An assessment of nucleic acid amplification testing for active mycobacterial infection

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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
Al-Ateah et al. (2012) Kingdom of Saudi Arabia	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=22 specimens 13 pleural fluids 3 pericardial fluids 2 synovial fluids 4 abdominal aspirates	AFB –ve: Xpert	3	0	0	19	None reported
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=20 specimens 5 joint fluid 12 pleural fluid 3 peritoneal fluid	AFB –ve: Xpert	4	0	2	14	None reported
Moure, Martin & Alcaide (2012) Spain	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=44 specimens 31 pleural fluid 7 joint fluid 3 ascitic fluid 3 pericardial fluid	AFB –ve: Xpert	13	0	22	9	None reported

AFB = acid-fast bacilli; 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 fine-needle aspirates

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
Makeshkumar, Madhavan & Narayanan (2014) India	Level III-2 Low risk of bias	L-J culture	N=12 FNA specimens	AFB (ZN) IS6110 PCR	2 1	3 3	0 1	7 7	None reported
Derese et al. (2012) Ethiopia	Level III-2 Some risk of bias	L-J culture	N=134 FNAs from lymph nodes	n=101 AFB (ZN) n=124 IS6110 nPCR	8 21	5 8	27 29	61 66	None reported
Pahwa et al. (2005) India	Level III-2 Some risk of bias	L-J medium culture	N=55 FNAs	AFB (ZN + FL) MPB64 PCR	14 17	5 5	5 1	31 32	None reported
Mittal et al. (2011) India	Level III-2 Some risk of bias	L-J culture	N=50 lymph node FNAs	AFB (ZN) IS6110 PCR AFB + NAAT	22 27 30	2 3 3	8 3 1	18 17 16	None reported
Therese, Jayanthi & Madhavan (2005) India	Level III-2 Some risk of bias	L-J culture	N=44 lymph node FNA specimens n=38	AFB (ZN) IS6110 PCR AFB + NAAT AFB –ve: IS6110 PCR	5 9 9 4	1 10 11 10	4 0 0 0	34 25 24 24	None reported

AFB = acid-fast bacilli; FL = fluorescent; FNA = fine-needle aspirate; L-J = Lowenstein-Jensen; NAAT = nucleic acid amplification test; nPCR = nested PCRPCR = polymerase chain reaction; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in fine-needle aspirates

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
Van Rie et al. (2013b) South Africa	Level III-2 Low risk of bias	MGIT culture	N=344 FNA specimens	HIV+ AFB (FL) Xpert AFB + NAAT	59 139 140	5 23 23	87 10 9	188 172 172	8/373 cultures were contaminated or non-interpretable 4/373 were NTM 5/373 had invalid Xpert results and were excluded from analysis
Ablanedo-Terrazas et al. (2014) Mexico	Level III-2 Low risk of bias	MGIT 960 liquid culture	N=68 lymph node FNAs	HIV+ AFB (ZN) Xpert AFB + NAAT	12 15 15	4 0 4	3 0 0	49 53 49	No invalid Xpert results were obtained
Ligthelm et al. (2011) South Africa	Level III-2 Low risk of bias	MGIT 960 liquid culture	N=48 lymph node FNAs	AFB (ZN) AFB (FL) Xpert AFB + NAAT	12 22 28 29	0 1 3 2	17 7 1 0	19 18 16 17	No invalid Xpert results were obtained
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=23 lymph nodes - n=20	AFB (FL) Xpert AFB + NAAT AFB –ve: Xpert	3 6 6 3	0 0 0 0	3 0 0 0	17 17 17 17	None reported
Biadglegne et al. (2014) Ethiopia and Germany	Level III-2 Some risk of bias	L-J and Gottsacker culture	N=213 FNAs from lymph nodes n=12 n=201	AFB (FL) Xpert AFB + NAAT AFB +ve Xpert AFB –ve Xpert	11 29 29 11 18	1 56 56 1 55	20 2 2 0 2	181 126 126 0 126	11/231 cultures were contaminated 8/231 Xpert results were indeterminate and excluded from analysis
Moure, Martin & Alcaide (2012) Spain	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=38 lymph nodes	AFB –ve: Xpert	24	0	10	4	None reported
Al-Ateah et al. (2012) Kingdom of Saudi Arabia	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=5 FNAs	AFB (FL) Xpert	2 2	1 0	0 0	2 3	None reported

