Estimating the Transmission Dynamics of Streptococcus pneumoniae from Strain Prevalence Data

Biometrics

Volumn 69, Issue 3, 2013, Pages 748-757

  Numminen, Elina ^a   Cheng, Lu ^a   Gyllenberg, Mats ^a   Corander, Jukka ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b ÅBO AKADEMI UNIVERSITY   (Finland)

Author keywords

Bayesian inference; Continuous time Markov chains; Epidemiology; Multi strain models; Transmission dynamics

Indexed keywords

BAYESIAN NETWORKS; CONTINUOUS TIME SYSTEMS; DYNAMICS; INFERENCE ENGINES; MARKOV PROCESSES; STRAIN;

APPROXIMATE BAYESIAN; BAYESIAN COMPUTATION; BAYESIAN INFERENCE; CONTINOUS TIME MARKOV CHAIN; HIGH RATE; METROPOLITAN AREA; MULTI-STRAIN MODELS; STREPTOCOCCUS PNEUMONIAE; TRANSMISSION DYNAMICS; YOUNG CHILDREN;

EPIDEMIOLOGY;

BACTERIAL DISEASE; BAYESIAN ANALYSIS; BIOMETRY; CHILD HEALTH; DATABASE; DISEASE PREVALENCE; DISEASE TRANSMISSION; EPIDEMIOLOGY; METROPOLITAN AREA; MODEL VALIDATION; POPULATION DYNAMICS; SIZE DISTRIBUTION;

NORWAY; OSLO [NORWAY];

BACTERIA (MICROORGANISMS); STREPTOCOCCUS PNEUMONIAE;

ARTICLE; BAYES THEOREM; BAYESIAN INFERENCE; BIOLOGICAL MODEL; BIOMETRY; CLASSIFICATION; COMPUTER SIMULATION; CONTINUOUS-TIME MARKOV CHAINS; DAY CARE; DISEASE TRANSMISSION; EPIDEMIC; EPIDEMIOLOGY; HETEROZYGOTE; HUMAN; METHODOLOGY; MICROBIOLOGY; MULTI-STRAIN MODELS; NORWAY; PNEUMOCOCCAL INFECTION; PRESCHOOL CHILD; PREVALENCE; PROBABILITY; SPECIES DIFFERENCE; STATISTICAL MODEL; STATISTICS; STREPTOCOCCUS PNEUMONIAE; TRANSMISSION DYNAMICS; VALIDATION STUDY;

BAYESIAN INFERENCE; CONTINUOUS-TIME MARKOV CHAINS; EPIDEMIOLOGY; MULTI-STRAIN MODELS; TRANSMISSION DYNAMICS;

BAYES THEOREM; BIOMETRY; CARRIER STATE; CHILD DAY CARE CENTERS; CHILD, PRESCHOOL; COMPUTER SIMULATION; EPIDEMICS; HUMANS; MARKOV CHAINS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; NORWAY; PNEUMOCOCCAL INFECTIONS; PREVALENCE; SPECIES SPECIFICITY; STOCHASTIC PROCESSES; STREPTOCOCCUS PNEUMONIAE;

EID: 84901191236     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/biom.12040     Document Type: Article

References (31)

