Tracking the source of an E. coli outbreak


Europe is currently in the grip of a deadly outbreak of Escherichia coli O104:H4—a rare strain of a common bacterium. Prior to last month, E. coli O104:H4 had only been identified as a cause of illness in one, single person. As of yesterday, the bacteria had sickened thousands and killed 27.

E. coli is a gut bacteria. There are E. coli living in your intestines right now. The good news is that those strains aren't dangerous. Instead, when people get sick from E. coli, it's usually the work of strains that live in the guts of animals, especially cows. These bugs, while as friendly to their bovine hosts as our E. coli are to us, release chemicals that are toxic to people. When we consume them—by getting meat juices on fresh vegetables or fruit, via manure sprayed on crops, or through contaminated water supplies—the foreign E. coli can make us very, very sick. And that sickness is difficult to treat. That's because some strains, including O104:H4, actually release more toxins when you try to fight them with antibiotics.

The European Center for Disease Prevention and Control has linked most of these recent cases back to the northern part of Germany, the victims either live there or had recently traveled through the region. So it's reasonable to assume that the contaminated food either came from there, or was eaten there. But that's the easy part. It's much, much harder to figure out what, exactly, it was that made people sick. Over the weekend, authorities thought they'd pinpointed the outbreak to a bad batch of organic salad sprouts. But, when preliminary tests of the sprouts turned up no evidence of contamination, they backed off and started pointing the finger at imported cucumbers and tomatoes from Spain. Today, the official opinion flip-flopped again. Direct tests of the sprouts are still turning up negative. But epidemiological studies show that people who ate the sprouts were 9 times more likely to become infected than those who had not.

That's enough evidence to affect the immediate public health response—shut down the farm, warn people off sprouts. But it's not necessarily going to be the final word on where this outbreak came from.

Top image: A graph showing examples of a bacterial growth mediums including a few of Escherichia coli (E.coli) bacterias displayed in a microbiological laboratory at the Bulgarian Food Safety Agency in Sofia June 9, 2011. The European Union on Wednesday upped compensation to 210 million euros from 150 million for farmers hit by plummeting sales, after Germany first blamed cucumbers from Spain and other salad vegetables, and then German bean sprouts. (REUTERS/Stoyan Nenov)

In fact, outbreaks of food-borne illness, in general, are tricky to pin down. Just think about the way you eat—lots of different foods, from different stores, coming from different places ... even different countries. You don't know where it came from. And you probably don't even have the best recall of what you specifically did and didn't eat over the course of the past week. That's important, because investigations of food-borne illness start with interviews. Epidemiologists compare the foods that sick people reported eating and compare them to the ones that healthy people ate. Any dish that shows up more frequently among the sick becomes a suspect. But then scientists still have to narrow down the ingredients. It's a slow investigation, and an imperfect one that, by its nature, can only happen long after the trails of evidence start to become fuzzy. The United States Centers for Disease Control explains how scientists can be mislead:

Some might think that the best investigation method would be just to culture all the leftover foods in the kitchen, and conclude that the one that is positive is the one that caused the outbreak. The trouble is that this can be misleading, because it happens after the fact. What if the Hollandaise sauce is all gone, but the spoon that was in the sauce got placed in potato salad that was not served at the function? Now, cultures of the potato salad yield a pathogen, and the unwary tester might call that the source of the outbreak, even though the potato salad had nothing to do with it. This means that laboratory testing without epidemiologic investigation can lead to the wrong conclusion.

As a result, it's not particularly unusual for investigations of food-borne illness to get the culprit wrong, or point to a couple of possible culprits and then later narrow it down after the outbreak has ended. It's also not surprising to statistically pinpoint a veggie villain that never actually tests positive for E. coli. In 2006, for instance, an American E. coli outbreak was traced to Taco Bell, but the specific vegetable involved was at first misidentified. The statistical investigation pointed to green onions, then later to shredded lettuce. But no food samples ever turned up positive for the strain of E. coli that made people sick. That's because the entire supply—even the entire supply from the same supplier—doesn't have to be contaminated for people to get sick. And scientists can't test every single green onion or, in this case, every single sprout.

This week, Reuters sent photographers into labs across Europe to see how that sampling and testing is done. In this series of photographs, you can follow along as whole sprouts are turned into liquified samples, and the samples are tested to see whether E. coli is present. The shots don't all come from the same places, but this will give you a good idea of what the process looks like. (All caption text by Reuters, not me.)


An Austrian scientist selects cress sprouts in the microbiological laboratory of the The Austrian Agency for Health and Food Safety (AGES) in Vienna June 9 , 2011. The German government has been criticised at home and around Europe for failing so far to pin down the cause of the E.coli outbreak that has killed 27 and stricken more than 2,700 people in 12 countries. All cases have been traced back to near Hamburg in northern Germany. (REUTERS/Leonhard Foeger)


Cress sprouts suspended in a culture medium are pictured in the microbiological laboratory of the The Austrian Agency for Health and Food Safety (AGES) in Vienna June 9 , 2011. (REUTERS/Leonhard Foeger)


Cress sprouts, suspended in a culture medium, are weighed in the microbiological laboratory of the The Austrian Agency for Health and Food Safety (AGES) in Vienna June 9 , 2011.(REUTERS/Leonhard Foeger)


Specialist Oksana Krivcenko prepares food sample to isolate the Escherichia coli (E.coli) bacteria strain at the Institute of Food Safety, Animal Health and Environment in Riga, Latvia, June 9, 2011.(REUTERS/Ints Kalnins)


Specialist Marina Soloviecika holds test-tubes as she works to isolate the Escherichia coli (E.coli) bacteria strain at the Institute of Food Safety, Animal Health and Environment in Riga June 9, 2011.(REUTERS/Ints Kalnins)


An Austrian scientist holds a petri dish with bacterial strains of EHEC bacteria (enterohaemorrhagic Escherichia coli.) in the microbiological laboratory of the The Austrian Agency for Health and Food Safety (AGES) in Vienna June 9 , 2011. (REUTERS/Leonhard Foeger )


  1. I remember reading about a case last year where someone (Joyce Carol Oates husband) died from e-coli in their lungs. I didn’t know that was possible.

    Can someone explain how e-coli ends up in the lungs, and what can be done to prevent this?

  2. I just loved this tweet from a few days ago:

    @danieltatarsky – In 1 week 18 die from eating cucumbers, everyone stops eating cucumbers. Every single week 100,000 die from smoking. No one stops. We’re nuts.

      1. I’m a non-smoker, but I think you’re onto something there. Cucumbers are just kinda good. Cigarettes must be better.

        1. [insert here dirty joke mentioning cigars and cucumbers, and highlight the “insert here” part and also the “insert here part” part.]

      2. Or, perhaps, cigarettes are 4 orders of magnitude more satisfying than cucumbers?

        Few things in life are as satisfying as a skillfully wielded cucumber.

        1. “Few things in life are as satisfying as a skillfully wielded cucumber.”

          that statement is completely factitious in quality and quantity.

    1. “Every single week 100,000 die from smoking. No one stops.”

      Maybe because that statement is completely factitious in quality and quantity. Know what? You’re right that there are too many chicken littles running around.

      Most of us live in artificial environments steeped in multiple toxins. Who knows how they interact? Really think you’re getting the lowdown when the regulators keep quiet about Roundup for decades?

      Know when we knew about radon? Know where all the fallout is? Know the chemical history of your locale? Didn’t think so. We’re all in that boat. Simplistic pap doesn’t help.

    2. While that’s pretty funny, the reason people stop eating cucumbers when there’s a deadly outbreak and don’t stop smoking deadly cigarettes is because a cigarette won’t SUDDENLY kill you, but that cucumber sandwich might (though, probably not, but you know how fear permeates culture).

  3. “Europe is currently in the grip of a deadly outbreak”

    Erm…that’s a bit strong. The outbreak is based in one part of one country (Northern Germany), and whilst it’s true that people have travelled and many, many people are affected, to suggest that it has a whole continent in its grip is silly.

    Great article, marred by sensational lead.

  4. Have you read the crackpots over at Natural News’s take on this?

    Mike Adams wrote an article on how this strain of e.coli was genetically engineered by Big Pharma to be as virulent and antibiotic resistent as possible, then Big Bad Pharma sprayed them on produce trucks or something and then ran like the devil.

    1. Genetically engineer superbug
    2. Release into food supply to create a “controlled outbreak”
    3. ????
    4. PROFIT

    Seriously I hate that guy.

    1. Well, c’mon. The first picture in the post says it all, I didn’t have to read further….Merck caused the outbreak.

  5. I am amazed that there has been no suspicion of “terrorism” and no claim of a “successful attack” by some whacko group. I presume that an outbreak on this scale would have produced a much different response in the USA.

    Two things: don’t eat raw veggies unless you are really sure of their provenance, and don’t believe everything you read.

    Two apparently innocent groups of food producers have now been possibly irreparably harmed by news releases which only guess at the source of the contamination.

    Perhaps I’ll just go and smoke a cigarette while I contemplate the idiocy of much of this. But only after I wash my hands very carefully.

  6. Over the weekend, authorities thought they’d pinpointed the outbreak to a bad batch of organic salad sprouts. But, when preliminary tests of the sprouts turned up no evidence of contamination, they backed off and started pointing the finger at imported cucumbers and tomatoes from Spain.

    This is temporally reversed from the actual events. The sprouts weren’t even implicated until after “the finger” was being pointed at Spanish cucumbers. (That is, there were accusations being made from Germany to Spain almost immediately on the first onset of cases)

  7. “Over the weekend, authorities thought they’d pinpointed the outbreak to a bad batch of organic salad sprouts. But, when preliminary tests of the sprouts turned up no evidence of contamination, they backed off and started pointing the finger at imported cucumbers and tomatoes from Spain. Today, the official opinion flip-flopped again.”

