TABLE 2.
Diagnostic potential of mutations at known resistance-conferring locia
| Drug | Gene | Mutation | Frequency | PPV | Sensitivity | Specificity |
|---|---|---|---|---|---|---|
| Rifampin | Any | 70 | 1 | 0.99 | 1 | |
| rpoB | D435Yb,c | 2 | 1 | 0.03 | 1 | |
| H445D/L/Yb,c | 19 | 1 | 0.27 | 1 | ||
| S450L/Wb,c | 49 | 1 | 0.69 | 1 | ||
| Isoniazid | Any | 72 | 0.99 | 0.97 | 0.96 | |
| katG | S315Tc | 71 | 1 | 0.97 | 1 | |
| inhA | c-15tc | 26 | 0.96 | 0.34 | 0.96 | |
| t-8a/cc | 26 | 1 | 0.36 | 1 | ||
| Ofloxacin | Any | 43 | 1 | 0.91 | 1 | |
| gyrA | A90Vc | 14 | 1 | 0.28 | 1 | |
| S91Pc | 4 | 1 | 0.08 | 1 | ||
| D94A/G/H/N/Yc | 25 | 1 | 0.50 | 1 | ||
| gyrB | D461N | 2 | 1 | 0.04 | 1 | |
| N499T | 1 | 1 | 0.02 | 1 | ||
| Kanamycin | Any | 40 | 0.90 | 0.73 | 0.91 | |
| rrs | a1400gc | 31 | 1 | 0.61 | 1 | |
| c1483tc | 1 | 1 | 0.02 | 1 | ||
| eis | g-10a | 2 | 0 | 0 | 0.96 | |
| c-14t | 6 | 0.67 | 0.08 | 0.96 | ||
| Amikacin | Any | 32 | 1 | 0.86 | 1 | |
| rrs | a1400gc | 31 | 1 | 079 | 1 | |
| c1483tc | 1 | 1 | 0.03 | 1 | ||
| Capreomycin | Any | 35 | 0.97 | 0.83 | 0.98 | |
| rrs | a1400gc | 31 | 1 | 0.72 | 1 | |
| c1483tc | 1 | 1 | 0.02 | 1 | ||
| tlyA | LOF | 3 | 0.67 | 0.05 | 0.98 | |
| Streptomycin | Any | 70 | 1 | 0.93 | 1 | |
| rpsL | K43R | 41 | 1 | 0.55 | 1 | |
| K88R | 3 | 1 | 0.04 | 1 | ||
| rrs | a513c | 19 | 1 | 0.25 | 1 | |
| a516t | 6 | 1 | 0.08 | 1 | ||
| gidB | LOF | 2 | 1 | 0.03 | 1 | |
| Pyrazinamide | Any | 3 | 1 | 0.16 | 1 | |
| pncA | LOF | 3 | 1 | 0.16 | 1 | |
| Ethambutol | Any | 63 | 0.98 | 0.90 | 0.96 | |
| embB | M306I/Vc | 38 | 0.97 | 0.53 | 0.96 | |
| G406D | 1 | 1 | 0.01 | 1 | ||
| Q497R | 24 | 1 | 0.34 | 1 | ||
| Ethionamide | Any | 65 | 0.35 | 1 | 0.42 | |
| ethA | LOF | 47 | 0.36 | 0.74 | 0.59 | |
| inhA | c-15tc | 26 | 0.50 | 0.57 | 0.82 | |
| t-8a/cc | 26 | 0.23 | 0.26 | 0.73 |
a
Isolates were included only if they had both phenotypic and genotypic resistance predictions. For each mutation, we show frequency of the mutation in the data set, positive predictive value (PPV), sensitivity, and specificity for predicting phenotypic resistance. Mutations are listed as either specific changes or as any loss-of-function (LOF) mutation, including nonsense mutations and frameshifts.
b
Mutation detectable by GeneXpert MTB/RIF.
c
Mutation detectable by MTBDRplus version 2.0 or MTBDRsl version 1.0.