeger, 123:384-386, 1961
11. J. F. Fisher, S. O. Meroueh, and S. Mobashery. Bacterial resistance to beta-lactam antibiotics: compelling opportunism, compelling opportunity. Chemical Reviews, 105(2):395-424, 2005
12. C. Fuda, M. Suvorov, S. B. Vakulenko, and S. Mobashery. The basis for resistance to beta-lactam antibiotics by penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus. The Journal of Biological Chemistry, 279(39):40802-40806, 2004
13. C. C. Fuda, J. F. Fisher, and S. Mobashery. Beta-lactam resistance in Staphylococcus aureus: the adaptive resistance of a plastic genome. Cellular and Molecular Life Sciences, 62(22): 2617-2633, 2005
14. M. Gardner. Mathematical games: The fantastic combinations of john conways new solitaire game life. Scientific American, 223(4):120-123, 1970
15. P. Giesbrecht, T. Kersten, H. Maidhof, and J. Wecke. Staphylococcal cell wall: morphogenesis and fatal variations in the presence of penicillin. Microbiology and Molecular Biology Reviews, 62 (4):1371-1414, 1998
16. M. Ginovart, D. Lopez, and J. Valls. Indisim, an individual-based discrete simulation model to study bacterial cultures. Journal of Theoretical Biology, 214(2):305-319, 2002
17. K. Graves-Woodward and R. F. Pratt. Reaction of soluble penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus with beta-lactams and acyclic substrates: kinetics in homogeneous solution. The Biochemical Journal, 332(3):755-761, 1998
18. V. Grimm. Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future? Ecological modelling, 115(2-3):129-148, 1999
19. M. J. Grimson and G. C. Barker. Continuum model for the spatiotemporal growth of bacterial colonies. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 49(2):1680-1684, 1994
20. L. L. Guan and K. Kamino. Bacterial response to siderophore and quorum-sensing chemical signals in the seawater microbial community. BMC Microbiology, 1:27, 2001
21. N. R. Jennings, K. Sycara, and M. J. Wooldridge. A roadmap of agent research and development. Autonomous Agents and Multi-Agent Systems, 1(1):7-38, 1998
22. W. M. M. Kirby. Extraction of a highly potent penicillin inactivator from penicillin resistant staphylococci. Science, 99(2579):452-453, 1944
23. J. U. Kreft, G. Booth, and J. W.Wimpenny. Bacsim, a simulator for individual-based modelling of bacterial colony growth. Microbiology, 144(12):3275-3287, 1998
24. A. M. Lacasta, I. R. Cantalapiedra, C. E. Auguet, A. Penaranda, and L. Ramirez-Piscina. Modeling of spatiotemporal patterns in bacterial colonies. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 59(6):7036-7041, 1999
25. S. B. Levy and B. Marshall. Antibacterial resistance worldwide: causes, challenges and responses. Nature Medicine, 10(12 Suppl):S122-129, 2004
26. R. A. Lewis, S. P. Curnock, and K. G. Dyke. Proteolytic cleavage of the repressor (blai) of betalactamase synthesis in Staphylococcus aureus. FEMS Microbiology Letters, 178(2):271-275, 1999
27. W. P. Lu, Y. Sun, M. D. Bauer, S. Paule, P. M. Koenigs, and W. G. Kraft. Penicillin-binding protein 2a from methicillin-resistant Staphylococcus aureus: kinetic characterization of its interactions with beta-lactams using electrospray mass spectrometry. Biochemistry, 38(20): 6537-6546, 1999
28. F. Malouin, J. Blais, S. Chamberland, M. Hoang, C. Park, C. Chan, K. Mathias, S. Hakem, K. Dupree, E. Liu, T. Nguyen, and M. N. Dudley. Rwj-54428 (mc-02,479), a new cephalosporin with high affinity for penicillin-binding proteins, including pbp 2a, and stability to staphylococcal beta-lactamases. Antimicrobial Agents and Chemotherapy, 47(2):658-664, 2003
