E. coli outbreak – PacBio data and PLoS One paper on 2001 O104:H4 strain

It’s been a while since my last post, mainly because my attention has had to return to other things (my day job, ASM, and holidays in the Australian Snowy Mountains).

But a fair bit has happened in the last few weeks on the E. coli front.

PacBio has released some data from an outbreak strain plus a few related strains. As far as I know this is the first time PacBio data has been released publicly so it’s a good opportunity to have a play…I will at some point but not tonight! The data includes very long reads (average ~3 kbp) but with 85% accuracy (ouch! but useful for assembly)…using their circularised read approach, they get much better accuracy (average ~98%) but much shorter reads (average 430 bp).

Muenster & Life Tech have now published their analysis of outbreak strain and the 2001 O104:H4 STEC strain from Germany in PLoS One. Data is available here at NCBI.

The key finding of interest, I think, is that the stx2 phage (i.e. Shiga toxin) was present in the 2001 strain – apparently identical and in the same position – suggesting that the phage was acquired by a common ancestor of the 2001 and 2011 German O104:H4 strains. However the stx2 phage does favour certain insertion sites, so it is still possible that this represents two separate acquisitions.

This is their model:

Mellman et al, PLoS One 2011 - Model for O104:H4 STEC evolutionMellman et al, PLoS One 2011 - Model for O104:H4 STEC evolution

The two strains carry different aggregative adhesion plasmids (AAF/III in 2001; AAF/I in 2011) and different resistance plasmids, consistent with some evolutionary time separating them.

The paper says that each strain has accumulated 87-95 SNPs among 1,444 chromosomal genes since they shared a common ancestor…but I’ve not looked in enough detail to be convinced the authors have corrected sufficiently for homopolymers.

Interestingly their tree suggests that the common ancestor of the 2001 & 2011 German strains is also the common ancestor of the African (stx2-free) EAEC strain Ec55989 (which has picked up 24 SNPs)…again I’m not sure whether this is correct until I inspect the data myself, and the lower number of SNPs in Ec55989 makes me a little suspicious that the others are over-estimates….since Ec55989 was isolated ~1999 I think so should have a similar number of SNPs to the 2001 strain. But still a very interesting development.

This is their tree:

Mellman 2011 PLoS One - minimum spanning tree