Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda
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Date
2012
Journal Title
Journal ISSN
Volume Title
Publisher
BMC Research Notes
Abstract
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 culturenegative
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).
Conclusion: 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.
Description
Keywords
Pulmonary tuberculosis, Smear-negative TB, Smear-negative TB, HIV-infected, HIV-TB co-infection, CD4 cell counts, Nucleic acid amplification tests, In-house PCR, Lowenstein-Jensen culture, Sensitivity, Specificity, Resource limited settings
Citation
Nakiyingi et al.: Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda. BMC Research Notes 2012 5:487. doi:10.1186/1756-0500-5-487