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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.