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Evaluation of the Performance of Stool Samples to Diagnose Pediatric Pulmonary Tuberculosis in Routine Care: A Cohort

Brekhna Aurangzeb^1,2, Atiqa Ambreen³, Iqbal Bano⁴

¹Centre of International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.

Open Forum Infectious Diseases

|November 5, 2025

Insights

Stool Xpert-Ultra shows moderate sensitivity for diagnosing childhood pulmonary tuberculosis (PTB) in children under 10. This noninvasive test is valuable for detecting additional PTB cases, particularly in older children and those with severe acute malnutrition (SAM).

Area of Science:

Pediatric infectious diseases
Microbiology
Diagnostic testing

Background:

The World Health Organization (WHO) suggests stool as an alternative respiratory sample for diagnosing pulmonary tuberculosis (PTB) in children under 10.
This study evaluated the diagnostic performance of stool Xpert-Ultra compared to microbiologically confirmed PTB (MC-PTB) in children under 15.

Purpose of the Study:

To assess the diagnostic accuracy of stool Xpert-Ultra for pulmonary tuberculosis in children.
To stratify performance by age and nutritional status.
To identify predictors of microbiological yield.

Main Methods:

Children under 15 with presumptive PTB had stool and respiratory samples tested using Xpert MTB/RIF-Ultra (Xpert-Ultra).
Microbiologically confirmed PTB (MC-PTB) was determined using a composite reference standard.
Logistic regression analyzed factors associated with microbiological positivity.

Main Results:

Stool Xpert-Ultra showed moderate sensitivity (47%) against MC-PTB in children under 10, and higher sensitivity (72%) in children aged 10 and above.
The test identified 11% more MC-PTB cases when respiratory samples were negative or unavailable.
Sensitivity was higher (64%) in severely acute malnourished (SAM) children. Age, sex, SAM status, and chest X-ray findings predicted microbiological positivity.

Conclusions:

Stool Xpert-Ultra has moderate sensitivity for diagnosing PTB in younger children but is a valuable noninvasive alternative.
It is particularly useful for detecting additional PTB cases in older children and those with SAM, where fewer cases were missed.

Read full analysis

Abstract

Background:

The World Health Organization (WHO) recommends stool as an alternative respiratory sample (RS) for diagnosing pulmonary tuberculosis (PTB) in children <10 years. This study assessed stool-Xpert-Ultra diagnostic performance against microbiologically confirmed (MC-PTB) cases identified based on the composite reference standard (CRS) in children <15 years, stratified by age and nutritional status.

Methods:

Children <15 years with presumptive PTB were assessed at 2 tertiary-care hospitals in Pakistan. Stools and RS were tested using Xpert MTB/RIF-Ultra (Xpert-Ultra) and culture. Using the CRS, PTB cases were MC-PTB or clinically confirmed. Nutritional status was classified using WHO criteria. Stool-Xpert-Ultra diagnostic performance was assessed against MC-PTB or positive RS-Xpert-Ultra. Logistic regression identified predictors of microbiological yields.

Results:

Among 650 children, we obtained 587 RS, 258 stool and 195 both stool and RS. Of 650, 264 (41%) had MC and 136 (21%) had clinically confirmed PTB. Stool-Xpert-Ultra had sensitivity, specificity, and accuracy of 47%, 88%, 77%, and 72%, 73%, 72% against MC-PTB in children <10 and ≥10, respectively. Stool-Xpert-Ultra performed similarly against RS-Xpert-Ultra in each age group. Stool-Xpert-Ultra detected 11% additional MC-PTB cases when RS was negative or unavailable. Stool-Xpert-Ultra had high sensitivity (64%) in severely acute malnourished (SAM) children. Age ≥10, female, SAM and TB-consistent chest X-rays were strongly associated with stool and RS microbiological positivity.

Conclusions:

Stool-Xpert-Ultra demonstrated moderate sensitivity against MC-PTB in <10. It identified additional MC-PTB cases when RS was unavailable or/negative, making it a valuable noninvasive alternative, especially in children ≥10 and with SAM, where it missed fewer cases.

Keywords:

Xpert-Ultra childhood pulmonary TB respiratory samples severe acute malnutrition stools

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