Journal
BMC INFECTIOUS DISEASES
Volume 15, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12879-015-1121-7
Keywords
Single nucleotide polymorphism; Lineages; Long sequence polymorphism; High-throughput
Categories
Funding
- Tuberculosis Research Unit (TBRU)
- United Sates National Institutes of Allergy and Infectious Diseases
- United States National Institutes of Health and Human Services [NO1-AI-95383, HHSN266200700022C/NO1-AI-70022]
- National Institutes of Health [R01 AI075637-01]
- Swiss National Science Foundation [PP0033-119205]
- Carnegie Corporation of New York
- Makerere University
- Henry Wheeler Center for Emerging and Neglected Diseases at the University of California, Berkeley
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Background: 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 (R) 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.
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