Peter Cock edited this page Aug 22, 2013 · 166 revisions

E. coli O104:H4 Genome Analysis Crowdsourcing

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:

  • TY2482 (BGI in collaboration with University Medical Centre Hamburg-Eppendorf)
  • LB226692 (Life Tech in-house in collaboration with University Hospital Muenster)
  • 5 isolates: H112180280 (released earlier with 454 scaffold) plus 4 additional isolates (Health Protection Agency, Colindale, UK)
  • 2 isolates, unnamed (Göttingen Genomics Lab, Germany)
  • 1 isolate, c22711 from PacBio, in addition to several related strains

A historical O104:H4 ST678 isolate from 2001 has also been sequenced:

  • Strain 01-09591 (HUSEC041) (University Hospital Muenster in collaboration with Life Tech)

Sequence reads





Visualization of results

Press coverage of Crowdsourcing efforts

  1. Scientists Rush to Study Genome of Lethal E. coli (http://www.sciencemag.org/content/332/6035/1249) [Science News]
  2. Eurosurveillance, Volume 16, Issue 24, 16 June 2011 "Another fascinating development stems from comparative genomics, available in real time, to elucidate the ancestral origin of the 2011 outbreak strain." (http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19890) [Eurosurveillance]
  3. E. Coli Sequencing Prompts Crowdsourcing Project to Annotate Genomes, Enabling Platform Comparisons (http://www.genomeweb.com/sequencing/e-coli-sequencing-prompts-crowdsourcing-project-annotate-genomes-enabling-platfo) [Genomeweb]
  4. The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later - June 20, 2011 http://blogs.nature.com/news/2011/06/the_german_e_coli_outbreak_40.html [Nature News]
  5. BBC News sprouting seeds are the cause of the outbreak
  6. Blogtalkradio - Assembly of German EHEC Sequence in less than 12 Hours (http://www.blogtalkradio.com/lifetechnologies/2011/06/28/assembly-of-german-ehec-sequence-in-less-than-12-hours)
  7. British scientist identifies genetic sequences in new E. coli strain (http://www.dw-world.de/dw/article/0,,15133914,00.html)
  8. Guest Post: International Crowdsourcing Initiative to Combat the E. Coli Breakout in Germany (http://www.ngsleaders.org/blogs.aspx?id=825&blogid=79)

Citable publications

  1. 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)

  2. 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)

  3. 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)

  4. 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.

  5. 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)

  6. 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)

  7. 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)

  8. 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)

  9. 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)

  10. 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)

  11. 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)

  12. 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).

  13. 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


  • Marina Manrique
  • Raquel Tobes
  • Nick Loman
  • Konrad Paszkiewicz
  • Torsten Seeman
  • Simon Gladman
  • Kat Holt
  • Pablo Pareja Tobes
  • Tim Dallman
  • Anthony Underwood
  • Raju Misra
  • Patrik D'haeseleer
  • Kwan Lab
  • Shrinivasrao Mane
  • Lisa Crossman
  • Scott Edmunds
  • Nico Petty

Many thanks to BGI, Life Technologies, the University Muenster, and the Health Protection Agency for the open release of these important datasets.