ON IMPORTANCE OF USING EVOLUTIONARILY ROBUST MARKERS FOR DETECTION OF MYCOBACTERIUM TUBERCULOSIS STRAINS OF LAM GENETIC FAMILY

Abstract

Aim. The clinical and epidemiological significance of the Latin American Mediterranean (LAM) genetic family of Mycobacterium tuberculosis determines the importance of the correct detection of LAM strains. In this study, a complex of molecular methods was used to analyze LAM strains in the population of M. tuberculosis in the Omsk region of Western Siberia, which is characterized by a high incidence of drug-resistant tuberculosis. Materials and methods. The collection included 207 strains of M. tuberculosis, isolated in the Omsk region in 2015 — 2016. The strains were subjected to spoligotyping, analysis of LAM-specific SNP Rv0129c 309G>A, and whole genome sequencing followed by bioinformatics analysis. Results. A comparison of the obtained CRISPR-spoligotyping profiles with the international SITVIT_WEB database, assigned 11 strains (5.3%) to the LAM genotype. At the same time, based on analysis of phylogenetic SNP in the gene Rv0129c, 30 isolates (14.5%) were assigned to LAM. Whole genome sequencing was performed for 4 isolates with different spoligotyping profiles. Conclusion. The results of this study show the limited utility of the decision rules implemented in SITVIT_WEB to define LAM family for isolates with long deleted blocks of spacers or abridged spoligoprofiles. The following approach can be recommended for detection of LAM isolates (1) primary spoligotyping, comparison with SITVIT_WEB, and mandatory interpretation in the light of expert knowledge; (2) detection of LAM-specific SNP (e.g., using PCR-RFLP).

Keywords

• mycobacterium tuberculosis
• evolution
• whole genome sequencing
• spoligotyping
• lam (latin-american mediterranean) genotype