Scrutiny of all the evidence and the whole food chain is narrowing down the culprit in the German E. coli outbreak to sprouts operations in the Hamburg region

Updated 9/06/2011

The mists of uncertainty are starting to clear in Germany, after much waxing and waning over the last few days.

To find the culprit good detective work on what people eat and where they eat has been essential. Sprouts have been added to the lists of suspect foods which included cucumbers and tomatoes. Faecal contamination of sprouts is a common cause of major food outbreaks, as they are not cooked and provide conditions for ready multiplication of bacteria when bean shoots are sprouted.
Furthermore, perceptive comments reported in the New York Times point out that the pattern of disease fits with a contamination source somewhere in the food chain local to the Hamburg region in Germany, and not from outside the country. This could be contamination of beans in the field, [manure on the farm,] contamination from washing water, contamination from infected workers in a processing plant, or from a broken pipe in a water or sewer system. We don’t yet know exactly.
Recent news specifically mentions a particular sprout farm that has now closed. See links at end of this post. Amazingly, the manager of the farm “can’t understand how the processes we have here and the accusations could possibly fit together”. Later news provided by Spiegel online provides strong confirmation that the farm is the culprit:

Growing Indications Sprouts Were Tainted 8th Jun 2011.Spiegel OnlineConfusion over the source of the deadly E. coli bacteria grew on Wednesday when health officials detected it on a discarded cucumber in the eastern city of Magdeburg. Meanwhile, German authorities said they had found two new clues pointing to a sprout farm that may have been a source of the germ.
Earlier on Wednesday, German authorities had said there were growing indications that bean sprouts delivered by an organic farm in Bienenbüttel first identified as a possible source on Sunday may indeed be a cause of the outbreak.Health officials found two fresh clues that point to the farm near the town of Uelzen in northern Germany, the regional Consumer Protection Ministry of Lower Saxony said.Ministry spokesman Gert Hahne said a total of 18 people infected with EHEC, the deadly strain of the bacteria, around the northern port city of Cuxhaven ate sprouts from the farm in a company cafeteria.In addition, three female workers at the farm suffered from diarrhea in the first half of May, and one of them is known to have been contaminated with EHEC. Their work included packaging the sprouts.The ministry spokesman said it was possible that one of the women accidentally “fed the pathogen into the operations of the company.” Or they might have been infected with EHEC at the farm.Reuters reported that a local doctor said a worker at the farm had become severely ill with E. coli and had part of her intestine removed. The 54-year-old woman developed bloody diarrhea followed by serious blood disorders.Anton Schafmayer, a doctor who operated on her, said she had eaten the sprouts. “It went very fast. Such a pace is very rare,” he told Reuters. “The surgery probably saved her. We removed a large part of the lower intestine.”The Lower Saxony ministry spokesman said that despite the additional clues pointing to the sprout farm, it was still possible that the nationwide epidemic stemmed from several sources.Four company canteens and three restaurants where people caught EHEC are now known to have been supplied by the Bienenbüttel farm — infecting about 100 of the more than 2,600 EHEC patients in Germany. So far, no EHEC bacteria have been found at the farm.

And there’s another interesting clue emerging from the molecular scientific laboratory work which suggests that the German germ implicated in causing disease has a very similar bacterial relative that has been present in Germany for at at least 10 years. The combination of opportunity for growth of relatively rare German germ that is present in manure and faeces in low quantities, plus local distribution produce to retail outlets in Hamburg explains many features of the outbreak.
Bacterial evolution occurs in real time primarily by gene swapping.
Speculation about whe
ther this is a completely new germ is probably beside the point.Changes to the spectrum of virulence and toxin genes is commonplace in gut bacteria and there are billions of opportunities for this to occur with such large populations of germs, so evolution of new variants occurs at a fast pace in these bacteria. This is nothing new to science, even even if such gene shuffling generates novel combinations of characteristics (see Natural GMOs Part 85 ). That’s just another day at the office for bacteria.
And it’s not mutations. Journalists need to stop mindlessly nattering about mutations when they discuss new germs.  A major part of E. coli variation comes from gene exchange between germs, not accidental DNA mutation within a lineage of germs. They mostly take in fresh genes from outside when they evolve.
Reshuffling of genes is thus what E. coli does naturally. An E. coli with a new combination of genes that are present somewhere among gut bacteria is still E. coli, and gene addition to E.coli is a basic fact of life.
Key words: Food chain, Molecular fingerprinting, Contamination, faeces, water, manure, soil , Pathogenic Escherichia coli, EHEC, EAEC, Natural GMO

Collected other relevant press cuttings:

JAMES KANTER and ALAN COWELL At NY Times provide one perceptive diagnosis of the epidemic

Published: June 3, 2011
Considering the fact that a high numbers of infections that were spread across a single region of one country, the bacterium probably entered the food chain after leaving farms, but before the produce was sold directly to consumers, said Jonathan Fletcher, a senior lecturer in microbiology at the University of Bradford in England.
“The distribution suggests this wasn’t at the point of origin because given the way food chains work these days that means it would have already spread more widely across Europe and possibly the world,” he said. “At the same time, this has already traveled far enough to suggest that not just one stall or supermarket was responsible.”

