Cyclospora outbreak tests RFK Jr.'s promise to overhaul food system, rebuild trust in CDC
Cyclospora presents a test for HHS Secretary Robert F. Kennedy Jr.'s promise to overhaul the food system and restore confidence in the agencies overseeing it.
ShanonG
Robert F. Kennedy Jr., US secretary of Health and Human Services (HHS), during a celebration at the Health and Human Services (HHS) headquarters in Washington, DC, US, on Thursday, Jan. 8, 2026.
Kent Nishimura | Bloomberg | Getty Images
Robert F. Kennedy Jr. took the helm of the U.S. Department of Health and Human Services last year promising to overhaul the U.S. food system and restore confidence in the agencies that oversee it.
The secretary of the Department of Health and Human Services now faces one of his biggest tests yet, as the country tries to contain an outbreak – or potentially multiple outbreaks – of foodborne illness. Two months and thousands of cases of cyclosporiasis later, it looks like the nation's already fragile system is faltering.
Experts have long said the U.S. is underprepared to rein in foodborne outbreaks. But after the Trump administration slashed key officials — from federal employees who investigate the source of illnesses to those who share information with the public — Kennedy appears to face an even more daunting task to contain the parasite and build trust in the administration's response.
"It is difficult to quantify precisely, but it is clear that the cuts to federal funding over the past year or so have reduced our capacity to respond to outbreaks like this," said Craig Hedberg, co-director of the Minnesota Integrated Food Safety Center of Excellence.
Kennedy earlier this week defended the handling of an outbreak of cyclosporiasis that has sickened at least 7,000 people in Michigan alone. (The official count from the Centers for Disease Control and Prevention, which has lagged behind state tallies, sits at nearly 4,200 cases). Kennedy said the ongoing outbreak of cyclosporiasis is "under control," contending criticisms that agency cuts have hampered the investigation are "invalid."
The U.S. Food and Drug Administration and the Centers for Disease Control and Prevention have narrowed their focus to shredded iceberg lettuce from Taylor Farms, a produce supplier for a range of restaurants and grocers. The FDA over the weekend said lettuce from the company tested positive for cyclospora, the parasite that causes the explosive diarrhea. The agency later walked that back, saying it was a false positive.
Donald Schaffner, chair of food science at Rutgers University, said he's never seen such a reversal before and called it a "pretty big screw up." Still, one former senior FDA food official said the agency was right to publicize the positive test because if it turned out to be a true positive, delaying the announcement could have caused more people to fall ill. And regardless of the test result, the agencies still see the lettuce as a likely culprit.
The about face, and the confusion it created over whether regulators still suspected the Taylor Farms lettuce was tied to the outbreak, underscored the difficulty Kennedy faces in trying to restore public confidence.
HHS spokesperson Emily Hilliard in a statement to CNBC said the FDA has been transparent with Taylor Farms throughout the investigation and the corrected lab result doesn't change the agency's findings.
Former federal health officials and independent food safety experts say they see the cyclospora response as a prime example of a system that's long been underfunded and overstrained, leaving the U.S. vulnerable to these kinds of outbreaks. And they fear budget cuts, policy delays and personnel turnover are exacerbating an already delicate situation.
In response, Hilliard said regulators have "mounted a robust, science-based response to this outbreak, working closely with health departments in all 50 states, rapidly identifying known sources, and ensuring Americans have the information they need to protect themselves."
She added, "FDA and CDC continue working together to use every available public health tool to identify additional sources of the outbreak and inform swift public health action."
The cyclospora challenge
Technician holding a specimen container with stool sample for cyclospora test.
Md Babul Hosen | Istock | Getty Images
Cyclospora is a parasite that's trickier to track than some other pathogens. Parasites don't grow outside the human body, making it harder to test for them and link cases to each other. Cyclospora tests are prone to false positives because the process for conducting them can sometimes make it look like there's a parasite in the sample when there's not, Schaffner said.
Some experts said the Trump administration funding cuts make that tall task even tougher.
Dr. Daniel Jernigan, former director of the CDC's National Center for Emerging and Zoonotic Infectious Diseases, pointed to the CDC's Division of Parasitic Diseases and Malaria losing $40 million in funds from the U.S. Agency for International Development after the Trump administration dismantled the organization. The agency anticipates recovering some funds, though it would represent one-quarter of the money it used to receive from USAID, according to Jernigan.
Jernigan estimates the group has lost about one-quarter of its staff because of the budget cuts. Some of those employees worked on other parasitic diseases like malaria, but would typically be tapped to help respond in an emergency situation like this one, he said. As a result of the cuts, CDC is trying to move the parasitic diseases groups to the Division of Foodborne, Water and Environmental Diseases, which Jernigan says is a good thing for optimizing foodborne disease investigation and control.
