Table 1. Sensitivity and specificity for resistance prediction of different tools.
| Antibiotic | Sanger | CASTB | PhyResSE | KvarQ | Mykrobe Predictor TB | TBProfiler | MTBseq | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #R | #S | Sens | Spec | Sens | Spec | Sens | Spec | Sens | Spec | Sens | Spec | Sens | Spec | |
| INH | 28 | 63 | 89 (72, 98) | 100 (92, 100) | 100 (82, 100) | 98 (91, 100) | 86 (67, 96) | 100 (92, 100) | 89 (72, 98) | 100 (92, 100) | 93 (76, 99) | 84 (73, 92) | 100 (82, 100) | 98 (91, 100) |
| RMP | 18 | 73 | 94 (73, 100) | 100 (93, 100) | 100 (74, 100) | 99 (93, 100) | 94 (73, 100) | 100 (93, 100) | 100 (74, 100) | 99 (93, 100) | 100 (74, 100) | 99 (93, 100) | 100 (74, 100) | 100 (93, 100) |
| SM | 37 | 54 | 30 (16, 47) | 100 (90, 100) | 100 (86, 100) | 100 (90, 100) | 57 (39, 73) | 100 (90, 100) | 57 (39, 73) | 100 (90, 100) | 57 (39, 73) | 100 (90, 100) | 100 (86, 100) | 100 (90, 100) |
| EMB | 15 | 76 | 53 (27, 79) | 100 (93, 100) | 94 (70, 100) | 100 (93, 100) | 53 (27, 79) | 100 (93, 100) | 47 (21, 73) | 99 (93, 100) | 94 (70, 100) | 99 (93, 100) | 100 (71, 100) | 100 (93, 100) |
| PZA | 11 | 80 | 45 (17, 77) | 100 (93, 100) | 100 (62, 100) | 99 (93, 100) | 45 (17, 77) | 100 (93, 100) | n.a. | n.a. | 100 (62, 100) | 99 (93, 100) | 100 (62, 100) | 99 (93, 100) |
Notes:
Evaluation of resistance deduction from whole-genome sequence data by programs CASTB, PhyResSE, KvarQ, Mykrobe Predictor TB, TBProfiler, and MTBseq, with sensitivity (Sens) and specificity (Spec) estimated with 95% confidence intervals compared to Sanger sequencing results (#R resistant, #S sensitive).
INH, isoniazid; RMP, rifampicin; SM, streptomycin; EMB, ethambutol; PZA, pyrazinamide.