title: Comparison of two molecular methods and an automated liquid culture system for the early detection of Mycobacterium tuberculosis from both pulmonary and extrapulmonary specimens in Kuwait.
abstract: OBJECTIVE
  Molecular methods for the detection of Mycobacterium tuberculosis (MTB) are widely used for the early diagnosis of tuberculosis (TB). The objectives of this study were to evaluate the performance of two molecular techniques for the detection of MTB for both pulmonary and extrapulmonary specimens in comparison with conventional culture techniques in Kuwait and to correlate the results with clinical and histopathological diagnosis.
  
  
  METHODS
  A total of 9,594 consecutive pulmonary (n=5,597) and extrapulmonary (n=3,997) specimens received by the Kuwait National TB Reference Laboratory from November 2011 to December 2015 were processed for direct smear microscopy for acid-fast bacilli using a Zhiel-Neelsen stain, Xpert MTB/RIF assay, ProbTec polymerase chain reaction (PCR), and growth in fully automated MGIT 960 system tubes. The clinical and histopathological diagnoses were correlated with the results.
  
  
  RESULTS
  For pulmonary specimens, the overall sensitivity and specificity of both molecular methods together were 90.7% and 99.7%, respectively. The sensitivity and specificity of the Xpert MTB/RIF assay were 90.1% and 99.4%, respectively. The sensitivity and specificity of ProbTec PCR were 86% and 99.6%, respectively. For extrapulmonary specimens, the overall sensitivity and specificity of both molecular methods together were 87% and 97.8%, respectively. The sensitivity and specificity of Xpert MTB/RIF assay were 89.5% and 97.2%, respectively. The sensitivity and specificity of ProbTec PCR were 73% and 97.8%, respectively. When clinical and histopathological correlations were made with the assumed false-positive results from both molecular methods, the corrected sensitivity and specificity for pulmonary specimens were 91% and 99.9%, respectively, and 89.6% and 99.8% for extrapulmonary specimens, respectively.
  
  
  CONCLUSIONS
  The performance of the Xpert MTB/RIF assay was superior to ProbTec PCR for the early detection of MTB from both pulmonary and extrapulmonary specimens.
authors.affiliation: Department of Microbiology, Faculty of Medicine, Kuwait University; Kuwait National TB Reference Laboratory, Kuwait. Electronic address: e.mokaddas@hsc.edu.kw.
authors.forename: E M
authors.initials: EM
authors.lastname: Mokaddas
authors.affiliation: Kuwait National TB Reference Laboratory, Kuwait.
authors.forename: H
authors.initials: H
authors.lastname: Saadaldeen
authors.affiliation: Department of Microbiology, Faculty of Medicine, Kuwait University.
authors.forename: S
authors.initials: S
authors.lastname: Ahmad
keywords: Extrapulmonary; GeneXpert TB/REF; Mycobacterium tuberculosis; ProbTec; Pulmonary