Xpert ® MTB/RIF assay for extrapulmonary tuberculosis and rifampicin resistance
Open accessAbstract
BACKGROUND: MTB/RIF (Xpert) is a World Health Organization (WHO)-recommended, rapid, automated, nucleic acid amplification assay that is used widely for simultaneous detection of Mycobacterium tuberculosis complex and rifampicin resistance in sputum specimens. This Cochrane Review assessed the accuracy of Xpert in extrapulmonary specimens. OBJECTIVES: To determine the diagnostic accuracy of Xpert a) for extrapulmonary TB by site of disease in people presumed to have extrapulmonary TB; and b) for rifampicin resistance in people presumed to have extrapulmonary TB. SEARCH METHODS: We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature (LILACS), Scopus, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number (ISRCTN) Registry, and ProQuest up to 7 August 2017 without language restriction. SELECTION CRITERIA: We included diagnostic accuracy studies of Xpert in people presumed to have extrapulmonary TB. We included TB meningitis and pleural, lymph node, bone or joint, genitourinary, peritoneal, pericardial, and disseminated TB. We used culture as the reference standard. For pleural TB, we also included a composite reference standard, which defined a positive result as the presence of granulomatous inflammation or a positive culture result. For rifampicin resistance, we used culture-based drug susceptibility testing or MTBDRplus as the reference standard. DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data, assessed risk of bias and applicability using the QUADAS-2 tool. We determined pooled predicted sensitivity and specificity for TB, grouped by type of extrapulmonary specimen, and for rifampicin resistance. For TB detection, we used a bivariate random-effects model. Recognizing that use of culture may lead to misclassification of cases of extrapulmonary TB as 'not TB' owing to the paucibacillary nature of the disease, we adjusted accuracy estimates by applying a latent class meta-analysis model. For rifampicin resistance detection, we performed univariate meta-analyses for sensitivity and specificity separately to include studies in which no rifampicin resistance was detected. We used theoretical populations with an assumed prevalence to provide illustrative numbers of patients with false positive and false negative results. MAIN RESULTS: We included 66 unique studies that evaluated 16,213 specimens for detection of extrapulmonary TB and rifampicin resistance. We identified only one study that evaluated the newest test version, Xpert MTB/RIF Ultra (Ultra), for TB meningitis. Fifty studies (76%) took place in low- or middle-income countries. Risk of bias was low for patient selection, index test, and flow and timing domains and was high or unclear for the reference standard domain (most of these studies decontaminated sterile specimens before culture inoculation). Regarding applicability, in the patient selection domain, we scored high or unclear concern for most studies because either patients were evaluated exclusively as inpatients at tertiary care centres, or we were not sure about the clinical settings.Pooled Xpert sensitivity (defined by culture) varied across different types of specimens (31% in pleural tissue to 97% in bone or joint fluid); Xpert sensitivity was > 80% in urine and bone or joint fluid and tissue. Pooled Xpert specificity (defined by culture) varied less than sensitivity (82% in bone or joint tissue to 99% in pleural fluid and urine). Xpert specificity was ≥ 98% in cerebrospinal fluid, pleural fluid, urine, and peritoneal fluid.Xpert testing in cerebrospinal fluidXpert pooled sensitivity and specificity (95% credible interval (CrI)) against culture were 71.1% (60.9% to 80.4%) and 98.0% (97.0% to 98.8%), respectively (29 studies, 3774 specimens; moderate-certainty evidence).For a population of 1000 people where 100 have TB meningitis on culture, 89 would be Xpert-positive: of these, 18 (20%) would not have TB (false-positives); and 911 would be Xpert-negative: of these, 29 (3%) would have TB (false-negatives).For TB meningitis, ultra sensitivity and specificity against culture (95% confidence interval (CI)) were 90% (55% to 100%) and 90% (83% to 95%), respectively (one study, 129 participants).Xpert testing in pleural fluidXpert pooled sensitivity and specificity (95% CrI) against culture were 50.9% (39.7% to 62.8%) and 99.2% (98.2% to 99.7%), respectively (27 studies, 4006 specimens; low-certainty evidence).For a population of 1000 people where 150 have pleural TB on culture, 83 would be Xpert-positive: of these, seven (8%) would not have TB (false-positives); and 917 would be Xpert-negative: of these, 74 (8%) would have TB (false-negatives).Xpert testing in urineXpert pooled sensitivity and specificity (95% CrI) against culture were 82.7% (69.6% to 91.1%) a
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For lymph node aspirate, evidence uses a composite reference because a composite reference standard is preferable for estimating accuracy.
“For lymph node aspirate, we provide evidence using a composite reference because, based on findings from the original review (Kohli 2018), we believe a composite reference standard is preferable for estimating accuracy.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
The Methods (Criteria for considering studies) say the review used a composite reference standard for pleural TB but decided against one for other forms of TB. The Discussion (Summary of main results) specifically says it used culture plus a latent class model for lymph node aspirate rather than a composite standard, citing inconsistent definitions, interpretive difficulty, and bias concerns. Page numbers are not available in the supplied copy. (LLM, conf=0.90)
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Experimental — accuracy not yet measuredWe added a sensitivity analysis limiting inclusion to studies that used one specimen per participant for Xpert Ultra.
