title: Using likelihood ratios to estimate diagnostic accuracy of a novel multiplex nested PCR in extra-pulmonary tuberculosis.
abstract: METHODS
  A tertiary care centre in Mumbai with a referral bias towards treatment failures.
  
  
  OBJECTIVE
  To standardise and evaluate a novel single tube multiplex nested polymerase chain reaction (PCR) targeting insertion sequence (IS) 6110, mpb64, rrs and rpoB  genes for rapid diagnosis of extra-pulmonary tuberculosis (EPTB).
  
  
  METHODS
  The PCR assay was evaluated among 489 consecutive consenting patients, and results were compared against a composite reference standard comprising smear microscopy, culture, clinical symptoms, radiological scan and  histology.
  
  
  RESULTS
  PCR assay reported a pooled sensitivity of 94.5% (242/256, 95%CI 91-97): 91.9% (125/136, 95%CI 86-96) for smear-negative composite reference standard (CRS) positive cases and 97.5% (117/120, 95%CI 93-99) for smear-positive CRS-positive cases. The PCR  positivity rate increased from 91.7% (235/256, 95%CI 88-95) when presence of IS6110 was considered alone for reporting a test as positive to 94.5% (242/256, 95%CI 91-97) when used in combination with other three gene targets, with a specificity of 96.4% (212/220, 95%CI 93-98).  A positive likelihood ratio of 26 (95%CI 13-51) and a negative likelihood ratio of 0.06 (95%CI 0.03-0.09) makes the test useful for ruling out and ruling in the disease.
  
  
  CONCLUSIONS
  Culture should not be replaced by PCR as a gold standard; however, PCR can be used as a rapid,  accurate tool in the diagnosis of EPTB.
authors.affiliation: P. D. Hinduja National Hospital and Medical Research Centre, Mahim, Mumbai, India.
authors.forename: V
authors.initials: V
authors.lastname: Vadwai
authors.forename: A
authors.initials: A
authors.lastname: Shetty
authors.forename: C
authors.initials: C
authors.lastname: Rodrigues
mesh_terms: D004269:DNA, Bacterial / Q000032:analysis*; D003937:Diagnosis, Differential; D006801:Humans; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D015203:Reproducibility of Results; D014376:Tuberculosis / Q000175:diagnosis* / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial