Table 3 Significant associations between genomic variants and drug resistance phenotypes identified by variant-based GWAS
Variant Locus | Variant Position | Type | Known Phenotype Association [13] | Lineage | Observed Phenotype Association (p-value) | PhyC |
|---|---|---|---|---|---|---|
rrs | 1,473,246 | inter | STM, AG | 2 | CAP(2 × 10−31), KAN(1.1 × 10−37) | 8 |
rrs | 1,473,246 | inter | STM, AG | 4 | KAN(6.7 × 10−31) | 15 |
rrs | 1,473,246 | inter | STM, AG | 2 + 4 | AMK(2.4 × 10−39), CAP(3.9 × 10−48), KAN(6.5 × 10−69), XDRvMDR(5.3 × 10−27) | 18 |
katG | 2,155,168 | NS | INH | 2 | XDR(2.1 × 10− 42) | 5 |
katG | 2,155,168 | NS | INH | 4 | INH(6.1 × 10−65), MDR(6 × 10−45), XDR(1.5 × 10−29) | 9 |
katG | 2,155,168 | NS | INH | 2 + 4 | INH(4.4 × 10–56), MDR(7.4 × 10−25) | 9 |
Rv0197 | 232,574 | NS | Novel | 4 | XDR(9.5 × 10−62) | 0 |
Rv0197 | 232,574 | NS | Novel | 2 + 4 | XDR(232,574;3.8 × 10−51) | 0 |
rpoB | 761,155 | NS | RMP | 2 | XDR(3.5 × 10− 25) | 4 |
rpoB | 761,155 | NS | RMP | 4 | MDR(1.2 × 10−27), PZA(1.9 × 10−28), RMP(2.6 × 10− 42, 7.1 × 10−31, 761,139;3.4 × 10−23), XDR(3.8 × 10− 57) | 7 |
rpoB | 761,139 | NS | RMP | 4 | RMP(3.4 × 10−23) | 3 |
rpoB | 761,155 | NS | RMP | 2 + 4 | MDR(5 × 10−23), PZA(6 × 10−26), RMP(2 × 10−38), XDR(1.3 × 10− 27) | 7 |
rpoB | 761,139 | NS | RMP | 2 + 4 | PZA(4 × 10− 23), RMP(2.2 × 10−29), | 7 |
recF | 4047 | S | Novel | 4 | XDR(1.2 × 10− 52) | 0 |
recF | 4047 | S | Novel | 2 + 4 | XDR(8.6 × 10−41) | 0 |
Rv1482c-fabG1 | 1,673,425 | inter | INH, ETH | 4 | INH(1.1 × 10−36) | 3 |
Rv1482c-fabG1 | 1,673,425 | inter | INH, ETH | 2 + 4 | INH(1.1 × 10− 35) | 14 |
rpsL | 781,687 | NS | STM | 2 | STM(3 × 10−27) | 4 |
rpsL | 781,687 | NS | STM | 2 + 4 | STM(6.3 × 10−28) | 6 |
argJ | 1,867,614 | S | Novel | 2 + 4 | XDR(6.9 × 10−26) | 0 |
gyrA | 7570 | NS | FQ | 4 | XDR(8.6 × 10−23) | 24 |
gyrA | 7582 | NS | FQ | 2 + 4 | CIP(1.3 × 10−24), FQ(4.6 × 10−22) | 44 |