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
Rachow et al. (2011) Tanzania	Level II Low risk of bias	MGIT and/or L-J media culture	N=249 sputum samples - n=51 n=198	AFB (ZN) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert	51 61 62 50 11	0 8 8 0 8	18 8 7 1 7	180 172 172 0 172	43/292 were Xpert indeterminate and excluded from final analysis
Walusimbi et al. (2013) Uganda	Level III-1 Low risk of bias	MGIT and/or L-J culture	N=369 AFB –ve HIV+ sputum specimens with valid results	HIV+ AFB –ve Xpert	21	16	22	310	57/430 specimens had contaminated cultures 19/430 had invalid Xpert results
Carriquiry et al. (2012) Peru	Level III-1 Low risk of bias	MGIT and/or L-J media culture	N=131 HIV+ patients - n=34 n=97	HIV+ AFB (ZN) Xpert AFB + NAAT AFB +ve: Xpert ABF –ve: Xpert	31 44 44 31 13	3 2 4 1 1	14 1 1 0 1	83 84 82 2 82	1 culture was contaminated 2 Xpert results were invalid and repeated
Nicol et al. (2011) South Africa	Level III-2 Low risk of bias	MGIT culture	N=452 children with at least one induced sputum sample	AFB (FL) Xpert	27 52	0 6	43 18	382 376	None reported
Zar et al. (2013) South Africa	Level III-2 Low risk of bias	MGIT culture	N=384 children with at least one induced sputum sample	AFB (FL) Xpert	4 13	1 3	26 17	353 351	None reported
Kurbatova et al. (2013) Russia	Level III-2 Low risk of bias	MGIT and/or L-J media culture	N=228 specimens	AFB (direct) AFB (FL) Xpert (direct) Xpert (conc.)	65 93 102 103	3 12 17 16	44 16 5 6	124 114 104 111	2/238 culture results were missing 8/238 had Indeterminate Xpert results
Bates et al. (2013) Zambia	Level III-2 Low risk of bias	MGIT culture	N=142 sputum specimens from children	AFB (FL) Xpert	3 9	7 2	7 1	125 130	None reported
Helb et al. (2010) Vietnam	Level III-2 Low risk of bias	MGIT and/or L-J media culture	N=107 patients - n=29 n=78	AFB Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert	29 67 67 29 38	0 0 0 0 0	53 15 15 0 15	25 25 25 0 25	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=56 sputum specimens - n=31 n=25	AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert	31 37 37 31 6	0 0 0 0 0	7 1 1 0 1	18 18 18 0 18	None reported
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=18 sputum specimens - n=14	AFB (FL) Xpert AFB + NAAT AFB –ve: Xpert	4 5 5 1	0 0 0 0	1 0 0 0	13 13 13 13	None reported
Hanrahan et al. (2014) South Africa	Level III-2 Some risk of bias	MGIT media culture	N=2,082 patients	AFB Xpert	186 299	10 47	186 107	1,472 1,638	None reported
Theron et al. (2012) South Africa	Level III-2 Some risk of bias	MGIT medium culture	N=480 sputum samples - n=286 - n=130	AFB (FL) Xpert AFB + NAAT HIV –ve: AFB (FL) Xpert AFB + NAAT HIV +ve: AFB (FL) Xpert AFB + NAAT	102 115 122 65 68 72 26 35 37	3 15 17 2 10 10 1 4 5	47 34 27 19 16 12 24 15 13	328 316 314 200 193 192 79 76 75	None reported
Sohn et al. (2014) Canada	Level III-2 Some risk of bias	Liquid culture	N=435 sputum samples - n=11 n=424	AFB (FL) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert	7 11 12 6 5	4 1 5 0 1	17 13 12 1 12	407 410 406 4 405	1/436 invalid Xpert result

AFB = acid-fast bacilli; FL = fluorescent; HIV = human immunodeficiency virus; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; Xpert = GeneXpert MTB/RIF NAAT; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in bronchoalveolar lavage, bronchial aspirates and washings

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
Min et al. (2010) Korea	Level III-2 Low risk of bias	Ogawa medium culture	N=136 bronchial aspirates	AFB stain (ZN) senX3-regX3 qPCR	20 39	1 1	45 26	70 70	None reported
Deshmukh et al. 2013 India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=13 BAL specimens	AFB (ZN) IS6110 PCR AFB + NAAT	2 5 5	0 2 2	3 0 0	8 6 6	None reported
Kibiki et al. (2007) Tanzania	Level III-2 Some risk of bias	L-J culture	N=116 BAL samples	HIV+ AFB (ZN) IS6110 PCR	16 27	1 42	12 1	87 46	4/120 specimens were contaminated (1 AFB +ve and 3 AFB –ve)

AFB = acid-fast bacilli; BAL = bronchoalveolar lavage; HIV = human immunodeficiency virus; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; 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 bronchoalveolar lavage, bronchial aspirates and washings

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
Theron et al. (2013) South Africa	Level III-2 Low risk of bias	MGIT medium culture	N=154 BAL specimens n=135 n=84 - n=46	AFB (FL) Xpert AFB –ve: Xpert HIV– AFB (FL) Xpert HIV– AFB –ve Xpert HIV+ AFB (FL) Xpert HIV+ AFB –ve Xpert	15 25 9 7 12 5 4 6 1	1 5 4 0 3 3 1 2 1	12 2 2 5 0 0 3 2 7	126 122 120 72 69 69 37 34 34	1/156 specimens had contaminated cultures 1/156 had Xpert error and was excluded from the analysis
Al-Ateah et al. (2012) Kingdom of Saudi Arabia	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=116 BAL specimens n=111	AFB (FL) Xpert AFB –ve: Xpert	4 5 1	1 0 0	2 1 1	109 110 109	None reported
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=40 specimens 31 bronchial aspirates 9 BAL n=35	AFB (FL) Xpert AFB + NAAT AFB –ve: Xpert	4 7 7 3	1 0 1 0	3 0 0 0	32 33 32 32	None reported

AFB = acid-fast bacilli; BAL = bronchoalveolar lavage; FL = fluorescent; HIV = human immunodeficiency virus; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; Xpert = GeneXpert MTB/RIF NAAT

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in gastric aspirates