Health Secretary Robert F. Kennedy Jr. summoned Susan Monarez, the director of the Centers for Disease Control and Prevention, to his office in Washington earlier this week to deliver an ultimatum.
She needed to fire career agency officials and commit to backing his advisers if they recommended restricting access to proven vaccines — or risk being fired herself, according to people familiar with the events.
Dr. Monarez’s refusal to do so led to an extraordinary standoff on Thursday that paralyzed the nation’s health agency, which is still reeling from mass layoffs and a shooting this month that killed a police officer and terrified employees.
Top officials have quit, Dr. Monarez’s future is in doubt and President Trump has yet to publicly back his health secretary.
The White House press secretary, Karoline Leavitt, said Mr. Trump had fired Dr. Monarez. “The secretary asked her to resign,” Ms. Leavitt said. “She said she would, and then she said she wouldn’t, so the president fired her, which he has every right to do.”
Lawyers for Dr. Monarez insisted that, because she had been confirmed by the Senate and served at the pleasure of the president, she would leave only if Mr. Trump personally instructed her to do so. They said she had chosen “protecting the public over serving a political agenda.”
The president himself was silent.
Dr. Monarez, who had been sworn in just one month earlier, had lost access to her agency email. Three other high-ranking officials, who had resigned in protest on Wednesday, were escorted out of the agency’s Atlanta headquarters. A new chief operating officer was installed.
And Mr. Kennedy, who had tried unsuccessfully to fire Dr. Monarez himself, fumed at a news briefing in Texas that the C.D.C. — an agency he has previously described as “a cesspool of corruption” — needed an overhaul.
“There’s a lot of trouble at C.D.C., and it’s going to require getting rid of some people over the long term in order for us to change the institutional culture,” he said.
Public health leaders said the health of all Americans was at stake.
With Dr. Monarez facing an uncertain future, and the agency’s top ranks depleted, leading public health experts wondered aloud on Thursday whether the C.D.C. could recover — and what might happen should a pandemic or other health crisis arise.
They said they fear the United States will be unable to handle a future pandemic or other health crisis.
“I think this is quite a negative and potentially catastrophic step for the country,” said Adm. Brett Giroir, a physician who helped lead the response to the coronavirus pandemic during Mr. Trump’s first term and advised Mr. Kennedy during the latest transition.
“I don’t know who’s in charge, honestly, and that’s frightening because the No. 1 thing you need is somebody in charge,” he added.
The Monday meeting was just the beginning of a tense back-and-forth between Dr. Monarez and her boss, the health secretary, according to people familiar with the events.
In addition to firing top C.D.C. leaders, Mr. Kennedy insisted that Dr. Monarez agree to accept whatever recommendations were made by the Advisory Committee on Immunization Policy, they said. The expert panel was recently reconstituted by Mr. Kennedy with new members who have questioned the safety of vaccines.
The committee is scheduled to meet again on Sept. 18 and 19, and may consider recommendations for a wide array of vaccines, including those for hepatitis B, Covid and respiratory syncytial virus, as well as a combination vaccine for measles, mumps, rubella and varicella, according to an agenda posted on the Federal Register.
After Dr. Monarez refused Mr. Kennedy’s demands, she called Senator Bill Cassidy, Republican of Louisiana and chair of the Senate health committee. He called Mr. Kennedy, which angered the health secretary, according to an administration official familiar with the events.
Mr. Kennedy summoned her back on Tuesday and reiterated his demands. On Wednesday, Dr. Monarez received a phone call from the White House personnel office telling her that she was being fired.
Dr. Richard Besser, chief executive of the Robert Wood Johnson Foundation and a former acting director of the C.D.C., said that he called Dr. Monarez on Wednesday, just by chance, to see how they could cooperate on public health matters.
He said she told him she did not expect to be long in her job — and that there were two things she would never do to keep it.
“One was anything that was deemed illegal, and the second was anything that she felt flew in the face of science,” he said. Dr. Monarez said she had been asked to do both, he continued — to fire agency leadership and “to rubber stamp A.C.I.P. recommendations that flew in the face of science.”
In Washington, senators from both parties expressed dismay at the events unfolding at the C.D.C. Mr. Cassidy, a physician who voted for Mr. Kennedy’s confirmation as health secretary after publicly agonizing over it, said on social media late Wednesday that the “high profile departures will require oversight” by his panel.
On Thursday, Mr. Cassidy called for a delay in the upcoming vaccine advisory committee meeting. Mr. Cassidy said that said if the meeting proceeds, “any recommendations made should be rejected as lacking legitimacy” given concerns about the panel “and the current turmoil in C.D.C. leadership.”
Senator Bernie Sanders, the Vermont independent and ranking member of the health panel, said the attempt to fire Dr. Monarez was “outrageous” and called for a hearing. His colleague on the committee, Senator Patty Murray, Democrat of Washington, demanded Mr. Kennedy’s “immediate termination.”
