TABLE 2.
Performance characteristics of tNGS compared to WGS and LPAa
| Test | Drug | Profile | pDST | Performance (95% CI) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| R | S | Sensitivity | Specificity | PPV | NPV | Concordance | Cohen's kappa | |||
| tNGS | RIF | R | 37 | 2 | 95.0 (83.0–99.0) | 97.0 (89.0–100) | 95.0 (83.0–99.0) | 97.0 (89.0–100) | 96.0 (90.0–99.0) | 0.92 (95% CI: 0.84–0.92) |
| S | 2 | 63 | ||||||||
| WGS | RIF | R | 36 | 1 | 97.0 (86.0–100) | 99.0 (92.0–100) | 97.0 (86.0–100) | 99.0 (92.0–100) | 98.0 (93.0–100) | 0.96 (95% CI: 90.0–0.96) |
| S | 1 | 66 | ||||||||
| LPA | RIF | R | 19 | 1 | 100 (82.0–100) | 93.0 (0.68–100) | 95.0 (75.0–100) | 100 (77.0–100) | 97.0 (85.0–100) | 0.94 (95% CI: 0.82–0.94) |
| S | 0 | 14 | ||||||||
| tNGS | INH | R | 37 | 1 | 88.0 (74.0–96.0) | 98.0 (91.0–100) | 97.0 (86.0–100) | 92.0 (83.0–97.0) | 94.0 (88.0–98.0) | 0.88 (95% CI: 78.0–88.0) |
| S | 5 | 61 | ||||||||
| WGS | INH | R | 37 | 2 | 92.0 (80.0–98.0) | 97.0 (89.0–100) | 95.0 (83.0–99.0) | 95.0 (0.87–99.0) | 95.0 (89.0–98.0) | 0.90 (95% CI: 0.81–90.0) |
| S | 3 | 62 | ||||||||
| LPA | INH | R | 16 | 1 | 89.0 (65.0–99.0) | 94.0 (70.0–100) | 94.0 (71.0–100) | 88.0 (64.0–99.0) | 91.0 (76.0–98.0) | 0.82 (95% CI: 63.0–0.82) |
| S | 2 | 15 | ||||||||
| tNGS | FQ | R | 32 | 0 | 100 (89.0–100) | 100 (95.0–100) | 100 (89.0–100) | 100 (95.0–100) | 100 (96.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 71 | ||||||||
| WGS | FQ | R | 30 | 0 | 100 (88.0–100) | 100 (95.0–100) | 100 (88.0–100) | 100 (95.0–100) | 98.0 (93.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 73 | ||||||||
| LPA | FQ | R | 17 | 0 | 100 (80.0–100) | 100 (79.0–100) | 100 (80.0–100) | 100 (79.0–100) | 100 (89.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 16 | ||||||||
| tNGS | AMG | R | 19 | 0 | 100 (82.0–100) | 100 (96.0–100) | 100 (82.0–100) | 100 (96.0–100) | 100 (96.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 84 | ||||||||
| WGS | AMG | R | 17 | 0 | 94.0 (0.73–100) | 100 (96.0–100) | 100 (80.0–100) | 99.0 (94.0–100) | 99.0 (95.0–100) | 0.97 (95% CI: 90.0–0.97) |
| S | 1 | 85 | ||||||||
| LPA | AMG | R | 19 | 1 | 100 (75.0–100) | 95.0 (75.0–100) | 93.0 (66.0–100) | 100 (82.0–100) | 97.0 (0.84–100) | 0.94 (95% CI: 0.82–0.94) |
| S | 0 | 13 | ||||||||
| tNGS | STM | R | 20 | 0 | 95.0 (76.0–100) | 100 (96.0–100) | 100 (83.0–100) | 99.0 (94.0–100) | 99.0 (95.0–100) | 0.97 (95% CI: 0.91–0.97) |
| S | 1 | 83 | ||||||||
| WGS | STR | R | 18 | 3 | 95.0 (74.0–100) | 96.0 (90.0–99.0) | 86.0 (64.0–97.0) | 99.0 (93.0–100) | 96.0 (90.0–99.0) | 0.88 (95% CI: 76.0–88.0) |
