Xpert MTB/RIF Ultra assay for tuberculosis disease and rifampicin resistance in children

Abstract

Background: In 2023, an estimated 1.3 million children (aged 0-14 years) became ill with tuberculosis, and 166,000 children (aged 0-15 years) died from the disease. Xpert MTB/RIF Ultra (Xpert Ultra) is a molecular World Health Organization (WHO)-recommended rapid diagnostic test that detects Mycobacterium tuberculosis complex and rifampicin resistance. This is an update of a Cochrane review first published in 2020 and last updated in 2022. Parts of the current update informed the 2024 WHO updated guidance for the diagnosis of tuberculosis.

Objectives: To assess the diagnostic accuracy of Xpert Ultra for detecting pulmonary tuberculosis, tuberculous meningitis, lymph node tuberculosis, and rifampicin resistance in children (aged 0-9 years) with presumed tuberculosis.

Search methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, three other databases, and three trial registers without language restrictions to 6 October 2023.

Selection criteria: For study design, we included cross-sectional and cohort studies and randomized trials that evaluated Xpert Ultra in HIV-positive and HIV-negative children aged birth to nine years. Regarding specimen type, we included studies evaluating sputum, gastric, stool, or nasopharyngeal specimens (pulmonary tuberculosis); cerebrospinal fluid (tuberculous meningitis); and fine needle aspirate or surgical biopsy tissue (lymph node tuberculosis). Reference standards for detection of tuberculosis were microbiological reference standard (MRS; including culture) or composite reference standard (CRS); for stool, we considered Xpert Ultra in sputum or gastric aspirates in addition to culture. Reference standards for detection of rifampicin resistance in sputum were phenotypic drug susceptibility testing or targeted or whole genome sequencing.

Data collection and analysis: Two review authors independently extracted data and assessed methodological quality using the tailored QUADAS-2 tool, judging risk of bias separately for each target condition and sample type. We conducted separate meta-analyses for detection of pulmonary tuberculosis, tuberculous meningitis, lymph node tuberculosis, and rifampicin resistance. We used a bivariate model to estimate summary sensitivity and specificity with 95% confidence intervals (CIs). We assessed certainty of evidence using the GRADE approach.

Main results: This update included 23 studies (including 9 new studies since the previous review) that evaluated detection of pulmonary tuberculosis (21 studies, 9223 children), tuberculous meningitis (3 studies, 215 children), lymph node tuberculosis (2 studies, 58 children), and rifampicin resistance (3 studies, 130 children). Seventeen studies (74%) took place in countries with a high tuberculosis burden. Overall, risk of bias and applicability concerns were low. Detection of pulmonary tuberculosis (microbiological reference standard) Sputum (11 studies) Xpert Ultra summary sensitivity was 75.3% (95% CI 68.9% to 80.8%; 345 children; moderate-certainty evidence), and specificity was 95.9% (95% CI 92.3% to 97.9%; 2645 children; high-certainty evidence). Gastric aspirate (12 studies) Xpert Ultra summary sensitivity was 69.6% (95% CI 60.3% to 77.6%; 167 children; moderate-certainty evidence), and specificity was 91.0% (95% CI 82.5% to 95.6%; 1792 children; moderate-certainty evidence). Stool (10 studies) Xpert Ultra summary sensitivity was 68.0% (95% CI 50.3% to 81.7%; 255 children; moderate-certainty evidence), and specificity was 98.2% (95% CI 96.3% to 99.1%; 2630 children; high-certainty evidence). Nasopharyngeal aspirate (6 studies) Xpert Ultra summary sensitivity was 46.2% (95% CI 34.9% to 57.9%; 94 children; moderate-certainty evidence), and specificity was 97.5% (95% CI 95.1% to 98.7%; 1259 children; high-certainty evidence). Xpert Ultra sensitivity was lower against CRS than against MRS for all specimen types, while the specificities were similar. Extrapulmonary tuberculosis Meta-analysis was not possible for lymph node tuberculosis and tuberculous meningitis due to low study numbers. Interpretation of results For a population of 1000 children, where 100 have pulmonary tuberculosis: In sputum: • 112 would be Xpert Ultra positive, of whom 75 would have pulmonary tuberculosis (true positives) and 37 would not (false positives). • 888 would be Xpert Ultra negative, of whom 863 would not have pulmonary tuberculosis (true negatives) and 25 would have pulmonary tuberculosis (false negatives). In gastric aspirate: • 151 would be Xpert Ultra positive, of whom 70 would have pulmonary tuberculosis (true positives) and 81 would not (false positives). • 849 would be Xpert Ultra negative, of whom 819 would not have pulmonary tuberculosis (true negatives) and 30 would have pulmonary tuberculosis (false negatives). In stool: • 85 would be Xpert Ultra positive, of whom 68 would have pulmonary tuberculosis (true positives) and 17 would not (false positives). • 915 would be Xpert Ultra negative, of whom 883 would not have pulmonary tuberculosis (true negatives) and 32 would have pulmonary tuberculosis (false negatives). In nasopharyngeal aspirate: • 68 would be Xpert Ultra positive, of whom 46 would have pulmonary tuberculosis (true positives) and 22 would not (false positives). • 932 would be Xpert Ultra negative, of whom 878 would not have pulmonary tuberculosis (true negatives), and 54 would have pulmonary tuberculosis (false negatives). Detection of rifampicin resistance Three studies with 76 children evaluated detection of rifampicin resistance (sputum only); two of these studies reported no cases and one reported rifampicin resistance in two children.

