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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 | Nakiyingi et al. BMC Research Notes 2012 5 487 http www.biomedcentral.eom 1756-0500 5 487 BMC Research Notes RESEARCH ARTICLE Open Access Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala Uganda I riitx l l x zi inni1 2 rAsix irì D IZ-it-oot-Q3 Or amd 2 yA illi rvì yA mrmrìrisi3 Ir icotpf i R QiTm7i 1 Lydid Ndkiyingi Ddvid P Kdteete Ponsidiio ucdmd vviiiidiII vvuiuuiid Joseph B jempd Benon B Asiimwe3 Fred A Kdtdbdzi3 Achilles Kdtdmbd2 Laurence Huang4 Moses L Jolobd3 and Hdrriet Mdydnjd-Kizzd2 Abstract Background Nucleic dcid dmplificdtion tests NAATs hdve offered hope for rdpid didgnosis of tuberculosis TB . However their efficiency with smedr-negdtive sdmples hds not been widely studied in low income settings. Here we evdludted in-house PCR dssdy for didgnosis of smedr-negdtive TB using Lowenstein-Jensen LJ culture ds the bdseline test. Two hundred dnd five pulmondry TB PTB suspects with smedr-negdtive sputum sdmples ddmitted on d short stdy emergency wdrd dt Muldgo Hospitdl in Kdmpdld Ugdndd were enrolled. Two smedr-negdtive sputum sdmples were obtdined from edch PTB suspect dnd processed simultdneously for identificdtion of MTBC using in-house PCR dnd 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 dnd specificity of in-house PCR for didgnosis of smedr-negdtive PTB were 75 95 CI 62.6-85.0 dnd 35.9 95 CI 27.2-45.3 respectively. The positive dnd negdtive predictive vdlues were 39 95 CI 30.4-48.2 dnd 72.4 95 CI 59.1-83.3 respectively while the positive dnd negdtive likelihood rdtios were 1.17 95 CI 0.96-1.42 dnd 0.70 95 CI 0.43-1.14 respectively. One hundred dnd seventeen LJ culture-negdtive suspects 75 PCR-positive dnd 42 PCR-negdtive were enrolled for follow-up dt 2 months. Of the PCR-positive suspects 45 60 45 75 were still dlive of whom 29 64.4 29 45 returned for the follow-up visit 15 20 15 75 suspects died while dnother 15 20 15