Fitting outbreak models to data from many small norovirus outbreaks

Epidemics

Volumn 6, Issue , 2014, Pages 18-29

  O'Dea, Eamon B ^a   Pepin, Kim M ^b,c   Lopman, Ben A ^d,e   Wilke, Claus O ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c Department of Ecosystem Science and Sustainability   (United States)

^d PUBLIC HEALTH ENGLAND   (United Kingdom)

^e NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

Author keywords

Generalized linear model; Health care associated infection; Norovirus; Parameter estimation; Stochastic epidemic model

Indexed keywords

ARTICLE; AUTUMN; EPIDEMIC; GROWTH RATE; HUMAN; LONG TERM CARE; NONHUMAN; NOROVIRUS; NOROVIRUS INFECTION; PRIORITY JOURNAL; SEASONAL VARIATION; SPRING; SUMMER; VIRUS TRANSMISSION; WINTER; CALICIVIRIDAE INFECTIONS; CLINICAL TRIAL; EPIDEMIOLOGY; HEALTH SURVEY; HOSPITAL; ISOLATION AND PURIFICATION; MATHEMATICAL COMPUTING; MULTICENTER STUDY; SEASON; STATISTICS AND NUMERICAL DATA; TIME; TRANSMISSION; UNITED KINGDOM; UNITED STATES;

CALICIVIRIDAE INFECTIONS; DISEASE OUTBREAKS; GREAT BRITAIN; HOSPITALS; HUMANS; LONG-TERM CARE; MATHEMATICAL COMPUTING; NOROVIRUS; POPULATION SURVEILLANCE; SEASONS; TIME FACTORS; UNITED STATES;

EID: 84892984911     PISSN: 17554365     EISSN: 18780067     Source Type: Journal    
DOI: 10.1016/j.epidem.2013.12.002     Document Type: Article

References (57)

