title: Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda.
abstract: BACKGROUND
  Nucleic acid amplification tests (NAATs) have offered hope for rapid diagnosis of tuberculosis (TB). However, their efficiency with smear-negative samples has not been widely studied in low income settings. Here, we evaluated in-house PCR assay for diagnosis of smear-negative TB using Lowenstein-Jensen (LJ) culture as the baseline test. Two hundred and five pulmonary TB (PTB) suspects with smear-negative sputum samples, admitted on a short stay emergency ward at Mulago Hospital in Kampala, Uganda, were enrolled. Two smear-negative sputum samples were obtained from each PTB suspect and processed simultaneously for identification of MTBC using in-house PCR and LJ culture.
  
  
  RESULTS
  Seventy two PTB suspects (35%, 72/205) were LJ culture positive while 128 (62.4%, 128/205) were PCR-positive. The sensitivity and specificity of in-house PCR for diagnosis of smear-negative PTB were 75% (95% CI 62.6-85.0) and 35.9% (95% CI 27.2-45.3), respectively. The positive and negative predictive values were 39% (95% CI 30.4-48.2) and 72.4% (95% CI 59.1-83.3), respectively, while the positive and negative likelihood ratios were 1.17 (95% CI 0.96-1.42) and 0.70 (95% CI 0.43-1.14), respectively. One hundred and seventeen LJ culture-negative suspects (75 PCR-positive and 42 PCR-negative) were enrolled for follow-up at 2 months. Of the PCR-positive suspects, 45 (60%, 45/75) were still alive, of whom 29 (64.4%, 29/45) returned for the follow-up visit; 15 (20%, 15/75) suspects died while another 15 (20%, 15/75) were lost to follow-up. Of the 42 PCR-negative suspects, 22 (52.4%, 22/42) were still alive, of whom 16 (72.7%, 16/22) returned for follow-up; 11 (26.2%, 11/42) died while nine (21.4%, 9/42) were lost to follow-up. Overall, more PCR-positive suspects were diagnosed with PTB during follow-up visits but the difference was not statistically significant (27.6%, 8/29 vs. 25%, 4/16, p = 0.9239). Furthermore, mortality was higher for the PCR-negative suspects but the difference was also not statistically significant (26.2% vs. 20% p = 0.7094).
  
  
  CONCLUSIONS
  In-house PCR correlates poorly with LJ culture for diagnosis of smear-negative PTB. Therefore, in-house PCR may not be adopted as an alternative to LJ culture.
authors.affiliation: Infectious Diseases Institute, Makerere University College of Health Sciences, Mulago Hospital Complex, Kampala, Uganda. lydikiyingi@yahoo.com
authors.forename: Lydia
authors.initials: L
authors.lastname: Nakiyingi
authors.forename: David P
authors.initials: DP
authors.lastname: Kateete
authors.forename: Ponsiano
authors.initials: P
authors.lastname: Ocama
authors.forename: William
authors.initials: W
authors.lastname: Worodria
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Sempa
authors.forename: Benon B
authors.initials: BB
authors.lastname: Asiimwe
authors.forename: Fred A
authors.initials: FA
authors.lastname: Katabazi
authors.forename: Achilles
authors.initials: A
authors.lastname: Katamba
authors.forename: Laurence
authors.initials: L
authors.lastname: Huang
authors.forename: Moses L
authors.initials: ML
authors.lastname: Joloba
authors.forename: Harriet
authors.initials: H
authors.lastname: Mayanja-Kizza
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D005260:Female; D006801:Humans; D008297:Male; D009169:Mycobacterium tuberculosis / Q000302:isolation & purification; D016133:Polymerase Chain Reaction / Q000379:methods*; D013183:Sputum / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000175:diagnosis*; D014454:Uganda
chemical_list: D017931:DNA Primers