Optimising pulmonary tuberculosis diagnosis in adults: diagnostic usefulness of stool gene xpert alone and in combination with sputum gene xpert at a referral centre in Northeastern Nigeria

Purpose Pulmonary tuberculosis (PTB) continues to be a major public health burden, a situation exacerbated by significant diagnostic gaps. Conventional testing relies heavily on sputum samples, but many patients are unable to produce adequate and qualitative sputum. This limitation leaves a number of cases undiagnosed. Microbiological diagnosis of pulmonary tuberculosis relies mainly on smear microscopy and Xpert MTB/RIF on sputum samples, but obtaining good-quality sputum samples may be difficult. Stool GeneXpert, a molecular diagnostic test, has shown potential as an alternative specimen for diagnosing PTB. This study aimed to evaluate the diagnostic performance of stool GeneXpert, both as a standalone test and in combination with sputum GeneXpert, for diagnosing PTB in adults in Northeastern Nigeria. Methods This retrospective descriptive study was conducted at the Federal Teaching Hospital, Gombe, in Northeastern Nigeria, and included data collected between January 2023 and October 2024. Adult patients suspected of having PTB and tested with sputum and/or stool GeneXpert were included. Data were collected from medical records, including demographic details, HIV status, diagnostic test results, and patient weight. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for stool GeneXpert and the combination of stool and sputum GeneXpert. McNemar test, Receiver Operating Characteristic (ROC) curve analysis, and logistic regression were used to evaluate diagnostic performance and identify factors influencing diagnostic outcomes. Results A total of 318 patients were included. The diagnostic yield of stool GeneXpert alone was 72.1%, higher than sputum GeneXpert at 64.3%. The combined stool and sputum GeneXpert testing achieved a diagnostic yield of 83.7%, with 100% sensitivity and 100% NPV. The McNemar test showed no significant difference between stool and sputum GeneXpert results (p = 0.164). However, combining both samples significantly improved detection (p = 0.000). ROC analysis demonstrated a modest discriminatory ability for stool GeneXpert (AUC = 0.621), which improved moderately when combined with sputum GeneXpert (AUC = 0.728). Conclusion Stool GeneXpert, particularly when combined with sputum GeneXpert, offers a promising alternative for diagnosing PTB, especially when sputum collection is difficult. The combined testing approach enhances diagnostic yield and may improve early detection and treatment outcomes for PTB in resource-limited settings. Further studies are warranted to confirm these findings and explore the broader applicability of stool GeneXpert.