Timing of Pathogen Adaptation to a Multicomponent Treatment

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Bourget, Romain ^a,b   Chaumont, Loïc ^a   Sapoukhina, Natalia ^a,b  

^a UNIVERSITÉ D'ANGERS   (France)

^b Universite d'Angers   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ARTICLE; COMBINATION CHEMOTHERAPY; CULTIVAR; DEATH; DISEASE TRANSMISSION; LIFE CYCLE; MIGRATION; MULTIGENE FAMILY; MUTATION; POPULATION SIZE; PREDICTION; PROBABILITY; STOCHASTIC MODEL;

ADAPTATION, PHYSIOLOGICAL; BIOLOGICAL EVOLUTION; COMBINED MODALITY THERAPY; COMMUNICABLE DISEASES; HOST-PATHOGEN INTERACTIONS; HUMANS; MARKOV CHAINS; MODELS, BIOLOGICAL; MUTATION; STOCHASTIC PROCESSES; TIME FACTORS;

EID: 84882627491     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071926     Document Type: Article

References (57)

1. McDonald BA, Linde C, (2002) Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 40: 349-379.
2. Read AF, Mackinnon MJ (2007) In: Stearns SC, Koella JC, editors, Evolution in Health and Disease, OUP Oxford, Oxford biology, chapter 11.
3. van den Bosch F, Gilligan CA, (2008) Models of fungicide resistance dynamics. Annu Rev Phytopathol 46: 123-147.
4. MacLean RC, Hall AR, Perron GG, Buckling A, (2010) The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nature Rev Genet 11: 405-414.
5. Lipsitch M, Levin BR, (1997) The population dynamics of antimicrobial chemotherapy. Antimicrob Agents Ch 41: 363-73.
6. Dieckmann U, Metz J, Sabelis M, Sigmund K (2005) Adaptive Dynamics of Infectious Diseases: In Pursuit of Virulence Management. Cambridge Studies in Adaptive Dynamics. Cambridge University Press.
7. Hill AVS, (2011) Vaccines against malaria. Philos Trans R Soc Lond B 366: 2806-2814.
8. Bloom BR, Murray CJL, (1992) Tuberculosis: Commentary on a reemergent killer. Science 257: 1055-1064.
9. Boni MF, (2008) Vaccination and antigenic drift in inuenza. Vaccine 26Supplement 3: C8-C14.
10. Mundt CC, (1990) Probability of mutation to multiple virulence and durability of resistance gene pyramids. Phytopathology 80: 221-223.
11. zur Wiesch PA, Kouyos R, Engelstdter J, Regoes RR, Bonhoeffer S, (2011) Population biological principles of drug-resistance evolution in infectious diseases. Lancet Infect Dis 11: 236-247.
12. Bonhoeffer S, Lipsitch M, Levin BR, (1997) Evaluating treatment protocols to prevent antibiotic resistance. Proc Natl Acad Sci USA 94: 12106-12111.
13. van den Bosch F, Gilligan C, (2003) Measures of durability of resistance. Phytopathology 93: 616-25.
14. Gandon S, Day T, (2007) The evolutionary epidemiology of vaccination. J R Soc Interface 4: 803-817.
15. Castle MD, Gilligan CA, (2012) An epidemiological framework for modelling fungicide dynamics and control. PLoS ONE 7: e40941.
16. Débarre F, Lenormand T, Gandon S, (2009) Evolutionary epidemiology of drug-resistance in space. PLoS Comput Biol 5: e1000337.
17. Fabre F, Rousseau E, Mailleret L, Moury B, (2012) Durable strategies to deploy plant resistance in agricultural landscapes. New Phytol 193: 1064-1075.
18. Day T, Gandon S, (2012) The evolutionary epidemiology of multilocus drug resistance. Evolution 66: 1582-97.
19. Bergstrom CT, Lo M, Lipsitch M, (2004) Ecological theory suggests that antimicrobial cycling will not reduce antimicrobial resistance in hospitals. Proc Natl Acad Sci USA 101: 13285-13290.
20. Massad E, Lundberg S, Yang HM, (1993) Modeling and simulating the evolution of resistance against antibiotics. Int J BioMed Comput 33: 65-81.
21. Hermsen R, Hwa T, (2010) Sources and sinks: A stochastic model of evolution in heterogeneous environments. Phys Rev Lett 105: 248104.
22. Rice SH, Papadopoulos A, (2009) Evolution with stochastic fitness and stochastic migration. PLoS ONE 4: e7130.
23. Restif O, Grenfell BT, (2006) Integrating life history and cross-immunity into the evolutionary dynamics of pathogens. Proc R Soc Lond B 273: 409-416.
24. D'Agata EM, Magal P, Olivier D, Ruan S, Webb GF, (2007) Modeling antibiotic resistance in hospitals: The impact of minimizing treatment duration. J Theor Biol 249: 487-499.
25. Reuter GEH (1961) Competition processes. Univ. California Press, volume II of Proc. 4th Berkeley Sympos. Math. Statist. and Prob. 421-430.
26. Phillips PC, (2008) Epistasis the essential role of gene interactions in the structure and evolution of genetic systems. Nature Rev Genet 9: 855-867.
27. Trindade S, Sousa A, Xavier KB, Dionisio F, Ferreira MG, et al. (2009) Positive epistasis drives the acquisition of multidrug resistance. PLoS Genet 5: e1000578.
28. Allen LJ (2003) An Introduction to Stochastic Processes with Biology Applications. Prentice Hall.
