Genomic data from Escherichia coli O104:H4 isolate TY-2482

Dataset type: Genomic
Data released on June 03, 2011

The May 2011 outbreak of an E. coli infection in Europe resulted in serious concerns about the potential appearance of a new deadly strain of bacteria, Escherichia coli O104:H4 TY-2482. In response to this situation, and immediately after the reports of deaths, the University Medical Centre Hamburg-Eppendorf and BGI-Shenzhen worked together to sequence the bacterium and assess its human health risk. The bacterium’s genome was first sequenced using Life Technologies; Ion Torrent sequencing platform. According to the results of the draft assembly, the estimated genome size of this new E. coli strain is about 5.2 Mb. Sequence analysis indicated this bacterium is an EHEC serotype O104 E. coli strain. Comparative analysis showed that this bacterium has 93% sequence similarity with the EAEC 55989 E. coli strain, which was isolated in the Central African Republic and known to cause serious diarrhea. This strain of E. coli, however, has also acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome. The acquisition of these genes may have occurred through horizontal gene transfer. To maximize its utility to the research community and aid those fighting the epidemic, this genomic data was released into the public domain under a CC0 license. To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to genomic data from the 2011 E. coli outbreak. This work is published from: China.

Additional details

Read the peer-reviewed publication(s):

Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N. J., Hentschke, M., … Yang, R. (2011). Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4. New England Journal of Medicine, 365(8), 718–724. doi:10.1056/nejmoa1107643 (PubMed: 21793736)
Kole, K., Lindeboom, R. G. H., Baltissen, M. P. A., Jansen, P. W. T. C., Vermeulen, M., Tiesinga, P., & Celikel, T. (2017). Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. GigaScience, 6(10). doi:10.1093/gigascience/gix082
Hung, L.-H., Shi, K., Wu, M., Young, W. C., Raftery, A. E., & Yeung, K. Y. (2017). fastBMA: scalable network inference and transitive reduction. GigaScience, 6(10). doi:10.1093/gigascience/gix078

Additional information:

https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki/

Accessions (data generated as part of this study):

SRA: SRP006916
BioProject: PRJNA67657





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
TY-2482562E. coli Escherichia coli Isolate:TY-2482
Isolation source:stool sample from patient with he...
Serovar:O104:H4
...
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Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
TY-2482Genome sequenceFASTQ1.51 GB2012-02-28
TY-2482OtherEXCEL33.5 KB2012-02-28
TY-2482Sequence assemblyFASTA1.47 MB2012-02-28
TY-2482Sequence assemblyFASTA1.55 MB2012-02-28
TY-2482Sequence assemblyFASTA1.57 MB2012-02-28
TY-2482Sequence assemblyFASTA1.68 MB2012-02-28
TY-2482Sequence assemblyFASTA50 KB2012-02-28
TY-2482Sequence assemblyFASTA1.57 MB2012-02-28
ReadmeTEXT1.4 KB2012-02-28
TY-2482Genome sequenceFASTQ7.8 MB2012-02-28
Displaying 1-10 of 18 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China M Li 31530068
Date Action
September 15, 2017 Relationship added : DOI 200029
September 15, 2017 Relationship removed : DOI 200029
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix082
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix078
March 12, 2018 Funder added : National Institutes of Health
July 30, 2018 Funder added : National Natural Science Foundation of China
August 21, 2018 Link added : PRJEB21098
August 21, 2018 Link removed : PRJEB21098
December 5, 2018 External Link removed : http://climb.genomics.cn/Ecoli_TY-2482 - no longer active, no alternative found