AFB = acid-fast bacilli; FL = fluorescent; FNA = fine-needle aspirate; HIV = human immunodeficiency virus; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria; Xpert = GeneXpert MTB/RIF NAAT; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of in-house NAAT compared with AFB microscopy and culture in abscesses/pus

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

Deshmukh et al. 2013

India

Level III-2

Low risk of bias

MGIT and/or L-J culture

N=94 pus specimens

AFB (ZN)
IS6110 PCR
AFB + NAAT

43
53
53

5
15
15

12
2
2

34
24
24

None reported

Makeshkumar, Madhavan & Narayanan (2014)

India

Level III-2

Low risk of bias

L-J culture

N=7 pus specimens

AFB (ZN)
IS6110 PCR

1
1

0
2

0
0

6
4

None reported

AFB = acid-fast bacilli; L-J = Lowenstein-Jensen; MGIT = Mycobacterium Growth Indicator Tubes; 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 abscesses/pus

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

Al-Ateah et al. (2012)

Kingdom of Saudi Arabia

Level III-2

Low risk of bias

MGIT and/or L-J culture

N=10 abscess aspirates

n=8

AFB (FL)
Xpert

AFB –ve: Xpert

2
3

0
0

1
0

7
7

None reported

Moure, Martin & Alcaide (2012)

Spain

Level III-2

Some risk of bias

MGIT and/or L-J culture

N=19 abscess aspirates

AFB –ve: Xpert

None reported

AFB = acid-fast bacilli; FL = fluorescent; 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 urine

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
Deshmukh et al. 2013 India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=53 urine specimens	AFB (ZN) IS6110 PCR AFB + NAAT	4 15 15	2 9 9	16 5 5	31 24 24	None reported
Makeshkumar, Madhavan & Narayanan (2014) India	Level III-2 Low risk of bias	L-J culture	N=8 urine specimens	AFB (ZN) IS6110 PCR	2 2	1 2	0 0	5 4	Not reported
Khosravi et al. (2010) Iran	Level III-2 Some risk of bias	L-J culture	N=200 urine samples	AFB (ZN) IS6110 nPCR	4 10	0 0	6 0	190 190	None reported
Ghaleb, Afifi & El-Gohary (2013) Egypt	Level III-2 Some risk of bias	BACTEC 12B and/or L-J culture	N=100 urine samples - n=99	AFB (ZN) IS6110 PCR AFB + NAAT AFB –ve IS6110 PCR	1 3 3 2	0 3 3 3	0 0 0 0	99 94 94 94	None reported
Khan, Cheema & Khan (2013) Egypt	Level III-2 Some risk of bias	L-J culture	N=50 urine samples	AFB (ZN) PCR	11 16	2 2	8 3	29 29	None reported

