Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666790 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15376136_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15376137_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15376138_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR15376139_subreads.fastq.gz | Fastqsanger.gz |
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Project description:This study characterises large chromosomal rearrangements (LCRs) and their associated phenotypes in E. coli O157 strains. RNA-seq was performed on wildtype strain 9000 and three derivative strains in which LCRs had occurred following experimental bovine colonisation. Gene expression differences between these strains was analysed when each was grown in either LB or M9 media.
2020-10-02 | GSE158899 | GEO
Project description:We describe the design and evaluate the use of a high density oligonuclotide microarray covering seven sequenced E. coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labelled genomic DNA to query the microarrays and subsequently analyse common virulence genes and phage elements, and perform whole genome comparisons, we observed that O175:H16 D1 is a K-12 like strain and confirmed that its phi3538 phage element originated from the E. coli 3538 strain with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains providing a likely explanation for their capability to transfer phi3538 between them. Analyses of control samples demonstrated that results using our custom designed microarray were representative of the true biology, e.g. by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7 percent of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis. Keywords: Genomic DNA hybridizations
2006-08-29 | GSE4690 | GEO
Project description:Background: Enterohemorrhagic Escherichia coli (EHEC) O157 causes severe food-bone illness in humans. The chromosome of O157 consists of 4.1-Mb backbone sequences shared by benign E. coli K-12, and 1.4-Mb O157-specific sequences encoding many virulence determinants such as Shiga toxin genes (stxs) and the locus of enterocyte effacement (LEE). Non-O157 EHECs belonging to clonal lineages distinct from O157 also cause similar illness in humans. According to the parallel evolution model, they have independently acquired the major virulence determinants, stxs and LEE. However, the genomic differences between O157 and non-O157 EHECs have not yet systematically been analyzed. Results: By using the microarray and Whole Genome PCR scanning analyses, we performed a whole genome comparison of 20 EHEC strains of O26, O111, and O103 serotypes with O157. In non-O157 EHEC strains, although genome sizes were similar with or rather larger than O157 and the backbone regions were well conserved, O157-specific regions were very poorly conserved. Only around 20% of the O157-specific genes were fully conserved in each non-O157 serotype. However, the non-O157 EHECs contained a significant number of virulence genes found on prophages and plasmids in O157, and also multiple prophages similar but significantly divergent from those in O157. Conclusion: Although O157 and non-O157 EHECs have independently acquired a huge amount of serotype- or strain-specific genes by lateral gene transfer, they share an unexpectedly large number of virulence genes. Independent infections of similar but distinct bacteriophages carrying these virulence determinants appear to be involved in the parallel evolution of EHEC. Keywords: comparative genomic hybridization, CGH
2007-08-23 | GSE7931 | GEO
Project description:Typical enteropathogenic Escherichia coli (EPEC) O55:H7 is regarded as the closest relative of enterohemorrhagic E. coli (EHEC) O157:H7. Both serotypes usually express the γ1 intimin subclass and trigger actin polymerazation by the Tir-TccP pathway. However, atypical O55:H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains. We show that the atypical O55:H7 strains, which express the θ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55:H7 and from the EPEC O55:H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by restriction fragment length polymorphism analysis of PCR products and DNA sequencing analysis of about 65-kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (≥ 40 kb) encoding the O55-antigen gene cluster and part of neighboring colanic acid gene cluster is involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria. Keywords: comparative genomic hybridization
2008-04-01 | GSE8889 | GEO
Project description:Transcriptional profiling of wt and ler- EPEC and O157 E. coli strains at mid log and early stationary growth phases
2013-03-31 | GSE38876 | GEO
Project description:Typical enteropathogenic Escherichia coli (EPEC) O55:H7 is regarded as the closest relative of enterohemorrhagic E. coli (EHEC) O157:H7. Both serotypes usually express the γ1 intimin subclass and trigger actin polymerazation by the Tir-TccP pathway. However, atypical O55:H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains. We show that the atypical O55:H7 strains, which express the θ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55:H7 and from the EPEC O55:H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by restriction fragment length polymorphism analysis of PCR products and DNA sequencing analysis of about 65-kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (⥠40 kb) encoding the O55-antigen gene cluster and part of neighboring colanic acid gene cluster is involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria. Keywords: comparative genomic hybridization Total 8 test samples were analyzed. Genomic DNA from each test strain and a reference strain (O157 Sakai) were labeled with Cy3 and Cy5, respectively, and were cohybridized on a single array. Labeling and hybridization were performed twice independently.
2010-05-22 | E-GEOD-8889 | biostudies-arrayexpress
Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more sensitive to oxidative stress than MG1655. A microarray study of these strains treated with sub-lethal concentrations (0.5mg/ml) of menadione revealed big differences in their responses. In E. coli O157 (Sakai), 540 genes responded significantly to the treatment compared to 121 genes in MG1655. One surprising finding from the microarray data was the observation that many iron-transport genes were up-regulated in E. coli O157 (Sakai) whereas relatively few were induced in MG1655 despite the fact that the bacteria were grown in a medium containing ample iron. We speculated that the induction of iron transport genes in an iron-rich medium might have contributed to the enhanced killing of E. coli O157 (Sakai) through triggering of a Fenton reaction. We speculated that the difference in sensitivity to oxidative stress might be due to differences in the intracellular iron content of E. coli O157 and MG1655. We found that E. coli O157 contains ~50% more iron than MG1655 and believe that during oxidative stress, this iron is released by damaged proteins. The greater levels of free iron in E. coli O157 will trigger a greater Fenton reaction that can damage the ferric uptake regulator (Fur), resulting in unregulated iron transport. In MG1655, the lower iron content results in a smaller Fenton reaction, enabling the cellular protection systems to limit damage and protect Fur.
2015-02-22 | GSE36130 | GEO
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies, a combination of microarray analyses and surface enhanced Raman spectroscopy (SERS) were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli O157:H7 on lettuce roots and compared to E. coli K12 using a hydroponic system (HS) which we have reported in the previous studies. Using microarray, after three days of interaction with lettuce roots, 94 and 109 genes of E. coli O157:H7 were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Only 8 genes were also found in the E. coli K12 up-regulated genes. No genes were found in the down-regulated genes clusters between those two strains. For E. coli O157:H7, forty out of the 94 up-regulated genes (43%) were involved in protein synthesis and were highly repressed compared to 40 out of 193 (23%) E. coli K12 up-regulated genes associated with protein synthesis. The wildtype of E.coli O157:H7 colonized two log CFU per root less compared to E. coli K12. Genes involved in biofilm modulation (bhsA and ybiM) were significantly up-regulated in E. coli O157:H7 and curli production (crl and csgA) were found important for E. coli K12 to attach to lettuce roots in the previous studies. BhsA mutant of E. coli O157:H7 was impaired in the colonization of lettuce roots. The SERS spectra of E. coli K12 and O157 controls (cells without interacting with roots) were very similar. The spectra of E. coli K12 and O157 exposed to the hydroponic system (HS) showed some differences in the nucleic acid, protein, and lipid regions compared with controls. The spectra of E. coli K12 HS cells exhibited significant differences compared to spectra from E. coli O157 HS cells in the RNA and protein regions. The overall band intensity of amide regions declined for E. coli O157 HS cells, while it increased for E. coli K12 HS cells. The intensity of the RNA bands of E. coli K12 HS cells were also found much higher than those of E. coli O157 HS cells. These findings were in agreement to our Microarray data. Our microarray and SERS data showed that E. coli K12 and O157:H7 behavior dramatically differently in colonizing on lettuce roots. Compared to K12, E. coli O157:H7 colonized less efficiently on lettuce roots.
2012-03-29 | GSE36885 | GEO
Project description:Pathogenic biofilms have been associated with persistent infections due to high resistance to antimicrobial agents while commensal biofilms often fortify host immune system. Hence, controlling biofilm formation of both pathogenic bacteria and commensal bacteria is important in bacteria-related diseases. We investigated the effect of plant flavonoids on biofilm formation of both enterohemorrhagic Escherichia coli O157:H7 and three commensal E. coli K-12 strains. Phloretin abundant in apples markedly reduced E. coli O157:H7 biofilm formation without affecting the growth of planktonic cells while phloretin did not harm commensal E. coli K-12 biofilms. Also, phloretin reduced E. coli O157:H7 attachment to human colon epithelial cells. Global transcriptome analyses revealed that phloretin repressed toxin genes (hlyE and stx2), autoinducer-2 importer genes (lsrACDBF), a curli gene (csgA), and a dozens of prophage genes in E. coli O157:H7 cells. Electron microscopy confirmed that phroretin reduced the curli production in E. coli O157:H7. In addition, phloretin suppressed TNF-α-induced inflammatory response in vitro using human colonic epithelial cells. Moreover, in the trinitrobenzene sulfonic acid (TNBS)-induced rat colitis model, phloretin significantly ameliorated colon inflammation and body weight loss. Taken together, our results suggest that phloretin may act as an inhibitor of E. coli O157:H7 biofilm formation as well as anti-inflammatory agent on inflammatory bowel diseases while leaving beneficial commensal E. coli biofilm intact.
2011-11-22 | GSE28144 | GEO
Project description:Secreted proteins constitute a major part of virulence factors that are responsible for pathogenesis caused by gram negative bacteria. Enterohemorrhagic Escherichia coli (E. coli), EHEC O157:H7 is the major pathogen often causing outbreaks. There is growing evidence that non-O157:H7 E. coli strains may also be involved in the recent outbreaks. However, there is no systematic study describing differential secreted proteins from non-O157:H7 E. coli strains. Here, we have applied isobaric tag-based TMT labeling combined with high-resolution Fourier transform mass spectrometry to study the differential secretome analysis of major non-O157:H7 E. coli strains, O103, O111, O121, O145, O26 and O45, which is known as diarrhea inducing non-O175:H7 ATCC “big six” serogroup E. coli strains. We identified 1,240 proteins quantitatively identified, 565 proteins were found to be secreted as predicted by PSORTb and SecretomeP. We identified 310 proteins containing signal peptide and 255 proteins as secreted. We identified 20 strain specific proteins with in big-six group and was confirmed by proteogenomics approach. Further we enriched and have shown relative expression of type III secretion system. To our knowledge, this study is the first comparative proteomic study on secretome of E. coli big six serogroup and the several of these strain specific secreted proteins can be further studied to develop potential markers for identification and strain level differentiation. Moreover, the results of this study can be utilized in several applications, including food safety, diagnostics of E. coli outbreaks, and biodefense.
2018-07-05 | PXD004372 | Pride