Identification of mycobacterium tuberculosis beijing genotype using three different molecular methods

Beijing strains constitute more than 1/4 of Mycobacterium tuberculosis (MT) genotypes. Beijing genotype is considered an important genotype because of its reasonable characteristics such as association with multi-drugs resistance TB. The aim of this study was to identify the genetic pattern of MT Beijing genotype using spoligotyping, variable number tandem repeat (VNTR) typing and RFLP-IS6110 methods. Materials ands 238 MT culture positive specimens (2007-2008) were genotyped by spoligotyping. Thereafter, the isolated Beijing genotype was subjected to VNTR typing and RFLP analysis. The results of Spoligotyping were analyzed using SPOLDB4 database. VNTR typing was used to identify alleles diversity in 9 locus (MPTR-A, ETR-A, ETR-B, ETR-C, ETR-D, ETR-E, ETR-F, QUB11B, QUB3232) of the isolated Beijing strains. The allelic diversity of VNTR was measured using Hunter Gaston Index (HGI). The spoligotyping of MT isolates revealed the following 8 patterns: Haarlem (27.7%), CAS1 (25.2%), EAI3 (21.8%), CAS2 (6.7%), T1 (6.3%), Beijing (5.5%), U (5%), T (0.4), EAI2 (1.2%). By VNTR typing, the QUB3232 locus was identified as the most distinctive (HGI≥0.6); ETR-F, ETR-E and QUB11b loci; as median distinctive loci (HGI≥0.4-0.6) and other loci as the weakest distinctive locus for Beijing families.The Beijing strains demonstrated diverse patterns in RFLP, 13/13(100%) and VNTR 10/13(77%). The ariety of genetic patterns revealed the reactivation in the studied population. As RFLP method is a time consuming and costly effective method, VNTR and spoligotyping method can be used as alternative methods for molecular epidemiology of MT.