Ms. Murray, who voted against Dr. Monarez’s confirmation, said in a statement that she once had “serious doubts about Director Monarez’s willingness to stand up against R.F.K. Jr.’s personal mission to destroy public health in America.”
She added: “I’m glad to say that I was wrong.”
The three officials who were ushered out the door by security on Thursday had coordinated their resignations. C.D.C. employees had planned to gather at agency headquarters in Atlanta. for a “clap-out” send-off to honor them, but the officials were forced to leave earlier. Still, hundreds of C.D.C. employees, including many in service uniforms, gathered at the agency to celebrate them.
The C.D.C. officials had decades of government experience, and all influenced vaccine policy.
Dr. Debra Houry, the C.D.C.’s chief medical officer, coordinated the various arms of the agency. Dr. Demetre Daskalakis ran the center that oversees respiratory illnesses and issues vaccine recommendations. Dr. Daniel Jernigan supervised the center that oversees emerging diseases and vaccine safety.
A fourth official, Dr. Jennifer Layden, who resigned a day earlier, led the office of public health data.
Dr. Jernigan said he had heard from Dr. Monarez that Mr. Kennedy’s office felt his position “was not needed anymore.” He decided to resign before his job could be eliminated, he said, in part hoping that would allow Dr. Monarez to continue as the director.
“If we were the problem, and she had the opportunity to actually stay, removing us as a problem I think was something that we were willing to do,” he said, adding that it was “important to have a strong, scientifically driven director.”
Dr. Jernigan said he was also increasingly uncomfortable with the things he was being asked to do, including providing data for a new analysis of vaccine safety data for potential links to autism, even though dozens of studies have already examined that claim and not found a connection.
Mr. Kennedy has hired David Geier, a discredited vaccine skeptic, to reanalyze the data, but Mr. Geier seemed to already have a conclusion in mind, Dr. Jernigan said.
“That approach to having a desire of what you want out of the data, and then looking at the data in order to find it — that, to me, is not the right way to ask scientific questions,” he added.
In an interview on Thursday morning, Dr. Houry and Dr. Daskalakis said there was no single move that pushed them to resign.
Rather, it was “death by a thousand paper cuts,” Dr. Houry said. “We had so many of these instances where we just couldn’t take it.”
The three had been contemplating leaving the agency for weeks, they said. But their distress escalated sharply after the new members of the vaccine advisory panel said that they would revisit the childhood and adolescent immunization schedules when they met again in the fall.
One vaccine that protects against hepatitis B was added to the committee’s agenda for its next meeting in September. Mr. Kennedy has long been critical of the vaccine.
Hepatitis B is a highly transmissible and dangerous pathogen that can be spread through sexual contact, needle stick injuries or from an infected mother to child, said Dr. Sean O’Leary, chair of the infectious disease committee for the American Academy of Pediatrics.
The vaccine has been shown to be safe and is given at birth to ensure that no cases are missed, he said. Any attempt to remove it from the immunization schedule would most likely face opposition, including from Senator Cassidy, he added.
Other recent moves also influenced the resignations.
Last week, Mr. Kennedy named Retsef Levi, a health analytics expert at the Massachusetts Institute of Technology, to lead the Covid vaccine working group, which was given a broad mandate.
Dr. Levi has called for the Covid vaccines to be pulled from the market. Last week, a spokesman for the Department of Health and Human Services defended the choice, saying the group’s members would work with federal experts and be receptive to diverse perspectives.
Dr. Daskalakis criticized the selection of Dr. Levi, saying he had no expertise in vaccines, “is frankly riddled with bias” and was assigned specifically to prevent the C.D.C.’s input to the discussion.
“That was, for me, one of the brightest red lines,” he said.
Mr. Kennedy signaled his intention to transform immunization policies when he fired all 17 independent scientific advisers to the C.D.C. and replaced them with eight people of his own choosing. (One later dropped out because of financial conflicts of interest.)
This week’s high-profile resignations are only the latest in a series of exits at the agency since Mr. Kennedy took office. In April, as the C.D.C. and other agencies were sharply pared down, some C.D.C. leaders were placed on administrative leave and a few took early retirement.
Two experts in vaccine policy left the agency in June, saying they feared for the lives of Americans if Mr. Kennedy were to continue unchecked.
Dr. Lakshmi Panagiotakopoulos oversaw the Covid vaccine working group before she resigned in June.
“It’s heartbreaking to witness such important, nuanced work being led by someone who has shown publicly at the A.C.I.P. meeting that he not only doesn’t understand the data, but is also dedicated to baseless conspiracy theories,” she said of Dr. Levi on Thursday.
The newest resignations are a sign of “how dire things are at the agency,” she said.
Sheryl Gay Stolberg covers health policy for The Times from Washington. A former congressional and White House correspondent, she focuses on the intersection of health policy and politics.
Apoorva Mandavilli reports on science and global health for The Times, with a focus on infectious diseases and pandemics and the public health agencies that try to manage them.
Christina Jewett covers the Food and Drug Administration, which means keeping a close eye on drugs, medical devices, food safety and tobacco policy.
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