Table:
Sensitivity and specificity of commercial and WGS-based tests for resistance diagnosis
| Commercial test |
randomForests-select WGS test |
Direct association-select WGS test |
All WGS test* |
|||||
|---|---|---|---|---|---|---|---|---|
| Sensitivity | Specificity | Sensitivity | Specificity | Sensitivity | Specificity | Sensitivity | Specificity | |
| Isoniazid | 83% (2759/3306) | 93% (4834/5201) | 88% (2900/3306) | 92% (4780/5201) | 89% (2956/3306) | 92% (4776/5201) | 92% (3029/3306) | 64% (3314/5201) |
| Rifamycins | 90% (2354/2624) | 93% (5361/5786) | 91% (2385/2624) | 92% (5341/5786) | 91% (2395/2624) | 92% (5338/5786) | 92% (2405/2624) | 89% (5178/5786) |
| Fluoroquinolones | 53% (452/854) | 94% (2626/2790) | 51% (439/854) | 95% (2637/2790) | 52% (440/854) | 95% (2641/2790) | 57% (488/854) | 86% (2406/2790) |
| Second-line injectables | 56% (517/921) | 86% (2179/2547) | 58% (535/921) | 84% (2136/2547) | 57% (524/921) | 86% (2185/2547) | 64% (594/921) | 80% (2027/2547) |
| Pyrazinamide | ·· | ·· | 65% (862/1324) | 95% (4660/4907) | 75% (996/1324) | 91% (4485/4907) | 78% (1030/1324) | 89% (4384/4907) |
| Ethambutol | ·· | ·· | 79% (1476/1863) | 86% (4702/5441) | 75% (1389/1863) | 88% (4772/5441) | 85% (1589/1863) | 74% (4042/5441) |
| Streptomycin | ·· | ·· | 76% (1601/2112) | 86% (3204/3726) | 77% (1627/2112) | 87% (3223/3726) | 91% (1928/2112) | 71% (2657/3726) |
Sensitivity is the percentage of resistant isolates classified as resistant. Specificity is the percentage of susceptible isolates classified as susceptible. WGS=whole genome sequencing.
*
Classifying fluoroquinolones and second-line injectables as susceptible if no isoniazid and no rifamycin resistance mutation found.