Table 1. Performance of Mykrobe during development of the variant panel.
TP, number of phenotypically resistant samples that correctly identified as resistant ("true positives"); FP, number of phenotypically susceptible samples which are falsely identified as resistant ("false positives"); TN, number of phenotypically susceptible samples that are correctly identified as susceptible ("true negatives"); FN, number of phenotypically resistant samples that are incorrectly identified as susceptible ("false negative"); VME, very major error rate (false-negative rate); ME, major error rate (false-positive rate); PPV, positive predictive value; NPV, negative predictive value. 95% binomial confidence intervals calculated using the Wilson score interval.
| (a) Candidate panel 1, Training dataset | ||||||||
|---|---|---|---|---|---|---|---|---|
| Drug | TP | FP | TN | FN | VME (95% CI) | ME (95% CI) | PPV (95% CI) | NPV (95% CI) |
| Ethambutol | 209 | 121 | 2807 | 22 | 9.52(6.4-14.0%) | 4.13(3.5-4.9%) | 63.33(58.0-68.3%) | 99.22(98.8-99.5%) |
| Isoniazid | 564 | 32 | 2538 | 38 | 6.31(4.6-8.5%) | 1.25(0.9-1.8%) | 94.63(92.5-96.2%) | 98.52(98.0-98.9%) |
| Rifampicin | 373 | 40 | 2714 | 11 | 2.86(1.6-5.1%) | 1.45(1.1-2.0%) | 90.31(87.1-92.8%) | 99.6(99.3-99.8%) |
| Amikacin | 56 | 3 | 702 | 8 | 12.5(6.5-22.8%) | 0.43(0.1-1.2%) | 94.92(86.1-98.3%) | 98.87(97.8-99.4%) |
| Capreomycin | 51 | 36 | 669 | 10 | 16.39(9.2-27.6%) | 5.11(3.7-7.0%) | 58.62(48.1-68.4%) | 98.53(97.3-99.2%) |
| Ciprofloxacin | 19 | 4 | 243 | 0 | 0.0(0.0-16.8%) | 1.62(0.6-4.1%) | 82.61(62.9-93.0%) | 100.0(98.4-100.0%) |
| Kanamycin | 11 | 1 | 528 | 6 | 35.29(17.3-58.7%) | 0.19(0.0-1.1%) | 91.67(64.6-98.5%) | 98.88(97.6-99.5%) |
| Moxifloxacin | 17 | 5 | 549 | 4 | 19.05(7.7-40.0%) | 0.9(0.4-2.1%) | 77.27(56.6-89.9%) | 99.28(98.2-99.7%) |
| Ofloxacin | 19 | 4 | 763 | 6 | 24.0(11.5-43.4%) | 0.52(0.2-1.3%) | 82.61(62.9-93.0%) | 99.22(98.3-99.6%) |
| Streptomycin | 344 | 18 | 1355 | 39 | 10.18(7.5-13.6%) | 1.31(0.8-2.1%) | 95.03(92.3-96.8%) | 97.2(96.2-97.9%) |
| (b) Candidate panel 2, Global dataset | ||||||||
| Drug | TP | FP | TN | FN | VME (95% CI) | ME (95% CI) | PPV (95% CI) | NPV (95% CI) |
| Ethambutol | 1338 | 434 | 3499 | 230 | 14.67(13.0-16.5%) | 11.03(10.1-12.1%) | 75.51(73.5-77.5%) | 93.83(93.0-94.6%) |
| Isoniazid | 2781 | 54 | 2704 | 184 | 6.21(5.4-7.1%) | 1.96(1.5-2.5%) | 98.1(97.5-98.5%) | 93.63(92.7-94.5%) |
