title: Utility of polymerase chain reaction in diagnosis of tuberculosis in our setup: a ten years experience.
abstract: OBJECTIVE
  To evaluate the yield of polymerase chain reaction (PCR) for detection of Mycobacterium tuberculosis from different clinical specimens.
  
  
  METHODS
  Observational study.
  
  
  METHODS
  Department of Microbiology, Armed Forces Institute of Pathology, Rawalpindi, from January 2001 to December 2010.
  
  
  METHODS
  Different clinical specimens received for Mycobacterium tuberculosis PCR were dealt during the study period. Contaminated samples like sputum were processed by the standard N-acetyl L-cysteine (NALC)-NaOH method. PCR protocols were followed as per manufacturer's manual. PCR was performed using a Thermal Cycler (Master Cycler, Eppendorf, Germany): an initial denaturation step at 94°C for 3 minutes was followed by 40 cycles of denaturation at 94°C for 30 seconds, annealing at 60°C for 30 seconds and extension at 72°C for 30 seconds and a final extension at 72°C for 7 minutes. The products were held at 4°C and later run on 1% agarose gel, stained with Ethidium bromide and visualized in ultraviolet (UV) transilluminator.
  
  
  RESULTS
  Out of a total 4620 samples for PCR, 299 were positive for Mycobacterium tuberculosis (6.5%). The percentage of samples from male patients were 63.2%. The mean age of patients was 38+11.5 years. Blood was the most frequent specimen received for PCR (46.66%), followed by body fluids (18.41%) and CSF (10.64%). Yield for different clinical samples was 63/471 for sputum (13.4%), 3/29 for endobronchial washings (10.3%), 59/851 for body fluids (6.9%) and 24/400 for urine (6%). Positive yield from blood was the lowest (101/2156, 4.7%).
  
  
  CONCLUSIONS
  PCR for Mycobacterium tuberculosis is a rapid and reliable method for the diagnosis of both pulmonary and extrapulmonary tuberculosis. The highest positive yield was obtained from sputum and lowest from blood specimens.
authors.affiliation: Department of Pathology, Combined Military Hospital, Nowshera. docfaisal@msn.com
authors.forename: Faisal
authors.initials: F
authors.lastname: Hanif
authors.forename: Aamer
authors.initials: A
authors.lastname: Ikram
authors.forename: Luqman
authors.initials: L
authors.lastname: Satti
authors.forename: Muhammad
authors.initials: M
authors.lastname: Roshan
authors.forename: Shahid Ahmad
authors.initials: SA
authors.lastname: Abbasi
mesh_terms: D000328:Adult; D017677:Age Distribution; D015331:Cohort Studies; D004269:DNA, Bacterial / Q000032:analysis; D003906:Developing Countries; D005260:Female; D006801:Humans; D015994:Incidence; D008297:Male; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000302:isolation & purification*; D010154:Pakistan / Q000453:epidemiology; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000706:statistics & numerical data; D012189:Retrospective Studies; D018570:Risk Assessment; D017678:Sex Distribution; D013048:Specimen Handling; D013997:Time Factors; D014376:Tuberculosis / Q000097:blood / Q000175:diagnosis* / Q000453:epidemiology
chemical_list: D004269:DNA, Bacterial