Xpert MTB/RIF diagnosis of childhood tuberculosis from sputum and stool samples in a high TB-HIV-prevalent setting

Utility of stool Xpert MTB/Rif assay in the diagnosis of pulmonary and abdominal tuberculosis in children - A study from Western India

BACKGROUND

Microbiological diagnosis of pediatric pulmonary and intestinal tuberculosis remains difficult due to difficulty in specimen collection such as with sputum, gastric aspirates or intestinal biopsies. Stool Xpert MTB/Rif may be useful as specimen collection is non-invasive.

OBJECTIVES

To determine the sensitivity and specificity of Stool Xpert for the diagnosis of pulmonary or intestinal tuberculosis in Indian children.

METHODS

We retrospectively compared the performance of stool Xpert, pulmonary sample Xpert (gastric lavage, sputum, bronchoalveolar lavage), and Mycobacteria Growth Indicator Tube (MGIT) for 52 children with pulmonary, intestinal or disseminated tuberculosis.

RESULTS

Thirty (57.7%) children had positive pulmonary Xpert results, while 17(32.7%) had positive stool Xpert results. The sensitivity and specificity of stool Xpert compared to pulmonary Xpert was 43.3% and 81.8%, respectively. On using MGIT as a reference, pulmonary Xpert had a higher sensitivity compared to stool Xpert (81.8% vs. 63.6%, respectively) but lower specificity (48.8%vs.75.6%, respectively). Kappa analysis showed fair agreement between stool and pulmonary Xpert results (0.23), and moderate agreement between stool and gastric lavage Xpert results (0.43). Stool Xpert was found to be equivalent to pulmonary Xpert in detecting tuberculosis in children younger than 5 years (36.4% in both; 4 children each tested positive out of 11). No patients with isolated intestinal tuberculosis had positive stool Xpert.

CONCLUSION

Stool Xpert may serve as a supplementary diagnostic tool in paediatric tuberculosis, particularly in young children where specimen collection is difficult. However, its lower sensitivity compared to pulmonary samples limits its potential as a standalone test.

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.

Analysis of unsuccessful tests and the effect of prolonged clinical sample preprocessing in the GeneXpert MTB/RIF assay

BACKGROUND

The GeneXpert MTB/RIF (Xpert) assay is a widely used technology for detecting Mycobacterium tuberculosis (MTB) in clinical samples. However, the study on the failure of the Xpert assay during routine implementation and its potential solutions is limited.

METHODS

We retrospectively analyzed the records of unsuccessful tests in the Xpert and the GeneXpert MTB/RIF Ultra (Ultra) assays between April 2017 and April 2021 at the Shanghai Public Health Clinical Center. To further investigate the effect of prolonged preprocessing on clinical sputum, an additional 120 sputum samples were collected for Xpert testing after 15 min, 3 h, and 6 h preprocessing. The analysis was performed by SPSS version 19.0 software.

RESULTS

A total of 11,314 test records were analyzed, of which 268 (2.37%) had unsuccessful test results. Among these, 221 (1.95%) were reported as "Error", 43 (0.38%) as "Invalid", and 4 (0.04%) as "No result". The most common clinical specimen for Xpert tests was sputum, accounting for 114 (2.17%) unsuccessful tests. The failure rate of urine specimens was lower than that of sputum (OR = 0.12, 95% CI: 0.02-0.88, χ2 = 6.22, p = 0.021). In contrast, the failure rate of stool specimens was approximately twice as high as that of sputum (OR = 1.93, 95% CI: 1.09-3.40, χ2 = 5.35, p = 0.014). In the prolonged preprocessing experiment, 102 cases (85%) yielded consistent results in Xpert tests. Furthermore, 7 cases (5.83%) detected an increase in MTB load, 8 cases (6.67%) detected a decrease in MTB load, and 3 cases (2.5%) yielded incongruent results in MTB and rifampicin resistance detection.

CONCLUSIONS

The primary cause of unsuccessful tests in the Xpert assay was reported as "Error". Despite varying failure rates depending on the samples, the Xpert assay can be applied to extrapulmonary samples. For paucibacillary specimens, retesting the remaining preprocessed mixture should be carefully considered.

Comparison of gastric lavage/sputum and stool specimens in the diagnosis of pediatric pulmonary tuberculosis- A pilot study

BACKGROUND AND OBJECTIVE

Global TB report 2021 mentions 11 % prevalence of pediatric TB, whereas 5.65% of the cases were reported from India in 2020. India features in the list of TB high burden countries, HIV-TB high burden and MDR-TB high burden countries. The diagnosis of pulmonary tuberculosis in children is difficult as they tend to swallow the sputum, invasive techniques of gastric aspirates needs to be followed and the disease itself is paucibacillary. The disease progresses rapidly in young children and hence rapid diagnosis is needed. Obtaining appropriate respiratory samples for diagnosis is difficult especially in primary care settings. Stool sample is easy to obtain and since children swallow sputum, it can be used to diagnose pulmonary tuberculosis. With this background, a pilot study was planned to evaluate the accuracy of the Xpert MTB/RIF assay for the detection of MTB in stool specimens obtained from pediatric pulmonary TB patients confirmed either by gastric lavage(GL) or sputum(SP) Xpert MTB/RIF assay. In addition, the results of microscopy of stool specimen were compared with that of gastric lavage/ sputum (GL/SP) specimen by Ziehl-Neelsen (ZN) and fluorescent light-emitting diode (LED) staining.

MATERIAL AND METHODS

A prospective study was carried out on 50 GL/SP Xpert MTB/RIF assay positive children (0-14 years). Stool specimens from these children were processed for Xpert MTB/RIF assay. The GL/SP and stool specimens were processed for ZN and Auramine O fluorescent microscopy as well.

RESULTS

Fluorescent staining detected acid fast bacilli (AFB) in 24 GL/SP and 16 stool specimens as compared to 20 GL/SP and 10 stool specimens by ZN staining. Stool Xpert MTB/ RIF assay was positive in 29 out of 50 children. Rifampicin resistance was detected in 13 of the 50 (26%) GL/SP specimens. Of these 13 children, rifampicin resistance was detected in 7 stool specimens, rifampicin indeterminate resistance was detected in one specimen and in the remaining 5 children, M.tuberculosis was not detected in stool.

CONCLUSION

Stool is a good non-invasive specimen for the detection of pulmonary TB in children, especially in remote areas, where invasive techniques cannot be performed for sample collection.

Evaluation of Xpert MTB/RIF Assay on Stool Samples for the Diagnosis of Pulmonary Tuberculosis among the Pediatric Population

Objective  Microbiological confirmation of tuberculosis (TB) in pediatric cases is challenging due to its paucibacillary nature and difficulty in specimen collection. This study aimed to validate stool as an alternative sample for the diagnosis of pediatric pulmonary TB via Xpert MTB/RIF (Xpert) assay. Materials and Methods  This cross-sectional study included 75 pediatric patients up to 10 years of age with signs and symptoms suggestive of TB. From each recruited patient, pulmonary and stool samples were collected in a sterile container. The collected samples were subjected to Ziehl-Neelsen staining, BACTEC MGIT 960 culture (MGIT), Xpert, and in-house multiplex polymerase chain reaction for TB diagnosis. Results  About 13.33% (10/75) of the pulmonary samples and, of them, 50% (5/75) of the stool samples were positive by Xpert assay. The sensitivity and specificity of Xpert assay with stool and pulmonary samples were 50 (95% confidence interval [CI]: 18.71-81.29%) and 100% (95% CI: 94.48-100%), respectively. Conclusion  The Xpert assay on stool samples showed limited sensitivity and good specificity in the diagnosis of pulmonary TB. Therefore, it can be proposed as an alternative screening sample to diagnose TB in pediatric cases for which getting a respiratory sample is extremely difficult. However, further studies with greater number of samples and multiple baseline variables are required to support our findings. Strategies to optimize stool Xpert assay should be performed to enhance the sensitivity of this method to detect Mycobacterium tuberculosis in children.

Detection of <i>Mycobacterium tuberculosis</i> in Peripheral Blood Mononuclear Cells from Patients with Pulmonary Tuberculosis

Background: Pulmonary tuberculosis is currently diagnosed using traditional techniques, such as smear production from sputum samples, to detect acid-fast bacilli (AFB) and bacteriological culture. The detection of Mycobacterium tuberculosis DNA in peripheral blood samples could potentially aid in tuberculosis diagnosis. Objectives: This study aimed to compare the effectiveness of polymerase chain reaction (PCR) assay on peripheral blood mononuclear cells (PBMCs) with established diagnostic techniques for detecting M. tuberculosis. Methods: We collected peripheral blood and sputum samples from 45 patients with smear-positive pulmonary tuberculosis. Standard microscopy and culture techniques were performed on both sputum and PBMC samples. The PCR was conducted on PBMC and sputum specimens using primers specific for the M. tuberculosis complex insertion sequence IS6110. Results: Thirty-nine sputum samples and 2 PBMC samples were determined to contain M. tuberculosis based on bacterial culture and biochemical tests. PCR results were positive for 32 (82%) sputum samples and 29 (75%) PBMC samples. None of the PBMCs tested positive through AFB staining. Conclusions: The M. tuberculosis PCR assay on PBMCs using IS6110 primers demonstrated high sensitivity and specificity in detecting M. tuberculosis DNA. However, the implementation of real-time PCR with a specific probe may further enhance the detection of M. tuberculosis DNA in peripheral blood.

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.

Trends in pediatric tuberculosis diagnosis utilizing xpert Mycobacterium tuberculosis/Rifampicin in a poor-resource, high-burden region: A retrospective, multicenter study

Background

The burden of tuberculosis (TB) in Nigeria remains high, and diagnosis in children, a challenge. We aimed to document yield from Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) as a mode of diagnosis for children and the variables associated with a positive result.

Methods

This was a retrospective review of TB treatment cards of children aged 0-15 years managed from January 2017 to December 2021 across six public tertiary institutions in Nigeria. The data obtained were analyzed using the descriptive and inferential statistics. Statistical significance was set at P < 0.05.

Results

Of 1489 children commenced on TB treatment, 1463 (97.9%) had sufficient data for analysis the median age of study participants was 60 months (interquartile range [IQR]: 24, 120), and 814 (55.6%) were males. Xpert MTB/RIF test was performed in 862 (59%) participants and MTB was detected in 171 (19.8%) participants, of which 6.4% (11/171) had RIF resistance reported. The use of Xpert MTB/RIF rose from 56.5% in 2017 to 64% in 2020 but fell to 60.9% in 2021. We found that older age (> 10 years), the presence of pulmonary TB (PTB), and a negative human immunodeficiency virus (HIV) status were associated with positive Xpert MTB/RIF tests (P = 0.002, 0.001, and 0.012, respectively).

Conclusion

The utilization of Xpert MTB/RIF in children increased in the years before the COVID-19 pandemic. Factors associated with MTB detection by Xpert MTB/RIF include older age, the presence of PTB, and a negative HIV status. Clinical and radiological evaluation continues to play vital roles in the diagnosis of childhood TB in Nigeria.

Pediatric Tuberculosis Management: A Global Challenge or Breakthrough?

Managing pediatric tuberculosis (TB) remains a public health problem requiring urgent and long-lasting solutions as TB is one of the top ten causes of ill health and death in children as well as adolescents universally. Minors are particularly susceptible to this severe illness that can be fatal post-infection or even serve as reservoirs for future disease outbreaks. However, pediatric TB is the least prioritized in most health programs and optimal infection/disease control has been quite neglected for this specialized patient category, as most scientific and clinical research efforts focus on developing novel management strategies for adults. Moreover, the ongoing coronavirus pandemic has meaningfully hindered the gains and progress achieved with TB prophylaxis, therapy, diagnosis, and global eradication goals for all affected persons of varying age bands. Thus, the opening of novel research activities and opportunities that can provide more insight and create new knowledge specifically geared towards managing TB disease in this specialized group will significantly improve their well-being and longevity.

High Mycobacterium tuberculosis Bacillary Loads Detected by Tuberculosis Molecular Bacterial Load Assay in Patient Stool: a Potential Alternative for Nonsputum Diagnosis and Treatment Response Monitoring of Tuberculosis

Not all patients produce sputum, yet most available TB tests use sputum. We investigated the utility of a novel RNA-based quantitative test, the tuberculosis molecular bacterial load assay (TB-MBLA), for the detection and quantification of Mycobacterium tuberculosis in stool. Stools from 100 adult individuals were treated with OMNIgene-sputum reagent and tested using Xpert MTB/RIF ultra (Xpert ultra), auramine O smear microscopy (smear), mycobacterial growth indicator tube (MGIT), and Lowenstein-Jensen (LJ) cultures. The remaining portions were frozen at −20°C and later tested by TB-MBLA. MGIT sputum culture was used as a TB confirmatory test and reference for stool tests. Sixty-one of 100 participants were already confirmed TB positive by MGIT sputum culture, 20 (33%) of whom were HIV coinfected. TB-MBLA detected M. tuberculosis in 57/100 stool samples, including 49 already confirmed for TB. The mean bacterial load measured by stool TB-MBLA was 5.67 ± 1.7 log₁₀ estimated CFU (eCFU) per mL in HIV-coinfected participants, which was higher than the 4.83 ± 1.59 log₁₀ eCFU per mL among the HIV-negative participants (P = 0.04). The sensitivities (95% confidence intervals [CI]) of stool assays were 80% (68 to 89) and 90% (79 to 98) for TB-MBLA and Xpert ultra, which were both higher than the 44% (32 to 58), 64% (51 to 76), and 62% (45 to 77) for smear, MGIT, and Lowenstein-Jensen (LJ) stool cultures, respectively. The specificity (95% CI) of stool assays was highest for smear, at 97% (87 to 100), followed by Xpert ultra at 91% (76 to 98), TB-MBLA at 79% (63 to 90), LJ at 80% (64 to 91), and MGIT at 62% (45 to 77). Twenty-six percent of MGIT and 21% of LJ stool cultures were indeterminate due to contamination. Detection and quantification of viable M. tuberculosis bacilli in stool raises its utility as an alternative to sputum as a sample type for TB diagnosis.

IMPORTANCE This paper highlights the value of stool as a sample type for diagnosis of tuberculosis. While other studies have used DNA-based assays like the Xpert MTB/RIF and culture to detect Mycobacterium tuberculosis in stool, this is the first study that has applied TB-MBLA, an RNA-based assay, to quantify TB bacteria in stool. The high microbial density and diversity in stool compromises the specificity and sensitivity of culture-based tests due to overgrowth of non-M. tuberculosis flora. Consequently, TB-MBLA becomes the most sensitive and specific test for the detection and quantification of viable TB bacteria in stool. Most crucially, this study raises the possibility of a nonsputum alternative sample type for diagnosis of TB among people who have difficulty in producing sputum.

Retrospective cohort analysis of survival of children living with HIV/AIDS in Mumbai, India

OBJECTIVES

To understand the survival in a cohort of children living with HIV/AIDS (CLHAs) and to study the factors associated with survival in CLHAs in government antiretroviral therapy (ART) centres in Mumbai, India.

DESIGN

This is a retrospective cohort analysis.

SETTING

Data from electronic ART records of children from 15 ART centres in Mumbai, Maharashtra, India.

PARTICIPANTS

2224 CLHAs registered in one of these ART centres from 2004 until October 2019. CLHAs up to the age of 18 at the time of registration were considered for these analyses.

PRIMARY AND SECONDARY OUTCOMES

We accessed the following data: date of test, date of initiation of ART, date of last follow-up, age at the time of registration, gender, potential route of infection, baseline CD4 counts, ART regimen, adherence and presence of co-infection (TB). We estimated the survival probabilities, plotted the Kaplan-Meier survival graphs and estimated HRs for mortality.

RESULTS

The mortality rate in our population was 22.75 (95% CI 20.02 to 25.85) per 1000 person-years. The 1-year survival was 0.92 (95% CI 0.91 to 0.93), 0.89 (95% CI 0.88 to 0.91) at 5 years and 0.85 (95% CI 0.83 to 0.87) at 10 years after initiation of ART. Children with adherence less than 80% had lowest survival in the first year (0.54, 95% CI 0.46 to 0.61). It reduced drastically at 5 and 10 years. After adjusting for demographic and clinical parameters, mortality was associated with poor adherence (<80%) (HR 11.70, 95% CI 8.82 to 15.53; p<0.001). However, CD4 counts of greater than 200 and age more than 1 year were protective.

CONCLUSIONS

Poor adherence to ART and low CD4 counts were significantly associated with higher mortality. Adherence counselling should be an important component of CLHA monitoring in all ART centres. It is also important to identify children early in the infection and start ART medications appropriately.

Variable Diagnostic Performance of Stool Xpert in Pediatric Tuberculosis: A Systematic Review and Meta-analysis

BACKGROUND

Difficult specimen collection and low bacillary load make microbiological confirmation of tuberculosis (TB) in children challenging. In this study, we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of Xpert on stool for pediatric tuberculosis.

METHODS

Our search included studies from 2011 through 2019, and specific search terms were used to retrieve articles from Pubmed, EMBASE, BIOSIS, ClinicalTrials.gov, and Google Scholar. Risk of bias was assessed using the QUADAS 2 tool. The protocol was registered in PROSPERO (CRD42018083637). Summary estimates of sensitivity and specificity were conducted using meta-disc Software assuming a random-effects model.

RESULTS

We identified 12 eligible studies, which included data from 2177 children, of whom 295 (13.6%) had bacteriologically confirmed TB on respiratory specimens. The pooled sensitivity of Xpert MTB/RIF on stool specimens compared with bacteriologically confirmed tuberculosis with respiratory specimens was 0.50 (95% CI, 0.44-0.56) with an I 2 of 86%, which was statistically significant (P < .001). The pooled specificity was 0.99 (95% CI, 0.98-0.99; I 2 = 0.0%; P = .44).

CONCLUSIONS

Despite the observed heterogeneity, stool may be considered an additional specimen to support diagnosis of pulmonary TB in children, especially in settings where it is impossible to get respiratory samples. Further studies should evaluate its optimization as a diagnostic tool.

Xpert® MTB/RIF assay testing on stool for the diagnosis of paediatric pulmonary TB in Tanzania

SETTING

Six health facilities in Dar es Salaam, Tanzania.

OBJECTIVE

To evaluate the use of stool specimens in the diagnostic workup of paediatric TB using the Xpert^® MTB/RIF assay.

DESIGN

Between December 2018 and May 2019, we performed a cross-sectional diagnostic study of children aged between 1 month and 14 years with presumptive TB. A single stool specimen was tested using Xpert. The result was compared with the reference microbiological standard for respiratory or gastric specimens tested using Xpert and/or solid culture. The sensitivity, specificity and predictive values of stool Xpert assay were assessed.

RESULTS

A total of 225 children with a median age of 2.17 years (IQR 1.16-5.19) were enrolled; 165/225 (73.3%) were aged <5 years. Of 225 children, 8 (3.6%) were diagnosed with TB as they were culture- or Xpert-positive on sputum/gastric aspirate. The stool Xpert assay showed a sensitivity of 62.5% (95% CI 25-92) and specificity of 100% (95% CI 98-100) against the reference standard.

CONCLUSION

Use of the Xpert assay on stool specimens had a moderate sensitivity and high specificity in the diagnosis of pulmonary TB in children. Our data adds to the body of evidence for the use of Xpert assay on stool as a non-respiratory specimen to complement conventional methods used to diagnose the disease.

Tuberculosis diagnostic accuracy of stool Xpert MTB/RIF and urine AlereLAM in vulnerable children

BACKGROUND

Non-sputum based diagnostic approaches are crucial in children at high risk of disseminated tuberculosis [TB] who cannot expectorate sputum. We evaluated the diagnostic accuracy of Xpert MTB/RIF from stool and urine AlereLipoarabinomannan [LAM] test in this group of children.

METHODS

Hospitalised children with presumptive TB and either age <2 years, HIV-positive or severe malnutrition were enrolled in a diagnostic cohort. At enrolment, we attempted to collect two urine, two stool and two respiratory samples. Urine and stool were tested with AlereLAM and Xpert MTB/RIF, respectively. Respiratory samples were tested with Xpert MTB/RIF and mycobacterial culture. Both a microbiological and a composite clinical reference standard were used.

RESULTS

The study enrolled 219 children; median age 16.4 months, 72 (32.9%) HIV-positive and 184 (84.4%) severely malnourished. Twelve (5.5%) and 58 (28.5%) children had confirmed and unconfirmed TB respectively. Stool and urine were collected in 219 (100%) and 216 (98.6%) children. Against the microbiological reference standard the sensitivity and specificity (n/N, 95% confidence intervals) of stool Xpert MTB/RIF was 50.0% (6/12, 21.1-78.9) and 99.1% (198/200 96.4-99.9), while that of urine AlereLAM was 50.0% (6/12, 21.1-78.9) and 74.6% (147/197, 67.9-80.5) respectively. Against the composite reference standard sensitivity was reduced to 11.4% (8/70) for stool and 26.2% (17/68) for urine, with no major difference by age group (<2 and >2 years) or HIV status.

CONCLUSION

The Xpert MTB/RIF assay has excellent specificity on stool, but sensitivity is suboptimal. Urine AlereLAM is compromised by poor sensitivity and specificity in children.

Evaluation of stool GeneXpert MTB/RIF for the diagnosis of pulmonary tuberculosis among presumptive patients in Tanzania

Background

Diagnosis of pulmonary tuberculosis remains grim, especially in resource-limited settings. Low quality of sputum, particularly among seriously ill, HIV/AIDS, and pediatric patients might result in missing the diagnosis. This study evaluated the performance of GeneXpert MTB/RIF for the detection of pulmonary tuberculosis on stool specimens as an alternative to respiratory specimens.

Methods

A cross-sectional study design was used to evaluate the performance of GeneXpert MTB/RIF to detect TB in stool specimens from presumptive TB patients. Sputum culture on Lowenstein-Jensen media was used as the gold standard. Recruitment of patients into the study was conducted in 12 selected health facilities in Tanzania. Two sputa and a stool specimen were collected from each study participant. Both sputa and stool samples were tested at their respective study sites of collection using GeneXpert, and their respective portions shipped to the Central Tuberculosis Reference Laboratory for testing by stool GeneXpert and sputum culture in the LJ media. Statistical analysis was performed using STATA software version 14.1.

Results

A total of 590 presumptive tuberculosis patients were enrolled in this study. Their median age was 35 years (IQR = 21–47 years). More than half (57.5%, n = 339) of the study participants, were males. Children aged below 15 years constituted 17.6% (n = 104) of the study participants. A total of 75 tuberculosis cases were detected by sputum culture. The sensitivity and specificity of Stool GeneXpert conducted at CTRL was 84% (95% CI: 81.0–87.0%), and 93.4% (CI: 98.5–99.9%) respectively. The overall sensitivity and specificity of stool GeneXpert at the peripheral laboratories was 63.0% (95% CI: 47.8–76.1) and 76.7% (95% CI: 72.1–81.4), respectively.

Conclusion

Findings from this study suggest that stool is a potential alternative to respiratory specimen for use in routine diagnosis of tuberculosis, especially when obtaining a respiratory specimen is challenging.

Laboratory development of a simple stool sample processing method diagnosis of pediatric tuberculosis using Xpert Ultra

Stool samples are alternatives to respiratory samples for bacteriological confirmation of childhood tuberculosis but require intensive laboratory processing before molecular testing to remove PCR inhibitors and debris. We aimed to develop a centrifuge-free processing method for use in resource-limited settings based on a sucrose-flotation method that showed good sensitivity for childhood tuberculosis diagnosis. In an in vitro study using Xpert MTB/RIF Ultra on stool samples spiked with defined bacterial concentrations of Mycobacterium tuberculosis (MTB), we compared different simplification parameters to the reference sucrose-flotation method. Best methods were selected based on the rate of invalid/error results and on sensitivity, compared to the reference method on stools spiked at 10³ colony forming units (CFU)/g MTB. For final selection, we tested the best parameter combinations at 10² CFU/g. Out of 13 different parameter combinations, three were tested at 10² CFU/g. The best combination used 0.5 g stool, manual shaking, no filtration, 30-min sedimentation, and a 1:3.6 dilution ratio. This method gave 10% invalid/error results and a sensitivity of 70% vs 63% at 10³ CFU/g and 53% vs 58% at 10² CFU/g compared to the reference method. This pre-clinical study was able to develop a centrifuge-free processing method to facilitate stool Xpert Ultra testing.

Rapid detection of Mycobacterium tuberculosis in children using blood and urine specimens

INTRODUCTION

Laboratory and clinical features of childhood tuberculosis (TB) are non-specific and establishing an accurate diagnosis remains a challenge. This study evaluated a Single tube nested-PCR (STNPCR) to detect genomic DNA of Mycobacterium tuberculosis complex in blood and urine.

METHODS

Biological samples were obtained from children (<15 years old) with clinical suspicion of pulmonary and extrapulmonary TB at public hospitals in Recife-Pernambuco, Brazil. Cultures yielded negative results in a majority of childhood TB cases, which are generally paucibacillary. A set of clinical, epidemiological, radiological, and laboratory criteria with evident clinical improvement after anti-TB treatment were frequently used to define childhood TB cases.

RESULTS

Ninety children with clinical suspicion were enrolled in this study (44 with TB and 46 without TB). The pulmonary TB group had 20 confirmed cases and 46 negative controls, while the extrapulmonary TB group had 24 confirmed cases. The STNPCR showed sensitivities to pulmonary and extrapulmonary TB of 47.4% and 52.2% (blood) and 38.8% and 20% (urine), respectively. Considering the low performance of STNPCR on separate samples, we decided to perform a combined analysis (parallel sensitivity analysis) of the results from blood and urine samples. The parallel sensitivity increased to 65% in blood and 62.5% in urine. The specificity in both samples ranged from 93.5-97.8%.

CONCLUSIONS

Although STNPCR showed moderate sensitivity, the specificity is high; therefore, the test can be used as an auxiliary tool to diagnose TB in children. It is a rapid test that demonstrated better performance than other diagnostic tests in paucibacillary samples as it does in childhood tuberculosis.

Xpert MTB/RIF and Xpert MTB/RIF Ultra assays for active tuberculosis and rifampicin resistance in children

BACKGROUND

Every year, at least one million children become ill with tuberculosis and around 200,000 children die. Xpert MTB/RIF and Xpert Ultra are World Health Organization (WHO)-recommended rapid molecular tests that simultaneously detect tuberculosis and rifampicin resistance in adults and children with signs and symptoms of tuberculosis, at lower health system levels. To inform updated WHO guidelines on molecular assays, we performed a systematic review on the diagnostic accuracy of these tests in children presumed to have active tuberculosis.

OBJECTIVES

Primary objectives • To determine the diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for (a) pulmonary tuberculosis in children presumed to have tuberculosis; (b) tuberculous meningitis in children presumed to have tuberculosis; (c) lymph node tuberculosis in children presumed to have tuberculosis; and (d) rifampicin resistance in children presumed to have tuberculosis - For tuberculosis detection, index tests were used as the initial test, replacing standard practice (i.e. smear microscopy or culture) - For detection of rifampicin resistance, index tests replaced culture-based drug susceptibility testing as the initial test Secondary objectives • To compare the accuracy of Xpert MTB/RIF and Xpert Ultra for each of the four target conditions • To investigate potential sources of heterogeneity in accuracy estimates - For tuberculosis detection, we considered age, disease severity, smear-test status, HIV status, clinical setting, specimen type, high tuberculosis burden, and high tuberculosis/HIV burden - For detection of rifampicin resistance, we considered multi-drug-resistant tuberculosis burden • To compare multiple Xpert MTB/RIF or Xpert Ultra results (repeated testing) with the initial Xpert MTB/RIF or Xpert Ultra result SEARCH METHODS: We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), Scopus, the WHO International Clinical Trials Registry Platform, ClinicalTrials.gov, and the International Standard Randomized Controlled Trials Number (ISRCTN) Registry up to 29 April 2019, without language restrictions.

SELECTION CRITERIA

Randomized trials, cross-sectional trials, and cohort studies evaluating Xpert MTB/RIF or Xpert Ultra in HIV-positive and HIV-negative children younger than 15 years. Reference standards comprised culture or a composite reference standard for tuberculosis and drug susceptibility testing or MTBDRplus (molecular assay for detection of Mycobacterium tuberculosis and drug resistance) for rifampicin resistance. We included studies evaluating sputum, gastric aspirate, stool, nasopharyngeal or bronchial lavage specimens (pulmonary tuberculosis), cerebrospinal fluid (tuberculous meningitis), fine needle aspirates, or surgical biopsy tissue (lymph node tuberculosis).

DATA COLLECTION AND ANALYSIS

Two review authors independently extracted data and assessed study quality using the Quality Assessment of Studies of Diagnostic Accuracy - Revised (QUADAS-2). For each target condition, we used the bivariate model to estimate pooled sensitivity and specificity with 95% confidence intervals (CIs). We stratified all analyses by type of reference standard. We assessed certainty of evidence using the GRADE approach.

MAIN RESULTS

For pulmonary tuberculosis, 299 data sets (68,544 participants) were available for analysis; for tuberculous meningitis, 10 data sets (423 participants) were available; for lymph node tuberculosis, 10 data sets (318 participants) were available; and for rifampicin resistance, 14 data sets (326 participants) were available. Thirty-nine studies (80%) took place in countries with high tuberculosis burden. Risk of bias was low except for the reference standard domain, for which risk of bias was unclear because many studies collected only one specimen for culture. Detection of pulmonary tuberculosis For sputum specimens, Xpert MTB/RIF pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 64.6% (55.3% to 72.9%) (23 studies, 493 participants; moderate-certainty evidence) and 99.0% (98.1% to 99.5%) (23 studies, 6119 participants; moderate-certainty evidence). For other specimen types (nasopharyngeal aspirate, 4 studies; gastric aspirate, 14 studies; stool, 11 studies), Xpert MTB/RIF pooled sensitivity ranged between 45.7% and 73.0%, and pooled specificity ranged between 98.1% and 99.6%. For sputum specimens, Xpert Ultra pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 72.8% (64.7% to 79.6%) (3 studies, 136 participants; low-certainty evidence) and 97.5% (95.8% to 98.5%) (3 studies, 551 participants; high-certainty evidence). For nasopharyngeal specimens, Xpert Ultra sensitivity (95% CI) and specificity (95% CI) were 45.7% (28.9% to 63.3%) and 97.5% (93.7% to 99.3%) (1 study, 195 participants). For all specimen types, Xpert MTB/RIF and Xpert Ultra sensitivity were lower against a composite reference standard than against culture. Detection of tuberculous meningitis For cerebrospinal fluid, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 54.0% (95% CI 27.8% to 78.2%) (6 studies, 28 participants; very low-certainty evidence) and 93.8% (95% CI 84.5% to 97.6%) (6 studies, 213 participants; low-certainty evidence). Detection of lymph node tuberculosis For lymph node aspirates or biopsies, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 90.4% (95% CI 55.7% to 98.6%) (6 studies, 68 participants; very low-certainty evidence) and 89.8% (95% CI 71.5% to 96.8%) (6 studies, 142 participants; low-certainty evidence). Detection of rifampicin resistance Xpert MTB/RIF pooled sensitivity and specificity were 90.0% (67.6% to 97.5%) (6 studies, 20 participants; low-certainty evidence) and 98.3% (87.7% to 99.8%) (6 studies, 203 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We found Xpert MTB/RIF sensitivity to vary by specimen type, with gastric aspirate specimens having the highest sensitivity followed by sputum and stool, and nasopharyngeal specimens the lowest; specificity in all specimens was > 98%. Compared with Xpert MTB/RIF, Xpert Ultra sensitivity in sputum was higher and specificity slightly lower. Xpert MTB/RIF was accurate for detection of rifampicin resistance. Xpert MTB/RIF was sensitive for diagnosing lymph node tuberculosis. For children with presumed tuberculous meningitis, treatment decisions should be based on the entirety of clinical information and treatment should not be withheld based solely on an Xpert MTB/RIF result. The small numbers of studies and participants, particularly for Xpert Ultra, limits our confidence in the precision of these estimates.

