title: Genotypic, Phenotypic and Clinical Validation of GeneXpert in Extra-Pulmonary and Pulmonary Tuberculosis in India.
abstract: BACKGROUND
  Newer molecular diagnostics have brought paradigm shift in early diagnosis of tuberculosis [TB]. WHO recommended use of GeneXpert MTB/RIF [Xpert] for Extra-pulmonary [EP] TB; critics have since questioned its efficiency.
  
  
  METHODS
  The present study was designed to assess the performance of GeneXpert in 761 extra-pulmonary and 384 pulmonary specimens from patients clinically suspected of TB and compare with Phenotypic, Genotypic and Composite reference standards [CRS].
  
  
  RESULTS
  Comparison of GeneXpert results to CRS, demonstrated sensitivity of 100% and 90.68%, specificity of 100% and 99.62% for pulmonary and extra-pulmonary samples. On comparison with culture, sensitivity for Rifampicin [Rif] resistance detection was 87.5% and 81.82% respectively, while specificity was 100% for both pulmonary and extra-pulmonary TB. On comparison to sequencing of rpoB gene [Rif resistance determining region, RRDR], sensitivity was respectively 93.33% and 90% while specificity was 100% in both pulmonary and extra-pulmonary TB. GeneXpert assay missed 533CCG mutation in one sputum and dual mutation [517 & 519] in one pus sample, detected by sequencing. Sequencing picked dual mutation [529, 530] in a sputum sample sensitive to Rif, demonstrating, not all RRDR mutations lead to resistance.
  
  
  CONCLUSIONS
  Current study reports observations in a patient care setting in a high burden region, from a large collection of pulmonary and extra-pulmonary samples and puts to rest questions regarding sensitivity, specificity, detection of infrequent mutations and mutations responsible for low-level Rif resistance by GeneXpert. Improvements in the assay could offer further improvement in sensitivity of detection in different patient samples; nevertheless it may be difficult to improve sensitivity of Rif resistance detection if only one gene is targeted. Assay specificity was high both for TB detection and Rif resistance detection. Despite a few misses, the assay offers major boost to early diagnosis of TB and MDR-TB, in difficult to diagnose pauci-bacillary TB.
authors.affiliation: Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Urvashi B
authors.initials: UB
authors.lastname: Singh
authors.affiliation: Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Pooja
authors.initials: P
authors.lastname: Pandey
authors.affiliation: Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Girija
authors.initials: G
authors.lastname: Mehta
authors.affiliation: Rajan Babu Institute for Pulmonary Medicine and Tuberculosis, Delhi, India.
authors.forename: Anuj K
authors.initials: AK
authors.lastname: Bhatnagar
authors.affiliation: Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Anant
authors.initials: A
authors.lastname: Mohan
authors.affiliation: Department of Neurology, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Vinay
authors.initials: V
authors.lastname: Goyal
authors.affiliation: Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Vineet
authors.initials: V
authors.lastname: Ahuja
authors.affiliation: WHO, Country Office for India, New Delhi, India.
authors.forename: Ranjani
authors.initials: R
authors.lastname: Ramachandran
authors.affiliation: Central TB Division, Government of India, New Delhi, India.
authors.forename: Kuldeep S
authors.initials: KS
authors.lastname: Sachdeva
authors.affiliation: Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Jyotish C
authors.initials: JC
authors.lastname: Samantaray
mesh_terms: D000293:Adolescent; D000328:Adult; D000995:Antitubercular Agents / Q000494:pharmacology; D058491:Bacterial Load; D024881:Drug Resistance, Bacterial; D005260:Female; D005838:Genotype; D006801:Humans; D007194:India; D008297:Male; D008826:Microbial Sensitivity Tests / Q000379:methods / Q000592:standards; D008875:Middle Aged; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics*; D010641:Phenotype; D011446:Prospective Studies; D012015:Reference Standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013183:Sputum / Q000382:microbiology; D014376:Tuberculosis / Q000175:diagnosis* / Q000382:microbiology*; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis* / Q000382:microbiology*; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents