Comparison of Xpert Mtb/Rif with Histology for the Detection of Mycobacterium Tuberculosis in Formalin Fixed Paraffin Embedded Tissues at Aga Khan University Hospital, Nairobi

Date of Award


Document Type


Degree Name

Master of Medicine (MMed)

First Supervisor/Advisor

Dr. Samuel Gakinya

Second Supervisor/Advisor

Dr. Zahir Moloo

Third Supervisor/Advisor

Dr. Shahin Sayed


Pathology (East Africa)


Background: Diagnosis of extrapulmonary tuberculosis (EPTB) continues to be a challenge due to the complexity of the causative organism and the wide array of pathologic features seen in this infection. A number of studies have shown polymerase chain reaction (PCR) for EPTB to be a feasible, sensitive and specific test for diagnosis of tuberculosis (TB) of which, the World Health Organisation (WHO) has given recommendations. As pertains EPTB, Xpert MTB/RIF may be used in place of conventional tests such as microscopy, histopathology and culture in lymph nodes and other tissues from patients suspected to have EPTB. It has been demonstrated that Xpert MTB/RIF can be used for fresh or frozen tissues specimens with good results. However, the use of formalin fixed paraffin embedded (FFPE) tissues, a widely available and rich source of clinical material, on the Xpert platform is yet to be described.

Objectives: The aim of this study was to demonstrate the potential utility of Xpert MTB/RIF in the detection of Mycobacterium tuberculosis from FFPE tissues with histological features suggestive of tuberculosis. We compared Xpert MTB/RIF to histology for the detection of Mycobacterium tuberculosis from FFPE tissues. In those cases with a positive Xpert result, we determined the prevalence of rifampicin resistance in EPTB.

Methods: Eighty randomly selected archived FFPE tissues exhibiting histological features suggestive of TB (necrotizing granulomatous inflammation, non-necrotizing granulomatous inflammation, chronic inflammation, necrotizing inflammation and suppurative inflammation) from January 1, though December 31, 2014 were retrieved. All the cases were subjected to microscopic evaluation of Haematoxylin and Eosin (H&E) stained and Ziehl-Neelsen (ZN) slides. With prior deparaffinization and lysis, all cases were also subjected to the Xpert MTB/RIF assay. Only 79 cases were included in the final analysis. This was after exclusion of one case due to an error in the Xpert MTB/RIF assay. The outcome measures were proportions of positively identified cases by each test. The data were analysed using chi - square test.

Results: Xpert MTB/RIF assay detected 32.9% more cases than microscopy (53.2% versus 20.3%) which was statistically significant, (p= 0.002). None of the cases tested positive for rifampicin resistance. Seven cases however, had an indeterminate rifampicin resistance result.

Conclusion: With prior deparaffinization and lysis, FFPE tissues can also be subjected to the Xpert MTB/RIF assay. A validation study to determine the clinical utility of this assay for FFPE tissues is recommended.

This document is available in the relevant AKU library