“In the previous review (Kohli 2018), we added post hoc a sensitivity analysis limiting inclusion to studies that used one specimen per participant. In this review, we performed a similar sensitivity analysis for Xpert Ultra.”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
For Xpert MTB/RIF in CSF, studies that evaluated only one specimen per participant had lower pooled sensitivity (63.5%) and lower pooled specificity (96.1%) than all studies (71.1% and 98.0%).
“However, for Xpert MTB/RIF in CSF, in comparison with all studies, (sensitivity of 71.1% (60.9 to 80.4), and specificity of 98.0% (97.0 to 98.8)), studies that evaluated only one specimen per participant had lower pooled sensitivity at 63.5% (47.6 to 76.3) and lower pooled specificity at 96.1% (94.2 to 97.4).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
In the original review, sensitivity analyses by type of extrapulmonary specimen found little difference for most analyses.
“For Xpert MTB/RIF, in the original review we performed sensitivity analyses by type of extrapulmonary specimen and found that for most analyses, the sensitivity analyses made little difference to any of these findings (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
For CSF, the pooled proportion of inconclusive Xpert MTB/RIF results was 0.9% (95% CrI 0.3 to 1.9).
“We previously reported that for CSF, of 2096 tests performed, the pooled proportion of inconclusive Xpert MTB/RIF results was 0.9% (95% CrI 0.3 to 1.9) (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
For lymph node aspirates, the pooled proportion of inconclusive Xpert MTB/RIF results was 1.0% (95% CrI 0.4 to 2.0).
“We previously reported that for lymph node aspirates, in the 1134 tests performed, the pooled proportion of inconclusive Xpert MTB/RIF results was 1.0% (95% CrI 0.4 to 2.0) (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
For pleural fluid, the pooled proportion of inconclusive Xpert MTB/RIF results was 1.2% (95% CrI 0.4 to 2.6).
“We previously reported that for pleural fluid, of 1416 tests performed the pooled proportion of inconclusive Xpert MTB/RIF results was 1.2% (95% CrI 0.4 to 2.6) (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
For rifampicin resistance testing, of 1003 tests performed, the pooled proportion of indeterminate Xpert MTB/RIF results was 2.6% (95% CrI 1.4 to 4.3).
“We previously reported that for rifampicin resistance testing, of 1003 tests performed, the pooled proportion of indeterminate Xpert MTB/RIF results was 2.6% (95% CrI 1.4 to 4.3) (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
In 10 studies involving 6975 specimens with 141 NTMs, Xpert MTB/RIF was negative in all specimens.
“For Xpert MTB/RIF, we previously reported that in 10 studies involving 6975 specimens with 141 NTMs, Xpert MTB/RIF was negative in all specimens (Kohli 2018).”
From Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults (2021) · cites this paper as Kohli 2018
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- Authors
- Kohli, M., Schiller, I., Dendukuri, N., Dheda, K., Denkinger, C. M., Schumacher, S. G., & Steingart, K. R.
- Affiliations
- McGill University (CA)
- McGill University Health Centre (CA)
- University of Cape Town (ZA)
- FIND (CH)
- Liverpool School of Tropical Medicine (GB)
- Corresponding author
- Steingart, Karen R
- ORCID
- Venue
- Cochrane Database of Systematic Reviews
- Publisher
- Wiley
- Published
- 2018-08-27
- Volume
- 8
- Pages
- CD012768-CD012768
- ISSN
- 1361-6137 (ISSN-L)
- 1465-1858
- PMC
- PMC6513199
- OpenAlex
- W2748797449
- Cited by
- 245
- References
- 218
- Citations by year
- 2026: 13 · 2025: 12 · 2024: 34 · 2023: 28 · 2022: 33 · 2021: 44 · 2020: 45 · 2019: 34 · 2018: 1 · 2017: 1
- FWCI
- 4.53
- Type
- journal article
- Language
- en
- Update notices
- new_version (2021-01-15)
- Open access
- bronze
- doi.org
- Locations
- Cochrane Database of Systematic Reviews (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- Funders
- Beijing University of Chinese Medicine
- Topics
- Health Sciences › Medicine › Infectious Diseases › Tuberculosis Research and Epidemiology
- Health Sciences › Medicine › Surgery › Infectious Diseases and Tuberculosis
- Health Sciences › Medicine › Surgery › Diagnosis and treatment of tuberculosis
- Keywords
- Xpert MTB/RIF, extrapulmonary tuberculosis, rifampicin resistance, Mycobacterium tuberculosis complex, diagnostic accuracy, tuberculous meningitis, pleural tuberculosis, tuberculous lymphadenitis, osteoarticular tuberculosis, urogenital tuberculosis, tuberculous pericarditis, tuberculous peritonitis, nucleic acid amplification tests, latent class analysis, sensitivity and specificity
- MeSH terms
- Antibiotics, Antitubercular, Bacterial Proteins, False Negative Reactions, False Positive Reactions, Humans, Mycobacterium tuberculosis, Reagent Kits, Diagnostic, Reference Standards, Rifampin, DNA-Directed RNA Polymerases, Sensitivity and Specificity, Tuberculosis, Tuberculosis, Meningeal, Drug Resistance, Bacterial
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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