The Incidence of Tuberculosis in Infants, Siaya District, Western Kenya

BACKGROUND

Infants are a target population for new tuberculosis (TB) vaccines. TB incidence estimates are needed to guide the design of trials. To determine the TB incidence and cohort retention among young children using comprehensive diagnostic methods in a high burden area.

METHODS

Infants 0-42 days were enrolled. Through 4 monthly follow-up and unscheduled (sick) visits up to the age of 2 years, infants with presumptive TB based on a history of contact, TB symptoms or pre-determined hospitalization criteria were admitted to a case verification ward. Two induced sputa and gastric aspirates were collected for culture and GeneXpert. Mantoux and HIV tests were done. Clinical management was based on the Keith Edwards score. Cases were classified into microbiologically confirmed or radiologic, diagnosed by blinded expert assessment. Cox regression was used to identify risk factors for incident TB and study retention.

RESULTS

Of 2900 infants enrolled, 927 (32%) developed presumptive TB, 737/927 (80%) were investigated. Sixty-nine TB cases were diagnosed (bacteriologic and radiologic). All TB incidence was 2/100 person-years of observation (pyo) (95% CI: 1.65-2.65). Nine were bacteriologic cases, incidence 0.3/100 pyo. The radiologic TB incidence was 1.82/100 pyo. Bacteriologic TB was associated with infant HIV infection, higher Keith Edwards scores. Completeness of 4-month vaccinations and HIV infection were positively associated with retention.

CONCLUSIONS

TB incidence was high. An all TB endpoint would require a sample size of a few thousand children, but tens of thousands, when limited to bacteriologic TB.

Diagnostic accuracy of molecular detection of Mycobacterium tuberculosis in pediatric stool samples: A systematic review and meta-analysis

BACKGROUND

Stool is a promising specimen option to diagnose pediatric tuberculosis (TB), but studies have reported a wide range of test sensitivities. We conducted a meta-analysis to assess the accuracy of Xpert MTB/RIF or 'in-house' molecular tests on stool samples against culture or Xpert MTB/RIF on respiratory samples or clinically-diagnosed unconfirmed TB and aimed to identify factors that contribute to the heterogeneity of reported sensitivity.

METHODS

We searched EMBASE and Pubmed databases and conference abstract books for studies reporting molecular stool testing against a clinical or microbiological reference standard among children.

RESULTS

We identified 16 studies that included 2,481 children in stool test analyses. Pooled specificity was 98% [95%CI: 96-99], pooled sensitivity was 57% [95%CI: 40-72] against culture and 3% [95%CI: 2-6] among children with clinically-diagnosed, unconfirmed TB. There was much heterogeneity. Sensitivity was higher among children with a smear-positive sputum test. Rifampin resistance in stool was reported in two studies and detected in 5/14 children (36%).

CONCLUSION

Our results suggest molecular stool tests have potential as diagnostic rule-in tests, but it is challenging to optimize sensitivity due to between-study variation in methodology and test procedures. Therefore, we recommend future research with rigorous study design and standardized results reporting.

Detection of Mycobacterium tuberculosis in pediatric stool samples using TruTip technology

Background

Rapid and accurate diagnosis of childhood tuberculosis (TB) is challenging because children are often unable to produce the sputum sample required for conventional tests. Stool is an alternative sample type that is easy to collect from children, and studies investigating the use of stool for molecular detection of Mycobacterium tuberculosis (Mtb) have led to promising results. Our objective was to evaluate stool as an alternative specimen to sputum for Mtb detection in children. We did so using the TruTip workstation (Akonni Biosystems), a novel automated lysis and extraction platform.

Methods

We tested stool samples from 259 children aged 0–14 years old, in Lima, Peru who presented with TB symptoms. Following extraction with TruTip, we detected the presence of Mtb DNA by IS6110 real-time PCR. We calculated assay sensitivity in two groups: (1) children with culture confirmed TB (N = 22); and (2) children with clinically-diagnosed unconfirmed TB (N = 84). We calculated specificity among children in whom TB was ruled out (N = 153). Among children who were diagnosed with TB, we examined factors associated with a positive stool test.

Results

Assay sensitivity was 59% (95% confidence interval [CI]: 39–80%) and 1.2% (95% CI: 0.0–6.5%) in children with culture-confirmed and clinically-diagnosed unconfirmed TB, respectively, and specificity was 97% (95% CI: 93–99%). The assay detected Mtb in stool of 7/7 children with smear-positive TB (100% sensitivity; 95% CI: 59–100%), and in 6/15 of children with smear-negative, culture-confirmed TB (40% sensitivity; 95% CI: 16–68%). Older age, smear positivity, culture positivity, ability to produce sputum and cavitary disease were associated with a positive stool result.

