There is a growing interest for the use of stool samples as an alternative to respiratory samples for the diagnosis of intrathoracic TB in children unable to produce sputum. Unlike respiratory samples, stool samples require processing before molecular testing. Several groups have already evaluated different processing methods. However, it is difficult to know which method has the best accuracy and potential for use at Primary Health Care level, due to the difference in study designs and populations. Therefore, in this study, the investigators propose to evaluate the accuracy of different promising stool processing methods in the same population within the same study with an adapted design. Furthermore, no study has so far evaluated for stool testing the new Xpert MTB/RIF Ultra cartridge that has a lower level of detection than the previous Xpert MTB/RIF cartridge. The investigators propose to evaluate the accuracy of Xpert MTB/RIF Ultra (Ultra) performed on stool samples collected from children with presumptive TB and processed using four different processing methods (Standard sucrose flotation method, optimized sucrose flotation method, SPK, and SOS) against bacteriological results from respiratory specimens and to perform a head-to-head comparison of the diagnostic accuracy and feasibility of these different methods in Uganda and Zambia. The selection of processing methods was based on accuracy results, degree of simplification allowing their introduction at PHC level, and finding from the TB-Speed in-vitro stool processing study. The standard sucrose flotation method is kept to assess if results obtained with the optimised sucrose-flotation method in our in-vitro study can be reproduced in-vivo

This is a diagnostic study evaluating the diagnostic accuracy of the Ultra assay in stools with a two-stage sequential design starting as a cohort of children with presumptive TB enriched in a second stage with Ultra positive TB cases on respiratory sample. It is both an ancillary to the TB-Speed HIV (C18-27) and the TB-Speed SAM (C18-28) studies and a study enrolling children from routine not enrolled in those two studies.

This design was chosen to be able to evaluate the sensitivity and specificity of the Ultra assay in a smaller sample size that is usually required by a "classical" prospective cohort design and avoiding the bias of overestimation of the sensitivity classically associated with the case-control design. In order to quickly generate data on appropriate stool processing method, and to contribute to the planned WHO recommendations for stool Ultra testing (expected 2nd semester 2020), a two-stage sequential design will be used. Indeed, knowing that on average only 10-15% of children with presumptive TB in a community-based setting will be confirmed, in order to reach the sample size of confirmed cases for the evaluation of sensitivity, 7 to 10 times more children with presumptive TB would need to be enrolled in a prospective design. On the other hand, the number of children with presumptive TB not confirmed with TB for the estimation of the specificity would be reached much earlier. In addition, based on the previous study results, it is known that the specificity of Xpert MTB/RIF assay in stool is high (99% CI:98-99), which would result in a relatively small sample size to evaluate the specificity of the Ultra in stools.

During the first stage, the investigators will offer to join all consecutive presumptive TB cases presenting at study sites to estimate specificity with the expected precision and calculate a preliminary sensitivity estimate. During the second stage, the investigators will keep enrolling only those from TB Speed studies and routine care who are Xpert positive on respiratory samples in order to estimate sensitivity with the expected precision.

This two-stage sequential design first estimating specificity then sensitivity has been described by Wruck et al. as an efficient way of validating diagnostic tests when the prevalence of the disease is low. It would not be feasible to consecutively enrol all children with presumptive TB to describe an expected sensitivity of 60% with 10% precision as this would require over 900 patients, of which, approximately 800 would be culture negative. In the two-stage process described by Wruck, only reference standard positive samples from the original population are selected in stage 2. The investigators adapted this design to the TB context as culture results will only be available after enrollment (and if the child is positive, only after the child has started treatment), hence selecting only those who are Ultra positive on respiratory samples for the second cohort as a way of enriching the study population with a subpopulation that has a higher TB prevalence probability, before their true disease status is confirmed. Other comparable diagnostic studies have either used greater resources to include larger samples sizes or have resorted to reporting imprecise estimates of sensitivity. To our knowledge, this is a relatively unique approach to study design for accuracy studies, with few published examples.

With such design, there should be no bias on the evaluation of the specificity similarly to a classical prospective design because this evaluation will be done among consecutively enrolled children with presumptive TB only. The sensitivity estimates may not be generalizable to all culture confirmed TB children due to the sampling approach. Xpert positive children will be more likely to have higher biological loads, causing a possible inflation of the sensitivity. However, the results will provide valuable information on variations of sensitivities of the different stool processing methods within this population.

An interim analysis will be carried out after the completion of the prospective cohort in order to describe specificity and preliminary results of the sensitivity and the agreement between the processing methods. The recruitment of participants will not be put on hold during the interim analysis. A final analysis will be conducted at the end of the study to describe sensitivity as well as the secondary end points.

Inclusion Criteria for the prospective cohort:

1. Children < 15 years old

2. Presumptive intra-thoracic TB based on at least one criterion among the following:

   • Persistent cough for more than 2 weeks
   • Persistent fever for more than 2 weeks
   • Recent failure to thrive (documented clear deviation from a previous growth trajectory in the last 3 months or Z score weight/age < 2)
   • Failure of broad-spectrum antibiotics for treatment of pneumonia
   • Suggestive CXR features

   OR History of contact with a TB case and any of the symptoms listed under point 2 with shorter duration (< 2 weeks) if the child is HIV infected or presents with SAM.

3. Signed informed consent by parent or guardian and assent signed by children ≥ 7 years old

Inclusion Criteria for the enrichment cohort:

1. Children < 15 years old

2. Presumptive TB based on at least one criterion among the following:

   • Persistent cough for more than 2 weeks
   • Persistent fever for more than 2 weeks
   • Recent failure to thrive (documented clear deviation from a previous growth trajectory in the last 3 months or Z score weight/age < 2)
   • Failure of broad-spectrum antibiotics for treatment of pneumonia
   • Suggestive CXR features

   OR History of contact with a TB case and any of the symptoms listed under point 2 with shorter duration (< 2 weeks) if the child is HIV infected or presents with SAM.

3. One positive Xpert (MTB/Rif or Ultra) result from at least one respiratory sample: sputum, NPA or GA

4. Signed informed consent by parent or guardian and assent signed by children ≥ 7 years old

Exclusion Criteria for prospective and enrichment cohorts:

1. > 5 days of antituberculosis treatment in the last 3 months
2. History of tuberculosis preventive therapy in the last 3 months
3. Confirmed extrapulmonary TB only

Individual participant data will be available after de-identification

Access to data will be given after the publication of the main study results based on global data.

Data can be requested by members or partners of the TB-Speed consortium or by external research groups.

They can be used for secondary analyses of the TB-Speed project, country specific analyses, contribution to individual data meta-analysis and analyses that are not related to the research thematic of TB-Speed project.

The request for access to data will need to be sent to the Publication Committee accompanied by a concept paper describing the objectives of the analysis/study, how the data will be used, the list of data or material requested and how the original contributors will be credited.

Once the application is approved, data will be released under a data and/or material sharing agreement that secures the term of use.