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      Diagnostic accuracy of Xpert MTB/RIF Ultra and culture assays to detect Mycobacterium Tuberculosis using OMNIgene-sputum processed stool among adult TB presumptive patients in Uganda

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          Abstract

          Background

          Stool is a potential sample for diagnosing Mycobacterium tuberculosis ( Mtb) in patients with difficulty in expectorating. However, high mycobacterial culture contamination rates and Xpert MTB/RIF Ultra test error rates on stool samples have limited its use. OMNIgene SPUTUM (OM-S) is a sample transport reagent with characteristics of sputum decontamination while maintaining viable Mtb. We evaluated the impact of OM-S on Mtb diagnostic yield from stool using smear microscopy, Xpert MTB/RIF Ultra, and culture among presumptive TB patients.

          Methods

          Paired stool and expectorated sputum samples were collected from consecutive Ugandan adults undergoing diagnostic evaluation for pulmonary TB between June 2018 and June 2019. Stool was divided into 2 portions: one was homogenized in OM-S (OM-S stool) and the other in PBS (PBS stool) as control. Both sputum and processed stool were tested for Mtb using concentrated smear fluorescence microscopy (CFM), Xpert MTB/RIF Ultra (Xpert) and Mycobacteria Growth Indicator Tube (MGIT) culture. Sensitivity, specificity, and predictive values for each test were calculated against sputum MGIT culture as the reference standard.

          Results

          Of the 200 participants, 120 (60%) were male, 73 (37%) were HIV positive (median CD4 120 cells/uL (IQR 43–297)) and 128 (64%) had confirmed pulmonary TB by sputum MGIT culture. Seven (4%) OM-S stool Xpert samples reported errors while 47 (25%) and 103 (61%) were contaminated on OM-S stool MGIT and PBS stool MGIT, respectively. OM-S stool MGIT was able to accurately diagnose 56 of the contaminated PBS stool MGIT samples compared to only 5 of the contaminated OM-S stool MGIT samples diagnosed by PBS stool MGIT.

          Sensitivity (95% Confidence Interval, CI) 89% (83–94) for OM-S stool Xpert was higher compared to that of OM-S stool MGIT 60% (51–69) and PBS stool MGIT 42% (32–52). Specificity (95%CI) 91% (82–97) was also higher for OM-S stool Xpert compared to OM-S stool MGIT 64% (51–75) and PBS stool MGIT 26% (16–38).

          Conclusion

          Stool processed with OM-S showed potential to improve Mtb diagnostic yield and reduce rates of indeterminate results when tested on Xpert and MGIT culture. The method may thus be of value in Mtb detection among patients with difficulty to expectorate.

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          Most cited references28

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          Rapid molecular detection of extrapulmonary tuberculosis by the automated GeneXpert MTB/RIF system.

          In total, 521 nonrespiratory specimens (91 urine, 30 gastric aspirate, 245 tissue, 113 pleural fluid, 19 cerebrospinal fluid [CSF], and 23 stool specimens) submitted to the German National Reference Laboratory for Mycobacteria (NRL) from May 2009 to August 2010 were comparatively investigated with the new molecular-based GeneXpert MTB/RIF (Xpert) assay system and conventional liquid and solid culture methods. Twenty (3.8%) of the 521 specimens gave no interpretable result. Whereas the sensitivity of the Xpert assay with tissue specimens was 69.0% (20 out of 29 culture-positive cases detected), 100% sensitivity was found with the urine and stool specimens. The combined sensitivity and specificity of the Xpert assay were calculated to be 77.3% and 98.2%, respectively.
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            Diagnostic accuracy of the Xpert MTB/RIF assay for extrapulmonary and pulmonary tuberculosis when testing non-respiratory samples: a systematic review

            Background Although the evidence base regarding the use of the Xpert MTB/RIF assay for diagnosis of pulmonary tuberculosis (TB) when testing respiratory samples is well established, the evidence base for its diagnostic accuracy for extrapulmonary and sputum-scarce pulmonary TB when testing non-respiratory samples is less clearly defined. Methods A systematic literature search of 7 electronic databases (Medline, EMBASE, ISI Web of Science, BIOSIS, Global Health Database, Scopus and Cochrane Database) was conducted to identify studies of the diagnostic accuracy of the Xpert assay when testing non-respiratory samples compared with a culture-based reference standard. Data were extracted and study quality was assessed using the QUADAS-2 tool. Sensitivities and specificities were calculated on a per-sample basis, stratified by sample type and smear microscopy status and summarised using forest plots. Pooled estimates were calculated for groups with sufficient data. Results Twenty-seven studies with a total of 6,026 non-respiratory samples were included. Among the 23 studies comparing Xpert and culture done on the same samples, sensitivity was very heterogeneous with a median sensitivity of 0.83 (IQR, 0.68–0.94) whereas specificities were typically very high (median, 0.98; IQR, 0.89–1.00). The pooled summary estimates of sensitivity when testing smear-positive and smear-negative samples were 0.95 (95% CI 0.91–1.00) and 0.69 (95% CI 0.60-0.80), respectively. Pooled summary estimates of sensitivity varied substantially between sample types: lymph node tissue, 0.96 (95% CI, 0.72-0.99); tissue samples of all types, 0.88 (95% CI, 0.76–0.94); pleural fluid, 0.34 (95% CI, 0.24–0.44); gastric aspirates for diagnosis of sputum-scarce pulmonary TB, 0.78 (IQR, 0.68 – 0.85). Median sensitivities when testing cerebrospinal fluid and non-pleural serous fluid samples were 0.85 (IQR, 0.75-1.00) and 0.67 (IQR, 0.00-1.00), respectively. Conclusion Xpert detects with high specificity the vast majority of EPTB cases with smear-positive non-respiratory samples and approximately two-thirds of those with smear-negative samples. Xpert is a useful rule-in diagnostic test for EPTB, especially when testing cerebrospinal fluid and tissue samples. In addition, it has a high sensitivity for detecting pulmonary TB when using gastric aspirate samples. These findings support recent WHO guidelines regarding the use of Xpert for TB diagnosis from non-respiratory samples. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0709-7) contains supplementary material, which is available to authorized users.
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              Childhood pulmonary tuberculosis: old wisdom and new challenges.

              Childhood tuberculosis is neglected in endemic areas with resource constraints, as children are considered to develop mild forms of disease and to contribute little to the maintenance of the tuberculosis epidemic. However, children contribute a significant proportion of the disease burden and suffer severe tuberculosis-related morbidity and mortality, particularly in endemic areas. This review provides an overview of well-documented concepts and principles, and demonstrates how this "old wisdom" applies to current and future challenges in the field of childhood tuberculosis; the aim was to articulate some of the most pressing issues, to provide a rational framework for discussion, and to stimulate thought and further scientific study. The prechemotherapy literature that described the natural history of disease in children identified three central concepts: (1) the need for accurate case definitions, (2) the importance of risk stratification, and (3) the diverse spectrum of disease pathology, which necessitates accurate disease classification. The relevance of these concepts and their application to pertinent issues such as the diagnosis of childhood tuberculosis are discussed. The concepts are also linked to the basic principles of antituberculosis treatment, providing a simplified approach to the diagnosis and treatment of childhood tuberculosis that is independent of resource constraints. The main challenges for future research are highlighted and in conclusion it is emphasized that the infrastructure provided by the directly observed therapy, short-course strategy, combined with well-targeted interventions, slightly improved resources, and greatly improved political commitment, may lead to a dramatic reduction in tuberculosis-related morbidity and mortality among children.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: ValidationRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: SupervisionRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Writing – review & editing
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Methodology
                Role: Data curationRole: InvestigationRole: SupervisionRole: Writing – review & editing
                Role: InvestigationRole: ResourcesRole: Writing – review & editing
                Role: ResourcesRole: Supervision
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                21 April 2023
                2023
                : 18
                : 4
                : e0284041
                Affiliations
                [1 ] Infectious Diseases Research Collaboration, Kampala, Uganda
                [2 ] Department of Biochemistry and Sports Science, Makerere University, Kampala, Uganda
                [3 ] Division of Infection and Global Health, School of Medicine, University of St. Andrews, Scotland, United Kingdom
                [4 ] China Uganda Friendship Hospital Naguru, Kampala, Uganda
                [5 ] Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
                [6 ] Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States of America
                [7 ] Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, United States of America
                [8 ] Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, United States of America
                [9 ] Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States of America
                Hangzhou Red Cross Hospital, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0003-1793-5251
                https://orcid.org/0000-0002-4742-2791
                https://orcid.org/0000-0003-0073-9879
                https://orcid.org/0000-0002-8629-9992
                Article
                PONE-D-22-28442
                10.1371/journal.pone.0284041
                10121033
                37083706
                6fe82609-5155-4c97-be84-8dff218920ef
                © 2023 Sessolo et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 14 October 2022
                : 22 March 2023
                Page count
                Figures: 3, Tables: 4, Pages: 14
                Funding
                Funded by: Academy for Health Innovation Uganda
                Award ID: RFA 003/2017
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000050, National Heart, Lung, and Blood Institute;
                Award ID: 2R01HL128156-05A1
                Award Recipient :
                Funded by: DNAgenotek Inc.
                Funded by: SPUTUM
                Award Recipient :
                This study was funded by The Academy for Health Innovation Uganda (RFA 003/2017, awarded to AS) through the Infectious Disease Institute of Makerere University. The parent study in which our study was nested was funded by the National Heart, Lung, and Blood Institute under the I AM OLD grant (2R01HL128156-05A1, awarded to LH) through Professor Laurence Huang of University of California San Francisco. The IAM OLD grant provided the funding to support participant enrolment. DNAgenotek Inc. the manufacturers of the OMNIgene. SPUTUM provided the reagent free of charge, received by AS. Funders had no role in study design, data collection and analysis and in manuscript preparation/write up.
                Categories
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