Conclusion

Testing of stool samples with the TruTip workstation and IS6110 amplification yielded sensitivity and specificity estimates comparable to other tests such as Xpert. Future work should include detection of resistance using the TruTip closed amplification system and assay optimization to improve sensitivity in children with low bacillary loads.

Diagnostic Accuracy of Stool Xpert MTB/RIF for Detection of Pulmonary Tuberculosis in Children: a Systematic Review and Meta-analysis

Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB.

Invasive collection methods are often required to obtain samples for the microbiological evaluation of children with presumptive pulmonary tuberculosis (PTB). Nucleic acid amplification testing of easier-to-collect stool samples could be a noninvasive method of diagnosing PTB. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of testing stool with the Xpert MTB/RIF assay (“stool Xpert”) for childhood PTB. Four databases were searched for publications from January 2008 to June 2018. Studies assessing the diagnostic accuracy among children of stool Xpert compared to a microbiological reference standard of conventional specimens tested by mycobacterial culture or Xpert were eligible. Bivariate random-effects meta-analyses were performed to calculate pooled sensitivity and specificity of stool Xpert against the reference standard. From 1,589 citations, 9 studies (n = 1,681) were included. Median participant ages ranged from 1.3 to 10.6 years. Protocols for stool processing and testing varied substantially, with differences in reagents and methods of homogenization and filtering. Against the microbiological reference standard, the pooled sensitivity and specificity of stool Xpert were 67% (95% confidence interval [CI], 52 to 79%) and 99% (95% CI, 98 to 99%), respectively. Sensitivity was higher among children with HIV (79% [95% CI, 68 to 87%] versus 60% [95% CI, 44 to 74%] among HIV-uninfected children). Heterogeneity was high. Data were insufficient for subgroup analyses among children under the age of 5 years, the most relevant target population. Stool Xpert could be a noninvasive method of ruling in PTB in children, particularly those with HIV. However, studies focused on children under 5 years of age are needed, and generalizability of the evidence is limited by the lack of standardized stool preparation and testing protocols.

GeneXpert of stool versus gastric lavage fluid for the diagnosis of pulmonary tuberculosis in severely ill adults

PURPOSE

Stool is an alternative specimen matrix for tuberculosis (TB) tests, because Mycobacterium tuberculosis (MTB) can be swallowed and detected in the samples from digestive tract. We aimed to assess the performance of GeneXpert on stool and gastric lavage fluid (GALF) in diagnosing TB among patients with severe pulmonary TB.

METHODS

We enrolled adults with suspected pulmonary TB who were unable to produce sputum at visit between January 2016 and June 2018. Bacteriological samples consisted of one transtracheal aspirate sputum specimen, one stool specimen and/or one gastric lavage fluid specimen. Bacterial culture of transtracheal aspirate sputum provided the gold standard.

RESULTS

Of 65 individuals recruited for analysis, MGIT culture identified the presence of MTB in 32 samples. Overall, 29 of 32 stool samples from culture-positive cases were detected by the GeneXpert test, demonstrating a sensitivity of 90.6%. For GALF, 13 patients were detected as infected with MTB by GeneXpert, yielding a sensitivity of 56.5%. The statistical analysis revealed that GeneXpert showed significantly better sensitivity in detecting MTB from stool samples than GALF samples (P = 0.003). Among individuals with GeneXpert-positive stool, the percentage of individuals with comorbid diabetes was significantly higher than among individuals with GeneXpert-negative stool (19.4% vs. 2.9%, P = 0.034).

CONCLUSIONS

In conclusion, our data reveal that GeneXpert provides a higher detection rate on stool compared to GALF, indicating stool should be considered as an alternative for adult TB patients unable to produce sputum. Individuals with diabetes are more likely to have positive GeneXpert stool than nondiabetic individuals.

Recent Innovations in Diagnosis and Treatment of Pediatric Tuberculosis

PURPOSE OF REVIEW

Tuberculosis is leading cause of global morbidity and mortality and a significant proportion of the burden of disease occurs in children. In the past 5 years, a number of innovations have improved the diagnosis and treatment for children with both latent tuberculosis infection and active disease.

RECENT FINDINGS

This review discusses three key areas of innovation. First, we assess utilization and performance of interferon-gamma release assays (IGRAs) in different clinical and epidemiologic scenarios. Recent literature has demonstrated good performance of IGRAs for diagnosis of latent tuberculosis infection, particularly in low-incidence settings such as TB control programs in North America. For high-incidence populations, or when testing is done for possible active TB disease, IGRA performance has some important limitations, but IGRA sensitivity when measured against culture proven disease may be better than earlier studies suggested. The second area of innovation is in increased uptake of nucleic acid amplification (NAA) tests and broader application in non-sputum samples for both pediatric pulmonary and extrapulmonary tuberculosis. Finally, recent studies have provided solid evidence in support of shorter treatment courses for pediatric latent tuberculosis infection, such as 12 weeks of weekly isoniazid and rifapentine or 4 months daily rifampin, that improve compliance and may reduce resources required for TB control. Many recent innovations in pediatric tuberculosis relate to an improved understanding of how to optimally use existing tests and treatments. Until diagnostic tests and interventions such as vaccination are developed that can dramatically alter the paradigm of pediatric TB management and control, it is important for stakeholders to have a nuanced understanding of tools currently available.