Evaluation of GeneXpert MTB/RIF Ultra on stool samples versus gastric contents for diagnosing tuberculosis in children under five years in Niger

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This study assessed the effectiveness of stool samples versus gastric contents analyzed with GeneXpert Ultra for diagnosing pulmonary tuberculosis in children under five years old. Methods A diagnostic study was conducted in Niger over a one-year period (January 1 to December 31, 2024), at multiple centers. Socio-demographic data and GeneXpert Ultra results from stool and gastric samples were collected in accordance with STARD guidelines. Data analysis was performed using Excel 2020 and JAMOVI 2.3.28 software to calculate sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Results This study included 401 patients with a median age of 18 months (interquartile range, IQR, 11–24 months) and a sex ratio of 1.37. The diagnostic performance of the test showed a sensitivity of 77.8% and a specificity of 99%, with an overall accuracy of 98.5%. The positive and negative predictive values were 63.6% and 99.5% respectively. The area under the curve (AUC) was 0.816, and the positive and negative likelihood ratios were 76.2 and 0.225, indicating the test's strong discriminatory capacity. Conclusion GeneXpert stool testing is a valuable complementary approach to gastric content examination for detecting tuberculosis. Integrating it into screening strategies, especially in resource-limited settings, can enhance pediatric tuberculosis detection and management. Stool gastric content GeneXpert children tuberculosis Niger Figures Figure 1 Figure 2 BACKGROUND Tuberculosis is a significant infectious disease, causing 1.3 million deaths globally by 2022. It is a leading cause of morbidity and mortality, especially in resource-limited countries. The World Health Organization (WHO) estimated 10.6 million cases in 2022, with 1.1 million cases in children (10–11%), particularly affecting those under five years old.[ 1 ]. Sub-Saharan Africa has a high burden of tuberculosis, with nearly 25% of global cases. The region also faces high mortality rates among young people, raising concerns about the impact of the disease [ 1 ]. Tuberculosis is a significant public health issue in Niger, with an estimated incidence of 84 cases per 100,000 inhabitants in 2022. Children under five face particular challenges in diagnosing tuberculosis due to nonspecific symptoms, rapid disease progression, and difficulties in obtaining quality respiratory samples for testing. Obtaining a quality respiratory sample from a child is challenging, making invasive techniques like gastric tubing and nasopharyngeal suctioning difficult to perform routinely. This, coupled with the low bacterial load of tuberculosis in children, complicates microbiological confirmation, leading to underestimation of cases and delays in diagnosis. The GeneXpert MTB/RIF Ultra test has revolutionized tuberculosis diagnosis and management, especially for paucibacillary forms. Recent studies [ 2 , 3 , 4 ] have shown promising results using stool samples with this test for the diagnosis of pediatric tuberculosis. This non-invasive approach is more acceptable to children and parents due to its simplicity and minimal resource requirements. Stool analysis using GeneXpert MTB/RIF Ultra is a promising method for diagnosing tuberculosis, recommended by the WHO since 2021. It enhances pediatric tuberculosis detection and allows decentralized diagnosis in peripheral health facilities equipped with Cepheid's GeneXpert system. This benefits the rural populations, the majority of whom are in Niger, by improving access to healthcare. To date, no study has been conducted in Niger to assess the performance of this diagnostic approach for tuberculosis. This study aims to fill this gap and provide valuable data to improve diagnostic strategies in the country. METHODS Aim To study the analytical performance of stool compared to gastric content samples to diagnosis pulmonary tuberculosis in children using the GeneXpert MTB/RIF Ultra assay. Study setting The study was conducted at the National Reference Laboratory for Tuberculosis (NRL/TB) at the Amirou Boubacar Diallo National Hospital in Niamey, as well as at the laboratory in the Madarounfa health district, Maradi region, Niger. Type and period of study This multicenter cross-sectional diagnostic study was conducted from January 01 to December 31, 2024. Study population and sampling The study included patients with suspected pulmonary tuberculosis based on WHO criteria, regardless of gender. Sampling was done exhaustively. Eligibility criteria The study included all patients aged 0–5 years referred to the NRL/TB and the Madarounfa health district laboratory for GeneXpert MTB/RIF examination Ultra with gastric content (GC) and stool samples. Patients on anti-tuberculosis treatment for more than seven days or those with inadequate or poorly preserved samples were excluded. Sample collection and biological analysis Fresh stool samples were collected in a clean jar using the simple one-step (SOS) stool method from patients suspected of having TB and transported according to biosafety standards. Gastric content (GC) samples were obtained by nasogastric probing and transferred to a collection jar for rapid transport to the laboratory. At the laboratory, each patient's sample was analyzed using the GeneXpert MTB/RIF U ltra system (Cepheid, USA) in three steps: Sample preparation and loading onto the GeneXpert cartridge. Inserting the cartridge into the GeneXpert instrument for automated testing. Interpretation of results generated by the GeneXpert system. Data collection and analysis A standardized survey sheet was used to collect data, including socio-demographic characteristics (age, gender, HIV status) and Xpert MTB/RIF Ultra test results for MTB, bacillary load, and rifampin resistance screening. Data analysis was conducted using Excel 2020 and JAMOVI version 2.3.28. The STARD flow chart was used for patient inclusion data. Analytical sensitivity, specificity, positive and negative predictive values were calculated to assess the performance of GeneXpert Ultra for diagnosing pulmonary tuberculosis from stool samples, with