Subquestions (for a linked evidence approach): Accuracy What is the accuracy of NAAT in the diagnosis of patients with suspected MTB, compared with AFB microscopy and culture? What is the accuracy of NAAT plus AFB microscopy in the diagnosis of patients with suspected MTB, compared with AFB microscopy alone? What is the accuracy of in-house NAAT compared with commercial NAAT in the diagnosis of patients with suspected MTB, using culture as the reference standard? What is the accuracy of NAAT in the detection of genetic mutations on the rpoB gene that are associated with rifampicin resistance? What is the accuracy of NAAT in the diagnosis of NTM in patients suspected of having an NTM infection, compared with culture? Change in management Does AFB microscopy plus NAAT to determine the presence of MTB and rifampicin resistance change patient management, compared with management decisions made based on AFB microscopy alone, in patients with a high pre-test probability of active TB? Does AFB microscopy plus NAAT to determine the presence of MTB and rifampicin resistance change patient management, compared with management decisions made based on AFB microscopy alone, in patients with a low-pre-test probability of TB? Does NAAT plus culture change patient management, compared with culture plus other tests, in patients suspected of having an NTM infection? Effectiveness of change in management To what extent does treating patients who have rifampicin-resistant MTB infections with alternative treatments result in better health outcomes for the patient and their contacts? What is the health impact of early versus delayed treatment of TB on the individual and their contacts? What adverse events (AEs) are associated with inappropriate antibiotic treatment for TB? Diagnostic assessment framework This assessment uses the theoretical framework outlined in the MSAC Guidelines for the assessment of diagnostic technologies (). This means that evidence of the clinical effectiveness of diagnosing MTB or NTB using NAAT requires either:
Appendix A Health Expert Standing Panel and Assessment Group Health Expert Standing Panel (HESP) Member Expertise or affiliation Jim Black Associate Professor, Nossal Institute for Global Health, Melbourne School of Population and Global Health Assessment group AHTA, University of Adelaide, South Australia Name Position Judy Morona Senior Research Officer Arlene Vogan Health Economist Sharon Kessels Research Officer Debra Gum Senior Research Officer Joanne Milverton Research Officer Jacci Parsons Team Leader (Medical HTA) Skye Newton Team Leader (Medical HTA) Camille Schubert Senior Health Economist Tracy Merlin Managing Director Noted conflicts of interest There were no conflicts of interest.
Al-Ateah et al. () 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) Xpert AFB + NAAT AFB +ve: Xpert AFB –ve: Xpert AFB (FL) Xpert 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. () 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. () 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) Xpert 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. () Level III-2 Solid L-J N=160 HIV+ sputum or HIV+ AFB (ZN) 8 2 4 146 Repeated Xpert
Chile Low risk of bias and liquid media culture mouthwash specimens Xpert 11 1 1 147 MTB/RIF assays were performed for patients who had discordant results Teo et al. () 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) Xpert 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. () 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. () 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
Helb et al. () 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. () 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. () 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. () 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. () 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. () 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
Al-Ateah et al. () 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. () 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 77 Diagnostic accuracy of Xpert NAAT compared with AFB microscopy and culture in gastric aspirates Study Country Evidence level and risk of bias Reference standard Population Samples Tests results results results results Inconclusive results Bates et al. () 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. () 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 () 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 78 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 results results results results Inconclusive results El Khechine et al. () 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 79 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 results results results results Inconclusive results Bhigjee et al. () 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. () 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 () 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. () 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
