Evaluation of the Diagnostic Performance of GeneXpert MTB/RIF assay for Extra-pulmonary Tuberculosis: A Retrospective Study from Pakistan

Objective: A retrospective cross sectional study was conducted to evaluate the diagnostic performance of Cepheid GeneXpert MTB/RIF assay (Xpert assay) for the Extra-pulmonary tuberculosis (EPTB). This study retrieved and analyzed the record of Provincial TB Reference Laboratory (PTRL), Hayatabad Medical Complex, Peshawar, Pakistan from January 2019 to December 2022. Materials and Methods: Different EPTB specimens received to the PTRL for routine diagnosis from EPTB suspected patients were recruited consecutively and anonymously. All the specimens were digested and decontaminated by NALC-NaOH method except CSF. Afterward, all the specimens were cultured on solid and liquid medium and tested by Xpert assay. The overall and for each individual sample, diagnostic performance of Xpert assay was measured by sensitivity, specificity and predictive values using culture as a gold standard. Results: A total of 2174 EPTB samples were recruited after meeting the inclusion criteria and the pooled sensitivity, specificity, positive predictive value and negative predictive value of Xpert assay was 67%, 94%, 52% and 96% respectively. Moreover, Xpert assay showed variable sensitivities for different EPTB specimens including Pus, Tissue biopsy, Urine, CSF, Pleural fluid, Pericardial fluid and Ascitic fluid i.e., 91, 83, 80, 67, 46, 44 and 36%, respectively. The specificity ranged from 85% in CSF to 99% in Urine. Conclusion: Xpert assay can early detect EPTB cases for prompt treatment but there is low certainty of negative result to rule out EPTB.