Don't get the wrong idea about The New England Journal of Medicine's report about the Salmonella Saintpaul outbreak investigation of 2008. While it more clearly than ever breaks down the path of the tortured investigation — and, most importantly, why the link to tomatoes was mistaken — it manages to poke the industry yet again on the traceback issue. It is vindication for tomatoes but not absolution for the industry.

From the discussion part of the report:

This outbreak of foodborne disease in the United States was one of the largest salmonella outbreaks ever identified. Because many salmonella illnesses are not confirmed by culture, it is likely that many more occurred than were identified.

The results of multiple investigations indicate that jalapeño peppers were the major vehicle for transmission, and serrano peppers were also a vehicle. These findings include epidemiologic associations between illness and consumption of hot peppers, the convergence of tracebacks to a single farm that grew both types of peppers but not tomatoes, and isolation of the outbreak strain from agricultural water and serrano peppers collected on that farm. The consumption of jalapeño peppers was not specifically implicated in either study in which this hypothesis was explicitly tested (studies 2 and 3). However, study 2 implicated foods typically made or consumed with hot peppers, and study 3 implicated the presence of jalapeño peppers in the home. One explanation for the results of study 2 could be that produce items are consumed in small quantities as ingredients of other dishes and might not be recognized or always remembered after several weeks, making the implication of such items more difficult. In study 3, the respondent was often the food preparer, who would be likely to know the ingredients.

Early in the outbreak, raw tomatoes were thought to be a vehicle because study 1, conducted by standard methods, yielded a strong association between illness and consumption of raw tomatoes. Tomatoes have been implicated in many salmonella outbreaks. The initial finding that tomatoes were a source was supported by the observation that the number of new cases decreased shortly after the national tomato alert. The Texas survey, in which case subjects from early in the outbreak were specifically asked about the consumption of hot peppers and tomatoes, showed a high frequency of tomato consumption, which was similar to the frequency found in study 1, whereas fewer than half of those surveyed reported eating hot peppers. However, tomato tracebacks did not converge on any one geographic location, supplier, or growing area, and the FDA analyses of tomato samples did not identify salmonella.

The observed epidemiologic association with tomatoes may reflect collinearity between tomatoes and hot peppers, meaning that an association was identified because tomatoes were often eaten with hot peppers. It could also reflect amplified growth of salmonella in food items, such as salsa, containing both tomatoes and contaminated hot peppers. The decline in cases shortly after the nationwide tomato advisory could be explained if avoidance of raw tomatoes indirectly reduced exposure to contaminated hot peppers. The low frequency of reported hot-pepper consumption in the Texas survey could be due to unrecognized exposure to hot peppers as ingredients in other foods.

Salsa and guacamole, both foods typically containing tomatoes and hot peppers, were implicated repeatedly in cluster investigations; these foods may have provided a medium for salmonella growth. Cut or diced tomatoes require prompt refrigeration because of the potential for salmonella growth. However, salsa and guacamole are kept at room temperature for hours in some commercial settings. The addition of both fresh garlic and lime juice to salsas can suppress the growth of salmonella.

On the basis of FDA investigations, pepper contamination probably occurred on the farm. This may not be unusual; a small survey of Mexican farms that grow chile peppers indicated that 6 of 14 irrigation-water samples (43%) and 3 of 5 pepper rinses (60%) yielded salmonella (none of the serotypes were Saintpaul). From 1972 through 1999, only 1.2% of human salmonella isolates that were serotyped at public and private laboratories in Mexico were serotype Saintpaul.

This outbreak investigation highlights the recurring challenges of epidemiologic identification of ingredients in foods that are commonly consumed, rapid identification and investigation of local clusters, the need to continue exploring hypotheses during an ongoing outbreak, and produce tracing in the supply chain.

Traceback issues such as commingling, repacking, varying degrees of product documentation throughout the supply chain, difficulty in linking incoming with outgoing shipments to the next level in the distribution chain, and the complexity of the distribution chain continue to hinder product-tracing efforts. Improvements in product-tracing systems and the ability of the systems to work together are needed for more rapid tracing of implicated products through the supply chain in order to maximize public health protection and minimize the economic burden to industry.

In addition, an understanding of the mechanisms and ecologies that can lead to contamination of produce on farms and the institution of additional control measures from the source throughout the supply chain are critical for preventing similar outbreaks in the future.