| Pyrazinamide | 750 | 177 | 2408 | 264 | 26.04(23.4-28.8%) | 6.85(5.9-7.9%) | 80.91(78.3-83.3%) | 90.12(88.9-91.2%) |
| Rifampicin | 2634 | 60 | 2990 | 136 | 4.91(4.2-5.8%) | 1.97(1.5-2.5%) | 97.77(97.1-98.3%) | 95.65(94.9-96.3%) |
| Amikacin | 100 | 5 | 1495 | 21 | 17.36(11.6-25.1%) | 0.33(0.1-0.8%) | 95.24(89.3-97.9%) | 98.61(97.9-99.1%) |
| Capreomycin | 97 | 26 | 1600 | 42 | 30.22(23.2-38.3%) | 1.6(1.1-2.3%) | 78.86(70.8-85.1%) | 97.44(96.6-98.1%) |
| Ciprofloxacin | 1 | 4 | 33 | 4 | 80.0(37.6-96.4%) | 10.81(4.3-24.7%) | 20.0(3.6-62.4%) | 89.19(75.3-95.7%) |
| Kanamycin | 88 | 3 | 1410 | 47 | 34.81(27.3-43.2%) | 0.21(0.1-0.6%) | 96.7(90.8-98.9%) | 96.77(95.7-97.6%) |
| Moxifloxacin | 14 | 1 | 85 | 3 | 17.65(6.2-41.0%) | 1.16(0.2-6.3%) | 93.33(70.2-98.8%) | 96.59(90.5-98.8%) |
| Ofloxacin | 329 | 19 | 1348 | 59 | 15.21(12.0-19.1%) | 1.39(0.9-2.2%) | 94.54(91.6-96.5%) | 95.81(94.6-96.7%) |
| Streptomycin | 462 | 32 | 2276 | 217 | 31.96(28.6-35.6%) | 1.39(1.0-2.0%) | 93.52(91.0-95.4%) | 91.3(90.1-92.3%) |
| (c) Candidate panel 3, prospective dataset | ||||||||
| Drug | TP | FP | TN | FN | VME (95% CI) | ME (95% CI) | PPV (95% CI) | NPV (95% CI) |
| Ethambutol | 71 | 48 | 4171 | 1 | 1.39(0.2-7.5%) | 1.14(0.9-1.5%) | 59.66(50.7-68.0%) | 99.98(99.9-100.0%) |
| Isoniazid | 312 | 19 | 3931 | 17 | 5.17(3.3-8.1%) | 0.48(0.3-0.7%) | 94.26(91.2-96.3%) | 99.57(99.3-99.7%) |
| Pyrazinamide | 102 | 23 | 4047 | 23 | 18.4(12.6-26.1%) | 0.57(0.4-0.8%) | 81.6(73.9-87.4%) | 99.43(99.2-99.6%) |
| Rifampicin | 133 | 35 | 4140 | 0 | 0.0(0.0-2.8%) | 0.84(0.6-1.2%) | 79.17(72.4-84.6%) | 100.0(99.9-100.0%) |
| Amikacin | 3 | 0 | 59 | 1 | 25.0(4.6-69.9%) | 0.0(0.0-6.1%) | 100.0(43.9-100.0%) | 98.33(91.2-99.7%) |
| Capreomycin | 3 | 0 | 59 | 0 | 0.0(0.0-56.1%) | 0.0(0.0-6.1%) | 100.0(43.9-100.0%) | 100.0(93.9-100.0%) |
| Ciprofloxacin | 30 | 3 | 199 | 19 | 38.78(26.4-52.7%) | 1.49(0.5-4.3%) | 90.91(76.4-96.9%) | 91.28(86.8-94.3%) |
| Kanamycin | 4 | 0 | 54 | 0 | 0.0(0.0-49.0%) | 0.0(0.0-6.6%) | 100.0(51.0-100.0%) | 100.0(93.4-100.0%) |
| Moxifloxacin | 19 | 3 | 41 | 1 | 5.0(0.9-23.6%) | 6.82(2.3-18.2%) | 86.36(66.7-95.2%) | 97.62(87.7-99.6%) |
| Ofloxacin | 21 | 3 | 42 | 1 | 4.55(0.8-21.8%) | 6.67(2.3-17.8%) | 87.5(69.0-95.7%) | 97.67(87.9-99.6%) |
| Streptomycin | 36 | 16 | 685 | 21 | 36.84(25.5-49.8%) | 2.28(1.4-3.7%) | 69.23(55.7-80.1%) | 97.03(95.5-98.0%) |