Improving diagnosis of tuberculosis (TB), especially in children

In 2019, 29% of the estimated 10 million new cases of TB went undiagnosed. Particularly in children and people living with the human immunodeficiency virus (PLHIV), TB is often not recognized. Such patients frequently have nonspecific signs and symptoms and laboratory confirmation of their disease is hardly possible due to its paucibacillary nature and the difficulty to obtain sputum. Without a laboratory confirmation drug resistant TB cannot be detected. Misdiagnosis and delays in the start of correct treatment contribute significantly to the increased morbidity and mortality among these patient groups.



Stool as an alternative specimen type to use for Xpert testing

The laboratory diagnosis of TB relies on the detection of Mycobacterium tuberculosis complex (MTB) bacteria in a sample of a patient with presumptive TB. Sputum is the most commonly used sample for pulmonary TB. For some people, especially children, it is difficult to spontaneously expectorate sputum.

Alternative methods to get a sputum sample are rather unpleasant or even painful for the patient and are usually not available at the primary healthcare level, where most patients are diagnosed. Stool is an alternative sample for the diagnosis of pulmonary TB because the MTB bacteria may be swallowed and end up in their stool, which can be easily collected.



Detecting MTB and rifampicin resistance

The Xpert MTB/RIF (Xpert) assay and the more sensitive Xpert MTB/RIF Ultra (Xpert Ultra) assay (Cepheid, Sunnyvale, CA) are quick and easy cartridge-based assays that detect MTB and rifampicin resistance by using the polymerase chain reaction (PCR) technique to amplify the DNA of the MTB bacteria. The GeneXpert instruments, in which these assays are run, are widely available at secondary health care level and their availability at primary healthcare level is rapidly expanding in most countries to increase case finding, with the aim to reach the END TB strategy.

Various recent studies have demonstrated that both the Xpert and the more sensitive Xpert Ultra assaycan be used to detect MTB in stool with high specificity 1,2. Thus, Xpert and Xpert Ultra testing on stool can be used as a rule-in test near the point of care. In 2020, the WHO recommended stool for the diagnosis of TB in children and adults.



Stool samples

Stool samples naturally contain substances that may result in unsuccessful Xpert or Xpert Ultra assay test results due to inhibition of the PCR amplification or due to clogging of the filter in the test cartridge. Therefore, optimal processing of stool samples before Xpert or Xpert Ultra assay testing is of the utmost importance. Previously published stool processing methods contain somewhat complex procedures and require centrifugation, bead-beating, dilution and/or filtration steps and additional supplies.

However, these are not available at in the typical primary health care level laboratories, which hampers their uptake and usefulness for the diagnosis of TB in children. Therefore, KNCV set out to develop a stool processing method that can be applied at the primary health care level.


KNCV’s SOS stool method

We have developed a simple stool processing method for the detection of MTB in stool, in which stool processing is limited to only one release-and-sedimentation step. We therefore refer to it as the “simple one-step (SOS) stool method”. The SOS stool method makes use of the standard Xpert or Xpert Ultra assay test kit and does not require additional essential supplies or equipment. The SOS stool processing method was validated and the proof of principle was demonstrated in a routine setting 3. The SOS stool method can potentially be rolled out to any Xpert site, bringing a bacteriologically confirmed TB diagnosis closer to the point of care.

The SOS Stoolbox

The SOS Stoolbox is KNCV’s online package to support countries with the implementation of the SOS stool method for Xpert or Xpert Ultra assay testing. Currently, the SOS Stoolbox consists of the following downloadable documents.

These are the first versions of the documents, based on the currently available knowledge on the SOS stool processing method. Research for optimization of the method is still ongoing. The current documents may be replaced by updated ones when new evidence becomes available. Soon, the SOS Stoolbox will be expanded with additional documents.



Training, ongoing studies and webinars

It is advised that laboratory staff take a short course to be able to correctly apply the method. Training materials will soon become available in the SOS Stoolbox and it is already possible to sign up for a course organized by KNCV. Currently, studies are ongoing to investigate whether further optimization of the SOS stool method is required (PODTEC study), whether other transport media may yield better results, compare the method head-to-head with other stool processing methods (FIND and TB Speed study), and to investigate the potential cost effectiveness of the method (SOS-TBIM study). Online webinars will be organized in due time to disseminate the results of these studies.

Sign up

If you want to receive information on webinars or other news on the SOS stool method, then you soon will be able to sign up here. If you want to sign up for a course, then check out the information on the SOS stool method training. For other questions you can send an email to



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KNCV has been fighting TB since its establishment in 1903. Over the past 117 years, the organization has acquired indispensable knowledge and experience in the field of effective TB control, resulting in pre-elimination in the Netherlands and significant contributions to global evidence generation, policy development and TB program implementation worldwide.

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Tuberculosis is still one of the major causes of preventable death in the world and claims over 4000 lives a day, leading to over 1,5 million deaths a year.

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