title: Comparative Study of GeneXpert with ZN Stain and Culture in Samples of Suspected Pulmonary Tuberculosis.
abstract: BACKGROUND
  Tuberculosis remains one of the deadliest communicable diseases. There are number of tests available for the diagnosis of tuberculosis but conventional microscopy has low sensitivity and culture although gold standard, but takes longer time for positivity. On the other side, Nucleic acid amplification techniques due to its rapidity and sensitivity not only help in early diagnosis and management of tuberculosis especially in patients with high clinical suspicion like immunocompromised patients, history of contact with active tuberculosis patient etc., but also curtail the transmission of the disease.
  
  
  OBJECTIVE
  To evaluate the sensitivity, specificity, positive predictive value and negative predictive value of Nucleic acid amplification assay (GeneXpert) using respiratory samples in patients with suspected pulmonary tuberculosis and compare with AFB smear microscopy (Ziehl Neelsen stain) and Acid Fast Bacilli (AFB) culture.
  
  
  METHODS
  We retrospectively reviewed the respiratory samples of suspected pulmonary tuberculosis (including Bronchoalveolar lavage and sputum) of 170 patients from Jan 2015 to Nov 2015 for ZN stain, culture and GeneXpert (Xpert(®) MTB/Rif assay). The sensitivity, specificity, PPV and NPV of GeneXpert and ZN microscopy were calculated using Liquid culture of Mycobacterium tuberculosis as gold standard.
  
  
  RESULTS
  A total of 170 patient samples were evaluated in final analysis. Of these, 14 samples were positive by all three methods used in our study. The overall sensitivity, specificity, PPV and NPV of GeneXpert were 86.8%, 93.1%, 78.5% and 96% respectively and for BAL sample, 81.4%, 93.4%, 73.3% and 95.7% respectively. The overall sensitivity and specificity of AFB smear microscopy were 22.2%, % and 78.5% respectively and for BAL sample 22.2% and 100% respectively. For AFB negative samples sensitivity and specificity were 79.1% and 93.1% respectively.
  
  
  CONCLUSIONS
  GeneXpert has a higher sensitivity than AFB smear microscopy in respiratory samples. GeneXpert can be a useful tool for early diagnosis of patients with high clinical suspicion of pulmonary tuberculosis. Positive GeneXpert, but culture negative results should be read cautiously and be well correlated with clinical and treatment history of the patient. The other major advantage of Gene Xpert is that it simultaneously detects Rifampicin resistance and especially beneficial in patient with MDR and HIV associated tuberculosis and should be studied further.
authors.affiliation: Consultant Microbiologist, Department of Microbiology, Oncquest Laboratories Limited , New Delhi, India .
authors.forename: Monika
authors.initials: M
authors.lastname: Agrawal
authors.affiliation: Junior Consultant Microbiologist, Department of Microbiology, Oncquest Laboratories Limited , New Delhi, India .
authors.forename: Ashish
authors.initials: A
authors.lastname: Bajaj
authors.affiliation: Manager Molecular Biology, Department of Molecular Biology, Oncquest Laboratories Limited , New Delhi, India .
authors.forename: Vinay
authors.initials: V
authors.lastname: Bhatia
authors.affiliation: Director, Department of Molecular Biology and R&D, Oncquest Laboratories Limited , New Delhi, India .
authors.forename: Sarjana
authors.initials: S
authors.lastname: Dutt
keywords: Acid fast bacilli; Bronchoalveolar lavage; Smear microscopy; Sputum