An article on titled, "E. coli and Friends," gives a good description of several foodborne pathogens featured at  Reporter Jen Christensen profiles E. coli, Salmonella, Campylobacter, and Listeria, and describes how health officials determine which pathogen is responsible for illness:

Tracking Down the Culprits

When stomach symptoms occur, people tend to attribute the cause to a “bug” rather than food. Clues suggesting a possible foodborne pathogen include severe symptoms and having more than one person is affected – especially if the symptoms occur in several families. A physician may contact the local health department to determine if other cases have been reported. In addition, stool samples may be sent to a lab for testing.

It can take quite a bit of detective work to track down a source of foodborne illness. Not everyone who eats a contaminated food product gets sick (typically the very young, very old, patients with chronic medical conditions and those with weak immune systems are most susceptible). The severity of symptoms may also vary.

Health officials gather data on patient characteristics, how long they have been sick and places they may have visited days before the onset of illness. Hopefully, common traits will begin to emerge, such as “everyone ate at the same restaurant” or “ate the same food.” Suspect food items may be tested for the presence of bacteria or toxins. As more clues emerge, experts may be able to narrow down or pinpoint the source of the problem. In some cases (as with the peanut butter/salmonella link recently), an investigation may lead to an extensive recall of a particular food item.

The E. coli Reference Center at Penn State University is the nation’s largest repository for E. coli strains, holding more than 70,000 strains collected over the last 40 years. The bacteria are frozen to enable researchers to study and track changes or genetic mutations that may make the illness more difficult to treat. Older samples are stored at room temperature in “slants,” or test tubes containing a solid growth medium to preserve the culture. The lab can also test a current sample for the bacteria and look for genes associated with those causing the most serious illness.