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Feasibility, usefulness and cost analysis of Gene Xpert to increase case detection

A nurse examines a patient's medication chart at the National Institute of Diseases of Chest and Hospital in Dhaka, Bangladesh. © 2014 Probal Rashid, Courtesy of Photoshare

Research Overview

TRAction is currently funding a research study in Bangladesh exploring the effectiveness of Gene Xpert technology to increase case detection of hard-to-detect Tuberculosis (TB) cases & drug-resistant strains.

Bangladesh currently ranks 6th among 22 TB high-burden countries in the world. In spite of considerable progress in providing TB services, an estimated 300,000 new cases are detected per year in this country.

In Bangladesh, The National TB Control Programme (NTP) coordinates the diagnosis, reporting and treatment of TB cases according to WHO guidelines. Most TB cases are diagnosed through passive case finding. Three sputum specimens are obtained from TB suspects for sputum-smear microscopy. A new smear-positive TB case is diagnosed on the basis of one or more sputum specimens testing positive for acid fast bacilli. Conventional microscopy cannot detect TB bacilli when the concentration is less than 5000 bacilli per ml of sputum.  In Bangladesh, 65% of the pulmonary TB can be detected by conventional microscopy and the rest (35%) remain un-diagnosed. These group of TB patients are called smear negative pulmonary TB.  Smear-negative TB has to be diagnosed on the basis of symptoms, clinical features, and supportive chest X-ray findings.

Recent evidence has shown Xpert MTB/RIF— a tool for early diagnosis tuberculosis, can diagnose 72.5% of suspected cases with smear negative pulmonary tuberculosis. Xpert MTB/RIF is a real-time PCR that detects DNA of mycobacterium tuberculosis and rifampicin resistance simultaneously. It has high sensitivity and specificity, and can identify 98% rifampicin-resistant mycobacterium within 2 hours. The Xpert MTB/RIF assay is simple and user friendly, requires minimum biosafety facilities, and little hands-on technical time.

Project Location

Bangladesh: Dhaka

Research Objectives

  1. Evaluate the feasibility and usefulness of Gene Xpert for detection of smear negative pulmonary and extra pulmonary TB.
  2. Determine the diagnostic accuracy of Gene Xpert MTB/RIF assay compared to the gold standard (culture) for detection of smear negative pulmonary and extra pulmonary TB.
  3. Assess cost and outcomes of diagnostic approaches by Gene Xpert and culture using samples from smear negative pulmonary and extra pulmonary TB suspects.

Study Approach

Smear-negative PTB was studied in Shyamoli Chest Disease Clinic, at the National Institute of Diseases of Chest and Hospitals, and at the division-level TB hospitals of Rajshahi and Sylhet. TB lymphadenitis was studied in Bangabandhu Sheikh Mujib Medical University.  Clinical specimens (smear-negative sputum samples, lymph node aspirates, and other extra-pulmonary clinical specimens) from presumptive TB cases were tested by GXP and by conventional culture. Drug susceptibility testing (DST) was performed by proportion method.

Key Findings

This study demonstrated detection of 23.5% additional EPTB cases and 13.3% smear negative cases by using GeneXpert MTB/RIF. A subset of smear negative presumptive pulmonary TB cases were tested with GeneXpert in prison (n=594) and also in the urban slum (n=408); researchers found that using GeneXpert MTB/RIF can increase the total bacteriological case detection at least by 25% in both groups.

To explore operational barriers and challenges associated with the introduction of GeneXpert at study facilities, researchers conducted key informant interviews with 22 purposively selected staff members (microbiologists, clinical pathologists, junior consultants, laboratory technologists and program organizers) and conducted a record review. Findings revealed that there was a serious gap in machine maintenance with the problem of module failure. It was reported that hands-on training received by the staff on GeneXpert test and machine maintenance was not adequate. There was no operative manual for the machine maintenance nor written standard operating procedure (SOP) for the test.

Lessons Learned

The National TB Control Programme should include GXP test for rapid diagnosis of smear-negative PTB and EPTB cases. However there were some challenges associated with this research.  Challenges highlighted included power failures in summer time and lack of Information, Education and Communication (IEC) materials and location mark of the centres. Before scaling up GeneXpert MTB/RIF further, these issues should be carefully addressed.

Research into Action

The results of this study hold implications in shifting the dynamic in TB control in Bangladesh, and adds to the global evidence base on Gene Xpert technology. Policymakers can act on increasing the availability and utilization of Gene Xpert technology to curb the spread of TB. Stakeholders in the Ministry of Health, the national & international organizations working in TB control will benefit from the evidence generated by this study.

Implemented by

International Centre for Diarrheal Disease Research (icddr,b)

Principle Investigator: Dr. Zeaur Rahim

Project Status

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