An assessment of nucleic acid amplification testing for active mycobacterial infection
- Bu səhifədəki naviqasiya:
- False-positive results False-negative results True-negative results
- Study Country Evidence level and risk of bias Reference standard
| Study
Country |
Evidence level and risk of bias |
Reference standard |
Population Samples |
Tests |
True-positive results |
False-positive results |
False-negative results |
True-negative results | |
|
Inconclusive results | |||||||||
|
Park et al. (2013) Korea
|
Level III-1 Low risk of bias |
Liquid and/or solid culture |
N=320 pulmonary specimens n=26 n=294
|
AFB Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
13 19 22 10 9 |
13 6 19 0 6 |
10 4 1 3 1 |
284 291 278 13 278 |
None reported |
|
Tortoli et al. (2012) Italy
|
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=1,413 extrapulmonary samples |
AFB (FL) Xpert |
98 188 |
12 32 |
140 50 |
1163 1143 |
61/1,493 specimens grew NTM 17/1,493 had indeterminate Xpert results and were excluded from analysis |
|
Bates et al. (2013) Zambia
|
Level III-2 Low risk of bias |
MGIT culture |
N=930 mixed pulmonary specimens from children |
AFB (FL) Xpert |
15 42 |
43 16 |
30 7 |
842 865 |
None reported |
|
Al-Ateah et al. (2012) Kingdom of Saudi Arabia |
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=239 specimens - n=43 n=196 N=183 non-sputum - n=12
n=171 N=67 extrapulmonary - n=7
n=60 |
AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert AFB (FL)
AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert AFB (FL)
AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
41 58 59 41 17 10 21 22 10 11 6 16 17 6 10 |
1 0 1 0 0 1 0 1 0 0 0 0 0 0 0 |
20 4 3 1 3 13 3 2 1 2 11 2 1 1 1 |
177 177 176 1 176 159 159 158 1 158 50 49 49 0 49 |
None reported |
|
Malbruny et al. (2011) France
|
Level III-2 Low risk of bias |
MGIT and Coletsos slants |
N=180 specimens - n=17 n=163 |
AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
15 29 29 15 14 |
2 2 4 0 2 |
16 2 2 0 2 |
147 147 145 2 145 |
None reported |
|
Malbruny et al. (2011) France
|
Level III-2 Low risk of bias |
MGIT and Coletsos slants |
N=162 non-sputum - n=13 n=149 N=89 extrapulmonary - n=5
n=84 |
AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert AFB (FL)
AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
11 24 24 11 13 4 12 12 4 8 |
2 2 4 0 2 1 2 3 0 2 |
15 2 2 0 2 10 2 2 0 2 |
134 134 132 2 132 74 73 72 1 72 |
- |
|
Balcells et al. (2012) Chile
|
Level III-2 Low risk of bias |
Solid L-J and liquid media culture |
N=160 HIV+ sputum or mouthwash specimens |
HIV+ AFB (ZN) Xpert |
8 11 |
2 1 |
4 1 |
146 147 |
Repeated Xpert MTB/RIF assays were performed for patients who had discordant results |
|
Teo et al. (2011) Singapore |
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=153 specimens - n=58 n=95 N= 122 pulmonary - n=52
n=70 N=31 extrapulmonary - n=6
n=25 |
AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert : AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert AFB (FL)
AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
47 70 70 47 23 43 56 56 43 13 4 14 14 4 10 |
11 8 14 5 3 9 5 11 3 2 2 3 3 2 1 |
30 7 7 0 7 19 6 6 0 6 11 1 1 0 1 |
65 68 62 6 62 51 55 49 6 49 14 13 13 0 13 |
9/162 respiratory specimens gave invalid GeneXpert results |
|
Ioannidis et al. (2011) Greece
|
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=92 AFB -ve mixed specimens |
AFB –ve: Xpert |
19 |
5 |
3 |
65 |
12/105 cultures were contaminated 1/105 had invalid Xpert result |
|
Deggim et al. (2013) Switzerland |
Level III-2 Low risk of bias |
MGIT 960 liquid and Middlebrook 7H11 culture |
N=77 mixed specimens - n=19
n=58 |
AFB (FL) Xpert AFB + NAAT AFB +ve Xpert AFB –ve Xpert
|
14 15 15 14 1 |
5 2 7 0 2 |
4 3 3 0 3 |
