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Table 1 Mutations detected in all strains analyzed

From: Sequence analysis for detection of first-line drug resistance in Mycobacterium tuberculosis strains from a high-incidence setting

Gene

Mutation

Strains phenotypically susceptible to INH (n=)

Strains phenotypically resistant to INH (n=)

katG

wild type

65

4(1)

 

Ala291Thr (gct/act); Ser315Thr (agc/acc)

 

1

 

Trp300Cys (tgg/tgc)

 

1

 

Thr302Arg (acg/agg)

 

1

 

Ser315Thr (acg/acc)

 

21

 

Asp329 (gac/ggac frameshift)

 

1

 

Arg463Leu (cgg/ctg)(2)

 

2

 

Gln471Arg (cag/cgg); Ser315Thr (agc/acc)

 

1

 

Strains phenotypically susceptible to RIF (n=)

Strains phenotypically resistant to RIF (n=)

rpoB

wild type

76

 
 

Thr481Ala (acc/gcc)(3)

 

1

 

Leu511Pro (ctg/ccg)(4)

1

 
 

Asp516Tyr (gac/tac)(4)

3

 
 

His526Tyr (cac/tac)

 

3

 

His526Arg (cac/cgc)

 

3

 

Ser531Leu (tcg/ttg)

 

8

 

Leu533Pro (ctg/ccg)(4)

1

1

 

Strains phenotypically susceptible to SM (n=)

Strains phenotypically resistant to SM (n=)

rpsL

wild type

56

21

 

Lys43Arg (aag/agg)

 

11

 

Lys88Arg (aag/agg)

1

8

gidB

wild type

26 (2 with mutations in rrs/rpsL)

15 (10 with mutations in rpsL)

 

Leu16Arg (ctt/cgt)

4

2

 

Leu16Arg (ctt/cgt); Gln127stop (caa/taa); Ala161Ala (gcc/gcg)

1

 
 

Leu16Arg (ctt/cgt); Ala161Ala (gcc/gcg)

2

1 (Lys43Arg in rpsL)

 

Leu16Arg (ctt/cgt); Ala200Glu (gcg/gag)

 

2

 

Leu16Arg (ctt/cgt); Ala205Ala (gca/gcg)

 

1 (Lys43Arg in rpsL)

 

Gly34Ala (ggg/gcg)

 

1

 

Pro38 (ccc/cc frameshift)

 

1 (Lys88Arg in rpsL)

 

Val65Gly (gtc/ggc)

 

1

 

Gly69Asp (ggt/gat)

1

2

 

Gly71Arg (gga/aga)

 

1

 

Val88Ala (gta/gca)

 

1

 

Leu91Pro (cta/cca)

 

1

 

Gly92Asp (gaa/gac)

1

 
 

Gly92Asp (gaa/gac); Ala205Ala (gca/gcg)

 

3 (Lys43Arg in rpsL)

 

Ser100Phe (tct/ttt)

 

1

 

Val110Val (gtg/gtt); Ala205Ala (gca/gcg)

4

 
 

Ala138Val (gcg/gtg)

 

2

 

Ala200Glu (gcg/gag) + Ala205Ala (gca/gcg)

 

1

 

Ala205Ala (gca/gcg)

18

4 (3 with mutations in rpsL)

 

Strains phenotypically susceptible to EMB (n=)

Strains phenotypically resistant to EMB (n=)

embB

wild type

82

4(5)

 

Met306Ile (atg/ata)

 

6

 

Met306Val (atg/gtg)

 

1

 

Trp332Arg (tgg/cgg)

 

1

 

Gln497Lys (cag/aag)(3)

 

1

 

Gln1002Arg (cag/cgc)(3)

 

2

 

Strains phenotypically susceptible to PZA (n=)

Strains phenotypically resistant to PZA (n=)

pncA

wild type

84

3

 

−11 (a/g)

 

1

 

Ile5 (atc/atcc frameshift)

 

1

 

Thr47Ala (acc/gcc)

2

 
 

Tyr64 (tat/tata frameshift)

 

1

 

Lys96Glu (aag/gag)

1

 
 

Gln141 (cag/cag acggcgccag (insertion of 10 bp → frameshift)

 

1

 

Ala146Glu (gcg/gag)

 

1

 

Gly162Asp (ggt/gat)

 

1

 

Leu172Pro (ctg/ccg)

 

1

  1. Sequence analysis and drug susceptibility testing has been repeated for all strains showing discrepant results.
  2. Abbreviations: INH, isoniazid; RIF, rifampin; SM, streptomycin; EMB, ethambutol; PZA, pyrazinamide.
  3. (1)Those strains were additionally sequenced in the promoter region of inhA and ahpC. Two of them carried a mutation in inhA at position −15 (C → T) and one in ahpC at −57 (C → T).
  4. (2)Arg463Leu is a phylogenetic SNP [23] and was excluded for further analysis.
  5. (3)These mutations were identified by sequence analysis of the complete gene.
  6. (4)These mutations confer low-level RIF resistance.
  7. (5)These strains were sequenced in the complete embCAB operon. One strain carried a mutation in embC [Val981Leu (gtg/ctg)].