title: Use of real time polymerase chain reaction for detection of M. tuberculosis, M. avium and M. kansasii from clinical specimens.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. arnoldbaino@yahoo.co.uk.|Uganda-CASE Research Collaboration, Kampala, Uganda. arnoldbaino@yahoo.co.uk.
authors.forename: Arnold
authors.initials: A
authors.lastname: Bainomugisa
authors.affiliation: Department of Medical Microbiology, College of Health sciences, Makerere University, Kampala, Uganda. wampande@covabs.mak.ac.ug.|Department of Bio molecular Resources and Bio laboratory Sciences, College of Veterinary Medicine, Animal resource and Bio-security, Kampala, Uganda. wampande@covabs.mak.ac.ug.
authors.forename: Eddie
authors.initials: E
authors.lastname: Wampande
authors.affiliation: Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. muchwachris@yahoo.com.|Uganda-CASE Research Collaboration, Kampala, Uganda. muchwachris@yahoo.com.
authors.forename: Chris
authors.initials: C
authors.lastname: Muchwa
authors.affiliation: Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. jpakol01@gmail.com.|Uganda-CASE Research Collaboration, Kampala, Uganda. jpakol01@gmail.com.
authors.forename: Joseph
authors.initials: J
authors.lastname: Akol
authors.affiliation: Uganda-CASE Research Collaboration, Kampala, Uganda. mubirip@gmail.com.
authors.forename: Paul
authors.initials: P
authors.lastname: Mubiri
authors.affiliation: Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. henricosk705@yahoo.com.|Uganda-CASE Research Collaboration, Kampala, Uganda. henricosk705@yahoo.com.
authors.forename: Henry
authors.initials: H
authors.lastname: Ssenyungule
authors.affiliation: Department of Bio molecular Resources and Bio laboratory Sciences, College of Veterinary Medicine, Animal resource and Bio-security, Kampala, Uganda. matovue@vetmed.mak.ac.ug.
authors.forename: Enock
authors.initials: E
authors.lastname: Matovu
authors.affiliation: Joint Clinical Research Centre, P.O. Box 10005, Kampala, Lubowa, Uganda. sxo81@case.edu.|Uganda-CASE Research Collaboration, Kampala, Uganda. sxo81@case.edu.
authors.forename: Sam
authors.initials: S
authors.lastname: Ogwang
authors.affiliation: Department of Medical Microbiology, College of Health sciences, Makerere University, Kampala, Uganda. mlj10@case.edu.|Uganda-CASE Research Collaboration, Kampala, Uganda. mlj10@case.edu.
authors.forename: Moses
authors.initials: M
authors.lastname: Joloba
mesh_terms: D015658:HIV Infections; D006801:Humans; D009161:Mycobacterium / Q000235:genetics / Q000302:isolation & purification*; D060888:Real-Time Polymerase Chain Reaction / Q000592:standards; D012680:Sensitivity and Specificity; D014397:Tuberculosis, Pulmonary / Q000382:microbiology*; D014454:Uganda