ORIGINAL ARTICLE Xpert MTB/RIF diagnosis of childhood tuberculosis from sputum and stool samples in a high TB-HIV-prevalent setting Patrick Orikiriza 1,2 & Margaret Nansumba 1 & Dan Nyehangane 1 & Mathieu Bastard 3 & Ivan Taremwa Mugisha 1 & Denis Nansera 4 & Juliet Mwanga-Amumpaire 1,4 & Yap Boum II 1,4 & Elias Kumbakumba 4 & Maryline Bonnet 1,2,5 Received: 14 April 2018 /Accepted: 2 May 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract The Xpert MTB/RIF assay is a major advance for diagnosis of tuberculosis (TB) in high-burden countries but is limited in children by their difficulty to produce sputum. We investigated TB in sputum and stool from children with the aim of improving paediatric TB diagnosis. A prospective cohort of children with presumptive TB, provided two sputum or induced sputum at enrolment in a regional referral hospital in Uganda. Stool was collected from those started on TB treatment. All specimen were tested for Xpert MTB/RIF, mycobacteria growth indicator tube (MGIT), Lowenstein Jensen cultures and microscopy (except stool). We compared TB detection between age categories and assessed the performance of Xpert MTB/RIF in sputum and stool. Of the 392 children enrolled, 357 (91.1%) produced at least one sputum sample. Sputum culture yield was 13/357 (3.6%): 3/109 (2.6%), 3/89 (3.2%), 3/101 (2.6%) and 4/44 (8.2%) among children of < 2, 2–5, ≥ 5–10 and > 10 years, respectively (p = 0.599). Xpert MTB/RIF yield was 14/350 (4.0%): 3/104 (2.9%), 4/92 (4.3%), 3/88 (2.9%) and 4/50 (.0%), respectively (p = 0.283). Sensitivity and specificity of Xpert MTB/RIF in sputum against sputum culture were 90.9% (95% CI 58.7–99.8) and 99.1% (99.1–99.8). In stool, it was 55.6% (21.2–86.3) and 98.2% (98.2–100) against Xpert MTB/RIF and culture in sputum. Only a minority of children had microbiologically confirmed TB with a higher proportion in children above 10 years. Although sensitivity of Xpert MTB/RIF in stool was low, with good optimization, it might be a good alternative to sputum in children. Keywords Childhood tuberculosis . Stool . Sputum . Xpert MTB/RIF Introduction Childhood tuberculosis (TB) diagnosis continues to be a ma- jor challenge. To date, there is no optimum diagnostic test in children and their exact TB burden remains unknown [1, 2]. In a 2017 WHO report, it was estimated that approximately 1 million children below 15 years developed TB in 2016 but only 45% were notified [3]. This could be explained by the fact that that current diagnosis of TB in children relies on a thorough assessment of evidence derived from a careful his- tory of exposure, clinical examination, tuberculin skin test and chest X-ray when available, and rarely bacteriological confir- mation [4, 5]. Because of limited bacteriological confirmation, it is possible that in the absence of an expert opinion, clinical judgement could be misleading as it is mostly subjective. In the absence of non-sputum-sensitive diagnostic tests, micro- biological tests rely on examination of respiratory sample but are limited by difficulty in obtaining a sputum specimen in children and the paucibacillary nature of childhood intratho- racic TB [6]. Based on a recent meta-analysis, the sensitivity (95% con- fidence intervals) of the Xpert MTB/RIF as compared to that of culture is 62% (51–73) for sputum or sputum induction and 66% (51–81) for gastric lavage or aspirate with specificities of 98% (97–99) and 98% (96–99) respectively [7]. However, Xpert MTB/RIF is still constrained by difficulty in using spu- tum induction, or gastric aspirate or lavage, in health facilities of limited resource settings [8]. This has influenced a lot of interest in the use of stool specimen to detect TB bacilli from * Patrick Orikiriza patrick.orikiriza@epicentre.msf.org 1 Epicentre Mbarara Research Centre, P.O Box 1956, Mbarara, Uganda 2 Université de Montpellier, Montpellier, France 3 Epicentre, Paris, France 4 Mbarara University of Science and Technology, Mbarara, Uganda 5 IRD UMI233/ INSERM U1175, Montpellier, France European Journal of Clinical Microbiology & Infectious Diseases https://doi.org/10.1007/s10096-018-3272-0