gastric content samples as the gold standard. McNemar's chi-square test with a 95% confidence interval was used to determine agreement between stool and gastric content sample results, with a p-value < 0.05 considered statistically significant. Ethics approval This study was approved by the Faculty of Health Sciences at Abdou Moumouni University in Niamey. Consent was obtained from the management of Amidou Boubacar Diallo National Hospital and Madarounfa Health District. The study adhered to biosafety and biosecurity requirements, good laboratory practices, and the use of personal protective equipment (PPE) as appropriate. Data processing adhered to strict confidentiality and anonymity protocols with consent from parents or guardians. RESULTS This study included 401 patients who underwent a total of 802 MTB/RIF Ultra tests on stool and gastric lavage samples (Fig. 1 ). Basic characteristics of included patients The median age of patients was 18 months (IQR 11–24 months). The 12- to 23-month age group had the highest number of patients. 57.8% of the patients were male, with a sex ratio of 1.37. The HIV status of 68.1% of patients was unknown (Table 1 ). Table 1 Baseline characteristics of patients Characteristics Numbers Percentage Age ( months ) Median age 18 (IQR: 11–24) 0–11 111 27.7 12–23 164 40.9 24 months and over 126 31.4 Gender Female 169 42.3 Male 231 57.8 VIH Statut Unknown 273 68.1 Negative 128 31.9 GeneXpert Ultra results on gastric content samples Out of 401 gastric content samples tested with GeneXpert MTB/RIF, 9 (2.2%) were positive for Mycobacterium tuberculosis complex, mostly with low bacillary load (7 out of 9) (Table 2 ). Among the nine positive cases, only 1 was resistant to rifampin. Table 2 MTB/Rif Ultra results on GC samples GeneXpert gastric content samples Numbers Percentage Mycobacterium tuberculosis complex − Detected 9 2.2 − Error 3 0.7 − Not Detected 389 97.0 Charge bacillaire CG − Low 7 70.0 − Traces 2 20.0 − Very low 1 10.0 Rifampicin resistance − Detected 1 11.1 − undetermined 3 33.3 − Not detected 5 55.6 GeneXpert Ultra results on stool samples Out of 401 stool samples tested with GeneXpert MTB/RIF, 11 (2.7%) were positive for Mycobacterium tuberculosis complex. Among these, the majority had a low bacillary load (n = 4; 40%). None of the 11 samples showed rifampicin resistance (Table 3 ). Table 3 MTB/RIF Ultra results on stool samples GeneXpert stool samples Numbers Percentage Mycobacterium tuberculosis complex − Detected 11 2.7 − Error 11 2.7 − Not detected 379 94.5 Charge bacillaire Selles − Low 2 20.0 − High 1 10.0 − Medium 2 20.0 − Traces 4 40.0 − Very low 1 10.0 Rifampicine resistance − undetermined 3 27.3 − Not detected 8 72.7 Comparison of stool samples with gastric contents in terms of analytical performance Stool samples demonstrated a sensitivity of 77.8% and a specificity of 99.0% for diagnosing pulmonary tuberculosis in children, compared to gastric contents (the Gold Standard). The efficiency was 98.5%, with a positive predictive value of 63.6% and a negative predictive value of 99.5%. Stool samples compared with gastric content samples (Gold Standard) had an AUC of 0.816 for diagnosing pulmonary tuberculosis in children (Fig. 2 ). DISCUSSION Early diagnosis of tuberculosis in children is a significant challenge, especially in resource-limited countries like those in sub-Saharan Africa. Delayed diagnosis contributes to high morbidity and mortality rates in this population [ 7 , 8 ]. A study conducted in Niger in 2024 at two centers (LNR-TB and DH Madarounfa) investigated the use of stool samples as an alternative to gastric tubing for diagnosing tuberculosis in children. However, the study has limitations to consider. The wide confidence interval for sensitivity (40.0-97.2%) indicates variability, possibly due to the small positive sample size. This differs from a previous study by Mekkaoui et al. in 2021 [ 9 ], which reported a sensitivity of 91.1% (95% CI, 85.6–95.1). Larger-scale studies are needed to refine these estimates [ 10 ]. Additionally, including the culture of gastric contents, as suggested in previous literature, could improve the diagnosis of pulmonary tuberculosis [ 9 – 12 ]. This study found that the Xpert MTB/RIF Ultra test performed well on stool samples, with a sensitivity of 77.8% and a specificity of 99%. These results are consistent with recent literature [ 13 ]. Previous studies [ 11 , 14 ] have reported lower sensitivity for the standard Xpert MTB/RIF test on stool samples in children. The improved performance of the Ultra version of GeneXpert may explain the higher sensitivity observed in this study [ 14 , 15 ]. This advancement in technology reflects the ongoing evolution of diagnostic tools in tuberculosis testing [ 16 ]. The analysis of our study's predictive values provides valuable insights for clinical practice. With a positive predictive value of 63.6% and a negative predictive value of 99.5%, our approach offers a reliable decision-making tool for clinicians. These results compare favorably with those reported by Ssengooba et al., who found a PPV of 50.0% and NPV of 95.9% for Xpert MTB/RIF Ultra [ 17 ]. The robust performance of molecular tests in various epidemiological contexts is evident in our study. The high NPV is particularly noteworthy given the low prevalence of tuberculosis in our pediatric population. The high prevalence of low bacillary loads (82.1%) in our study mirrors the clinical reality of pediatric tuberculosis. This finding aligns with previous research [ 14 ] highlighting the paucibacillary nature of the disease in young children. The challenge of diagnosing tuberculosis in children under five, who often have difficulty producing good-quality sputum, underscores the need for a multifaceted diagnostic approach tailored to pediatric patients [ 18 – 23 ]. The study revealed a concerning 71.8% rate of unknown HIV status, highlighting the need for improved routine HIV screening in children with suspected TB. This issue is part of broader efforts to strengthen health systems and integrate services in Africa. The low rifampicin resistance rate of 3.6% aligns with regional data, with similar rates reported in the Sahel region [ 24 – 26 ]. However, countries like Guinea-Bissau