WASHINGTON — One-quarter of the federal government shut down at 12:01 a.m. Saturday — including the Food and Drug Administration.

Republican leadership in the House suggested around 7:30 p.m. Friday there would be no further votes on legislation to fund the government ahead of the midnight deadline, teeing up a partial shutdown.

The FDA, however, won’t feel the full effects of the shutdown until Wednesday, since nearly all of its staff would not have worked over the weekend or on the federal holidays Monday and Tuesday. Beginning Wednesday, about 40 percent of the agency’s employees will be furloughed; the majority are either considered “essential” or have their work funded by user fees paid for by the drug and device industry.

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Although talks are expected to begin again on Saturday, it’s not yet clear whether congressional negotiators will be able to work out a deal with President Trump before Wednesday.

FDA employees whose jobs are considered essential to public safety won’t be furloughed. For example, the FDA will still implement recalls of harmful food and drugs, but they will stop routine inspections of manufacturing plants.

A shutdown will have other palpable effects on the agency, too, such as slowing down the drug approval process and halting some administrative actions, senior officials told STAT earlier this year, in the days leading up to the January 2018 shutdown.

In a letter to staff Thursday night, FDA Commissioner Scott Gottlieb said that the timing of the shutdown was unfortunate.

“I deeply regret that we face these challenges at any time – and especially at this time of the year,” he wrote. “I remain optimistic that Congress will work quickly to maintain the government’s funding so we may continue to carry out all of the activities that support our important mission.”

The partial shutdown will not affect most public health work done by other agencies, like the National Institutes of Health or the Centers for Disease Control and Prevention, since much of the Department of Health and Human Services was already funded through a bill passed in September.

The shutdown will also effectively doom a bipartisan effort to pass a major piece of public health legislation that is supposed to help the government respond to public health emergencies. That bill would have renewed some programs created back in 2006 that expired on either September 30 or December 19.

In a short-term funding bill that never made its way to the president’s desk, lawmakers had included provisions that would have prolonged two specific measures through February 8. And in a separate piece of legislation, lawmakers also attempted to extend all of the programs many years into the future. Neither has yet been signed into law.

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