Genetic family trees show the German outbreak of E coli is a member of small family of germs called EAEC — that includes an African germ — and is distinct from EHECs

The latest news is that the German outbreak strain of Escherichia coli is a member of small family of germs called EAEC that includes an African member (Ec55989 ). This family is clearly distinct from classical EHEC (=STEC)  bacteria such as E. coli O157:H7. The Pundit will now start calling them  EAEC/STEC recombinant or hybrid germs, or alternatively Shigatoxin production EAECs.

Family tree for E. coli using genome sequence data.
Just hours back, as part of an astonishingly fast international crowdsourcing effort, Konrad Paszkiewicz from University of Exeter and Kat Holt University of Melbourne have taken great advantage of genome data kindly and very wisely freely made available to the scientific community by the several E. coli genome sequencing groups. Konrad and Kat have just now completed a preliminary family tree for the germs based on relevant genetic point mutation changes in the “genome backbone” genes.
In Kat Holt’s words:

The result clearly shows that the outbreak genomes (green) are very similar to Ec55989 (also green, labelled ‘reference’), and very different to other sequenced E. coli (note in particular the group of EHEC O157:H7 on the middle left, which are very distant from the outbreak strains). Since this is a network, it would reveal if there were major recombinations between this strain and the other E. coli chromosomes, which there aren’t. This confirms that the outbreak strain is truly an EAEC, with very close similarity to Ec55989 and not to classical EHEC. This is backed by the presence of an EAEC plasmid, [optional mini-chromosome] carrying aggregative adhesion fimbrial cluster I (AAF/I; agg operon; see this post for details [genes involved in attachment to the gut lining]). 

Alternative tree for E. coli based on “Splits” method.

This analysis by Konrad and Kat based on point mutations (called SNPs in geeky jargon) occuring in genes that do not have high inter-strain mobility (backbone genes) , and it thus avoids the genealogy confusion caused by mobile genes such as bacterial virus DNA (phages).

Not only that, Mike the Mad Biologist has a very recent posting explaining about EAEC germ biology, and where they might come from and where they might hide

Crowdsourcing rules, OK!

Written by David Tribe

David Tribe’s research career in academia and industry has covered molecular genetics, biochemistry, microbial evolution and biotechnology. He has over 60 publications and patents. Dr. Tribe's recent activities focus on agricultural policy and food risk management. He teaches graduate programs in food science and risk management as a Senior Lecturer in the Department of Agriculture and Food Systems, University of Melbourne.


  1. Somehow this article was “sheltered” from web searches for a while. Old, but still interesting.
    “The deadly new strain of E.coli that has killed 18 people in Europe risks spreading from person to person in Britain, the Health Protection Agency warned last night.
    “As seven cases of the food poisoning bacteria were diagnosed in Britain, the agency said that the mutant strain was so virulent that sufferers risked spreading the infection to friends and relations through close contact.
    –Killer E.coli strain infects first victims in Britain, The Guardian, 2 Jun 2011

  2. Thanks, David, this is fascinating. I have read that BfR believes the evidence is pointing towards the seeds used on the farm as a likely vector, does this mean that manure is an unlikely source of the contamination on the seed farm?
    Does this narrow down the possible sources or is it possible for humans to infect animals who then re-infect us? I’m wondering, generally, where this steers the investigation, shouldn’t it be pretty easy to check the suppliers of the seeds? Oops, I realize thats alot of questions, sorry.

    1. I think its important to keep a completely open mind and wait for good evidence to be discovered and analysed rigorously. The conclusions should driven from specific evidence using prior knowledge to guide the search. The genetics is pointing to the possible importance of a human carrier component. Clearly the background science says the infection could be transmitted by the seed (E. coli can live even inside the seed). The cautions from RKI/other agencies against several different kinds of sprout could indicate several different things. One only is a common source on the Lower-Saxony farm.That’s about all we know from outside. The seed information does NOT rule out manure. The evidence says manure at the Lower-Saxony farms is not very likely the cause, but the farms the seed came from may be a very different story. They may be non-German and non-organic.

        1. Thanks, David, I’m surprised we haven’t heard anything about the seed farms yet.

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