(Reuters) – The U.S. Food and Drug Administration has warned Pfizer Inc for failing to quickly report serious and unexpected potential side effects from its drugs already on the market.

In a 12-page warning letter to Pfizer Chief Executive Jeffrey Kindler, the FDA cited numerous examples involving some of the company’s top-known brands, including impotence drug Viagra, cholesterol pill Lipitor and seizure medicine Lyrica.

The delays in reporting side effects date back as far as 2004 and have grown in recent years, according to the FDA’s letter that was released by Pfizer on Wednesday.

Ronald Pace, director of the FDA’s New York office, told Pfizer in the letter dated May 26 that it had not properly documented or investigated reported problems in patients after the drugs were approved for use.

“FDA expects drug manufacturers to establish and implement reasonable mechanisms to assure that all serious and unexpected experiences are promptly recorded and investigated,” Pace wrote.

Pace asked Kindler to arrange a meeting between the company and the agency over the violations. Pfizer said it received the letter June 3.

The FDA conducted a 6-week inspection of Pfizer’s New York headquarters in July and August of 2009, where agency inspectors found system-wide lapses at the world’s largest drugmaker.

The patient reports “contained serious and unexpected adverse events… that were not submitted until they were identified during the FDA inspection,” Pace wrote. Efforts to fix the problem “have been shown to be ineffective,” he added.

In a statement, Pfizer said it would work with the FDA to satisfy the agency “and to assure optimal surveillance and reporting of post-marketing adverse events.”

But it also said that such individual reports are just one part of its overall monitoring of the drugs it sells and that it “believes we provide complete and accurate data to determine the benefit and risk profile for all of our medicines, and to enable their safe and appropriate use.”

In its letter, the FDA cited multiple examples of reporting lapses.

For example, while Viagra and similar medications are known to cause serious visual problems, including blindness, Pfizer failed to report cases related to its drug within the agency’s 15-day deadline “by misclassifying and/or downgrading reports to non-serious without reasonable justification.”

And with Pfizer’s now withdrawn painkiller Bextra, FDA granted the company a waiver allowing 60 days to forward any complaints, a window of time the drugmaker still missed.

The FDA said Pfizer initially blamed the problems on a new computerized system to handle the reports, saying staff were not properly trained. In a September 2009 response to the agency, Pfizer told the agency it would update user manuals, better train its staff in the computerized reporting system and take other action.

Despite those steps, the FDA said in its letter that the company’s actions were “inadequate.”

Pfizer told the FDA that its reporting improved after May 2009, but did not include any data backing up that claim, the FDA said. Additionally, the company did not prove to the FDA that it trained all the employees it said it would.

According to the FDA, the company’s delays in telling the agency about reported complaints have only grown. About 4 percent of Pfizer’s 80,560 reports were sent late from March 2006 through December 2008 compared with 9 percent from December 2008 to June 2009, the letter said.

Additionally, the FDA cited Pfizer for not immediately telling the FDA about thefts and significant losses of its medications.

FDA’s Pace requested an immediate meeting and asked for the problems to be fixed within 15 days, or an explanation provided if it would take longer. He also called for Pfizer to submit a revised plan to fix the problems.

Failure to fix the problems could result in legal action without notice and the FDA could delay action in approving the company’s pending drugs, among other penalties, Pace said in the letter.

(Reporting by Susan Heavey, additional reporting by Lisa Richwine; Editing by Tim Dobbyn)

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