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

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

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
Bhanu et al. (2005) India	Level III-1 Low risk of bias	L-J culture	N=14 endometrial biopsies	AFB (ZN) mpt64 PCR	1 1	0 7	0 0	13 6	3 negative PCR included in analysis were found to be inhibitory
Deshmukh et al. 2013 India	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=164 tissue specimens	AFB (ZN) IS6110 PCR AFB + NAAT	37 57 57	7 3 3	23 3 3	97 84 84	None reported
Sharma et al. (2013) India	Level III-2 Low risk of bias	L-J culture	N=50 endoscopic ileocaecal biopsies	AFB (ZN) M-PCR	1 2	1 0	0 29	47 19	None reported
Shukla et al. (2011) India	Level III-2 Some risk of bias	L-J culture	N=38 endometrial biopsies	AFB –ve: IS6110 nPCR	2	26	0	10	None reported
Bhanothu, Theophilus & Rozati (2014) India	Level III-2 Some risk of bias	L-J culture	N=191 endometrial or ovarian biopsies n=37 n=154	AFB (ZN) TCR4 PCR AFB + NAAT AFB +ve: TCR4 PCR AFB –ve: TCR4 PCR	37 77 77 37 40	0 80 80 0 80	41 1 1 0 1	113 33 33 0 33	None reported
Therese, Jayanthi & Madhavan (2005) India	Level III-2 Some risk of bias	L-J culture	N=9 tissue biopsies - n=8	AFB (ZN) IS6110 PCR AFB + NAAT AFB –ve: IS6110 PCR	1 1 1 0	0 4 4 4	0 0 0 0	8 4 4 4	None reported
Keys et al. (2012) Australia	Level III-2 Some risk of bias	Culture	N=5 pleural biopsies from children	AFB PCR AFB + NAAT	1 3	0 2	2 0	2 0	1/6 specimens had an inconclusive PCR result

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

Table Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in tissue biopsies

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
Al-Atteah et al. (2012) Kingdom of Saudi Arabia	Level III-2 Low risk of bias	MGIT and/or L-J culture	N=16 tissue biopsies	AFB (FL) Xpert	2 8	0 0	6 1	8 7	None reported
Malbruny et al. (2011) France	Level III-2 Low risk of bias	MGIT and Coletsos slants	N=6 vertebral biopsies	AFB (FL) Xpert AFB + NAAT	1 1 1	0 0 0	0 0 0	5 5 5	None reported
Moure, Martin & Alcaide (2012) Spain	Level III-2 Some risk of bias	MGIT and/or L-J culture	N=20 tissue biopsies	AFB –ve: Xpert	5	0	7	8	None reported

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 NAAT compared with drug sensitivity testing for the detection of drug-resistant MTB infections

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
Carriquiry et al. (2012) Peru	Level III-1 Low risk of bias	DST	N= 39 culture-positive sputum samples	Xpert RIF	6	3	0	30	None reported
Vadwai et al. (2011) India	Level III-2 Low risk of bias	DST with MGIT SIRE	N=125 culture-positive extrapulmonary specimens	Xpert RIF	39	5	1	80	None reported
Kurbatova et al. (2013) Russia	Level III-2 Low risk of bias	DST	N=99 culture-positive Xpert-valid sputum specimens	Xpert (conc) vs L-J or MGIT Xpert (conc) vs L-J DST Xpert (conc) vs MGIT DST	57 45 55	1 2 2	5 5 1	38 30 40	10/109 specimens had invalid Xpert RIF results 2/109 specimens had contaminated MGIT DST 25/109 specimens had contaminated L-J DST
Bates et al. (2013) Zambia	Level III-2 Low risk of bias	DST with MGIT SIRE	N=52 culture-positive gastric lavage specimens	RIF resistance Xpert RIF Multi- drug resistance Xpert RIF	2 2	1 1	0 0	49 49	6/788 specimens were contaminated and excluded from analysis
Lee et al. (2013) Korea	Level III-2 Low risk of bias	DST on Ogawa medium	N=35 culture-positive Xpert-positive bronchoscopy samples	Xpert RIF	2	0	0	33	None reported
Ioannidis et al. (2011) Greece	Level III-2 Low risk of bias	GenoType MTBDRplus and confirmed by DST	N=32 culture-positive, GeneXpert-valid mixed samples	Xpert RIF	3	1	0	28	None reported
Hillemann et al. (2011) Germany	Level III-2 Low risk of bias	DST	N=29 culture-positive non-respiratory specimens	Xpert RIF	0	1	0	28	3/29 culture-positive specimens by Xpert NAAT had an indeterminate RIF resistance result
Theron et al. (2013) South Africa	Level III-2 Low risk of bias	DST with MGIT SIRE	N=27 culture-positive BAL samples	RIF resistance Xpert RIF MDR Xpert RIF	1 1	3 3	0 0	23 23	None reported
Deggim et al. (2013) Switzerland	Level III-2 Low risk of bias	BACTEC MGIT 960	N=18 culture-positive mixed specimens	Xpert RIF	0	2	0	16	None reported
Sohn et al. (2014) Canada	Level III-2 Some risk of bias	DST	N=501 culture-positive sputum samples	Xpert RIF	1	1	0	499	1/502 specimens had contaminated cultures 44/502 had invalid Xpert results and were repeated
Halse et al. (2010) USA	Level III-2 Some risk of bias	DST	N=143 culture-positive mixed specimens	rpoB pyrosequencing	2	1	1	139	None reported
Marlowe et al. (2011) USA	Level III-2 Some risk of bias	DST	N=130 culture-positive respiratory specimens	Xpert RIF	0	3	0	127	None reported
Zeka, Tasbakan & Cavusoglu (2011) Turkey	Level III-2 Some risk of bias	DST	N=89 culture-positive mixed specimens N=58 pulmonary N=31 extrapulmonary	RIF resistance Xpert RIF MDR Xpert RIF	1 1	0 0	0 4	88 84	None reported
Biadglegne et al. (2014) Ethiopia and Germany	Level III-2 Some risk of bias	BacT/Alert 3D DST	N=32 culture-positive FNA samples	Xpert RIF	2	1	0	29	None reported

