An assessment of nucleic acid amplification testing for active mycobacterial infection

Appendix Analysis of diagnostic accuracy data

Table 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

Figure 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

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

-	Non-sputum Sensitivity [95%CI]	Non-sputum Specificity [95%CI]	Extrapulmonary Sensitivity [95%CI]	Extrapulmonary Specificity [95%CI]
AFB All NAAT In-house NAAT Commercial NAAT AFB (ZN) AFB (FL)	- 46% [37, 55] k=35 46% [34, 59] k=25 46% [35, 57] k=10 46% [34, 59] k=26 46% [35, 57] k=10	- 98% [97, 99] k=35 98% [96, 99] k=25 99% [98, 99] k=10 98% [96, 99] k=26 96% [90, 99] k=10	- 44% [33, 55] k=29 43% [29, 58] k=21 48% [34, 63] k=8 46% [31, 61] k=21 42% [32, 53] k=7	- 98% [96, 99] k=29 98% [96, 99] k=21 91% [81, 96] k=8 98% [95, 99] k=21 99% [97, 99] k=7
NAAT All NAAT In-house NAAT Commercial NAAT	- 91% [83, 94] k=35 91% [79, 96] k=25 90% [83, 94] k=10	- 92% [84, 96] k=35 88% [75, 95] k=25 96% [90, 99] k=10	- 91% [83, 96] k=29 91% [78, 97] k=21 90% [83, 94] k=8	- 89% [79, 95] k=29 86% [70, 95] k=21 92% [85, 96] k=8
AFB + NAAT All NAAT In-house NAAT Commercial NAAT	- 94% [91, 96] k=18 100% [87, 100] k=11 94% [90, 96] k=7	- 83% [70, 91] k=18 56% [11, 93] k=11 92% [82, 97] k=7	- 94% [91, 96] k=17 93% [87, 96] k=10 94% [91, 97] k=7	- 81% [68, 90] k=17 70% [49, 85] k=10 91% [81, 96] k=7

AFB = acid-fast bacilli; CI = confidence interval; FL = fluorescent staining; NAAT = nucleic acid amplification test; TB = tuberculosis; ZN = Ziehl-Neelsen staining

Figure Forest plot showing the pooled sensitivity and specificity values for AFB, NAAT and AFB plus NAAT compared with culture, according to specimen type

AFB = acid-fast bacilli; BAL = bronchoalveolar lavage; CSF = cerebrospinal fluid; FNA = fine-needle aspirate; NAAT = nucleic acid amplification test

Figure Forest plot of the sensitivity and specificity of NAAT 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

NAAT = nucleic acid amplification test; TB = tuberculosis

Figure Forest plot of the sensitivity and specificity of NAAT 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 41 and 42.

NAAT = nucleic acid amplification test; TB = tuberculosis

Figure Forest plot of the sensitivity and specificity of AFB plus NAAT 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

Figure Forest plot of the sensitivity and specificity of AFB plus NAAT 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 43 and 44.

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

Figure Forest plot of the sensitivity and specificity of NAAT compared with culture in AFB-positive specimens, grouped according to type of NAAT and 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; high incidence = > 100 cases per 100,000 people

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

Figure Forest plot of the sensitivity and specificity of NAAT compared with culture in AFB-negative specimens, grouped according to use of in-house or commercial NAAT and 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; high incidence = > 100 cases per 100,000 people

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

Figure Forest plot of the sensitivity and specificity of AFB and/or NAAT compared with culture in HIV-positive patients suspected of having TB

Incidence of TB based on WHO estimates from 2012

AFB = acid-fast bacilli; BAL = bronchoalveolar lavage; FNA = fine-needle aspirate; NAAT = nucleic acid amplification test; TB = tuberculosis

Figure Forest plot of the sensitivity and specificity of AFB and/or NAAT compared with culture in HIV-negative patients suspected of having TB

Incidence of TB based on WHO estimates from 2012

AFB = acid-fast bacilli; BAL = bronchoalveolar lavage; HIV = human immunodeficiency virus; NAAT = nucleic acid amplification test; TB = tuberculosis

Figure Forest plot of the sensitivity and specificity of AFB and NAAT compared with culture or a clinical reference standard in diagnosing NTM infections

^a Estimated pooled values were obtained using the metan command in Stata 12.1

Incidence of TB based on WHO estimates from 2012

AFB = acid-fast bacilli; CRS = clinical reference standard; HIV = human immunodeficiency virus; MAC = Mycobacterium avium complex; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria

Figure Forest plot of the sensitivity and specificity of culture compared with a clinical reference standard and subgroup analysis of NAAT compared with culture, based on HIV and AFB status

^a Estimated pooled values were obtained using the metan command in STATA 12.1

Incidence of TB based on WHO estimates from 2012

AFB = acid-fast bacilli; CRS = clinical reference standard; HIV = human immunodeficiency virus; MAC = Mycobacterium avium complex; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria.