Comparison of 0104:H4 strain TY 2482 chromosome to other sequenced E. coli
- who Nico Petty, University of Queensland
- what Comparison of TY-2482 chromosome to other sequenced E. coli
- date 22/06/2011
To illustrate the similarities and differences between the German outbreak strain of enteroaggregative-haemorrhagic E. coli (EAHEC) and EAEC and EHEC, I took the BGI complete sequence of the chromosome of strain TY-2482 (from 16/6/11), re-cut it to start at the same place as the other fully sequenced E. coli genomes in the databases, and compared it to its closest sequenced relative EAEC strain 55989, and the prototypical EHEC strain O157:H7 Sakai using ACT.
I’ve highlighted the major regions of difference in strain TY-2482 compared to 55989 (prophages are coloured pink, non-prophage regions are coloured green). I’ve also highlighted the Shiga toxin-encoding prophage (which is similar, but not identical, to the stx prophage in TY-2482) and the Locus of Enterocyte Effacement (LEE) pathogenicity island in Sakai (which is absent in TY-2482). The blue criss-crossing lines are due to repeated sequences throughout the chromosome, most of which are associated with a number of related prophages.
Then I compared the German outbreak strain to all other fully sequenced E. coli genomes available in the public databases using BRIG.
I used the chromosome of TY-2482 as the central reference, and the presence of TY-2482 sequences in other E. coli genomes is shown in the coloured rings (the genomes in the merged rings are - EHEC O157:H7 strains: EC4115, EDL933, Sakai, TW14359, TW14588; EHEC non-O157: O26:H11 str. 11368, O103:H2 str. 12009, O111:H- str. 11128; Other pathotypes: O55:H7 str. CB9615, O127:H6 str. E2348/69, O83:H1 str. NRG 857C, UM146, 536, UTI89, CFT073, E24377A, H10407, UMNK88, IAI39, IHE3034, S88, UMN026, APEC01; Lab/enviromental: BW2952, DH1, DH10B, MG1655, W3110, BL21, REL606, ATCC8739, KO11, W, SMS-3-5; Commensal: ABU83972, ED1a, HS, IAI1, SE11, SE15). I’ve not included the other strains that have been sequenced from this outbreak as Kat Holt has already shown that there are no obvious differences in the chromosomes of the separate isolates.
Regions of difference from EAEC strains 55989 and 042 are highlighted in the outside ring (prophages are purple, non-prophage regions are red). NB: I’ve not marked up all the prophage regions in TY-2482, just the phage that are either not found in, or are significantly different from, the prophages in 55989.