In a food contamination mystery that stretched throughout the spring and summer, more than 1,300 people in 43 states, the District of Colombia and Canada were sickened in what has been called the largest food-borne outbreak in the last decade, surpassing the almost 700 salmonella cases from contaminated peanut butter in late 2006. The case has baffled officials, who have not only been unable to trace the source of the bacteria, but even pinpoint what type of food is responsible.

Initially, the Food and Drug Administration blamed the outbreak on raw tomatoes-particularly the red round, plum and Roma varieties-and banned them from supermarket shelves and restaurant menus around the country. The ban lasted more than a month and is estimated to have cost the tomato industry more than $100 million. When the tomato ban did not quell the outbreak, the FDA started looking for other sources. In July, it issued a warning against raw jalapeno and serrano peppers. Officials admitted, however, that they were unconvinced that the peppers were the sole explanation for the outbreak either, since many victims insisted that they had never eaten any. The inconsistencies led some investigators to examine farms that may have grown tomatoes in the spring before switching to peppers later, while others looked at fresh cilantro as another possible suspect. 

In mid-July, officials had a breakthrough when they discovered a jalapeno pepper contaminated with the same bacterial strain responsible for the outbreak-a rare type known as Salmonella saintpaul that is only usually seen in 25 cases a year-in a food distribution warehouse in Texas. The FDA was hopeful that this discovery, along with the discovery of contaminated serrano peppers and irrigation water at a farm in Mexico, would be the clues that would lead them to the source of the contamination, but it only added to the confusion. Many officials resigned themselves to the possibility that the origin of the contamination might never be found.

This long-running saga has raised an important question. Why was this outbreak so difficult to solve? In contrast, it took officials a mere two weeks to link an E. coli outbreak to bags of fresh spinach in 2006. The problem is that this recent salmonella outbreak has proven to be much more complex than other cases. One reason is that the outbreak quickly spread throughout the country, making it difficult to pinpoint a region of origin for the bacteria. In addition, there were few geographic clusters of disease for investigators to focus on-a factor further complicated by the fact that many cases go unreported in the first place. The CDC estimates that for every one salmonella case reported to the government, 30 or 40 more go unrecognized, making it difficult for investigators to determine accurate disease patterns.

Perhaps the biggest obstacle to solving the mystery has been the way in which the suspected foods are sold. Unlike bagged spinach or jars of peanut butter, tomatoes, for example, are generally sold loose by weight or are repackaged during shipping to meet customer demand. This means that no consistent bar code stays with these products as they travel from the farm to the table. The closest rule to govern this process comes from the Bioterrorism Act of 2002, in which the FDA only requires produce handlers to document one step forward and one step back in the supply chain (and this does not even apply to farmers or retailers). As such, the trail of a particular fruit or vegetable can quickly become obscured, making trace-back almost impossible.

Some states have enacted their own rules for tomato farmers in particular, mandating electronic tracking systems on boxes that can trace the products through the entire supply chain. According to many critics, this kind of exception needs to become the rule in order to prevent future outbreaks from spiraling out of control. 

"With unfortunate events like this, Americans are becoming aware that food safety and national security are synonymous," said Rep. Tim Mahoney (D-FL). "We clearly need to examine and overhaul our food safety system to ensure that the food we grow and import is safe." 

Morgan O'Rourke is editor in chief of Risk Management.