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.


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Comments (30)
taxslave's Avatar
taxslave    Jun 5th, 2011
That is rather embarrassing. Much like the US blaming Canada for the 911 attacks. Am I right that E.coli comes from feces contaminated food?
Tonington's Avatar
Tonington    Jun 5th, 2011
Quote: Originally Posted by taxslave --

That is rather embarrassing. Much like the US blaming Canada for the 911 attacks. Am I right that E.coli comes from feces contaminated food?

It's a fecal-oral transmission of disease. It can come about by improper sanitation in food preparation, from contamination on the farms with manure spreading, contaminated water used for irrigation, and even flies or airborne particles.
petros's Avatar
petros    Jun 5th, 2011
And well drawn drinking water...it has no problems living in the ground.
Tonington's Avatar
Tonington    Jun 5th, 2011
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+1
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.
petros's Avatar
petros    Jun 5th, 2011
What is the total score on "Super Bugs" these days? MRSA is one I've experienced and my wife. I got it post operative she just plain picked it up from working in a hospital. She did okay with the treatment but I had an evil reaction to the vancomyacin and had to stop treatment and switch to a synthetic antibiotic.
Tonington's Avatar
Tonington    Jun 5th, 2011
I have no idea, I would imagine it's a lot. I know for sure of eight bacterial species that can be found in that group, but the number of strains, I have no sweet clue.
karrie's Avatar
karrie    Jun 5th, 2011
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People have so many produce items that they don't wash, it never ceases to blow me away. Pre-peeled carrots, snap peas, bean sprouts (apparently the culprit in Germany), spinach (cause of recent outbreaks in NA), melons, pineapples.... the lists go on and on.

Stop and think for one second about what kind of bathroom facilities the person picking your produce is being provided with, and you will ALWAYS, wash EVERYTHING.
Tonington's Avatar
Tonington    Jun 5th, 2011
On a related note, I read recently of a husband and wife. Can't remember which, but one partner had an aggressive C. difficile infection, and they weren't responding to treatment. In the gut, the clinicians found an abnormal population of microbes, some that shouldn't have been there.

They ended up taking a stool sample from the healthy partner, and transplanting it into the gut of the sick partner. The turn around was very fast. Weight loss stopped, and they regained their health very quickly.

The hope is, that some day, the microbiologists will know their stuff well enough that instead of using a stool sample, they can just select a cocktail of species to trasnplant in the gut. Once those species out-compete the exotics in the gut, the normal gut population can return.
petros's Avatar
petros    Jun 5th, 2011
Quote: Originally Posted by Tonington --

On a related note, I read recently of a husband and wife. Can't remember which, but one partner had an aggressive C. difficile infection, and they weren't responding to treatment. In the gut, the clinicians found an abnormal population of microbes, some that shouldn't have been there.

They ended up taking a stool sample from the healthy partner, and transplanting it into the gut of the sick partner. The turn around was very fast. Weight loss stopped, and they regained their health very quickly.

The hope is, that some day, the microbiologists will know their stuff well enough that instead of using a stool sample, they can just select a cocktail of species to trasnplant in the gut. Once those species out-compete the exotics in the gut, the normal gut population can return.

"Phage Therapy". I've been looking into what the options are. Only linezolid will work for me but I'll always remain at high risk of re-infection and need to be cultured for every infection that does come along.

$3500 for 10 days of linezolid. Safeway tried to weasle out of the 10X Airmiles for that Rx.
Retired_Can_Soldier's Avatar
Retired_Can_Soldier    Jun 5th, 2011
German Beansprouts!

Those god damned Germans! Two world wars and now this.

Will they ever learn?