Authors' conclusions: Xpert Ultra sensitivity was moderate in sputum, gastric aspirate, and stool specimens. Nasopharyngeal aspirate had the lowest sensitivity. Xpert Ultra specificity was high against both MRS and CRS. We were unable to determine the accuracy of Xpert Ultra for detecting tuberculous meningitis, lymph node tuberculosis, and rifampicin resistance due to a paucity of data.

Funding: This update was funded through WHO.

Registration: The protocol for this review was originally published through Cochrane in 2019. The protocol for this update was a generic protocol that consolidated previously published Cochrane protocols of Xpert Ultra for tuberculosis detection and can be accessed at https://osf.io/26wg7/. Protocol (2019) DOI: 10.1002/14651858.CD013359 Original review (2020) DOI: 10.1002/14651858.CD013359.pub2 Review update (2022) DOI: 10.1002/14651858.CD013359.pub3.

1

Clinical pathway of Xpert Ultra in children presumed to have tuberculosis.

2

Study flow diagram.

3

Risk of bias and applicability concerns summary: reviews authors' judgements about each domain for each included study. Judgements are based on the sputum specimen type, unless the study did not include sputum specimens, in which case judgements are based on the specimen type listed: Aurilio 2022 (EPTB), Babo 2023 (stool), Chabala 2023 (GA), de Haas 2022 (stool), Lounnas 2025 (stool), Parigi 2021 (GA), Pradhan 2022 (EPTB)

4

Risk of bias and applicability concerns graph: review authors' judgements about each domain presented as percentages across included studies.

5

Forest plots of Xpert Ultra sensitivity and specificity for diagnosis of pulmonary tuberculosis in children in all specimen types and against all reference standards. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
FN: false negative; FP: false positive; TN: true negative; TP: true positive. For stool specimens, microbiological reference standard is used because Xpert on sputum specimens was included in the reference standard.

6

Forest plots of Xpert Ultra sensitivity and specificity in sputum and gastric aspirate for pulmonary tuberculosis by age group, all with culture reference standard. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
FN: false negative; FP: false positive; TN: true negative; TP: true positive.

7

Forest plots of Xpert Ultra sensitivity and specificity in stool and nasopharyngeal specimens for pulmonary tuberculosis by age group, all with microbiological reference standard. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
FN: false negative; FP: false positive; TN: true negative; TP: true positive. For stool specimens, microbiological reference standard is used because Xpert on sputum specimens was included in the reference standard.

8

Forest plots of Xpert Ultra sensitivity and specificity for pulmonary tuberculosis by specimen type, HIV status, and reference standard. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
FN: false negative; FP: false positive; TN: true negative; TP: true positive. For stool specimens, microbiological reference standard is used because Xpert on sputum specimens was included in the reference standard.

9

Forest plots of Xpert Ultra sensitivity and specificity for pulmonary tuberculosis by specimen type and comorbidity, all with microbiological reference standard. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
FN: false negative; FP: false positive; TN: true negative; TP: true positive. For stool specimens, microbiological reference standard is used because Xpert on sputum specimens was included in the reference standard.

10

Forest plot of Xpert Ultra sensitivity and specificity for rifampicin resistance. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
TP: true positive; FP: false positive; FN: false negative; TN: true negative.

11

Forest plot of Xpert Ultra sensitivity and specificity for diagnosis of extrapulmonary tuberculosis in children. The squares represent the sensitivity and specificity of each study, the black lines their confidence intervals (CIs).
CSF: cerebrospinal fluid; EPTB: extrapulmonary tuberculosis; FP: false positive; FN: false negative; TN: true negative; TP: true positive.