1. Anderson R.M., May R.M. Infectious Diseases of Humans: Dynamics and Control 1992, Oxford University Press, USA.
2. Becker N. An estimation procedure for household disease data. Biometrika 1979, 66:271-277.
3. Becker N.G. Analysis of Infectious Disease Data 1989, Chapman and Hall/CRC.
4. Becker N.G. Analysis of infectious disease data from a sample of households. Lecture Notes-Monograph Series 1991, 18:27-40.
5. Bolker B., Skaug H. R2admb: ADMB to R interface functions. R package version 0.7.5.1 2011.
6. Cannon J.L., Lindesmith L.C., Donaldson E.F., Saxe L., Baric R.S., Vinjé J. Herd immunity to GII.4 noroviruses is supported by outbreak patient sera. Journal of Virology 2009, 83:5363-5374.
7. Centers for Disease Control and Prevention Norovirus outbreak in an elementary school-District of Columbia, February 2007. MMWR 2008, 56:1340-1343.
8. Centers for Disease Control and Prevention Updated norovirus outbreak management and disease prevention guidelines. MMWR 2011, 60:1-18.
9. Committee to Reduce Infection Deaths State laws on reporting HAIs 2011, http://www.hospitalinfection.org/legislation.shtml.
10. Ding J.L., Chen X.R. Asymptotic properties of the maximum likelihood estimate in generalized linear models with stochastic regressors. Acta Mathematica Sinica, English Series 2006, 22:1679-1686.
11. Ding J.L., Chen X.R. Large-sample theory for generalized linear models with non-natural link and random variates. Acta Mathematicae Applicatae Sinica, English Series 2006, 22:115-126.
12. Evans M.R., Meldrum R., Lane W., Gardner D., Ribeiro C.D., Gallimore C.I., Westmoreland D. An outbreak of viral gastroenteritis following environmental contamination at a concert hall. Epidemiology and Infection 2002, 129:355-360.
13. Fahrmeir L. Consistency and asymptotic normality of the maximum likelihood estimator in generalized linear models. The Annals of Statistics 1985, 13:342-368.
14. Forrester M., Pettitt A.N. Use of stochastic epidemic modeling to quantify transmission rates of colonization with Methicillin-Resistant Staphylococcus aureus in an intensive care unit. Infection Control and Hospital Epidemiology 2005, 26:598-606.
15. Fournier D.A., Skaug H.J., Ancheta J., Ianelli J., Magnusson A., Maunder M.N., Nielsen A., Sibert J. AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models. Optimization Methods and Software 2011, 27:233-249.
16. Glass R.I., Parashar U.D., Estes M.K. Norovirus gastroenteritis. New England Journal of Medicine 2009, 361:1776-1785.
17. Grota P.G., Stone P.W., Jordan S., Pogorzelska M., Larson E. Electronic surveillance systems in infection prevention: organizational support, program characteristics, and user satisfaction. American Journal of Infection Control 2010, 38:509-514.
18. Halloran M.E., Longini I.M., Struchiner C.J. Design and Analysis of Vaccine Studies 2009, Springer.
19. Halpin H., Shortell S.M., Milstein A., Vanneman M. Hospital adoption of automated surveillance technology and the implementation of infection prevention and control programs. American Journal of Infection Control 2011, 39:270-276.
20. Hayakawa Y., O'Neill P.D., Upton D., Yip P.S. Bayesian inference for a stochastic epidemic model with uncertain numbers of susceptibles of several types. Australian and New Zealand Journal of Statistics 2003, 45:491-502.
21. Heijne J.C.M., Rondy M., Verhoef L., Wallinga J., Kretzschmar M., Low N., Koopmans M., Teunis P.F.M. Quantifying transmission of norovirus during an outbreak. Epidemiology 2012, 23:277-284.
22. Heijne J.C.M., Teunis P., Morroy G., Wijkmans C., Oostveen S., Duizer E., Kretzschmar M., Wallinga J. Enhanced hygiene measures and norovirus transmission during an outbreak. Emerging Infectious Diseases 2009, 15:24-30.
23. Höhle M. Additive-multiplicative regression models for spatio-temporal epidemics. Biometrical Journal 2009, 51:961-978.
24. Hohle M., Jorgensen E., O'Neill P.D. Inference in disease transmission experiments by using stochastic epidemic models. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2005, 54:349-366.
25. Huggins R.M., Yip P.S.F., Lau E.H.Y. A note on the estimation of the initial number of susceptible individuals in the general epidemic model. Statistics & Probability Letters 2004, 67:321-330.
26. Isakbaeva E.T., Widdowson M.A., Beard R.S., Bulens S.N., Mullins J., Monroe S.S., Bresee J., Sassano P., Cramer E.H., Glass R.I. Norovirus transmission on cruise ship. Emerging Infectious Diseases 2005, 11:154-158.
27. Kalbfleisch J.D., Prentice R.L. The Statistical Analysis of Failure Time Data 2002, Wiley. 2nd edition.
28. Keeling M.J. Models of foot-and-mouth disease. Proceedings. Biological Sciences 2005, 272:1195-1202.
29. Kuusi M., Nuorti J.P., Maunula L., Minh Tran N.N., Ratia M., Karlsson J., von Bonsdorff C.H. A prolonged outbreak of Norwalk-like calicivirus (NLV) gastroenteritis in a rehabilitation centre due to environmental contamination. Epidemiology and Infection 2002, 129:133-138.
30. Kypraios T. A note on maximum likelihood estimation of the initial number of susceptibles in the general stochastic epidemic model. Statistics & Probability Letters 2009, 79:1972-1976.