54 57 52 5 52 |
2/79 had invalid Xpert results |
|
Zeka, Tasbakan & Cavusoglu (2011) Turkey
|
Level III-2 Some risk of bias |
MB/BacT liquid and/or L-J culture |
N=429 mixed specimens n=32 n=397
|
AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
31 71 71 31 40 |
1 6 7 0 6 |
58 18 18 0 18 |
339 334 333 1 333 |
None reported |
|
Marlowe et al. (2011) USA
|
Level III-2 Some risk of bias |
Culture |
N=216 pulmonary specimens n=126 n=90
|
AFB Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert
|
87 116 118 85 31 |
39 4 39 4 0 |
43 14 12 2 12 |
47 82 47 35 47 |
1/217 bronchial specimen was found to be PCR inhibitory and was excluded from analysis |
|
Moure, Martin & Alcaide (2012) Spain
|
Level III-2 Some risk of bias |
MGIT and/or L-J culture |
N=147 AFB –ve extrapulmonary specimens |
AFB –ve: Xpert |
63 |
0 |
45 |
39 |
2/149 specimens had Xpert indeterminate results |
AFB = acid-fast bacilli; FL = fluorescent; HIV = human immunodeficiency virus; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria; TB = tuberculosis; Xpert = GeneXpert MTB/RIF NAAT; ZN = Ziehl-Neelsen
Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in sputum
|
Study Country |
Evidence level and risk of bias |
Reference standard |
Population Samples |
Tests |
True-positive results |
False-positive results |
False-negative results |
True-negative results |
Inconclusive results |
|
Davis et al. (2009) Uganda
|
Level II Low risk of bias |
L-J Middlebrook and MGIT cultures |
N=100 sputum samples - n=63
n=37 |
AFB (ZN) secA1 PCR AFB + NAAT AFB +ve: secA1 PCR AFB –ve secA1 PCR |
55 62 63 54 8 |
8 6 11 3 3 |
8 1 0 1 0 |
29 31 26 5 26 |
27/127 AFB microscopy results not recorded and excluded from analysis |
|
Mashta et al. (2011) India
|
Level III-1 Low risk of bias |
L-J liquid medium culture |
N=463 sputum samples - n=228 n=235 |
AFB (MB) IS6110 -devR PCR AFB + NAAT AFB +ve IS6110 -devR PCR AFB –ve IS6110 -devR PCR
|
148 69 157 60 9 |
80 71 115 32 35 |
44 123 39 88 39 |
191 200 152 48 152 |
Contaminated samples (4%) were identified and patients were called to collect a second sample |
|
Nakiyingi et al. (2012) Uganda
|
Level III-1 Some risk of bias |
L-J liquid medium culture |
N=181 patients with AFB –ve sputum samples |
AFB –ve IS6110 PCR |
48 |
75 |
16 |
42 |
5/205 cultures were contaminated 19/205 PCR results were unavailable |
|
Ekrami et al. (2011) Iran
|
Level III-1 Some risk of bias |
L-J solid medium culture |
N=152 sputum samples |
AFB (ZN) IS6110 PCR IS6110 nPCR) |
90 78 94 |
6 8 6 |
16 28 12 |
40 38 40 |
None reported |
|
Chakravorty et al. (2006) India
|
Level III-2 Low risk of bias |
L-J solid medium culture |
N=506 sputum samples from 506 patients |
USP AFB (ZN) devR PCR IS6110 PCR |
273 269 272 |
39 52 65 |
0 4 1 |
194 181 168 |
None reported |
|
Michelon et al. (2011) Brazil
|
Level III-2 Low risk of bias |
Culture |
N=469 sputum specimens N=295 induced sputum specimens N=174 spontaneous sputum specimens |
AFB IS6110 PCR AFB + NAAT AFB
AFB + NAAT AFB
AFB + NAAT |
62 65 75 55
60 7
15 |
7 7 12 5
2
|
14 10 1 6
8
|
386 387 381 229
224 157
157 |
4/476 (3 induced and 1 spontaneous) specimens were PCR inhibitory 3/479 (induced) gave indeterminate results |
|
Jiang et al. (2012) China
|
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=207 sputum samples - n=51 n=156 |
AFB (ZN) 16S qRT-PCR AFB + NAAT AFB +ve: 16S qRT-PCR AFB –ve: 16S qRT-PCR
|
24 28 28 24 4 |
27 21 43 5 16 |
6 2 2 0 2 |
150 156 134 22 134 |
None reported |
|
Suzuki et al. (2006) Japan
|
Level III-2 Low risk of bias |
MGIT culture |
N=138 sputum specimens n=55 n=83
|
: AFB dnaJ PCR-ICA AFB + NAAT AFB +ve: dnaJ PCR-ICA AFB –ve: dnaJ PCR-ICA
|
53 41 57 39 1 |
2 5 5 2 3 |
20 32 16 14 19 |
63 60 60 0 60 |
None reported |
|
El Khechine et al. (2009) France
