title: Characterizing Mycobacterium tuberculosis isolates from Karachi, Pakistan: drug resistance and genotypes.
abstract: OBJECTIVE
  To study the prevalence, risk factors, and genotypes of drug-resistant Mycobacterium tuberculosis in Karachi.
  
  
  METHODS
  Pulmonary tuberculosis (TB) patients were recruited in a cross-sectional study (2006-2009). Drug susceptibility testing was performed for culture-positive cases (n=1004). Factors associated with drug resistance were evaluated using logistic regression analysis. Strains were typed using spoligotyping and mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR). The associations of genotype and drug resistance were explored using the Chi-square test.
  
  
  RESULTS
  Resistance rates - new and previously treated - were as follows: multidrug-resistant (MDR)-TB, 2.4% and 13.9%, respectively; rifampin (RIF) monoresistance, 0.1% and 0.6%, respectively; any isoniazid (INH) resistance, 8.9% and 28.5%, respectively; and INH monoresistance, 3.0% and 6.3%, respectively. Prior TB treatment was a risk factor for MDR-TB (adjusted odds ratio (AOR) 6.8, 95% confidence interval (CI) 3.5-13.1) and INH monoresistance (AOR 2.4, 95% CI 1.1-5.2). Additional risk factors included low socioeconomic status for INH monoresistance (AOR 3.3, 95% CI 1.7-6.5), and belonging to Balouchi (AOR 9.2, 95% CI 2.5-33.4), Sindhi (AOR 4.1, 95% CI 1.2-13.5), or Pakhtun (AOR 3.4, 95% CI 1.0-11.2) ethnicity for MDR-TB. Although Central Asian strain (55.6%) was the most prevalent genotype, MDR-TB was significantly associated with Haarlem (H) genogroup (crude OR 9.2, 95% CI 3.6-23.8).
  
  
  CONCLUSIONS
  An MDR-TB rate of 2.4% is reported in new patients. Low RIF monoresistance supports the use of RIF as a marker for MDR-TB in this population. The need to strengthen TB care in the identified at-risk groups is emphasized. Based on INH resistance rates, a review of national treatment/prevention regimens relying on INH is suggested.
authors.affiliation: Department of Pathology and Microbiology, Aga Khan University, Stadium Road, PO Box 3500, Karachi 74800, Pakistan.
authors.forename: Afsheen
authors.initials: A
authors.lastname: Ayaz
authors.forename: Zahra
authors.initials: Z
authors.lastname: Hasan
authors.forename: Sana
authors.initials: S
authors.lastname: Jafri
authors.forename: Raunaq
authors.initials: R
authors.lastname: Inayat
authors.forename: Rafique
authors.initials: R
authors.lastname: Mangi
authors.forename: Abid Ali
authors.initials: AA
authors.lastname: Channa
authors.forename: Faisal Riaz
authors.initials: FR
authors.lastname: Malik
authors.forename: Asho
authors.initials: A
authors.lastname: Ali
authors.forename: Yasraba
authors.initials: Y
authors.lastname: Rafiq
authors.forename: Rumina
authors.initials: R
authors.lastname: Hasan
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D003430:Cross-Sectional Studies; D024901:Drug Resistance, Multiple, Bacterial; D005260:Female; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D058889:Molecular Typing; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification*; D010154:Pakistan / Q000453:epidemiology; D015995:Prevalence; D012307:Risk Factors; D018088:Tuberculosis, Multidrug-Resistant / Q000453:epidemiology* / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology* / Q000382:microbiology; D055815:Young Adult