Combination of single nucleotide polymorphism and variable-number tandem repeats for genotyping a homogenous population of Mycobacterium tuberculosis Beijing strains in China

The standard 15- and 24-locus Variable Number Tandem Repeats (VNTR) genotyping have demonstrated adequate discriminatory power and small homoplasy effect for tracing tuberculosis (TB) transmission and predicting M. tuberculosis lineages in European and North-American countries. However, its validity of the definition of transmission in homogenous M. tuberculosis populations in high-TB burden settings has been questioned. Here, we genotyped a population based collection of 191 Beijing strains based on standard 15-locus VNTR (VNTR-15) and 8 Single Nucleotide Polymorphisms (SNPs) in Shanghai, China. Limited discriminatory power and high rates of VNTR homoplasy were observed in the homogenous population of evolutionarily "modern" Beijing strains. Additional typing of three hypervariable loci (VNTR3820, VNTR4120 and VNTR3232) was performed to VNTR-15 based clusters. High variations of hypervariable alleles were observed in clusters with inconsistent SNP sublineages. We concluded that SNPs and hypervariable VNTR loci are helpful to enhance discriminatory power and decrease VNTR homoplasy effect for defining clusters. We recommended the combination of standard VNTR-15 and SNPs as fist-line typing methods and the hypervariable loci as second-line typing of clustered strains for molecular epidemiology studies in homogenous M. tuberculosis populations.