An assessment of nucleic acid amplification testing for active mycobacterial infection

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
Bates et al. (2013) Zambia	Level III-2 Low risk of bias	MGIT culture	N=788 gastric aspirates from children	AFB (FL) Xpert	12 33	23 5	36 15	717 735	None reported
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=33 gastric aspirates - n=30	AFB (FL) Xpert AFB + NAAT AFB –ve: Xpert	3 5 5 2	0 0 0 0	2 0 0 0	28 28 28 28	None reported
Moure, Martin & Alcaide (2012) Spain	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=6 gastric aspirates	AFB –ve: Xpert	2	0	1	3	2/8 specimens had an Xpert indeterminate result

AFB = acid-fast bacilli; FL = fluorescent; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; Xpert = GeneXpert MTB/RIF NAAT

Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in stools

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
El Khechine et al. (2009) France	Level III-2 Low risk of bias	L-J for stools	N=134 stool samples	AFB (ZN) IS6110 qPCR AFB + NAAT	9 13 13	0 11 11	4 0 0	121 110 110	None reported

AFB = acid-fast bacilli; L-J = Lowenstein-Jensen; NAAT = nucleic acid amplification test; qPCR = quantitative (real-time) polymerase chain reaction; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in cerebrospinal fluid

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
Bhigjee et al. (2007) South Africa	Level III-2 Low risk of bias	7H11 medium culture and MGIT culture	N=126 CSF specimens from 68 patients	AFB –ve: IS6110-MPB64 PCR qPCR	18 18	9 16	2 2	97 90	None reported
Deshmukh et al. 2013 India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=60 CSF specimens	AFB (ZN) IS6110 PCR AFB + NAAT	2 10 10	0 19 19	12 4 4	46 27 27	None reported
Desai et al. (2006) India	Level III-2 Low risk of bias	L-J culture	N=30 CSF specimens	AFB (ZN) IS6110 PCR	1 8	0 12	19 0	22 10	None reported
Makeshkumar, Madhavan & Narayanan (2014) India	Level III-2 Low risk of bias	L-J culture	N=25 CSF specimens	AFB –ve: IS6110 PCR	0	9	0	16	None reported
Ani et al. (2009) Nigeria	Level III-2 Low risk of bias	L-J slope culture	N=5 CSF specimens from children	AFB –ve IS6110 PCR	0	0	0	5	None reported
Therese, Jayanthi & Madhavan (2005) India	Level III-2 Some risk of bias	L-J culture	N=120 CSF specimens - n=119	AFB (ZN) IS6110 PCR AFB + NAAT AFB –ve: IS6110 PCR	1 1 1 0	0 37 37 37	0 0 0 0	119 82 82 82	None reported
Baveja et al. (2009) India	Level III-2 Some risk of bias	L-J and BACTEC culture	N=100 CSF specimens from children	AFB (ZN) MPB64 PCR	2 22	0 0	20 0	78 78	None reported
Shukla et al. (2011) India	Level III-2 Some risk of bias	L-J culture	N=16 CSF specimens	AFB –ve: IS6110 nPCR	0	12	0	4	None reported

AFB = acid-fast bacilli; CSF = cerebrospinal fluid; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; nPCR = nested PCR; PCR = polymerase chain reaction; qPCR = quantitative (real-time) PCR; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in cerebrospinal fluid

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
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=15 CSF specimens	AFB –ve: Xpert	1	0	0	14	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=14 CSF specimens	AFB –ve: Xpert	0	0	0	14	None reported
Moure, Martin & Alcaide (2012) Spain	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=14 CSF specimens	AFB –ve: Xpert	2	0	0	12	None reported

AFB = acid-fast bacilli; CSF = cerebrospinal fluid; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; Xpert = GeneXpert MTB/RIF NAAT

Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in body fluids

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
Maurya et al. (2011a) India	Level III-1 Low risk of bias	BACTEC culture	N=102 pleural effusions - n=17 n=85	AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve IS6110 PCR AFB –ve IS6110 PCR	15 45 45 15 30	2 17 18 1 16	32 2 2 0 2	53 38 37 1 37	None reported
Singh et al. (2006) India	Level III-1 Low risk of bias	L-J culture	N=85 bone-marrow aspirates	AFB –ve MPB64 PCR	1	18	0	66	None reported
Bhanu et al. (2005) India	Level III-1 Low risk of bias	L-J culture	N=16 endometrial aspirates	AFB (ZN) mpt64 PCR	0 0	1 1	0 8	15 7	1 negative PCR included in analysis was found to be inhibitory
Makeshkumar, Madhavan & Narayanan (2014) India	Level III-2 Low risk of bias	L-J culture	N=119 CSF specimens 59 ascetic fluid, 54 pleural fluid, 6 synovial fluid	AFB (ZN) IS6110 PCR	1 0	0 28	0 1	118 90	None reported
Deshmukh et al. 2013 India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=52 body fluid specimens	AFB (ZN) IS6110 PCR AFB + NAAT	3 12 12	0 7 7	13 4 4	36 29 29	None reported
Ani et al. (2009) Nigeria	Level III-2 Low risk of bias	L-J slope culture	N=25 fluid specimens from children 11 gastric wash 5 ascitic fluid 9 pleural effusions	AFB –ve IS6110 PCR	12	0	0	13	None reported
Therese, Jayanthi & Madhavan (2005) India	Level III-2 Some risk of bias	L-J culture	N=107 specimens 104 peritoneal and 3 pericardial n=106	AFB (ZN) IS6110 PCR AFB + NAAT AFB –ve: IS6110 PCR	1 2 2 1	0 64 64 64	2 1 1 1	104 40 40 40	None reported
Bhanothu, Theophilus & Rozati (2014) India	Level III-2 Some risk of bias	L-J culture	N=11 pelvic fluids	AFB (ZN) TCR4 PCR AFB + NAAT	7 11 11	0 0 0	0 0 0	4 0 0	None reported

AFB = acid-fast bacilli; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; M-PCR = multiplex PCR; NAAT = nucleic acid amplification test; PCR = polymerase chain reaction; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in body fluids