Loop-mediated isothermal amplification as alternative to PCR for the diagnosis of extra-pulmonary tuberculosis

BACKGROUND: The main challenge in combatting extra-pulmonary tuberculosis (EPTB) is the lack of a rapid, reliable and inexpensive diagnostic test for the detection of Mycobacterium tuberculosis. OBJECTIVE: To evaluate the diagnostic potential of an L-serine dehydratase gene (sdaA) loop-mediated isothermal amplification (LAMP) assay for the detection of M. tuberculosis in clinical specimens from presumptive EPTB patients. METHODS: An in-house sdaA LAMP assay was used to analyse clinical specimens (n= 315) for the diagnosis of EPTB compared with culture and the composite reference standard (CRS) comprising culture and polymerase chain reaction (PCR) using insertion sequence (IS) 6110 and mpb64 as target genes. RESULTS: The sdaA LAMP assay showed the highest sensitivity (93.3%) in comparison to culture; the sensitivity of IS6110 PCR, mpb64 and sdaA PCR assay was respectively 80%, 86.7% and 90%. In comparison to CRS, the LAMP assay had a sensitivity of 92.5% and a specificity of 99.2%, with a high positive (121.11) and a low negative likelihood ratio (0.08). CONCLUSION: Due to its speed, simplicity, sensitivity and specificity, the sdaA LAMP assay is a potential diagnostic test for the diagnosis of EPTB, particularly in resource-limited settings.