31. Lau E.H.Y., Yip P.S.F. Estimating the basic reproductive number in the general epidemic model with an unknown initial number of susceptible individuals. Scandinavian Journal of Statistics 2008, 35:650-663.
32. L'Ecuyer P., Simard R., Chen E., Kelton W. An object-oriented random-number package with many long streams and substreams. Operations Research 2002, 50:1073-1075.
33. Liang K.Y., Zeger S.L. Longitudinal data analysis using generalized linear models. Biometrika 1986, 73:13-22.
34. Lively C.M. An epidemiological model of host-parasite coevolution and sex. Journal of Evolutionary Biology 2010, 23:1490-1497.
35. Lopman B., Armstrong B., Atchison C., Gray J.J. Host, weather and virological factors drive norovirus epidemiology: time-series analysis of laboratory surveillance data in England and Wales. PLoS One 2009, 4:e6671.
36. Lopman B.A., Hall A.J., Curns A.T., Parashar U.D. Increasing rates of gastroenteritis hospital discharges in US adults and the contribution of norovirus, 1996-2007. Clinical Infectious Diseases 2011, 52:466-474.
37. Lopman B.A., Reacher M.H., Vipond I.B., Hill D., Perry C., Halladay T., Brown D.W., Edmunds W.J., Sarangi J. Epidemiology and cost of nosocomial gastroenteritis, Avon, England, 2002-2003. Emerging Infectious Diseases 2004, 10:1827-1834.
38. Lopman B.A., Reacher M.H., Vipond I.B., Sarangi J., Brown D.W.G. Clinical manifestation of norovirus gastroenteritis in health care settings. Clinical Infectious Diseases 2004, 39:318-324.
39. Meyer S., Elias J., Höhle M. A space-time conditional intensity model for invasive meningococcal disease occurrence. Biometrics 2012, 68:607-616.
40. O'Neill P.D., Marks P.J. Bayesian model choice and infection route modelling in an outbreak of Norovirus. Statistics in Medicine 2005, 24:2011-2024.
41. R Development Core Team R: A Language and Environment for Statistical Computing 2010, R Foundation for Statistical Computing, Vienna, Austria, ISBN 3-900051-07-0.
42. Rida W.N. Asymptotic properties of some estimators for the infection rate in the general stochastic epidemic model. Journal of the Royal Statistical Society. Series B (Methodological) 1991, 53:269-283.
43. Rosenthal N.A., Lee L.E., Vermeulen B.A.J., Hedberg K., Keene W.E., Widdowson M., Cieslak P.R., Vinjé J. Epidemiological and genetic characteristics of norovirus outbreaks in long-term care facilities, 2003-2006. Epidemiology and Infection 2011, 139:286-294.
44. Scallan E., Hoekstra R.M., Angulo F.J., Tauxe R.V., Widdowson M., Roy S.L., Jones J.L., Griffin P.M. Foodborne illness acquired in the United States-major pathogens. Emerging Infectious Diseases 2011, 17:7-15.
45. Shao Q.X. Some properties of an estimator for the basic reproduction number of the general epidemic model. Mathematical Biosciences 1999, 159:79-96.
46. Sukhrie F.H.A., Teunis P., Vennema H., Copra C., Thijs Beersma M.F.C., Bogerman J., Koopmans M. Nosocomial transmission of norovirus is mainly caused by symptomatic cases. Clinical Infectious Diseases 2012, 54:931-937.
47. Teunis P., Heijne J.C.M., Sukhrie F., van Eijkeren J., Koopmans M., Kretzschmar M. Infectious disease transmission as a forensic problem: who infected whom?. Journal of the Royal Society Interface 2013, 10:20120955.
48. Thornley C.N., Emslie N.A., Sprott T.W., Greening G.E., Rapana J.P. Recurring norovirus transmission on an airplane. Clinical Infectious Diseases 2011, 53:515-520.
49. Vignaux T., Muller K., Helmbold B. SimPy Manual 2012, Available at http://simpy.sourceforge.net.
50. Venable W.N., Ripley B.D. Statistics Complements to Modern Applied Statistics with S 2002, Available at http://www.stats.ox.ac.uk/pub/MASS4/. 4th edition.
51. Voirin N., Roche S., Vanhems P., Giard M., David-Tchouda S., Barret B., Ecochard R. A multiplicative hazard regression model to assess the risk of disease transmission at hospital during community epidemics. BMC Medical Research Methodology 2011, 11:53.
52. Wickham H. ggplot2: Elegant Graphics for Data Analysis 2009, Springer, New York.
53. Wikswo M.E., Cortes J., Hall A.J., Vaughan G., Howard C., Gregoricus N., Cramer E.H. Disease transmission and passenger behaviors during a high morbidity Norovirus outbreak on a cruise ship, January 2009. Clinical Infectious Diseases 2011, 52:1116-1122.
54. Wilkinson G.N., Rogers C.E. Symbolic description of factorial models for analysis of variance. Applied Statistics 1973, 22:392-399.
55. Yen C., Wikswo M.E., Lopman B.A., Vinje J., Parashar U.D., Hall A.J. Impact of an emergent norovirus variant in 2009 on norovirus outbreak activity in the United States. Clinical Infectious Diseases 2011, 53:568-571.
56. Zelner J.L., King A.A., Moe C.L., Eisenberg J.N.S. How infections propagate after point-source outbreaks: an analysis of secondary norovirus transmission. Epidemiology 2010, 21:711-718.
57. Zelner J.L., Lopman B.A., Hall A.J., Ballesteros S., Grenfell B.T. Linking time-varying symptomatology and intensity of infectiousness to patterns of norovirus transmission. PLoS ONE 2013, 8:e68413.