3 results on '"Egor Shitikov"'
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2. Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia
- Author
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Konstantin G. Skryabin, Elena N. Ilina, Nikolai A. Bazaleev, Tatjana G. Smirnova, Alexey V. Beletsky, Tatjana V. Parfenova, Afanas'ev Mv, Dmitry G. Alekseev, Elena Larionova, Egor Shitikov, A. V. Mardanov, Nikolai V. Ravin, Dmitri E. Kamashev, Dmitry S. Ischenko, Vadim M. Govorun, Maja V. Malakhova, L.N. Ikryannikova, and Larisa Chernousova
- Subjects
Bacterial Diseases ,Extensively Drug-Resistant Tuberculosis ,Antitubercular Agents ,Genome ,Russia ,Genome Databases ,Genome Sequencing ,Genome Evolution ,Phylogeny ,Genetics ,0303 health sciences ,Comparative Genomic Hybridization ,Multidisciplinary ,Phylogenetic tree ,Multi-Drug-Resistant Tuberculosis ,High-Throughput Nucleotide Sequencing ,Genomics ,3. Good health ,Functional Genomics ,Phenotype ,Infectious Diseases ,GenBank ,Medicine ,Research Article ,DNA, Bacterial ,Sequence analysis ,Science ,Molecular Sequence Data ,Sequence Databases ,Context (language use) ,Microbial Sensitivity Tests ,Biology ,Mycobacterium ,Mycobacterium tuberculosis ,03 medical and health sciences ,Genome Analysis Tools ,medicine ,Humans ,Tuberculosis ,030304 developmental biology ,Comparative genomics ,Sequence Assembly Tools ,030306 microbiology ,Extensively drug-resistant tuberculosis ,Comparative Genomics ,medicine.disease ,biology.organism_classification ,Siberia ,Genome, Bacterial - Abstract
Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes--drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998-1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4(XDR), belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4(XDR) may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment.
- Published
- 2013
3. Unusual Large-Scale Chromosomal Rearrangements in Mycobacterium tuberculosis Beijing B0/W148 Cluster Isolates
- Author
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Tatiana Otten, Elena N. Ilina, Elena Nosova, Yulia D Isaeva, Anna Vyazovaya, Julia Bespyatykh, Peter K Yablonsky, Olga Narvskaya, Dmitry G. Alexeev, Igor Mokrousov, Egor Shitikov, Viacheslav Zhuravlev, Boris Vishnevsky, Irina Y. Karpova, Dmitry S. Ischenko, Vadim M. Govorun, and Elena S. Kostryukova
- Subjects
Bacterial Diseases ,Antitubercular Agents ,Genome ,Russia ,Drug Resistance, Multiple, Bacterial ,Genome Databases ,Genomic library ,Genome Sequencing ,Genome Evolution ,Phylogeny ,Chromosomal inversion ,Genetics ,0303 health sciences ,Multidisciplinary ,biology ,Phylogenetic tree ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Genomics ,Chromosomes, Bacterial ,3. Good health ,Infectious Diseases ,Medicine ,Restriction fragment length polymorphism ,Research Article ,DNA, Bacterial ,China ,Sequence analysis ,Science ,Mycobacterium ,Mycobacterium tuberculosis ,03 medical and health sciences ,Genome Analysis Tools ,Tuberculosis ,Humans ,Biology ,Tuberculosis, Pulmonary ,030304 developmental biology ,Comparative genomics ,Evolutionary Biology ,Sequence Assembly Tools ,030306 microbiology ,Computational Biology ,Tropical Diseases (Non-Neglected) ,Genomic Evolution ,Comparative Genomics ,biology.organism_classification ,Chromosome Inversion ,Structural Genomics ,Genome, Bacterial - Abstract
The Mycobacterium tuberculosis (MTB) Beijing family isolates are geographically widespread, and there are examples of Beijing isolates that are hypervirulent and associated with drug resistance. One-fourth of Beijing genotype isolates found in Russia belong to the B0/W148 group. The aim of the present study was to investigate features of these endemic strains on a genomic level. Four Russian clinical isolates of this group were sequenced, and the data obtained was compared with published sequences of various MTB strain genomes, including genome of strain W-148 of the same B0/W148 group. The comparison of the W-148 and H37Rv genomes revealed two independent inversions of large segments of the chromosome. The same inversions were found in one of the studied strains after deep sequencing using both the fragment and mate-paired libraries. Additionally, inversions were confirmed by RFLP hybridization analysis. The discovered rearrangements were verified by PCR in all four newly sequenced strains in the study and in four additional strains of the same Beijing B0/W148 group. The other 32 MTB strains from different phylogenetic lineages were tested and revealed no inversions. We suggest that the initial largest inversion changed the orientation of the three megabase (Mb) segment of the chromosome, and the second one occurred in the previously inverted region and partly restored the orientation of the 2.1 Mb inner segment of the region. This is another remarkable example of genomic rearrangements in the MTB in addition to the recently published of large-scale duplications. The described cases suggest that large-scale genomic rearrangements in the currently circulating MTB isolates may occur more frequently than previously considered, and we hope that further studies will help to determine the exact mechanism of such events.
- Published
- 2014
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