Foodborne illness investigations have slowed and food recalls have plummeted to their lowest levels in years because of disruptions in America’s multi-layered food safety system caused by the novel coronavirus, a USA TODAY investigation found.

The pandemic struck the system at every level — from the federal agencies tasked with stopping contaminated food before it leaves farms and factories to the state health departments that test sick residents for foodborne illnesses like E. coli.

Experts say there is no evidence yet of resulting widespread health issues, but food safety advocates say Americans are now more at risk.

“We have so many different safeguards built into our system, and one by one COVID is knocking pieces out,” Sarah Sorscher, deputy director of regulatory affairs at the Center for Science in the Public Interest.

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The U.S. Food and Drug Administration in March announced it would postpone in-person inspections of the nation’s food factories, canneries, and poultry farms. As a result, the number of FDA inspections dropped from an average of more than 900 a month to just eight in April. Along with that tumbled FDA citations issued for unsafe conditions — from hundreds a month to nearly zero in April. 

The number of product recalls followed suit. 

Companies primarily issue recalls themselves and report them to the FDA. Weekly reports from the FDA shows the number of recalls dropping from 173 in February to 105 in March to 70 in April.

The U.S. Department of Agriculture also oversees food recalls. Their numbers, too, dropped from an average of more than 10 a month to an unprecedented zero in March and just two in April. Between January and April, the USDA listed just seven food recalls — the lowest number for that period in at least a decade.

A USDA spokesperson said by email the agency is “continuing to meet all inspection obligations” and that it has further pushed the food industry for more “accountability” in providing safe products. 

The agency “is proactively engaging with industry to improve production practices and reduce the number of recalls and we are seeing the results of these efforts,” the spokesperson wrote.

Meanwhile, some state health departments are so busy with COVID-19 that they’re struggling to keep up with the typical foodborne illness workload, which could be decreasing anyway as fewer Americans seek treatment for stomach ailments, choosing instead to stay home instead of seeing their doctor. 

State health agencies typically interact with local doctors and hospitals to gather information that’s then loaded into a nationwide “PulseNet” database administered by the CDC. 

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PulseNet activity started plummeting in April, said Dr. Robert Tauxe, director of the CDC’s foodborne illness division. It saw a 50% decline in E. coli samples being entered into the system and a 25% drop in Salmonella cases compared to five-year averages. 

Despite this, Tauxe said, the changes have “not interrupted our ability to detect and investigate foodborne outbreaks.”

“We are still detecting new clusters that are being investigated every week,” he added. “The number of clusters identified is about the same as that seen in previous years.”

Yet the number of completed federal investigations of foodborne outbreaks also fell both at the CDC and the FDA.

Through May 7, the CDC has solved two outbreaks: a mushroom outbreak that sickened three dozen people and killed four across the country, and a clover sprouts outbreak that sickened 51, primarily in Utah.

That’s behind the pace of the agency’s recent history. By the same time last year, there had been recalls of products across five different outbreaks, which sickened more than 300. The pace was in line with the CDC’s annual average of 13 completed investigations dating to 2011.

The CDC’s Tauxe cautioned that not every investigation leads to a recall, and says the agency “Continues to work with our public health partners to detect outbreaks.”

Information from the FDA’s website also indicates a drop in completed investigations resulting in food recalls this year. While the agency has had two investigations so far — also the mushrooms and clover sprouts — that’s less than half the pace of 2018 and 2019, which both saw 16 investigations completed over the course of a year. However, it is not unprecedented, and exceeds the pace of investigations in 2011 and 2015.

The number of open, internal FDA investigations has dropped even more dramatically on a monthly level, according to statistics provided to USA TODAY. Last December, the agency had been tracking 15 investigations, a record high. But by the middle of February, that number dropped to nine, and by the middle of April, just two.

In an email, Frank Yiannas, FDA’s deputy commissioner for food policy and response, said the agency’s foodborne illness section is still “fully staffed and on the job” working to identify outbreaks. He noted the mushroom investigation remains ongoing, leading to recalls of products on April 7 and 15.

FDA inspections plummet

Ordinarily, the FDA visits thousands of food production facilities each year to conduct safety inspections. Examples from recent inspections show troubling findings reported with straightforward language.

“You did not exclude pests from your food plant to protect against contamination of food,” read one.

“You did not take an adequate measure to protect against inclusion of metal or extraneous material in food,” read another.

But on March 18, the agency announced it would “postpone” almost all such inspections as employees began teleworking.

The number of inspections and citations swiftly plummeted. In 2018 and 2019, the FDA averaged about 900 inspections a month, leading to 600 citations. In March, the numbers fell to 307 inspections and 167 citations. In April, just eight inspections took place, leading to two citations.

The FDA was already limited in how often they were inspecting facilities, with federal regulations requiring a visit just once every three to five years, said Tony Corbo, senior government affairs representative from the nonprofit Food & Water Watch.

“You already have a weak inspection system, that’s been made weaker,” Corbo said.

