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By Andrea Shalal, Leah Douglas, Ahmed Aboulenein and Ted Hesson

WASHINGTON (Reuters) -Almost half of the probationary workers at the U.S. Centers for Disease Control and Prevention and others at the National Institutes of Health are being forced out as President Donald Trump overhauls government agencies, sources familiar with the job cuts told Reuters on Friday.

One source familiar with the CDC layoffs said managers had no say on the criteria and that about 45% of probationary employees would be let go.

An unspecified number of employees at the National Institutes of Health were also fired, two sources familiar with the NIH cuts told Reuters.

A spokesperson for the U.S. Department of Health and Human Services, which oversees the CDC and NIH, confirmed it was taking action on an order to streamline and restructure.

Some of those fired from the CDC on Friday were first-year fellows in the agency's two-year Epidemic Intelligence Service program, which trains healthcare professionals to investigate diseases, a second source familiar with the CDC cuts told Reuters.

Second-year fellows were waiting to be told if they would also be fired later on Friday, the source said. The CDC has between 120 and 180 EIS officers in any given year across the first- and second-year classes, its website shows.

Scientists at the NIH received instructions late on Friday to terminate probationary employees in their research laboratories and clinics, one source, an NIH scientist, said.

"I literally can't work" without the terminated staff members, the scientist said. "There's not going to be any research." Patients would have to be turned away because of the terminations, the scientist said.

The NIH may need to temporarily close some facilities due to lack of qualified personnel, said a second source, a U.S. health official.

A "huge" number of nurses from the NIH Clinical Center were also fired, the official said. Some employees who have been with the agency for decades and not on probation also received dismissal notices, the official said.

A total of around 5,200 probationary employees across HHS were being let go, STAT News reported.

The Associated Press reported on Friday that 1,300 probationary employees at the CDC were being let go, citing a federal official. The CDC had 12,000 employees as of last year.

The moves came on the first full day for Secretary of Health and Human Services Robert F. Kennedy Jr., who was confirmed on Thursday despite being an avowed vaccine skeptic and critic of the CDC and other agencies under his watch.

The CDC is a sweeping agency that is used as a public health model around the world to track and respond to infectious disease outbreaks, including recommending licensed vaccines such as routine vaccines used in childhood and those given during the COVID-19 pandemic.

The NIH is the country's top public funder of medical research. It has long been in Kennedy's crosshairs, and he said in November he would act quickly to fire 600 people there and replace them all with new hires. The agency employs nearly 20,000 people.

"HHS is following the administration's guidance and taking action to support the president's broader efforts to restructure and streamline the federal government," an HHS spokesperson said when asked about the cuts.

"This is to ensure that HHS better serves the American people at the highest and most efficient standard."

The CDC did not respond to a request for comment. The NIH did not immediately respond to a request for comment.

The CDC layoffs were part of a verbal notice from HHS in a meeting with CDC leaders, AP reported, citing a federal official who was at the meeting.

The U.S. government began firing thousands of people at multiple agencies on Thursday as Trump and billionaire Elon Musk accelerate their purge of America's federal bureaucracy, Reuters reported.

Trump has tasked Musk and his team at the Department of Government Efficiency, a temporary government agency, with undertaking a massive downsizing of the 2.3 million-strong civilian federal workforce.