Madhavan & Narayanan () India Low risk of bias IS6110 PCR 2 2 0 4 Khosravi et al. () 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 () 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 () 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 88 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 results results results results Inconclusive results Bhanu et al. () 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. () 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
by DST Hillemann et al. () 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. () 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. () 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. () 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. () 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. () 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 () 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. () 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 91 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 results results results results Notes Abdalla et al. () 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. () 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. () 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. () The Netherlands Level III-2 Low risk of bias Culture N=238 MTB 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+
blinded or blinding not known) Quality: Low risk of bias Patient selection Index test Comparator ? Reference std ? Flow and timing Applicability: C1, P1 71 respiratory including sputum, BAL 8 non-respiratory including ascetic fluid, pleural fluid, biopsy tissue confirm or rule out TB in newly identified suspect cases Exclusion None stated NALC-NaOH and centrifuged for sedimentation of mycobacteria manufacturer’s instructions for respiratory specimens Non-respiratory specimens were tested similarly were confirmed by ZN staining growth detection DST was performed using the BACTEC MGIT 960 system Derese et al. () Ethiopia Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection ? Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=134 FNA samples from lymph nodes Mean age 28.6 ± 12.7 years HIV status not reported Inclusion Retrospective study on previously collected FNA specimens stored at –80 °C to diagnose lymphadenitis TB Exclusion None stated Specimens were decontaminated using NALC-NaOH method and centrifuged for sedimentation of mycobacteria PCR was performed using IS1081 primers AFB microscopy with ZN staining Four L-J medium (two with glycerol and two with pyruvate) slopes were incubated and examined weekly for 8 consecutive weeks Desai et al. () India Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Patient selection Index test Comparator Reference std ? N=30 CSF samples Age and HIV status not reported Inclusion In-house patients with a provisional diagnosis of tuberculous meningitis and had 2 mL of CSF available for study Sample split in two The first 1-mL portion was centrifuged and used for AFB microscopy and culture, and the second 1-mL portion was stored at −20 °C and used for DNA extraction and PCR PCR targeting IS6110 was performed ZN-stained smears L-J solid medium
12 lymph node punctures 11 urine 5 pus 2 semen 6 stool receiving anti-TB therapy for more than 6 days or who had completed treatment less than 12 months before the date of enrolment Drouillon et al. () France Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator ? Reference std ? Flow and timing Applicability: C1, P1 N=179 pulmonary specimens (sputa and gastric fluids) were collected from 100 patients Age and HIV status not reported Inclusion Consecutive, patients with suspected TB between April and October 2004 Exclusion None stated A minimum of 2 mL of pulmonary specimen was collected Some was used directly for the DNA extraction The remainder was decontaminated using NALC-NaOH solution qPCR was performed to amplify and detect the IS6110 sequence Method not specified Culture was performed using MGIT liquid media and Coletsos slants Ekrami et al. () Iran Level III-1: A comparison against independent, blinded reference standard among non-consecutive patients Quality: Some risk of bias Patient selection Index test ? Comparator ? Reference std ? Flow and timing Applicability: C1, P2 N=152 sputum samples Age and HIV status not reported Inclusion Patients who were suspected of having pulmonary TB Exclusion Not reported Processed according to standard routine diagnostic procedures using the NALC-NaOH method PCR and nPCR Purified DNA was amplified using primers specific to IS6110 and two specific pairs of external and internal primers for this bacterium ZN-stained AFB microscopy L-J solid medium culture
