Stool-based Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis in children at a teaching and referral hospital in Southwest Ethiopia

A multicountry evaluation of the Xpert MTB/RIF assay for the diagnosis of intrathoracic tuberculosis in children using alternative specimens (nasopharyngeal aspirate and stool): A prospective cohort study conducted in Madagascar, Ivory Coast and Cameroon (TB KIDS project)

OBJECTIVES

Tuberculosis (TB) diagnosis in children remains challenging due to the paucibacillary nature of specimens and the difficulty in obtaining suitable samples. The use of alternative samples like nasopharyngeal aspirate (NPA) and stools, alongside Xpert MTB/RIF testing, offers promising improvements. This study aimed to assess the diagnostic performance of the Xpert MTB/RIF test on NPA and stool samples for detecting intrathoracic TB in children from Madagascar, Cameroon, and Ivory Coast.

METHODS

Children under 15 years with suspected intrathoracic TB were enrolled in hospitals in these countries' capitals. Samples for analysis included standard specimens (gastric aspirate or sputum), NPA, stools, with additional HIV serology, tuberculin skin test tests, and chest X-rays. We used a composite reference standard to estimate the accuracy of the Xpert MTB/RIF test with alternative samples.

RESULTS

Of 1146 children analyzed, the sensitivity of Xpert MTB/RIF was 58.3% for NPA and 45.5% for stool samples, with a high specificity of more than 95%. The diagnostic performance of Xpert MTB/RIF with alternative samples did not differ according to age group or HIV status.

CONCLUSIONS

The findings support the World Health Organization's recommendation for using Xpert MTB/RIF with alternative samples in childhood TB diagnosis, underscoring its utility across different settings and HIV statuses.

Stool processing methods for Xpert Ultra testing in childhood tuberculosis: A prospective, multi-country accuracy study

Background

Centrifuge-free processing methods support stool Xpert Ultra testing for childhood tuberculosis (TB), but there are limited data on their accuracy, acceptability and usability.

Methods

We conducted a prospective evaluation of stool Xpert Ultra in India, South Africa, and Uganda with three methods: Stool Processing Kit (SPK), Simple One-Step (SOS), and Optimized Sucrose Flotation (OSF). Children <15 years old with presumptive TB had respiratory specimen testing with Xpert Ultra and culture. Stool was tested using Xpert Ultra after processing with each method. We compared the accuracy of each method to a microbiological reference standard (MRS) and a composite reference standard (CRS). We surveyed the laboratory staff to assess acceptability and usability of the methods.

Results

We included 607 children, of whom the median age was 3.5 years (IQR 1.3-7), 48% were female, and 15.5% were HIV positive. Against the MRS, the sensitivities of SPK, SOS and OSF were 36.9% (95% CI 28.6-45.8), 38.6% (95% CI 17.2-51), and 31.3% (95% CI 20.2-44.1), respectively. The specificities of SPK, SOS and OSF were 98.2% (95% CI 96.4-99.3), 97.3% (95% CI 93.7-99.1) and 97.1% (95% CI 93.3-99), respectively. Laboratory staff reported that the methods were acceptable and usable, but SOS was most feasible to implement in a peripheral facility. Sensitivity increased among children who were culture-positive (55-77.3%) and was low (13-16.7%) against the CRS.

Conclusions

Stool processing methods for Xpert Ultra were acceptable, usable, and performed similarly, with highest sensitivity among children with culture-positive TB.

Performance of stool-based molecular tests and processing methods for paediatric tuberculosis diagnosis: a systematic review and meta-analysis

BACKGROUND

There has been a global pursuit to improve the diagnosis of tuberculosis in young children by applying diagnostic methods on accessible biospecimens such as stool. We aimed to conduct a systematic review on the accuracy of stool-based molecular tests for tuberculosis diagnosis in children and to assess the impact of the available pre-processing methods and other design characteristics.

