title: Comparison of Xpert MTB/RIF Assay and GenoType MTBDRplus DNA Probes for Detection of Mutations Associated with Rifampicin Resistance in Mycobacterium tuberculosis.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: Arfatur
authors.initials: A
authors.lastname: Rahman
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: Mahfuza
authors.initials: M
authors.lastname: Sahrin
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: Sadia
authors.initials: S
authors.lastname: Afrin
authors.affiliation: Oregon Health and Science University, Portland, United States of America.
authors.forename: Keith
authors.initials: K
authors.lastname: Earley
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: Shahriar
authors.initials: S
authors.lastname: Ahmed
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: S M Mazidur
authors.initials: SM
authors.lastname: Rahman
authors.affiliation: International Center for Diarrheal Disease Research, Dhaka, Bangladesh.
authors.forename: Sayera
authors.initials: S
authors.lastname: Banu
mesh_terms: D000995:Antitubercular Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D015342:DNA Probes; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics*; D054908:Extensively Drug-Resistant Tuberculosis / Q000188:drug therapy / Q000382:microbiology*; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D012293:Rifampin / Q000494:pharmacology*; D013183:Sputum / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D015342:DNA Probes; C505805:rpoB protein, Mycobacterium tuberculosis; D012321:DNA-Directed RNA Polymerases; D012293:Rifampin