Wampande, Eddie M.Hatzios, Stavroula K.Achan, BeatriceMupere, EzekielNsereko, MaryMayanja, Harriet K.Eisenach, KathleenBoom, W HenryGagneux, SebastienJoloba, Moses L.2015-11-032015Wampande, Eddie M., Stavroula K. Hatzios, Beatrice Achan, Ezekiel Mupere, Mary Nsereko, Harriet K. Mayanja, Kathleen Eisenach, W Henry Boom, Sebastien Gagneux, and Moses L. Joloba. 2015. “A single-nucleotide-polymorphism real-time PCR assay for genotyping of Mycobacterium tuberculosis complex in peri-urban Kampala.” BMC Infectious Diseases 15 (1): 396. doi:10.1186/s12879-015-1121-7. http://dx.doi.org/10.1186/s12879-015-1121-7.1471-2334http://nrs.harvard.edu/urn-3:HUL.InstRepos:23474048Background: Accurate and high-throughput genotyping of Mycobacterium tuberculosis complex (MTBC) may be important for understanding the epidemiology and pathogenesis of tuberculosis (TB). In this study, we report the development of a LightCycler® real-time PCR single-nucleotide-polymorphism (LRPS) assay for the rapid determination of MTBC lineages/sublineages in minimally processed sputum samples from TB patients. Method Genotyping analysis of 70 MTBC strains was performed using the Long Sequence Polymorphism-PCR (LSP-PCR) technique and the LRPS assay in parallel. For targeted sequencing, 9 MTBC isolates (three isolates per MTBC lineage) were analyzed for lineage-specific single nucleotide polymorphisms (SNPs) in the following three genes to verify LRPS results: Rv004c for MTB Uganda family, Rv2962 for MTB lineage 4, and Rv0129c for MTB lineage 3. The MTBC lineages present in 300 smear-positive sputum samples were then determined by the validated LRPS method without prior culturing. Results: The LSP-PCR and LRPS assays produced consistent genotyping data for all 70 MTBC strains; however, the LSP-PCR assay was 10-fold less sensitive than the LRPS method and required higher DNA concentrations to successfully characterize the MTBC lineage of certain samples. Targeted sequencing of genes containing lineage-specific SNPs was 100 % concordant with the genotyping results and provided further validation of the LRPS assay. Of the 300 sputum samples analyzed, 58 % contained MTBC from the MTBC-Uganda family, 27 % from the MTBC lineage 4 (excluding MTBC Uganda family), 13 % from the MTBC lineage 3, and the remaining 2 % were of indeterminate lineage. Conclusion: The LRPS assay is a sensitive, high-throughput technique with potential application to routine genotyping of MTBC in sputum samples from TB patients. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1121-7) contains supplementary material, which is available to authorized users.en-USSingle nucleotide polymorphismLineagesLong sequence polymorphismHigh-throughputJournal Article2015-11-0310.1186/s12879-015-1121-7