Table 2.
GyrB amino acid polymorphisms identified in the N. abscessus (n = 29), N. cyriacigeorgica (n = 30), and N. nova (n = 29) strains
| Species |
Amino acid (nucleotides) at the indicated positions (1–4)a |
|||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N. farcinica DSM 43665b | 160 | 161 | 164 | 181 | 183 | 185 | 187 | 188 | 233 | 237 | 238 | 240 | 257 | 258 | 259 | 260 | 262 | 265 | 292 | 349 |
| N. abscessus strainsc | ||||||||||||||||||||
| DSM 44432b (n = 11) | 10 Glu (GAG) | 38 Lys (AAG) | 87 Asp (GAC) | 109 Ala (GCC) | ||||||||||||||||
| Mutatedb (n = 18) | Lys (AAG) | Gln (CAG) | Glu (GAA) | Ser (TCC) | ||||||||||||||||
| Frequency (%) | 3.4 | 3.4 | 58.6 | 10.3 | ||||||||||||||||
| N. cyriacigeorgica strainsd | ||||||||||||||||||||
| DSM 44484c (n = 8) | 29 Val (GTC) | 32 Ala (GCC) | 49 Ile (ATC) | 53 Pro (CCG) | 55 Thr (ACG) | 106 Thr (ACC) | 108 Val (GTC) | 125 Ala (GCC) | 126 Glu (GAG) | 127 Ala (GCG) | 128 Gln (CAG) | 130 Thr (ACC) | ||||||||
| Mutatedc (n = 22) | Ile (ATC) | Asp (GAC) | Val (GTT) | Ala (GCG) | Ser (TCC), Lys (AAG) | Ala (GCC) | Ile (ATC) | Glu (GAG) | Gln (CAG) | Thr (ACG) | Pro (CCG), Ala(GCG) | Ala (GCC) | ||||||||
| Frequency (%) | 3.3 | 3.3 | 3.3 | 43.3 | 36.7 6.6 | 6.6 | 20.0 | 23.3 | 23.3 | 23.3 | 66.6 3.3 | 50.0 | ||||||||
| N. nova strainse | ||||||||||||||||||||
| DSM 44481d (n = 8) | 51 Gly (GGT) | 101 Glu (GAG) | 105 Asp (GAT) | 126 Ala (GCG) | 129′ | 131 Hys (CAG) | 157 Pro (CCG) | 215 Val (GTG) | ||||||||||||
| Mutatedd (n = 21) | Asp (GAC), Ser (AGC) | Gln (CAG) | Glu (GAG) | Thr (ACC), Ser (AGC), Asn (AAC) | Pro (CCG) | Pro (CCG), Arg (CGG) | Ala (GCG) | Phe (TTC) | ||||||||||||
| Frequency (%) | 3.4, 3.4 | 62.0 | 62.0 | 44.8, 10.34, 3.4 | 65.5 | 62, 3.4 | 68.9 | 3.4 | ||||||||||||
Amino acid polymorphism positions (modified nucleotides are underlined) with respect to the complete genome sequence of reference strain N. farcinica DSM 43665T (accession no. NC_006361), N. abscessus DSM 44432T (accession no. AB447398), N. cyriacigeorgica DSM 44484T (accession no. GQ496121), and N. nova DSM 44481T (accession no. GQ496102).
All the N. farcinica strains harbored the same GyrB as N. farcinica DSM 43665T (accession no. NC_006361).
No. of GyrB types, 5; HGDI, 0.94; divergence, 0.5 to 1.4%.
No. of GyrB types, 9; HGDI, 0.94; divergence, 0.4 to 4.3%.
No. of GyrB types, 11; HGDI, 0.81; divergence, 0.4 to 2.6%.