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Table 2 Prevalence of pneumococcal pneumonia (PPN) in case-patients and performance of real-time polymerase chain reaction (qPCR) and urine antigen test (UAT): conventional analysis with UAT as a gold standard vs. Bayesian latent class models (BLCM) (n = 353)

From: Pneumococcal pneumonia prevalence among adults with severe acute respiratory illness in Thailand - comparison of Bayesian latent class modeling and conventional analysis

  Conventional analyses
Mean (95% CI)
BLCM
Median (95% CrI)
Primary Adjusted Binary qPCR model Continuous qPCR model
27 UAT positives considered true positives UAT sensitivity is 75% and specificity is 100% qPCR and UAT qPCR and UAT
Prevalence 8% (5–11%) 10% (7–15%) 10% (7–16%) 11% (7–17%)
Sensitivity of qPCR 96% (81–100%)   96% (83–100%)  
Specificity of qPCR 74% (69–79%)   75% (71–79%)  
PPV of qPCR 23% (16–32%)   31% (20–44%)  
Mean qPCR Ct among PPN 25.6 (24.2–26.9)    25.7 (24.6–27)
Mean qPCR among Non-PPN 31 (30–32)    32.4 (31.4–33.4)
Sensitivity of UAT 100% (assumed) 75% (published) 72% (53–87%) 67% (51–83%)
Specificity of UAT 100% (assumed) 100% (assumed) 99.5% (98.5–99.9%) 99.5% (98.6–99.9%)
PPV of UAT 100% 100% 94% (83–99%) 95% (83–99%)
Probability of PPV of UAT < 90% 0 0 18% 17%