1. Anderson, R. M. and May, R. M. (1991). Infectious Diseases of Humans: Dynamics and Control. Oxford: Oxford University Press. 757 p.
2. Auranen, K., Mehtälä, J., Tanskanen, A., and Kaltoft, M. S. (2010). Between-strain competition in acquisition and clearance of pneumococcal carriage-Epidemiologic evidence from a longitudinal study of day-care children. American Journal of Epidemiology 171, 169-176.
3. Ball, F., Mollison, D., and Scalia-Tomba, G. (1997). Epidemics with two levels of mixing. Annals of Applied Probability 7, 46-89.
4. Beaumont, M. A. (2010). Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics 41, 379-406.
5. Bernardo, J. M. and Smith, A. F. M. (1994). Bayesian Theory. Wiley Series in Probability and Statistics. Chichester: John Wiley & Sons 586 p.
6. Bogaert, D., De Groot, R., and Hermans, P. W. (2004). Streptoccus pneumoniae colonisation: The key to pneumococcal disease. The Lancet Infectious Diseases 4, 144-54.
7. Brooks-Pollock, E., Becerra, M. C., Goldstein, E., Cohen, T., and Murray, M. B. (2011). Epidemiologic inference from the distribution of tuberculosis cases in households in Lima, Peru. The Journal of Infectious Diseases 203, 1582-9.
8. Cobey, S. and Lipsitch, M. (2012). Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes. Science 335, 1376.
9. Donkor, E. S., Bishop, C. J., Antonio, M., Wren, B., and Hanage, W. P. (2011). High levels of recombination among Streptoccus pneumoniae isolates from the Gambia. mBio 2, e00040-11.
10. Dunais, B., Pradier, C., Carsenti, H., Sabah, M., Mancini, G., Fontas, E., and Dellamonica, P. (2004). Influence of child care on nasopharyngeal carriage of Streptoccus pneumoniae and Haemophilus influenzae. The Pediatric Infectious Disease Journal 22, 589-92.
11. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22, 403-434.
12. Feil, E. J., Smith, J. M., Enright, M. C., and Spratt, B. G. (2000). Estimating recombinational parameters in Streptoccus pneumoniae from multilocus sequence typing data. Genetics 154, 1439-50.
13. Fraser, C., Hanage, W. P., and Spratt, B. G. (2005). Neutral microepidemic evolution of bacterial pathogens. Proceedings of the National Academy of Sciences 102, 1968-1973.
14. Fraser, C., Hanage, W. P., and Spratt, B. G. (2007). Recombination and the nature of bacterial speciation. Science 315, 476-480.
15. Hagenaars, T. J., Donnelly, C. A., and Ferguson, N. M. (2004). Spatial heterogeneity and the persistence of infectious diseases. Journal of Theoretical Biology 229, 349-359.
16. Hanage, W. P. (2010). Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete. Epidemics 2, 80-84.
17. Hoti, F., Erästö, P., Leino, T., and Auranen, K. (2009). Outbreaks of Streptoccus pneumoniae carriage in day care cohorts in Finland-Implications for elimination of transmission. BMC Infectious Diseases 9, 102.
18. Huang, S. S., Finkelstein, J. A., and Lipsitch, M. (2009). Modeling community-and individual-level effects of childcare center attendance on pneumococcal carriage. Clinical Infectious Diseases 40, 1215-22.
19. Hubbel, S. P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton: Princeton University Press. 448 p.
20. Kellner, J. D., Scheifele, D., Vanderkooi, O. G., MacDonald, J., Church, D. L., and Tyrrel, G. J. (2008). Effects of routine infant vaccination with the 7-valent pneumococcal conjugate vaccine on nasopharyngeal colonization with Streptoccus pneumoniae in children in Calgary, Canada. The Pediatric Infectious Disease Journal 27, 526-32.
21. Lipsitch, M., Abdullahi, O., D'Amour, A., Wen, X., Weienberger, D. M., Tchechen, E., and Scott, J. A. G. (2012). Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal serotypes in kenya with a Markov transition model. Epidemiology 23, 510-9.
22. Luciani, F., Sisson, S. A., Jiang, H., Francis, A. R., and Tanaka, M. M. (2009). The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences 106, 14711-14715.
23. Melegaro, A., Choi, Y., Pebody, R., and Gay, N. (2007). Pneumococcal carriage in United Kingdom families: Estimating serotype-specific transmission parameters from longitudinal data. American Journal of Epidemiology 166, 228-235.
24. Peet, R. K. (1974). The measurement of species diversity, Annual Review of Ecology and Systematics 5, 285-307.
25. Pritchard, J., Seielstad, M., Perez-Lezaun, A., and Feldman, M. (1999). Population growth of human Y chromosomes: A study of Y chromosome microsatellites. Molecular Biology and Evolution 16, 1791-1798.
26. Ratmann, O., Andrieu, C., Wiuf, C., and Richardson, S. (2009). Model criticism based on likelihood-free inference, with an application to protein network evolution. Proceedings of the National Academy of Sciences 106, 10576-10581.
27. Sisson, S. S., Fan, Y., and Tanaka, M. M. (2007). Sequential Monte Carlo without likelihoods. Proceedings of the National Academy of Sciences 104, 1760-1765.
28. Stone, P., Wilkinson-Herbots, H., and Isham, V. (2008). A stochastic model for head lice infections. Journal of Mathematical Biology 56, 746-764.
29. Vestrheim, D. F., Høiby, E. A., Aaberge, I. S., and Caugant, D. A. (2008). Phenotypic and genotypic characterization of Streptoccus pneumoniae strains colonizing children attending day-care centers in Norway. Journal of Clinical Microbiology 46, 2508-2518.
30. Vestrheim, D. F., Høiby, E. A., Aaberge, I. S., and Caugant, D. A. (2010). Impact of a pneumococcal conjugate vaccination program on carriage among children in Norway. Clinical and Vaccine Immunology 17, 325-334.
31. Weinberger, D. M., Trzcinski, K., Lu, Y. J., Bogaert, D., Brandes, A., Galagan, A., Anderson, P. W., Malley, R., and Lipsitch, M. (2009). Pneumococcal capsular polysaccharide structure predicts serotype prevalence. PLOS Pathogens 5, e1000476.