title: Performance evaluation of three commercial molecular assays for the detection of Mycobacterium tuberculosis from clinical specimens in a high TB-HIV-burden setting.
abstract: BACKGROUND
  A major challenge faced by countries with a high burden of tuberculosis (TB) is early detection especially in individuals with paucibacillary disease which is common in HIV endemic settings. Remarkable efforts have been made globally to accelerate the development and expansion of new diagnostic technologies that allow better and earlier diagnosis of active tuberculosis particularly directly from clinical specimens with a few commercial options available. These include GenoType MTBDRplus Version 2.0 (Hain Lifescience), Xpert® MTB/RIF (Cepheid) and Anyplex™ plus MTB/NTM/DR-TB Real-time detection (Seegene). We evaluated the diagnostic performance of these three commercial molecular assays for the detection of Mycobacterium tuberculosis complex from clinical specimens in a high TB-HIV-burden setting.
  
  
  METHODS
  This was a retrospective laboratory-based study using stored remnant sediments from clinical specimens of presumptive pulmonary TB cases. A stratified sample of smear positive TB, smear negative TB and TB culture negatives was included. All the samples were tested on the three molecular assays following the manufacturers' instructions; except for Anyplex™plus, for which DNA extraction was performed using the NucliSENS® easyMAG® platform (bioMerieux). Samples were also processed for liquid TB culture and time-to-culture positivity was recorded.
  
  
  RESULTS
  Of the 90 sediments processed, 81 were analyzable across all three systems. The overall sensitivity was highest for Xpert® MTB/RIF (89.1%) followed by GenoType MTBDRplus (70.9%) and Anyplex™ plus (65.5%). The specificity and sensitivity in smear positive cases was comparable across all systems. There was a significant difference in sensitivity between Xpert® MTB/RIF and the other two assays for smear-negative cases (P < 0.05). The performance in cases where the time-to-culture positivity was ≥ 20 days was also significantly poorer for both Anyplex™ plus and GenoType MTBDRplus compared to Xpert® MTB/RIF (P < 0.05). Xpert® MTB/RIF achieved 100% specificity, while Anyplex™ plus and GenoType MTBDRplus achieved 96.2 and 92.3% respectively.
  
  
  CONCLUSIONS
  The Xpert® MTB/RIF was superior to the other two assays for the detection of TB in smear negative specimens notably when bacterial loads are very low in sputum. It is important that studies reporting on test performance stratify their results by time-to-culture positivity to accurately assess clinical performance especially in high HIV settings.
authors.affiliation: Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. mashofong@yahoo.com.|National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa. mashofong@yahoo.com.
authors.forename: M M Z
authors.initials: MM
authors.lastname: Matabane
authors.affiliation: Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. farzana.ismail@up.ac.za.|National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa. farzana.ismail@up.ac.za.
authors.forename: F
authors.initials: F
authors.lastname: Ismail
authors.affiliation: Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. strydom.kathy@gmail.com.|National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa. strydom.kathy@gmail.com.
authors.forename: K A
authors.initials: KA
authors.lastname: Strydom
authors.affiliation: National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa. oonwuegbuna@gmail.com.
authors.forename: O
authors.initials: O
authors.lastname: Onwuegbuna
authors.affiliation: National Institute for Communicable Diseases: Centre for Tuberculosis, Johannesburg, South Africa. shaheedvo@nicd.ac.za.
authors.forename: S V
authors.initials: SV
authors.lastname: Omar
authors.affiliation: Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. naziri@nicd.ac.za.|National Institute for Communicable Diseases: Centre for Tuberculosis, Johannesburg, South Africa. naziri@nicd.ac.za.
authors.forename: N
authors.initials: N
authors.lastname: Ismail
mesh_terms: D058491:Bacterial Load / Q000235:genetics; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000382:microbiology; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity; D057089:Pathology, Molecular / Q000379:methods*; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D013019:South Africa; D013183:Sputum / Q000382:microbiology; D014376:Tuberculosis / Q000453:epidemiology / Q000382:microbiology*; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis / Q000382:microbiology