The CDC is falling deeper into crisis. What it means for the nation’s health.

Senior officials resigned this week from the Centers for Disease Control and Prevention, revolting against efforts to upend U.S. vaccine policy that they warned could lead to resurgences of preventable disease. But months of upheaval at the agency have already undercut its work to shield Americans from harm, officials and public health experts said, with the worst possibly yet to come.

Under the Trump administration, the agency has slashed billions in funding, shed hundreds of employees and rolled back programs to help Americans quit smoking and to prevent infant and maternal deaths, including support for monitoring sudden unexpected infant deaths. Funding for programs to prevent drowning, youth violence and sexual assault is in limbo, while they are under review by the U.S. DOGE Service.

The consequences of some of these cuts have been muted or delayed because they have yet to take effect or have been halted by courts. But public health workers and experts say the CDC’s troubles could grow worse as the agency loses career staff who could intervene. And they say a bigger crisis in credibility is already unfolding.

“I never have seen an instance of an advanced, affluent country with among the finest scientific resources and leaders in the world be under assault, not from small pockets of the public or people who have unusual beliefs, but from the government itself,” said Allan M. Brandt, a public health historian at Harvard University. “This has just been radically unprecedented.”

Months of tension erupted this week with the ouster of the agency’s director, Susan Monarez, and resignation of senior leaders. In a rare moment of open defiance against the Trump administration, CDC staffers rallied Thursday in support of the departing leaders outside their Atlanta campus.

Health and Human Services Secretary Robert F. Kennedy Jr., a longtime anti-vaccine activist who has repeatedly attacked the credibility of CDC, sent an email to employees late Thursday telling them he wanted to restore trust and credibility to the agency.

“Your daily efforts — often unseen — save lives,” he wrote. “Reform does not diminish your work; it strengthens it.”

States and local government officials who depend on the CDC for much of their funding say they haven’t been able to tap CDC experts in a health crisis, or can no longer operate certain programs. They are bracing for it to get worse: Trump’s proposed budget for next year would cut the 11,500-employee agency’s budget from $9.1 billion to about $4.2 billion.

Communities big and small have felt the pinch of CDC cuts this year, scaling back vaccination efforts in Georgia and the response to a lead hazard crisis in Milwaukee that resulted in the closure of several schools after children tested positive for lead poisoning.

Mike Totoraitis, commissioner of the Milwaukee Health Department, said his department wanted the expertise of the CDC team this spring to figure out the full scope of the problem and how to best conduct surveillance for signs of poisoning. But those CDC employees had been placed on leave as part of job cuts, and the CDC denied a formal request for help.

The CDC later reinstated its lead experts in June.

“Seeing the administration at HHS seemingly devalue public health and create such turmoil within the nation’s — arguably the global — most preeminent public health authority is concerning,” Totoraitis said.

“Scientific independence is what builds trust,” said Marion Koopmans, director of the pandemic and disaster preparedness center in the Netherlands. “Political interventions really erode that trust.”

CDC epidemiologists track and analyze chronic disease trends such as rising obesity and declining drug overdose deaths. Investigators help states piece together outbreaks, such as this year’s measles surge in Texas. Researchers craft campaigns to educate the public on emerging health threats and avoiding harms from violence and smoking. Employees screen travelers and animals at U.S. airports for disease.

This had been their work for decades, seldom the subject of fierce political debates.

Then coronavirus came. Republicans criticized the CDC’s guidance on masks and other measures as too cautious, leading to unreasonably long school shutdowns, rising mental health woes and other social problems. It also galvanized the anti-vaccine movement, which seized on distrust of coronavirus vaccines to cast doubt on other shots. Among those leading the charge was Kennedy — who now oversees the agency he last year decried as a “cesspool of corruption.”

After Donald Trump won the presidency again, the CDC came under scrutiny. His first choice to lead the CDC, Dave Weldon, was a former congressman who had accused the agency of covering up evidence of vaccine risks. In Trump’s first week back in office, his administration blocked the agency from public communications and purged its websites of diversity and gender topics. In the months that followed, the CDC lost hundreds of employees and saw key offices shuttered. On Aug. 8, a gunman attacked the agency’s Atlanta headquarters in a brazen assault that terrified and angered staff.

Trump administration officials said their goal is to strengthen the CDC.

“We need strong leadership that will go in there and that will be able to execute on President Trump’s broad ambitions to restore this agency to gold standard science and to what it was when we were growing up, which was the most respected health agency in the world,” Kennedy said in a Thursday interview on Fox News.

The July confirmation of Monarez, a longtime federal government scientist Trump nominated because Weldon lacked the votes for confirmation, relieved agency staffers who saw her as a potential buffer against Kennedy. People familiar with her firing said she resisted pressure from Kennedy and other officials to change vaccine policy and fire senior staff.

Three senior leaders resigned Wednesday after Monarez’s ouster, saying Kennedy and his allies were undermining and politicizing vaccine policy. Kennedy in June had purged the CDC committee that recommends immunizations, replacing its members with individuals who have criticized long-standing vaccine recommendations.

Based on demands for data and internal discussions, agency scientists and the leaders who resigned this week said the newly reformulated committee appears poised to rescind some immunization recommendations at its mid-September meeting. The potential targets include hepatitis B shots at birth, an RSV immunization for babies, coronavirus vaccines for otherwise healthy children and young adults and a combined vaccine for measles, mumps, rubella and chicken pox. The committee previously said it would revisit the childhood immunization schedule and scrutinize the cumulative effects of all the shots administered to children.

Career scientists who worked on these vaccine issues said they have been ignored, pushed out or quit in frustration.

“For people who don’t pay attention to vaccines, some of the few remaining people who want vaccines to stay at CVS just left the CDC,” said Anna Yousaf, a CDC infectious diseases physician who has researched the effectiveness of coronavirus vaccines, speaking in her personal capacity.

Kennedy and other health officials in the Trump administration say they are not anti-vaccine, but want Americans to be able to make informed decisions backed by reliable safety and effectiveness data.

Tom Inglesby, director of the Johns Hopkins Center for Health Security at the Bloomberg School of Public Health, noted two of the senior leaders who resigned led divisions that are the backbone of CDC’s pandemic preparedness. He described their centers as “gold standard” with specialized labs to identify new pathogens, experts to deploy in dangerous outbreaks and the expertise to write guidance during a health emergency.

“If these cornerstones of CDC lose their talent, their scientific excellence and independence, we lose major national pandemic preparedness capacity,” said Inglesby, a former Biden administration health adviser.

“Countries like Canada have tried to pull their weight in supporting infection prevention efforts and vaccination efforts in other countries,” she said. “But the U.S. CDC was always special — bigger, better, enormously capable, always willing to help.”

In U.S. communities, the Trump administration’s slashing of more than $11 billion in COVID-era CDC grants to local and state communities has upended public health efforts.

A KFF Health News analysis this month showed that blue states and cities clawed back much of the money through court battles while GOP-led states that did not challenge the cuts lost funding. For example, the health department in Columbus, Ohio, lost $3 million, forcing it to lay off 11 employees who investigated disease outbreaks.

The administration also shut down the CDC’s Office on Smoking and Health, which funded nearly $100 million to state programs that included anti-smoking campaigns and hotlines designed to help smokers quit.

About 2,000 CDC employees were laid off, although several hundred have been brought back. The cuts hampered operations at labs that analyzed sexually transmitted diseases such as hepatitis C.

In a post on X Friday, HHS deputy secretary Jim O’Neill confirmed that he would serve as acting director of CDC, and said the Trump administration is refocusing the CDC on its original mission of protecting Americans from infectious-disease.

“We are helping the agency earn back the trust it had squandered,” he wrote.

Some CDC employees are bracing for what they and many medical experts say could be a death knell for the credibility of public health in America: A declaration from Kennedy that vaccines can cause autism.

For more than two decades, the agency has fought to combat what public health experts have described as one of the most persistent sources of vaccine misinformation that has been thoroughly debunked through dozens of studies spanning the globe.

Before becoming HHS secretary, Kennedy repeatedly falsely linked vaccines to a rise in cases of autism in the United States, accusing the CDC of suppressing research into the claims. He hired David Geier, a promoter of the link, to review CDC vaccine databases to study the issue, unsettling career CDC officials tasked with working with him.

Dan Jernigan, who helped oversee the CDC’s infectious-disease response, told the Post he quit in part because HHS was demanding Geier be given access to sensitive vaccine safety data as part of examining autism.

“What we see is a desire to go back and try and find those links that had been identified not to be there previously,” Jernigan said.