But Martin Wiedmann, a professor of food safety at Cornell University, said the impact should be limited. He said the food companies themselves were and still are the primary testers of food safety, and that whatever amount of layered protection came from federal oversight was worth suspending to cut down on the risk of inspectors becoming infected.

“The FDA is the final safeguard of the system,” he said.

The FDA has modified other guardrails, too. Over the past two months, the agency has eased rules ensuring the safety of consumer-grade eggs, requiring supplement manufacturers to report “adverse events,” and compelling food companies to audit food safety practices at ingredient suppliers.

Sorscher said she understands the need for temporary changes to protect workers from COVID-19 but that the loss of on-the-ground auditors is a “red flag.” The chaos causes food manufacturers to connect with new suppliers. Normally, they’d first evaluate the safety of those suppliers, but that line of defense is now hindered.

“A lot of supply chains are being disrupted right now, so it’s really important that if a company is working with a new supplier, they’re able to ensure food safety,” Sorscher said.

The FDA’s Yiannas defended the agency, saying it is using “layers” of protection that include modifying an algorithm to scrutinize food imports and enhancing remote inspections. The agency also continues to conduct “mission critical” in-person inspections.

“FDA believes these alternative activities strike the right balance,” Yiannas said, “between the realities of the unprecedented present situation in which certain travel is not possible yet still provide regulatory oversight, while protecting the health and well-being of our workforce and those working in regulated industry.”

Some companies also are continuing private audits of their factories, and Sorscher noted that companies are still legally responsible for addressing food safety risks internally. But she said she worries about what happens if private inspectors and staff also become impacted by COVID-19.

“FDA isn’t inspecting, and what if the (company’s) food safety person is out sick?” Sorscher said. “When that last support falls, and that person in industry whose job it is to handle food safety isn’t there, then we could have an outbreak and we may not even know it.”

Meat plants packed with risk

While the FDA has curtailed its in-person inspections of food factories, the USDA has remained on the job in the nation’s meat processing plants, where federal regulations require inspectors to be present at least once a day, if not around the clock.

But issues with the system are now widely known. As previously reported by USA TODAY, last month more than 1,000 inspectors were off the job after falling ill with COVID-19 or because they are considered high risk for medical complications from the disease. 

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The USDA says it has enough inspectors to cover all sites. But the agency has also issued an unprecedented number of “line speed waivers” that allow poultry plants to run at higher speeds with fewer inspectors.

In April, the department granted 15 poultry plants the waivers, which according to the Federal Register, means they have to keep at least one line averaging above the standard production speed. The waivers mean fewer USDA inspectors are physically inspecting carcasses.

Proponents argue the companies still have to implement other safety checks, like taking microbial swabs of carcasses to look for contaminants like salmonella.

But to critics like Corbo, the strain on meatpacking inspections could undercut safety.

“You’ve got these inspectors going into these plants. They may be sick or their attention may be diverted because of the pandemic,” Corbo said. “There may be issues that surface there where they’re not fully concentrating on their food safety task.”

Feedback loop broken

Another weak link in the food safety chain involves doctors, patients and health departments.  

Typically, outbreak investigations start at the local level, when a sick patient visits a doctor and a stool sample is taken. Those samples are then collected through a series of commercial and public health laboratories before being uploaded into the PulseNet database.

But hospitals and health departments are understandably focused on COVID-19, said William Marler, an attorney with Marler Clark in Seattle who specializes in food safety.

“If a kid gets acute kidney failure caused by E. coli, normally there would be a health worker there interviewing them to find out the common denominator for their illness,” Marler said. “Are they able to do that? I think the answer is probably not.”

There are additional signs such shortfalls may be occurring.

On a national call with consumer groups last week, CDC officials said several state health departments reported trouble keeping up with stool sample testing and asked for federal support. One state, which was not identified by the CDC, requested further help with interviewing patients to determine what they ate.

Janet Hamilton, executive director of the Council of State and Territorial Epidemiologists says her organization has also been holding weekly COVID-19 calls with health officials from across the country. 

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Asked about whether state health departments were struggling to keep up with foodborne illness responsibilities, Hamilton did not offer specifics but said such agencies were being crunched by years of budget cuts even before coronavirus.

“Of course protecting the nation’s food supply is critical,” Hamilton said, “but what we need is consistent, dedicated funding to support our public health infrastructure, to ensure we’re ready to respond to foodborne illnesses, as well as any other kind of outbreak.”

Many experts said they believe the drop-off in sampling may be caused by Americans choosing to stay home rather than seek treatment and testing for stomach problems.

“There’s no question that people who have called us over the last couple of months, have gone, ‘I don’t really want to go to the doctor because of COVID,’” Marler said. “Clearly some of the mild cases of foodborne illness are not going to get caught.”

Marler added that there may also be changes to risk factors for foodborne illness, with less eating out at restaurants and more people eating out at home.

But he said we probably won’t not have all the answers until after the pandemic has subsided.

“It’s going to be an interesting time after all this is over,” he said, “to sort of do an analysis of the whole food safety system and what impact COVID did or did not have.”

Contributing: Sky Chadde, Midwest Center for Investigative Reporting

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