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“We were going to see if she was able to weather the storm. And when she was not, we were done,� said Houry, one of at least four CDC leaders who resigned this week. She was the agency’s deputy director and chief medical officer.

The White House confirmed late Wednesday that Monarez was fired because she was not "aligned with� agenda and had refused to resign. She had been less than a month ago.

Trump's health secretary, , declined during an appearance on “Fox & Friends� to directly comment on the CDC shake-up. But he said he continues to have concerns about CDC officials hewing to the administration's health policies.

“So we need to look at the priorities of the agency, if there’s really a deeply, deeply embedded, I would say, malaise at the agency,� Kennedy said. “And we need strong leadership that will go in there and that will be able to execute on President Trump’s broad ambitions.�

A lawyer for Monarez said the termination was not legal — and that she would not step down — because she was informed of her dismissal by staff in the presidential personnel office and that only Trump himself could fire her. Monarez has not commented.

Dr. Richard Besser, a former CDC acting director, said that when he spoke with Monarez on Wednesday, she vowed not to do anything that was illegal or that flew in the face of science. She had refused directives from the Department of Health and Human Services to fire her management team.

She also would not automatically sign off on any recommendations from a handpicked by Kennedy, according to Besser, now president of the Robert Wood Johnson Foundation, which helps support The Associated Press Health and Science Department.

Houry and Dr. Demetre Daskalakis, who resigned as head of the National Center for Immunization and Respiratory Diseases, said Monarez had tried to make sure scientific safeguards were in place.

Some concerned the Advisory Committee on Immunization Practices, a group of outside experts who make recommendations to the CDC director on how to use vaccines. The recommendations are then adopted by doctors, school systems, health insurers and others.

Kennedy is a longtime leader in the anti-vaccine movement, and in June, he abruptly dismissed the entire panel, accusing members of being too closely aligned with manufacturers. He replaced them with that included several vaccine skeptics and then he shut the door that had long helped form vaccine recommendations.

Recently, Monarez tried to replace the official who coordinated the panel's meetings with someone who had more policy experience. Monarez also pushed to have slides and evidence reviews posted weeks before the committee's meetings and have the sessions open to public comment, Houry said.

HHS officials nixed that and called her to a meeting in Washington on Monday, Houry said.

When it became clear that Monarez was out, other top CDC officials decided they had to leave, too, Houry and Daskalakis said.

“I came to the point personally where I think our science will be compromised, and that's my line in the sand,� Daskalakis said.

Monarez's lawyers, Mark Zaid and Abbe David Lowell, said in a statement that when she refused “to rubber-stamp unscientific, reckless directives and fire dedicated health experts, she chose protecting the public over serving a political agenda. For that, she has been targeted.�

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The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education and the Robert Wood Johnson Foundation. The AP is solely responsible for all content.