| S | 1 | 82 | ||||||||
| tNGS | EMB | R | 0 | 0 | NA | 100 (94.0–100) | NA | 100 (94.0–100) | 100 (94.0–100) | NA |
| S | 0 | 56 | ||||||||
| WGS | EMB | R | 0 | 0 | NA | 97.0 (88.0–100) | NA | 100 (94.0–100) | 97.0 (88.0–100) | NA |
| S | 2 | 56 | ||||||||
| tNGS | PZA | R | 20 | 1 | 83.0 (63.0–95.0) | 99.0 (93.0–100) | 95.0 (76.0–100) | 95.0 (88.0–99.0 | 95.0 (89.0–98.0) | 0.88 (95% CI: 74.0–86.0) |
| S | 4 | 79 | ||||||||
| WGS | PZA | R | 20 | 2 | 87.0 (66.0–97.0) | 98.0 (91.0–100) | 91.0 (71.0–99.0) | 96.0 (90.0–99.0) | 95.0 (89.0–98.0) | 0.86 (95% CI: 74.0–86.0) |
| S | 3 | 79 | ||||||||
| tNGS | LZD | R | 5 | 0 | 100 (48.0–100) | 100 (96.0–100) | 100 (48.0–100) | 100 (96.0–100) | 100 (97.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 102 | ||||||||
| WGS | LZD | R | 5 | 0 | 100 (48.0–100) | 100 (96.0–100) | 100 (48.0–100) | 100 (96.0–100) | 100 (96.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 98 | ||||||||
| tNGS | CFZ | R | 0 | 0 | NA | 100 (97.0–100) | NA | 100 (97.0–100) | 100 (97.0–100) | NA |
| S | 0 | 107 | ||||||||
| WGS | CFZ | R | 0 | 0 | NA | 100 (96.0–100) | NA | 100 (96.0–100) | 100 (96.0–100) | NA |
| S | 0 | 103 | ||||||||
| tNGS | BDQ | R | 0 | 0 | NA | 100 (96.0–100) | NA | 98.0 (93.0–100) | 98.0 (93.0–100) | NA |
| S | 2 | 103 | ||||||||
| WGS | BDQ | R | 2 | 0 | 100 (16.0–100) | 100 (96.0–100) | 100 (16.0–100) | 100 (96.0–100) | 100 (96.0–100) | 1.00 (95% CI: 1.00–1.00) |
| S | 0 | 99 | ||||||||
| tNGS | ETH | R | 8 | 1 | 73.0 (39.0–94.0) | 99.0 (94.0–100) | 89.0 (52.0–100) | 97.0 (91.0–99.0) | 96.0 (90.0–99.0) | 0.78 (95% CI: 0.57–78.0) |
| S | 3 | 91 | ||||||||
| WGS | ETH | R | 7 | 2 | 70.0 (35.0–93.0) | 98.0 (92.0–100) | 78.0 (40.0–97.0) | 97.0 (91.0–99.0) | 95.0 (89.0–98.0) | 0.71 (95% CI: 0.47–71.0) |
| S | 3 | 91 | ||||||||
a
For samples with available pDST results, tNGS, WGS, and LPA results were assessed to study their sensitivity, specificity, positive predictive value, negative predictive value, concordance, and agreement Cohen’s kappa with 95% CI. tNGS—targeted next-generation sequencing; WGS—whole-genome sequencing; LPA—line probe assay; pDST—phenotypic drug susceptibility testing; RIF—rifampicin; INH—isoniazid; FQ—fluoroquinolone; AMG—aminoglycoside; STR—streptomycin; EMB—ethambutol; PZA—pyrazinamide; LZD—linezolid; CFZ—clofazimine; BDQ—bedaquiline; ETH— ethionamide; R—resistant; S—susceptible; PPV—positive predictive value; NPV—negative predictive value. CI—confidence interval; NA—not available.