title: Nucleic acid amplification tests for diagnosis of smear-negative TB in a high HIV-prevalence setting: a prospective cohort study.
abstract: BACKGROUND
  Nucleic acid amplification tests are sensitive for identifying Mycobacterium tuberculosis in populations with positive sputum smears for acid-fast bacilli, but less sensitive in sputum-smear-negative populations. Few studies have evaluated the clinical impact of these tests in low-income countries with high burdens of TB and HIV.
  
  
  METHODS
  We prospectively enrolled 211 consecutive adults with cough ≥2 weeks and negative sputum smears at Mulago Hospital in Kampala, Uganda. We tested a single early-morning sputum specimen for Mycobacterium tuberculosis DNA using two nucleic acid amplification tests: a novel in-house polymerase chain reaction targeting the mycobacterial secA1 gene, and the commercial Amplified® Mycobacterium tuberculosis Direct (MTD) test (Gen-Probe Inc, San Diego, CA). We calculated the diagnostic accuracy of these index tests in reference to a primary microbiologic gold standard (positive mycobacterial culture of sputum or bronchoalveolar lavage fluid), and measured their likely clinical impact on additional tuberculosis cases detected among those not prescribed initial TB treatment.
  
  
  RESULTS
  Of 211 patients enrolled, 170 (81%) were HIV-seropositive, with median CD4+ T-cell count 78 cells/µL (interquartile range 29-203). Among HIV-seropositive patients, 94 (55%) reported taking co-trimoxazole prophylaxis and 29 (17%) reported taking antiretroviral therapy. Seventy-five patients (36%) had culture-confirmed TB. Sensitivity of MTD was 39% (95% CI 28-51) and that of secA1 was 24% (95% CI 15-35). Both tests had specificities of 95% (95% CI 90-98). The MTD test correctly identified 18 (24%) TB patients not treated at discharge and led to a 72% relative increase in the smear-negative case detection rate.
  
  
  CONCLUSIONS
  The secA1 and MTD nucleic acid amplification tests had moderate sensitivity and high specificity for TB in a predominantly HIV-seropositive population with negative sputum smears. Although newer, more sensitive nucleic acid assays may enhance detection of Mycobacterium tuberculosis in sputum, even currently available tests can provide substantial clinical impact in smear-negative populations.
authors.affiliation: Division of Pulmonary & Critical Care Medicine, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America. Lucian.Davis@ucsf.edu
authors.forename: J Lucian
authors.initials: JL
authors.lastname: Davis
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.forename: William
authors.initials: W
authors.lastname: Worodria
authors.forename: Henry
authors.initials: H
authors.lastname: Masur
authors.forename: Adithya
authors.initials: A
authors.lastname: Cattamanchi
authors.forename: Charles
authors.initials: C
authors.lastname: Huber
authors.forename: Cecily
authors.initials: C
authors.lastname: Miller
authors.forename: Patricia S
authors.initials: PS
authors.lastname: Conville
authors.forename: Patrick
authors.initials: P
authors.lastname: Murray
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Kovacs
mesh_terms: D000328:Adult; D015331:Cohort Studies; D015897:Comorbidity; D015658:HIV Infections / Q000150:complications / Q000175:diagnosis / Q000453:epidemiology*; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000302:isolation & purification; D021141:Nucleic Acid Amplification Techniques / Q000379:methods / Q000592:standards*; D016133:Polymerase Chain Reaction / Q000379:methods*; D015995:Prevalence; D011446:Prospective Studies; D012680:Sensitivity and Specificity; D014376:Tuberculosis / Q000150:complications / Q000175:diagnosis* / Q000453:epidemiology