U.S. Food and Drug Administration Commissioner Scott Gottlieb said some parties were using "the excuse" of the ongoing partial government shutdown — now into its fourth week and the longest in U.S. history — to "advance misleading narratives."

"We've seen some inaccurate narratives," Gottlieb wrote on Twitter on Jan. 15. "As the challenges grow, I fear that we'll see more parties inadvertently or deliberately blame the shutdown."

Gottlieb did not identify any particular company or party in his tweets, so it was unclear whom he meant or what narratives he was describing.

The commissioner also tweeted that his agency was getting "many questions" related to a "particular biotech firm" and also inquiries about when regulators could continue to accept medical product applications during the lapse in funding.

Those tweets came shortly after one company, Aimmune Therapeutics Inc., reported on Jan. 14 that the FDA told the biotech the regulatory work on its application to market an oral immunotherapy to treat peanut allergy in pediatric patients was put on hold until the shutdown ended.

The shutdown is now 26 days long.

In December 2018, Aimmune said it was seeking a priority review under the Prescription Drug User Fee Act — the law that permits the FDA to collect user fees from drugmakers to assist with regulatory work on new drug applications.

The FDA is not permitted to divulge information about a company's pending application. It is unclear if the biotech Gottlieb was tweeting about was Aimmune. But several of the commissioner's tweets over two days on Jan. 14 and 15 were about applications for allergenic products — the type of drug Aimmune is seeking to market in the U.S and whose application review has now been stalled, which the biotech attributed to the shutdown.

A spokeswoman for Aimmune told S&P Global Market Intelligence the company had paid user fees to the FDA a week before it filed its application on Dec. 21, 2018, just hours before the government shutdown started at midnight — a closure that was triggered when Congress failed to fund a quarter of the nation's federal agencies, including Gottlieb's.

On Jan. 15, Gottlieb tweeted that the FDA has about four to five weeks' worth of user fees on hand for the review work on new medicine applications, though he noted that estimate could change.

The agency also has about "three months of runway" on the medical device side.

Gottlieb did not provide dollar amounts for those user fees and he has not responded to questions about how much funding the FDA has available to review applications for generic drugs and lower-cost versions of biologic therapies, or biosimilars.

He did, however, acknowledge that generic drug and biosimilar programs would be impacted if the shutdown continues.

User fee vs. non-user fee programs

For products covered by a user fee program, if the manufacturer submitted the application and paid any required fees before the shutdown, the FDA can use its "limited carryover user fee funding to continue reviewing the application," Gottlieb explained on Twitter on Jan. 14.

He noted the FDA is not permitted to accept new medical product applications that require a payment or any new user fees during the shutdown.

For products not covered by a user fee program, like most blood and allergenic extract products, the FDA does not have carryover user fee funding to continue reviewing pending or accepting new applications, Gottlieb said.

"These product categories are not associated with a user fee program," Gottlieb said. "As a result, during the lapse, FDA activities for products are limited to emergency work involving safety of human life, such as monitoring for adverse events and, if warranted, taking action to protect patients."

Gottlieb returned to Twitter early the next morning, emphasizing that because blood and allergenic products are not covered by user fee programs, routine review activity ceased related to those categories.

"This fact is widely understood in allergenic product category," he wrote on Jan. 15. "This industry segment negotiated to be excluded from user fee agreements, so it's widely understood that they're not covered by user fees but by budget authority, which lapsed."

Gottlieb said some companies try to submit applications "under pathways that aren't open to them."

He again did not identify any specific company, but he said "Allergenic-type products only meet criteria to fall outside the allergenic category in very specific circumstances."

The commissioner said when confusion occurs on application submissions and user fee payments, "it's highly unfortunate and we always try hard to provide clarification where appropriate."

"As a general matter, if all of a sponsor's interactions are with the allergenic products division, it's an indication that it's an allergenic product," Gottlieb said.

Some FDA inspectors returning to work

Meanwhile, Gottlieb also disclosed on Twitter that he was bringing back about 400 of the more than 7,000 employees who had been furloughed. The vast majority of those returning are inspectors and their support staff.

Of those 400, 150 will be focused on inspections of food product plants, 100 for medical device manufacturing facilities, 70 for plants where drugs are made and 90 for biologic therapy facilities, he said.

The commissioner described the drug and device facilities as "high-risk" manufacturing sites.

Gottlieb insisted none of the FDA's regular inspections had been missed during the shutdown.

"None were scheduled," he said on Twitter on Jan. 15. "Normally the schedule for the first week back from Christmas would have been reduced, but unclear how many we would have scheduled but for the shutdown. Not many. Maybe a few dozen. They'll be scheduled going forward, starting today."