Genotypic, Phenotypic and Clinical Validation of GeneXpert in Extra-Pulmonary and Pulmonary Tuberculosis in India

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.

A Three-Year Experience with GeneXpert MTB/RIF Assay in Tuberculosis Control Programme (RNTCP)- A Clinical Study

“…Despite a few misses, the assay offers major boost to early diagnosis of TB and MDR-TB, in difficult to diagnose pauci-bacillary TB. [15] The Xpert MTB/RIF assay demonstrated a high capability to detect MTBC DNA in AFB microscopy-negative samples of pulmonary and extrapulmonary origin. With the exception of a specimen harbouring a mixed MTBC population, the assay correctly retrieved information from the rpoB hot spot region regarding RMP resistance.…”

Making a Positive Diagnosis of Intestinal Tuberculosis with the Aid of New Biologic and Histologic Features: How Far Have We Reached?

“…Thus, the advantage of the Gene Xpert assay is achievement of a rapid diagnosis at a point of care and additional information about drug resistance, rather than an additional yield. An Indian study [35] included pulmonary ( n = 384) and extrapulmonary ( n = 761) samples. Among the latter, the sensitivity of the Gene Xpert assay was 88% and its specificity was 91%.…”

GeneXpert MTB/RIF Assay: A Revolutionizing Method for Rapid Molecular Detection of Mycobacterium Tuberculosis in Comparison to Other Conventional Methods

“…Furthermore, Singh et al, 2016, demonstrated a sensitivity of 100% and specificity of 100% for pulmonary samples by using GeneXpert assay. In addition, Agrawal et al, 2016, reported that the sensitivity and specificity of GeneXpert in sputum were 100% and 90% that is compatible with the study of Sharma et al, 2015who found a sensitivity of 96.9% and a specificity of 99.8%.…”