Genetic relationship of Mycobacterium tuberculosis strains based on single nucleotide polymorphism analysis of the selected virulence genes

Abstract

Tuberculosis (TB) remains a major infectious disease that threatens human health not only in Korea but also in the whole world. The emerging anti–tuberculosis drug resistant M. tuberculosis makes TB situation worse than before and the incidence of drug resistant M. tuberculosis is continuously increasing these days. Therefore, epidemiological investigations of M. tuberculosis are very helpful to identify the infectious and transmission routes, domestic or global TB incidences. Molecular epidemiological studies using SNP analysis made it possible to get phylogeny, drug resistance and virulence through analysis in nucleotide polymorphisms. However, molecular epidemiological studies using SNP need the appropriate genetic loci to be selected and the results are dependent on the genes and their numbers in order. Clustering of M. tuberculosis with convenience and accuracy, the SNPs of virulence genes of M. tuberculosis were compared to those of traditional molecular epidemiological method and of existing SNP information. This study includes 10 reference M. tuberculosis strains, 66 clinical M. tuberculosis isolates, 2 strains of M. bovis and M. africanum. Those SNPs of 22 selected virulence genes were identified from total 79 strains. They were classified into clusters based on genetic similarities and the genetic characters were investigated. Distinctive 8 clusters could cover all the 79 strains included in this study and 10 reference strains located in the clusters representing distinctive genetic characters. 66 clinical M. tuberculosis isolates were located in different clusters according to their SNP characters. Two strains of M. bovis and M. africanum were made as an independent cluster and could be distinguish from M. tuberculosis strains. To minimize the numbers of virulent genes that fulfill the purpose of this study, 22 virulent genes were further investigated and 14 virulent genes were selected finally. The molecular epidemiological study using SNP of virulent genes could discriminate M. tuberculosis strains based on genetic characteristics as of traditional molecular epidemiological methods, and could identify their genetic characteristics more conveniently and accurately compared to those of existing molecular epidemiological methods based on SNP. These results suggest that SNP analysis of limited set of virulent genes can make it easy to access of M. tuberculosis epidemiology and can contribute to TB control consequently.