Most people think of foodborne illness outbreaks as spanning a few days or weeks. But, with current technology, disease detectives can find patients of a single outbreak spread across several years and multiple states.

That is the case with an ongoing outbreak of Listeria illnesses linked to fresh peaches that began in 2018. So far, 11 patients have been identified, most recently found in August this year. One of the patients died. Recent recalls of peaches, nectarines, and plums have been initiated while public health officials continue investigating the outbreak.

The links between people sickened in the outbreak this year and the initial patient in 2018 were made possible using whole genome sequencing (WGS). Whole genome sequencing has been likened to fingerprinting used in criminal investigations, but WGS allows the Centers for Disease Control and Prevention to look at millions of pieces of data.

“WGS examines more than 4.5 million ‘letters’ of the genetic code in disease-causing bacteria such as Salmonella. Bacteria closely related by WGS are more likely to have originated from the same source than more distantly related bacteria,” said John Besser, who retired in 2019 as Deputy Chief of the Enteric Diseases Laboratory Branch at the CDC. He continues to work on CDC-related projects through the Association of Public Health Laboratories.

“Ill persons in a WGS cluster will likely have shared exposure, such as a contaminated food product. By focusing on WGS clusters, investigators can detect outbreaks when they are small, even if cases are dispersed over multiple states or widely separated in time.”

Besser likened WGS to “Star Trek” medicine. He said the technique helps identify ongoing outbreaks and allows public health officials and industry to look into the future and make adjustments to enhance food safety. He said using WGS in the foodborne disease arena is much like what the National Transportation Safety Board does with airplane accidents. It provides information that can help prevent future failures in food safety systems.

Art Lang, the former Director of the CDC’s Food Safety Office, said WGS has eliminated time constraints when it comes to outbreak investigations and allowed public health officials to link illnesses across great distances. Lang said before the mid-1990s, residents or healthcare professionals recognized most “unusual” events, and outbreaks were investigated by the local or state health departments, such as the deadly 1993 Jack-in-the-Box E. coli outbreak traced to hamburgers.

“Subtyping methods (WGS) have helped investigators to focus on clusters of illness due to the same organism with a very similar ‘fingerprint,’ ” said Lang, who has also been a CDC Epidemic Intelligence Service officer. He has served on the Executive Committee of the National Advisory Committee on Microbiological Criteria for Foods.

Lang said in the late 1990s, PFGE (pulsed-field gel electrophoresis) technology helped eliminate the limitation of place. But now, with WGS, public health officials can detect more multistate outbreaks than ever. Any single health department might have only 1 or 2 cases reported, but something unusual can now be seen from the national level.

“In the past, epidemiologists often ignored product recall information because they rarely led to detection of an outbreak. Today, this is no longer the case. It is definitely what happened in the 2014 stone fruit outbreak,” Lang said.

“Whole genome sequencing has made the invisible visible. We have not recognized patterns of illness, i.e., R.E.P.S. (repeating, emerging or persistent strains) are emerging.” 

The current outbreak of Salmonella illnesses traced to cantaloupe is another example of how WGS allows disease detectives to identify outbreak patients across long distances, said Greg Hedberg, a professor at the University of Minnesota’s School of Health since 1999. He is also Co-Director of the Minnesota Integrated Food Safety Center of Excellence. 

The cantaloupe outbreak stretches from coast to coast in the United States and has sickened 117 people. A corresponding outbreak in Canada has sickened 63 people. One person in Canada has died, and the United States has recorded two deaths. Multiple recalls of whole and fresh-cut cantaloupe have been initiated.

“The current cantaloupe outbreak involves an unusual type of Salmonella,” Hedberg said, making use of WGS even more critical than in some outbreaks.

Hedberg said that compared to previous methods, modern technology provides much more granular data on a molecular level, which shows a relationship between outbreak strains. For example, he said, an outbreak linked to Salmonella in Malt-O-Meal cereal was linked to an outbreak 10 years later in a cereal made at the same plant. Remodeling at the plant had released the contaminant.

Another example of how WGS has enhanced outbreak investigations is the Listeria outbreak traced to Blue Bell ice cream. The outbreak was first detected in 2014, but ultimately, patients were found dating back to 2010. 

Peter Gerner-Smidt, who retired in 2020 as chief of the enteric diseases laboratory branch at CDC and PulseNet — a database with over 300,000 genomes — said WGS allowed outbreak investigators to identify patients dating back several years because Listeria patients popped up on the radar screen when the outbreak strain of Listeria was uploaded to the PulseNet database. Those patients would not have been linked to the more recent ones if older technology had been the only option.

“The Blue Bell outbreak gave rise to a new outbreak category: ‘low and slow’ outbreaks, i.e., outbreaks with few cases dispersed over a long time, even years, that in the past could not be recognized,” said Gerner-Smidt who was in charge of introducing and implementing WGS in routine lab surveillance of foodborne infections in this country before he retired from the CDC. 

“It may be difficult to understand that now we may detect and solve outbreaks with two or three cases spread out over the years, but that is possible if you use WGS with integrated surveillance of people and food production.”