Computational protocol: Diagnostic accuracy of pulmonary host inflammatory mediators in the exclusion of ventilator-acquired pneumonia

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Protocol publication

[…] Sample size was estimated from the derivation study post-test probability (PTP) of VAP using the IL-1β threshold value for exclusion. Below the threshold, IL-1β excluded VAP with a PTP of 2.8% (95% CI 0.1% to 15.9%). To improve the external validity of this result, a sample size was based on narrowing the 95% CI. We estimated that 24% of patients would have confirmed VAP based on the derivation cohort. A sample size of 140 was estimated to allow a 95% CI for a PTP of 3% to be 0% to 8%, which was judged tight enough for potential clinical use. We, therefore, planned to recruit 160 patients to allow for a dropout rate of approximately 15%.Statistical analysis was performed using SPSS V.19 (Chicago, Illinois, USA) and R 3.0.0. Comparisons for non-normally distributed continuous data were made with the Mann–Whitney U test, otherwise with the Student t test. Binary outcomes were analysed using the χ2 test.Since the objective was to validate a rule-out for VAP, the statistical analysis was performed to determine the maximum sensitivity and negative predictive value (NPV). Patients were dichotomised into a VAP group and non-VAP group according to growth in BAL fluid of >104 cfu/mL or ≤104 cfu/mL. Individual biomarkers that were significantly different between groups were analysed by receiver operator characteristic (ROC) procedures. Biomarkers were log10 transformed with the addition of a constant of one before being tested in combination. Log10 transformed biomarkers were entered into a logistic regression model and ROC curves were constructed from the predictive model. Cut-points for individual biomarkers and combinations were determined by fixing a minimum NPV of 95%. The diagnostic rules, diagnostic performance measures and associated 95% CIs were derived using the OptimalCutpoints library in R3.0.0. […]

Pipeline specifications

Software tools SPSS, OptimalCutpoints
Applications Miscellaneous, Medical phenotype analysis
Organisms Homo sapiens
Diseases Infection, Pneumonia, Pneumonia, Ventilator-Associated