In this wiki we aim to gather all the results of the analysis of the E. coli O104:H4 strain responsible for the May/June 2011 outbreak in Germany and Europe.
TEN isolates from the outbreak have been sequenced so far:
A historical O104:H4 ST678 isolate from 2001 has also been sequenced:
Scheutz F, Møller Nielsen E, Frimodt-Møller J, Boisen N, Morabito S, Tozzoli R, Nataro JP, Caprioli A. Characteristics of the enteroaggregative Shiga toxin/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June 2011. Euro Surveill. 2011;16(24):pii=19889. (http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19889)
Martina Bielaszewska, Alexander Mellmann, Wenlan Zhang, Robin Kock, Angelika Fruth, Andreas Bauwens, Georg Peters, Helge Karch, Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study, The Lancet Infectious Diseases, In Press, Corrected Proof, Available online 22 June 2011, ISSN 1473-3099. (http://dx.doi.org/10.1016/S1473-3099(11)70165-7) (http://www.sciencedirect.com/science/article/pii/S1473309911701657)
Li, D; Xi, F; Zhao, M; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, C; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen, Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Song, Y; Zhao, X; Chen, F; Yin, X; Rohde, H; Liang, Y; Li, Y and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011): Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. (http://dx.doi.org/10.5524/100001)
Frank C, Werber D, Cramer JP, Askar M, Faber M, Heiden MA, Bernard H, Fruth A, Prager R, Spode A, Wadl M, Zoufaly A, Jordan S, Stark K, Krause G; the HUS Investigation Team. Epidemic Profile of Shiga-Toxin-Producing Escherichia coli O104:H4 Outbreak in Germany - Preliminary Report. N Engl J Med. 2011 Jun 22. [Epub ahead of print] PubMed PMID: 21696328.
Manrique, Marina, Pareja-Tobes, Pablo, Pareja-Tobes, Eduardo, Pareja, Eduardo, and Tobes, Raquel. Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system. Available from Nature Precedings (http://dx.doi.org/10.1038/npre.2011.6001.1) (2011)
Cheung MK, Li L, Nong W, and Kwan HS. 2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST. Available from Nature Precedings (http://dx.doi.org/10.1038/npre.2011.6110.1) (2011)
Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, et al. (2011) Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. PLoS ONE 6(7): e22751. (http://dx.doi.org/10.1371/journal.pone.0022751)
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, et al. (2011) Origins of the E. coli strain causing an outbreak of haemolytic-uremic syndrome in Germany. N Engl J Med. (http://dx.doi.org/10.1056/NEJMoa1106920)
Rohde H, Qin J, Cui Y, Li D, Loman NJ, et al. (2011) Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4. N Engl J Med. (http://dx.doi.org/10.1056/NEJMoa1107643)
Crossman, Lisa. Large scale expansion of mobile elements in specific hotspot regions of the German outbreak Escherichia coli O104:H4. Available from Nature Precedings (http://hdl.handle.net/10101/npre.2011.6466.1) (2011)
Monecke S, Mariani-Kurkdjian P, Bingen E, Weill FX, Baliere C, Slickers P, Ehricht R. (2011) Presence of Enterohemorrhagic Escherichia coli ST678/O104:H4 in France prior to 2011. Appl Environ Microbiol, published online ahead of print. (http://dx.doi.org/10.1128/AEM.06524-11) (http://aem.asm.org/cgi/content/abstract/AEM.06524-11v1)
Cheung MK, Li L, Nong W, and Kwan HS. 2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment. BMC Research Notes, 4:533 (http://www.biomedcentral.com/1756-0500/4/533/abstract).
Ahmed SA et al. 2012. Genomic Comparison of Escherichia coli O104:H4 Isolates from 2009 and 2011 Reveals Plasmid, and Prophage Heterogeneity, Including Shiga Toxin Encoding Phage stx2. PLoS One, 11:e48228.
If you're working with such dataset and want to share your results, please feel free to edit the wiki. You just need a GitHub account, which is just an email and a password. If you want to submit your data, read this: how to contribute
Many thanks to BGI, Life Technologies, the University Muenster, and the Health Protection Agency for the open release of these important datasets.
Last edited by Peter Cock,