title: Performance of the G4 Xpert®MTB/RIF assay for the detection of Mycobacterium tuberculosis and rifampin resistance: a retrospective case-control study of analytical and clinical samples from high- and low-tuberculosis prevalence settings.
abstract: BACKGROUND
  The Xpert®MTB/RIF (Xpert) assay is a rapid PCR-based assay for the detection of Mycobacterium tuberculosis complex DNA (MTBc) and mutations associated with rifampin resistance (RIF). An updated version introduced in 2011, the G4 Xpert, included modifications to probe B and updated analytic software.
  
  
  METHODS
  An analytical study was performed to assess Xpert detection of mutations associated with rifampin resistance in rifampin-susceptible and -resistant isolates. A clinical study was performed in which specimens from US and non-US persons suspected of tuberculosis (TB) were tested to determine Xpert performance characteristics. All specimens underwent smear microscopy, mycobacterial culture, conventional drug-susceptibility testing and Xpert testing; DNA from isolates with discordant rifampin resistance results was sequenced.
  
  
  RESULTS
  Among 191 laboratory-prepared isolates in the analytical study, Xpert sensitivity for detection of rifampin resistance associated mutations was 97.7% and specificity was 90.8%, which increased to 99.0% after DNA sequencing analysis of the discordant samples. Of the 1,096 subjects in the four clinical studies, 49% were from the US. Overall, Xpert detected MTBc in 439 of 468 culture-positive specimens for a sensitivity of 93.8% (95% confidence interval [CI]: 91.2%-95.7%) and did not detect MTBc in 620 of 628 culture-negative specimens for a specificity of 98.7% (95% CI: 97.5%-99.4%). Sensitivity was 99.7% among smear-positive cases, and 76.1% among smear-negative cases. Non-determinate MTBc detection and false-positive RIF resistance results were low (1.2 and 0.9%, respectively).
  
  
  CONCLUSIONS
  The updated Xpert assay retained the high sensitivity and specificity of the previous assay versions and demonstrated low rates of non-determinate and RIF resistance false positive results.
authors.affiliation: Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, MSB I-689, Newark, NJ, 07103, USA. Dharannj@njms.rutgers.edu.
authors.forename: Nila J
authors.initials: NJ
authors.lastname: Dharan
authors.affiliation: Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, MSB I-689, Newark, NJ, 07103, USA.|Current address: Sackler School of Graduate Biomedical Science - Tufts University, Boston, MA, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Blakemore
authors.affiliation: University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Sloutsky
authors.affiliation: University of Massachusetts Medical School, Worcester, MA, USA.
authors.forename: Devinder
authors.initials: D
authors.lastname: Kaur
authors.affiliation: Orange County Health Care Agency, Santa Ana, CA, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Alexander
authors.affiliation: Orange County Health Care Agency, Santa Ana, CA, USA.
authors.forename: Minoo
authors.initials: M
authors.lastname: Ghajar
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY, USA.
authors.forename: Kimberlee A
authors.initials: KA
authors.lastname: Musser
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, NY, USA.
authors.forename: Vincent E
authors.initials: VE
authors.lastname: Escuyer
authors.affiliation: Florida Department of Health, Jacksonville, FL, USA.
authors.forename: Marie-Claire
authors.initials: MC
authors.lastname: Rowlinson
authors.affiliation: Florida Department of Health, Jacksonville, FL, USA.
authors.forename: Susanne
authors.initials: S
authors.lastname: Crowe
authors.affiliation: Clínica y Laboratorio de Tuberculosis, Hospital General Tijuana, Tijuana, Mexico.
authors.forename: Rafael
authors.initials: R
authors.lastname: Laniado-Laborin
authors.affiliation: Foundation for Innovative New Diagnostics, Geneva, Switzerland.
authors.forename: Eloise
authors.initials: E
authors.lastname: Valli
authors.affiliation: Foundation for Innovative New Diagnostics, Geneva, Switzerland.
authors.forename: Pamela
authors.initials: P
authors.lastname: Nabeta
authors.affiliation: Cepheid, Sunnyvale, CA, USA.
authors.forename: Pamela
authors.initials: P
authors.lastname: Johnson
authors.affiliation: Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 South Orange Avenue, MSB I-689, Newark, NJ, 07103, USA. Allandda@njms.rutgers.edu.
authors.forename: David
authors.initials: D
authors.lastname: Alland
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000904:Antibiotics, Antitubercular; D001681:Biological Assay; D016022:Case-Control Studies; D004269:DNA, Bacterial / Q000032:analysis; D003906:Developing Countries; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D005189:False Positive Reactions; D005260:Female; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods; D015995:Prevalence; D012189:Retrospective Studies; D012293:Rifampin; D012680:Sensitivity and Specificity; D014376:Tuberculosis / Q000175:diagnosis* / Q000453:epidemiology / Q000382:microbiology; D014481:United States / Q000453:epidemiology; D055815:Young Adult
chemical_list: D000904:Antibiotics, Antitubercular; D004269:DNA, Bacterial; D012293:Rifampin
keywords: Diagnostics; G4; GeneXpert; Tuberculosis; Xpert