    Um… what?
    The Spanish cucumbers were assumed to be the source like two weeks ago because e. coli were found on one.
    Then it turned out that was a different strain.
    The sprout-theory has turned up a few days ago and although the first tests were negative, the authorities nevertheless stuck with saying that the sprouts were the likely cause because that’s where the evidence was pointing. So, no offense, but you’ve got that bit in there completely wrong.

  8. “BERLIN (AP) — German vegetable sprouts caused the E. coli outbreak that has killed 31 people and sickened nearly 3,100, investigators announced Friday after tracking links to the bacteria from patients in hospital beds to restaurants and then farm fields.

    “Reinhard Burger, president of the Robert Koch Institute, Germany’s national disease control center, said the pattern of the outbreak had produced enough evidence to draw that conclusion even though no tests on sprouts from an organic farm in Lower Saxony had come back positive for the E. coli strain behind the outbreak.”

    I would never buy sprouts from the market due to outbreaks of salmonella that have happened in the past. Each week I have two batches of sprouts (broccoli, radish, mung beans, etc.) that I grow at home, so I know it’s safe if you DIY.

    People are lulled into thinking that “organic” means a safer product. Actually, it’s industrial farming that’s the culprit. Cross-contamination and inadequate rinsing is a set-up for disaster.

  9. â–¼
    You want to know about the source and path of EHEC pathogen HUSEC041, the E-coli clone, hybridized with Central African variant?

    Can’t find them in food?

    I’ll give you some hints, you decide if they mean anything. :

    Germany is world largest importer of cut flowers.
    Kenya, with 60,000 tonnes of cut flowers, one of the worlds main exporters.
    About 1,000 tons of roses were flown from Kenya into Germany for Mother’s Day (8 May) alone.

    Flowers get transported in moist temperate conditions which benefit e-coli bacteria.

    The Hamburg Blumengrossmarkt (Flower wholesale market) is a big entry point for Kenyan Flowers.

    Kenya is in eastern central Africa.
    Kenya’s rural west repeatedly experiences large outbreaks of bloody diarrhea epidemics triggered by Escherichia coli.

    Kenya traditionally has massive cattle farming (eg, the Maasai).
    Cow dung is used there in many ways: cooking, construction, fertilizers,
    cow manure-bio-gas power-generation and related “Guelleduengung” {there seems to be no english term for that on the internet!} …
    Cow dung is an almost universal fertilizer, used for a great variant of cultured plants, like flowers.

    The outbreak in Northern Germany, with its center being Hamburg, mostly affects women, did especially at the beginning of the epidemic.
    Around 70% of the infected are now woman, at first 90%.
    Particularly affected are women aged 19-40 or respectively 55 years.

    This is the population group which:

    – Represents the largest share of purchasers of cut flowers.

    – Which is most commonly gifted with flowers.

    – Which mainly deals with flowers, cuts them, arranges them,
    changes their water, and the like.
    Cut flowers are typically dealt with in the kitchen, near and in the sink, where vegetables and fruit are cleaned and prepared also.

    On German (still common} weekly open air markets, the cut flower stands are typically in direct vicinity of the veggie stand, because of the shared, identical customer-base.

    Supermarket chains, such as for example Aldi Nord, sell cut flowers from Kenya with the entry point of Hamburg. (for ridiculously little money, it’s a shame, needs fair trade}

    (Typical scene: Woman comes home with groceries, nibbles on a carrot while putting stuff into the fridge, snackis on a strawberry while cutting off the flowers, putting them in a vase. The knife is swiftly rinsed off in between uses.)

    Thanks for your attention.
    I happen to live around here and although I don’t tend to harbor unreasonable angst, I read and heard about this from the start. Being interested in anything I thought about it, and this is what I came up with.
    All the other theories sounded dumb to start with. This seems obvious.

    I started trying to tell my thoughts to a host of institutions, including the police, medical universities and the health ministry – alas they have no time to hear me on the phone or read my e-mails. To busy with EHEC. Uhh… good luck!

    Currently the investigations deal exclusively with food, as it’s a “foodborne” pathogen.

    Maybe someone among the readers has the means to mention this to someone in charge?

    I strongly feel that some investigation into this scenario would be advised, and also, simultaneously, inquests should be made with hospitals, organizations and agencies in Kenya to find out if the bloody diarrhea epidemic there, has become conspicuous, shows suspicious changes.
    It should be found out if tests for HUSEC041 can be done in Kenya.

    (All Sources: Google, verify yourself =])

    Btw. although the world is not fearstricken and Europe currently in the grip of a deadly outbreak, it isn’t as harmless as some readers here like to think. Only a few of the infected die while in state of the art medical care, many more have kidney damage and neural damage that will be permanent.

  10. Gokulram Arunasalam
    It is quite scary that e.coli was found in fresh vegetables – something people would eat raw as salads. Goes again to show that food – vegetables or meat need to be treated properly (washed well, boiled, cooked in heat etc).

    1. And that is the funny part.
      Serotype O104:H4 was really not found much on veggies. In the few samples it was found, there is strong indication that the contamination was secondary. Not the source, but a relay. The source has NOT been found. Still.

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