A model-based Bayesian estimation of the rate of evolution of VNTR loci in Mycobacterium tuberculosis

PLoS Computational Biology

Volumn 8, Issue 6, 2012, Pages

  Aandahl, R Zachariah ^a   Reyes, Josephine F ^b   Sisson, Scott A ^a   Tanaka, Mark M ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

TUBES (COMPONENTS);

BAYESIAN ESTIMATIONS; DETAILED MODELS; LINEAR MODELING; MODEL-BASED OPC; MOLECULAR EPIDEMIOLOGY; MUTATION RATES; MYCOBACTERIUM TUBERCULOSIS; POPULATION GENETIC MODELS; TANDEM REPEATS; VARIABLE NUMBER;

BAYESIAN NETWORKS;

ARTICLE; BACTERIUM ISOLATE; BAYESIAN LEARNING; CLADISTICS; DISEASE PREDISPOSITION; DISEASE TRANSMISSION; GENE LOCUS; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HETEROZYGOSITY; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MUTATION RATE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; STATISTICAL MODEL; VARIABLE NUMBER OF TANDEM REPEAT; BAYES THEOREM; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; COMPUTER SIMULATION; EVALUATION; GENETICS; HUMAN; LUNG TUBERCULOSIS; MICROBIOLOGY; MUTATION; NUCLEIC ACID DATABASE; PATHOGENICITY;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

BACTERIAL DNA;

BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, NUCLEIC ACID; DNA, BACTERIAL; EVOLUTION, MOLECULAR; HUMANS; LINEAR MODELS; MINISATELLITE REPEATS; MODELS, GENETIC; MUTATION; MYCOBACTERIUM TUBERCULOSIS; TUBERCULOSIS, PULMONARY;

EID: 84864044587     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002573     Document Type: Article

References (57)

