Nearly 100 patients treated with specialized medical scopes at 39 VA centers between 2010 and 2015 tested positive for multidrug-resistant infections, and officials said they couldn’t rule out the possibility that the devices may have been a factor in some cases.

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Potentially deadly “superbug” infections like those spread by contaminated medical scopes at civilian hospitals in Seattle and elsewhere may have occurred at U.S. Veterans Affairs medical centers as well — though the risk is very low — a federal investigation has found.

Nearly 100 patients treated with specialized medical scopes at nearly 40 VA centers between 2010 and 2015 tested positive for multidrug-resistant infections known as CRE, and officials said they couldn’t rule out the possibility that the devices may have been a factor in at least a dozen cases.

However, officials with the Veterans Health Administration Office of Public Health reported that an analysis of more than 40,000 patient records found no widespread evidence of the problem, and concluded that “any transmission appears highly unlikely.”

The investigation results, released in response to a public-records request by The Seattle Times, are the VA’s first acknowledgment that infections tied to hard-to-clean duodenoscopes — similar to those detected at Seattle’s Virginia Mason Medical Center — may have occurred within the veterans’ medical system.

Previously, VA officials in Washington, D.C., said they didn’t know whether any infections from carbapenem-resistant Enterobacteriaceae, or CRE, tied to the scopes had occurred at federal centers. Local officials said none had been reported.

“There have been no CRE infections at any VA facility, according to the National Office of Sterile Processing,” Chad Hutson, a spokesman for the VA Puget Sound Health Care System, said in a March 4 email, noting he was referring to local sites.

A patient-safety advocate and prominent critic of the scopes called the VA report “a bombshell” in light of the agency’s previous position.

“The VA’s statement raises questions about what the VA knew and when they knew it,” said Lawrence F. Muscarella, a Philadelphia expert on contaminated duodenoscopes.

The VA launched the investigation after reports of scope-associated infections in Seattle and Los Angeles, said Dr. Mark Holodniy, who authored the report.

“We went ahead and did this proactively,” he said.

The new analysis of nearly 56,000 procedures in more than 40,000 veterans between January 2010 and February 2015 detected nearly 5,000 CRE isolates in 2,300 patients.

During that time, 97 patients who were treated with the specialized medical scopes at 39 VA centers were infected with at least one CRE isolate, the report found. Twenty patients had the infections before the procedures.

The patients received either ERCP, endoscopic retrograde cholangiopancreatography, or EUS, endoscopic ultrasonography, procedures that diagnose and treat problems of the pancreas, bile ducts and liver. Nearly 700,000 ERCP procedures are performed in the U.S. each year.

“It was unclear whether their CRE infection was due to their duodenoscopy procedure,” the report said.

At 17 VA medical centers, a single patient who underwent the procedures tested positive for CRE, which officials said likely indicated little chance it was spread by a tainted scope.

“We cannot definitively rule out the possibility that these patients developed their infection as a result of their procedure, however, as there were no additional patients found at these sites, there was not a clear linkage to a duodenoscopy procedure,” the report said.

But at 22 other VA centers, multiple patients who received ERCP/EUS developed CRE infections. At eight centers, 42 patient pairs were reported to have had procedures within six months of each other at the same site, and both tested positive for the same germ.

After review, 36 pairs were ruled out because the device serial numbers and models didn’t match, the cases were miscoded or patients didn’t actually receive treatment in the same location. That left a half-dozen in which infections could have been linked to contaminated scopes.

“There were six pairs that we could not completely rule out the possibility of transmission,” the report found.

For three of those, the scope models and serial numbers were not available, and officials were unable to determine whether the patients had been exposed to the same duodenoscope. In the other three pairs, the same scope was used.

However, the scopes were also used on other patients in the interim, without incident, the report found. “Thus, transmission of CRE within these pairs appears highly unlikely,” officials concluded.

There were several limitations to the report, including uncertainty over whether all VA centers were correctly identifying CRE, inability to use molecular fingerprinting to determine whether patients were infected with the same strain of bacteria, and lack of consistency in identifying the make and model of the scopes. The review was limited to patients with CRE detected at VA sites; patients with infections diagnosed elsewhere might not have been identified.

Lisa McGiffert, director of the Safe Patient Project for Consumers Union, said those significant caveats make it difficult to tell whether the infections were actually tied to the scopes.

“I suspect the VA is among the more sophisticated in surveillance and that seems a bit shocking considering the lack of documentation for these infections,” she said in an email.

But Holodniy said the VA “investigated this to the fullest extent possible,” given the data the agency had. He said he was pleased to find no evidence of CRE spread.

“I was quite relieved and, frankly, very proud of the system,” he said. “We pay attention to the details so that we don’t have this kind of a problem. That speaks volumes to the processes that have been put in place in sterile processing.”

The VA launched the investigation at 150 medical centers and associated sites after reports of outbreaks of multidrug-resistant infections at hospitals in Seattle, Los Angeles and elsewhere tied to the scopes. Health officials determined that the devices could not be cleaned even after medical staff followed manufacturers’ directions.

VA officials did not disclose the locations of the 39 medical centers with CRE-infected patients. But Hutson, spokesman for the Puget Sound center, said no infections tied to ERCP have been reported at that site.

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The federal Food and Drug Administration and the Centers for Disease Control and Prevention have issued guidelines aimed at helping hospitals prevent the spread of infections by contaminated scopes. Last week, the FDA issued additional guidelines, while also acknowledging that it might be impossible to clean the scopes as they’re designed.

Several patients locally and nationwide, and Virginia Mason officials, are suing one of the leading manufacturers of the scopes, Olympus America.

Dr. Andrew Ross, head of gastroenterology at Virginia Mason, has said his hospital had to implement a $1 million “test-and-hold” program to stop the local outbreak linked to 39 infections, including 18 deaths, between 2012 and 2014.

FDA officials and now VA officials have said that the risk of contracting deadly infections is low. FDA officials say that the benefits of using the duodenoscopes outweigh those risks, and that they’re lifesaving procedures in people who need them. Holodniy agreed.

“I would say to that patient in front of me, if they needed that procedure, they should go ahead and have that procedure in the VA,” he said.