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
Maurya et al. (2011b) India	Level III-1 Low risk of bias	BACTEC culture	N=328 extrapulmonary specimens n=37 n=291	AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR	23 140 140 23 117	14 63 71 6 57	128 11 11 0 11	163 114 106 8 106	20/479 specimens had contaminated cultures and were excluded from analysis
Fan et al. (2014) China	Level III-1 Low risk of bias	MGIT liquid culture	N=200 respiratory samples	AFB –ve: SAT-TB PCR	57	6	4	133	None reported
Kim et al. (2008) Korea	Level III-2 Low risk of bias	Ogawa media culture	N=2,973 specimens	AFB (FL + ZN) IS6110 PCR AFB + NAAT	118 142 148	2 56 56	79 55 49	2,774 2,720 2,720	None reported
Deshmukh et al. (2013) India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=463 specimens - n=111 n=352 N= 436 non-sputum - n=105 n=331	AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR	96 165 165 96 69 91 152 152 91 61	15 75 75 15 60 14 72 72 14 58	88 19 19 0 19 79 18 18 0 18	264 204 204 0 204 152 194 194 0 194	3/466 cultures grew NTM and were excluded from analysis
Deshmukh et al. (2013) India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=423 extrapulmonary - n=103 n=320	AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR	89 147 147 89 58	14 70 70 14 56	76 18 18 0 18	244 188 188 0 188	-
Ben Kahla et al. (2011) Tunisia	Level III-2 Low risk of bias	L-J culture	N=316 specimens - n=60 n=256	All: AFB (FL) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR	50 48 51 47 1	10 6 14 2 4	5 7 4 3 4	251 249 247 8 247	23/333 sputum samples were contaminated and not included in analysis
Therese, Jayanthi & Madhavan (2005) India	Level III-2 Low risk of bias	L-J culture	N=280 extrapulmonary clinical samples n=9 n=271	AFB (ZN) IS6110 PCR AFB + NAAT AFB +ve: IS6110 PCR AFB –ve: IS6110 PCR	8 13 13 8 5	1 115 116 0 115	6 1 1 0 1	265 151 150 1 150	None reported
Jiang et al. (2012) China	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=235 mixed samples - n=60 n=175 N=28 extrapulmonary - n=9 n=19	AFB (ZN) 16S qRT-PCR AFB + NAAT AFB +ve: 16S qRT-PCR AFB –ve: 16S qRT-PCR AFB (ZN) 16S qRT-PCR AFB + NAAT AFB +ve: 16S qRT-PCR AFB –ve: 16S qRT-PCR	28 34 34 28 6 4 6 6 4 2	32 25 49 8 17 5 4 6 3 1	8 2 2 0 2 2 0 0 0 0	167 174 150 24 150 17 18 16 2 16	None reported
Makeshkumar, Madhavan & Narayanan (2014) India	Level III-2 Low risk of bias	L-J culture	N=178 extrapulmonary specimens	AFB (ZN) IS6110 PCR	6 4	4 44	0 2	168 128	None reported
Gholoobi et al. (2014) Iran	Level III-2 Low risk of bias	L-J culture	N=30 mixed specimens	AFB (ZN) 16S-23S PCR rpoB PCR IS6110 PCR	9 8 5 7	3 4 0 0	3 4 7 5	15 15 18 18	None reported
Ani et al. (2009) Nigeria	Level III-2 Low risk of bias	L-J slope culture	N=40 mixed specimens from children N=30 non-sputum samples	AFB –ve: IS6110 PCR	4 0	18 12	0 0	18 18	None reported
Halse et al. (2010) USA	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=1,309 specimens - n=267 n=1,042 N=1,196 pulmonary - n=248 n=948 N=113 extrapulmonary - n=19 n=94	AFB (ZN) IS6110 rpoB qPCR AFB + NAAT AFB +ve: IS6110 rpoB qPCR AFB –ve: IS6110 rpoB qPCR AFB (ZN) IS6110 rpoB qPCR AFB + NAAT AFB +ve: IS6110 rpoB qPCR AFB –ve: IS6110 rpoB qPCR AFB (ZN) IS6110 rpoB qPCR AFB + NAAT AFB +ve: IS6110 rpoB qPCR AFB –ve: IS6110 rpoB qPCR	225 253 254 224 29 211 235 236 210 25 14 18 18 14 4	42 1 43 0 1 37 1 38 0 1 5 0 5 0 0	45 17 16 1 16 38 14 13 1 13 7 3 3 0 3	997 1,038 996 42 996 910 946 909 37 909 87 92 87 5 87	7/1,316 specimens had no PCR result Inconclusive PCR: (not reproducible) 5 respiratory specimens 2 non-respiratory Indeterminate PCR: (PCR inhibition) 3 respiratory specimens
Drouillon et al. (2009) France and Italy	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=607 specimens N=548 pulmonary N=59 extrapulmonary	AFB (ZN + FL) qRT-PCR AFB (ZN + FL) qRT-PCR AFB (ZN + FL) qRT-PCR	61 115 60 105 1 10	0 13 0 11 0 2	70 16 59 14 11 2	476 463 429 418 47 45	1/633 specimen was culture contaminated, 12/633 were PCR-2 inhibited, 13/633 were positive NTM and excluded from analysis
Shukla et al. (2011) India	Level III-2 Some risk of bias	L-J culture	N=140 specimens - n=40 n=100 N=86 pulmonary - n=40 n=46 N=54 extrapulmonary	AFB (ZN) IS6110 nPCR AFB + NAAT AFB +ve: IS6110 nPCR AFB –ve: IS6110 nPCR AFB (ZN) IS6110 nPCR AFB + NAAT AFB +ve: IS6110 nPCR AFB –ve: IS6110 nPCR AFB –ve: IS6110 nPCR	38 46 48 36 10 38 44 46 36 8 2	2 58 60 0 58 2 20 22 0 20 38	10 2 0 2 0 8 2 0 2 0 0	90 34 32 2 32 38 20 18 2 18 14	Not reported
Drouillon et al. (2007) France	Level III-2 Some risk of bias	MGIT or Coletsos slants	N=168 pulmonary specimens	AFB IS6110 qPCR	11 20	0 9	21 12	136 127	11/179 cultures were contaminated and excluded from analysis
Sharma et al. (2012) India	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=80 extrapulmonary specimens n=79	AFB (ZN) M-PCR AFB + NAAT AFB –ve M-PCR	1 3 3 2	0 63 63 63	2 0 0 0	77 14 14 14	None reported

AFB = acid-fast bacilli; FL = fluorescent; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria; nPCR = nested PCR; PCR = polymerase chain reaction; qPCR = quantitative (real-time) PCR; qRT-PCR = quantitative (real-time) reverse transcription PCR; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in mixed specimens