Bayesian Estimation of Pneumonia Etiology: Epidemiologic Considerations and Applications to the Pneumonia Etiology Research for Child Health Study

Maria Deloria-Knoll, Wei Fu, Qiyuan Shi, Christine Prosperi, Zhenke Wu, Laura Hammitt, Daniel R. Feikin, Henry C. Baggett, Stephen R.C. Howie, J. Anthony G. Scott, David R. Murdoch, Shabir A. Madhi, Donald M. Thea, W. Abdullah Brooks, Karen L. Kotloff, Mengying Li, Daniel E. Park, Wenyi Lin, Orin S. Levine, Katherine O’Brien, Scott Zeger (2017). Clinical Infectious Diseases

Abstract

In pneumonia, specimens are rarely obtained directly from the infection site, the lung, so the pathogen causing infection is determined indirectly from multiple tests on peripheral clinical specimens, which may have imperfect and uncertain sensitivity and specificity, so inference about the cause is complex. Analytic approaches have included expert review of case-only results, case–control logistic regression, latent class analysis, and attributable fraction, but each has serious limitations and none naturally integrate multiple test results. The Pneumonia Etiology Research for Child Health (PERCH) study required an analytic solution appropriate for a case–control design that could incorporate evidence from multiple specimens from cases and controls and that accounted for measurement error. We describe a Bayesian integrated approach we developed that combined and extended elements of attributable fraction and latent class analyses to meet some of these challenges and illustrate the advantage it confers regarding the challenges identified for other methods.

Keywords: Bayesian theorem, etiologic estimations, pneumonia, epidemiologic methods, statistical models

Bibtex

@Article{DeloriaKnoll2017b,
  author          = {Deloria Knoll, Maria and Fu, Wei and Shi, Qiyuan and Prosperi, Christine and Wu, Zhenke and Hammitt, Laura L and Feikin, Daniel R and Baggett, Henry C and Howie, Stephen R C and Scott, J Anthony G and Murdoch, David R and Madhi, Shabir A and Thea, Donald M and Brooks, W Abdullah and Kotloff, Karen L and Li, Mengying and Park, Daniel E and Lin, Wenyi and Levine, Orin S and O'Brien, Katherine L and Zeger, Scott L},
  title           = {Bayesian Estimation of Pneumonia Etiology: Epidemiologic Considerations and Applications to the Pneumonia Etiology Research for Child Health Study.},
  journal         = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
  year            = {2017},
  volume          = {64},
  pages           = {S213--S227},
  month           = jun,
  issn            = {1537-6591},
  completed       = {2018-02-22},
  country         = {United States},
  doi             = {10.1093/cid/cix144},
  issn-linking    = {1058-4838},
  issue           = {suppl_3},
  nlm-id          = {9203213},
  owner           = {NLM},
  pii             = {3858226},
  pmc             = {PMC5447849},
  pmid            = {28575370},
  revised         = {2019-01-12},
}