Mycobacterium tuberculosis CCDC5079
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA19585 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Drug-susceptible clinical isolate
| PRJNA21053 | ENA
Project description:Transcriptional profile comparison among Beijing and non-Beijing M. tuberculosis isolates. Three M. tuberculosis strains were compared. The laboratory reference strain, H37Rv, belongs to the Euro-American or lineage 4. Two clinical isolates of the East-Asian or lineage 2: 98_1663 is a pre-Beijing or Group 1 isolate, and HN878 is a Beijing or Group 5 isolate. Three replicates were performed for each comparison using two different biological samples.
2016-06-24 | E-GEOD-83677 | biostudies-arrayexpress
Project description:Mycobacterium tuberculosis (MTB) Beijing genotype is associated with high virulence and drug resistance worldwide. In Colombia, the Beijing genotype circulates since 1997 predominantly on the pacific coast, being the Beijing-Like SIT-190 more prevalent. This genotype conforms to a drug-resistant cluster and shows a fatal outcome in patients. To better understand virulence determinants, we performed a transcriptomic analysis with a Beijing-Like SIT-190 isolate (BL-323), and Beijing-Classic SIT-1 isolate (BC-391) in progressive tuberculosis (TB) murine model. RNA was extracted from mice lungs on days 3, 14, 28, and 60. On average, 0.6% of the total reads mapped against MTB genomes and of those, 90% against coding genes. The strains were independently associated as determined by hierarchical cluster and multidimensional scaling analysis. Gene ontology showed that in strain BL-323 enriched functions were related to host immune response and hypoxia, while proteolysis and protein folding were enriched in the BC-391 strain. Altogether, our results suggested a differential transcriptional program when evaluating these two closely related strains. The data presented here could potentially impact the control of this emerging, highly virulent and drug resistance genotype.
2022-03-24 | GSE198877 | GEO
Project description:Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) strains and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018-2021, obtained from the analysis of whole genome sequence data. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB (HR-MTB), 7 were resistant only to one antibiotic (3 were resistant only to ethambutol and 3 isolate to streptomycin while one isolate showed resistance to fluoroquinolones), 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB (pre-XDR). This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of TB infection.
2023-11-17 | E-MTAB-13058 | biostudies-arrayexpress
Project description:Tuberculosis continues as an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Contrary, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune- suppression, including Nkiras, Dleu2 and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.
2021-03-25 | GSE169541 | GEO
Project description:The identification of multidrug resistant (MDR), extensively and totally drug resistant Mycobacterium tuberculosis (Mtb), in vulnerable sites such as Mumbai, is a grave threat to the control of tuberculosis. The current study aimed at explaining the rapid expression of MDR in Directly Observed Treatment Short Course (DOTS) compliant patients, represents the first study comparing global transcriptional profiles of 3 pairs of clinical Mtb isolates, collected longitudinally at initiation and completion of DOTS. While the isolates were drug susceptible (DS) at onset and MDR at completion of DOTS, they exhibited identical DNA fingerprints at both points of collection. The whole genome transcriptional analysis was performed using total RNA from H37Rv and 3 locally predominant spoligotypes viz. MANU1, CAS and Beijing, hybridized on MTBv3 (BuG@S) microarray, and yielded 36, 98 and 45 differentially expressed genes respectively. Genes encoding transcription factors (sig, rpoB), cell wall biosynthesis (emb genes), protein synthesis (rpl) and additional central metabolic pathways (ppdK, pknH, pfkB) were found to be down regulated in the MDR isolates as compared to the DS isolate of the same genotype. Up regulation of drug efflux pumps, ABC transporters, trans-membrane proteins and stress response transcriptional factors (whiB) in the MDR isolates was observed. The data indicated that Mtb, without specific mutations in drug target genes may persist in the host due to additional mechanisms like drug efflux pumps and lowered rate of metabolism. Furthermore this population of Mtb, which also showed reduced DNA repair activity, would result in selection and stabilization of spontaneous mutations in drug target genes, causing selection of a MDR strain in the presence of drug pressures. Efflux pump such as drrA may play a significant role in increasing fitness of low level drug resistant cells and assist in survival of Mtb till acquisition of drug resistant mutations with least fitness cost. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-134]
2013-04-24 | E-BUGS-134 | biostudies-arrayexpress
Project description:Transcriptional profile comparison among Beijing and non-Beijing M. tuberculosis isolates.
2016-06-24 | GSE83677 | GEO
Project description:Autophagy is a conserved lysosomal-dependent cellular degradation process shown to play a key role in immune defense against Mycobacterium tuberculosis inside host macrophages. Induction of autophagy enhances mycobacterial phagosome acquisition of lysosomal hydrolases, resulting in the destruction of intracellular M. tuberculosis reference strain H37Rv and strains belonging to the East African Indian genotype. However, our previous study showed that strains belonging to the hypervirulent M. tuberculosis Beijing genotype have a special ability to resist autophagic killing but the mechanism involved remains unclear. In this study, we carried out whole transcriptome analyses of host macrophages infected with the autophagy resistant Beijing strain compared to that of H37Rv. Our results identified several genes that are differentially regulated in the Beijing strain-infected host cells including those function in the lysosome positioning pathway. Host macrophages depleted of Kxd1 and Pleckhm2, two proteins in this pathway, can now enhance the lysosomal hydrolase acquisition into the Beijing phagosomes and restrict the bacterial survival upon autophagy induction. High-content image analysis showed an increase in lysosome numbers at the cell periphery in host cells infected with the autophagy resistant Beijing strain in a Pleckhm2-dependent manner. Taken together, these data indicated that the M. tuberculosis Beijing strain escapes autophagic elimination by upregulating the lysosome positioning pathway resulting in an increase in lysosome relocation toward the cell periphery and therefore sparing the mycobacteria from autophagic restriction. Our work thus identified new strategy employed by M. tuberculosis to evade autophagy which may provide potential new targets for drug discovery against tuberculosis
2021-03-02 | GSE151633 | GEO
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