Cyclospora outbreak tests RFK Jr.'s promise to overhaul food system, rebuild trust in CDC

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."

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.