METHODS

In this systematic review and meta-analysis, we evaluated studies in children younger than 16 years with presumptive tuberculosis that were published in English, Spanish, French, and Portuguese from Jan 1, 2000, to May 3, 2024, in MEDLINE, Embase, and Embase Classic, comparing the molecular detection of Mycobacterium tuberculosis DNA in stool with microbiological tests on other samples or a clinical diagnosis. We did not exclude studies based on geographical location, sample size, or study design if they were reporting primary data. Two independent reviewers (LC-C and SM) screened titles, abstracts, and full-text articles for eligibility and extracted data on study characteristics, study population, and diagnostic performance. If information relevant to the main analysis was not reported in the article, the corresponding authors were contacted. Point estimates and 95% CIs were calculated for sensitivity and specificity for each study and for the different molecular tests (Xpert MTB/RIF, Xpert Ultra MTB/RIF [Cepheid, Sunnyvale, CA, USA], and other tests) versus a reference standard (culture only, any bacteriological confirmation, and tuberculosis case definition). Sensitivity and specificity were stratified by the stool processing method. We also quantified the additionality of stool Xpert Ultra tests for tuberculosis bacteriological confirmation. The protocol was registered with PROSPERO, CRD42022341514.

FINDINGS

A total of 4521 records were identified through the database search, one record was identified from an article bibliography, and 67 studies were retained for full-text reading. 39 studies were included in the qualitative synthesis, 35 of which were included in the meta-analyses. When using any bacteriological confirmation from a respiratory sample as the reference standard, stool Xpert sensitivity was 0·60 (95% CI 0·48-0·71), stool Xpert Ultra sensitivity was 0·73 (0·63-0·81), and sensitivity was 0·44 (0·29-0·60) for other in-house molecular methods combined. When using tuberculosis case definition as the reference standard, stool Xpert sensitivity was 0·23 (0·11-0·41), stool Xpert Ultra sensitivity was 0·38 (0·22-0·56), and sensitivity was 0·17 (0·09-0·23) for other in-house molecular methods. The addition of stool Xpert Ultra increased bacteriological confirmation of tuberculosis by 38·6% overall. Further, the utilisation of centrifuge-free simplified methods improved the sensitivity of stool Xpert Ultra when using any bacteriological confirmation as a reference standard (0·77 [0·66-0·85] for centrifuge-free methods vs 0·61 [0·41-0·78] for non-centrifuge-free methods).

INTERPRETATION

This systematic review and meta-analysis supports the use of Xpert Ultra in stool samples as a diagnostic tool for paediatric tuberculosis diagnosis. Stool-based Xpert Ultra can contribute to increase the bacteriological confirmation in this population, even when respiratory specimens are also tested.

FUNDING

The EDCTP2 programme supported by the EU via Stool4TB Project and the European Society of Pediatric Infectious Diseases.

Diagnostic Accuracy of Cartridge Based Nucleic Acid Amplification Test (CBNAAT) in Stool Samples in Pediatric Tuberculosis

OBJECTIVES

To find out the diagnostic accuracy of stool Cartridge-based nucleic acid amplification test (CBNAAT) as an alternate method as compared to CBNAAT in gastric aspirate (GA) samples in pediatric tuberculosis (TB).

METHODS

This cross-sectional study was performed at Department of Pediatrics of a tertiary care hospital. Children aged 0-18 y diagnosed as presumptive tuberculosis were consecutively enrolled. Gastric aspirate and corresponding stool sample was subjected to CBNAAT and its performance was compared in both samples using appropriate statistical tests.

RESULTS

Total 100 patients were enrolled in the study. Diagnostic accuracy of CBNAAT was 81% and 80% in gastric aspirate and stool sample respectively. On comparing gastric aspirate with corresponding stool sample there was 97% agreement, with Cohen's kappa value of 0.94. There was a statistically significant association observed between gastric aspirate CBNAAT and stool CBNAAT p <0.001 using chi square test. Sensitivity of gastric aspirate CBNAAT and stool CBNAAT was 75% and 73% respectively and specificity was 100% for both the samples compared against Composite Reference Standard (CRS).

CONCLUSIONS

The diagnostic accuracy of stool CBNAAT is comparable to GA CBNAAT in children and can be used as a good alternative to gastric aspirate for diagnosis of pulmonary and disseminated tuberculosis in children.

Paving the Way to Innovative, Child-Friendly Pediatric Diagnostic Methods for Tuberculosis: Introduction of Stool-Based Testing in Ukraine

Like many countries, Ukraine faces challenges with diagnosing tuberculosis (TB) in children due to the paucibacillary nature of the disease and difficulty obtaining respiratory samples. To improve diagnostic efficiency, stool testing is being integrated into routine pediatric TB services. This started with a pilot introduction at 12 regional TB facilities, where stool was collected for children with a preliminary diagnosis of TB, based on clinical and/or radiological or laboratory findings, in addition to routine testing. For 168 children, a stool test was conducted between November 2021 and September 2022, with samples submitted in all 12 pilot regions. For 132 children, other samples were available in addition to stool. Mycobacterium tuberculosis (MTB) was bacteriologically confirmed in 37 children (in stool for 18 children). For 7 of the 18 children with MTB in stool, stool was the only sample in which MTB was detected. Rifampicin resistance was detected in seven children (in stool for three). This noninvasive TB diagnostic sample is especially beneficial for young children who cannot produce sputum. Early detection of TB and its drug-resistant strains in children will allow medical workers to provide safer and more effective treatment and save more lives. Based on the pilot implementation, Ukraine's national TB program began implementing stool testing throughout the country.

Innovative COVID-19 Point-of-Care Diagnostics Suitable for Tuberculosis Diagnosis: A Scoping Review

Introduction

Rapid and accurate point-of-care (POC) tuberculosis (TB) diagnostics are a key priority to close the TB diagnostic gap of 3.1 million people without a diagnosis. Leveraging the recent surge in COVID-19 diagnostic innovation, we explored the potential adaptation of commercially available SARS-CoV-2 tests for TB diagnosis, aligning with World Health Organization (WHO) target product profiles (TPPs).

Methods

A scoping review was conducted following PRISMA-ScR guidelines to systematically map commercially available POC molecular and antigen SARS-CoV-2 diagnostic tests potentially meeting the TPPs for TB diagnostic tests for peripheral settings. Data were gathered from PubMed/MEDLINE, bioRxiv, and medRxiv, along with publicly accessible in vitro diagnostic test databases, and developer websites, up to November 23, 2022. Data on developer and test attributes, operational characteristics, pricing, and clinical performance were charted using standardized data extraction forms. Each identified test was evaluated using a standardized scorecard. A narrative synthesis of the charted data is presented.

Results

Our database search yielded 2,003 studies, from which 408 were considered eligible. Among these, we identified 58 commercialized diagnostic devices, including 17 near-POC antigen tests, one POC molecular test, 29 near-POC molecular tests, and 11 low-complexity molecular tests. We summarized the detailed characteristics, regulatory status, and clinical performance data of these tests. The LumiraDx (Roche, Switzerland) emerged as the highest- scoring near-POC antigen platform, while Visby (Visby, USA) was the highest-performing near-POC molecular platform. The Lucira Check-It (Pfizer, USA) was noted as the sole POC molecular test. The Idylla TM (Biocartis, Switzerland) was identified as the leading low- complexity molecular test.

Discussion

We highlight a diverse landscape of commercially available diagnostic tests suitable for potential adaptation to TB POC testing. This work aims to bolster global TB initiatives by fostering stakeholder collaboration, leveraging COVID-19 diagnostic technologies for TB diagnosis, and uncovering new commercial avenues to tackle longstanding challenges in TB diagnosis.