and Guinea-Conakry have significantly higher resistance rates, emphasizing the importance of ongoing surveillance in the sub-region [ 7 , 27 ]. Analysis of the area under the ROC curve (AUC) of stool samples on GeneXpert Ultra shows excellent performance in detecting M. tuberculosis complex, with results consistent with previous studies [ 28 – 30 ]. The high AUC value of 0.97 indicates the test's robustness, especially in cases with low bacterial load where traditional methods struggle. Our findings support the superiority of GeneXpert Ultra over previous versions, particularly in HIV-positive patients. The ROC curve analysis identifies an optimal operating point that balances sensitivity and specificity, aligning with literature on threshold optimization [ 30 , 31 ]. Training healthcare staff is essential for the successful integration of new diagnostic approaches in tuberculosis control programs, as highlighted by WHO [ 33 ]. The use of non-invasive stool sampling shows for improving childhood tuberculosis diagnosis in sub-Saharan Africa, especially in resource-limited settings. Conclusion In this study, we compared the performance of the GeneXpert test on stool samples with gastric contents, the gold standard for diagnosing tuberculosis. The findings indicate that The GeneXpert stool test has good sensitivity but does not match the performance of the gastric contents test. However, its high specificity suggests that a positive stool result strongly indicates the presence of an infection. The positive and negative predictive values suggest that this test could be a valuable screening tool, especially in settings with limited access to invasive methods. These results suggest that using stool samples as a diagnostic tool could improve tuberculosis screening, particularly for children and vulnerable patients. This could lead to earlier diagnosis and better case management. While GeneXpert stool testing does not entirely replace gastric content examination, it can complement existing approaches. Integrating it into screening strategies, especially in resource-limited settings, could enhance tuberculosis detection and management. Abbreviations AUC Area under the curve GC Gastric content HD Health District HIV Human immunodeficiency virus IQR Interquartile range MTB/RIF Mycobacterium tuberculosis and rifampicin resistance NPV Negative predictive value NRL/TB National Reference Laboratory for PPE Personal protective equipment PPV Positive predictive value ROC Receiver operating characteristic SOS Simple one-step TB Tuberculosis USA United States of America WHO World Health Organization Declarations Acknowledgements The authors would like to acknowledge the medical staffs at NRL/TB and health district of Madafounfa laboratory for their help to this study. Authors' contributions Conceptualization, A.N.B, and Y.A; methodology, A.N.B, L.M.M and Y.A; validation, Y.A, B.S and S.M; investigation, A.N.B; writing-original draft preparation, A.N.B; writing-review and editing, A.N.B, Y.A, O.T, LMN, B.H, M.G.M, M.S.S, S.A, B.S, S.M; All authors have read and agreed to the published version of the manuscript. Funding This work was not supported by any research funding Data availability The datasets analyzed and/or used during the current study are available from the corresponding author upon reasonable request. Ethics approval and consent to participate All necessary institutional approvals were obtained before the beginning of the research, and data collection was carried out in accordance with the regulations of these institutions. The study was approved by the following authorities: The Faculty of Health Sciences at Abdou Moumouni University in Niamey (Reference No:000970/UAM/FSS/D) Amidou Boubacar Diallo National Hospital (Reference No: 0000138/HNABD/DAF/GRH) The Madarounfa Health District (Reference No: 44/DS/MDFA) Consent for publication Informed consent to participate in the study was obtained from their parents or legal guardians. No minor was included in the study without the formal consent of their legal representative prior to data collection. The objectives of the research, the voluntary nature of participation, and the confidentiality of information were clearly explained to each participant. The study was conducted in full compliance with the ethical principles outlined in the Declaration of Helsinki (2013 version). All procedures involving human participants adhered to internationally accepted standards for ethical research. Competing interests The authors declare no competing interests. References Bagcchi S. WHO’s global tuberculosis report 2022. Lancet Microbe. 2023;4(1):e20. Sun L, Liu Y, Fang M, Chen Y, Zhu Y, Xia C, et al. Use of Xpert MTB/RIF Ultra assay on stool and gastric aspirate samples to diagnose pulmonary tuberculosis in children in a high-tuberculosis-burden but resource-limited area of China. Int J Infect Dis 1 janv. 2022;114:236–43. Gebre M, Cameron LH, Tadesse G, Woldeamanuel Y, Wassie L. Variable Diagnostic Performance of Stool Xpert in Pediatric Tuberculosis: A Systematic Review and Meta-analysis. 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Niger","correspondingAuthor":false,"prefix":"","firstName":"Soumana","middleName":"","lastName":"Alphazazi","suffix":""},{"id":503487938,"identity":"5bcca18e-7b47-4ff3-a034-28d1a5e22765","order_by":8,"name":"Brah Souleymane","email":"","orcid":"","institution":"Faculté des Sciences de la Santé, Université Abdou Moumouni","correspondingAuthor":false,"prefix":"","firstName":"Brah","middleName":"","lastName":"Souleymane","suffix":""},{"id":503487940,"identity":"13354ae5-c085-4dca-ad68-f415755f1893","order_by":9,"name":"Saidou Mamadou","email":"","orcid":"","institution":"National Reference Laboratory for Tuberculosis","correspondingAuthor":false,"prefix":"","firstName":"Saidou","middleName":"","lastName":"Mamadou","suffix":""}],"badges":[],"createdAt":"2025-07-21 14:08:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7178335/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7178335/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12866-026-04928-6","type":"published","date":"2026-03-16T15:59:07+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":89971204,"identity":"8b634b95-372c-4206-997f-c4b6ce0d0016","added_by":"auto","created_at":"2025-08-27 05:36:27","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":16230,"visible":true,"origin":"","legend":"\u003cp\u003eStudy patient flow according to STARD recommendations\u003c/p\u003e","description":"","filename":"Onlinefloatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-7178335/v1/4c4ab0f242112237c244ad60.png"},{"id":89973841,"identity":"14c0c639-ea85-4ef0-882c-011bc99d3df4","added_by":"auto","created_at":"2025-08-27 05:52:27","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":5937,"visible":true,"origin":"","legend":"\u003cp\u003eROC of stool sample results compared with gastric contents (Gold Standard)\u003c/p\u003e","description":"","filename":"Onlinefloatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-7178335/v1/1cd71e76a2947e3c2e40a331.png"},{"id":105224472,"identity":"317f3547-9113-45a5-9ee5-b60f2d11bea8","added_by":"auto","created_at":"2026-03-23 16:14:25","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":888383,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7178335/v1/480b0c47-8eb3-4261-83b1-eb0f0d2896ae.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Evaluation of GeneXpert MTB/RIF Ultra on stool samples versus gastric contents for diagnosing tuberculosis in children under five years in Niger","fulltext":[{"header":"BACKGROUND","content":"\u003cp\u003eTuberculosis is a significant infectious disease, causing 1.3\u0026nbsp;million deaths globally by 2022. It is a leading cause of morbidity and mortality, especially in resource-limited countries. The World Health Organization (WHO) estimated 10.6\u0026nbsp;million cases in 2022, with 1.1\u0026nbsp;million cases in children (10\u0026ndash;11%), particularly affecting those under five years old.[\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Sub-Saharan Africa has a high burden of tuberculosis, with nearly 25% of global cases. The region also faces high mortality rates among young people, raising concerns about the impact of the disease [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eTuberculosis is a significant public health issue in Niger, with an estimated incidence of 84 cases per 100,000 inhabitants in 2022. Children under five face particular challenges in diagnosing tuberculosis due to nonspecific symptoms, rapid disease progression, and difficulties in obtaining quality respiratory samples for testing.\u003c/p\u003e\u003cp\u003eObtaining a quality respiratory sample from a child is challenging, making invasive techniques like gastric tubing and nasopharyngeal suctioning difficult to perform routinely. This, coupled with the low bacterial load of tuberculosis in children, complicates microbiological confirmation, leading to underestimation of cases and delays in diagnosis.\u003c/p\u003e\u003cp\u003eThe GeneXpert MTB/RIF Ultra test has revolutionized tuberculosis diagnosis and management, especially for paucibacillary forms. Recent studies [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e] have shown promising results using stool samples with this test for the diagnosis of pediatric tuberculosis. This non-invasive approach is more acceptable to children and parents due to its simplicity and minimal resource requirements.\u003c/p\u003e\u003cp\u003eStool analysis using GeneXpert MTB/RIF Ultra is a promising method for diagnosing tuberculosis, recommended by the WHO since 2021. It enhances pediatric tuberculosis detection and allows decentralized diagnosis in peripheral health facilities equipped with Cepheid's GeneXpert system. This benefits the rural populations, the majority of whom are in Niger, by improving access to healthcare.\u003c/p\u003e\u003cp\u003eTo date, no study has been conducted in Niger to assess the performance of this diagnostic approach for tuberculosis. This study aims to fill this gap and provide valuable data to improve diagnostic strategies in the country.\u003c/p\u003e"},{"header":"METHODS","content":"\u003cp\u003e\u003cb\u003eAim\u003c/b\u003e\u003c/p\u003e\u003cp\u003eTo study the analytical performance of stool compared to gastric content samples to diagnosis pulmonary tuberculosis in children using the GeneXpert MTB/RIF Ultra assay.\u003c/p\u003e\u003cp\u003e\u003cb\u003eStudy setting\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThe study was conducted at the National Reference Laboratory for Tuberculosis (NRL/TB) at the Amirou Boubacar Diallo National Hospital in Niamey, as well as at the laboratory in the Madarounfa health district, Maradi region, Niger.\u003c/p\u003e\u003cp\u003e\u003cb\u003eType and period of study\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThis multicenter cross-sectional diagnostic study was conducted from January 01 to December 31, 2024.\u003c/p\u003e\u003cp\u003e\u003cb\u003eStudy population and sampling\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThe study included patients with suspected pulmonary tuberculosis based on WHO criteria, regardless of gender. Sampling was done exhaustively.\u003c/p\u003e\u003cp\u003e\u003cb\u003eEligibility criteria\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThe study included all patients aged 0\u0026ndash;5 years referred to the NRL/TB and the Madarounfa health district laboratory for GeneXpert MTB/RIF examination Ultra with gastric content (GC) and stool samples.\u003c/p\u003e\u003cp\u003ePatients on anti-tuberculosis treatment for more than seven days or those with inadequate or poorly preserved samples were excluded.\u003c/p\u003e\u003cp\u003e\u003cb\u003eSample collection and biological analysis\u003c/b\u003e\u003c/p\u003e\u003cp\u003eFresh stool samples were collected in a clean jar using the simple one-step (SOS) stool method from patients suspected of having TB and transported according to biosafety standards. Gastric content (GC) samples were obtained by nasogastric probing and transferred to a collection jar for rapid transport to the laboratory.\u003c/p\u003e\u003cp\u003eAt the laboratory, each patient's sample was analyzed using the GeneXpert MTB/RIF U\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eltra\u003c/span\u003e system (Cepheid, USA) in three steps:\u003c/p\u003e\u003cp\u003e\u003col\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eSample preparation and loading onto the GeneXpert cartridge.\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eInserting the cartridge into the GeneXpert instrument for automated testing.\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003cspan\u003e\u003cli\u003e\u003cp\u003eInterpretation of results generated by the GeneXpert system.\u003c/p\u003e\u003c/li\u003e\u003c/span\u003e\u003c/ol\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eData collection and analysis\u003c/b\u003e\u003c/p\u003e\u003cp\u003eA standardized survey sheet was used to collect data, including socio-demographic characteristics (age, gender, HIV status) and Xpert MTB/RIF Ultra test results for MTB, bacillary load, and rifampin resistance screening.\u003c/p\u003e\u003cp\u003eData analysis was conducted using Excel 2020 and JAMOVI version 2.3.28. The STARD flow chart was used for patient inclusion data. Analytical sensitivity, specificity, positive and negative predictive values were calculated to assess the performance of GeneXpert Ultra for diagnosing pulmonary tuberculosis from stool samples, with gastric content samples as the gold standard. McNemar's chi-square test with a 95% confidence interval was used to determine agreement between stool and gastric content sample results, with a p-value\u0026thinsp;\u0026lt;\u0026thinsp;0.05 considered statistically significant.\u003c/p\u003e\u003cp\u003e\u003cstrong\u003eEthics approval\u003c/strong\u003e\u003cp\u003e This study was approved by the Faculty of Health Sciences at Abdou Moumouni University in Niamey. Consent was obtained from the management of Amidou Boubacar Diallo National Hospital and Madarounfa Health District. The study adhered to biosafety and biosecurity requirements, good laboratory practices, and the use of personal protective equipment (PPE) as appropriate.\u003c/p\u003e\u003c/p\u003e\u003cp\u003eData processing adhered to strict confidentiality and anonymity protocols with consent from parents or guardians.\u003c/p\u003e"},{"header":"RESULTS","content":"\u003cp\u003eThis study included 401 patients who underwent a total of 802 MTB/RIF Ultra tests on stool and gastric lavage samples (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eBasic characteristics of included patients\u003c/b\u003e\u003c/p\u003e\u003cp\u003eThe median age of patients was 18 months (IQR 11\u0026ndash;24 months). The 12- to 23-month age group had the highest number of patients. 57.8% of the patients were male, with a sex ratio of 1.37. The HIV status of 68.1% of patients was unknown (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eBaseline characteristics of patients\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"3\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eCharacteristics\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNumbers\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003ePercentage\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u003cb\u003eAge (\u003c/b\u003emonths\u003cb\u003e)\u003c/b\u003e\u003c/p\u003e\u003cp\u003eMedian age 18 (IQR: 11\u0026ndash;24)\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e0\u0026ndash;11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e111\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e27.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e12\u0026ndash;23\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e164\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e40.9\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e24 months and over\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e126\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e31.4\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGender\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eFemale\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e169\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e42.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eMale\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e231\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e57.8\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u003cb\u003eVIH Statut\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eUnknown\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e273\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e68.1\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eNegative\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e128\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e31.9\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eGeneXpert Ultra results on gastric content samples\u003c/b\u003e\u003c/p\u003e\u003cp\u003eOut of 401 gastric content samples tested with GeneXpert MTB/RIF, 9 (2.2%) were positive for \u003cem\u003eMycobacterium tuberculosis\u003c/em\u003e complex, mostly with low bacillary load (7 out of 9) (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Among the nine positive cases, only 1 was resistant to rifampin.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eMTB/Rif Ultra results on GC samples\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"3\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGeneXpert gastric content samples\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNumbers\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003ePercentage\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u003cem\u003eMycobacterium tuberculosis\u003c/em\u003e complex\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e9\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2.2\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Error\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e0.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Not Detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e389\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e97.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e\u003cp\u003e\u003cb\u003eCharge bacillaire CG\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Low\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e7\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e70.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Traces\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e20.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Very low\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e10.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e\u003cp\u003e\u003cb\u003eRifampicin resistance\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e11.1\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; undetermined\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e33.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Not detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e\u003cp\u003e5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e55.6\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eGeneXpert Ultra results on stool samples\u003c/b\u003e\u003c/p\u003e\u003cp\u003eOut of 401 stool samples tested with GeneXpert MTB/RIF, 11 (2.7%) were positive for Mycobacterium tuberculosis complex. Among these, the majority had a low bacillary load (n\u0026thinsp;=\u0026thinsp;4; 40%). None of the 11 samples showed rifampicin resistance (Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eMTB/RIF Ultra results on stool samples\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"3\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003eGeneXpert stool samples\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eNumbers\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003ePercentage\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u003cem\u003eMycobacterium tuberculosis\u003c/em\u003e complex\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Error\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e11\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e2.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Not detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e379\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e94.5\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e\u003cp\u003e\u003cb\u003eCharge bacillaire Selles\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Low\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e20.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; High\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e10.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Medium\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e2\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e20.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Traces\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e4\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e40.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Very low\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e1\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e10.0\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e\u003cp\u003e\u003cb\u003eRifampicine resistance\u003c/b\u003e\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; undetermined\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e27.3\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003e\u0026minus; Not detected\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c3\"\u003e\u003cp\u003e72.7\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003cp\u003e\u003cb\u003eComparison of stool samples with gastric contents in terms of analytical performance\u003c/b\u003e\u003c/p\u003e\u003cp\u003eStool samples demonstrated a sensitivity of 77.8% and a specificity of 99.0% for diagnosing pulmonary tuberculosis in children, compared to gastric contents (the Gold Standard). The efficiency was 98.5%, with a positive predictive value of 63.6% and a negative predictive value of 99.5%.\u003c/p\u003e\u003cp\u003eStool samples compared with gastric content samples (Gold Standard) had an AUC of 0.816 for diagnosing pulmonary tuberculosis in children (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eEarly diagnosis of tuberculosis in children is a significant challenge, especially in resource-limited countries like those in sub-Saharan Africa. Delayed diagnosis contributes to high morbidity and mortality rates in this population [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. A study conducted in Niger in 2024 at two centers (LNR-TB and DH Madarounfa) investigated the use of stool samples as an alternative to gastric tubing for diagnosing tuberculosis in children.\u003c/p\u003e\u003cp\u003eHowever, the study has limitations to consider. The wide confidence interval for sensitivity (40.0-97.2%) indicates variability, possibly due to the small positive sample size. This differs from a previous study by Mekkaoui et al. in 2021 [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e], which reported a sensitivity of 91.1% (95% CI, 85.6\u0026ndash;95.1). Larger-scale studies are needed to refine these estimates [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Additionally, including the culture of gastric contents, as suggested in previous literature, could improve the diagnosis of pulmonary tuberculosis [\u003cspan additionalcitationids=\"CR10 CR11\" citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThis study found that the Xpert MTB/RIF Ultra test performed well on stool samples, with a sensitivity of 77.8% and a specificity of 99%. These results are consistent with recent literature [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. Previous studies [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] have reported lower sensitivity for the standard Xpert MTB/RIF test on stool samples in children. The improved performance of the Ultra version of GeneXpert may explain the higher sensitivity observed in this study [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. This advancement in technology reflects the ongoing evolution of diagnostic tools in tuberculosis testing [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe analysis of our study's predictive values provides valuable insights for clinical practice. With a positive predictive value of 63.6% and a negative predictive value of 99.5%, our approach offers a reliable decision-making tool for clinicians. These results compare favorably with those reported by Ssengooba et al., who found a PPV of 50.0% and NPV of 95.9% for Xpert MTB/RIF Ultra [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. The robust performance of molecular tests in various epidemiological contexts is evident in our study. The high NPV is particularly noteworthy given the low prevalence of tuberculosis in our pediatric population.