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Despite tremendous advances in diagnostic laboratory technology, identifying the pathogen(s) causing pneumonia remains challenging because the infected lung tissue cannot usually be sampled for testing. Consequently, to obtain information about pneumonia etiology, clinicians and researchers test specimens distant to the site of infection. These tests may lack sensitivity (eg, blood culture, which is only positive in a small proportion of children with pneumonia) and/or specificity (eg, detection of pathogens in upper respiratory tract specimens, which may indicate asymptomatic carriage or a less severe syndrome, such as upper respiratory infection). While highly sensitive nucleic acid detection methods and testing of multiple specimens improve sensitivity, multiple pathogens are often detected and this adds complexity to the interpretation as the etiologic significance of results may be unclear (ie, the pneumonia may be caused by none, one, some, or all of the pathogens detected). Some of these challenges can be addressed by adjusting positivity rates to account for poor sensitivity or incorporating test results from controls without pneumonia to account for poor specificity. However, no classical analytic methods can account for measurement error (ie, sensitivity and specificity) for multiple specimen types and integrate the results of measurements for multiple pathogens to produce an accurate understanding of etiology. We describe the major analytic challenges in determining pneumonia etiology and review how the common analytical approaches (eg, descriptive, case-control, attributable fraction, latent class analysis) address some but not all challenges. We demonstrate how these limitations necessitate a new, integrated analytical approach to pneumonia etiology data.

Original publication

DOI

10.1093/cid/cix147

Type

Journal article

Journal

Clin Infect Dis

Publication Date

15/06/2017

Volume

64

Pages

S197 - S204

Keywords

attributable fraction analysis, case-control analysis, etiology, latent class analysis., pneumonia, Blood Culture, Case-Control Studies, Child, Cross-Sectional Studies, Diagnostic Techniques, Respiratory System, Female, Humans, Lung, Male, Multicenter Studies as Topic, Pneumonia, Pneumonia, Bacterial, Pneumonia, Viral, Sensitivity and Specificity, Specimen Handling