29. Bourget R (2013) Modélisation stochastique des processus d'adaptation d'une population de pathogène aux rsistances génétiques des hôtes. Ph.D. thesis, Université d'Angers.
30. Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem-US 81: 2340-2361.
31. Ethier SN, Kurtz TG (2005) Markov processes: characterization and convergence. Wiley series in probability and statistics;Wiley-Interscience paperback series.
32. Novozhilov AS, Karev GP, Koonin EV, (2006) Biological applications of the theory of birth-and-death processes. Brief Bioinform 7: 70-85.
33. Bourget R, Chaumont L, Sapoukhina N (2012) Exponentiality of first passage times of continuous time markov chains. Under revision.
34. Sapoukhina N, Durel CE, Le Cam B, (2009) Spatial deployment of gene-for-gene resistance governs evolution and spread of pathogen populations. Theor Ecol 2: 229-238.
35. Handel A, Regoes RR, Antia R, (2006) The role of compensatory mutations in the emergence of drug resistance. PLoS Comput Biol 2: e137.
36. Rhodes TD, Nikolaitchik O, Chen J, Powell D, Hu WS, (2005) Genetic recombination of human immunodeficiency virus type 1 in one round of viral replication: Effects of genetic distance, target cells, accessory genes, and lack of high negative interference in crossover events. J Virol 79: 1666-1677.
37. Collingham YC, Huntley B, (2000) Impacts of habitat fragmentation and patch size upon migration rates. Ecol Appl 10: 131-144.
38. Otten W, Bailey DJ, Gilligan CA, (2004) Empirical evidence of spatial thresholds to control invasion of fungal parasites and saprotrophs. New Phytol 163: 125-132.
39. Ohtsuki A, Sasaki A, (2006) Epidemiology and disease-control under gene-for-gene plant-pathogen interaction. J Theor Biol 238: 780-794.
40. Suzuki SU, Sasaki A, (2011) How does the resistance threshold in spatially explicit epidemic dy namics depend on the basic reproductive ratio and spatial correlation of crop genotypes? J Theor Biol 276: 117-125.
41. Scherer A, McLean A, (2002) Mathematical models of vaccination. Brit Med Bull 62: 187-199.
42. Michea-Hamzehpour M, Pechere JC, Marchou B, Auckenthaler R, (1986) Combination therapy: a way to limit emergence of resistance? Am J Med 80: 138-142.
43. Anderson N, Martin PJ, Jarrett RG, (1988) Mixtures of anthelmintics: A strategy against resistance. Aust Vet J 65: 62-64.
44. Hooper J, Custer D, Schmaljohn C, Schmaljohn A, (2000) Dna vaccination with vaccinia virus l1r and a33r genes protects mice against a lethal poxvirus challenge. Virology 266: 329-339.
45. Kelly J, Gepts P, Miklas P, Coyne D, (2003) Tagging and mapping of genes and qtl and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crop Res 82: 135-154.
46. Michelmore R, Wong J, (2008) Classical and molecular genetics of bremia lactuca, cause of lettuce downy mildew. Eur J Plant Pathol 122: 19-30.
47. Carriére Y, Tabashnik B, (2001) Reversing insect adaptation to transgenic insecticidal plants. Proc R Soc Lond B 268: 1475-1480.
48. Berkhoff E, de Wit E, Geelhoed-Mieras M, Boon A, Symons J, et al. (2006) Fitness costs limit escape from cytotoxic t lymphocytes by inuenza a viruses. Vaccine 24: 6594-6596.
49. Fabre F, Bruchou C, Palloix A, Moury B, (2009) Key determinants of resistance durability to plant viruses: Insights from a model linking within- and between-host dynamics. Virus Res 141: 140-149.
50. Lannou C, Mundt CC, (1997) Evolution of a pathogen population in host mixtures: rate of emergence of complex races. Theor Appl Genet 94: 991-999.
51. Leach JE, Vera Cruz CM, Bai J, Leung H, (2001) Pathogen fitness penalty as a predictor of durability of disease resistance genes. Annu Rev Phytopathol 39: 187-224.
52. Cuevas JM, Moya A, Sanjuán R, (2005) Following the very initial growth of biological rna viral clones. J Genl Virol 86: 435-443.
53. Ayme V, Souche S, Caranta C, Jacquemond M, Chadoeuf J, et al. (2006) Different mutations in the genome-linked protein vpg of potato virus y confer virulence on the pvr23 resistance in pepper. Mol Plant Microbe Interact 19: 557-563.
54. Carrasco P, Dars J, Agudelo-Romero P, Elena S, (2007) A real-time rt-pcr assay for quantifying the fitness of tobacco etch virus in competition experiments. J Virol Methods 139: 181-188.
55. Labbé P, Sidos N, Raymond M, Lenormand T, (2009) Resistance gene replacement in the mosquito culex pipiens: Fitness estimation from long-term cline series. Genetics 182: 303-312.
56. Kimura M, (1968) Evolutionary rate at the molecular level. Nature 217: 624-626.
57. Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R, (2010) Viral mutation rates. J Virol 84: 9733-9748.