Table.
In-vitro selected variants in Rv0678, atpE, and other genes conferring resistance to bedaquiline and clofazimine
| Mutation | Number of times selected | Bedaquiline MIC (mg/L) | Bedaquiline MIC fold increase | Clofazimine MIC (mg/L) | Clofazimine MIC fold increase | ||
|---|---|---|---|---|---|---|---|
| Wild-type ancestor | .. | 0·25 to 0·50 | .. | 0·5 to 1·0 | .. | ||
| Rv0678 | |||||||
| Promotor | −10_–9insG | 1 | 2 | 4 to 8 | 1 | 1 to 2 | |
| 6fs* | 16_17delG | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| 9fs* | 26_27delAG | 1 | 2 | 4 to 8 | NA | NA | |
| 14fs* | 40_41delC | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 17fs | 49_50delA | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 21fs | 62_63delA | 1 | 2 | 4 to 8 | 1 | 1 to 2 | |
| Gly24Val* | 71G→T | 3 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Gly25Ser | 73G→A | 1 | 2 | 4 to 8 | NA | NA | |
| 30fs | 89_90delG | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Arg38Ter | 112C→T | 4 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Arg38Pro | 113G→C | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Leu40Ser | 119T→C | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| 40fs | 120_121delG | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Leu43Pro | 128T→C | 5 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| Leu43Arg | 128T→G | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Leu44Pro* | 131T→C | 4 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Arg50Trp | 148C→T | 16 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Gln51Arg | 152A→G | 2 | 2 | 4 to 8 | 4 | 4 to 8 | |
| Glu54Ter | 160G→T | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Glu55Ter* | 163G→T | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Ala57Glu | 170C→A | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Ala62Asp* | 185C→A | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Ser63Gly | 187A→G | 3 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 64fs* | 192_193insG | 18 | 1 to 4 | 2 to 16 | 2 to 4 | 2 to 8 | |
| 65fs* | 193_194delG | 13 | 1 to 2 | 2 to 8 | 2 to 4 | 2 to 8 | |
| Gly66Glu | 197G→A | 1 | 2 | 4 to 8 | 1 | 1 to 2 | |
| Ser68Gly* | 202A→G | 9 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| Arg72Trp | 214C→T | 2 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| Arg72Leu | 215G→T | 3 | 2 to 4 | 4 to 16 | 4 to 6 | 4 to 12 | |
| Leu74Pro* | 221T→C | 8 | 1 to 2 | 2 to 8 | 2 to 4 | 2 to 8 | |
| 76fs* | 228_229insT | 1 | 2 | 4 to 8 | NA | NA | |
| Phe79Val | 235T→G | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Phe79Cys | 236T→G | 2 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Ala84Val | 251C→T | 2 | 1 to 2 | 2 to 8 | 1 to 2 | 1 to 4 | |
| 88fs | 263_264insT | 1 | 2 | 4 to 8 | 1 | 1 to 2 | |
| 92fs | 274_275insA | 3 | 1 | 2 to 4 | 2 | 2 to 4 | |
| 94fs | 281_282delG | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 97fs | 291_292insA | 2 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 98fs | 292_293delA | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Ala99Val* | 296C→T | 17 | 1 to 2 | 2 to 8 | 1 to 2 | 1 to 4 | |
| Ala102Thr* | 304G→A | 4 | 1 to 4 | 2 to 16 | 2 to 4 | 2 to 8 | |
| Gly103Arg | 307G→C | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| Leu114Pro | 341T→C | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Gln115Ter | 343C→T | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Ala118Asp* | 353C→A | 1 | 1 | 2 to 4 | 2 | 2 to 4 | |
| 120fs* | 360_361delG | 8 | 1 to 4 | 2 to 16 | 2 to 4 | 2 to 8 | |
| Gly121Glu | 362G→A | 3 | 2 | 4 to 8 | 2 to 4 | 2 to 8 | |
| Leu122Pro | 365T→C | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 125fs | 374_375delT | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Leu125Pro | 374T→C | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Arg132Pro | 395G→C | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Arg135Trp | 403C→T | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Leu136Pro | 407T→C | 2 | 2 | 4 to 8 | 2 to 4 | 2 to 8 | |
| 139fs | 417_418insCGGGATCTGTTGGCATATAT | 3 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| 142fs | 425_426delT | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 142fs | 426_427insTTGGCATA | 1 | 2 | 4 to 8 | NA | NA | |
| Tyr145Ter* | 435T→G | 6 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| Ser151Pro | 451T→C | 1 | 2 | 4 to 8 | 2 | 2 to 4 | |
| Leu154Pro | 461T→C | 2 | 2 | 4 to 8 | 2 | 2 to 4 | |
| 155fs | 465_466insC | 2 | 1 to 2 | 2 to 8 | 2 | 2 to 4 | |
| Arg156Ter | 466C→T | 3 | 2 | 4 to 8 | 2 | 2 to 4 | |
| atpE | |||||||
| Asp28Gly | 83A→G | 1 | ≥10 | ≥20 | NA | NA | |
| Asp28Val | 83A→T | 3 | ≥8 | ≥16 | NA | NA | |
| Glu61Asp* | 183G→C | 4 | 2 to ≥10 | 4 to ≥20 | 1 | 1 to 2 | |
| Glu61Asp | 183G→T | 3 | ≥10 | ≥20 | 1 to 2 | 1 to 4 | |
| Ala63Pro* | 187G→C | 7 | ≥10 | ≥20 | 1 to 2 | 1 to 4 | |
| Other | .. | 13 | 2 | 4 to 8 | 1 to 2 | 1 to 4 | |
The genotype of each variant was identified by whole-genome sequencing. The 13 mutants under the category Other do not have any variant in a resistance-associated gene. MIC was established by resazurin microtitre assay and compared with the drug-susceptible wild-type ancestor to describe MIC fold increase. Each single mutant was tested at least one time with biological duplicates. MICs of independently selected mutants with the same mutation were pooled together and represented as a range. Additional details including variant position, selection drug, and selection concentration are included in appendix 3 (p 1). fs=frameshift. MIC=minimum inhibitory concentration. NA=not available.
One or more selected mutants harbour a variant in a second gene; further details are given in appendix 3 (p 4).