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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

Assemblies

Annotations

Analysis

• 2-Jun Nick Loman EHEC genome assembly
• 3-Jun Mike the Mad Biologist I Don't Think the German Outbreak E. coli Strain Is Novel: Something Very Similar Was Isolated Ten Years Ago...
• 3-Jun Marina Manrique (Era7) Automatic annotation of E. coli TY2482
• 3-Jun Simon Gladman Automatic annotation of E. coli TY2482
• 4-Jun Kat Holt Two strain SNP comparison
• 5-Jun David Studholme Comparisons of E. coli TY2482 against previously sequenced E. coli genomes
• 5-Jun Kat Holt EHEC genomes – plasmid
• 5-Jun Konrad Paszkiewicz TY2482,-LB226692-vs-Genbank-Ecoli
• 5-Jun Phylogeo HUSEC41 German outbreak strains are not that ‘new’
• 5-Jun Mariam Rizkallah Automatic annotations with RAST
• 5-Jun Kat Holt Comparative genomics - acquired material
• 5-Jun Raquel Tobes Preliminary functional manual annotation of E. coli TY-2482
• 5-Jun Raquel Tobes Identification of genes involved in colonization, adhesion, pathogenicity and metal resistance
• 5-Jun Raquel Tobes Analysis of TY-2482 genome plasticity
• 6-Jun David Vallenet Explore LB226692 annotations with MicroScope
• 6-Jun Kat Holt EAEC plasmids and aggregative fimbriae
• 7-Jun Kat Holt Gene content and horizontal transfer analysis
• 7-Jun Wolfgang Gerlach Taxonomic analysis of 3057 genes from TY-2482 with CARMA3
• 7-Jun Raquel Tobes & Marina Manrique (Era7) Automatic annotation of E. coli TY2482 BGI V2 assembly
• 8-Jun Raquel Tobes & Marina Manrique (Era7)Automatic annotation of E. coli LB226692 genome
• 8-Jun David Studholme A cluster of E. coli 55989 genes missing from outbreak strain TY22428. Is this a T6SS?
• 8-Jun Kat Holt Annotation of phage in the latest (6/6; HiSeq data) assembly
• 8-Jun Kat Holt Typing schemes & PCR targets for the outbreak strain
• 9-Jun Scott Weissman & Kat Holt Plasmid MLST analysis of IncI/blaCTX-M plasmid
• 9-Jun Nico Petty via Kat Holt More detailed analysis of prophage
• 9-Jun Konrad Paszkiewicz Pfam domain comparison
• 10-Jun Raquel Tobes Mauve comparison of E. coli H112180280 and TY-2482 strains
• 10-Jun Kwan lab The outbreak strains have similar pathogencity as Ecoli EAEC strain 55989: Alignment of virulence factors from VFDB
• 11-Jun Kat Holt EAEC plasmid comparison with new scaffold assemblies
• 11-Jun Kat Holt Comparison of new BGI and HPA scaffolds
• 11-Jun Kat Holt Resistance genes in the same scaffold as chromosome
• 11-Jun Günter Klambauer, Martin Heusel, Djork-Arné Clevert and Sepp Hochreiter Copy number analysis of the outbreak strain
• 11-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of BGI V3 assembly of E. coli TY-2482 genome
• 11-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of HPA assembly of E. coli H112180280 genome
• 12-Jun Kat Holt Analysis and manual annotation of chromosomal insertion containing adhesin/pathogenicity island plus multiple drug resistance operons
• 13-Jun Kat Holt Biofilm-associated genes and acquired pic mucinase
• 12-Jun Patrik D'haeseleer Alignment of all three assemblies with 55989 and plasmids
• 13-Jun Kwan Lab [The outbreak strains harbor the whole set of EAEC secreted proteins] (http://hskwanfptcuhk.blogspot.com/2011/06/outbreak-strains-harbor-whole-set-of.html)
• 14-Jun Peter Slickers Read length matters: identifying the phiStx2 att site
• 14-Jun Lisa Crossman Salmonella matches & annotations on two TY2482 plasmid scaffolds
• 14-Jun Konrad Paszkiewicz & Kat Holt SNP-base phylogeny confirms similarity of E. coli outbreak to EAEC Ec55989