El Khechine et al. () France Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P1 N=134 patients each with one sputum and one stool sample Mean age 37 ± 15 years HIV status not reported Inclusion Sputum specimens and stool specimens collected from patients suspected of having pulmonary TB Exclusion Not reported Respiratory tract specimens were digested and decontaminated using the NALC-NaOH method Stool specimens were filtered using a faecal specimen filtration vial kit qPCR amplification and detection of IS6110 Direct ZN-stained microscopy of sputum or filtered stool Decontaminated sputum was inoculated into a BACTEC 9000 bottle and incubated in an automated BACTEC 9000 MB system for 2 months Stool culture: in L-J medium for 2 months Ereqat et al. () Palestine Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=95 sputum samples from 84 patients Mean age 46.4 ± 2.5 years HIV status not reported Inclusion Patients suspected of having pulmonary TB Exclusion Not reported The sputum samples were processed using the NALC-NaOH method DNA was extracted from ZN-stained material scraped off from the microscopic slides PCR used primers targeting a 123-bp segment of IS6110 ZN-stained AFB microscopy L-J medium culture (37 °C, up to 8 weeks) Fan et al. () China Level III-1: A comparison against independent, blinded reference standard among non-consecutive patients Quality: Low risk of bias Patient selection Index test N=200 AFB –ve respiratory samples Mean age 43 ± 18 years 120 sputum 80 BAL Inclusion Patients suspected of pulmonary TB > 18 years of age with abnormal CXR findings that had three consecutive negative AFB microscopy Not reported Simultaneous amplification and testing for MTB (SAT-TB) assay MTB 16S rRNA was reverse transcribed to generate a 170-bp DNA fragment in a real-time PCR AFB microscopy MGIT culture was performed in the BD BACTEC MGIT960 Mycobacteria Culture System
Comparator Reference std Flow and timing Applicability: C1, P2 results or were sputum scarce Exclusion Patients who were AFB +ve or HIV+ or were missing culture specimens George, Mony & Kenneth () India Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test Comparator Reference std ? Flow and timing Applicability: C1, P2 N=78 sputum samples Age and HIV status not reported Inclusion TB suspects Exclusion Not reported Sputum samples were decontaminated using NALC-NaOH method and stored at –20 °C Decontaminated sputum was processed using the Amplicor respiratory specimen preparation kit LAMP assay specific for the rimM sequence of MTB and Mycobacterium bovis AUR fluorescence microscopy L-J culture and MGIT culture Ghaleb, Afifi & El-Gohary () Egypt Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=100 urine samples 75 males with mean age 37.5 ±7.5 years 25 females with mean age 37.0 ± 9.0 years HIV status not reported Inclusion Patients with symptoms suggestive of renal TB Exclusion None reported Urine specimens were treated with method for the decontamination PCR targeting IS6110 AFB microscopy with ZN staining L-J solid and BACTEC 12B liquid culture
known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P1 reported indications for TB Exclusion None GeneXpert instrument bacterial colonies were investigated with the GenoType MTBDRplus assay and confirmed by DST using the proportion method on L-J culture medium and/or MGIT for RIF Jiang et al. () China Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=235 mixed specimens: sputum (88.1%), pleural fluid (3.0%), lymph node (3.0%), CSF (2.1%), urine (1.7%), abscess and exudate (1.7%) and faeces (0.4%) Age and HIV status not reported Inclusion Clinical specimens were obtained from patients with suspected TB Exclusion None Respiratory specimens were decontaminated with NALC-NaOH Extrapulmonary specimens from closed and normally sterile sites were used directly without decontamination after a single centrifugation qRT-PCR using MTB 16S rRNA-specific primers AFB smears with ZN stain Liquid MGIT 960 and solid L-J cultures Keys et al. () Australia Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection ? Index test ? Comparator ? Reference std ? Flow and timing ? N=6 pleural biopsied from children Age and HIV status not reported Inclusion Children with clinical suspicion of TB with both respiratory and constitutional symptoms Exclusion None stated Not reported PCR, details not provided AFB microscopy Culture
