title: Diagnosis of Pulmonary Tuberculosis and Detection of Resistance to Rifampin and Isoniazid through Direct Molecular Methods in Stool Samples.
abstract: BACKGROUND
  Tuberculosis (TB) is an infectious disease that is caused by Mycobacterium tuberculosis (M.tb). TB has high morbidity and mortality around the world.
  
  
  OBJECTIVE
  To evaluate molecular-based methods performed directly on stool samples for the diagnosis of pulmonary tuberculosis (PTB) and to determine the susceptibility to Rifampicin (RMP) and Isoniazid (INH).
  
  
  METHODS
  This is a descriptive study evaluating the performance of the PCR-based method for direct PTB diagnosis and to determine the susceptibility of RMP and INH using stool samples from PTB patients. The study was conducted between March 2011 and March 2014.
  
  
  METHODS
  Three stool samples and three sputum samples (n=300 stool and 300 sputum) were collected from 100 PTB patients (75 pretreatment and 25 follow up). Stool samples (n=60) were also collected from 20 healthy individuals to serve as controls. DNA was extracted from stool samples using Chelex®-100. PTB was diagnosed using a Genekam®kit. RMP and INH susceptibility testing was performed using the Genotype MTBDRplus®assay. The sputum Lowenstein Jensen (LJ) culture and agar proportion method (PM) of drug susceptibility testing for INH and RMP were considered to be the gold standard methods for comparing the results of the molecular methods.
  
  
  RESULTS
  The Genekam kit showed 100% sensitivity and 95.24% specificity for diagnosing new patients and showed 100% sensitivity and 80% specificity for follow-up patients. The Genotype MTBDR-plus assay showed 86.4% and 100% sensitivity and 98.1% and 97.8% specificity for determining INH and RMP sensitivity, respectively, in newly diagnosed patients and 85.7% and 94.4% sensitivity and specificity, respectively, for both INH and RMP in follow-up patients.
  
  
  CONCLUSIONS
  Molecular-based methods are promising techniques for the diagnosis and susceptibility testing of PTB when the ease of sample collection and the speed of diagnosis are taken into consideration. However, they are not as useful for assessing follow-up patients.
authors.affiliation: Department of Medical Laboratory Technology, College of Applied Medical Science, University of Hafr Albatin, Hafr Al Batin, Saudi Arabia.
authors.forename: Sulaiman Ali Al
authors.initials: SA
authors.lastname: Yousef
authors.affiliation: Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia kabdelraheem@ksu.edu.sa khalidfp7@gmail.com.|Botany Department, Faculty of Science, Sohag University, Sohag, Egypt.
authors.forename: Khalid Abdullah Ali
authors.initials: KA
authors.lastname: AbdelRahim
authors.affiliation: Department of Clinical Pathology, Clinical Microbiology Unit, Faculty of Medicine, Assiut University Hospital, Egypt.
authors.forename: Asmaa O
authors.initials: AO
authors.lastname: Ahmed
authors.affiliation: Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Khalid Salmeen
authors.initials: KS
authors.lastname: Almaary
authors.affiliation: Department of Medical Laboratory Technology, College of Applied Medical Science, University of Hafr Albatin, Hafr Al Batin, Saudi Arabia.
authors.forename: Ahmed Mohamed Ali
authors.initials: AM
authors.lastname: Mohamed
mesh_terms: D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D002648:Child; D005243:Feces / Q000382:microbiology*; D005260:Female; D006801:Humans; D007538:Isoniazid / Q000627:therapeutic use*; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction / Q000379:methods*; D012293:Rifampin / Q000627:therapeutic use*; D018088:Tuberculosis, Multidrug-Resistant / Q000175:diagnosis* / Q000188:drug therapy* / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis* / Q000188:drug therapy* / Q000382:microbiology; D055815:Young Adult
chemical_list: D007538:Isoniazid; D012293:Rifampin
keywords: Egypt; Genekam; MDR-TB; MTDR-plus; Stool; Tuberculosis