E. coli O157, O121, and O26 read data from Swedish cattle
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ABSTRACT:
PROVIDER: PRJEB55252 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10038400_1.fastq.gz | Fastqsanger.gz | |||
| ERR10038400_2.fastq.gz | Fastqsanger.gz | |||
| ERR10038500_1.fastq.gz | Fastqsanger.gz | |||
| ERR10038500_2.fastq.gz | Fastqsanger.gz | |||
| ERR10038700_1.fastq.gz | Fastqsanger.gz |
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Project description:STEC O121 from Swedish cattle 2017-2019
| PRJEB57416 | ENA
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:Evaluation of Enriched Background Microflora of Wheat flour Spiked with E. coli O157 and E. coli O121 through metagenomics
| PRJNA430401 | ENA
Project description:O157:H7 from Swedish cattle, 454 sequencing
| PRJNA215274 | ENA
Project description:In this study, 140 cattle STEC isolates belonging to serogroups O157, O26, O145, O121, O103 and O45 were characterized for 38 virulence-associated genes, antimicrobial resistance profiles and genotyped by PFGE. The majority of isolates carried both stx1 and stx2 concurrently, stx2c, and stx2d; plasmid-encoded genes ehxA, espP, subA and saa but lacked katP and etpD and eaeA. Possession of eaeA was significantly associated with the presence of nle genes, katP, etpD, ureC and terC. However, saa and subA, stx1c and stx1d were only detected in eaeA negative isolates. A complete OI-122 and most non-LEE effector genes were detected in only two eaeA positive serotypes, including STEC O157:H7 and O103:H2. The eaeA gene was detected in STEC serotypes that are commonly implicated in severe humans disease and outbreaks including STEC O157:H7, STEC O145:H28 and O103:H2. PFGE revealed that the isolates were highly diverse with very low rates of antimicrobial resistance. In conclusion, only a small number of cattle STEC serotypes that possessed eaeA, had the highest number of virulence-associated genes, indicative of their high virulence. Further characterization of STEC O157:H7, STEC O145:H28 and O103:H2 using whole genome sequencing will be needed to fully understand their virulence potential for humans.
| S-EPMC6695430 | biostudies-literature
Project description:BackgroundShiga-toxin producing Escherichia coli (STEC) have emerged as important foodborne pathogens, among which seven serogroups (O26, O45, O103, O111, O121, O145, O157) are most frequently implicated in human infection. The aim was to determine if a light scattering sensor can be used to rapidly identify the colonies of STEC serogroups on selective agar plates.Methodology/principal findingsInitially, a total of 37 STEC strains representing seven serovars were grown on four different selective agar media, including sorbitol MacConkey (SMAC), Rainbow Agar O157, BBL CHROMagarO157, and R&F E. coli O157:H7, as well as nonselective Brain Heart Infusion agar. The colonies were scanned by an automated light scattering sensor, known as BARDOT (BActerial Rapid Detection using Optical scattering Technology), to acquire scatter patterns of STEC serogroups, and the scatter patterns were analyzed using an image classifier. Among all of the selective media tested, both SMAC and Rainbow provided the best differentiation results allowing multi-class classification of all serovars with an average accuracy of more than 90% after 10-12 h of growth, even though the colony appearance was indistinguishable at that early stage of growth. SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns. Colony scatter images were also tested with samples derived from pure and mixed cultures, as well as experimentally inoculated food samples. BARDOT accurately detected O157 and O26 serovars from a mixed culture and also from inoculated lettuce and ground beef (10-h broth enrichment +12-h on-plate incubation) in the presence of natural background microbiota in less than 24 h.ConclusionsBARDOT could potentially be used as a screening tool during isolation of the most important STEC serovars on selective agar plates from food samples in less than 24 h.
| S-EPMC4138183 | biostudies-literature
Project description:Sequencing of 30 Swedish cattle from different local breeds
| PRJEB60564 | ENA
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
Project description:Escherichia coli serogroups O26, O45, O103, O111, O121, O145, and O157 are the causative agents of human diseases, and LAMP assays have been developed for detection of the seven leading STEC serogroups.ObjectiveTo evaluate existing LAMP assays for detection of the seven STEC serogroups, if necessary, to improve these assays and to promote their practical application.MethodsPure DNA extract from 23 strains reserved in our lab was used to evaluate the existing LAMP assays. The existing LAMP assays were modified via adding 1% tetramethylene sulfoxide and 5% dimethyl sulfoxide as well as optimizing reaction temperature.ResultsThe detection limit of the modified LAMP assays was 0.1-1 pg per reaction, equivalent to 25-250 cfu per reaction, the non-specific amplification can completely be eliminated with optimal amplifying temperature, and the modified LAMP assays can specifically and sensitivly amplify targeted O serogroup-specific gene (wzx or wzy) of any concerned Escherichia coli serogroup as commercial kit Isothermal Master Mix did.ConclusionIn conclusion, the LAMP assays were highly susceptible to non-specific amplification caused by primer dimers, and these modified methods were free of non-specific amplification and can rapidly and reliably detect the seven major Shiga toxin-producing E. coli serogroups.
| S-EPMC5870286 | biostudies-literature
Project description:Total RNA from rectal tissues of E. coli O157 super-shedders and non-shedders were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR. Fifteen of differentially expressed genes were related to innate and adaptive immune functions and were down-regulated in super-shedders, which could be one of reasons for super-shedding phenomenon.
2016-03-20 | GSE67099 | GEO