Food Safety in North America

Since the creation of PulseNet in 1996, more than one-half billion pounds of contaminated food have been recalled due, in part, to PulseNet activities.

Dr. Doyle is quick to point out that PulseNet has revolutionized the detection and investigation of foodborne disease outbreaks, especially in multiple sites across the country which, before PulseNet, often went undetected or were detected only after they grew very large.

“PulseNet, in collaboration with FDA’s GenomeTrakr, is rapidly adopting whole genome sequencing as its next generation fingerprinting method,” Dr. Doyle says. “This will enable more rapid detection of outbreaks, as well as increasing CDC’s ability to identify outbreaks having only a few cases, and enabling FDA to better track outbreaks back to their source.”

What’s more, the success of PulseNet USA inspired the formation of its collaborator, PulseNet International, which now spans some 82 member countries in Canada, Europe, Latin America and the Caribbean, Asia Pacific, the Middle East, and Africa; and includes some 126 laboratories.

Whole Genome Sequencing

Dr. Doyle greatly appreciates all the benefits the landmark tool whole genome sequencing offers for solving foodborne illness puzzles and mysteries.

“Sequencing allows scientists to trace pathogens right to the source,” he says. “One recent example is the Salmonella contamination of frozen raw scraped ground tuna that infected 425 people in 28 states in 2012 and was traced to India. The genome sequencing led to this discovery.”

Whole genome sequencing reveals the complete DNA makeup of an organism, enabling scientists to better understand variations both within and between species. This in turn facilitates the differentiation between organisms with a precision that other technologies do not allow.

Having utilized whole genome sequencing since 2008, FDA says on its website that it is using this technology to perform basic foodborne pathogen identification during foodborne illness outbreaks and applying it in novel ways that have the potential to help reduce foodborne illnesses and deaths over the long term, both in the U.S and abroad.

With its ever-decreasing cost and continually increasing speed, genome sequencing is used to identify pathogens isolated from food or environmental samples. Dr. Doyle concurs that these can then be compared to clinical isolates from patients. According to FDA, if the pathogens found in the food or food production environment match the pathogens from the sick patients, a reliable link between the two can be made, which helps define the scope of a foodborne illness outbreak.

This type of testing has traditionally been done using methods such as pulsed-field gel electrophoresis (PFGE), but there are some strains of Salmonella spp. that PFGE is unable to differentiate. FDA explains that whole genome sequencing performs the same function as PFGE but has the power to differentiate virtually all strains of foodborne pathogens, no matter what the species. Its ability to differentiate between even closely related organisms thus allows outbreaks to be detected with fewer clinical cases and provides the opportunity to stop outbreaks sooner and avoid additional illnesses.

However, FDA asserts the most promising and far-reaching public health benefit may come from pairing a foodborne pathogen’s genomic information with its geographic location and applying the principles of evolutionary biology to determine the relatedness of the pathogens. That’s because, FDA explains, the genomic information of a species of foodborne pathogen found in one geographic area is different than the genomic information of the same species of pathogen found in another area.

Knowing the geographic areas that pathogens are typically associated with can be a powerful tool in tracking down the root source of contamination for a food product, especially multi-ingredient food products whose ingredients come from different states or countries, FDA notes.