Computational protocol: The diagnostic accuracy of three rapid diagnostic tests for typhoid fever at Chittagong Medical College Hospital, Chittagong, Bangladesh

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Protocol publication

[…] The Standards for Reporting of Diagnostic Accuracy reporting guidelines were followed . The sensitivity, specificity and predictive values with 95% confidence intervals were calculated. Laboratory‐confirmed typhoid cases were defined if the patient's blood culture and/or blood PCR was positive for Typhi or Paratyphi A (composite reference standard positive). Cases that were not typhoid were defined if the patient's blood culture and blood PCR was negative for Typhi or Paratyphi A (composite reference standard negative).Analysis was performed using SPSS version 22 (IBM SPSS Statistics, Chicago, IL, USA). The Bayesian LCM as described by Dendukuri and Joseph was used to approximate the prevalence, sensitivities and specificities of all tests. The Bayesian LCM does not assume that any test is perfect, but considers that each test could be imperfect in diagnosing the true disease status. The true disease status of the patient population is then defined on the basis of overall prevalence (the probability that a patient with suspected typhoid fever is truly infected with S. Typhi). LCMs estimate prevalence and accuracy of each test based on the observed frequency of the possible combinations of test results. The model assumed that no other prior information (non‐informative priors) about the unknown parameters (prevalence, sensitivities and specificities) was available except the specificity of blood culture was set at 100% and that there was a correlation between the blood culture and PCR result. The median values of all the parameters were reported together with the 95% credible intervals . The Bayesian LCM was run using WinBUGS 1.4 (Medical Research Council, and Imperial College London, UK). […]

Pipeline specifications

Software tools SPSS, WinBUGS
Applications Drug design, Miscellaneous
Organisms Salmonella enterica, Homo sapiens, Salmonella enterica subsp. enterica serovar Typhi
Diseases Dengue, Leptospirosis, Malaria, Typhoid Fever