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STEC O104:H4 from Spain and Italy

ABSTRACT: Genomic characterization of Shiga toxin-producing Escherichia coli (STEC) O104:H4 clinical strains isolated in Spain and Italy

PROVIDER: PRJEB27813 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2704795.fastq.gz	Fastqsanger.gz
	ERR2704795_1.fastq.gz	Fastqsanger.gz
	ERR2704795_2.fastq.gz	Fastqsanger.gz
	ERR2704796.fastq.gz	Fastqsanger.gz
	ERR2704796_1.fastq.gz	Fastqsanger.gz

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Differential RNA-Seq (dRNA-seq) of Escherichia coli O104:H4

Project description:We performed a high-throughput mapping of the 5’ end transcriptome of the pAA plasmid of the clinical Escherichia coli O104:H4 (E. coli O104:H4) isolate LB226692. We employed differential RNA-sequencing (dRNA-seq), a terminator exonuclease (TEX)-based RNA-seq approach allowing for the discrimination of primary and processed transcripts. This method has proven to be a powerful tool for the mapping of transcription start sites (TSS) and detection of non-coding RNAs (ncRNAs) in bacteria. We catalogued pAA-associated TSS and processing sites on a plasmid-wide scale and performed a detailed analysis of the primary transcriptome focusing on pAA virulence gene expression.

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RpoS acts as a global repressor of virulence gene expression in Escherichia coli O104:H4 and enteroaggregative E. coli

Project description:In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. The rpoS ATG>ATA SNP was associated with enhanced EAEC-specific virulence gene expression. Deletion of rpoS in E. coli O104:H4 Dstx2 and typical EAEC resulted in a similar effect. Both rpoS ATG>ATA and DrpoS strains exhibited stronger virulence-related phenotypes in comparison to wild type. Using promoter-reporter gene fusions, we demonstrated that wild-type RpoS repressed aggR, encoding the main regulator of EAEC virulence. In summary, our work demonstrates that RpoS acts as a global repressor of E. coli O104:H4 virulence, primarily through an AggR-dependent mechanism.

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Project description:Escherichia coli is a diverse species of bacteria. Some isolates of E. coli can cause hemorrhagic uremic syndrome in humans through consumption of contaminated food. We hypothesize that secreted and surface-associated proteins in E. coli may contribute to bacterial persistence in food products and to pathogenicity in humans. Here we report the proteomic analyses of secretomes from two serotypes of E. coli, O157:H7 and O104:H4, that cause human foodborne illness. The secreted proteins were isolated from the liquid cultures and analyzed by liquid chromatography-tandem mass spectrometry. We report 57 secreted proteins for O157:H7 and 67 for O104:H4 with increased abundance in minimal medium. As signature proteins, O157:H7 expressed intimin and translocated intimin receptor. By contrast, O104:H4 expressed enteroaggregative fimbriae, serine protease autotransporters, Shiga toxin, and beta-lactamase. The E. coli O104:H4 released more cytosolic proteins into the culture media than the O157:H7 serotype, indicating that it might be a leaky strain. The differential abundance of two transpeptidases YbiS and YnhG, along with other lipoproteins in O157:H7 indicates that this serotype secretes several peptidol-lipoprotein components of biofilm. In addition, we observed differential abundance of several ABC transporters, proteases and lipoproteins, which give each strain a unique survival strategy and drug resistance. The identification of secreted proteins will enable us understand better how these bacteria persist in food products and cause human disease.

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