Skip to main content

Advertisement

Table 2 Accuracy of whole genome drug resistance analysis compared to reported resistance phenotype when applied to in silico determination of resistance from raw sequence data.

From: Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

Drug Sample size Resistant (%) Sensitivity (95% CI) Specificity (95% CI) Accuracy (95% CI) China Sen/Spec Pakistan Sen/Spec Malawi Sen/Spec Portugal Sen/Spec Russia Sen/Spec Canada Sen/Spec
INH 693 305 (44) 92.8 (89.9-95.7) 100 (100–100) 96.8 (95.5-98.1) 88.0/100 100/100 92.6/100 94.6/100 100/100 -/100
RMP 694 264 (38) 96.2 (93.9-98.5) 98.1 (96.8-99.4) 97.4 (96.2-98.5) 95.7/97.7 97.3/100 100/98.2 96.9/100 90.9/90.0 -/100
EMB 484 150 (31) 88.7 (83.6-93.8) 81.7 (77.6-85.8) 83.9 (80.6-87.2) 83.6/71.3 100/42.7 100/80 85.7/68.1 100/80.0 -/100
STR 487 225 (46.2) 87.1 (82.7-91.5) 89.7 (86.0-93.4) 88.5 (85.7-91.3) 86.8/91.0 95.8/44.4 61.5/95.6 86.8/81.5 100/100 -/100
PZA 307 110 (35.8) 70.9 (62.4-79.4) 93.9 (90.6-97.2) 85.7 (81.7-89.6) NT 51.3/- 66.7/94.8 80.6/100 100/60.0 -/100
ETH 334 155 (46.4) 73.6 (66.7-80.5) 93.3 (89.6-97.0) 84.1 (80.2-88.1) 38.9/97.3 66.7/90.3 NT 84.9/84.6 NT NT
MOX 42 10 (23.8) 60.0 (29.6-90.4) 68.7 (52.6-84.8) 66.7 (52.4-80.9) NT NT NT 83.3/56.2 25.0/100 NT
OFX 313 117 (37.4) 85.5 (79.1-91.9) 94.9 (91.8 · 98.0) 91.4 (88.3-94.5) 77.8/95.1 -/100 NT 92.1/93.2 NT NT
AMK 193 76 (39.4) 82.9 (74.4-91.4) 98.3 (96.0-100) 92.2 (88.4-96.0) NT 86.5/100 NT 79.5/98.2 NT NT
CAP 358 89 (24.9) 60.7 (50.6-70.8) 90.7 (87.2-94.2) 83.2 (79.4-87.1) 50.0/97.0 85.7/21.7 NT 57.7/98.0 100/91.7 NT
KAN 118 118 (37.3) 87.3 (81.3-93.3) 93.4 (89.9-96.9) 91.1 (88.0-94.3) 71.4/97.0 83.8/- NT 98.0/88.7 80.0/33.3 NT
MDR 693 262 (37.8) 91.2 (87.8-94.6) 98.4 (97.2-99.6) 95.8 (94.3-97.3) 86.3/100 97.3/100 100/98.2 95.8/100 90.9/90.0 -/100
XDR 601 54 (9) 75.9 (64.5-87.3) 98.4 (97.3-99.5) 96.3 (94.8-97.8) 60.9/99.1 -/100 -/100 96.3/88.9 25.0/100 -/100
  1. AMK, amikacin; CAP, capreomycin; CI, confidence interval; EMB, ethambutol; ETH, ethionamide; INH, isoniazid; KAN, kanamycin; MDR, multi-drug resistance; MOX, moxifloxacin; OFX, ofloxacin; NT, not tested; PZA, pyrazinamide; RMP, rifampicin; Sen, sensitivity; Spec, specificity; STR, streptomycin; XDR, extensive drug resistance.