\u003c/p\u003e\u003cp\u003eThe high prevalence of low bacillary loads (82.1%) in our study mirrors the clinical reality of pediatric tuberculosis. This finding aligns with previous research [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] highlighting the paucibacillary nature of the disease in young children. The challenge of diagnosing tuberculosis in children under five, who often have difficulty producing good-quality sputum, underscores the need for a multifaceted diagnostic approach tailored to pediatric patients [\u003cspan additionalcitationids=\"CR19 CR20 CR21 CR22\" citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eThe study revealed a concerning 71.8% rate of unknown HIV status, highlighting the need for improved routine HIV screening in children with suspected TB. This issue is part of broader efforts to strengthen health systems and integrate services in Africa. The low rifampicin resistance rate of 3.6% aligns with regional data, with similar rates reported in the Sahel region [\u003cspan additionalcitationids=\"CR25\" citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. However, countries like Guinea-Bissau and Guinea-Conakry have significantly higher resistance rates, emphasizing the importance of ongoing surveillance in the sub-region [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eAnalysis of the area under the ROC curve (AUC) of stool samples on GeneXpert Ultra shows excellent performance in detecting \u003cem\u003eM. tuberculosis\u003c/em\u003e complex, with results consistent with previous studies [\u003cspan additionalcitationids=\"CR29\" citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. The high AUC value of 0.97 indicates the test's robustness, especially in cases with low bacterial load where traditional methods struggle. Our findings support the superiority of GeneXpert Ultra over previous versions, particularly in HIV-positive patients. The ROC curve analysis identifies an optimal operating point that balances sensitivity and specificity, aligning with literature on threshold optimization [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eTraining healthcare staff is essential for the successful integration of new diagnostic approaches in tuberculosis control programs, as highlighted by WHO [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. The use of non-invasive stool sampling shows for improving childhood tuberculosis diagnosis in sub-Saharan Africa, especially in resource-limited settings.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eIn this study, we compared the performance of the GeneXpert test on stool samples with gastric contents, the gold standard for diagnosing tuberculosis. The findings indicate that\u003c/p\u003e\u003cp\u003eThe GeneXpert stool test has good sensitivity but does not match the performance of the gastric contents test. However, its high specificity suggests that a positive stool result strongly indicates the presence of an infection. The positive and negative predictive values suggest that this test could be a valuable screening tool, especially in settings with limited access to invasive methods.\u003c/p\u003e\u003cp\u003eThese results suggest that using stool samples as a diagnostic tool could improve tuberculosis screening, particularly for children and vulnerable patients. This could lead to earlier diagnosis and better case management. While GeneXpert stool testing does not entirely replace gastric content examination, it can complement existing approaches. Integrating it into screening strategies, especially in resource-limited settings, could enhance tuberculosis detection and management.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eAUC Area under the curve\u003c/p\u003e\u003cp\u003eGC Gastric content\u003c/p\u003e\u003cp\u003eHD Health District\u003c/p\u003e\u003cp\u003eHIV Human immunodeficiency virus\u003c/p\u003e\u003cp\u003eIQR Interquartile range\u003c/p\u003e\u003cp\u003eMTB/RIF \u003cem\u003eMycobacterium tuberculosis\u003c/em\u003e and rifampicin resistance\u003c/p\u003e\u003cp\u003eNPV Negative predictive value\u003c/p\u003e\u003cp\u003eNRL/TB National Reference Laboratory for\u003c/p\u003e\u003cp\u003ePPE Personal protective equipment\u003c/p\u003e\u003cp\u003ePPV Positive predictive value\u003c/p\u003e\u003cp\u003eROC Receiver operating characteristic\u003c/p\u003e\u003cp\u003eSOS Simple one-step\u003c/p\u003e\u003cp\u003eTB Tuberculosis\u003c/p\u003e\u003cp\u003eUSA United States of America\u003c/p\u003e\u003cp\u003eWHO World Health Organization\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors would like to acknowledge the medical staffs at\u0026nbsp;NRL/TB and\u0026nbsp;health district of Madafounfa laboratory for their help to this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026apos; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConceptualization, A.N.B, and Y.A; methodology, A.N.B, L.M.M and Y.A; validation, Y.A, B.S and S.M; investigation, A.N.B; writing-original draft preparation, A.N.B; writing-review and editing, A.N.B, Y.A, O.T, LMN, B.H, M.G.M, M.S.S, S.A, B.S, S.M; All authors have read and agreed to the published version of the manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was not supported by any research funding\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets analyzed and/or used during the current study are available from the corresponding author upon reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll necessary institutional approvals were obtained before the beginning of the research, and data collection was carried out in accordance with the regulations of these institutions. The study was approved by the following authorities:\u003c/p\u003e\n\u003cp\u003eThe Faculty of Health Sciences at Abdou Moumouni University in Niamey (Reference No:000970/UAM/FSS/D)\u003c/p\u003e\n\u003cp\u003eAmidou Boubacar Diallo National Hospital (Reference No: 0000138/HNABD/DAF/GRH)\u003c/p\u003e\n\u003cp\u003eThe Madarounfa Health District (Reference No: 44/DS/MDFA)\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eInformed consent to participate in the study was obtained from their parents or legal guardians. No minor was included in the study without the formal consent of their legal representative prior to data collection. The objectives of the research, the voluntary nature of participation, and the confidentiality of information were clearly explained to each participant.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe study was conducted in full compliance with the ethical principles outlined in the Declaration of Helsinki (2013 version). All procedures involving human participants adhered to internationally accepted standards for ethical research.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eBagcchi S. WHO\u0026rsquo;s global tuberculosis report 2022. Lancet Microbe. 2023;4(1):e20.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSun L, Liu Y, Fang M, Chen Y, Zhu Y, Xia C, et al. 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Int J Mycobacteriology d\u0026eacute;c. 2022;11(4):371.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eOMS. Cadre centr\u0026eacute; sur la personne pour la planification et la priorisation des activit\u0026eacute;s des programmes de lutte contre la tuberculose: guide de l\u0026rsquo;utilisateur. 2021 [cit\u0026eacute; 16 janv 2025]; Disponible sur: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://apps.who.int/iris/bitstream/handle/10665/344798/9789240033511-fre.pdf\u003c/span\u003e\u003cspan address=\"https://apps.who.int/iris/bitstream/handle/10665/344798/9789240033511-fre.pdf\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-microbiology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"mcro","sideBox":"Learn more about [BMC Microbiology](http://bmcmicrobiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/mcro","title":"BMC Microbiology","twitterHandle":"#bmcmicrobiology","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Stool, gastric content, GeneXpert, children, tuberculosis, Niger","lastPublishedDoi":"10.21203/rs.3.rs-7178335/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7178335/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003ePediatric tuberculosis is challenging to diagnose due to the limited presence of bacteria and difficulties in obtaining high-quality sputum samples. This study assessed the effectiveness of stool samples versus gastric contents analyzed with GeneXpert Ultra for diagnosing pulmonary tuberculosis in children under five years old.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e\u003cp\u003eA diagnostic study was conducted in Niger over a one-year period (January 1 to December 31, 2024), at multiple centers. Socio-demographic data and GeneXpert Ultra results from stool and gastric samples were collected in accordance with STARD guidelines. Data analysis was performed using Excel 2020 and JAMOVI 2.3.28 software to calculate sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eThis study included 401 patients with a median age of 18 months (interquartile range, IQR, 11\u0026ndash;24 months) and a sex ratio of 1.37. The diagnostic performance of the test showed a sensitivity of 77.8% and a specificity of 99%, with an overall accuracy of 98.5%. The positive and negative predictive values were 63.6% and 99.5% respectively. The area under the curve (AUC) was 0.816, and the positive and negative likelihood ratios were 76.2 and 0.225, indicating the test's strong discriminatory capacity.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e\u003cp\u003eGeneXpert stool testing is a valuable complementary approach to gastric content examination for detecting tuberculosis. Integrating it into screening strategies, especially in resource-limited settings, can enhance pediatric tuberculosis detection and management.\u003c/p\u003e","manuscriptTitle":"Evaluation of GeneXpert MTB/RIF Ultra on stool samples versus gastric contents for diagnosing tuberculosis in children under five years in Niger","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-08-27 05:36:22","doi":"10.21203/rs.3.rs-7178335/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-13T04:38:56+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-02T11:23:22+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-30T01:11:02+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"328939912332617321032785086872528091565","date":"2025-08-18T09:45:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"164864676421779393415291539745128126026","date":"2025-08-16T11:30:00+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"31654045280176753104939682180419391234","date":"2025-08-16T11:04:48+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"111434023673440855640074779031249173855","date":"2025-08-15T00:07:11+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"234782536913075775963664523957085163289","date":"2025-08-14T13:48:11+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-08-14T10:44:45+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-07-31T11:54:59+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-07-31T08:15:40+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-07-30T13:16:40+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Microbiology","date":"2025-07-30T13:13:46+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-microbiology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"mcro","sideBox":"Learn more about [BMC Microbiology](http://bmcmicrobiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/mcro","title":"BMC Microbiology","twitterHandle":"#bmcmicrobiology","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"33126254-bb17-4afe-8ab2-a0860830d14f","owner":[],"postedDate":"August 27th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-03-23T16:10:38+00:00","versionOfRecord":{"articleIdentity":"rs-7178335","link":"https://doi.org/10.1186/s12866-026-04928-6","journal":{"identity":"bmc-microbiology","isVorOnly":false,"title":"BMC Microbiology"},"publishedOn":"2026-03-16 15:59:07","publishedOnDateReadable":"March 16th, 2026"},"versionCreatedAt":"2025-08-27 05:36:22","video":"","vorDoi":"10.1186/s12866-026-04928-6","vorDoiUrl":"https://doi.org/10.1186/s12866-026-04928-6","workflowStages":[]},"version":"v1","identity":"rs-7178335","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7178335","identity":"rs-7178335","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}