Table 2. Effect of prior culture on spoligotyping analysis for MTBc lineage detection.
| Lineages/Groups | All patients a % (n = 199) | All sputa b % (n = 196) | Culture positive sputa b % (n = 143) | Culture Negative & Contaminated sputa | Culture Negative sputa (only) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| % (n = 53) | Odds ratio (OddPos cult / OddNeg & Cont cult) with 95% CI | % Difference (PPos cult—PNeg & Cont cult) with 95% CI | p-value c | % (n = 36) | Odds ratio (OddPos cult / OddNeg cult) with 95% CI | % Difference (PPos cult -PNeg cult) with 95% CI | p-value c | ||||
| Lineage 1 (Indo-Oceanic) | 8.0 | 8.2 | 9.1 | 5.7 | 1.67 (0.46 to 6.04) | 3.4 (-5.2 to 12.1) | 0.565 * | 8.3 | 1.1 (0.3 to 4.1) | 0.8 (-9.7 to 11.2) | 1 * |
| Lineage 2 (East Asian Beijing) | 5.6 | 5.6 | 6.3 | 3.8 | 1.71 (0.36 to 8.09) | 2.5 (-4.7 to 9.8) | 0.730 * | 5.6 | 1.14 (0.23 to 5.55) | 0.7 (-8.1 to 9.5) | 1 * |
| Lineage 3 (East African Indian) | 1.0 | 1.0 | 1.4 | 0 | - | 1.4 (-1.8 to 4.6) | 0.1 * | 0 | - | 1.4 (-2.5 to 5.3) | 1 * |
| Lineage 4 (Euro-American) | 51.8 | 51.5 | 55.2 | 41.5 | 1.74 (0.92 to 3.29) | 13.7 (-2.1 to 29.5) | 0.087 | 30.5 | 2.81 (1.30 to 6.03) | 24.7 (6.4 to 43.0) | 0.008 |
| Lineage 5 (M. Africanum West African 1) | 25.1 | 25.0 | 21 | 35.8 | 0.48 (0.24 to 0.94) | -14.9 (-28.6 to -1.2) | 0.033 | 41.7 | 0.37 (0.17 to 0.8) | -20.7 (-36.6 to -4.8) | 0.011 |
| Lineage 6 (M. Africanum West African 2) | 8.5 | 8.7 | 7 | 13.2 | 0.49 (0.18 to 1.36) | -6.2 (-15.1 to 2.7) | 0.17 | 13.9 | 0.47 (0.15 to 1.43) | -6.9 (-17.1 to 3.3) | 0.182 |
| Modern lineages (L2 + L3 + L4) | 58.3 | 58.2 | 62.9 | 45.3 | 2.05 (1.09 to 3.87) | 17.7 (2.1 to 33.2) | 0.026 | 36.1 | 3.0 (1.43 to 6.31) | 26.8 (8.7 to 44.9) | 0.004 |
| Ancestral lineages (L1 + L5 + L6) | 41.7 | 41.8 | 37.1 | 54.7 | 0.49 (0.26 to 0.92) | -17.7 (-33.2 to -2.1) | 63.9 | 0.33 (0.16 to 0.7) | -26.8 (-44.9 to -8.7) | ||
| Other than M. africanum (L1 + L2 + L3 + L4) | 66.3 | 66.3 | 72.0 | 50.9 | 2.48 (1.30 to 4.72) | 21.1 (6.2 to 36.0) | 0.006 | 44.4 | 3.22 (1.55 to 6.7) | 27.6 (10.3 to 44.9) | 0.002 |
| M. africanum (L5 + L6) | 33.7 | 33.7 | 28 | 49.1 | 0.40 (0.21 to 0.77) | -21.1 (-36.0 to -6.2) | 55.6 | 0.31 (0.15 to 0.65) | -27.6 (-44.9 to -10.3) | ||
a Based on sputum results in 196 patients, and culture results in 3 patients (for whom direct spoligotyping failed: 2 ‘Lineage 4’ strains and 1 ‘Lineage 5’ strain).
b Direct spoligotyping (on sputa). L: Lineage.
c p-values were calculated using the two-group proportion test (independent groups).
* p-values were calculated using the Fisher Exact test (independent groups).