Was World-Wide E. coli O104:H4 Outbreak Caused by Sprouts?

Associated Press reporter Tomislav Skaro reported from Hamburg this morning that the Lower Saxony agriculture ministry was sending an alert Sunday warning people to stop eating the sprouts, which are often used in mixed salads, ministry spokesman Gert Hahne told The Associated Press.
“Bean sprouts have been identified as the product that likely caused the outbreak,” Hahne said. “Many restaurants that suffered from an E. coli outbreak had those sprouts delivered.”
Hahne said the sprouts were grown on a farm in Lower Saxony in northern Germany. He did not elaborate but planned a news conference later Sunday.  Hahne said while official test results have not yet conclusively shown that the Lower Saxony-grown sprouts were to blame, “all indications speak to them being” the cause.
However, authorities have kept their warning against eating tomatoes, cucumbers or lettuce.
The head of Germany’s national disease control center raised the death toll to 22 Sunday — 21 people in Germany and one in Sweden — and said another 2,153 people in Germany have been sickened. That figure includes 627 people who have developed Hemolytic Uremic Syndrome.  The World Health Organization said 10 other European nations and the U.S. have reported a total of 90 other victims.

New clues found in tracing the origin of the deadly E coli strain and an appeal for the sharing of additional data

2011-06-05 20:54:46 BGI website
… we are now tracing the history of the bacteria, as this latest analysis indicates that the two German strains (01-09591 originally isolated in 2001 and TY2482 from the 2011 outbreak) have identical profiles for all 12 virulence/fitness genes and 7 MLST housekeeping genes. However, at some point over this 10-year period the new 2011 outbreak strain seems to have developed the ability to resist many additional types of antibiotics. The latest data is now pointing to this candidate, as it now seems the African strain (strain 55989) is genetically more “distant” as the Shiga-toxin-producing gene and tellurite-resistance-genes were shown to be absent. (see for our detailed comparison). The utility of so quickly sharing our initial data is further supported as the link to this original strain has already been independently verified by other groups: See also ColiScope where the sequence of strain 55989 was first displayed (, with option chromosome EC55989_EC55v2)

E.coli death toll rises to 22

Irish Times 7/06/2011
Photo caption Two security guards patrol in front of the organic farm suspected to be the source of the E.coli outbreak that has killed 22 and made more than 2,200 people ill across Europe. Photograph: Fabian Bimmer/Reuters
German scientists were working today to confirm an organic vegetable farm as the source of an outbreak of E.coli bacteria that has killed 22 people and caused a food scare across Europe.
The search for the source of the outbreak is proving very difficult, the Lower Saxony state agriculture ministry said.
E.coli tests on 23 of the 40 samples of beansprouts from the farm in north Germany have proved negative, and the tests are not expected to be completed in the short term, the ministry said in a statement.
The manager of the farm said he could not understand how it could be the source of an infection that is usually transmitted through faeces, or food or water contaminated with faecal bacteria.
The Shiga toxin-producing E.coli (STEC) strain found in this outbreak is known to be able to lurk in cows’ intestines.
“I can’t understand how the processes we have here and the accusations could possibly fit together,” Klaus Verbeck told the regional newspaper Neue Osnabruecker Zeitung….continues.

Waffling over E. coli cause points to ‘incompetence,’ US expert says

German probe of deadly outbreak fails to pinpoint source

Sprouts? Cucumbers? Authorities Still Searching for Source of E. Coli

Bacteria like E. coli can flourish on certain types of farms. Here’s a look at why.
(A readable discussion of food risks)

Netherlands finds E. coli again in beet sprouts; Thailand finds E. coli in European cabbage
Doug Powell

Seek and ye shall find.
But countries still won’t test their way to a safe food supply.
Testing is extremely useful for validating safety procedures and to have a sense of what’s out there.
There’s lots of various E. coli out there.
RNW reports for the second time this week the Dutch Food Quality Authority (nVWA) has found sprouts contaminated with the EHEC bacterium, although it is not the O104 variant. A spokesperson for the Authority said on Friday that the beet seed sprouts have been withdrawn from the market on the orders of Health Minister Edith Schippers.
Meanwhile, Thailand said on Saturday that it had detected E. coli in cabbage imported from Europe and was checking whether it was the lethal strain involved in a killer outbreak in northern Germany. 
On Friday Thailand said that E. coli found in avocados a day earlier was not the deadly strain that has swept Europe in recent weeks. 
Testing has a role — make it meaningful.

