Comparative Genomic Hybridization of E. coli and Shigella species to determine the relatedness of isolates from Neobladders
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ABSTRACT:
ORGANISM(S): Shigella Shigella flexneri Escherichia coli Shigella boydii Shigella dysenteriae Shigella sonnei
PROVIDER: GSE27326 | GEO | 2011/07/25
SECONDARY ACCESSION(S): PRJNA137305
REPOSITORIES: GEO
Similar Datasets
Project description:Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder Isolates were included in the study that represent the prototype strains of multiple pathovars. No replicates were included in the final comparisons
2011-07-24 | E-GEOD-27326 | biostudies-arrayexpress
Project description:Background Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all serotypes. Results For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames, with a mean number of 729 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. Conclusion These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships. Keywords: comparative genomic hybridization
2007-07-01 | GSE5212 | GEO
Project description:Comparative Genomic Hybridization of E. coli and Shigella species to determine the relatedness of isolates from Neobladders
| PRJNA137305 | ENA
Project description:Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated the variability of important eco-physiological functions such as carbon substrate uptake and breakdown capabilities as well as stress defence mechanisms in the genomes of commensal and pathogenic E. coli strains. Furthermore, eco-physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high affinity substrate uptake systems. Our results indicate that the major eco-physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation. Keywords: comparative genomic hybridisation
2006-12-05 | GSE6407 | GEO
Project description:Although the majority of previous work on campylobacteriosis has centered on the species Campylobacter jejuni, Campylobacter coli, the sister group to C. jejuni, is also a significant problem, but remains a much less studied organism. The purpose of this study was to develop and apply an expanded 16 locus MLST genotyping scheme to a large collection of C. coli isolates sampled from a wide range of host species, and to complete microarray comparative genomic hybridizations for these same strains, in order to: (1) determine whether host specific clones, genotypes, or clonal complexes are evident and (2) evaluate whether there are particular genes comprising the dispensable portion of the C. coli genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of the expanded MLST data suggest that (1) host preferred groups have tended to evolve in the diversification of C. coli, (2) this has happened repeatedly, at different times, throughout the evolutionary history of the species, and (3) recombination has played varying roles in the diversification of the different groups. Concomitant with the information on evolutionary history derived from the MLST data, the microarray data suggests that a combination of common ancestry in some cases and lateral gene transfer in others are behind a tendency for sets of genes to be common to isolates derived from particular hosts. Keywords: comparative genomic hybridization
2010-02-02 | GSE16787 | GEO
Project description:This study using LC/MS/MS performed proteomics for identifying Escherichia coli, Shigella and some species of Neisseria
2023-10-20 | PXD046250 | iProX
Project description:We compared the transcriptional profiles of 12 E. coli O157:H7 isolates grown to stationary phase in LB broth. These isolates possess the same two enzyme PFGE profile and are related temporally or geographically to the above outbreak. These E. coli O157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig.
2011-11-01 | GSE33131 | GEO
Project description:Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (“pan-genome”) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Keywords: Comparative genomic hybridizations
2008-01-22 | GSE8595 | GEO
Project description:Escherichia coli is an important human pathogen, among others a cause of severe diarrhea diseases and urinary tract infections. The ability to distinguish different pathogenic E. coli subspecies is crucial for correct treatment of the infection. Characterization and quantification of clinical isolates proteomes can provide details of the organisms’ metabolism and specific virulence factors. We performed a systematic quantitative proteomic analysis on a representative selection of 16 pathogenic and 2 commensal E. coli strains, together with 5 pathogenic Shigella strains. The analysis yielded a dataset of more than 4 thousand proteins, with an average of 2 thousand proteins per strain and 980 proteins common to all strains. Statistical comparison of label-free quantitative levels of 750 proteins, which were quantified in all strains, revealed that levels of a majority of the shared proteins vary substantially among specific strains. Theses quantitative protein profiles clearly distinguished E. coli strains from Shigella and largely separated commensal E. coli strains from intestinal and extraintestinal E. coli isolates.
2020-10-19 | PXD005760 | Pride
Project description:Shigella sonnei as an enteric pathogen, can benefit from outcompeting gut commensals such as Escherichia coli and there can be several mechanisms that assist in interbacterial competition. It is, therefore, important to understand these mechanisms as they provide insights into the interactions of these pathogens in the complex environment they exist. We used our novel Bulk Phenotyping of Epidemiological Replicates (BPER) pipeline combined with bacterial Genome Wide Association Studies (GWAS) on a previously described real-world collection of S. sonnei isolates (n=165) to demonstrate the vital role that colicins could have played in shaping the observed epidemiology of S. sonnei. We then used targeted mass spectrometry on representative S. sonnei isolates to detect colicin sequences in cell free supernatants, which further validated our BPER results to suggest the vital role of colicins. Here, we also introduce BPER as an epidemiologically relevant way of phenotypic testing in the laboratory where the phenotypic results can be interpreted with much more relevance to the effects of those phenotypes in natural settings.
2023-10-24 | PXD036656 | Pride