Comparison of Xpert MTB/RIF Assay and GenoType MTBDR<i>plus</i> DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in <i>Mycobacterium tuberculosis</i>

<div><p>Background</p><p>GeneXpert MTB/RIF (Xpert) and Genotype MTBDR<i>plus</i> (DR<i>plus</i>) are two World Health Organization (WHO) endorsed probe based molecular drug susceptibility testing (DST) methods for rapid diagnosis of drug resistant tuberculosis. Both methods target the same 81 bp Rifampicin Resistance Determining Region (RRDR) of bacterial RNA polymerase β subunit (<i>rpoB</i>) for detection of Rifampicin (RIF) resistance associated mutations using DNA probes. So there is a correspondence of the probes of each other and expected similarity of probe binding.</p><p>Methods</p><p>We analyzed 92 sputum specimens by Xpert, DR<i>plus</i> and LJ proportion method (LJ-DST). We compared molecular DSTs with gold standard LJ-DST. We wanted to see the agreement level of two molecular methods for detection of RIF resistance associated mutations. The 81bp RRDR region of <i>rpoB</i> gene of discrepant cases between the two molecular methods was sequenced by Sanger sequencing.</p><p>Results</p><p>The agreement of Xpert and DR<i>plus</i> with LJ-DST for detection of RIF susceptibility was found to be 93.5% and 92.4%, respectively. We also found 92.4% overall agreement of two molecular methods for the detection of RIF susceptibility. A total of 84 out of 92 samples (91.3%) had agreement on the molecular locus of RRDR mutation by DR<i>plus</i> and Xpert. Sanger sequencing of 81bp RRDR revealed that Xpert probes detected seven of eight discrepant cases correctly and DR<i>plus</i> was erroneous in all the eight cases.</p><p>Conclusion</p><p>Although the overall concordance with LJ-DST was similar for both Xpert and DR<i>plus</i> assay, Xpert demonstrated more accuracy in the detection of RIF susceptibility for discrepant isolates compared with DR<i>plus</i>. This observation would be helpful for the improvement of probe based detection of drug resistance associated mutations especially <i>rpoB</i> mutation in <i>M</i>. <i>tuberculosis</i>.</p>