"At the beginning of this response, the cuts because of the USAID [funding] made that division less capable of responding fast, and that's not rocket science," Jernigan said. "Just fewer people, you don't have the reserve."
HHS' Hilliard said the funds were dedicated to international activities and were not used to support the CDC's domestic foodborne disease response. She added that Trump's proposed fiscal year 2027 budget proposes a $33 million increase for food safety activities.
Jernigan suggests increasing that budget would help improve the agency's ability to respond to such outbreaks. CDC funding for food safety hasn't seen a meaningful increase since 2014, according to an analysis from George Washington University's Institute for Food Safety and Nutrition Security.
This fiscal year, the CDC's budget for food safety is $74 million, up $2 million from last year, according to the agency's operating plan. That food safety sum represents about 10% of funds for the CDC's emerging and zoonotic infectious diseases work.
CDC's FoodNet, or the Foodborne Diseases Active Surveillance Network, stopped mandatory reporting for six of eight pathogens it previously monitored, including cyclospora, because there hasn't been enough money forthe work, something experts say is a result of chronic underfunding of food safety. That program tracks foodborne illness outbreaks over time rather than identifying new outbreaks.
Kennedy earlier this week said cuts in the FoodNet program were for "redundant surveillance."
At the FDA, the agency's budget for food has long been a fraction of centers that oversee regulation of drugs and devices. This year, the food center's $1.17 billion budget represents about 17% of the agency's roughly $7 billion in total program level spending.
Food funding has lagged other areas in part because it disproportionately comes from congressional appropriations, whereas money for other centers, including those that oversee prescription drugs and tobacco products, largely comes from fees the industry pays for reviews of applications.
The so-called Department of Government Efficiency, which oversaw massive federal layoffs last year, spared the FDA's foodborne illness outbreak personnel from sweeping cuts, according to the former senior FDA official. The FDA's main press office was gutted, stripping the agency of outbreak communications expertise.
Some contend the FDA's messaging around the false positive sowed confusion about the investigation and how consumers should respond.
Ellen Shumaker, director of outreach for Safe Plates at North Carolina State University, said the FDA's recall communications have needed modernization for some time. She said the agency needs to give clear communications to consumers, telling them in plain language what concrete steps they can take. She added that the agency needs to more quickly classify how severe a recall is.
In this case, the FDA said illnesses started on May 17, yet it didn't issue a public notice until July 16, a timeline that suggests the response was slower than expected, said Frank Yiannas, former deputy commissioner of food policy and response at the FDA. One measure that he and other food safety experts say could have helped accelerate the response was the FDA's Food Traceability Rule, which was supposed to go into effect this year but was delayed by two-and-a-half years. The policy was designed to help the FDA quickly see where a food came from to respond to foodborne illness outbreaks.
Kennedy has repeatedly promised to rebuild trust in the CDC following the Covid-19 pandemic and restore its focus on infectious disease, and the cyclospora response gives him a chance to display any improvements to the agency's handling of a crisis. So far, experts said they have not seen the response get much better.
The state ripple effects
State and local health departments are also feeling the effects of the Trump administration's cuts. A May analysis from the Congressional Research Service found the administration terminated $5.78 billion in CDC grants to states.
Sarah Sorscher, director of regulatory affairs at the Center for Science in the Public Interest, said states use the block grants to fund epidemiologists and other specialists involved in investigating outbreaks.
In Kentucky, the group that's primarily responsible for conducting case interviews for foodborne illnesses has experienced a 30% to 50% decrease in staffing due to a reduction in federal grant funds, according to a spokesperson for the state's department of public health. The state anticipates more staff reductions next year due to additional cuts to federal grants next year.
Even so, one state hit hard by the outbreak said it has received federal help. The Ohio Department of Health requested federal help for the cyclospora investigation and will host several of the CDC's Epidemic Intelligence Service officers this week to assist, a spokesman told CNBC. The state agency has requested help from the CDC in prior responses, including a measles outbreak in 2022 and the East Palestine train derailment in 2023.
In the meantime, more people are falling ill. The CDC has received reports of more than 4,000 laboratory confirmed cases and is aware of more than 7,400 additional cases, many of them in Michigan and Ohio, that haven't been confirmed by a lab test yet.
And on Wednesday, the FDA reported a new outbreak among dozens of people linked to a product that hasn't been identified yet, meaning the health agencies have even more leads to investigate.