• 14-Jun Peter Slickers MLST and serotyping 55989 in silico
• 15-Jun Lisa Crossman [Rearrangements in the plasmids from TY2482 and H112180280] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 16-Jun Kat Holt BRIG visualisation of 4 available genomes
• 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of second HPA assembly of H112180280 isolate
• 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotations of BGI latest assembly (Illumina reads, no gaps) of the chromosome and 3 plasmids of the isolate TY-2482
• 16-Jun Marina Manrique & Raquel Tobes (Era7) Automatic annotation of G2L assembly of GOS1 isolate
• 17-Jun Marina Manrique & Raquel Tobes (Era7) [Automatic annotation of G2L assembly of GOS2 isolate] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/GOS2/seqProject/G2L/annotations/era7bioinformatics/Era7_GOS2_annotation)
• 17-Jun Lisa Crossman [Manual annotation of pTY1 and some comments] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 17-Jun Lisa Crossman [Metabolic pathway maps] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 18-Jun Kat Holt Visual comparison of five outbreak genomes using BGI 'complete' sequence (16/06/11) as reference
• 19-Jun Peter Slickers Regions of difference - an inventory of genomic islands, prophages and other accessory gene clusters.
• 21-Jun Kwan Lab [A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation - Part I] (http://hskwanfptcuhk.blogspot.com/2011/06/proposed-analytical-workflow-in.html)
• 21-Jun Lisa Crossman [Orthologous genes shared between pTY1&pTY2 and related plasmids, explanation and description.] (http://www.sequenceanalysis.co.uk/CrowdSourcing/) The pictures are shown [here] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/tree/master/strains/comparativeAnalysis/LisaCrossman)
• 22-Jun Nico Petty Comparison of 0104:H4 strain TY-2482 chromosome to other sequenced E. coli
• 23-Jun Kat Holt SNP analysis & plasmid copy number using read mapping for 4 HPA strains & TY2482
• 23-Jun Kwan Lab [German outbreak strains: Alignment-free whole-genome phylogeny suggested that EAEC 55989 is a close relative but not a direct parent] (http://hskwanfptcuhk.blogspot.com/2011/06/german-outbreak-isolates-alignment-free.html)
• 24-Jun Lisa Crossman [Incompatibility groups of plasmids suggest avian source connection] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 2-Jul Kwan Lab [Germany outbreak strains: Distinguishing Feature Analysis suggested the presence of an additional unique prophage element] (http://hskwanfptcuhk.blogspot.com/2011/07/germany-outbreak-strains-distinguishing.html)
• 8-Jul Kwan Lab [Germany E. coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST] (http://hskwanfptcuhk.blogspot.com/2011/07/germany-e-coli-outbreak-prophage.html)
• 8-Jul Lisa Crossman [Very brief comment on PacBio sequence] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 18-Jul Lisa Crossman [Antibiotic resistance gene cluster] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 25-Jul Lisa Crossman [Aggregative E.coli gene cluster frameshifts] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 28-Jul Lisa Crossman [2001 outbreak strain versus the current outbreak] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)
• 6-Aug Lisa Crossman [Requested Repost of TY2482 metabolic map data] (https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/blob/master/strains/TY2482/seqProject/BGI/analysis/Crossman_metabolic_maps/map.tar.gz)
• 13-Nov Lisa Crossman [online detective work - Egyptian seeds with Al-Jazeera news video] (http://www.sequenceanalysis.co.uk/CrowdSourcing/)

