title: Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates.
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.
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Egor A
authors.initials: EA
authors.lastname: Shitikov
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Bespyatykh
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation ; Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation.
authors.forename: Dmitry S
authors.initials: DS
authors.lastname: Ischenko
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation ; Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation.
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Alexeev
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Irina Y
authors.initials: IY
authors.lastname: Karpova
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Elena S
authors.initials: ES
authors.lastname: Kostryukova
authors.affiliation: Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation.
authors.forename: Yulia D
authors.initials: YD
authors.lastname: Isaeva
authors.affiliation: Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation.
authors.forename: Elena Y
authors.initials: EY
authors.lastname: Nosova
authors.affiliation: St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Mokrousov
authors.affiliation: St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation.
authors.forename: Anna A
authors.initials: AA
authors.lastname: Vyazovaya
authors.affiliation: St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Narvskaya
authors.affiliation: Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation.
authors.forename: Boris I
authors.initials: BI
authors.lastname: Vishnevsky
authors.affiliation: Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation.
authors.forename: Tatiana F
authors.initials: TF
authors.lastname: Otten
authors.forename: Viacheslav Iu
authors.initials: VIu
authors.lastname: Zhuravlev
authors.affiliation: Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation.
authors.forename: Valery Y
authors.initials: VY
authors.lastname: Zhuravlev
authors.affiliation: Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation.
authors.forename: Peter K
authors.initials: PK
authors.lastname: Yablonsky
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Elena N
authors.initials: EN
authors.lastname: Ilina
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Vadim M
authors.initials: VM
authors.lastname: Govorun
mesh_terms: D000995:Antitubercular Agents / Q000627:therapeutic use; D002681:China / Q000453:epidemiology; D007446:Chromosome Inversion; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000145:classification / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial / Q000187:drug effects / Q000235:genetics*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D012426:Russia / Q000453:epidemiology; D014397:Tuberculosis, Pulmonary / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D004269:DNA, Bacterial