BAL = bronchoalveolar lavage; DST = drug susceptibility testing; FNA = fine-needle aspirate; L-J = Lowenstein-Jensen; MDR = multidrug-resistant; MGIT = Mycobacterium Growth Indicator Tubes; RIF = rifampicin

Table Diagnostic accuracy of NAAT and AFB microscopy using culture as the reference standard for diagnosis of NTM

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	Notes
Abdalla et al. (2009) Brazil	Level II High risk of bias	L-J culture	N=27 FFPE skin biopsy MTB culture-negative specimens	AFB –ve In-house NTM-NAAT	1	13	0	13	Culture not performed on 3/34 specimens 4/34 were MTB C+
Bogner et al. (1997) Germany	Level III-1 Low risk of bias	BACTEC 12B and/or L-J culture	N=540 blood specimens	HIV+ In-house MAC-NAAT	12	2	34	492	Only MAC-positive and MAC-negative results considered Results include 6 MTB and 18 non-MAC NTM C+ specimens
Mahaisavariya et al. (2005) Thailand	Level III-1 High risk of bias	Culture	N=131 tissue biopsies 5 n=41 6 n=90	AFB In-house NTM-NAAT AFB +ve In-house MTM-NAAT AFB –ve In-house MTM-NAAT	15 16 7 9	26 31 5 26	21 20 8 12	69 64 21 43	11/131 specimens had no culture results and were included as culture-negative Results includes 2 MTB C+ specimens
Kox et al. (1997) The Netherlands	Level III-2 Low risk of bias	Culture	N=238 MTB culture-negative specimens n=53 n=185	AFB (ZN) In-house NTM-NAAT AFB +ve In-house NTM-NAAT AFB –ve In-house NTM-NAAT	32 37 31 6	22 27 17 10	7 2 1 1	177 172 4 168	21/259 specimens were MTB C+
Matsumoto et al. (1998) Japan	Level III-2 Low risk of bias	Ogawa culture	N=139 MTB culture-negative bronchial washings n=133	AFB (ZN) Comm MAC-NAAT AFB –ve Comm MAC-NAAT	4 10 6	2 1 1	8 2 2	125 126 124	2/141 specimens were MTB C+
Choi et al. (2012) Korea	Level III-2 Some risk of bias	MGIT culture	N=467 respiratory specimens that were MTB culture-negative	AFB (FL) Comm NTM-NAAT	6 29	0 0	36 13	425 453	64/531 specimens from patients suspected of MTB infections
Tran et al. (2014) USA	Level III-2 Some risk of bias	BACTEC MGIT 960 culture	N=456 respiratory specimens n=179 n=277	AFB (ZN) In-house MAC-NAAT AFB +ve In-house MAC-NAAT AFB –ve In-house MAC-NAAT	67 57 54 3	112 2 0 2	29 39 13 26	248 358 112 246	8/464 specimens had inconclusive or indeterminate PCR results 25/360 MAC culture-negative specimens grew other NTMs and 101/360 grew MTB but were included as culture-negative in the analysis
Gamboa et al. (1997) Spain	Level III-2 Some risk of bias	BACTEC 13A culture	N=101 specimens N=91 blood specimens N=10 BM specimens	HIV+, AFB –ve Comm MAC-NAAT Comm MAC-NAAT Comm MAC-NAAT	57 56 1	0 0 0	11 10 1	33 25 8	30/121 blood specimens were MTB culture-positive 5/15 BM specimens were MTB C+ 6/11 false-negative specimens were non-MAC NTM C+
Ninet et al. (1997) Switzerland	Level III-2 High risk of bias	BACTEC 13A culture	N=195 MTB culture-negative blood specimens	HIV+ Comm MAC-NAAT	14	0	24	157	6/201 were MTB C+ 4/24 false-negative specimens were non-MAC NTM C+
Frevel et al. (1999) Germany	Level III-2 High risk of bias	Culture	N=69 FFPE samples	In-house NTM-NAAT	5	14	0	50	Only NTM results considered MTB culture result unknown

