Skip to main content

Table 2 Significant associations between loci and drug resistance phenotypes identified by locus-based GWAS

From: Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

Locus Known Phenotype Association [13] Lineage Observed Phenotype Association P-value PhyC
rpoB RMP 2 XDR, RMP, MDR 1.9 × 10− 72, 5.2 × 10− 58, 1.4 × 10− 44 11
rpoB RMP 4 RMP, MDR, PZA, XDR, EMB 2 × 10− 94, 1.1 × 10− 35, 1.1 × 10− 33, 2.5 × 10− 30, 6.4 × 10− 23 23
rpoB RMP 2 + 4 RMP, MDR, XDR, PZA 1.6 × 10− 126, 4.1 × 10− 77, 4.1 × 10− 66, 2.1 × 10− 24 40
gyrA FQ 2 MOX, FQ, XDR, OFL 5.2 × 10− 117, 2.5 × 10− 45, 4.3 × 10− 23, 5.1 × 10− 22 21
gyrA FQ 4 FQ, CIP, XDR 4.1 × 10− 38, 5.4 × 10− 36, 6.5 × 10− 27 24
gyrA FQ 2 + 4 FQ, OFL, CIP 1.2 × 10− 63, 1.7 × 10− 32, 2.2 × 10− 26 44
pncA PZA 2 XDR 1.50 × 10− 25 0
pncA PZA 4 PZA 4.50 × 10− 103 3
pncA PZA 2 + 4 PZA, EMB, XDR 5.3 × 10− 101, 1.2 × 10− 29, 6.7 × 10− 22 6
embC-embA EMB 4 XDR, EMB 6.1 × 10− 69, 2.8 × 10− 26 8
embC-embA EMB 2 + 4 XDR, EMB 3.3 × 10− 37, 1.4 × 10− 23 13
katG INH 2 INH, MDR 3.6 × 10−34, 7.3 × 10−24 5
katG INH 4 INH 1.20 × 10−44 9
katG INH 2 + 4 INH, MDR 1.5 × 10−61, 1.5 × 10−36 9
embB EMB 2 EMB 7.20 × 10−27 14
embB EMB 4 EMB 1.80 × 10−56 31
embB EMB 2 + 4 EMB 3.30 × 10−55 41
gid STM 4 STM 7.40 × 10− 55 0
gid STM 2 + 4 STM 1.30 × 10−53 0
Rv1313c-Rv1314c   4 XDR 1.40 × 10−54 0
Rv1313c-Rv1314c   2 + 4 XDR 3.30 × 10−32 0
rpsL STM 2 STM 1.90 × 10−38 4
rpsL STM 4 STM 5.60 × 10−26 6
rpsL STM 2 + 4 STM 6.00 × 10−41 13
fadB4-Rv3142c   4 XDR 4.60 × 10−38 0
Rv0526   2 + 4 XDR 8.70 × 10−37 0
Rv1482c-fabG1 INH, ETH 4 INH 1.70 × 10−34 3
Rv1482c-fabG1 INH, ETH 2 + 4 INH 3.30 × 10−30 14
espE-espF   2 + 4 XDR 5.70 × 10−31 0
tuf   4 XDR 1.50 × 10−29 0
inhA INH, ETH 4 XDR 2.40 × 10−28 0
cut5b-Rv3725   4 XDR 5.10 × 10−27 0
Rv3007c   4 XDR 7.80 × 10−24 0
Rv2668   4 XDR 1.30 × 10−23 0
pip-Rv0841   2 + 4 XDR 8.60 × 10− 23 0
rrs STM, AG 2 KAN 1.40 × 10−22 8
moeX   4 XDR 5.50 × 10− 22 0
lipJ-cinA   2 + 4 XDR 6.20 × 10−22 0
Rv3128c-Rv3129   2 MDR 7.40 × 10−22 0
  1. (P-values <1E-21) Novel associations are given in bold. ‘PhyC’ column refers to the number of associations identified through PhyC analysis for the locus and lineage in question. AMK = Amikacin-resistance, AG = Aminoglycoside-resistance, CAP = Capreomycin-resistance, CIP = Ciprofloxacin-resistance, EMB = Ethambutol-resistance, ETH = Ethionamide-resistance, FQ = Fluoroquinolone-resistance, INH = Isoniazid-resistance, KAN = Kanamycin-resistance, MDR = Multidrug-resistant, OFL = Ofloxacin-resistance, PAN = pan-susceptible (no known drug-resistance), PZA = Pyrazinamide-resistance, RMP = Rifampicin-resistance, STM = Streptomycin-resistance, XDR = Extensively drug-resistant