WASHINGTON — Susan Monarez, less than a month into the job as director of the Centers for Disease Control and Prevention, entered a meeting Monday with Health Secretary Robert F. Kennedy Jr. in his office in Washington, D.C., along with his deputy, Stefanie Spear. They asked for her resignation, citing concerns about insubordination and her integrity, including instances related to vaccine policy.

When she refused, Kennedy offered her another choice: Accept all recommendations from the agency’s vaccine advisory committee, whose members he had replaced with hand-picked allies who shared his hostile views about childhood immunizations, and fire a number of high-level officials at the agency.

Barely two weeks after the shooting at the agency’s main campus, Monarez declined again to step dow

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