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Deng awarded UGA Creative Research Medal for salmonella classification software By Sharon Dowdy

University of Georgia food microbiologist Xiangyu Deng’s work in the emerging field of bioinformatics led to his selection as a Creative Research Medal winner for 2017. 

The medal is one of the prestigious honors bestowed annually by the UGA Research Foundation. Awards are given to outstanding faculty, postdoctoral fellows and graduate students in recognition of excellence in research, scholarly creativity and technology commercialization at UGA.

Deng, an assistant professor of food microbiology with the Center for Food Safety (CFS) on the UGA Griffin campus, was recognized for creating a cloud-based software tool that quickly classifies strains of salmonella, one of the most prevalent foodborne pathogens in the United States and worldwide. The Centers for Disease Control and Prevention (CDC) estimates that 1 million foodborne illnesses and 380 deaths in the U.S. each year can be linked to nontyphoidal salmonella.

The SeqSero system identifies serotypes, or distinct strains of salmonella, from infected humans, animals, foods and the environment using whole genome sequencing. This system allows for accurate, fast “fingerprinting” of any salmonella strain and replaces a complicated, time-consuming laboratory protocol. Analysis time using SeqSero takes just minutes — analysis using the old system took days — while adding no extra cost.

SeqSero was developed by UGA College of Agricultural and Environmental Sciences food science graduate student Shaokang Zhang, under Deng’s direction, and was created with funding from the food industry in collaboration with the CDC’s National Salmonella Reference Laboratory. The CDC’s Enteric Diseases Laboratory Branch has adopted SeqSero for its routine processing of salmonella genomes.

“Earning the Creative Research Medal is a well-deserved distinction for one of our rising stars in the Center for Food Safety. The impact of Dr. Deng’s creation on public health is enormous,” said Francisco Diez, director of the CFS. “SeqSero has been widely adopted by the CDC, the U.S. Food and Drug Administration, the U.S. Department of Agriculture, multiple state health departments and more than 20 regulatory agencies of European, Asian and North American countries.” 

Deng compares the SeqSero system to a crime investigation. “For investigation and surveillance purposes, you need to be able to profile your suspects at different levels, from general demographics to fingerprints. If your suspects are salmonella, serotype determination, or serotyping, is the first step of your profiling,” he said. “It’s now possible to do all the profiling with whole genome sequencing, and it saves a lot of time and (steps in) workflow.”

In addition to saving time, SeqSero cuts out the need to maintain hundreds of reagents, or substances used for chemical analyses. “This is a highly desirable bioinformatics system and allows for push-button, fast, straightforward and accurate identification of salmonella serotypes from raw data that comes directly off sequencers,” Deng said. “There are more than 2,500 serotypes described for salmonella, and SeqSero focuses primarily on more common serotypes while also being able to ID many rare serotypes.”

Salmonella bacteria look alike under a microscope, but can be separated into many serotypes based on two structures on their surface, Deng explained. Serotyping forms the basis of the U.S. and international surveillance systems of salmonella.

It took the UGA team a year to develop the highly sophisticated food safety tool that has been publicly available for two years. It is supported by all major internet browsers and mobile devices and can easily be used by novices and bioinformatics experts alike, according to Deng.

For more on CFS, visit www.ugacfs.org.

(Sharon Dowdy is a news editor with the University of Georgia College of Agricultural and Environmental Sciences.)

Xiangyu Deng
Xiangyu Deng

Xiangyu Deng, an assistant professor of food microbiology with the Center for Food Safety (CFS) on the UGA Griffin campus.

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Xiangyu Deng, an assistant professor of food microbiology with the Center for Food Safety (CFS) on the UGA Griffin campus. Download Image
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