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Table 4 GeneXpert MTB/RIF diagnostic system performance for PTB and EPTB in relation to LJ culture as the reference standard

From: Diagnostic utility of GeneXpert MTB/RIF assay versus conventional methods for diagnosis of pulmonary and extra-pulmonary tuberculosis

Specimen type PTB (n = 449) EPTB (n = 133) PTB EPTB
Sputum BAL Pleural fluid CSF Ascetic fluid Pus Urine
No. 430 (95.8 %) 19 (4.2 %) 26 (19.5 %) 62 (46.6 %) 19 (14.3 %) 12 (9.0 %) 14 (10.5 %) 449 133
True- positive 106 4 7 12 5 3 3 110 31
False- positive 0 1 2 4 1 0 1 1 9
True- negative 272 12 13 40 11 5 7 284 75
False negative 12 0 2 1 1 2 2 12 7
Invalid or error 40 (9.3 %) 2 (10.5 %) 2 (7.7 %) 5 (8.1 %) 1 (5.3 %) 2 (16.7 %) 1 (7.1 %) 42 (9.4 %) 11 (8.3 %)
Sensitivity 89.8% 100% 77.8% 92.3% 83.3% 60.0% 60.0% 90.2% 81.6%
Specificity 87.2% 80.0% 76.5% 81.6% 84.6% 71.4% 77.8% 86.9% 78.9%
PPV 100 % 80.0% 77.8% 75.0% 83.3% 100% 75% 99.1% 77.5%
NPV 95.8 100% 86.7% 97.6% 91.7% 71.4% 77.8% 95.9% 91.5%
False- positive rate 0.0% 20% 11.8% 10.2% 7.7% 0.0% 11.1% 0.3% 9.5%
False -negative rate 4.2% 0% 22.2% 0% 16.7% 40.0% 40.0% 9.8% 18.5 %