The agency has lost a third of its work force this year. The Trump administration maintains that the losses are necessary, but critics say that there is no real plan, only animosity. Months before Robert F. Kennedy Jr. became health secretary, officials at the Centers for Disease Control and Prevention began preparing for his arrival.
Dr. Debra Houry, who was then the agency’s chief medical officer, read three books by Mr. Kennedy, as well as another by the current nominee for surgeon general, Dr. Casey Means, an ally of Mr. Kennedy.
Dr. Houry plowed through the Project 2025 blueprint and another report by the conservative American Enterprise Institute, in addition to reviewing the America First agenda. She guided directors of the C.D.C. centers as they prepared detailed briefs on Mr. Kennedy’s concerns, such as access to vaccine safety data and separating the measles vaccine from those for mumps and rubella.
Her first meeting with the Trump transition team, on Dec. 20, seemed cordial enough, and she allowed herself to hope that agency might even fare well. It has not.