ETR-VNTR and SNP-typing of principal genotypic groups of Mycobacterium tuberculosis strains circulating in Kyiv
Aim is to determine the genetic profiles of Mycobacterium tuberculosis (MBT) strains that circulate in Kyiv by VNTR (Varied Number of Tandem Repeats), SNP-typing (Singe Nucleotide Polymorphism) methods and deletion analysis, and assess the effectiveness of the chosen comprehensive strategies of genotyping. Methods. 120 isolates from patients with pulmonary tuberculosis in Kyiv were characterized by PCR typing methods: ETR-VNTR (for ETR (Exact Tandem Repeats) A, B, C, D, E loci), SNP-typing of group-specific SNP katG463 and gyrA95 by RFLP (Restriction Fragment Length Polymorphism) and deletion PCR analysis (TbD1 deletion). Results. We found the most common genetic MBT variants, which correspond to the families of the first "principal genotypic group," (PGG-1) Beijing (42435) and PGG-2 LAM (22232). The population is composed of PGG-1 strains (56.7%) PGG-2 strains (29.2 %), and PGG-3 strains (14.2 %). 92.6 % of strains belonging to PGG-1 strains made up strains from family Beijing. Group-specific SNP-typing somewhat increases the discriminatory ability of VNTR-typing based on 5 ETR loci. Conclusions. Genotyping based on SNP- and VNTR- typing more adequately reflects the evolutionary relationship of Mycobacterium tuberculosis strains than VNTR-typing based on MIRU and ETR and requires further optimization to improve the discriminatory ability of the method.
Key words: Mycobacterium tuberculosis complex, genotyping, ETR-, VNTR-, SNP-typing.