Applicability: C1, P1 Khan, Cheema & Khan () Egypt Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator ? Reference std ? Flow and timing ? Applicability: C1, P2 N=50 urine samples Median age of patients 38 years (range 20–76) HIV status not reported Inclusion Patients with symptoms suggestive of GUTB Exclusion None reported Urine specimens were treated using method for the decontamination PCR, details not provided AFB microscopy with ZN staining Culture on L-J medium Khosravi et al. () Iran Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=200 urine samples Mean age 37.8 years HIV status not reported Inclusion Patients with symptoms suggestive of renal TB Exclusion None reported Three urine samples collected on three consecutive days as early morning urine, pooled and concentrated nPCR targeting IS6110 AFB microscopy with ZN staining Culture on L-J medium with a conventional identification procedure Kibiki et al. () Tanzania Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias N=120 BAL samples from 120 HIV+ patients Mean age 39 years Inclusion HIV+ patients aged > 17 years with features of chest infection and referred for bronchoscopy > 80% had previous BAL samples were pre-treated by decontamination with and centrifuged The sediment was used for the different PCR (40 cycles) targeting IS6110 Direct smears were examined for AFB after ZN staining MTB culture was performed using L-J solid medium, with a maximum incubation period of 8 weeks
Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 antibiotic treatment for pneumonia Exclusion Pregnant women and patients with oxygen saturation < 90% under 6 L/minute diagnostic tests Kim et al. () Korea Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=2,973 patients Age and HIV status not reported n=1,134 pulmonary specimens: 863 sputum 271 bronchial aspirate n=1,839 extrapulmonary specimens: 834 pleural fluid 313 CSF 248 urine 147 tissue 109 pus 59 peritoneal fluid 34 blood 12 gastric aspirate 9 pericardial fluid 7 bone marrow 67 other Inclusion Patients who visited Kyung Hee Medical Center between July 2003 and July 2006 for TB diagnosis Exclusion None Sputum, bronchial aspirate, urine and pus were incubated with NaOH and then centrifuged Tissues were minced with scissors and treated with proteinase K and then centrifuged Cerebrospinal and other body fluids were centrifuged without any pre-treatment nPCR using primers targeting IS6110 AUR-stain positive specimens were confirmed with ZN microscopy Specimens were inoculated onto 3% Ogawa media and then incubated for at least 8 weeks at 37 °C Kurbatova et al. () Russia Level III-2: A comparison with reference standard (not blinded or blinding not known) N=238 sputum specimens from 201 patients Age and HIV status not reported Inclusion Adults (> 17 years of age) with presumptive or recently diagnosed pulmonary TB Sputum samples were homogenised and split into two portions. From one portion, 1.0 mL was tested by Xpert The Xpert MTB/RIF assay was performed according to the manufacturer’s instructions Direct and AUR fluorescence microscopy Sample was inoculated onto L-J solid medium and BACTEC MGIT 960 liquid medium
Quality: Low risk of bias Patient selection ? Index test Comparator Reference std ? Flow and timing Applicability: C1, P2 Exclusion Receiving anti-TB drugs within 60 days prior to specimen collection and a smear prepared for ZN microscopy The remaining portion (≥ 3 mL) was decontaminated with NALC-NaOH and centrifuged for culture and Xpert The results were obtained using the Xpert MTB/RIF software Culture-based DST was performed using either the BACTEC MGIT 960 system or the absolute concentration method on L-J medium Lee et al. () Korea Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=35 culture-positive Xpert-positive bronchoscopy samples Age and HIV status not reported Inclusion Retrospective review of all records for patients with suspected PTB, among whom the AFB microscopy, culture and Xpert assays were performed using bronchial washings or BAL Exclusion Patients diagnosed with sputum AFB +ve PTB before bronchoscopy or who had received anti-TB medication for ≥ 2 weeks within 90 days before bronchoscopy Samples were decontaminated with NaOH and centrifuged for AFB microscopy, culture and Xpert The Xpert MTB/RIF assay was performed following the manufacturer’s instructions The AFB smears were examined after AUR staining Culture-based DST was performed using the proportion method on 3% Ogawa medium Lee, Chen & Peng () Taiwan Level III-2: A comparison with reference standard (not blinded or blinding not known) N=150 sputum specimens Age and HIV status not reported Inclusion Suspected TB patients admitted to Kaohsiung Medical University Hospital Decontamination using NALC-NaOH treatment, and subsequent concentration by LAMP assay for detection of 16S rRNA in clinical isolates of MTB using an ELISA detection system AFB staining (method not specified) Mycobacterial culture (method not specified)
Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing ? Applicability: C1, P2 Exclusion Not reported centrifugation Ligthelm et al. () South Africa Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=48 lymph node FNAs Mean age of patients 27.9 ± 15.1 years 36/48 had unknown HIV status 9/12 (75%) patients tested were HIV+ Inclusion All patients referred for FNA biopsy with possible TB lymphadenitis Exclusion Inadequate sample for testing Sample used directly. The Xpert MTB/RIF assay was performed following the manufacturer’s instructions AFB smears with both ZN staining and fluorescence microscopy MGIT 960 for growth detection Makeshkumar, Madhavan & Narayanan () India Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=178 extrapulmonary specimens Age and HIV status not reported 59 ascetic fluid 54 pleural fluid 25 CSF 12 FNA 8 urine 7 pus 6 synovial fluid 7 other Inclusion All clinically suspected extrapulmonary TB patients who were visiting SRM Medical College Hospital during the period May 2008 – May 2009 Exclusion None Sterile body fluid samples (ascitic fluid, pleural fluid, CSF, synovial fluid, pericardial fluid and pancreatic cyst fluid) were centrifuged Pus specimens were decontaminated using Petroff’s method Biopsy and skin tissue samples were ground and then centrifuged PCR using primers targeting IS6110 AFB microscopy with ZN stain Specimens were inoculated onto solid L-J medium and examined every second day during the first week and weekly for up to 8 weeks
Applicability: C1, P2 Maurya et al. () India Level III-1: A comparison against independent, blinded reference standard among non-consecutive patients Quality: Low risk of bias Patient selection Index test Comparator Reference std Flow and timing Applicability: C1, P2 N=328 extrapulmonary specimens from new cases suspected of TB Mean patient age 39.8 ± 16.1 years HIV status not reported Lymph node aspirates, cold abscesses, pleural fluid, CSF, synovial fluid, ascetic fluid, urine, gastric aspirate, pus, bone marrow, wound and pus swabs, and biopsy tissues Inclusion Non-repeated specimens from suspected cases of extrapulmonary TB Exclusion None stated Specimens were divided into two parts and kept at −20 °C until processing (method not described) PCR was performed using IS6110 primer sequences Smear examination was by ZN staining BACTEC vials were incubated and interpreted as per the Becton Dickinson instruction manual Michelon et al. () Brazil Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test Comparator Reference std ? Flow and timing Applicability: C1, P2 N=476 sputum specimens Age and HIV status not reported 301 induced sputum specimens 175 spontaneous sputum specimens: 47 patients with a single collection that were processed in duplicate 128 patients with two collections on different days that were processed at a single time Inclusion Samples of suspected TB patients Exclusion Not reported All samples were treated with Mycobacterial culture and AFB microscopy were carried out for all clinical samples and the association of these results was chosen as the gold standard PCR amplification reactions were performed with biotinylated primers derived from IS6110 This was followed by a microwell hybridisation assay to detect the amplified product Method not reported Method not reported
Rachow et al. () Tanzania Level II: A comparison against independent, blinded reference standard among consecutive patients Quality: Low risk of bias Patient selection Index test Comparator Reference std Flow and timing Applicability: C1, P2 N=292 patients with sputum samples (each provided three samples, results were recorded from morning sample) Mean age 39.2 ± 13.8 years 58.9% were HIV+ Inclusion Patients with symptoms suggestive of pulmonary TB Exclusion Not able to produce sputum at recruitment, lost to follow-up during recruitment procedures Sputum samples were split into two aliquots, one of which was stored at –80 ºC; the other was processed for standard AFB microscopy and culture Sputa were decontaminated using the NALC-NaOH method Frozen sputa were thawed and processed according to the Xpert MTB/RIF assay test procedure AFB microscopy with ZN staining L-J solid and MGIT liquid culture Santos et al. () Brazil Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P2 N=218 sputum samples 60 non-Indigenous 158 Indigenous Age and HIV status not reported Inclusion Non-Indigenous and Indigenous patients presenting with respiratory symptoms and suspected of pulmonary TB, providing sputum sample Exclusion Not reported 48 samples had to be transported in cetylpyridinium chloride solution and were then homogenised PCR targeting IS6110 AFB microscopy using direct and concentrated techniques 48 samples were stained with bromothymol blue L-J medium culture (using NaOH as decontaminant) Sharma et al. () India Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? N=80 osteoarticular TB (OATB) specimens 67 synovial fluid 13 pus Age and HIV status not reported Inclusion Specimens received for AFB staining and culture for diagnosis of OATB Exclusion None stated The specimens were concentrated by centrifugation M-PCR with primers targeting IS6110 and MPB64 AFB microscopy with ZN staining Culture was on L-J medium
