The implementation of Xpert MTB/RIF assay for diagnosis of tuberculosis in Nepal: A mixed-methods analysis

PLoS One. 2018 Aug 10;13(8):e0201731. doi: 10.1371/journal.pone.0201731. eCollection 2018.


Background: Tuberculosis (TB) is a major public health problem in low and middle-income countries. Early detection and enrolment of TB cases is a challenge for National TB Programs.

Objective: To understand the performance and feasibility for scale-up of Xpert MTB/RIF assay for the TB diagnosis in Nepal.

Design: Implementation research employed mixed-method sequential explanatory design. The results of Xpert MTB/RIF assay were analysed in 26 TB diagnostic centres where Xpert machines had been installed before 2015. In-depth interviews and focus group discussions were conducted with stakeholders, purposively selected to represent experiences in centres that were functioning well, poorly or not functioning.

Results: During a one-year period in 2015/16, 23,075 Xpert MTB/RIF assays were performed in 21 diagnostic centres with 22,288 people also tested by sputum microscopy. Among these, 77% had concordant (positive or negative) results, demonstrating fair agreement (Kappa score, 0.3) between test results. Test failure and positivity rates in diagnostic centres ranged from 2.6% to 13.4% and 6.5% to 49%, respectively. The number of cartridges per positive result varied from 2.3 to 10.2. Xpert assay was positive in 3314 (15% of all cases) sputum smear microscopy negative cases. Of 4280 bacteriologically confirmed cases by Xpert assay, 355 (8%) were rifampicin resistant. Xpert machines were no longer functioning regularly throughout the year in 5 diagnostic centres. The main barriers for effective implementation of Xpert in Nepal were the lack of: timely supply of cartridges; replacement of damaged modules; maintenance of Xpert machines; and stock verification for timely procurement of cartridges. Inadequate laboratory infrastructure for maintaining functional Xpert equipment further challenges implementation and scale-up.

Conclusion: The implementation of Xpert MTB/RIF assay has increased case-finding of TB and MDR-TB in Nepal. However, there is a need to improve laboratory performance and strengthen laboratory infrastructure for optimal utilisation and scale-up of Xpert.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Early Diagnosis
  • Humans
  • Microscopy
  • Nepal
  • Sputum / microbiology
  • Tuberculosis, Pulmonary / diagnosis*

Grant support

This research was a part of postgraduate thesis. The scholarship for this degree was funded by the Special Programme for Research and Training in Tropical Diseases at the World Health Organization (WHO/TDR) and Universitas Gadjah Mada, Indonesia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.