Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Russian "successful" clone B0/W148 of Mycobacterium tuberculosis Beijing genotype: a multiplex PCR assay for rapid detection and global screening.

ABSTRACT: We describe a multiplex PCR assay to detect the Mycobacterium tuberculosis Beijing genotype variant B0/W148, which is considered a "successful" clone of M. tuberculosis, widespread in Russia. Specificity and sensitivity of the assay were 100% based on the analysis of a collection of 516 M. tuberculosis isolates of different genotypes and origins. This assay may be used for accurate and simple detection and surveillance of this clinically and epidemiologically important variant of M. tuberculosis.

SUBMITTER: Mokrousov I

PROVIDER: S-EPMC3486266 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Russian "successful" clone B0/W148 of Mycobacterium tuberculosis Beijing genotype: a multiplex PCR assay for rapid detection and global screening.

Mokrousov Igor I Narvskaya Olga O Vyazovaya Anna A Otten Tatiana T Jiao Wei-Wei WW Gomes Lia Lima LL Suffys Philip N PN Shen A-Dong AD Vishnevsky Boris B

Journal of clinical microbiology 20120829 11

We describe a multiplex PCR assay to detect the Mycobacterium tuberculosis Beijing genotype variant B0/W148, which is considered a "successful" clone of M. tuberculosis, widespread in Russia. Specificity and sensitivity of the assay were 100% based on the analysis of a collection of 516 M. tuberculosis isolates of different genotypes and origins. This assay may be used for accurate and simple detection and surveillance of this clinically and epidemiologically important variant of M. tuberculosis ...[more]

PMID: 22933595

Similar Datasets

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster.

Project description:Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the "success" of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 394 cluster strains were used to describe the main genetic features of the population. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrated that expression of the whiB6 which contains cluster-specific polymorphism (a151c) increased almost 40 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 was increased by more than 7 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes. In summary, our analysis allowed us to summarize the available results and also to obtain fundamentally new data.

| S-EPMC6917788 | biostudies-literature

Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster.

Project description:Beijing B0/W148, a "successful" clone of Mycobacterium tuberculosis, is widespread in the Russian Federation and some countries of the former Soviet Union. Here, we used label-free gel-LC-MS/MS shotgun proteomics to discover features of Beijing B0/W148 strains that could explain their success. Qualitative and quantitative proteome analyses of Beijing B0/W148 strains allowed us to identify 1,868 proteins, including 266 that were differentially abundant compared with the control strain H37Rv. To predict the biological effects of the observed differences in protein abundances, we performed Gene Ontology analysis together with analysis of protein-DNA interactions using a gene regulatory network. Our results demonstrate that Beijing B0/W148 strains have increased levels of enzymes responsible for long-chain fatty acid biosynthesis, along with a coincident decrease in the abundance of proteins responsible for their degradation. Together with high levels of HsaA (Rv3570c) protein, involved in steroid degradation, these findings provide a possible explanation for the increased transmissibility of Beijing B0/W148 strains and their survival in host macrophages. Among other, we confirmed a very low level of the SseA (Rv3283) protein in Beijing B0/W148 characteristic for all «modern» Beijing strains, which could lead to increased DNA oxidative damage, accumulation of mutations, and potentially facilitate the development of drug resistance.

| S-EPMC4928086 | biostudies-literature

Tuberculous spondylitis in Russia and prominent role of multidrug-resistant clone Mycobacterium tuberculosis Beijing B0/W148.

