The effects on mycobacterial interspersed repetitive units-variable-number tandem repeat of loci with same allelic diversity in mycobacterium tuberculosis Beijing genotype strains

Abstract

Qbjective To investigate the effects on mycobacterial interspersed repetitive units-variable-number tandem repeat(MIRU-VNTR)genotyping of loci with same allelic diversity in Mycobacterium tuberculosis Beijing genotype strains. Method R 2.9.1 software was used to construct phylogenetic tree based on two 9 and two 12 MIRU-VNTR loci combinations which have the same loci except MIRU40/MIRU16 and MIRU39/MIRU31 respectively.The Hunter-Gaston index, cluster rate and the characteristic of genotype were analyzed of two combinations. Results The phylogenetic tree based on the two 9 loci combination can be both divided into three groups.There is only one identical strain in group Ⅲ which accounts for 2.0% and 1.6% in the two 9 loci combinations, respectively.The phylogenetic tree based on the two 9 loci combination can be also devided into three groups.There is no identical strain in the three groups of the two 12 loci combinations. Conclusion Loci with the same allelic diversity have significant effects on MIRU-VNTR genotyping of Mycobacterium tuberculosis Beijing genotype strains.The effects on genotyping of loci that have the same or similar allelic diversity should also be considered besides the Hunter-Gaston index and cluster rate. Key words: Mycobacterium tuberculosis; Beijing family genotype; Mycobacterial interspersed repetitive units-variable-number tandem repeat; Diversity