TABLE 3.
Results from Illumina MiSeq whole-genome sequencing for detection of mutations in the emb B, pncA, gyrA, rrs, and rpsL genes of isolates originally defined in 1993 by LJ culture as resistant to isoniazid and rifampind
| Gene (antibiotic) | No. of isolates in which gene was found present by WGS/total no. tested (%) | Description of mutation(s) present by WGSb |
|
|---|---|---|---|
| Codon/nucleotide | No. of isolates | ||
| embB (EMB) | 34/96a (35.4) | Met306Ile | 14 |
| Met306Val | 7 | ||
| Gln497Argc | 3 | ||
| Thr11Xaac | 1 | ||
| Leu17Xaa, Gly25Xaa, Asp456Xaa, Met306Xaa | 1 | ||
| Met306Xaa | 1 | ||
| Gly406Aspc | 1 | ||
| Gln51Proc | 1 | ||
| Asp354Alac | 1 | ||
| Met306Xaa, Gly406Xaa | 1 | ||
| Glu378Alac | 1 | ||
| Tyr319Serc | 1 | ||
| Gln139Hisc | 1 | ||
| pncA (PZA) | 40/96 (41.7) | Trp68Gly | 1 |
| Asp8Asn | 2 | ||
| Trp68STOP | 1 | ||
| −11A>R | 1 | ||
| Phe13Leu | 1 | ||
| Trp68Arg | 1 | ||
| Cys72Try | 1 | ||
| Ins A pos 193 | 4 | ||
| Ala134Arg | 1 | ||
| Leu35Arg | 3 | ||
| Gln10Pro | 1 | ||
| Glu37STOP | 1 | ||
| Gly97Asp | 1 | ||
| Thr100Ile | 1 | ||
| Thr159Ala | 1 | ||
| Gly108Arg | 1 | ||
| Cys14Arg | 1 | ||
| His71Xaa | 1 | ||
| Thr168Xaa | 1 | ||
| Ile6Thr | 1 | ||
| Gln10Xaa | 1 | ||
| Leu35Arg, Val163Ala | 1 | ||
| Thr153Ile | 1 | ||
| Del G pos 7, Del G pos 391 | 1 | ||
| Thr76Pro | 2 | ||
| Phe106Ser | 1 | ||
| Leu4Ser | 1 | ||
| Ser164Leu | 1 | ||
| Ins G pos 392, Ins G pos 393 | 3 | ||
| His71Xaa, Thr168Xaa | 1 | ||
| Thr100Ile, Ile159Ala | 1 | ||
| gyrA (FQL) | 36/96 (37.5) | Ser91Pro | 1 |
| Ser95Thr, Gly668Asp | 12 | ||
| Gln613Glu | 10 | ||
| Ser95Thr, Gln21Glu, Gly668Asp | 1 | ||
| Cys254Arg | 1 | ||
| Gly247Ser | 4 | ||
| Ala90Xaa, Ser95Thr | 1 | ||
| Ser741Pro | 1 | ||
| Val384Ala | 1 | ||
| Leu252Arg | 1 | ||
| Glu21Gln, Ser95Thr, Gly668Asp | 1 | ||
| Asp89Xaa | 1 | ||
| Glu21Gln, Asp94Ala, Ser95Thr, Glt668Asp | 1 | ||
| rrs [16rRNA] (AMK, KAN) | 27/96 (11.3) | 1484G>T | 2 |
| 1403G>R, 1404T>Y | 1 | ||
| 492C>T | 15 | ||
| 517C>T | 4 | ||
| A514A>C | 2 | ||
| A1401A>R | 1 | ||
| 1260G>R, 1278A>W | 1 | ||
| 492C>T, 1260G>R, 1278A>W, 1445C>Y | 1 | ||
| rpsL (SM) | 11/96 (4.6) | Lys43Arg | 9 |
| Lys88Arg | 2 | ||
a
Includes all isolates successfully sequenced as per Table 2.
b
Novel mutations present by WGS are in bold type; bold type and underlining indicate that the mutation also conferred resistance phenotypically.
c
Discordant isolates (resistant by LJ and mutations present by WGS, but susceptible by LPA).
d
Abbreviations: LJ, Löwenstein-Jensen; LPA, line probe assay; WGS, whole-genome sequencing; PZA, pyrazinamide; EMB, ethambutol; FLQ, fluoroquinolone; AMK, amikacin; KAN, kanamycin; SM, streptomycin.