Students gain experience tracking, testing for salmonella
Posted December 14, 2015 | View original publication
Students earning degrees in food science and technology typically leave campus prepared to join the industry in areas such as product development, quality assurance and food marketing.
With the help of a course led by the University of Nebraska-Lincoln’s Andrew Benson, UNL students are broadening their professional prospects by learning to identify and track sources of foodborne illness that afflict about 1 in 6 Americans each year.
Food science programs rarely instill the knowledge and skills that students need to investigate foodborne pathogens such as salmonella, Benson said. Companies often send contaminated samples to third-party labs for specialized genetic testing, he said, with most industry workers having little knowledge of what goes into that testing.
To address this knowledge gap, which Benson described as “more like a chasm,” he introduced a new facet to his Food Microbiology Laboratory course for undergraduate and graduate students.
“The idea is to give the students exposure to a combination of the standard diagnostic microbiology and high-resolution methods used to systematically track (harmful) organisms,” said Benson, the W.W. Marshall Distinguished Professor of Biotechnology. “This is the only undergraduate laboratory course in food science I am aware of in the world that teaches students about what’s going on under the hood with genomic technology (while) showing them the bigger picture of how all the parts work together.”
Benson’s students gain this understanding while systematically testing and tracking salmonella in raw agricultural commodities. Multiple companies working in safety testing, sequencing and bioinformatics — including Neogen Corporation, GeneSeek, Illumina and Metagenome Analytics — have committed time and resources to the laboratory course at no charge.
Metagenome Analytics, a bioinformatics startup led by Benson and headquartered at UNL’s Nebraska Innovation Campus, has also partnered with Neogen and GeneSeek to develop one of the products used by the students.
“Nebraska Innovation Campus provides a unique platform that encourages industry partners to contribute to all three phases of UNL’s land grant mission: research, teaching and outreach,” Benson said. “I don’t think there are many places where the contributions of these companies could have been pulled together as seamlessly as they have here.”
The lab emphasizes source-tracking to determine whether salmonella cultured from a large number of raw agricultural samples are genetically related to one another. This is the same strategy that the Nebraska Public Health Laboratory or the Centers for Disease Control and Prevention would use to genetically match salmonella isolated from patients and determine whether they were part of an outbreak, Benson said.
In addition to conducting traditional, time-consuming salmonella testing, students use emerging technologies from the partnering companies to implement new tests that can accelerate the process and provide much finer levels of detection. According to Benson, this technology has either been commercialized within the last two years or, in some cases, will enter the food industry shortly after current UNL students do.
“These novel activities are an example of the progressive mindset of the Department of Food Science and Technology,” said Rolando Flores, professor and department head. “We are committed to innovation and bringing our students the latest developments in commercialized technologies in research to provide for outstanding training at the undergraduate and graduate levels.”
With the assistance of a Neogen research scientist and high-end molecular testing system flown in to Nebraska Innovation Campus, each pair of students begins by performing salmonella analyses of 10 different agricultural samples. They then use a next-generation DNA sequencing service co-developed by Neogen, GeneSeek and Metagenome Analytics that shrinks a critical testing stage from two weeks to just two days. Reagents, or tests, for this service were also provided free of charge by Illumina.
The students conclude their lab exercise with a genetic fingerprinting method that is used heavily by researchers but only recently adopted in the food research industry. By sequencing seven sections of a genome from each salmonella isolate, the students can search for isolates with genetic matches across all of the salmonella found among the 130 original raw agricultural samples. This process is identical to the way microbiologists track sources of salmonella or other pathogenic organisms, Benson said.
Because many of the technologies and techniques featured in the lab are also new to the industry, students are in the unique position of learning them at the same time as their future employers, Benson said.
In this way, he said, Nebraska Innovation Campus can help bridge the chasm separating the biotechnology sector and food industry by training future professionals who will work at the interface between the basic and applied sciences critical to public health.
Benson also credited the support of current and former students such as teaching assistants Mallory Suhr, Carlos Gomes-Neto and Brandon Nguyen, who prepared materials for the exercises. With their help, Benson said he plans to expand the existing lab into a more in-depth graduate course. He is also exploring opportunities to develop workshops for those working in the food industry and public health sector.
“It’s extremely rewarding to hear from former students currently working in the food industry who remember the great salmonella hunt and the lessons they learned about systematic scientific inquiry,” Benson said. “I look forward to capitalizing on the opportunity to reach more food industry professionals with this exercise.”