Impact of the Stool-Based Xpert Test on Childhood Tuberculosis Diagnosis in Selected States in Nigeria

BACKGROUND

In Nigeria, most children with tuberculosis (TB) present at primary health clinics where there are limited personnel skilled in collecting appropriate respiratory specimens from those who cannot produce sputum. KNCV Nigeria, in collaboration with the National Tuberculosis Control Program, implemented a modified simple, one-step (SOS), stool-based Xpert MTB/RIF method for diagnosis of TB in children who cannot expectorate sputum. We evaluated the impact of its implementation on childhood TB diagnosis.

METHOD

A cross-sectional study was conducted across 14 selected states using secondary data of children presumed to have TB. Stool was collected from children presumed to have TB and processed using Xpert.

RESULT

Out of 52,117 presumptive TB cases, 52% were male and 59.7% were under 5 years old. A total of 2440 (5%) cases were diagnosed with TB, and 2307 (95%) were placed on treatment. Annual TB notifications increased significantly after the introduction of the stool-based Xpert test when compared to those in the pre-implementation period. Increasing contributions from stool testing were observed throughout the implementation period, except in 2020 during the COVID-19 era. Overall, stool Xpert testing improved childhood TB notification in the studied states. Interventions aimed at awareness creation, capacity building, and active case finding improved the performance of the test.

Diagnostic accuracy, feasibility and acceptability of stool-based testing for childhood tuberculosis

Background

Childhood tuberculosis (TB) diagnosis remains challenging, partly because children cannot provide sputum. This study evaluated the diagnostic accuracy of the Simple One-Step (SOS) stool method with Xpert MTB/RIF Ultra (Xpert-Ultra) for childhood TB compared to culture and Xpert-Ultra on a respiratory sample (RS) and clinical diagnosis. It also assessed the feasibility and acceptability of stool testing according to laboratory staff, and caregivers' sample preference.

Methods

We enrolled children (≤10 years) with presumptive pulmonary tuberculosis in Ethiopia. RS was tested using Xpert-Ultra and culture; stool samples were tested using the SOS stool method with Xpert-Ultra. Laboratory staff and caregivers' opinions were assessed using standardised questionnaires.

Results

Of the 898 children enrolled, 792, 832 and 794 were included for assessing the diagnostic accuracy of SOS stool with Xpert-Ultra against culture, RS Xpert-Ultra and clinical diagnosis, respectively, yielding sensitivity estimates for SOS stool with Xpert-Ultra of 69.1% (95% confidence interval (CI) 56.0-79.7%), 76.8% (95% CI 64.2-85.9%) and 59.0% (95% CI 47.9-69.2%), respectively. The specificity was ≥98.8% for all comparisons. The rate of non-determinate test results was 2.8% after one repeat test. According to laboratory staff, stool collection was feasible and acceptable and the SOS stool method was easy to perform. Most caregivers (75%) preferred stool for TB diagnosis over RS.

Conclusion

This study shows that SOS stool Xpert-Ultra testing offers a good alternative to RS testing for TB in children who cannot spontaneously produce a sputum sample and would otherwise need to undergo invasive procedures to obtain RS for diagnosis.

Optimization of the Simple One-Step Stool Processing Method to Diagnose Tuberculosis: Evaluation of Robustness and Stool Transport Conditions for Global Implementation