AFB = acid-fast bacilli; BM = bone marrow; C+ = culture positive; Comm = commercial; FFPE = formalin fixed, paraffin embedded; FL = fluorescent; HIV = human immunodeficiency virus; MTB = Mycobacterium tuberculosis; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria; PCR = polymerase chain reaction; ZN = Ziehl-Neelsen

Table Diagnostic accuracy of NAAT, AFB microscopy and culture using a clinical reference standard for diagnosis of NTM

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	Notes
Abdalla et al. (2009) Brazil	Level II High risk of bias	CRS	N=27 FFPE skin biopsy MTB culture-negative specimens	AFB –ve In-house NTM-NAAT Culture	12 1	2 0	0 11	13 15	Culture not performed on 3/34 specimens 4/34 were MTB culture-positive
Phillips et al. (2005) Ghana	Level III-2 Low risk of bias	CRS	Biopsy specimens N=65 N=70 N=65	AFB (ZN) In-house MU-NAAT Culture	23 59 27	0 0 0	32 1 28	10 10 10	5/70 specimens did not have microscopy and culture results and were excluded from the analysis
Kox et al. (1997) The Netherlands	Level III-2 Some risk of bias	CRS	N=238 MTB culture-negative specimens	In-house NTM-NAAT Culture	74 38	5 0	2 37	157 162	21/259 specimens were MTB culture-positive
Gazzola et al. (2008) Italy	Level III-2 Some risk of bias	CRS	N=110 MTB culture-negative specimens N=67 blood specimens N=43 BM specimens	HIV+ MAC-NAAT Culture MAC-NAAT Culture MAC-NAAT + culture AFB MAC-NAAT Culture MAC-NAAT + culture	10 13 6 10 10 1 4 3 6	1 0 0 0 0 0 1 0 1	8 9 5 5 1 6 3 4 1	91 92 56 56 56 36 35 36 35	4/71 blood specimens were MTB culture-positive 3/46 BM specimens were MTB culture-positive

AFB = acid-fast bacilli; BM = bone marrow; Comm = commercial; CRS = clinical reference standard; FFPE = formalin fixed, paraffin embedded; HIV = human immunodeficiency virus; MTB = Mycobacterium tuberculosis; MU = M. ulcerans; NAAT = nucleic acid amplification test; NTM = non-tuberculous mycobacteria; PCR = polymerase chain reaction

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