Emails reveal: FDA was warned years ago about superbugs in medical scopes

State and federal health officials privately urged the Food and Drug Administration nearly six years ago to alert hospitals about contamination risks from specialized medical scopes that have been tied to a recent series of deadly superbug outbreaks.

The 2009 appeal came after duodenoscopes were linked to drug-resistant infections in dozens of Florida hospital patients, including 15 who died. In emails and a phone briefing, epidemiologists at the Florida Department of Health and the Centers for Disease Control and Prevention warned that the infections occurred because hospitals were having trouble cleaning the scopes properly, records obtained by USA TODAY show.

"This is likely not an issue limited to FL hospitals and it's quite concerning," Arjun Srinivasan, a CDC infection control expert, warned in an email sent to six FDA officials on April 22, 2009. "Some type of educational alert (to hospitals) will be useful … It could be brief, but it would probably be best if the alert came jointly from CDC and FDA. We also will likely want manufacturers to do an educational initiative."

Seven months later, the agencies mentioned duodenoscopes in the 57th paragraph of a general advisory on proper cleaning and disinfection of all medical scopes, including those used in colonoscopies and other common procedures. The two-sentence passage noted that special care was needed to clean trapped bacteria from a mechanism at the tip of the duodenoscopes, which are used in the U.S. about 650,000 times a year for procedures in the bile and pancreatic ducts.

It took five more years — until this winter — for the FDA to issue a specific warning that duodenoscopes pose exceptional contamination risks that can persist even after meticulous cleaning. By then, the scopes had been tied to superbug cases in Chicago, Seattle, Los Angeles, Pittsburgh, Hartford and elsewhere. Scores of patients were sickened, most with CRE, a drug-defying bacteria with mortality rates of 40% or more.

At least 15 of those patients died (in those cases, as in Florida, not all the deaths were attributed specifically to CRE because some victims also had other serious illnesses.)

Roger Sanderson, a Florida epidemiologist who helped push for a federal alert on duodenoscope safety in 2009, says he'd hoped for more than the passing reference in a general advisory on medical scope safety.

"What they had was down on page six or seven; how many people do you think got to that page?" says Sanderson, now retired. The cleaning challenges with duodenoscopes were unique and especially risky, he adds. "We thought it was a problem, we talked about an alert. We were not talking about scopes in general; we were talking about that scope."

Officials at the FDA, which regulates medical devices, insist the reference to duodenoscopes in the 2009 advisory was adequate based on what was known at the time. They say it wasn't until September 2013 that there was sufficient evidence of the scopes' risks to consider a more detailed warning, and it took 17 more months to evaluate what sort of advisory was needed.

"When the FDA had enough understanding of the issues we issued a safety communication in February to communicate publicly and to provide recommendations to mitigate the risk associated with the transmission of infections by duodenoscopes," the FDA said in a written statement.

The revelation that the FDA was urged to issue such a warning years earlier adds a new layer to a burgeoning debate over the speed and adequacy of the agency's efforts to alert practitioners and patients to the contamination issue. USA TODAY obtained the correspondence through an open records request to the Florida Department of Health, which played a central role in the 2009 discussions of duodenoscopes' risks.

"The FDA missed numerous red flags," says Rep. Ted Lieu, D-Calif, who has requested congressional hearings on the matter. "They knew for years that these scopes were difficult to clean, and when they realized that they should have begun issuing safety alerts and had the manufacturers look at (developing) new designs.

"This isn't one or two people dying," Lieu adds. "This is multiple people dying across America and hundreds, potentially thousands being exposed to superbugs."

A new 'superbug' in Florida

CRE was a newly emerging superbug when Sanderson investigated the outbreak at two central Florida hospitals in late 2008.

Sanderson traced the infections to patients who had undergone a procedure called ERCP, in which a duodenoscope is run down a person's throat to treat upper-intestinal blockages, such as gallstones or tumors. On Feb. 15, 2009, he relayed his initial findings in an email to Srinivasan at the CDC.

"Interesting outbreak," he wrote, "and kind of scary."

Sanderson found that technicians cleaning duodenoscopes at both hospitals did not follow protocols for cleaning the devices' "elevator" mechanism, which controls tiny tools that can remove blockages or insert stents in intestinal ducts. The elevator has a channel that must be purged of biological debris — a multi-step process in which the elevator is set at precise angles and scrubbed out with tiny, specialized brushes.

In a follow-up email to Srinivasan, Sanderson reported that investigators had brushed the channel of a duodenoscope at one hospital and pushed out a clump of accumulated tissue that was rife with bacteria, including CRE. Scores of patients had been treated with the scope and were at risk of infection, he wrote, calling it "a serious problem that demands attention now." (The state has not released the hospitals' names.)

Srinivasan told Sanderson the FDA would be very interested in the investigation, and he included Sanderson in the email he sent to FDA officials a few weeks later to suggest that hospitals be alerted about the scopes' contamination problems.

"Roger and I are worried," Srinivasan wrote in the message. "These scopes are used infrequently in many places and hence staff might be less aware of how to clean them, there is a real chance that these issues might be more widespread."

A hard-to-clean scope

Infection control experts have fretted for years about the cleaning hurdles posed by duodenoscopes, which have been linked to infection risks for decades.

In 2008 — around the time of the CRE outbreak in Florida — the CDC issued a broad guidance document on hospital disinfection that specifically noted the challenges of cleaning duodenoscopes properly.

