Table 2 Performance of three NGS in specific pathogen types.

From: Comparative diagnostic performance of metagenomic and two targeted sequencing methods in lower respiratory infection

Type

Technology

No. of samples categorized as:

Accuracy

Sensitivity

Specificity

PPV

NPV

TP

FP

FN

TN

G+

mNGSa

86

7

1

111

96.10% (92.49 − 98.01%)

98.85% (93.77 − 99.80%)

94.07% (88.26 − 97.10%)

92.47% (85.27 − 96.31%)

99.11% (95.12 − 99.84%)

A_tNGSb

35

10

52

108

69.76% (63.15 − 75.63%)

40.23% (30.55 − 50.74%)

91.53% (85.10 − 95.33%)

77.78% (63.73 − 87.46%)

67.50% (59.91 − 74.27%)

C_tNGSa

84

19

3

99

89.27% (84.29 − 92.81%)

96.55% (90.35 − 98.82%)

83.90% (76.22 − 89.44%)

81.55% (72.98 − 87.86%)

97.06% (91.71 − 98.99%)

G-

mNGSa

86

10

6

103

92.20% (87.70 − 95.14%)

93.48% (86.49 − 96.98%)

91.15% (84.47 − 95.12%)

89.58% (81.88 − 94.24%)

94.50% (88.51 − 97.45%)

A_tNGSb

66

2

26

111

86.34% (80.97 − 90.38%)

71.74% (61.81 − 79.92%)

98.23% (93.78 − 99.51%)

97.06% (89.90 − 99.19%)

81.02% (73.64 − 86.71%)

C_tNGSa

91

15

1

98

92.20% (87.70 − 95.14%)

98.91% (94.10 − 99.81%)

86.73% (79.25 − 91.79%)

85.85% (77.96 − 91.23%)

98.99% (94.50 − 99.82%)

DNA virus

mNGSab

82

4

9

110

93.66% (89.45 − 96.26%)

90.11% (82.26 − 94.71%)

96.49% (91.32 − 98.63%)

95.35% (88.64 − 98.18%)

92.44% (86.25 − 95.97%)

A_tNGSa

74

2

17

112

90.73% (85.98 − 93.99%)

81.32% (72.10 − 88.00%)

98.25% (93.83 − 99.52%)

97.37% (90.90 − 99.28%)

86.82% (79.91 − 91.61%)

C_tNGSb

89

29

1

86

85.37% (79.88 − 89.55%)

98.89% (93.97 − 99.80%)

74.78% (66.13 − 81.83%)

75.42% (66.94 − 82.31%)

98.85% (93.77 − 99.80%)

RNA virus

A_tNGSa

61

8

4

132

94.15% (90.05 − 96.62%)

93.85% (85.22 − 97.58%)

94.29% (89.13 − 97.08%)

88.41% (78.75 − 94.01%)

97.06% (92.68 − 98.85%)

C_tNGSa

61

10

4

130

93.17% (88.86 − 95.89%)

93.85% (85.22 − 97.58%)

92.86% (87.35 − 96.07%)

85.92% (75.98 − 92.17%)

97.01% (92.58 − 98.83%)

Fungi

mNGSa

81

6

6

112

94.15% (90.05 − 96.62%)

93.10% (85.76 − 96.80%)

94.92% (89.35 − 97.65%)

93.10% (85.76 − 96.80%)

94.92% (89.35 − 97.65%)

A_tNGSa

80

7

7

111

93.17% (88.86 − 95.89%)

91.95% (84.31 − 96.05%)

94.07% (88.26 − 97.10%)

91.95% (84.31 − 96.05%)

94.07% (88.26 − 97.10%)

C_tNGSa

79

4

8

114

94.15% (90.05 − 96.62%)

90.80% (82.89 − 95.27%)

96.61% (91.61 − 98.67%)

95.18% (88.25 − 98.11%)

93.44% (87.59 − 96.64%)

  1. G+, gram-positive bacteria; G-, gram-negative bacteria; TP, true positive, samples of all diagnostic pathogens detected by NGS; FP, false positive, samples with negative diagnosis but pathogen identification via NGS; FN, false negative, samples with negative NGS result but diagnostic pathogen; TN, true negative, samples with negative result of both diagnosis and NGS; PPV, positive predictive value; NPV, negative predictive value; Lowercase letters represent the test results for differences between two technologies. A significant difference is represented only if one “a” and the other is “b” (Padj < 0.017), otherwise no significant difference is represented (Padj > 0.017).
Back to article page