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A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data

Phillips, MT; Meiring, JE; Voysey, M; Warren, JL; Baker, S; Basnyat, B; Clemens, JD; ... Pitzer, VE; + view all (2021) A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data. Statistics in Medicine 10.1002/sim.9159. (In press). Green open access

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Abstract

Decisions about typhoid fever prevention and control are based on estimates of typhoid incidence and their uncertainty. Lack of specific clinical diagnostic criteria, poorly sensitive diagnostic tests, and scarcity of accurate and complete datasets contribute to difficulties in calculating age-specific population-level typhoid incidence. Using data from the Strategic Typhoid Alliance across Africa and Asia program, we integrated demographic censuses, healthcare utilization surveys, facility-based surveillance, and serological surveillance from Malawi, Nepal, and Bangladesh to account for under-detection of cases. We developed a Bayesian approach that adjusts the count of reported blood-culture-positive cases for blood culture detection, blood culture collection, and healthcare seeking—and how these factors vary by age—while combining information from prior published studies. We validated the model using simulated data. The ratio of observed to adjusted incidence rates was 7.7 (95% credible interval [CrI]: 6.0-12.4) in Malawi, 14.4 (95% CrI: 9.3-24.9) in Nepal, and 7.0 (95% CrI: 5.6-9.2) in Bangladesh. The probability of blood culture collection led to the largest adjustment in Malawi, while the probability of seeking healthcare contributed the most in Nepal and Bangladesh; adjustment factors varied by age. Adjusted incidence rates were within or below the seroincidence rate limits of typhoid infection. Estimates of blood-culture-confirmed typhoid fever without these adjustments results in considerable underestimation of the true incidence of typhoid fever. Our approach allows each phase of the reporting process to be synthesized to estimate the adjusted incidence of typhoid fever while correctly characterizing uncertainty, which can inform decision-making for typhoid prevention and control.

Type: Article
Title: A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/sim.9159
Publisher version: http://dx.doi.org/10.1002/sim.9159
Language: English
Additional information: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2021 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.
Keywords: Mathematical & Computational Biology, Public, Environmental & Occupational Health, Medical Informatics, Medicine, Research & Experimental, Statistics & Probability, Research & Experimental Medicine, Mathematics, incidence estimation, passive surveillance, reporting pyramid, typhoid fever, AFRICA, BURDEN
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
URI: https://discovery.ucl.ac.uk/id/eprint/10134345
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