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

Background Pediatric 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. 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.