Impact of Gene Xpert in resource limited settings to meet End TB strategy


  • Nazish Babar Associate Professor Microbiology, Department of Pathology Gajju Khan Medical College, Swabi, Pakistan
  • Asim Ali Shah Incharge Microbiology/Virology Gajju Khan Medical College, Swabi, Pakistan
  • Asfandyar Babar Final year BDS Shifa College of Dentistry, Islamabad, Pakistan
  • Sara Najeeb Associate Professor Microbiology Mohi-ud-din Islamic Medical College, Mirpur, Azad Kashmir
  • Zainab Abdul Rahman


Gene Xpert MTB/RIF assay, MDR-TB, Mycobacterium tuberculosis, Rifampicin


Background: Gene Xpert is the most sensitive technique for early diagnosis of TB/MDR TB, which enables the physicians to start an effective treatment much sooner, as the results are obtained within 2 hours, especially in life threatening conditions like tuberculous meningitis.

Objective: The main objective in conducting this study was to extensively analyze the diagnostic accuracy of Gene Xpert MTB/RIF assay in cases of both pulmonary and extra pulmonary TB, versus the standard conventional methods like Ziehl Neelsen smear microscopy.

Setting: This study was conducted from 28th of August, 2023 to 31st of March, 2024 at Microbiology Laboratory MTI- GKMC/BKMC, Swabi.

Material and methods: After seeking permission from IRB, samples received both from pulmonary and/or extra-pulmonary sites, were subjected to formation of smear followed by microscopy on Ziehl Neelsen staining, and further subjection to Gene Xpert analysis.


Out of the total 863 samples, 78 were detected positive on Gene Xpert, with an overall positivity of 9.03%, whereas the overall positivity on microscopy was lower i.e. 8.45%. Overall Rifampicin resistance as seen on Gene Xpert analysis was 1.28%, as only one pus sample out of a total of 78 pulmonary and extra pulmonary samples, was detected to be Rifampicin resistant. Diagnostic performance of Gene Xpert MTB/RIF in comparison with Microscopy was calculated using the following 2X2 table, taking Gene Xpert as a standard which showed a sensitivity of 93.58% and specificity of 100%, a positive predictive value was calculated to be 100%, a negative predictive value of 99.36% with an accuracy of 99.42%.

Conclusion: Gene Xpert MTB/RIF assay has proven to be a highly sensitive user friendly technique for diagnosing TB and resistance against rifampicin simultaneously for both pulmonary and extra pulmonary TB.





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