Table 2.
Generalized linear mixed model analysis was conducted on clustered and non-clustered MDR-TB isolates
| Rv number | Gene | Position | SNP | Amino acid changes | P value | OR (95%CI) |
|---|---|---|---|---|---|---|
| Rv0239 | vapB24 | 289,179 | A76C | Thr26Pro | 0.994 | - |
| Rv0239 | vapB24 | 289,300 | C197T | Ser66Phe | 9.999E-01 | - |
| Rv0298 | - | 363,375 | C124A | Leu42Met | 0.776 | 1.192(0.355–4.004) |
| Rv0298 | - | 363,464 | G213A | Arg71Arg | 0.022 | 6.104(1.295–28.782) |
| Rv0300 | vapB2 | 363,996 | T171C | Gly57Gly | 0.177 | 2.174(0.704–6.716) |
| Rv0657c | vapB6 | 753,562 | T56C | Ile19Thr | 0.202 | 0.547(0.216–1.383) |
| Rv0657c | vapB6 | 753,589 | A29C | Asp10Ala | 0.420 | 0.604(0.177–2.057) |
| Rv0662c | vapB7 | 755,873 | C151T | Arg51Cys | 0.730 | 1.137(0.547–2.366) |
| Rv0662c | vapB7 | 755,947 | G77A | Arg26His | 0.530 | 1.473(0.439–4.946) |
| Rv0664 | vapB8 | 758,548 | G17T | Cys6Phe | 0.580 | 1.375(0.445–4.247) |
| Rv1241 | vapB33 | 1,384,315 | G38A | Arg13Gln | 0.169 | 3.575(0.582–21.976) |
| Rv1246c | relE | 1,388,827 | A152T | Asn51Ile | 0.998 | - |
| Rv1494 | mazE4 | 1,686,299 | T29G | Ile10Ser | 0.061 | 0.434(0.181–1.039) |
| Rv1740 | vapB34 | 1,967,783 | A79G | Thr27Ala | 0.997 | - |
| Rv1740 | vapB34 | 1,967,844 | C140A | Ala47Glu | 0.466 | 1.235(0.7-2.181) |
| Rv1740 | vapB34 | 1,967,897 | G193C | Glu65Gln | 0.674 | 1.349(0.335–5.438) |
| Rv1943c | mazE5 | 2,195,025 | A323G | Glu108Gly | 0.839 | 0.92(0.411–2.058) |
| Rv1943c | mazE5 | 2,195,321 | G27A | Thr9Thr | 0.863 | 0.891(0.241–3.289) |
| Rv1955 | higB | 2,201,720 | T2C | Val1? | 0.408 | 1.332(0.675–2.63) |
| Rv1955 | higB | 2,201,808 | C90G | Asp30Glu | 0.853 | 0.936(0.465–1.883) |
| Rv1956 | higA | 2,202,491 | A354G | Ala118Ala | 0.995 | - |
| Rv1956 | higA | 2,202,500 | C363T | His121His | 0.265 | 3.36(0.399–28.29) |
| Rv1956 | higA | 2,202,582 | G445T | Ala149Ser | 0.990 | - |
| Rv1959c | parE1 | 2,203,869 | G109A | Glu37Lys | 0.053 | 8.02(0.975–65.957) |
| Rv1959c | parE1 | 2,203,890 | C88T | Gln30* | 5.510E-09 | 33.215(10.233–107.81) |
| Rv1960c | parD1 | 2,204,092 | C134T | Thr45Ile | 0.002 | 4.464(1.693–11.768) |
| Rv1962A | vapB35 | 2,205,283 | G267A | Arg89Arg | 0.154 | 3.743(0.609–23.024) |
| Rv1962A | vapB35 | 2,205,371 | T179G | Val60Gly | 0.999 | - |
| Rv1962A | vapB35 | 2,205,451 | G99A | Lys33Lys | 0.185 | 0.471(0.155–1.434) |
| Rv1962A | vapB35 | 2,205,511 | G39A | Thr13Thr | 0.359 | 0.716(0.35–1.463) |
| Rv1991A | mazE6 | 2,234,736 | G156A | Arg52Arg | 4.610E-04 | 38.321(4.981-294.819) |
| Rv2009 | vapB15 | 2,258,096 | C67T | Arg23Trp | 0.116 | 2.379(0.808–7.005) |
| Rv2142c | parE2 | 2,402,439 | C72T | Asp24Asp | 0.175 | 0.479(0.165–1.387) |
| Rv2274c | mazF8 | 2,546,601 | A205G | Ile69Val | 0.576 | 0.62(0.116–3.313) |
| Rv2274c | mazF8 | 2,546,684 | G122T | Gly41Val | 0.986 | - |
| Rv2274c | mazF8 | 2,546,803 | G3A | Met1? | 0.204 | 0.479(0.154–1.493) |
| Rv2526 | vapB17 | 2,851,303 | G213C | Glu71Asp | 0.060 | 3.33(0.95-11.677) |
| Rv2545 | vapB18 | 2,867,913 | T131G | Leu44Arg | 0.075 | 2.357(0.918–6.055) |
| Rv2547 | vapB19 | 2,868,659 | C54G | Ala18Ala | 0.003 | 2.066(1.278–3.339) |
| Rv2547 | vapB19 | 2,868,787 | A182G | Asp61Gly | 0.083 | 3.022(0.865–10.554) |
| Rv2595 | vapB40 | 2,925,594 | G103A | Asp35Asn | 0.997 | - |
| Rv2601A | vapB41 | 2,930,254 | G185A | Gly62Asp | 0.973 | 1.018(0.357–2.903) |
| Rv2653c | - | 2,976,616 | C294G | His98Gln | 1.000E + 00 | - |
| Rv2653c | - | 2,976,654 | C256T | Leu86Phe | 0.983 | - |
| Rv2653c | - | 2,976,830 | A80C | Gln27Pro | 0.201 | 0.337(0.064–1.783) |
| Rv2654c | - | 2,977,157 | T78G | Ala26Ala | 0.021 | 0.041(0.003–0.611) |
| Rv2830c | vapB22 | 3,137,058 | C167T | Ala56Val | 0.581 | 0.78(0.323–1.884) |
| Rv2862A | vapB23 | 3,174,748 | T2C | Ile1? | 0.047 | 2.735(1.012–7.388) |
| Rv2865 | relF | 3,177,660 | G124A | Ala42Thr | 0.172 | 0.541(0.224–1.306) |
| Rv2866 | relG | 3,177,884 | C63A | Arg21Arg | 0.986 | - |
| Rv2871 | vapB43 | 3,183,210 | A73G | Thr25Ala | 0.991 | - |
| Rv3181c | - | 3,550,092 | G52T | Val18Phe | 0.915 | 1.069(0.313–3.656) |
| Rv3385c | vapB46 | 3,799,821 | C123T | Asp41Asp | 9.998E-01 | - |
| Rv3385c | vapB46 | 3,799,874 | G70A | Ala24Thr | 0.004 | 7.973(1.911–33.263) |
| Rv3407 | vapB47 | 3,826,316 | G65T | Arg22Leu | 0.994 | - |
| Rv3407 | vapB47 | 3,826,501 | C250T | Arg84Cys | 0.203 | 0.809(0.584–1.121) |
| Rv3697A | vapB48 | 4,140,319 | C145T | Arg49Cys | 0.990 | - |
| Rv3697A | vapB48 | 4,140,384 | G80A | Gly27Glu | 0.998 | - |
SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval