Validation of genexpert machine using extrapulmonary samples at national tuberculosis referral laboratory in Lesotho

Abstract

INTRODUCTION: The battle against tuberculosis (TB) is still a major public health scourge in Lesotho. Unfortunately, TB not only affects the lungs; it can also be found in other extrapulmonary areas such as the skin, brain, lymph nodes, genitourinary tract, and bones/joints. The GeneXpert is a sophisticated molecular assay that rapidly detects pulmonary TB and its resistance to rifampicin in sputum. The traditional culture TB-detection methods are still used for TB diagnosis of nonrespiratory samples. The magnitude of delayed diagnosis of extrapulmonary tuberculosis (EPTB) can be addressed if rapid and effective methods are implemented. We sought to validate the GeneXpert System using two different cartridges; Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) and Xpert Ultra in the National Tuberculosis Reference Laboratory (NTRL) using extrapulmonary samples in this study. METHODOLOGY: This study was mainly experimental, but existing data from the NTRL database were also included. The assessment of the Xpert MTB/RIF and Xpert Ultra was comparable to culture for identifying Mycobacterium tuberculosis in extrapulmonary clinical specimens. Extrapulmonary samples from various health facilities in Lesotho were tested using the culture method (gold standard) and the GeneXpert as method to be validated. Patients from all ages and genders were included. Statistical analysis was conducted on IBM’s Statistical Package for Social Sciences (version 26). RESULTS: A total of 352 samples were analysed from 2016 to 2019. Pleural fluid was the most collected sample type (39.2%), followed by ascitic fluid (14.2%) and cerebrospinal fluid (13.6%). Of the 352 samples tested, 34 EPTB cases were detected by the GeneXpert assays and culture methods. Twenty-one cases tested positive by the GeneXpert assays alone, while only one tested positive by the culture method, and the two methods were able to both detect M. tuberculosis in 12 specimens. The sensitivity and specificity of the GeneXpert assays were 92.3% and 87.1%, respectively. Pleural EPTB was predominant in males aged 21 to 40 years. CONCLUSION: The findings from this study prove that pleural TB was the most prevalent EPTB. The outcomes of GeneXpert assays in this study do not replace culture as the gold method; however, the GeneXpert assays showed increased sensitivity and a better turn-around time of less than two hours, which can assist clinicians in making a prompt diagnosis.