Quality, Safety, Traceability: Protecting the Food Supply for US Consumers

This collaboration is an example of how public health laboratories help protect US consumers from pathogens in imported foods.

“FDA requested ongoing sampling of these imported enoki mushrooms for Listeria, which never would have occurred to us because no one in Maryland was sick,” Urban said. “We isolated two strains from products on Maryland stores shelves that were part of this outbreak. The producers were then put on import alerts so they could not just freely import products into the US—they had to prove their products were safe. This is prevention. This is exactly the kind of work we’re trying to do.”

Critical Partnerships 

All food products, whether produced domestically or imported, must meet US food safety requirements. According to Donald A. Prater, DVM, principal deputy director of the Human Foods Program at the FDA, the agency regulates about 80% of the food supply, with the remainder—including meat, poultry and processed egg products—regulated by the US Department of Agriculture.

As part of its Food Traceability Rule, FDA uses a risk-ranking tool to determine which foods must meet additional tracing requirements. Across the nearly 400 ports of entry where food enters the US, food products are screened using a tool called Predictive Risk-based Evaluation for Dynamic Import Compliance Targeting (PREDICT). This risk-based analytics tool electronically reviews prior notice entries, flagging risky products and entries with incomplete or inaccurate data. Using PREDICT, FDA can make quick admissibility decisions when a food is offered for import—including whether to physically examine the product or take a product sample.

Collecting and testing samples is a resource-intensive process that requires locating the product in a warehouse, inspecting the labeling, using a specific methodology to collect and process a sample, and sending it to a laboratory. FDA relies on its own laboratories and on state public health laboratories for sampling and testing. Broadly, this work includes routine surveillance testing, targeted assignments based on specific findings or historical trends, and testing for chemical hazards or pathogens that occur in new geographic locations or due to outbreaks.

Eight FDA laboratories primarily conduct regulatory surveillance of imported foods. Seven of those laboratories have microbiology capabilities, and all eight can perform various chemical analyses. Four additional laboratories are engaged in applied science activities, including method development, validation, and platform and matrix extensions, according to Prater. The Food Emergency Response Network (FERN), a 170-member network of federal, state, local, Tribal and territorial laboratories, also conducts regulatory testing when needed.

“We rely on our collective efforts with other public health laboratories,” Prater said. “We have great cooperation and we’re always looking to share what we’ve learned and how we can improve and work more efficiently and effectively to protect consumers. The value of working together as a food system is immeasurable in terms of protecting public health.”

Angela Poates, lead specialist for global health next generation sequencing and bioinformatics for APHL, said public health laboratories are the “boots on the ground” in defending the US food supply. As APHL’s lead for PulseNet International, a network focused on surveillance and detection of foodborne outbreaks caused by bacterial enteric pathogens, Poates and her colleagues work to help public health laboratories in eight global regions increase their foodborne pathogen, enteric and antimicrobial pathogen surveillance capacities.

“We’re helping to build food safety globally, which protects the US because we have many ingredients and food items coming into our country,” she said. “A coordinated outbreak response among public health laboratories, regulatory bodies, and industry suppliers is important for a fast outbreak response. Everybody has a part to play.” 

Evolutions in Testing 

Foodborne disease testing has evolved rapidly during the past two decades. Public health laboratories have moved from primarily using methods such as pulsed-field gel electrophoresis to whole genome sequencing (WGS). Standardizing the use of WGS has improved the precision of pathogen identification, as well as the speed and efficiency with which public health and regulatory agencies can respond to foodborne outbreaks. 

With FDA funding, Urban’s laboratory modernized its methods. “We brought on sophisticated screening tools, so we don’t have to test every food item with cumbersome, laborious and tedious methods,” he said. “Our partnership with FDA has been critical. Most states, including Maryland, don’t have the funding or infrastructure to throw money at a problem and build capacity at a moment’s notice.” 

As an example, Urban cites the use of high-resolution mass spectrometry techniques to identify what made a Maryland woman sick after she ingested Nut Diet Max brand Nuez de la India seeds—marketed as India nuts, commonly known as candlenuts—in 2023.  

“She ended up in the hospital with bradycardia,” Urban said. “We tested the food and, like whole genome sequencing where you get the genetic fingerprint, we applied a chemical fingerprint. Through analysis, we learned these were yellow oleander seeds, which are highly toxic. High-resolution mass spectrometry is a relatively new technology for identifying unknowns.” 

WGS is a critical tool in connecting the dots of foodborne illness, especially those that stretch beyond state or national borders. 

“All public health labs in the nation now use next-generation sequencing as their primary testing methodology for foodborne illness and disease surveillance on the clinical side,” said Kelly Oakeson, PhD, chief scientist, Next Generation Sequencing and Bioinformatics at the Utah Public Health Laboratory, noting that every laboratory has at least one next generation sequencer for surveillance work as part of the US Centers for Disease Control and Prevention's (CDC’s) PulseNet. 

“That same foundation of technology, training and technique means that if I get a result here in Utah, I can directly compare that result to my neighbor’s results in Idaho or New York or anywhere across the nation,” he said.  

Through FDA’s GenomeTrakr network, public health and university laboratories collect and share genomic data for foodborne and other pathogens that could affect the nation’s food supply. With access to these data, public health officials compare and analyze pathogens in real time to enable rapid response. 

No single technology has been as transformational in protecting the nation’s food safety as WGS.  

“Access to genomic profiles of pathogens has been instrumental in solving outbreaks and protecting the public, especially in situations where there are few cases or where cases have occurred over a period of years,” said Prater. “The ability to link and have confidence in the attribution to a particular outbreak or case has meant we can solve outbreaks we hadn’t been able to before.” 

Domestically, PulseNet has focused on validating protocols and decentralizing training of all laboratories on these protocols, according to Poates. “That made it easy to make sure all laboratories are using the same methods to detect outbreaks using whole-genome sequencing and that results are seamless. That doesn’t work on a global scale for many reasons,” she said. “You have countries with vast differences in financial resources, human resources and capabilities. The important thing is to have methods that are validated so the results are reliable. That’s the work we’ve been doing recently with PulseNet International.” 

Still, some variability isn’t always a bad thing, Poates said. “We’re working on validating different full genome sequencing methods,” she says. “Having the ability to use more than one technology provides flexibility for labs. Since some methods are more cost effective than others, we need this variability globally. But we want to make sure results are comparable so we can analyze them in a similar way for cluster detection and outbreaks.” 

An Emerging Workforce 

Investing in sophisticated technologies to test for foodborne pathogens also requires investing in a trained laboratory workforce. Poates said most international laboratories she has worked with now have a sequencer.

“The difficulty is that they may not have the infrastructure to support data that comes off the instrument or the epidemiological experts to analyze and interpret data,” she says. PulseNet International trains international laboratories on sequencing instrumentation and on equipment that may have been purchased for respiratory virus surveillance that can also be leveraged for enteric surveillance. 

Domestically, Oakeson has seen a workforce divide between bioinformatics experts and wet lab scientists. “I think you can do both,” he said. “That’s a bridge we’re trying to build on the workforce development side. It’s our job to take wet lab scientists and train them on how to do bioinformatics. Now, we’re adding the genomic epidemiology component too.” 

Urban says the Public Health Laboratory Fellowship Program: an APHL-CDC Initiative has helped him meet emerging workforce needs in his laboratory.  

“I’ve mentored 12 different fellows each for two-year appointments over the last three years,” he said. “I have people at the bench who are amazing and love what they do. Seven out of the 70 scientists I have here are APHL fellows. The program is an excellent way to increase workforce when funding decreases and to bring new laboratorians into public health.” 

Another benefit of developing a food safety workforce is that these laboratory skills are broadly useful, according to Poates.  

“One of the reasons this work is so important is because the wet laboratory, bioinformatics and epidemiology skills laboratories are trained in for food safety are transferrable to other pathogens,” she said. “This enhances overall pandemic preparedness greatly and encourages lab-epi communication, which is important in all forms of outbreak response. Even though we might be focused on foodborne pathogen capacity-building efforts, we’re building global pandemic preparedness and global health security.”

Funding Food Safety

The laboratory results critical to maintaining a robust food safety system require significant resources. Yet federal and state agencies often face spending constraints that affect these resources. FDA’s Laboratory Flexible Funding Model (LFFM)—first announced in 2020—has allowed some public health laboratories like MDH to further invest in protecting food safety. “In our case, there were 14 possible projects across microbiology, chemistry and radiochemistry,” Urban said. “We were funded for all but one of them. Now, all the disciplines we use in environmental testing, we can apply to food safety.”

Urban says LFFM funding for MDH continues. “We couldn’t do what we do without this grant; even with shrinking budgets, my view is we should be doing more, not less, because public health demands it,” he said. “I feel my role as one of the recipients of this grant is to hand wins to FDA, so they can go to Congress and get more funding. I come from academia, where you almost never get a grant without showing preliminary data. That’s the model I’ve adopted in public health. We are always doing more.”

As an environmental sciences laboratory, most of Urban’s work is testing air, water and food samples. His lab responds to outbreaks and illnesses, but “what we really want to do is prevent harmful exposures before they happen. We do surveillance testing of products already on store shelves for a variety of threats that could be present,” he said. “We went from testing a few hundred samples per year to testing about 2,000 samples.”

Testing products before isolates from ill people are sequenced is a shift from approaches that test products only after people become ill. “We have the funding and the mandate to do it,” Urban said. “If we can find pathogens before people get sick, that’s worthwhile and it’s what we should be doing. You can quantify how much we’re saving in emergency room costs and show that this is a good investment. But you can only do that if you have data.”

“We saw a reduction in the amount of funding we usually get for food safety activities in our most recent award from CDC,” Oakeson said. “We had to scramble to find ways to make up for those shortcomings because we don’t get a lot of support from state tax dollars. We used different funding mechanisms to fill in and make sure we can keep doing what we do to keep the food supply safe.”

Oakeson and his colleagues have also implemented strategies to help stretch laboratory resources. “In Utah, we’ve validated the ability to use a quarter of the volume of reagents needed for sequencing,” he said. “Previously, a reagent kit would be good for about 96 samples, but we now use that same kit and test 384 samples. We’ve been able to get more bang for our buck by using innovative techniques. We’ve shared those procedures and protocols with other public health labs across the nation so they can see those same cost savings.”

Sharing results and methodologies, and training together, has helped refine how state, federal and international laboratories work together.

“We're getting better at what we do,” said Prater. “It doesn't mean we don't have a need for additional resources. We're always advocating to make sure we have sufficient resources, not only for FDA laboratories but for our state partners as well.” 

Oakeson says he’s constantly looking to improve the efficiency of laboratory processes. Consolidating workflows is one area of focus. “If I can do one set of workflows in the laboratory to get my sequence data generated and prevent the need for additional workflows on the data analysis side, that helps my data scientists do that work as simply and as streamlined as possible,” he said. The update of CDC’s PulseNet to PulseNet 2.0, with its cloud-based solution for data analysis, has also improved efficiency, according to Oakeson.

Process improvements have helped public health laboratories meet the ever-growing demands of protecting the US food supply, even as available resources dwindle. “There’s always a new pathogen or virus that we need to address, but funding rarely increases,” he said.

That’s because public health works well in the background. “We need to keep public health and food safety at the forefront of people’s minds,” Oakeson says. “It’s important that people know what we’re doing and how we’re protecting them.”