reference standard among non-consecutive patients Quality: Low risk of bias Patient selection Index test Comparator Reference std Flow and timing Applicability: C1, P2 reported origin alone or associated with cervical lymphadenopathy, ascites, bone marrow transplant, as well as those with pyrexia accompanying renal failure or aplastic anaemia were investigated for TB Exclusion None processing 8 weeks Sohn et al. () Canada Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Some risk of bias Patient selection Index test ? Comparator Reference std ? Flow and timing Applicability: C1, P1 N=436 sputum samples Median age of patients 44 years (IQR 31–61) 12/49 (24%) patients tested were HIV+ Inclusion Consecutive patients aged > 17 years, referred for evaluation of suspected active pulmonary TB Exclusion Not reported Not reported The Xpert MTB/RIF was performed at the TB clinic according to the standard protocol for unprocessed samples, per the manufacturer AFB microscopy with AUR staining Liquid culture on three processed samples was followed by phenotypic DST at the provincial reference laboratory Suzuki et al. () Japan Level II: A comparison against independent, blinded reference standard among consecutive patients Quality: Low risk of bias Patient selection Index test ? N=138 sputum specimens Age and HIV status not reported Inclusion Patients hospitalised in Minami–Yokohama National Hospital, under suspicion of TB during a designed period Exclusion The clinical specimens were treated with Sputerzyme and then decontaminated using the NALC-NaOH method PCR–ICA DNA amplification with labelled primers targeting dnaJ and using detection of the amplified product by application on a sample pad of the test Specimens were fixed and stained with AUR, and their fluorescence was examined using microscopy The presence of AFBs was Specimens were inoculated into MGIT 960 tubes Growth of MTB was evaluated on the consumption of oxygen in the medium, as
Flow and timing Applicability: C1, P2 Walusimbi et al. () Uganda Level III-1: A comparison against independent, blinded reference standard among non-consecutive patients Quality: Low risk of bias Patient selection Index test Comparator: Reference std Flow and timing Applicability: C1, P2 N=430 AFB –ve, HIV+ sputum samples Median age 34 years (IQR 29–40) 369 had valid culture and Xpert results Inclusion HIV+ patients with symptoms of TB, giving consent, providing spot and early-morning sputum sample Exclusion Patients on TB treatment or unable to produce sputum The samples were digested and decontaminated using the NALC-NaOH method, and then concentrated by centrifugation For the Xpert MTB/RIF assay, a sample reagent was added to the processed sample in a 3:1 ratio The mixture was introduced into a cartridge, which was then loaded into the GeneXpert instrument, where the test was performed automatically When sufficient residual was available, repeat testing was carried out when an ‘invalid’ or ‘error’ result was obtained Fluorescent microscopy (unprocessed) using standard AUR reagent Culture using MGIT and L-J medium Zar et al. () South Africa Level III-2: A comparison with reference standard (not blinded or blinding not known) Quality: Low risk of bias Patient selection Index test Comparator Reference std ? Flow and timing Applicability: C1, P1 N=384 children with induced sputum samples Median age 38.3 months (IQR 21.2–56.5) 31/384 (8%) were HIV+ Inclusion Consecutive children < 15 years of age presenting from 1 August 2010 to 30 July 2012 with suspected pulmonary TB Exclusion None reported Samples were decontaminated using standard NALC-NaOH procedure and concentrated by centrifugation The treated specimen sample was transferred to the Xpert MTB/RIF cartridge and test was run in the GeneXpert instrument Fluorescent AFB microscopy using AUR MGIT culture was done using 0.5 mL of resuspended pellet on sputum specimens and incubated for up to 6 weeks
