Use of real time polymerase chain reaction for detection of M. tuberculosis, M. avium and M. kansasii from clinical specimens

Arnold Bainomugisa, Eddie Wampande, Chris Muchwa, Joseph Akol, Paul Mubiri, Henry Ssenyungule, Enock Matovu, Sam Ogwang, Moses Joloba

The incidence of M. tuberculosis (MTB) and non tuberculous Mycobacterium species (NTMs) like M. avium and M. kansasii has increased due to Human Immunodeficiency Virus (HIV) epidemic. Therefore accurate, rapid and cost effective methods for the identification of these NTMs and MTB are greatly needed for appropriate TB management. Thus in this study we evaluated the performance of Lightcycler® Mycobacterium detection assay to detect MTB, M. avium and M. kansasii in sputum specimens. A total of 241 baseline minimally processed sputum specimens from individual adult TB suspected patients were analyzed by Mycobacterium detection assay (Real-time-PCR) on a LightCycler 480® while using liquid culture as a reference standard. Real time PCR had a sensitivity of 100% (95% CI 96-100) and 100% (CI 19-100) for detection of MTB and M. avium respectively. Additionally the assay had a specificity of 99% (95% CI 96-99) and 95% (95% CI 91-97) for identification of MTB and M. avium respectively. The positive predictive value (PPV) for Real time PCR to identify MTB and M. avium among the specimens was 98% (95% CI 94-99) and 15% (95% CI 2-45) respectively. The kappa statistics for Real time PCR to identify MTB and M. avium was 0.9 (95% CI 0.9-1.0) and 0.3 (95%CI-0.03-0.5) respectively. The median time to detection for Real time PCR assay was 2 hours while overall median time to detection for MGIT-positive cultures was 8 days. The sample unit cost for Real time PCR was $ 12 compared to $ 20 for the reference liquid culture. The Light cycler® Mycobacterium detection assay rapidly and correctly identified MTB and M avium thus has the potential to be adopted in a clinical setting.