An assessment of nucleic acid amplification testing for active mycobacterial infection


Appendix D Analysis of diagnostic accuracy data



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Appendix D Analysis of diagnostic accuracy data


Table 93 Prevalence of MTB culture-positive patients in included studies

-

Overall [range]

> 100 [range]

100–10 [range]

< 10 [range]

All studies

-

-

-

-

All NAAT

Overall k=68

AFB +ve k=28

AFB –ve k=39

HIV+ k=7

HIV+, AFB –ve k=2

HIV– k=6

HIV–, AFB +ve k=4

HIV–, AFB –ve k=5


-

30% [1–81]

80% [27–100]

19% [1–72]

30% [16–42]

15% [12–19]

38% [8–77]

75% [27–100]

29% [6–50]


-

33% [2–81]

81% [27–100]

18% [1–50]

30% [16–42]

15% [12–19]

38% [8–77]

75% [27–100]

29% [6–50]


-

29% [1–71]

82% [47–98]

23% [2–72]

30% [22–34]

-

-



-

-


-

24% [6–60]

72% [54–88]

15% [4-48]

-

-

-



-

-


In-house NAAT

Overall k=44

AFB +ve k=16

AFB –ve k=23
-

32% [1–81]

80% [47–100]

17% [1-44]
-

36% [2–81]

86% [65–100]

20% [1–44]
-

29% [1–71]

74% [47–98]

13% [2–31]
-

24% [12–60]

69% [54–84]

5% [4–5]


Xpert

Overall k=24

AFB +ve k=12

AFB –ve k=16
-

27% [5–77]

78% [27–100]

23% [1–72]
-

27% [5–77]

67% [27–100]

14% [1–50]
-

29% [8–50]

92% [64–98]

37% [10-72]
-

24% [6–60]

74% [64–88]

18% [4–48]

Sputum specimens

-

-

-

-

All NAAT

Overall k=30

AFB +ve k=14

AFB –ve k=16

HIV+ k=3

HIV+, AFB +ve k=1

HIV– k=2

HIV–, AFB +ve k=1

HIV–, AFB –ve k=1


-

37% [5–81]

76% [27–100]

25% [4–100]

35% [34–38]

12%


42% [8–77]

27%


50%

-

42% [7–81]

78% [27–100]

34% [9–100]

38% (k=1)

12%


42% [8–77]

27%


50%

-

38% [5–71]

80% [47–100]

24% [4–56]

34% [34–34]

-

-



-

-


-

15% [6–28]

59% [54–64]

5% [4–6]


-

-

-



-

-


In-house NAAT

Overall k=18

AFB +ve k=9

AFB –ve k=10
-

41% [5–81]

76% [47–98]

26% [4–100]
-

58% [41–81]

85% [65–95]

40% [20–100]
-

34% [1–71]

72% [47–98]

14% [4–24]
-

13% [12–15]

54% (k=1)

5% (k=1)


Xpert

Overall k=12

AFB +ve k=5

AFB –ve k=7
-

32% [6–77]

76% [27–100]

23% [4–56]
-

26% [7–77]

64% [27–100]

23% [9–50]
-

49% [34–68]

96% [91–100]

42% [28–56]
-

17% [6–28]

64% (k=1)

5% [4–6]


Non-sputum specimens

-

-

-

-

All NAAT

Overall k=35

AFB +ve k=11

AFB –ve k=19

HIV+ k=4

HIV+, AFB –ve k=1

HIV– k=3

HIV–, AFB +ve k=2

HIV–, AFB –ve k=3


-

27% [1–67]

80% [44–100]

18% [0–72]

26% [16–42]

19%


34% [14–46]

94% [88–100]

24% [6–38]


-

29% [2–67]

86% [62–100]

14% [0–44]

27% [16–42]

19%]


34% [14–46]

94% [88–100]

24% [6–38]


-

24% [1–48]

68% [44–92]

32% [2–72]

30% [22–34]

-

-



-

-


-

23% [10–60]

79% [74–85]

9% [7–10]

-

-

-



-

-


In-house NAAT

Overall k=25

AFB +ve k=8

AFB –ve k=13
-

27% [1–67]

79% [44–100]

15% [0–44]
-

29% [2–67]

86% [62–100]

15% [0–44]
-

21% [1–40]

44% (k=1)

19% [2–32]
-

27% [10–60]

74% (k=1)

7% (k=1)


Xpert

Overall k=10

AFB +ve k=4

AFB –ve k=6
-

26% [6–60]

84% [67–92]

24% [1–72]
-

28% [6–60]

92% (k=1)

6% [1–10]
-

28% [13–48]

76% [67–85]

41% [8–72]
-

16% [16–16]

92% (k=1)

10% (k=1)

AFB = acid-fast bacilli; HIV = human immunodeficiency virus; MTB = Mycobacterium tuberculosis; NAAT = nucleic acid amplification test; Xpert = GeneXpert MTB/RIF NAAT

Forest plot of the sensitivity and specificity of AFB microscopy compared with culture, grouped according to use <a href=of in-house or commercial NAAT, for studies conducted in countries with low and medium incidence of TB" align="bottom" width="931" height="508" border="0">

Figure 38 Forest plot of the sensitivity and specificity of AFB microscopy compared with culture, grouped according to use of in-house or commercial NAAT, for studies conducted in countries with low and medium incidence of TB

Incidence of TB based on WHO estimates from 2012: low incidence = ≤ 10 cases per 100,000 people; medium incidence = 10–100 cases per 100,000 people

AFB = acid-fast bacilli; NAAT = nucleic acid amplification test; TB = tuberculosis



Forest plot of the sensitivity and specificity of AFB microscopy compared with culture, grouped according to use of in-house or commercial NAAT, for studies conducted in countries with high incidence of TB

Figure 39 Forest plot of the sensitivity and specificity of AFB microscopy compared with culture, grouped according to use of in-house or commercial NAAT, for studies conducted in countries with high incidence of TB

Incidence of TB based on WHO estimates from 2012: high incidence = > 100 cases per 100,000 people. The combined values are for all studies in both Figures 38 and 39

AFB = acid-fast bacilli; NAAT = nucleic acid amplification test; TB = tuberculosis

Table 94 Pooled sensitivity and specificity of AFB and NAAT in non-sputum specimens compared with extrapulmonary specimens



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