Dr Jay Bhattacharya, the director of the National Institutes of Health, will take on an additional role in the Administration of US President Donald Trump as acting director of the Centers for Disease Control and Prevention (CDC), long seen as a leading reference point for public health policy not only in the US but worldwide. 

Bhattacharya succeeds Dr Jim O’Neill, a science and tech investor who has been acting CDC director since August 2025.  O’Neill, who lacks any medical or research experience, is now being tapped to oversee the National Sciences Foundation in what critics described as a “musical chairs leadership shakeup for science agencies.”

Bhattacharya, meanwhile, will lead both NIH and CDC until President Trump appoints a permanent director for the latter – reflecting the tightening grip of a small coterie of Health Secretary Robert F Kennedy Jr and Trump confidantes around the leading US health policy, science and research institutions.

A permanent appointee to head the CDC would require Senate confirmation. Susan Monarez, the first Senate-confirmed CDC director under the Trump administration, led the agency briefly in 2025, before being ousted by Kennedy Jr just 29 days into her tenure.

In Senate testimony about her firing, Monarez told the Senate Health Committee members that she refused Kennedy’s requests to “replace evidence with ideology,” in pre-approving vaccine recommendation changes and in firing career public health officials.

Bhattacharya will have to balance managing the nation’s premier biomedical agency headquartered in Bethesda, Maryland, with running the federal public health agency, in Atlanta, Georgia. But the geographic distance is not the only challenge the incoming director faces.

Now positioned to reduce US vaccine schedules

The CDC vaccine advisory committee, also hand-picked by Kennedy, has made clear that its recommendations aim to reduce the number of shots American children should get, with the committee’s most recent recommendations dropping six common vaccines. The changes made good on Kennedy’s promises to reverse decades of US vaccine policy. 

As CDC’s acting director, hand-picked by Kennedy and a close ally, Bhattacharya is positioned to oversee further rollbacks in vaccine schedules, although the NIH director has stated he does support vaccinations for major childhood diseases. 

“The measles epidemic [is] best solved by parents vaccinating their children for measles,” he said during a Senate hearing in early February. The US has seen a resurgence in measles cases in the past year, fueled by misinformation and falling vaccination coverage. South Carolina reported nearly a thousand cases since October.

Along with the festering vaccine debate, the CDC has also seen mass layoffs as well as closures of departments that monitor infectious disease trends, support mental health, and manage tobacco and substance use prevention. 

Kennedy and his team claim that they have acted to reduce what they term “bureaucratic bloat” and conflicts of interest in the nation’s medical agencies. But some critics, including Dr James Alwine, speaking on behalf of  the alliance ‘Defend Public Health’,  argue that the movement championed by Kennedy is a new form of conflict of interest. 

“They promote ‘Medical Freedom,’ which is simply underwriting the largely unregulated multi-billion dollar wellness industry,” Alwine , an emeritus professor of cancer biologist at the University of Pennsylvania, said in a statement to Health Policy Watch.

“And the negative results of [this] movement are appearing as vaccine hesitancy rises, with increased cases of measles, whooping cough, flu, tetanus, mumps, and more. Children are suffering and dying.”

COVID-19 contrarian

Bhattacharya rose to prominence during the COVID-19 pandemic as an outspoken critic of the US management of the pandemic – particularly state-mandated shutdowns, as well as CDC  recommendations regarding vaccination and public use of masks.  A Stanford economist and physician, Bhattacharya co-wrote the Great Barrington Declaration, which argued for minimal COVID restrictions to boost ‘natural’ herd immunity.

The declaration was embraced by the Trump Administration and conservative news outlets. But critics pointed out that achieving herd immunity for COVID-19 without vaccines is both unethical and improbable. 

Bhattacharya will have to contend with an agency gutted of its top leadership after conflicts with Secretary Kennedy over vaccine recommendations. 

“I resigned because CDC leaders were reduced to rubber stamps, supporting policies not based in science and putting American lives at risk,” said Dr Debra Houry, a career CDC official and former CDC Chief Medical Officer, during Senate testimony on her resignation in September 2025.

“Secretary Kennedy censored CDC science, politicized its processes, and stripped leaders of independence.”

Image Credits: C-SPAN, HHS Photo by Amy Rossetti, National Cancer Institute on Unsplash.