homeless shelters, behavioural treatment programs, dialysis centres) Fan et al. () Tuberculosis center for diagnosis and treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China Conducted at: Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China Prospective cohort Level: III-3 Quality: 17.5/26 Some risk of bias N=280/335 included Mean age: 43 ± 18 years 54 (25%) females Inclusion: Patients with abnormal chest radiographic findings compatible with active TB (TB suspects), > 18 years of age, sputum scarce or with negative AFB microscopy Exclusion: AFB-positive patients and HIV positive patients SAT-TB assay (in-house) and culture (liquid medium) NA CIM: time to detection of TB Guerra et al. () School of Medicine, Johns Hopkins University, Baltimore, MD, USA Conducted at: Baltimore City Health Department, USA Historical control study Level: III-3 Quality: 14.5/26 High risk of bias N=107 (50 in NAAT group and 57 in non-NAAT group) Median age NAAT: 46.5 years, non-NAAT: 47 years 20 (40%) females in NAAT group, 11 (19.3%) females in non-NAAT group 18 (36%) HIV infected in NAAT group (10 unknown), 19 (33.3%) HIV infected in group (10 unknown) Inclusion: AFB-positive pulmonary TB suspects undergoing initial diagnostic evaluation between December 2000 and March 2006 Exclusion: Anti-TB therapy for > 6 days prior to sputum collection Amplified MTD Direct Test, AFB microscopy and culture for MTB AFB microscopy and culture Unnecessary TB treatment time Concordance between MTB results and definitive diagnosis, compared with no MTB results Hanrahan et al. () University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, USA Prospective cohort study Level: III-3 Quality: 16.5/26 Some risk of bias N=641 (50 NAAT-positive, 591 NAAT-negative) Median age: 35 years (IQR 415 (65%) females Inclusion: TB suspects presenting at the clinic, providing consent Exclusion: Not reported Xpert MTB/RIF assay, sputum AFB FL microscopy and liquid culture for MTB NA Number of cases starting TB treatment Median time to TB treatment
Conducted at: Primary care clinic in Johannesburg, South Africa 443 (69%) HIV infected 36 (6%) unknown Kwak et al. () Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea Conducted at: Seoul National University Hospital Retrospective cohort Level: III-3 Quality: 16.5/26 Some risk of bias N=681 patients requested for NAAT Median age: 61 years (IQR 47.5–73.0) 255 (37.4%) females 5 (0.7%) HIV infected Inclusion: Patients in whom NAAT was requested due to suspicion of pulmonary TB between 1 January 2011 and 31 May 2013 Exclusion: Not reported Xpert MTB/RIF assay, mycobacterial culture (liquid and/or solid) and AFB microscopy NA Time to report of results from laboratory Time to confirmation of results by physician Time to treatment Lacroix et al. () University of Sherbrooke, Sherbrooke, Quebec, Canada Conducted at: Public Health Department in Montegrie (Quebec) Retrospective cohort Level: III-3 Quality: 12/26 High risk of bias N=115/134 included (77 NAAT, 38 no NAAT) 43 (37.4%) females 7 (9.9%) HIV infected Inclusion: Contagious (pulmonary, laryngeal, miliary) active TB cases declared to the Public Health Department between 1 January 1998 and 30 June 2007 Exclusion: Non-respiratory TB, clinical case not confirmed by culture or PCR, incomplete file, previous episode of TB, incidentally found cases PCR (in-house, not specified) No PCR (culture, AFB microscopy, chest X-ray) Average delay in diagnosis
N=277 (out of 346 identified contacts) 44 did not comply with protocol 25 refused consent and positive culture for MTB Exclusion Patients with HIV and their contacts No written informed consent Failure to comply with study protocol reference ≤ 1 month delay Analysis of clinical risk factors ORs and their 95%CIs were calculated by means of univariate and multivariate logistic regression Golub et al. () Maryland, USA Prospective cohort study Level: III-2 Quality: 16/26 High risk of bias N=124 total patients with pulmonary TB included 34 excluded due to no contacts identified/tested N=54 (44%) born in USA US patients: 65% male 72% black 59% < 50 years of age 57% AFB sputum-positive 19% chest X-ray with cavitation 385 contacts, of whom 310 (81%) skin tested Inclusion All verified pulmonary TB patients who reported to the Maryland Department of Health and Mental Hygiene between 1 June 2000 and 30 November 2001 and their close contacts Close contacts included those living in the same household, working in a closed environment with patient, and reported close friends and relatives Exclusion No contacts identified or no contacts tested Treatment delay either: ≤ 60 days or ≤ 90 days Delay treated as a dichotomous variable, analysed for cut-offs of 60 and 90 days Total treatment delay defined as interval from first TB symptoms to initiation of treatment for TB Treatment delay > 60 days Treatment delay > 90 days Number of contacts infected TST-positive (tested at baseline and 10–12 weeks