Comparison of Xpert MTB/RIF Assay and GenoType MTBDRplus DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis

• Published in: PloS one Vol. 11; no. 4; p. e0152694
• Main Authors: Rahman, Arfatur, Sahrin, Mahfuza, Afrin, Sadia, Earley, Keith, Ahmed, Shahriar, Rahman, S M Mazidur, Banu, Sayera
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 07.04.2016; Public Library of Science (PLoS)
• Subjects: Antimicrobial agents; Antitubercular Agents - pharmacology; Bacteria; Bacterial Proteins - genetics; Biology and Life Sciences; Chemotherapy; Comparative analysis; Deoxyribonucleic acid; Disease; DNA; DNA Mutational Analysis - methods; DNA Probes; DNA sequencing; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; Drug resistance; Drug Resistance, Bacterial - drug effects; Drug Resistance, Bacterial - genetics; Extensively Drug-Resistant Tuberculosis - drug therapy; Extensively Drug-Resistant Tuberculosis - microbiology; Gene mutation; Genetic aspects; Genotype & phenotype; Genotypes; Health surveillance; Humans; Hybridization; Medical screening; Medicine and Health Sciences; Microbial Sensitivity Tests - methods; Mutation; Mycobacterium; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Physiological aspects; Probes; Public health; Research and Analysis Methods; Ribonucleic acid; Rifampin; Rifampin - pharmacology; RNA; RNA polymerase; RpoB protein; Sputum; Sputum - microbiology; Test procedures; Tuberculosis; United States; Bangladesh; China; Pakistan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0152694

GeneXpert MTB/RIF (Xpert) and Genotype MTBDRplus (DRplus) 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 (rpoB) 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. We analyzed 92 sputum specimens by Xpert, DRplus 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 rpoB gene of discrepant cases between the two molecular methods was sequenced by Sanger sequencing. The agreement of Xpert and DRplus 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 DRplus and Xpert. Sanger sequencing of 81bp RRDR revealed that Xpert probes detected seven of eight discrepant cases correctly and DRplus was erroneous in all the eight cases. Although the overall concordance with LJ-DST was similar for both Xpert and DRplus assay, Xpert demonstrated more accuracy in the detection of RIF susceptibility for discrepant isolates compared with DRplus. This observation would be helpful for the improvement of probe based detection of drug resistance associated mutations especially rpoB mutation in M. tuberculosis.