Project description:Extrapulmonary and, in particular, spinal tuberculosis (TB) constitutes a minor but significant part of the total TB incidence. In spite of this, almost no studies on the genetic diversity and drug resistance of Mycobacterium tuberculosis isolates from spinal TB patients have been published to date. Here, we report results of the first Russian and globally largest molecular study of M. tuberculosis isolates recovered from patients with tuberculous spondylitis (TBS). The majority of 107 isolates were assigned to the Beijing genotype (n = 80); the other main families were T (n = 11), Ural (n = 7), and LAM (n = 4). Multidrug resistance (MDR) was more frequently found among Beijing (90.5%) and, intriguingly, Ural (71.4%) isolates than other genotypes (5%; P < 0.001). The extremely drug-resistant (XDR) phenotype was exclusively found in the Beijing isolates (n = 7). A notable prevalence of the rpoB531 and katG315 mutations in Beijing strains that were similarly high in both TBS (this study) and published pulmonary TB (PTB) samples from Russia shows that TBS and PTB Beijing strains follow the same paradigm of acquisition of rifampin (RIF) and isoniazid (INH) resistance. The 24-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat (MIRU-VNTR) subtyping of 80 Beijing isolates further discriminated them into 24 types (Hunter Gaston index [HGI] = 0.83); types 100-32 and 94-32 represented the largest groups. A genotype of Russian successful clone B0/W148 was identified in 30 of 80 Beijing isolates. In conclusion, this study highlighted a crucial impact of the Beijing genotype and the especially prominent role of its MDR-associated successful clone B0/W148 cluster in the development of spinal MDR-TB in Russian patients.

| S-EPMC4356832 | biostudies-other

Author Correction: System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster.

Project description:An amendment to this paper has been published and can be accessed via a link at the top of the paper.

| S-EPMC7060307 | biostudies-literature

Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-09-25 | GSE269919 | GEO

Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates.

Project description: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.

| S-EPMC3885621 | biostudies-literature

Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 [whiB6_RNA-seq]

Project description:Among the multidrug-resistant (MDR) clones of Mycobacterium tuberculosis (Mtb) that were epidemiologically particularly successful, the 100-32 MDR Beijing clone, also called B0/W148 clone, has emerged since the early sixties. These B0/W148 strains belonging to the lineage 2 within the global Mtb phylogeny, are the main contributors to the MDR epidemic in Russia and Eastern Europe, and since the USSR’s fall, have also propagated to Western Europe. Among the various mutations that were identified as being specific for the MDR B0/W148 clone, we focused on two found in the transcriptional regulators KdpDE and WhiB6 and characterized in a H37Rv strain background the transcriptional profile associated with these mutations and their potential impact on the in vitro and in vivo growth characteristics.

2024-09-25 | GSE269918 | GEO

Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 [kdpDE_RNA-seq]

2024-09-25 | GSE269917 | GEO

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster

Project description:Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the “success” of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 200 cluster strains from the NCBI were used to describe the main genetic features of the population, as well as the level of resistance. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrate that expression of the whiB6 which contains cluster-specific polymorphism (T4338371G) increased by more than 50 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 is increased almost 30 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes.

2020-05-26 | PXD013509 | Pride

Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains

Project description:Nowadays proteomics is the one of the major instruments for editing and correct decryption of genomic information. Genomic correction of socially significant pathogens, like Mycobacterium tuberculosis, is by far the most relevant. We conducted proteogenomic analysis of W-148 strain, which belong to the Beijing B0/W148 cluster. Strains of this cluster possess unique pathogenic properties and have a unique genome organization. Taking into account a high similarity of cluster strains at the genomic level we analysed MS/MS datasets obtained for 63 clinical isolates of Beijing B0/W148. Based on H37Rv and W-148 annotations we identified 2,546 proteins, representing more than 60 % of total proteome. A set of peptides (n=404), specific for W-148 was found in comparison with H37Rv. Start sites for 32 genes were corrected based on combination of LC-MS/MS proteomic data with genomic six frame translation. Additionally, presence of peptides for 10 pseudogenes has been confirmed. Thus, the data obtained by us undoubtedly shows the need for conducting genome annotation based on proteomic data. Corrected during the study W-148 genome annotation will allow to use it in studies on Beijing B0/W148 cluster strains.

2018-10-08 | PXD009489 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data