E. coli strain in Germany is not novel

By Tonington
June 06, 2011
E. coli
E. coli -Unknown
Last night officials announced that the most likely source of this E. coli outbreak is from bean sprouts grown in Germany, which is a huge embarrassment for Germany after initially blaming the Spanish. Bean sprouts, have long been a source of both E.coli and Salmonella sp. caused illnesses over the years.

When the story first broke, there were many that were calling this a new or novel strain of E. coli. That was based on the sequencing of the genome, which actually breaks the genomic DNA up into about a few thousand pieces. The technology used is quite marvelous, it allows for rapid sequencing of genomes by using basically the world's smallest pH meter, to measure the H+ ions that are released when nucleotides are added to templates and incorporated into a strand of DNA.

Anyways, it turns out that initial reports of this sequence being novel were wrong. Once the sequence was published, labs around the world could begin analyzing the data. Using other techniques, such as multi-locus sequencing typing (think of it as being able to tell the difference between plagiaized copies of work, by analyzing the percentage of overlap, only with the DNA it's the addition of new words or letters to the same word).

The end result-which by the way is a marvel of modern science communication- is that this particular E. coli has been encountered before, in 2001 to be exact. There is a database that molecular results can be used to search for, and sure enough, this strain is a match for ST678 typing.

It's pretty remarkable in this day and age that scientists can confirm their results using different sequencing techniques, with colleagues so far away, and so quickly. I get the feeling sometimes that the public doesn't understand how difficult this can be, such as with new flu types...

A nice bit of work, now let's hope they can get all the contaminated food recalled, and work towards meaningful changes with respect to food safety. Germany actually has better access to illness reports than Canada does...this easily could happen here. I was particularly concerned with the lack of response from Canada Food Inspection Agency.

The discussion of most importance, beyond improving the networks available for screening illness in hospitals and clinics for early detection, is the drug resistance of this pathogen.

This was sort of a side line interest for academics as the illness spread, as E.coli is a gram negative bacteria...treating gram negative bacteria with anti-biotics makes the illness worse, because the illness isn't actually caused by the bacteria itself, but by the toxins it excretes. So, anti-biotic use means a large rush of toxic chemicals which makes the disease far worse.

Other strains of E.coli do not have this level of antibiotic resistance, but the ease with which genes are transferred horizontally between bacteria, it's only a matter of time before that happens.

So here's my public service announcement, do not use anti-microbials for everyday disinfection. We as a society do far too much of that, and all that does is add a selection pressure, which hastens the resistance these microbes develop.

This strain in Germany is resistant to at least 12 drugs, from almost ten different classes of anti-biotic.

If you want to disinfect your hands, use ordinary rubbing alcohol. As the alcohol evaporates, it carries the microbes off your skin in aerosols. Safe, effective, cheap, and it won't contribute to drug resistance in our pathogens.