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PROVIDER: PRJNA1142750 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
2012-08-30 | GSE39667 | GEO
Project description:Crohn’s disease (CD) is a severe chronic immune-mediated granulomatous inflammatory disease of the gastrointestinal tract. Its pathogenesis mechanisms remain obscure. One of the factors of CD pathogenesis is reduced diversity of gut microbiota which is accompanied by the characteristic increase of representation of Escherichia coli strains, several of which are able to penetrate the mucin layer, adhere to the epithelial cells, cross the epithelial barrier, and colonize macrophages. During the internalization, these E. coli strains can modulate macrophages’ defensive functions in a way that allows them to survive in a presence of such negative factors as low pH, oxidative stress, proteolytic enzymes and antimicrobial solutions. These strains were collectively assigned to the adhesive–invasive group of E. coli (AIEC). Earlier we sequenced 28 E. coli isolates from 10 patients with CD [Rakitina DV et al. Genome analysis of E. coli isolated from Crohn disease patients. BMC Genomics. 2017, 18(1):544. doi: 10.1186/s12864-017-3917-x] It has been demonstrated that the majority of enteropathogens feature specific metabolic pathways allowing them to use alternative carbon sources which leads to survivability and enhaced competitiveness in the host organism. Previously, we demonstrated that virulent properties of CD isolates are dependent on the carbon source: prolonged growth on propionate containing medium stimulates virulent properties while prolonged growth on glucose reduces these properties to levels indistinguishable from laboratory strain K-12 MG1655 [Pobeguts OV et al. Propionate Induces Virulent Properties of Crohn’s Disease-Associated Escherichia coli. Frontiers in Microbiology. 2020, 11:1460. doi: 10.3389/fmicb.2020.01460]. Thus, cultivation of E. coli on different growth mediums: M9 supplied with propionate and glucose made it possible to distinguish two states of each CD isolate: active (aAIEC) and inactive (iAIEC). In order to identify the major changes that occur upon change of carbon source, we carried out LC–MS-based proteomic analysis of aAIEC and iAIEC states of three CD isolates of E. coli ZvL2 (RCE07), BruB2 (RCE03) and К5 (RCE06) grown on glucose and propionate.
2020-11-17 | PXD022286 | Pride
Project description:Infection caused by bacteria from environmental reservoirs such as E. coli and S. uberis have not decreased in prevalence. Lack of success in controlling bovine mastitis due to S. uberis is associated with the route of infection which is not well understood and there is inadequate information on pathogenesis of S. uberis. Therefore, this study was to investigate the virulence factors of S. uberis using comparative genome analyses using isolates from cows with clinical mastitis and isolates from cows with a low cell count in their milk using a Subtracted Diversity Array (SDA). This study also reports the construction and validation of a microarray capable of fingerprinting the virulent and non-virulent isolates using the SDA technique.
2016-12-31 | GSE63835 | GEO
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison
2012-08-30 | E-GEOD-39667 | biostudies-arrayexpress
Project description:Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression. A498 cell line has been validated as a model of uropathogenic E. coli infection; the cells express functional receptors for bacterial virulence ligands and the response to virulent strains reflects human UTI. The cells were infected with asymptomatic and pathogenic E. coli in vitro, and harvested RNA was subjected to whole genome transcriptome analysis. A498 human kidney epithelial cells were infected with the asymptomatic (E. coli 83972) or virulent strains (E. coli CFT073) for 4 hours. The cells with culture medium alone were used as a control. The experiment was performed in biological duplicates or triplicates.
2013-02-23 | E-GEOD-43790 | biostudies-arrayexpress
Project description:Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression. A498 cell line has been validated as a model of uropathogenic E. coli infection; the cells express functional receptors for bacterial virulence ligands and the response to virulent strains reflects human UTI. The cells were infected with asymptomatic and pathogenic E. coli in vitro, and harvested RNA was subjected to whole genome transcriptome analysis.
2013-02-23 | GSE43790 | GEO
Project description:Transcriptional profiling of Asymptomatic Bacteriuria (ABU) Escherichia coli strain 83972 comparing the progenitor wild type strain ABU83972 with its re-isolates from human bladder colonization (PI-2, PII-4, PIII-4) and in vitro cultivation experiment (4.9).
2011-01-15 | GSE19917 | GEO
Project description:Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression. Therapeutic urinary tract inoculation with the prototype ABU strain E. coli 83972 is a safe alternative approach in patients with therapy-resistant recurrent UTI. The strain establishes persistent bacteriuria, protecting patients against super-infection with more virulent strains. Using this protocol, we examined if the establishment of asymptomatic bacterial carriage alters host gene expression.
2013-02-23 | GSE43838 | GEO
Project description:Urinary tract infections (UTIs) constitute a highly relevant model of microbial adaptation, in which the contrasting effects of pathogens and commensals on host tissues are clearly displayed. While virulent Escherichia coli cause severe, potentially life-threatening disease by breaking the inertia of the mucosal barrier and infecting the kidneys, the most common outcome of bacteriuria is an asymptomatic carrier state resembling commensalism at other mucosal sites. It remains unclear if the lack of destructive inflammation merely reflects low virulence or if carrier strains actively inhibit disease associated responses in the host. To address this question, we examined the effects of asymptomatic bacterial carriage on host gene expression. Therapeutic urinary tract inoculation with the prototype ABU strain E. coli 83972 is a safe alternative approach in patients with therapy-resistant recurrent UTI. The strain establishes persistent bacteriuria, protecting patients against super-infection with more virulent strains. Using this protocol, we examined if the establishment of asymptomatic bacterial carriage alters host gene expression. After antibiotic treatment to remove prior infection, patients were inoculated with E. coli 83972 through a catheter. Blood samples were obtained before and 24 h after inoculation.
2013-02-23 | E-GEOD-43838 | biostudies-arrayexpress
Project description:Transcriptional profiling of Asymptomatic Bacteriuria (ABU) Escherichia coli strain 83972 comparing the progenitor wild type strain ABU83972 with its re-isolates from human bladder colonization (PI-2, PII-4, PIII-4) and in vitro cultivation experiment (4.9). Wild type vs. re-isolate cells. Biological replicates: 3 wild type, 3 re-isolates, independently grown and harvested. One replicate per array.
2011-01-15 | E-GEOD-19917 | biostudies-arrayexpress