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

posted in: Syndicated | 6

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!

Follow David Tribe:

David Tribe is an applied geneticist, teaching graduate/undergrad courses in food science, food safety, biotechnology and microbiology at the University of Melbourne.