title: Genotype MTBDRsl line probe assay shortens time to diagnosis of extensively drug-resistant tuberculosis in a high-throughput diagnostic laboratory.
abstract: BACKGROUND
  Conventional culture-based drug susceptibility testing (DST) for the second-line antituberculosis drugs is slow, leading to diagnostic delay with associated exacerbation of transmission, amplification of resistance, and increased mortality.
  
  
  OBJECTIVE
  To assess the diagnostic performance of the GenoType MTBDRsl line probe assay (LPA) for the rapid detection of mutations conferring resistance to ofloxacin (OFX), amikacin (AMK), and ethambutol and to determine the impact of implementation on the turnaround time in a high-throughput diagnostic laboratory.
  
  
  METHODS
  Six hundred and fifty-seven direct patient acid-fast bacilli smear-positive specimens resistant to isoniazid, rifampin, or both according to the GenoType MTBDRplus assay were consecutively tested, using the GenoType MTBDRsl LPA. The diagnostic performance was assessed relative to the "gold standard" culture-based method, and the laboratory turnaround times for both methods were determined.
  
  
  RESULTS
  A total of 516 of 657 patient specimens had valid results for both tests. The sensitivity for detecting OFX, AMK, and extensive drug resistance, using the GenoType MTBDRsl LPA, was 90.7% (95% confidence interval [CI], 80.1-96.0%), 100% (95% CI, 91.8-100%), and 92.3% (95% CI, 75.9-97.9%), respectively, and the specificity for detection was 98.1% (95% CI, 96.3-99.0%), 99.4% (95% CI, 98.2-99.8%), and 99.6% (95% CI, 98.5-99.9%), respectively. Implementation of this test significantly reduced the turnaround time by 93.3% (P < 0.001), calculated from the date that the specimen was received at the laboratory to reporting second-line results. In addition, a significant increase in diagnostic yield of 20.1% and 19.3% (P < 0.001) for OFX and AMK resistance, respectively, was obtained for isolates that were either contaminated or had lost viability.
  
  
  CONCLUSIONS
  The GenoType MTBDRsl LPA is a rapid and reliable DST that can be easily incorporated into the diagnostic algorithm. This assay significantly improved diagnostic yield (P < 0.001) while simultaneously decreasing diagnostic delay for reporting second-line DST. The rapid dissemination of second-line DST results will guide initiation of appropriate treatment, thereby reducing transmission and improving treatment outcome.
authors.affiliation: National Health Laboratory Service (NHLS), Tuberculosis Reference Laboratory, Green Point, Cape Town, South Africa.
authors.forename: Marinus
authors.initials: M
authors.lastname: Barnard
authors.forename: Rob
authors.initials: R
authors.lastname: Warren
authors.forename: Nico
authors.initials: N
authors.lastname: Gey Van Pittius
authors.forename: Paul
authors.initials: P
authors.lastname: van Helden
authors.forename: Marlein
authors.initials: M
authors.lastname: Bosman
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Streicher
authors.forename: Gerrit
authors.initials: G
authors.lastname: Coetzee
authors.forename: Richard
authors.initials: R
authors.lastname: O'Brien
mesh_terms: D000583:Amikacin; D000995:Antitubercular Agents; D024901:Drug Resistance, Multiple, Bacterial / Q000187:drug effects / Q000235:genetics; D004977:Ethambutol; D054908:Extensively Drug-Resistant Tuberculosis / Q000175:diagnosis / Q000235:genetics* / Q000382:microbiology; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D015242:Ofloxacin; D010430:Pentosyltransferases / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D012293:Rifampin; D012680:Sensitivity and Specificity; D013019:South Africa; D013183:Sputum / Q000382:microbiology; D013997:Time Factors
chemical_list: D000995:Antitubercular Agents; D005819:Genetic Markers; D000583:Amikacin; D004977:Ethambutol; D015242:Ofloxacin; C540269:EmbB protein, Mycobacterium tuberculosis; D010430:Pentosyltransferases; D012293:Rifampin