Announcements

• 2-Jun Announcement of sequencing reads
• 5-Jun New clues found in tracing the origin of the deadly E coli strain and an appeal for the sharing of additional data
• 6-Jun EHEC: Scientists of Münster identify genome sequence of a comparable strain of the year 2001
• 6-Jun A de novo assembly of E. coli TY-2482 and free and validated diagnostic protocols and primers
• 7-Jun Oh no sequences! (Era7) annotates the second BGI assembly of E. coli TY-2482 with BG7 system
• 8-Jun Oh no sequences! (Era7) annotates E. coli LB226692 with BG7 system
• 9-Jun PATRIC Bioinformatics Resource centre has annotated the two genomes (using RAST) and provide comparative gene analysis
• 9-Jun Life Tech have released reads for LB226692 also added under 'Sequence reads' above.
• 10-Jun [Health Protection Agency UK Release 454 Genome of O104:H4 strain (H112180280)] (http://www.hpa-bioinformatics.org.uk/lgp/genomes)
• 11-Jun [BGI new scaffold released using paired end Illumina data] (ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/Escherichia_coli_TY-2482.scaffold.20110610.fa.gz) ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/Escherichia_coli_TY-2482.scaffold.20110610.fa.gz
• 13-Jun [PATRIC analysis looks at unique and divergent proteins in the two genomes] (http://enews.patricbrc.org/1197/unique-and-divergent-proteins-in-e-coli-outbreak-strains/)
• 16-Jun Two new genomes released from Göttingen Genomics Lab (note, username and password for FTP site is EAHEC_GOS)
• 16-Jun [BGI new scaffold assembled to single-base resolution without gaps released] (http://www.genomics.cn/en/news_show.php?type=show&id=660)
• 19-Jun Peter Slickers - I have started Wiki page "Regions of difference" for the collaborative annotation of genomic islands, prophages and other accessory gene clusters. Please contribute to this page in order to get a comprehensive inventory of all ROD present in the outbreak strain.
• 21-Jun Kat Holt MiSeq reads & assemblies available for HPA's H112180280 (previously sequenced by 454) plus 4 additional strains posted by HPA UK
• 23-Jun NCBI has Bioproject page organizing data publicly accessible at NCBI - (http://www.ncbi.nlm.nih.gov/bioproject/68275)
• 6-Jul Pacific Biosciences sequence an outbreak isolate, plus 7 African O104 EAEC strains 4 other EAEC strains (http://blog.pacificbiosciences.com/2011/06/smrt-technology.html)
• 13-Jul ASM Makes Research Publications on Enterohemorrhagic E. coli Freely Available (http://tiny.cc/3ri84)
• 20-Jul Univ. Muenster and Life Technologies have released Ion Torrent reads and a genome assembly of the historical HUSEC041 (ST678) E. coli O104:H4 isolate from 2001
• 1-Nov-2012 About 17 month after the outbreak a consortium initiated and supported by US military has published the first high-quality and fully assembled genome of an outbreak-related O104:H4 isolate alongside with two genomes of historical O104:H4 isolates from the Republic of Georgia. Initially a combination of Illumina and 454 sequencing was used, augmented with more than 400 PCR sequencing reactions for each genome to fill gaps and resolve repeated elements. Genbank entries: 1: outbreak-related isolate 2011C-3493, 2: historical isolate 2009EL-2050, 3: historical isolate 2009EL-2071.

Visualization of results

• 6-Jun Pablo Pareja Tobes(Era7) Era7-E.-coli-TY2482-annotation-with-BG7-system:-results-visualization
• 10-Jun Pablo Pareja Tobes(Era7) Visualization of GO annotation results from Automatic annotation of E. coli TY2482
• 2-Dec Pablo Pareja Tobes (Era7) Graph Visualizations of GO annotation results from automatic annotation of BGI V4 assembly

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] (http://www.bbc.co.uk/news/uk-13918692)
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.

Contributing

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

Contributors

• 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.