TABLE 2.
MTBDRplus line-probe assay (LPA) results and associated mutations observed by Illumina MiSeq whole-genome sequencing (WGS) for confirmation of rifampin-isoniazid resistance as originally defined by LJ culture in 20-year-old M. tuberculosis isolates (n = 240)
| Resistance category results by LPA (no. tested/total no.; %) | No. of isolates selected for WGS (total n = 111) | Description of mutations by WGSa |
No. of isolates (total n = 96) with indicated mutation(s) | |
|---|---|---|---|---|
| rpoB | katG | |||
| RIF+INH resistant (171/240; 71.3%) | 42b | Ser531Leu | Ser315Thr | 15 |
| His526Try | Ser315Thr | 7 | ||
| Ser531Leu | Ser315Thr, Arg463Leu | 3 | ||
| Ser526Asp/TyrSTOP | Ser315Thr | 2 | ||
| Ser531Leu | Ser315Ile | 1 | ||
| Asp516Val | Ser315Thr/SerSTOP | 1 | ||
| Ser531Thr | Ser315Thr | 1 | ||
| Asp516Val | Ser315Asn | 1 | ||
| Thr525Pro | DelCpos526, Ser315Thr | 1 | ||
| Asp516Val | Ser315Ile | 1 | ||
| His526Asp | Ser315Asn | 1 | ||
| Leu533Pro | Ser315Asn | 1 | ||
| His526Leu | Trp91Arg, Arg463Leu | 1 | ||
| Thr480Ala, Ser531Leu | Ser315Thr | 1 | ||
| His526Tyr | Ser315Arg | 1 | ||
| Ser531Leu | Ser315Thr, Arg463Leu, Ala464Leu | 1 | ||
| His526Tyr | Trp91Arg, Ser140Gly, Arg463Leu | 1 | ||
| Gln409Arg, Ser450Leu | Arg463Leu | 1 | ||
| His 526 Tyr | Ile200Thr (inhA gene) | 1 | ||
| RIF monoresistant (44/240; 18.3%) | 44c | His531Leu | No mutations | 4 |
| His531Leu | Arg463Leu | 2 | ||
| His531Leu | Del2185G | 1 | ||
| His531Leu | Pro131Arg, Arg463Leu | 1 | ||
| His531Leu | Tyr98Cys | 1 | ||
| His531Leu | Ser315Thr | 1 | ||
| His531Leu | Asp381Glu | 1 | ||
| His531Leu | Pro232Arg | 1 | ||
| His531Leu | Asp1426Arg | 1 | ||
| His531Leu | del 1426G (Missense) | 1 | ||
| His531Leu | Pro29Ser, Met420Thr | 1 | ||
| His531Leu | Pro232Ala | 1 | ||
| His531Leu | Ser100Ala (inhA gene) | 1 | ||
| His526Tyr | Arg463Leu | 2 | ||
| His526Tyr | Ins19A | 1 | ||
| His526Tyr | Phe594Ser | 1 | ||
| His526Tyr | Gln88STOP | 1 | ||
| His526Asp | Gly699Glu | 1 | ||
| His526Asp | Leu378Arg | 1 | ||
| Ser531Trp | Ala122Gly/Ala | 1 | ||
| Ser531Trp | Trp477STOP | 1 | ||
| Ser522Leu | Trp412STOP | 1 | ||
| Asp516Val | Arg463Leu | 1 | ||
| Asp516Val | Ins576A | 1 | ||
| Gln253Arg, His256Arg | No mutations | 1 | ||
| His526Arg | Trp198STOP | 1 | ||
| Leu511Pro/LeuSTOP | Gly699GLU | 1 | ||
| DelC526 | Arg463Leu, Trp477STOP | 1 | ||
| Wild type | Arg463Leu, Del entire codon pos 480 | 1 | ||
| INH monoresistant (5/240; 2%) | 5 | Val251Phe | Thr380Ile | 2 |
| Ser522Leu | Ser315Thr, Arg463Leu | 1 | ||
| Val249Met, Val251Tyr | Ser315Thr, Arg463Leu | 1 | ||
| Ser531Leu | Ser315Thr | 1 | ||
| RIF + INH susceptible (20/240; 8.3%) | 15d | Wild type | Wild type | 4 |
| Ser531Leu | No mutations | 2 | ||
| No mutations | Ser315Thr, W198STOP | 1 | ||
| His526Leu/His (mixed) | Ser315Thr | 1 | ||
| Ser531Leu | Pro232Ala | 1 | ||
| Ser531Leu | Glu553Lys | 1 | ||
| His526Leu/Ala | Gly299Ser | 1 | ||
| Ile572Phe/IleSTOP | Arg104Trp | 1 | ||
| Asp516Val | DelGpos1284 | 1 | ||
| Ile572Phe/IleSTOP | Gly299Arg/GlySTOP | 1 | ||
| Ser531Leu/SerSTOP | Arg463Leu | 1 | ||
a
Novel mutations present by WGS are shown in bold type.
b
Randomly selected from the 171 isolates.
c
Sequencing failed in 10 isolates (DNA concentration was too low for WGS), leaving 34 isolates with WGS results.
d
Sequencing failed in 5 isolates (DNA concentration was too low for WGS), leaving 15 isolates with WGS results.