Seattle’s Swedish Medical Center and 20 other hospitals tested dozens of specialized medical scopes every day for a month — and found bacteria remained even after rigorous cleaning.

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Medical scopes used at 21 Providence Health & Services hospitals in Washington and four other states remained contaminated with bacteria even after cleaning — the same problem that has led to possibly deadly infections in Seattle and across the U.S.

No infections were detected and no patients were harmed during the four-month trial last year, hospital officials said. But the systemwide survey confirmed their worst suspicions, according to Dr. Jack Brandabur, a gastroenterologist at Swedish Medical Center, part of the Providence system.

“We were expecting to find the same thing that others had reported, that despite adherence to strict guidelines, despite all that, bacteria can at times remain on these scopes,” said Brandabur, who led the study published recently in the journal Gastrointestinal Endoscopy.

Staff at 21 Providence hospitals tested 106 duodenoscopes and linear echoendoscopes for 30 days each by cleaning them according to manufacturers’ directions, then culturing them to see if they grew bacteria.

Microbial contamination was detected in 5 percent of more than 4,000 individual specimens collected after cleaning. Of those, 0.6 percent were bacteria that can pose a risk to human health.

The study is one of “very few systematic evaluations” of germs that linger on cleaned scopes, said Dr. Alex Kallen, a medical epidemiologist and outbreak response coordinator with the Centers for Disease Control and Prevention (CDC). No national estimates exist.

“The issue of persistent contamination remains an important one,” Kallen said in an email.

Although the Providence contamination numbers appear low, they’re confounding to the crew that oversees the extensive, multistep cleaning process aimed at the scopes used to diagnose and treat problems of the gastrointestinal tract.

“For us, we feel we’ve taken every precaution and then some,” said Shannan Hove, the registered nurse in charge of the Swedish endoscopy unit. “Nobody knew there was a problem until the problem was there.”

In the past two years, however, it’s become clear there is a problem with duodenoscopes, medical devices used to confirm and treat problems with digestive ducts. These scopes are specialized tools with particularly difficult-to-clean components, not the simpler devices used for common colonoscopies.

In Seattle, an outbreak of multi-drug-resistant bacteria at Virginia Mason Medical Center led to 39 infectionstied to the scopes between 2012 and 2014. Eighteen of those patients died, although what role, if any, that the infections played in their deaths isn’t clear.

A January report commissioned by U.S. Sen. Patty Murray, D-Wash., found that at least 250 people worldwidewere sickened in 25 incidents of antibiotic-resistant infections linked to the scopes between 2012 and 2015.

More recently, the federal Food and Drug Administration (FDA) reported that up to 350 patients at 41 medical facilities in the U.S. and around the world were infected by or exposed to contaminated scopes during a wider time span, between 2010 and 2015.

Duodenoscopes are used nearly 700,000 times a year in the U.S. for a procedure known as ERCP, or endoscopic retrograde cholangiopancreatography, which examines digestive ducts. Experts say those are necessary, even lifesaving procedures that avoid the risks of surgery.

Echoendoscopes, which have a similar design, are used in endoscopic ultrasound, procedures that obtain images and information about the digestive tract. They also can transmit infections, reports show.

Providence officials began their study after the Virginia Mason outbreak became public. Now they’re cooperating on another analysis with the FDA and CDC to determine whether double doses of high-level disinfection can eradicate all bacteria from the scopes. Results are expected in August.

In the first study, Providence staff between March and July 2015 took samples from sites on 106 scopes representing all three manufacturers, Olympus, Pentax and Fujinon. The hospitals operate in Washington and four other states: Alaska, California, Montana and Oregon. Two of the scopes tested grew intestinal bugs on several occasions and were sent back to the manufacturers for investigation and repair.

There was a wide variation in the number of positive specimens per hospital, from zero to more than 30 percent, but no striking difference in positive tests among the different models or manufacturers of the scopes, the type of cleanser or the automatic flushing system used, the study found.

However, the study did suggest that one brand of scope-washing machine, the Custom Ultrasonics Automated Endoscope Reprocessor, or AER, performed better than another brand, Medivator. Scopes cleaned in the Custom Ultrasonics machines showed no evidence of dangerous pathogens, while some scopes cleaned in the Medivator brand machines did.

That’s significant because the Senate report was critical of Custom Ultrasonics, saying that the firm’s products were used by nine of the 16 U.S. hospitals that had documented infections related to contaminated scopes.

FDA officials recalled the Custom Ultrasonics machines last November, citing safety concerns, but reversed the action in May, with the stipulation that they not be used to clean duodenoscopes.

Kallen, of the CDC, said the Providence study was not robust enough to determine a true difference in positive cultures in different brands of scope-washing machines. And FDA officials would not say whether the analysis influenced the decision to rescind the recall.

“Based on information from the company, the FDA has determined that the products may remain in the field for reprocessing other endoscopes during this validation,” an emailed statement said.

Lawrence Muscarella, who has tracked endoscope infections and is a former director of infection control at Custom Ultrasonics, called the FDA’s actions “odd, if unprecedented.”

“To date, the FDA has informally told the press it reversed the recall, but never told the public this by way of a formal safety notice, which can leave hospitals very confused,” he said.

He also questioned whether Providence officials truly know the extent of the device contamination. There are areas of the endoscope that cannot be accessed and brushed, so they wouldn’t have been available for testing, either.

“Therefore, the duodenoscope can be heavily contaminated, despite few or no bacteria being recovered during sampling,” he noted.

Patients undergoing ERCP or endoscopic ultrasound should talk with their doctors and carefully weigh the need for the procedures against the relatively low risk of infection from bacteria spread by scopes, according to the FDA and the CDC.

Muscarella suggests patients consider delaying treatment or seeking alternatives if the problem is not urgent. He also suggests that patients ask to be tested to confirm that they have no evidence of infection from or colonization with drug-resistant bacteria before any procedure.

“Any infections that you contract shortly after the procedure could therefore be due to the endoscopic procedure, which would be important for you to know,” he wrote.