later) Van der Oest, Kelly & Hood () Waikato Health District, New Zealand Retrospective cohort study Level: III-2 Quality: 11/26 High risk of bias N=244 (189 new cases, 37 relapse cases, 18 unclassified): 52% male 110 (45%) Maori 46 (19%) non-Indigenous New Zealanders 81 (33%) born overseas, 40 of whom were refugees number with length of Inclusion All notified cases of TB who were residing in the Waikato Health District at the time of notification from 1 January 1992 to 31 December 2001 No diagnostic delay Delay defined as time between development of symptoms and of the case Increasing diagnostic delay Favourable treatment outcome as defined by WHO (i.e. cure or treatment completed) Statistical analysis Logistic regression was used for multivariate and univariate comparisons Chi-square test
diagnostic delay reported 152 (62% of cases) outcome of treatment reported for 214 (88%) of cases AFB = acid-fast bacilli; HIV = human immunodeficiency virus; OR = odds ratio; TB = tuberculosis; TST = tuberculin skin test; WHO = World Health Organization Table 99 Study profiles of included studies on the effectiveness of change in management due to rifampicin-resistance mutations being identified Study setting Study design Quality appraisal Study population Selection criteria Intervention Comparator Outcomes Drobniewski et al. () UK Cohort study Level: III-2 Quality: 19/26 Some risk of bias N=90 MDR-TB patients 36 born in UK, 7 in Pakistan, 5 in India, 4 in Bangladesh, 20 in Africa, 4 in Europe, 1 each from USA, Australia, Philippines, Japan, Trinidad, Jamaica All cases were to at least isoniazid and RIF, and 29 and 33 cases were resistant to pyrazinamide and ethambutol, respectively Inclusion All mycobacterial cultures identified by the Public Health Laboratory Service, Mycobacterium Reference Unit, Scottish Mycobacteria Reference Laboratory, and PHLS Regional Centres for Mycobacteria Treatment with at least three drugs to which the bacterium was susceptible Treatment with fewer drugs to which the bacterium was susceptible Median survival period Chance of death Lam et al. () Thailand Retrospective chart review Level: III-2 Quality: 18.5/26 Some risk of bias N=190 RIF-resistant or patients Inclusion Patients with DST results demonstrating infection with or MDR-TB who were registered for TB treatment during October 2004 – September 2008 at health facilities within the Thailand TBAactive Surveillance Network Exclusion Patients from health facilities operated by private practitioners, Treatment other than Category II Category II treatment (streptomycin, isoniazid, ethambutol, RIF and pyrazinamide) Odds for poor outcome (treatment fail, death)
non-governmental organisations, or facilities serving solely as referral centres, patients with incomplete laboratory data and patients with NTM infection or a change in diagnosis Meyssonnier et al. () France Retrospective cohort study Level: III-2 Quality: 18/26 Some risk of bias N=39 RIF-mono-resistant TB patients, data about treatment and outcome were available for 30 patients 19 males (49%), median age 43 years (IQR 29–58) Foreign born 18 (46%) Inclusion All patients diagnosed with TB reported to the national network in France between 2005 and 2010 Treatment with antibiotics other than RIF Treatment with RIF-containing antibiotic regimen Health outcomes (recovery, lost to death, relapse) IQR = interquartile range; MDR = multidrug-resistant; NTM = non-tuberculous mycobacteria; RIF = rifampicin; TB = tuberculosis; DST = drug susceptibility testing Table 100 Study profiles of SRs assessing the safety and adverse effects of active TB therapies Author Country Study design Quality appraisal Research question Included studies (N) Population Intervention Comparator Outcomes Forget and Menzies () Canada Systematic review (literature search of Medline, relevant articles from authors’ files and pearled references from cited articles) Quality appraisal: poor High risk of bias Research question: NS Included studies: NS Active TB patients Latent TB patients TB patients on multidrug regimens Isoniazid, rifampicin, pyrazinamide, ethambutol, streptomycin Multidrug regimens Various Discontinuation rate AE rate Mortality rate Risk factors for development of AEs Frydenberg & Graham () Australia Systematic review (literature search of PubMed, EMBASE and Cochrane Library Reference, hand-search of reference lists) Research question: To review the frequency and manifestations of toxicities in children to current first-line anti-TB therapy Children (0–18 years of age) undergoing first-line therapy for TB, or therapy for latent TB Anti-TB agents, isoniazid, rifampicin, pyrazinamide, ethambutol, streptomycin Combination therapies NS Adverse reaction incidence AE rate mono-resistant