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.

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 )