29. W. Materi and D. S. Wishart. Computational systems biology in drug discovery and development: methods and applications. Drug Discovery Today, 12(7-8):295-303, 2007
30. J. T. Murphy and R. Walshe. Micro-gen: an agent-based model of bacteria-antibiotic interactions in batch culture. In Proceedings of the 20th Annual European Simulation and Modelling Conference, pages 239-242. Eurosis-ETI, October 23-25, 2006
31. J. T. Murphy, R. Walshe, and Marc Devocelle. Agent-based model of methicillin-resistant Staphylococcus aureus and antibiotics in batch culture. In Proceedings of 21st Annual European Simulation and Modelling Conference, pages 409-414. Eurosis-ETI, October 20-22, 2007
32. J. T.Murphy, R.Walshe, and M. Devocelle. A computational model of antibiotic-resistance mechanisms in methicillin-resistant Staphylococcus aureus (MRSA). Journal of Theoretical Biology, 254(2):284-293, 2008
33. J. T. Murphy, R. Walshe, and M. Devocelle. Modelling the population dynamics of antibioticresistant bacteria: An agent-based approach. International Journal of Modern Physics C, 20 (3):435-457, 2009
34. H. C. Neu. The crisis in antibiotic resistance. Science, 257(5073):1064-1073, 1992
35. J. B. Nielsen and J. O. Lampen. Membrane-bound penicillinases in gram-positive bacteria. The Journal of Biological Chemistry, 257(8):4490-4495, 1982
36. G. W. Niven, T. Fuks, J. S. Morton, S. A. Rua, and B. M. Mackey. A novel method for measuring lag times in division of individual bacterial cells using image analysis. Journal of Microbiological Methods, 65(2):311-317, 2006
37. S. R. Norris, C. W. Stratton, and D. S. Kernodle. Production of a and c variants of staphylococcal beta-lactamase by methicillin-resistant strains of Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 38(7):1649-1650, 1994
38. R. R. Regoes, C. Wiuff, R. M. Zappala, K. N. Garner, F. Baquero, and B. R. Levin. Pharmacodynamic functions: a multiparameter approach to the design of antibiotic treatment regimens. Antimicrobial Agents and Chemotherapy, 48(10):3670-3676, 2004
39. D. Skinner and C. S. Keefer. Significance of bacteremia caused by Staphylococcus aureus. Archives of Internal Medicine, 68:851-875, 1941
40. S. J. Sorensen, M. Bailey, L. H. Hansen, N. Kroer, and S. Wuertz. Studying plasmid horizontal transfer in situ: a critical review. Nature Reviews Microbiology, 3(9):700-710, 2005
41. M.W. van der Woude and A. J. Baumler. Phase and antigenic variation in bacteria. Clinical microbiology reviews, 17(3):581-611, 2004
42. C. Walsh. Molecular mechanisms that confer antibacterial drug resistance. Nature, 406(6797): 775-781, 2000
43. R. Walshe. Modelling bacterial growth patterns in the presence of antibiotic. In Proceedings of the 11th IEEE International Conference on Engineering of Complex Computer Systems, pages 177-188, Washington, DC, USA, 15-17 August 2006. IEEE Computer Society
44. D. S. Wishart, C. Knox, A. C. Guo, S. Shrivastava, M. Hassanali, P. Stothard, Z. Chang, and J. Woolsey. Drugbank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research, 34(Database issue):D668-672, 2006
45. G. D. Wright. The antibiotic resistome: the nexus of chemical and genetic diversity. Nature Reviews Microbiology, 5(3):175-186, 2007
46. H. Z. Zhang, C. J. Hackbarth, K. M. Chansky, and H. F. Chambers. A proteolytic transmembrane signaling pathway and resistance to beta-lactams in staphylococci. Science, 291(5510): 1962-1965, 2001
47. D. J. Zygmunt, C. W. Stratton, and D. S. Kernodle. Characterization of four beta-lactamases produced by Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 36(2):440-445, 1992