European Centre for Disease Prevention and Control

Is this E.coli strain a mutation and how does this affect the current outbreak? (2 June 2011)
The WHO has recently stated that this strain of E.coli “is a unique strain that has never been isolated from patients before” and there may be “various characteristics that make it more virulent and toxin-producing”.
The WHO reference laboratory has been able to confirm that this appears not to be a classical STEC. However, some reports of mutation ar
e incorrect. In simple terms “mutation” refers to a modification of a gene whereas the current issue raised by the WHO is better explained as a matter of acquiring extra genes or natural genetic recombination which is often seen with bacteria.

Thanks to Andy Apel, other press mentions of a sprout farm:

E. coli: What we know and need to
By Maryn McKenna   June 8, 2011  |  5:47 pm  |  Categories: Science Blogs, Superbug

One sharp comment on a particular organic industry response comes from from Ron Bailey at Reason:

Organic Folks Don Their Tin Foil Hats To Explain Outbreak of Deadly E. Coli Bacteria

Ronald Bailey | June 6, 2011

Nearly a score of people have died from infections from a deadly strain of E. coli bacteria in Germany. Thousands more have been sickened. German health authorities at first blamed Spanish cucumbers and more recently organic bean sprouts. Both appear to have been exonerated and the search for the source of contamination goes on.
In the meantime, some of the more unhinged proponents of organic fo
ods, evidently panicked by the claim that organic bean sprouts might be the source of the bacteria, have donned their tin foil hats and have figured out what’s really going on: the bacteria have been genetically engineered with the goal of discrediting organic foods: A small excerpt from the paranoid screed over at Natural News:
…if you can make people AFRAID of fresh vegetables — or even outlaw them altogether — then you can force the entire population onto a diet of dead foods and processed foods that promote degenerative disease and bolster the profits of the powerful drug companies.
It’s all part of the same agenda, you see: Keep people sick, deny them access to healing herbs and supplements, then profit from their suffering at the hands of the global drug cartels.
GMOs play a similar role in all this, of course: They’re designed to contaminate the food supply with genetic code that causes widespread infertility among human beings. And those who are somehow able to reproduce after exposure to GMOs still suffer from degenerative disease that enriches the drug companies from “treatment.”…
By the way, the most likely explanation of where this strain of e.coli was bioengineered is that the drug giants came up with it in their own labs. Who else has access to all the antibiotics and equipment needed to manage the targeted mutations of potentially thousands of e.coli colonies? The drug companies are uniquely positioned to both carry out this plot and profit from it. In other words, they have the means and the motive to engage in precisely such actions.
Aside from the drug companies, perhaps only the infectious disease regulators themselves have this kind of laboratory capacity. The CDC, for example, could probably pull this off if they really wanted to.
The proof that somebody bioengineered this e.coli strain is written right in the DNA of the bacteria. That’s forensic evidence, and what it reveals cannot be denied
. This strain underwent repeated and prolonged exposure to eight different classes of antibiotics, and then it somehow managed to appear in the food supply. How do you get to that if not through a well-planned scheme carried out by rogue scientists? There is no such thing as “spontaneous mutation” into a strain that is resistant to the top eight classes of brand-name antibiotic drugs being sold by Big Pharma today. Such mutations have to be deliberate.
In an email, one biotechnologist notes this irony:
Europe’s vaunted ‘farm to fork’ labeling and traceability system, which increases consumer confidence by allowing end user freedom of choice, and tracking to quickly identify and remove from the system any problematic foods, is only applied to GM foods, for which there have never been any documented cases of harm.
If you can stand it, you can marvel at Natural News‘ dark conspiracies here.


  1. I once heard that observed uptake of foreign genes by bacteria is almost entirely treating the foreign genes as food. It would be good to hear if this is accurate. Which would give us a more elegant account if true.

  2. Well in some ways yes. Perhaps better to say DNA is the only thing they eat, because they don’t eat their food, they absorb it as digested nutrients. They have no mouths or stomachs.

  3. Interesting and relevant comments at bacpathgenomics
    QUERY Posted by J. Brook on June 8, 2011 at 3:17 am
    So, was this new E. coli strain created in a lab? A biowarfare attack just before Merkel’s visit, when there’s so much at stake economically?
    Posted by kat on June 8, 2011 at 11:02 am
    No, there is basically zero chance of this. Bacteria do this all the time, they’ve been sharing genes for millenia and we are only just catching up and figuring out how they do it!
    As all the analysis shows (mine & others, collated here), all the genes present in this strain have been seen in E. coli before, and in fact there is an E. coli strain from Germany in 2001 which has all the same features. This is just a case of a bacteria that is usually seen in animals spilling over into the human food chain and causing some havoc.
    Unfortunate but not that unusual.

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