Background: Diagnosis of pediatric pulmonary tuberculosis (PTB) is a challenge. Symptoms are
nonspecific. Young children are unable to expectorate sputum samples; the procedures for obtaining
respiratory samples are invasive. Thus Mycobacterium tuberculosis cultures and smears
often are not performed. Stool samples were used as an alternative to respiratory samples for the
diagnosis of pediatric PTB using stool Xpert MTB/RIF and its sensitivity for detecting the DNA of
MTB in stool was determined. Methods: The study was a laboratory-based cross-sectional prospective
design. Stool specimen was collected from PTB suspected children (<15 years) attended in
Gertrude’s Children’s Hospital Nairobi and Kiambu District Hospital from September 2013 to
March 2014. Stool for Xpert was processed in two ways, direct and prior extraction of DNA using
QIAGEN stool DNA extraction kit. Result: A total sample of 91 stool specimen was collected from
patients. Of these 53 (58.2%) had sputum ZN smear microscopy. Six (11.3%) of them were confirmed
smear positive for PTB. Stool Gene Xpert was positive in all the six smear positive children.
Four (7.5%) smear negative patients tested positive by stool Gene Xpert test. This association is
significant (P = 0.000). Conclusion: This study reports that Mycobacterium tuberculosis DNA can be
detected in stool using Xpert testing with a higher sensitivity. Therefore stool which can easily be
obtained is an appropriate alternative sample for the diagnosis of PTB using Xpert assay for children
unable to give respiratory samples. Furthermore Xpert turn round time is less than 2 hours.
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