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Abstract
BackgroundNewer molecular diagnostics have brought paradigm shift in early diagnosis of tuberculosis [TB]. WHO recommended use of GeneXpert MTB/RIF [Xpert] for Extra-pulmonary [EP] TB; critics have since questioned its efficiency.MethodsThe present study was designed to assess the performance of GeneXpert in 761 extra-pulmonary and 384 pulmonary specimens from patients clinically suspected of TB and compare with Phenotypic, Genotypic and Composite reference standards [CRS].ResultsComparison of GeneXpert results to CRS, demonstrated sensitivity of 100% and 90.68%, specificity of 100% and 99.62% for pulmonary and extra-pulmonary samples. On comparison with culture, sensitivity for Rifampicin [Rif] resistance detection was 87.5% and 81.82% respectively, while specificity was 100% for both pulmonary and extra-pulmonary TB. On comparison to sequencing of rpoB gene [Rif resistance determining region, RRDR], sensitivity was respectively 93.33% and 90% while specificity was 100% in both pulmonary and extra-pulmonary TB. GeneXpert assay missed 533CCG mutation in one sputum and dual mutation [517 & 519] in one pus sample, detected by sequencing. Sequencing picked dual mutation [529, 530] in a sputum sample sensitive to Rif, demonstrating, not all RRDR mutations lead to resistance.ConclusionsCurrent study reports observations in a patient care setting in a high burden region, from a large collection of pulmonary and extra-pulmonary samples and puts to rest questions regarding sensitivity, specificity, detection of infrequent mutations and mutations responsible for low-level Rif resistance by GeneXpert. Improvements in the assay could offer further improvement in sensitivity of detection in different patient samples; nevertheless it may be difficult to improve sensitivity of Rif resistance detection if only one gene is targeted. Assay specificity was high both for TB detection and Rif resistance detection. Despite a few misses, the assay offers major boost to early diagnosis of TB and MDR-TB, in difficult to diagnose pauci-bacillary TB.
Highlights
Sequencing picked dual mutation [529, 530] in a sputum sample sensitive to Rif, demonstrating, not all RRDR mutations lead to resistance
In the absence of an efficient diagnostic modality for Tuberculosis [TB], the search for a tool that can overcome the dilemmas of the available diagnostic tests continues
Forty-one of 48 such patients with EPTB were resistant to Rifampicin by GeneXpert and were given treatment for MDR-TB, while four had gastrointestinal TB, and three had CNS-TB
Summary
In the absence of an efficient diagnostic modality for Tuberculosis [TB], the search for a tool that can overcome the dilemmas of the available diagnostic tests continues. In the wake of continued reports of high mortality and morbidity due to TB, WHO approved GeneXpert MTB/ RIF [Cepheid, Sunnyvale, CA, USA] in 2011 and recommended it for rapid implementation [1]. Gandhi et al reported that in a cohort of HIV-MDR-TB patients, 50% died before the culture/drug susceptibility testing [DST] report was generated [5]. It is towards this goal that rapid molecular diagnostics offering great promise have been developed [6]. WHO recommended use of GeneXpert MTB/RIF [Xpert] for Extra-pulmonary [EP] TB; critics have since questioned its efficiency
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