# TB detection in children using a novel stool-based GeneXpert assay

> **NIH NIH R01** · RBHS-NEW JERSEY MEDICAL SCHOOL · 2020 · $536,775

## Abstract

ABSTRACT
 Pediatric pulmonary tuberculosis (TB) remains a diagnostic challenge. Children swallow their sputum
rather than coughing it up, making analysis with standard TB tests difficult to perform. We led the development
and testing of the Xpert MTB/RIF (Xpert) assay, which simultaneously detects the presence of M. tuberculosis
and its susceptibility to the important first line drug rifampin in less than two hours. Hailed as a major advance
for detecting adult pulmonary TB, the test is suboptimal for detecting pediatric TB since sputum samples may
be difficult to obtain, and repeated testing is necessary for acceptable sensitivity. Here, we propose to adapt
the Xpert sputum assay so that it can be performed on the stool of pediatric TB suspects, developing a simple-
to-use kit that can rapidly detect TB in children. We will then test this assay using a newer assay cartridge
(Ultra) that is approximately 10 times more sensitive and almost twice as rapid as current Xpert MTB/RIF
cartridge. Our hypothesis is that swallowed M. tuberculosis currently detected in induced sputum samples or
gastric aspirates of pediatric patients should be concentrated and detectable in stool. Stool is the final
repository of all swallowed respiratory secretions and it is easily obtainable from infants and children, making it
an excellent test matrix. We will develop and test a simple sample processing bottle that can pre-process large
(> 1 gram) volumes of stool, removing particulate matter and PCR inhibitors, without compromising PCR TB
detection. The contents of the bottle will be able to be squeezed into the Xpert assay cartridge with little
difficulty or unpleasantness. The “Ultra stool” assay will be as easy to perform as the “Xpert sputum” assay,
and will have the same or better diagnostic sensitivity and specificity. The successful completion of this project
will literally transform pediatric pulmonary tuberculosis diagnosis. This proposal builds on an existing US –
South African collaboration focused on testing novel TB assays, enabling an established clinical and laboratory
team to work on this new problem. This project has the following four aims: 1) develop and test “out of
cartridge” sample processing protocols that maximize the sensitivity of the Ultra assay to detect M. tuberculosis
in stool. 2) Perform extensive analytic tests of the Ultra stool assay focusing on limit of detection, inclusivity,
specificity, effect of different stool samples, effect of different M. tuberculosis strains and susceptibility to
interfering substances. 3) Develop and test a simple stool pre-processing bottle. 4) Perform iterative evaluation
of the assay using stool samples from a cohort of children presenting with symptoms suggestive of pulmonary
TB .

## Key facts

- **NIH application ID:** 9823830
- **Project number:** 5R01AI131617-03
- **Recipient organization:** RBHS-NEW JERSEY MEDICAL SCHOOL
- **Principal Investigator:** David Alland
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $536,775
- **Award type:** 5
- **Project period:** 2017-12-05 → 2022-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9823830

## Citation

> US National Institutes of Health, RePORTER application 9823830, TB detection in children using a novel stool-based GeneXpert assay (5R01AI131617-03). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/9823830. Licensed CC0.

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