Summaries of genes in E. coli outbreak strain
- Summary of genome content (June 6)
- Comparison of new BGI and HPA scaffolds and mapping to major plasmids & phage
- Resistance genes inserted in the chromosome? (June 11)
- Biofilm-associated genes in the outbreak genome (June 13)
- New visual comparison of four outbreak genomes (June 16)
- Visual comparison of five outbreak genomes using BGI ‘complete’ sequence as reference (June 17)
- Plasmid copy number
- IncI MLST from Scott Weissman
- IncI blaCTX-M plasmid
- Aggregative (EAEC) plasmid and agg operon
- Updated aggregative (EAEC) plasmid using BGI & HPA scaffolds
- SNPs among HPA genomes and TY2482 (BGI)
- Phylogeny of outbreak and all available E. coli genomes (June 14)
- Point mutations between Ec55989 and outbreak genome TY2482 (June 15)
- First comparison between the two sequenced isolate genomes
- Latest assembly from BGI and reads from LifeTech
- Third strain sequenced by Health Protection Agency Collindale (UK) – 454, 13 scaffolds
Data & availability:
Update June 21. In addition to the 454 scaffold for H112180280, the UK’s Health Protection Agency has now posted Illumina MiSeq data (reads + assembly) for H112180280 and a further 4 isolates: http://www.hpa-bioinformatics.org.uk/lgp/genomes
Update June 17. BGI has now released a ‘complete’ assembly of their isolate, including one chromosome contig, the pAA and IncI plasmids (1 contig each) and a mini plasmid (1 contig).
Update June 16. Note 2 new genomes (454) now available from the Göttingen Genomics Lab, see comments section below for details.
Update June 13. BGI has now formally released their data, including reads, under Creative Commons 0 license. This is the most open license possible, and includes this statement:
The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
They have set up this page with links to, and details of, all the data available.
A similar formalisation is expected from HPA soon.
There are currently three genomes available, TY2482 (BGI) and LB226692 (LifeTech), H112180280 (HPA UK).
Assemblies are available:
- Life Tech, LB226692, http://www.ncbi.nlm.nih.gov/nuccore/AFOB00000000
- BGI, TY2482, http://www.ncbi.nlm.nih.gov/nuccore/AFOG0000000
- Updated TY2482 scaffold from BGI (June 11), ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/
- H112180280 (HPA UK) http://www.ncbi.nlm.nih.gov/nuccore/AFPN00000000
Reads of all three are also now available:
- Life Tech, LB226692, Ion Torrent reads [97 MB direct link]
- BGI, TY2482, Ion Torrent & HiSeq reads [ftp site; multiple files]
- *H112180280 (HPA UK) http://www.hpa-bioinformatics.org.uk/lgp/genomes [*file now removed]
See github wiki for more up-to-date data, annotation & crowdsourced analyses: https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki
Science: Scientists Rush to Study Genome of Lethal E. coli [Summary only; subscription required to read full article]