University of Georgia food scientist Xiangyu Deng has created a system that can identify subtypes of foodborne pathogens in a fraction of the time taken by traditional methods.

Quick detection and pathogen fingerprinting can save lives by helping to identify foodborne illness outbreaks and their victims, thereby making it easier to contain outbreaks.

“In outbreaks, time is very important. When a pathogen is detected in food, we then have to determine its subtype, or fingerprint,” Deng said in a university publication. “We need to shorten this process to the least amount of time possible.”

Deng is an assistant professor of food microbiology at the UGA Center for Food Safety in Griffin. His work was featured in the February issue of Applied and Environmental Microbiology, a leading journal in the field.

Detecting and subtyping a pathogen are separate processes now, but Deng has combined the two steps with “metagenomics analysis.”

“To prevent a pathogen from spreading, you have to first identify it by studying its DNA signatures,” Deng said. “Sometimes you only have a few cells of the pathogen in a food sample, just a tiny fraction of the resident microbial populations on the food.

“You could sequence the entire sample to identify the pathogen inside it, but that would not give you enough pathogen DNA signal for identification.”

Traditionally, the pathogen is separated from the food sample by growing cultures, which takes 24 to 48 hours.

To shorten the culture process, researchers in his lab apply tiny magnetic beads coated with antibodies that pull the pathogen cells out. Then they amplify the DNA of the captured pathogen cells so they have enough DNA to sequence.

“Using a new, very small sequencing tool that’s about the size of a USB drive, we can sequence while capturing the data in real time,” Deng said.

The small sequencer generates enough data for pathogen detection and subtyping in about 90 minutes, he said.

Deng tested the process on raw chicken breast, lettuce and black peppercorn samples that had been treated with salmonella. He also tested it on chicken parts collected at retail that were contaminated with different serotypes of salmonella. In one case, a small amount of salmonella was detected and subtyped from lettuce samples within 24 hours. Using standard methods, that would generally take two weeks, the scientist said.

The Centers for Disease Control and Prevention estimates that 1 million foodborne illnesses and 380 deaths in the U.S. each year are linked to nontyphoidal salmonella.

Identifying pathogenic bacteria before a food product is released into the market can reduce the number of people who get food poisoning, said Francisco Diez, director of the food safety center and an expert on enterohemorrhagic E. coli.

“Our center conducts cutting-edge research to ultimately protect the consumer,” he said. “The kind of scientific investigations the center conducts can be applied to solve contamination issues for the food industry.”