Running the data to identify clusters of a pathogen cropping up in different places is the easy part. Investigators also have to identify the source of the illness, which is all information that has to be collected manually. To do so, the CDC interviews patients to find out what foods they'd eaten and where recently. The amount of time they go back is dependent on the particular disease's incubation period, or how long it can remain in the human system between ingestion and showing symptoms.
The incubation period for E. coli, for example, is usually three to four days.
Once common food sources and eating establishments are identified, investigators develop hypotheses for the source of the illness. They test those hypotheses with both analytical studies and food testing. If sick people report having eaten a particular food more often than well people, to could be associated with the outbreak. Statistical testing enabled the CDC to determine the strength of a correlation for a particular food or eatery.
There could be a lot of reasons that it would be difficult to identify a particular trigger, like in the Chipotle outbreaks. The public often focuses on meat as the culprit, as happened early in the Chipotle cases. But a look at recent E. coli outbreaks in the U.S. show that vegetables like clover sprouts and spinach are often the culprits. These products can pick up the pathogens when the plants are fertilized in the field and not adequately cleaned prior to being served to consumers.
Steve Ells, co-CEO of the company, told the Associated Press that he doesn't think the company will ever know exactly which ingredient sickened customers in the larger outbreak. Still, he believes it was fresh foods like tomatoes or cilantro that had the bacteria.
One problem for the CDC in identifying fresh produce as the source of an outbreak is that by the time investigators find the food, the infected produce could be spoiled and no longer available for testing. Between physicians, state health authorities and CDC lab testing, the whole process can take weeks.
That means it's likely that once you read about people taken ill in the news, they were infected a while ago. The illnesses that were reported the week of Dec. 21 started between Nov. 18 and 26, for example.
An outbreak is considered to be over when there are no more new cases of the illness than health officials would expect in a normal population.