1. World Health Organization (2010) Global tuberculosis control 2010 World Health Organization.
2. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al. (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 6: e311.
3. Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, et al. (2008) Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog 4: e1000160.
4. Pepperell C, Hoeppner V, Lipatov M, Wobeser W, Schoolnik GK, et al. (2010) Bacterial genetic signatures of human social phenomena among M. tuberculosis from an Aboriginal Canadian population. Mol Biol Evol 27: 427-440.
5. Pepperell CS, Granka JM, Alexander DC, Behr MA, Chui L, et al. (2011) Dispersal of Mycobacterium tuberculosis via the Canadian fur trade. Proc Natl Acad Sci U S A 108: 6526-6531.
6. Sails AD, Barrett A, Sarginson S, Magee JG, Maynard P, et al. (2011) Molecular epidemiology of Mycobacterium tuberculosis in East Lancashire 2001-2009. Thorax 66: 709-713.
7. Thierry D, Brisson-Noel A, Vincent-Levy-Frebault V, Nguyen S, Guesdon JL, et al. (1990) Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis. J Clin Microbiol 28: 2668-2673.
8. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, et al. (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35: 907-914.
9. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-Gerdes S, et al. (2006) Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 44: 4498-4510.
10. Oelemann MC, Diel R, Vatin V, Haas W, Rüsch-Gerdes S, et al. (2007) Assessment of an optimized mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis. J Clin Microbiol 45: 691-697.
11. Tazi L, El Baghdadi J, Lesjean S, Locht C, Supply P, et al. (2004) Genetic diversity and population structure of Mycobacterium tuberculosis in Casablanca, a Moroccan city with high incidence of tuberculosis. J Clin Microbiol 42: 461-466.
12. Sola C, Filliol I, Legrand E, Lesjean S, Locht C, et al. (2003) Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol 3: 125-133.
13. Valcheva V, Mokrousov I, Narvskaya O, Rastogi N, Markova N, (2008) Utility of new 24-locus variable-number tandem-repeat typing for discriminating Mycobacterium tuberculosis clinical isolates collected in Bulgaria. J Clin Microbiol 46: 3005-3011.
14. Smittipat N, Billamas P, Palittapongarnpim M, Thong-On A, Temu MM, et al. (2005) Polymorphism of variable-number tandem repeats at multiple loci in My-cobacterium tuberculosis. J Clin Microbiol 43: 5034-5043.
15. Tanaka MM, Francis AR, (2005) Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information. Infect Genet Evol 5: 35-43.
16. Ohta T, Kimura M, (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22: 201-204.
17. Shriver MD, Jin L, Chakraborty R, Boerwinkle E, (1993) VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach. Genetics 134: 983-993.
18. Cornuet JM, Beaumont MA, Estoup A, Solignac M, (2006) Inference on microsatellite mutation processes in the invasive mite, varroa destructor, using reversible jump Markov chain Monte Carlo. Theor Popul Biol 69: 129-144.
19. Grant A, Arnold C, Thorne N, Gharbia S, Underwood A, (2008) Mathematical modelling of Mycobacterium tuberculosis VNTR loci estimates a very slow mutation rate for the repeats. J Mol Evol 66: 565-574.
20. Reyes JF, Tanaka MM, (2010) Mutation rates of spoligotypes and variable number tandem repeat loci in Mycobacterium tuberculosis. Infect Genet Evol 10: 1046-1051.
21. Supply P, Niemann S, Wirth T, (2011) On the mutation rates of spoligotypes and variable numbers of tandem repeat loci of Mycobacterium tuberculosis: Continued when tuning matters. Infect Genet Evol 11: 1191-1191.
22. Supply P, Niemann S, Wirth T, (2011) On the mutation rates of spoligotypes and variable numbers of tandem repeat loci of Mycobacterium tuberculosis. Infect Genet Evol 11: 251-252.
23. Tanaka MM, Reyes JF, et al. (2011) Mutation rate of VNTR loci in Mycobacterium tuberculosis: Response to Supply et al. Infect Genet Evol 11: 1189-1190.
24. Tanaka MM, Reyes JF, (2011) VNTR mutation in Mycobacterium tuberculosis: Lower rates for less variable loci. Infect Genet Evol 11: 1192-1192.
25. Jacquez JA, Simon CP, (1993) The stochastic SI model with recruitment and deaths I. Comparison with the closed SIS model. Math Biosci 117: 77-125.
26. Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
27. Tavare S, Balding DJ, Grifiths RC, Donnelly P, (1997) Inferring coalescence times from DNA sequence data. Genetics 145: 505-518.
28. Beaumont MA, Zhang W, Balding DJ, (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
29. Marjoram P, Molitor J, Plagnol V, Tavaré S, (2003) Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci U S A 100: 15324-15328.
30. Beaumont MA, (2010) Approximate Bayesian computation in evolution and ecology. Ann Rev Ecol Sys 41: 379-406.
31. Bertorelle G, Benazzo A, Mona S, (2010) ABC as a exible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 19: 2609-2625.
32. Luciani F, Sisson SA, Jiang H, Francis AR, Tanaka MM, (2009) The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 106: 14711-14715.
33. Tanaka MM, Francis AR, Luciani F, Sisson SA, (2006) Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data. Genetics 173: 1511-1520.
34. Drovandi CC, Pettitt AN, (2011) Estimation of parameters for macroparasite population evolution using approximate Bayesian computation. Biometrics 67: 225-233.
35. Sisson SA, Fan Y, (2011) Likelihood-free Markov chain Monte Carlo. In: Brooks SP, Gelman A, Jones G, Meng XL, editors. Handbook of Markov chain Monte Carlo Chapman and Hall/CRC Press pp. 319-341.
36. Csillery K, Blum MGB, Gaggiotti OE, Francois O, (2010) Approximate Bayesian computation (ABC) in practice. Trends Ecol Evol 25: 410-418.
37. Cohen T, Murray M, (2004) Modeling epidemics of multidrug-resistant M. tubercu-losis of heterogeneous fitness. Nat Med 10: 1117-1121.
38. Blower S, Mclean A, Porco T, Small P, Hopewell P, et al. (1995) The intrinsic transmission dynamics of tuberculosis epidemics. Nat Med 1: 815-821.
39. Sisson SA, Fan Y, Tanaka MM, (2007) Sequential Monte Carlo without likelihoods. Proc Natl Acad Sci U S A 104: 1760-1765 Errata (2009), 106, 16889.
40. Peters GW, Fan Y, Sisson SA, (2012) On sequential Monte Carlo, partial rejection control and approximate Bayesian computation. Stat Comput: in press.
41. Fearnhead P, Prangle D, (2012) Constructing summary statistics for approximate Bayesian computation: Semi-automatic ABC. J Roy Stat Soc B 74: 419-474.
42. Tafaj S, Zhang J, Hauck Y, Pourcel C, Hafizi H, et al. (2009) First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of Beijing multidrug-resistant isolates. J Clin Microbiol 47: 1581-1584.
43. Asgharzadeh M, Khakpour M, Salehi TZ, Kafil HS, (2007) Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to study Mycobacterium tuberculosis isolates from East Azarbaijan province of Iran. Pak J Biol Sci 10: 3769-3777.
44. Abadía E, Sequera M, Ortega D, Méndez M, Escalona A, et al. (2009) Mycobacterium tuberculosis ecology in Venezuela: epidemiologic correlates of common spoligotypes and a large clonal cluster defined by MIRU-VNTR-24. BMC Infect Dis 9: 122-134.
45. Nei M, (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A 70: 3321-3323.
46. Gelman A, Meng XL, Stern HS, (1996) Posterior predictive assessment of model fitness via realized discrepancies. Stat Sinica 6: 733-807.
47. Thornton K, Andolfatto P, (2006) Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
48. Reyes JF, Chan CHS, Tanaka MM, (2012) Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. Infect Genet Evol 12: 811-818.
49. Buard J, Bourdet A, Yardley J, Dubrova Y, Jeffreys A, (1998) Inuences of array size and homogeneity on minisatellite mutation. EMBO J 17: 3495-3502.
50. Dieringer D, Schlötterer C, (2003) Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res 13: 2242-2251.
51. Lai Y, Sun F, (2003) The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol Biol Evol 20: 2123-2131.
52. Kelkar Y, Tyekucheva S, Chiaromonte F, Makova K, (2008) The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 18: 30-38.
53. Seyfert A, Cristescu M, Frisse L, Schaack S, Thomas W, et al. (2008) The rate and spectrum of microsatellite mutation in Caenorhabditis elegans and Daphnia pulex. Genetics 178: 2113-2121.
54. Bazin E, Dawson KJ, Beaumont MA, (2010) Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical model. Genetics 185: 587-602.
55. Ewens WJ, (1972) The sampling theory of selectively neutral alleles. Theor Popul Biol 3: 87-112.
56. Blum MGB, Nunes MA, Prangle D, Sisson SA, (2012) A comparative review of dimension reduction methods in approximate Bayesian computation. http://arxiv.org/abs/1202.3819.
57. World Health Organization (2009) Tuberculosis Country Profiles: Epidemiology and Strategy. http://www.who.int/tb/country/data/profiles/en/index.html.