The incidence of foodborne infections in the U.S. from Campylobacter, Salmonella, and other virulent pathogens increased sharply last year, creating a major public health problem, according to CDC. Among its many consequences is a growing strain on the ability of federal, state, and local government agencies to identify and mitigate potential food safety concerns.
Partly in response, FDA in April announced a “Blueprint for a New Era of Smarter Food Safety,” in which government and industry would cooperate to leverage advances in digital technologies such as blockchain to enhance product traceability; artificial intelligence and machine learning to facilitate food import inspections; and new packaging and transportation approaches to help modernize the food industry and meet the growing demands of e-commerce.
While the Food Safety Modernization Act (FSMA) has enhanced oversight of the nation’s food supply, “we recognize that it’s time to look to the future of food safety once again with a view that builds on the progress we’re making with our regulatory framework, but also leverages the use of new and emerging technologies to create a more digital, traceable, and safer system,” said acting FDA Commissioner Norman “Ned” Sharpless, MD, and Deputy Commissioner Frank Yiannas in a recent joint statement.
Toward this end, FDA this year will hold a public meeting and gather stakeholder input on “smarter food safety.” The agency will also launch a pilot project using artificial intelligence to enhance its ability to review imports at ports of entry to ensure they meet U.S. food safety requirements. In addition, FDA will tap into its existing programs related to tracking the drug supply chain to see whether similar approaches might be adapted to tracking the nation’s food supply.
“When you look at how other industries digitally track the movement of planes, ride sharing, and delivery of packaged goods, it becomes clear that we must explore how these types of technologies could improve tracking when it comes to food,” Dr. Sharpless and Yiannas explained.
Pathogens on the Rise
The incidence of foodborne infections increased in 2018 compared to 2015-17, according to CDC’s latest Foodborne Diseases Active Surveillance Network (FoodNet) report, released in April. Surveillance from labs in 10 states confirmed more than 25,600 infections, nearly 5,900 hospitalizations, and 120 deaths that were caused by eight enteric pathogens commonly transmitted through food.
As in previous years, Campylobacter was the most prevalent, being responsible for 9,723 illnesses, 1,811 hospitalizations, and 30 deaths. This was followed by Salmonella with 9,084 illnesses, 2,416 hospitalizations, and 36 deaths. Campylobacter is commonly associated with consumption of raw or undercooked poultry and meat, while Salmonella is an issue in many types of food, including eggs, meat, poultry, fruits, vegetables, spices, and nuts.
Both bacteria can cause mild to severe illness, from uncomplicated diarrhea to severe systemic infections, such as Guillain-Barré syndrome (Campylobacter), an autoimmune disease that can cause paralysis, and reactive arthritis (Salmonella), which can cause acute, debilitating joint pain.
Other bacterial pathogens included Shiga toxin-producing E. coli (with 2,925 illnesses), Shigella (2,414 illnesses), Vibrio (537), Yersinia (465), and Listeria (126). While Listeria caused the fewest number of cases, it was also the most virulent, hospitalizing 96 percent of its victims and killing 21 percent of them.
Compared to 2015-17, incidences per 100,000 population increased by 12 percent for Campylobacter and 9 percent for Salmonella. Incidences skyrocketed for the parasite Cyclospora (399 percent), followed by the bacteria Vibrio (109 percent), Yersinia (58 percent), and Shiga-producing E. coli (26 percent).
Nationwide, the actual number of cases are much greater. This is because FoodNet collects data from public health departments in only 10 states, covering just 15 percent of the U.S. population. Additionally, the true number of foodborne illnesses always exceeds the reported number because many people who get sick do not seek, or necessarily require, medical treatment.
Some of last year’s increase may be due to greater use by the reporting laboratories of culture-independent diagnostic tests (CIDTs), CDC says. But produce itself was a major culprit, with romaine lettuce linked to two multistate outbreaks of E. coli O157 infections. CDC specifically tied the jump in Cyclospora infections to outbreaks associated with produce.
“More targeted prevention measures are needed on produce farms, food animal farms, and in meat and poultry processing establishments to make food safer and decrease human illness,” the CDC report said.
FDA this year began routine inspections of large farms for compliance with FSMA’s produce safety rule. While this will hopefully mitigate some of the contamination problems, more needs to be done. For example, in December 2018, USDA reported that 22 percent of establishments that produce chicken parts failed to meet the Salmonella performance standard.
Despite all the increased attention and effort on improving food safety, there seems to be no reduction in problems. During the first few months of this year alone CDC has been tracking Salmonella in turkey and in pre-cut melons, and E. coli in ground beef, among many others.
Limits of Diagnostics Tests
The public health labs that contribute data to FoodNet are increasingly using CIDTs, such as immunoassays and nucleic-acid amplified tests. CIDTs are faster and easier to perform than traditional culture-based methods, which require use of trained personnel. CIDTs can identify a general bacteria type within hours without having to culture or grow the pure bacteria strain (or isolate) in a laboratory, a process that typically takes days. But without the isolate, public health scientists are unable to determine the DNA subtype (“fingerprint”), its resistance pattern, or other characteristics necessary to detect outbreaks, track antibiotic resistance, monitor disease trends, and ultimately prevent outbreaks.
For example, PulseNet, the CDC-run network that connects public health and food regulatory agency laboratories, relies on the collection of DNA fingerprints of bacteria taken from sick patients to identify local and multistate outbreaks. The growing use of CIDTs is endangering PulseNet’s effectiveness.
“Without a DNA fingerprint of the bacteria, CDC and public health labs will not be able to find, monitor, and prevent foodborne disease outbreaks, track antibiotic resistance, or follow trends to know if prevention policies are working,” CDC says. Even in FoodNet, CIDTs “complicate data interpretation,” CDC says.
This is where advances in technology, such as whole genome sequencing (WGS) for pathogen detection and blockchain for product traceability are expected to yield big dividends for food safety.
WGS can map the genetic sequence of pathogens and other organisms with such precision that researchers can distinguish between different strains of a bacterium or even slight variations by geography within the same strain. Prior to WGS, scientists used such tools as polymerase chain reaction and pulsed-field electrophoresis (PFGE) to genotype microorganisms for diagnostic subtyping.
Last year, WGS replaced PFGE in PulseNet as the primary method for detecting and investigating Listeria outbreaks and is increasingly being used for Salmonella, E. coli, and Campylobacter.
“The more widespread use of WGS has also increased the number of detected outbreaks and subsequent investigations,” said then-FDA Commissioner Scott Gottlieb, MD, and Yiannas in a recent joint statement. But, they added, this has also increased FDA’s workload to identify and mitigate potential food safety concerns. “As part of the president’s 2020 budget, we’re also requesting additional resources to support the use of WGS and expand our ability to respond when we identify food contamination,” they explained.
Updating Technology Use
When it comes to food traceability, most companies keep records of one step back to identify the source and one step forward to where the food has gone, as required by federal law. And many companies keep these records on paper, not electronically. Investigators found this especially frustrating last year as they sought to determine the source of E. coli-tainted romaine lettuce. Had growers and shippers used electronic records and blockchain technology, tracing the origin might have taken minutes or even seconds, instead of weeks.
Blockchain uses a decentralized, secure ledger that’s shared by all parties in the supply chain to provide transparency on a product’s origins. It can greatly assist in warning consumers about risks with specific foods and in implementing more targeted and efficient recalls.
“Today’s technology can provide us with insights that were not possible even a handful of years ago,” says David Acheson, MD, former associate FDA commissioner for foods and founder and CEO of The Acheson Group. “But going even deeper than the DNA insights of an outbreak is the ability of today’s technology to trace a food forward, backward, and sideways. The technological ability is there, but with the regulatory requirement being only one forward/one back, the incentive is, unfortunately, a bit lacking,” Dr. Acheson says. “We can blame it on all sorts of things, but there’s no denying that the industry could, and can, do better.”
Tracing is only one area where technology can enhance food safety. “We’ll also be looking at how to leverage emerging technologies and other approaches that are being used in society and business sectors all around us, such as distributed ledgers, sensors, the Internet of Things, and artificial intelligence,” explained Dr. Sharpless and Yiannas—who before joining FDA last December had overseen the implementation of blockchain technology at Walmart.
“There’s a lot industry and government—whether it’s the states or the federal government—can do to advance food safety,” they added. “Tackling food safety is a shared responsibility, and there’s much more we can do together and in a manner that benefits people, food companies, and the planet.”
Dr. Acheson agrees. “We have to find a way to move faster in these types of outbreaks,” he says, “and that will require a commitment and resources from the government at the state and federal levels, likely new regulations, and, of course, industry at all levels—including retail and food service—using the technology that is already available.”