|
Level III-2 Low risk of bias |
BACTEC 9000 liquid culture |
N=134 sputum samples N=134 stool samples |
AFB (ZN) IS6110 qPCR AFB + NAAT |
13 18 18 |
2 10 10 |
7 0 0 |
112 106 106 |
None reported |
|
George, Mony & Kenneth (2011) India
|
Level III-2 Low risk of bias |
MGIT and/or L-J medium culture |
N=71 sputum samples - n=33 n=38 |
AFB (FL) LAMP AFB + NAAT AFB +ve: LAMP AFB –ve: LAMP
|
32 31 32 29 2 |
1 2 3 2 0 |
7 8 7 1 7 |
31 30 29 1 29 |
7/78 samples showed contamination for both L-J and MGIT cultures and were omitted from analysis |
|
Deshmukh et al. 2013 India
|
Level III-2 Low risk of bias |
MGIT and/or L-J culture |
N=27 sputum specimens |
AFB (ZN) IS6110 PCR AFB + NAAT |
5 13 13 |
1 3 3 |
9 1 1 |
12 10 10 |
None reported |
|
Ani et al. (2009) Nigeria
|
Level III-2 Low risk of bias |
L-J slope culture |
N=10 sputum specimens from children |
AFB –ve IS6110 PCR |
4 |
0 |
6 |
0 |
None reported |
|
Chakravorty et al. (2005) India
|
Level III-2 Some risk of bias |
L-J solid medium culture |
N=571 samples from 571 patients |
direct AFB (ZN) USP AFB (ZN) IS6110 PCR |
322 225 325 |
21 18 70 |
6 103 3 |
222 225 173 |
None reported |
|
Santos et al. (2006) Brazil
|
Level III-2 Some risk of bias |
L-J medium culture |
N=214 sputum samples - n=46 n=168 |
AFB (direct) AFB (conc.) IS6110 PCR AFB (conc.) + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR
|
14 17 38 38 17 21 |
1 4 24 26 2 22 |
30 27 6 6 5 1 |
169 166 146 144 22 124 |
4/218 samples were excluded due to contamination of culture tubes |
|
Lee, Chen & Peng (2009) Taiwan
|
Level III-2 Some risk of bias |
Culture (not specified) |
N=150 sputum samples |
AFB LAMP |
30 32 |
9 7 |
4 2 |
107 109 |
None reported |
|
de Albuquerque et al. (2014) Brazil
|
Level III-2 Some risk of bias |
L-J solid medium and 7H9 broth culture |
N=140 sputum specimens from 140 HIV+ patients |
HIV+ AFB (ZN) IS6110 qPCR |
37 41 |
0 1 |
10 6 |
93 92 |
None reported |
|
Marchi et al. (2008) Brazil
|
Level III-2 Some risk of bias |
L-J-MTBAC culture |
N=117 sputum specimens |
AFB (ZN) IS6110 PCR |
3 3 |
0 0 |
3 3 |
111 111 |
None reported |
|
Ereqat et al. (2011) Palestine |
Level III-2 Some risk of bias |
Culture |
N=95 samples from 84 patients n=13 n=82
|
AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR
|
7 10 10 7 3 |
6 20 20 6 14 |
4 1 1 0 1 |
78 64 64 0 64 |
None reported |
|
Shukla et al. (2011) India
|
Level III-2 Some risk of bias |
L-J culture |
N=40 AFB +ve sputum specimens |
AFB +ve: IS6110 nPCR |
36 |
0 |
2 |
2 |
None reported |
|
Gomez et al. (2011) Southern Texas (USA) and Mexico |
Level III-2 Some risk of bias |
MGIT liquid medium and L-J solid medium culture |
N=150 patients - n=101 n=49 |
AFB RD1 qPCR IS1081 qPCR IS6110 qPCR AFB + NAAT (IS6110 qPCR) AFB +ve: IS6110 qPCR AFB –ve: IS6110 qPCR |
99 102
104 107
96 8
|
2 0
2 0
|
8 5
0 3
|
41 43
43 41 2 41 |
32 had contaminated MGIT |
|
Haldar et al. (2007) India
|
Level III-2 Some risk of bias |
7H9 liquid media culture |
N=148 sputum samples |
Direct AFB (ZN) USP AFB (ZN) devR FL-PCR devR Gel-PCR IS6110 FL-PCR IS6110 Gel-PCR |
24 85 111
110 102 |
2 2 2
4 3 |
96 35 9
10 18 |
26 26 26
24 25 |
None reported |
AFB = acid-fast bacilli; FL = fluorescent; HIV = human immunodeficiency virus; LAMP = loop-mediated isothermal amplification; L-J = Lowenstein-Jensen; MB = methylene blue; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; nPCR = nested PCR; PCR = polymerase chain reaction; PCR-ICA = PCR-immunochromatographic assay; qPCR = quantitative (real-time) PCR; qRT-PCR = quantitative (real-time) reverse transcription PCR; USP = universal sample processing; ZN = Ziehl-Neelsen
Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in sputum
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