Photos: courtesy of University of Georgia
By Marcia Faye

They may be lurking in your vacuum cleaner bag, your child’s pet turtle droppings, or in the fresh onions you just sliced to garnish your cheeseburger. They might be in your burger, too. While they are naturally found in the intestinal tract of food livestock such as cows, pigs, or chickens, when they exhibit signs of being in your intestinal tract—you may find that for a few days your body feels as though it’s been taken over by an alien lifeform. They are Salmonella, rod-shaped, nearly always pathogenic bacteria that, according to the Centers for Disease Control and Prevention, account for about 1.35 million infections, 26,500 hospitalizations, and 420 deaths each year in the United States alone. Learn what one Illinois Institute of Technology alumnus is doing to decrease those numbers.

WHO: Xiangyu Deng (Ph.D. BIOL ’11), associate professor, University of Georgia and food microbiologist, University of Georgia Center for Food Safety

WHAT HE DOES: Deng investigates Salmonella bacteria, a leading cause of food poisoning, typically found in livestock. Salmonella often infects people when the excrement of cows, pigs, or chickens carrying the microorganisms enters the food chain.

WHY HE CAME TO ILLINOIS TECH: Deng, who was born in China, says that he wanted to pursue a scientific field in which he could produce tangible results. He was drawn to Chicago and to the National Center for Food Safety and Technology (now Illinois Tech’s Institute for Food Safety and Health), especially because of its government and industry collaborations.

NOTABLE ACCOMPLISHMENTS: In 2015 Deng and his team created SeqSero, a bioinformatics software tool that identifies more than 2,000 different serotypes of Salmonella from humans, animals, foods, and the environment within seconds by using whole genome [an organism’s complete set of DNA] sequencing. Whole genome sequencing offers a detailed and highly precise method of identifying strains of microorganisms by determining the order of the bases that comprise the bacterial DNA, thereby providing a unique fingerprinting analysis. According to Deng, the tool has been adopted routinely by more than 60 government, academic, and private institutions worldwide, including PulseNet, a national laboratory network for tracking foodborne pathogens, the Centers for Disease Control and Prevention, the United States Food and Drug Administration, and the U.S. Department of Agriculture. The team has analyzed more than 50,000 genomes, which are available for free on the Deng Laboratory website.

The team was most recently recognized for using machine learning techniques to predict the livestock sources of S. enterica Typhimurium infections, one of the most prevalent serotypes of the pathogen. They trained a machine learning classifier known as “random forest” with more than 1,300 S. enterica Typhimurium genomes from livestock and other sources, then used the algorithm to predict the livestock sources of the pathogen. The model averaged an accuracy rate of 83 percent and successfully predicted the root cause of seven out of eight major outbreaks that occurred in the U.S. from 1998 to 2013. Their approach helped to identify some 50 genetic prediction markers from entire genomes of the pathogen that are close to five million bases.

GREATEST CHALLENGE: “We don’t really know much about the mechanism behind the association of particular Salmonella strains to particular sources, for example, animal hosts such as poultry or pigs. That’s why we apply machine-learning techniques; we know little about food exposure and contamination sources of 95 percent of human infections of Salmonella in the U.S., but we do have a lot of genomic data. It’s a challenge to explain what we have found. We may be able to identify the genetic determinants of Salmonella-host association, if we can tease out mechanistic causation from coincidental correlation.”

WHAT’S NEXT: Deng’s lab recently received an FDA award to further develop and expand its source-attribution tool, expanding into more serotypes and more foods. The team is also exploring how the food microbiome—the entire community of microorganisms on a food sample—informs food safety, food quality, and the microbial ecology of overall food production environments. A piece of chicken, for example, may harbor more than 1 billion bacterial cells.