Table 3.
Breakdown of the relative diagnostic efficiencies of smear microscopy, Xpert Ultra, Xpert G4 and LPA tests in detecting Mycobacterium tuberculosis from pulmonary and extra-pulmonary samples under different culture and smear results categories.
| Parameter | All samples (both pulmonary and extra-pulmonary) | Pulmonary samples | Extra-pulmonary samples | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Auramine | Xpert Ultra | Xpert G4 | LPA | Auramine | Xpert Ultra | Xpert G4 | LPA | Auramine | Xpert Ultra | Xpert G4 | LPA | |
| Smear Negative-Culture Negative (SN-CN) | Smear Negative-Culture Negative (SN-CN) | Smear Negative-Culture Negative (SN-CN) | ||||||||||
| True Positive | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| True Negative | 131 | 73 | 129 | 25 | 65 | 40 | 64 | 8 | 66 | 33 | 65 | 17 |
| False Positive | 0 | 56 | 2 | 106 | 0 | 23 | 1 | 57 | 0 | 33 | 1 | 49 |
| False Negative | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Total | 131 | 129 †† | 131 | 131 | 65 | 63 †† | 65 | 65 | 66 | 66 | 66 | 66 |
| Sensitivity (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Specificity (CI), % | 100,00 (97,22-100,00) | 56,59 (47,58-65,29) | 98,47 (94,59-99,81) | 19,08 (12,75-26,87) | 100,00 (94,48-100,00) | 63,49 (50,40-75,27) | 98,46 (91,72-99,96) | 12,31 (5,47-22,82) | 100,00 (94,56-100,00) | 50,00 (37,43-62,57) | 98,48 (91,84-99,96) | 25,76 (15,78-38,01) |
| Positive predictive value (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Negative predictive value (CI), % | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| Smear Positive-Culture Positive (SP-CP) | Smear Positive-Culture Positive (SP-CP) | Smear Positive-Culture Positive (SP-CP) | ||||||||||
| True Positive | 48 | 47 | 43 | 43 | 41 | 40 | 37 | 38 | 7 | 7 | 6 | 5 |
| True Negative | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| False Positive | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| False Negative | 0 | 1 | 3 | 5 | 0 | 1 | 3 | 3 | 0 | 0 | 0 | 2 |
| Total | 48 | 48 | 46 §§ | 48 | 41 | 41 | 40 + 1 *** | 41 | 7 | 7 | 6 + 1 ††† | 7 |
| Sensitivity (CI), % | 100,00 (92,60-100,00) | 97,92 (88,93-99,95) | 93,48 (82,10-98,63) | 89,58 (77,34-96,53) | 100,00 (91,40-100,00) | 97,56 (87,14-99,94) | 92,50 (79,61-98,43) | 92,68 (80,08-98,46) | 100,00 (59,04-100,00) | 100,00 (59,04-100,00) | 100,00 (54,07-100,00) | 62,50 (24,49-91,48) |
| Specificity (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Positive predictive value (CI), % | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 | 100 |
| Negative predictive value (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Smear Negative-Culture Positive (SN-CP) | Smear Negative-Culture Positive (SN-CP) | Smear Negative-Culture Positive (SN-CP) | ||||||||||
| True Positive | 0 | 6 | 2 | 6 | 0 | 4 | 2 | 2 | 0 | 2 | 0 | 4 |
| True Negative | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| False Positive | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| False Negative | 15 | 9 | 13 | 9 | 9 | 5 | 7 | 7 | 6 | 4 | 6 | 2 |
| Total | 15 | 15 | 15 | 15 | 9 | 9 | 9 | 9 | 6 | 6 | 6 | 6 |
| Sensitivity (CI), % | 0,00 (0,00-21,80) | 40,00 (16,34-67,71) | 13,33 (1,66-40,46) | 40,00 (16,34-67,71) | 0,00 (0,00-33,63) | 44,44 (13,70-78,80) | 22,22 (2,81-60,01) | 22,22 (2,81-60,01) | 0,00 (0,00-45,93) | 33,33 (4,33-77,72) | 0,00 (0,00-45,93) | 66,67 (22,28-95,67) |
| Specificity (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Positive predictive value (CI), % | 0 | 100 | 100 | 100 | 0 | 100 | 100 | 100 | 0 | 100 | 0 | 100 |
| Negative predictive value (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Smear Positive-Culture Negative (SP-CN) | Smear Positive-Culture Negative (SP-CN) | Smear Positive-Culture Negative (SP-CN) | ||||||||||
| True Positive | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| True Negative | 0 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 |
| False Positive | 8 | 7 | 7 | 8 | 7 | 6 | 6 | 7 | 1 | 1 | 1 | 1 |
| False Negative | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Total | 8 | 8 | 8 | 8 | 7 | 7 | 7 | 7 | 1 | 1 | 1 | 1 |
| Sensitivity (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Specificity (CI), % | 0,00 (0,00-36,94) | 12,50 (0,32-52,65) | 12,50 (0,32-52,65) | 0,00 (0,00-36,94) | 0,00 (0,00-40,96) | 14,29 (0,36-57,87) | 14,29 (0,36-57,87) | 0,00 (0,00-40,96) | 0,00 (0,00-97,50) | 0,00 (0,00-97,50) | 0,00 (0,00-97,50) | 0,00 (0,00-97,50) |
| Positive predictive value (CI), % | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Negative predictive value (CI), % | 0 | 100 | 100 | 0 | 0 | 100 | 100 | 0 | 0 | 0 | 0 | 0 |
††2 Isolates were invalid. Adding them will amount to 131.
‡‡2 Isolates were invalid. Adding them will amount to 65.
§§2 Isolates were invalid/error. Adding them will amount to 46.
***1 Isolate was invalid/error. Adding it will amount to 41.
†††1 Isolate was invalid/error. Adding that will amount to 7.