By Donna Campisano, specialist, Communications, APHL

Last year, 113 people across 23 states were sickened with Salmonella Typhimurium after eating cucumbers. Another 61 people from 19 states developed Listeria monocytogenes after eating Boar’s Head liverwurst; 10 people died.  

These are just two of the many foodborne illness cases that made headlines recently. But what didn’t make headlines? Next generation sequencing (NGS), the revolutionary technology helping scientists pinpoint—with newfound speed and accuracy—the exact genetic makeup of a pathogen, which, in turn, can help them link illness clusters and zero in on the sickness-causing culprit.  

The ABCs of NGS 

NGS is a modern laboratory method that allows scientists to determine an organism’s complete DNA quickly and accurately. NGS is the technology used to perform whole genome sequencing, another laboratory procedure that determines the order of the nucleotides (chemical building blocks) in a genome.  

With the details that NGS provides, laboratory professionals can determine not only what pathogen (E. coli, Salmonella, Listeria or any number of other things) is affecting the sick person but also if it is the exact same strain found in other ill people or even in a particular food source. 

“NGS is a powerful tool that helps us understand how foodborne outbreaks start and spread, which is crucial for protecting public health.” 

“In food safety, this means we can identify and track bacteria that cause illness down to their genetic fingerprints,” said Kelly Oakeson, PhD, chief scientist, Next-Generation Sequencing and Bioinformatics, Utah Public Health Laboratory. “NGS allows us to compare the DNA of bacteria found in sick patients with bacteria found in food, production facilities or the environment. If the DNA matches, we can link cases together and trace the outbreak back to a common source. This helps public health agencies respond faster, issue recalls if needed and prevent more people from getting sick. It’s a powerful tool that helps us understand how foodborne outbreaks start and spread, which is crucial for protecting public health.” 

NGS: “Like reading every word of the book” 

Prior to the advent of NGS, laboratory scientists had to rely on culturing samples or using pulsed-field gel electrophoresis (or PFGE, a method that uses an electric field to separate large DNA molecules) to get genotyping information about a pathogen. But neither method gave scientists the kind of details that would help them link cases and uncover outbreaks with speed and confidence. 

“NGS is like reading every word of the book. With NGS, you get the entire story—every chapter, sentence and even typos.”

“PFGE, for example, is like judging books by their covers and titles,” Oakeson said. “You can group books into categories—mystery, romance, science fiction—based on the general look and feel, but you don’t know the exact details of the story inside. Similarly, PFGE gives you a broad pattern of a bacterial strain, which helps you group similar ones, but not with high precision. NGS is like reading every word of the book. With NGS, you get the entire story—every chapter, sentence and even typos. You can compare two books down to the exact wording, which allows for extremely accurate identification and comparison of bacterial strains.” 
 
But NGS does have its downsides, says Allison Gennety, specialist, Food Safety, at APHL. 

“The equipment is expensive, and you do need a good bioinformatics team to run it,” she said. “What’s more, if you’re a small laboratory that does minimal foodborne illness sampling, using NGS may not be cost-effective. You definitely get the most bang for your buck when you’re processing a lot of samples.” 

NGS in action

To demonstrate the usefulness of NGS, Oakeson points to a Salmonella outbreak tied to raw milk in Utah. 

During routine testing, Oakeson and his team identified a cluster of patients with genetically identical Salmonella strains. Epidemiologists were alerted, and after interviewing patients, they found that they all reported drinking raw milk from the same dairy. Raw milk samples were collected and sent to the laboratory, where they were also found to contain Salmonella. 

“Upon completing NGS,” Oakeson said, “we compared the genomes of the Salmonella from the clinical cases to those from the raw milk and confirmed they were genetically identical. This led the Utah Department of Agriculture and Food to halt the sale of raw milk from the dairy, effectively ending the outbreak.” 

Next steps for NGS

Experts say the future of NGS is bright. The technology is becoming faster and more affordable. And new advances—such as improvements in automation and the development of portable sequencers that can be used for on-site testing at dairies and farms, for example—are being made each day. The technology is also fostering more collaboration between local, state and federal agencies, with each using the same methods and databases to more effectively detect and stop outbreaks. 

“NGS allows us to detect outbreaks that previously would have gone unnoticed, link cases faster and track bacteria over time and geography. That level of precision has made food safety efforts more effective and more responsive than ever before.”

“NGS has transformed how we investigate foodborne illnesses,” Oakeson said. “It allows us to detect outbreaks that previously would have gone unnoticed, link cases faster and track bacteria over time and geography. That level of precision has made food safety efforts more effective and more responsive than ever before. It’s a great example of science making a real-world impact.” 

The post How Next Generation Sequencing Is Revolutionizing Food Safety  appeared first on APHL Blog.

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