Genetic Fingerprinting and the Tomato-Salmonella Outbreak


The search for the source of salmonella-tainted tomatoes that have sickened at least 613 people in 33 states has been powered by genetic fingerprinting – the technology that allows public health investigators to go beyond serotyping to identify clusters of illness. PFGE—pulsed-field gel electrophoresis—is the testing process used by the Centers for Disease Control and Prevention (CDC) and public health laboratories to analyze the DNA of bacterium. Specimens with indistinguishable DNA are said to share a common ancestry. When combined with epidemiological information, PFGE analysis has proven to be a powerful tool in outbreak detection.

Patti Waller, epidemiologist for Marler Clark, explains that the process begins with healthcare providers ordering stool cultures for patients presenting with symptoms of a food-borne illness. “As anyone who has toughed out a ‘stomach flu’ knows, not everyone goes to the doctor for what might be a foodborne illness,” Waller said from her office in Seattle. “When we do, doctors bound by insurance plan limits often can’t (or simply don’t) order stool sample tests, which is why the CDC estimates that for every person confirmed with salmonellosis, 38 ill persons go undetected. Now that there is so much awareness of this outbreak, many more tests are being done, which is why we are seeing the infection numbers shoot up around the country.”

Commercial labs commonly determine the presence of bacteria such as salmonella, but forward the specimen to a public health laboratory for confirmatory testing and serotyping. Public health labs are part of PulseNet, a national network of public health and food regulatory agency laboratories coordinated by the CDC. PulseNet participants perform standardized molecular subtyping (or “fingerprinting”) of foodborne disease-causing bacteria by PFGE.

“We keep hearing that salmonella saintpaul is rare, when in fact, it is the seventh most common serotype of salmonella reported to the CDC” said Waller. “What is truly rare in the current outbreak associated with tomatoes is the specific fingerprint of this strain, or subtype. It’s so uncommon, it seems to point to a single source of contamination.”