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. 2017 Nov;28(6):889-897.
doi: 10.1097/EDE.0000000000000719.

Bayesian Model Averaging with Change Points to Assess the Impact of Vaccination and Public Health Interventions

Esra Kürüm  1 , Joshua L Warren, Cynthia Schuck-Paim, Roger Lustig, Joseph A Lewnard, Rodrigo Fuentes, Christian A W Bruhn, Robert J Taylor, Lone Simonsen, Daniel M Weinberger
Affiliations

Bayesian Model Averaging with Change Points to Assess the Impact of Vaccination and Public Health Interventions

Esra Kürüm et al. Epidemiology. 2017 Nov.

Abstract

Background: Pneumococcal conjugate vaccines (PCVs) prevent invasive pneumococcal disease and pneumonia. However, some low-and middle-income countries have yet to introduce PCV into their immunization programs due, in part, to lack of certainty about the potential impact. Assessing PCV benefits is challenging because specific data on pneumococcal disease are often lacking, and it can be difficult to separate the effects of factors other than the vaccine that could also affect pneumococcal disease rates.

Methods: We assess PCV impact by combining Bayesian model averaging with change-point models to estimate the timing and magnitude of vaccine-associated changes, while controlling for seasonality and other covariates. We applied our approach to monthly time series of age-stratified hospitalizations related to pneumococcal infection in children younger 5 years of age in the United States, Brazil, and Chile.

Results: Our method accurately detected changes in data in which we knew true and noteworthy changes occurred, i.e., in simulated data and for invasive pneumococcal disease. Moreover, 24 months after the vaccine introduction, we detected reductions of 14%, 9%, and 9% in the United States, Brazil, and Chile, respectively, in all-cause pneumonia (ACP) hospitalizations for age group 0 to <1 years of age.

Conclusions: Our approach provides a flexible and sensitive method to detect changes in disease incidence that occur after the introduction of a vaccine or other intervention, while avoiding biases that exist in current approaches to time-trend analyses.

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Conflict of interest statement

D.M.W. had received an investigator-initiated research grant from Pfizer and consulting fees from Pfizer, Merck, and Affinivax. The other authors have no conflicts to report.

Figures

FIGURE 1.
FIGURE 1.
The plots on the left represent, IPD hospitalizations versus time for 10 US states by age group, showing observed IPD hospitalizations per month (black), model-averaged fitted values (orange, solid) with their 95% approximate pointwise confidence intervals (orange, dotted), and counterfactual predicted values (blue). The estimated decline at specific time points (green triangles) is shown, with their respective 95% bootstrap confidence intervals. The blue dots at the bottom represent the probability of a change occurring at that point. The color gets darker as the probability increases. The first and second sets of dots are for the first and second change points, respectively. The level plots on the right are posterior probabilities corresponding to the plots on the left for the locations of the first (x axis) and second (y axis) change points. The dashed lines represent the time that the PCV7 (January 2000) is introduced.
FIGURE 2.
FIGURE 2.
The plots on the right are ACP hospitalizations versus time for Brazil (first row), 10 US states (second row), and Chile (third row) for age group 0–12 months, showing observed ACP hospitalizations per month (black), model-averaged fitted values (orange, solid) with their 95% approximate pointwise confidence intervals (orange, dotted), and counterfactual predicted values (blue). The estimated decline at specific time points (green triangles) is shown, with their respective 95% bootstrap confidence intervals. The blue dots at the bottom represent the probability of a change occurring at that point. The color gets darker as the probability increases. In the second and third rows of the plot, the first and second sets of dots are for the first and second change points, respectively. The level plots on the right are posterior probabilities (in the second and third rows) corresponding to the plots on the left (in the second and third rows) for the locations of the first (x axis) and second (y axis) change points. The dashed lines represent the time that the pneumococcal conjugate vaccine is introduced.
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