Table 3. Common SNPs found in drug resistance related genes in isolates CSF-3053, 46-5069 and 43-13838.
The reference genome positions, nucleotide change, amino acid change and effect of single nucleotide polymorphisms in drug resistance related genes that are common to isolates CSF3053, 46-5069 and 43-13838. The protein variation was determined by Protein Variation Effect Analyzer (PROVEAN), a web based protein variation analysis tool (Choi et al., 2012).
| Position in reference genome (H37Rv, NC_000962.3) | Nucleotide change | Amino acid change | Protein variation effect | Gene | Associated drug | References |
|---|---|---|---|---|---|---|
| 6112 | G>C | Met291Ile | Deleterious | gyrB | Quinolones | Guillemin, Jarlier & Cambau (1998) |
| 7362 | G>C | Glu21Gln | Neutral | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) |
| 7585 | G>C | Ser95Thr | Neutral | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) and Kapur et al. (1995) |
| 8452 | C>T | Ala384Val | Deleterious | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) |
| 9143 | T>C | Ile614Ile | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) | |
| 9260 | G>C | Leu653Leu | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) | |
| 9304 | G>A | Gly668Asp (N) | Neutral | gyrA | Quinolones | Guillemin, Jarlier & Cambau (1998) |
| 412280 | T>G | His481Gln | Neutral | iniA | Ethambutol | Ramaswamy et al. (2003) |
| 575368 | T>C | Asp7Asp | Rv0486 | Isoniazid/Ethionamide | Projahn et al. (2011) | |
| 763031 | T>C | Ala1081Ala | rpoB | Rifampicin | Taniguchi et al. (1996) | |
| 763531 | G>C | Pro54Pro | rpoC | Rifampicin | Comas et al. (2012) | |
| 763884 | C>T | Ala172Val | Neutral | rpoC | Rifampicin | Comas et al. (2012) |
| 763886 | C>A | Arg173Arg | rpoC | Rifampicin | Comas et al. (2012) | |
| 1406312 | A>G | His343His | Rv1258c | Streptomycin | Siddiqi et al. (2004) | |
| 1417019 | C>T | Cys110Tyr | Deleterious | embR | Ethambutol | Ramaswamy et al. (2000) |
| 1674162 | C>T | Gly241Gly | fabG1 | Isoniazid | Lavender et al. (2005) | |
| 1792777 | T>C | Ile322Val | Neutral | Rv1592c | Isoniazid | Ramaswamy et al. (2003) |
| 1792778 | T>C | Glu321Glu | Rv1592c | Isoniazid | Ramaswamy et al. (2003) | |
| 2154724 | C>A | Arg463Leu | Neutral | katG | Isoniazid | Heym et al. (1995) |
| 2518132 | C>T | Thr6Thr | kasA | Isoniazid | Lee et al. (1999) | |
| 2519048 | G>A | Gly312Ser | Neutral | kasA | Isoniazid | Lee et al. (1999) |
| 2521342 | T>C | Asp200Asp | accD6 | Isoniazid | Ramaswamy et al. (2003) | |
| 3154414 | A>G | Ile73Thr | Neutral | efpA | Isoniazid | Ramaswamy et al. (2003) |
| 3571834 | T>G | Gln237Pro | Neutral | nudC | Isoniazid/Ethionamide | Wang et al. (2011) |
| 3647041 | A>G | Ser257Pro | Neutral | rmlD | Ethambutol | Ramaswamy et al. (2000) |
| 3647591 | A>G | Asn73Asn | rmlD | Ethambutol | Ramaswamy et al. (2000) | |
| 4049254 | G>A | Leu243Leu | folP1 | Para-aminosalicylic acid | Mathys et al. (2009) | |
| 4240671 | C>T | Thr270Ile | Neutral | embC | Ethambutol | Ramaswamy et al. (2000) |
| 4241042 | A>G | Asn394Asp | Deleterious | embC | Ethambutol | Ramaswamy et al. (2000) |
| 4242643 | C>T | Arg927Arg | embC | Ethambutol | Ramaswamy et al. (2000) | |
| 4243580 | G>A | Val116Val | embA | Ethambutol | Telenti et al. (1997) | |
| 4244420 | G>C | Val396Val | embA | Ethambutol | Telenti et al. (1997) | |
| 4245969 | C>T | Pro913Ser | Deleterious | embA | Ethambutol | Ramaswamy et al. (2000) and Telenti et al. (1997) |
| 4247578 | G>A | Leu355Leu | embB | Ethambutol | Telenti et al. (1997) | |
| 4247646 | A>C | Glu378Ala | Neutral | embB | Ethambutol | Telenti et al. (1997) |
| 4407588 | T>C | Ala205Ala | rsmG | Streptomycin | Okamoto et al. (2007) | |
| 4407873 | C>A | Val110Val | rsmG | Streptomycin | Okamoto et al. (2007) |