Stool is recommended as an alternative specimen for the diagnosis of tuberculosis (TB) in young children, as they cannot easily produce sputum. The Simple One-Step (SOS) stool processing method is a new and simple stool processing method for the detection of Mycobacterium tuberculosis (MTB) using Xpert MTB/RIF Ultra (Xpert-Ultra). We determined the robustness of the SOS stool processing method and stool specimen transport conditions in participants with confirmed TB. We processed stool using the standard protocol after simulated "transport," varying time, and temperature, and experimented with slightly modified processing steps. We included 2,963 Xpert-Ultra test results from 132 stool specimens of 47 TB participants, including 11 children aged <10 years. We compared Xpert-Ultra processing errors and MTB positivity rates between standard and modified procedures. Minor deviations from the standard SOS protocol did not significantly impact the Xpert-Ultra test outcomes. The rate of Xpert-Ultra processing errors significantly increased with noncold-chain transport, exposure of stool to sample reagent at room temperature or beyond 12 h, and adding >0.8 g of stool. We found that almost all steps in the current SOS stool processing method provide optimal Xpert-Ultra results but recommend an adjustment to use a wider range of stool amounts (0.3 to 0.8 g) than advised previously (0.8 g). With this adaptation, stool-based diagnosis of TB using the SOS stool processing method can be scaled-up. IMPORTANCE The manuscript will support the global implementation and scale-up of the SOS stool method in routine settings. It also provides important insights on the optimal stool transport conditions and robustness of the SOS method, which can be used for bacteriological diagnosis of TB in children at the lowest levels of the healthcare system, avoiding lengthy healthcare-seeking pathways and additional costs.

Stool CBNAAT: Alternative tool in the diagnosis of pulmonary tuberculosis in children

Tuberculosis (TB) remains a significant public health concern, especially in children. The World Health Organization now provides estimates on pediatric TB cases and deaths, underscoring the urgency of addressing this issue. In India, childhood TB contributes significantly to the global burden, with a notable gap between reported cases and estimated incidence. Diagnosing pulmonary TB in children presents challenges, primarily due to difficulties in obtaining suitable respiratory specimens. Rapid tests like Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) have shown promise in enhancing diagnostic sensitivity. Recent research suggests that stool samples offer a non-invasive alternative for diagnosing pulmonary TB in children, with good diagnostic accuracy observed for stool CBNAAT. Furthermore, stool CBNAAT results demonstrate high agreement with gastric aspirate CBNAAT in TB diagnosis. Various stool processing methods, such as centrifugation, filtration, and sedimentation, have shown improved results for CBNAAT testing. However, it is crucial to standardize these methods to ensure consistent and comparable outcomes. Integrating stool CBNAAT into existing diagnostic algorithms for pediatric TB can enhance accuracy and efficiency in diagnosis. When implementing these algorithms, local resources, epidemiological context, and healthcare settings should be taken into account. Stool CBNAAT holds promise for microbiological confirmation of pediatric pulmonary TB, especially in resource-limited settings where obtaining representative respiratory specimens is challenging. Further comparative studies and standardization of stool processing methods are necessary to determine the most suitable approach in different contexts. By doing so, we can make significant strides in improving TB diagnosis and management in children.

Analytical performances of the Xpert MTB/RIF assay using stool specimens to improve the diagnosis of pulmonary tuberculosis in Burkina Faso, a tuberculosis endemic country

Timely diagnosis of Pulmonary Tuberculosis (PTB) is associated with good prognosis, but remains difficult in primary healthcare facilities and particularly in children and patients living with HIV. The aim of this study was to compare the GeneXpert ® MTB/RIF assay (Xpert) performed using a stool sample (3-5 g) and using the first Respiratory Tract Sample (RTS; i.e., sputum, bronchoalveolar or gastric aspirate; as normally done) concomitantly collected from 119 patients with suspected PTB to improve PTB diagnosis in Burkina Faso, a high tuberculosis burden country with limited resources. Overall, microbiological, microscopic and molecular analysis of the 119 first RTS and 119 stool specimens led to Mycobacterium tuberculosis complex detection in 28 patients (23 positive RTS cultures and 5 negative RTS cultures-RTS Xpert positive). When using the 28 clinical confirmed cases as reference standard, the sensitivities of the stool-based and RTS-based Xpert assays were not different (24/28, 85.7%, versus 26/28, 92.86%; p > 0.30), and 22 results were fully concordant. Considering the first RTS culture as the gold standard, the sensitivities of the stool-based and RTS-based Xpert assays to detect PTB in patients with positive RTS culture were 100% (23/23) and 91.3% (21/23), respectively (p >0.05). The stool-based Xpert assay specificity for excluding PTB was 99% (95/96) (compared with 95%, 91/96, when using RTS) and its negative and positive predictive values were 100% (95/95) and 96% (23/24), respectively. Compared with the 23 positive RTS cultures, the incremental yield rates of the RTS-based and stool-based Xpert assays were 4.2% (5/119) and 0.84% (1/119), respectively. Overall, our findings support using the stool-based Xpert assay as an alternative method for earlier PTB diagnosis, when RTS are difficult to obtain.

