MOLECULAR DETECTION AND PHYLOGEOGRAPHY OF THE HYPERVIRULENT SUBTYPE OF MYCOBACTERIUM TUBERCULOSIS BEIJING 14717-15
МОЛЕКУЛЯРНАЯ ДЕТЕКЦИЯ И ФИЛОГЕОГРАФИЯ ГИПЕРВИРУЛЕНТНОГО СУБТИПА MYCOBACTERIUMTUBERCULOSIS BEIJING 14717-15
Mokrousov I.V. Vyazovaya A.A. Badleeva M.V. Gerasimova A.A. Belopolskaya O.B. Masharsky A.E. Kostyukova I.V. Zhdanova S.N. Mudarisova R.S. Avadenii I. Solovieva N.S. Naizabayeva D.A. Skiba Y.A. Zhuravlev V.Y. Pasechnik O.A. Ogarkov O.B.
January 2023Saint Petersburg Pasteur Institute
Russian Journal of Infection and Immunity
2023#13Issue 191 - 99 pp.
Aim. To develop a method for detecting Mycobacterium tuberculosis strains belonging to highly lethal, hypervirulent, multidrug-resistant Beijing 14717-15-cluster to be applied to screen for M. tuberculosis retrospective collections obtained from various regions of Russia. The collection included M. tuberculosis DNA samples obtained during population studies. Spoligotyping and genotyping of 24 variable number tandem repeats loci were performed according to standard protocols. Phylogenetic analysis was based on the whole genome sequencing data. Polymorphism at the genomic position 2423040 A > G, specific for the Beijing 14717-15 cluster, was detected using PCR-RFLP and HhaI restriction enzyme. The bioinformatic and phylogenetic analysis of whole genome sequencing data for 205 strains of the early ancient sublineage of the M. tuberculosis Beijing genotype showed that strains with the VNTR 14717-15 profile (according to MIRU-VNTRplus.org) and those close to it were grouped into one monophyletic cluster of related strains, which we defined as Beijing 14717-15-cluster. Among the SNPs specific for the 14717-15 cluster, we chose a functionally neutral SNP at the genomic position 2423040 A > G (Rv2161c Val33Ala) and developed a method for its detection in the PCR-RFLP format. Next, we applied this method to screening DNA collections from the regions of the European and Asian parts of Russia and Asian countries. The data demonstrate the presence of strains of the Beijing 14717-15 cluster only in the Asian region of Russia peaking in Buryatia (18%). We have developed a method for detection of the hypervirulent and highly lethal genetic cluster M. tuberculosis Beijing 14717-15 based on detection of the specific mutation in the Rv2161c gene using PCR followed by HhaI restriction of the PCR product and agarose gel electrophoresis to discriminate between wild-type and mutant alleles. The advantages of the proposed method are the speed, simple and unambiguous data interpretation, opportunity to detect contamination and mixed infection, suitability for efficient analysis of large collections of M. tuberculosis strains.
Beijing genotype , multidrug resistance , Mycobacterium tuberculosis , virulence , whole genome sequencing
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St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
Dorzhi Banzarov Buryat State University, Buryatia, Ulan-Ude, Russian Federation
Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, St. Petersburg, Russian Federation
Clinical Anti-tuberculosis Dispensary, Omsk, Russian Federation
Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
Almaty Branch of National Center for Biotechnology, Almaty, Kazakhstan
Al-Farabi Kazakh National University, Almaty, Kazakhstan
Omsk State Medical University, Omsk, Russian Federation
St. Petersburg Pasteur Institute
Dorzhi Banzarov Buryat State University
Resource Center “Bio-bank Center”
Clinical Anti-tuberculosis Dispensary
Scientific Centre of the Family Health and Human Reproduction Problems
St. Petersburg Research Institute of Phthisiopulmonology
Almaty Branch of National Center for Biotechnology
Al-Farabi Kazakh National University
Omsk State Medical University
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