"No other instrument is as complex, no other instrument (gets) as heavily contaminated with microorganisms — we've known this for 40 years," says William Rutala, an infection control expert at the University of North Carolina Hospitals and co-author of the 2008 CDC guidance. And when it comes to cleaning and disinfection, "no other instrument has such a narrow margin of safety."

It was assumed then that the scopes' problems could be solved by complying strictly with cleaning and disinfection guidelines, Rutala says. But the instructions, with dozens of steps, are far too complex to execute reliably in hospital environments, he adds, and research since then shows 10%-30% of duodenoscopes remain contaminated after reprocessing.

Last week, based on presentations by Rutala and other experts, an FDA advisory panel reached a broad consensus that duodenoscopes, as now designed, cannot be cleaned reliably under existing guidelines.

"These devices are not safe under current conditions," said panelist Irving Nachamkin, a microbiologist and director of laboratory medicine at the Hospital of the University of Pennsylvania in Philadelphia.

Despite such concerns, panelists endorsed the FDA's decision to encourage continued use of duodenoscopes. There was broad agreement that infection risks are low and the device remains the safest, least invasive way to perform important, potentially life-saving procedures.

Many participants urged the agency to press manufacturers for easier-to-clean scope designs. Several also recommended that hospitals be directed to sterilize the devices — a higher standard than the current disinfection requirement — and test them for residual bacteria before reuse.

The lingering issue, though, is whether the conversation about duodenoscope safety should have begun far earlier, as suggested in the wake of the Florida outbreak.

"People certainly were talking about the problem around that time, trying to understand the etiology of the contamination," Rutala says. "Should the FDA and the CDC have moved more quickly? That's a fair question."

The case for an alert

FDA officials were eager for more information after receiving the email from the CDC's Srinivasan about the CRE outbreak in Florida. The message was circulated to more than a dozen top FDA officials, including two who headed a general working group on medical scope safety.

On June 29, 2009, FDA and CDC officials held an inter-agency conference call to discuss the duodenoscope problem, including a "thorough" briefing from Sanderson and another Florida epidemiologist who helped in the CRE investigation. But the detailed warning that Sanderson hoped to see ended up as just that two-sentence mention in the general advisory on medical scope safety that came out the following November.

The FDA says it did not have enough evidence at that point to warrant a specific alert on duodenoscopes.

"The Florida outbreak, as with prior cases, was due to inadequate cleaning," the FDA said in a statement to USA TODAY. Since the agency attributed the problem to user error and not an inherent device flaw, it decided that a specific, stand-alone advisory to practitioners was not warranted.

Srinivasan says he supported the FDA's decision, in part because he worried that a dedicated alert on duodenoscopes might cause hospitals to pay less attention to thorough cleaning of other types of scopes. "We didn't want people to think that only ERCP scopes have challenges with reprocessing," he says.

The FDA says the need for a specific warning on duodenoscopes didn't begin to surface until September 2013, when the CDC tied the scopes to a CRE outbreak at Advocate Lutheran Hospital outside Chicago. That case was a "pivot point," FDA officials say, because the scopes caused infections despite being cleaned and disinfected properly.

"Upon learning of the 2013 Illinois outbreak, the FDA initiated a comprehensive review of the best available information" on duodenoscope infections, the agency said in its statement. "FDA (also) conducted an engineering assessment … leading us to believe that the design of these duodenoscopes creates significant challenges for reprocessing."

The FDA's review took almost a year and half. The resulting alert, in February, came soon after USA TODAY published a detailed investigation revealing the scopes' infection problems.

"The complex design of (duodenoscopes) may impede effective reprocessing," the multi-page advisory said, noting that the scopes can transmit superbugs even when cleaned properly. "Meticulously cleaning duodenoscopes … should reduce the risk of transmitting infection, but may not entirely eliminate it."

The FDA acknowledges that it lacks a defined policy on when to issue warnings as problems with medical devices come to light. Last week, officials asked the agency's advisory panel for guidance on what to do "when we have a medical device concern but do not yet have enough information to determine the most appropriate action."

The evidence of duodenoscopes' contamination problems grew slowly in the years immediately following the Florida CRE outbreak. Reports of duodenoscope-related outbreaks of antibiotic-resistant infections in Europe began cropping up in medical journals in 2010. And over the next few years, the FDA started seeing more and more signs of similar problems in the United States.

In data released last week, the FDA revealed that the number of reports it received on duodenoscope-related infections climbed from fewer than 10 in 2012 to nearly 70 in 2014 (each report can reflect multiple patients). In the first six weeks of 2015, more than 40 additional reports came in.

Even after the 2013 CRE outbreak in Chicago made it clear that the scopes' problems weren't just a matter of user error, the first public warning about the devices' contamination and infection risks came from the CDC, not the FDA. The CDC report, issued as an informational bulletin to health care providers, came out in January 2014. The FDA, which has regulatory responsibility for protecting the public from unsafe medical devices, would wait another 13 months before issuing its own alert.

The FDA "could have issued a statement at the very beginning of this (in 2009) at least saying that these scopes are really hard to clean," says Lieu, the California congressman. "They say, 'Well, we didn't know until the Fall of 2013 that these scopes could cause outbreaks even if cleaned 100% correctly.' But even under their own timeline, there was still no reason why they waited until 2015 to act."

Follow Investigative Reporter Peter Eisler on Twitter: @byPeterEisler