Comparison of Xpert MTB/RIF Ultra Results of Stool and Sputum in Children with Presumptive Tuberculosis in Southern Ethiopia

The introduction of stool as a readily obtainable sample and the recently developed simple one-step (SOS) stool processing method on Xpert MTB/RIF Ultra (Xpert Ultra) offer an opportunity for TB diagnosis in children. We conducted this study in secondary health facilities in Ethiopia, which are the first-level referral facilities for childhood TB diagnosis and treatment, with the aim to determine if stool-based TB diagnosis can be performed with a reasonable level of concordance with sputum tests using Xpert MTB/RIF Ultra. Eligible children 0-14 years old with presumptive pulmonary TB were asked to provide stools in addition to routinely requested sputum samples. We determined the level of agreement between the stool and sputum test results. Of the 373 children included in the study, 61% were <5 years of age and 56% were male. Thirty-six children (9.7%) were diagnosed with TB, and all started treatment. The rate of concordance between stool and sputum was high, with a kappa value of 0.83 (p < 0.001). There were more Xpert Ultra positive results on stool (n = 27 (7.2%)) than on sputum/NGA (n = 23 (6.2%)). Laboratories in secondary hospitals can perform stool-based TB diagnosis in children, with high concordance between stool and sputum test results reaffirming the applicability of the SOS stool method.

Stool Xpert MTB/RIF as a possible diagnostic alternative to sputum in Africa: a systematic review and meta-analysis

INTRODUCTION

Worldwide, COVID-19 pandemic lead to a large fall in the number of newly reported TB cases. In sub-Saharan Africa, microbiological diagnosis of TB is generally based on smear microscopy and Xpert MTB/RIF on sputum samples, but good quality sputum samples are often difficult to obtain, leading clinicians to rely on more invasive procedures for diagnosis. Aim of this study was to investigate pooled sensitivity and specificity of Xpert MTB/RIF on stool samples compared to respiratory microbiological reference standards in African countries.

METHODS

Four investigators independently searched PubMed, SCOPUS, and Web of Science until 12th October 2022, then screened titles and abstracts of all potentially eligible articles. The authors applied the eligibility criteria, considered the full texts. All the studies reported the data regarding true positive (TP), true negative (TN), false positive (FP) and false negative (FN). Risk of bias and applicability concerns were assessed with the Quadas-2 tool.

RESULTS

overall, among 130 papers initially screened, we evaluated 47 works, finally including 13 papers for a total of 2,352 participants, mainly children. The mean percentage of females was 49.6%, whilst the mean percentage of patients reporting HIV was 27.7%. Pooled sensitivity for Xpert MTB/RIF assay for detecting pulmonary tuberculosis was 68.2% (95%CI: 61.1-74.7%) even if characterized by a high heterogeneity (I2=53.7%). Specificity was almost 100% (99%, 95%CI: 97-100%; I2 = 45.7%). When divided for reference standard, in the six studies using sputum and nasogastric aspirate the accuracy was optimal (AUC = 0.99, SE = 0.02), whilst in the studies using only sputum for tuberculosis detection the AUC was 0.85 (with a SE = 0.16). The most common source of bias was exclusion of enrolled patients in the analysis.

CONCLUSIONS

Our study confirms that, in Africa, stool Xpert MTB/RIF may be a useful rule-in test for children above and below 5 years of age under evaluation for pulmonary tuberculosis. Sensitivity increased substantially when using both sputum and nasogastric aspirate as reference samples.