Determining the origin of the E. coli strain attacking Europe – Part 1

There is considerable interest in the origin of the E. coli strain infecting and killing people in Europe. At this point, there is insufficient evidence to establish the source. However, broadly speaking, there are two possibilities: a naturally occuring recombinant which likely began in the gut of a cow or a manipulated strain born in a laboratory. I realise that in even mentioning the second possibility, this blog will be lumped in with sites populated by frauds, the gullible, the ignorant and the mentally ill. This is unfortunate, but is not a reason to exclude an obvious possibility.

Our first task is to describe the genetic elements which are responsible for an E coli bacterium’s function. E coli have two types of DNA, a single large chromosome and smaller plasmids. The chromosome is about 5 million base pairs long and contains about 5,000 genes. In addition, bacteria may contain plasmids, small circular pieces of DNA which may encode proteins which allow a bacteria to resist antibiotics. Further, these plasmids can be exchanged between bacteria which may not be closely related. In an environment where antibiotics are in heavy use, such as an hospital, selection can favor strains of bacteria which have acquired resistance to such antibiotics via plasmid exchange. This is why antibiotic resistance can spread so quickly between different strains of bacteria.

Although pathogenic E coli have caused great harm to humans, laboratory strains of E coli have long been used both as an engine of discovery and to develop therapeutics. Children who did not produce enough growth hormone used to be given extracts taken from the pituitary glands of cadavers. This supply was expensive, limited and sometimes dangerous. Genetically engineered bacteria changed this by providing a limitless and safe supply of growth hormone. Many other therapeutics are now available due to genetic manipulation of bacteria.

Recombinant DNA technology in bacteria makes use of several tools.  Pieces of DNA can be cut using proteins called restriction enzymes. There are many types of restriction enzymes which recognise specific sequences of nucleotides. Plasmids are convenient tools for transferring genes into bacteria and amplifying genetic material. They can be engineered to contain sequences which make it easy to use restriction enzymes for modifying them. This technology is well-established and so easy to use that kits are available for High School students.

E. coli are capable of exchanging genetic material under natural conditions. They can also be easily manipulated in a laboratory. Determining whether a novel strain of a bacteria is natural or laboratory made is not an easy task. In the next blog in this series, I will discuss the existing evidence and what additional evidence would be useful in distinguishing between these two possibilities.

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3 thoughts on “Determining the origin of the E. coli strain attacking Europe – Part 1

  1. do you have the genome ? I just (only) know flu.
    So, compare with the mexflu-creation reassortment and how we determined
    that it’s (likely) natural.
    get several EHEC genomes (ignore the plasmids ?) align them.
    Get the new one and the ancestors that it recombined from.
    Compare the number of mutations between the strains.
    Can they already estimate when that recombination happened ?

    I found that one link to the Chinese webpage that sequenced it.
    But don’t understand their “run” files

  2. gsgs, the “run” files are raw sequences from a Next Generation sequencer. These are short sequences which have not yet been assembled into full length chromosomal and plasmid sequences. You are used to looking at “finished” sequences wherein the short sequences for individual viral genetic elements have already been assembled. Doing the assembly on the bacterial genome is much more difficult than small viral segments. There are rough drafts of the new ecoli genome, but the finished version is not ready yet.

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