Reprocessing Flexible Endoscopes

Flexible endoscopes have many advantages and are very helpful devices in modern medicine to diagnose and treat many diseases. They could, however, also put patient safety at risk when reprocessing fails or is performed inadequately.


Since the first reported use of an early flexible endoscope in 1805, these instruments have continued to develop, especially since the 1960s when fibre optics were introduced. These procedures are not only minimally invasive and therefore less painful for the patient, but also result in, if compared to classic surgical procedures, less complications such as surgical site infections. They also enable rapid screenings, diagnosis and even direct treatment. With more than 18 million gastrointestinal endoscopic procedures and at least a half million bronchoscopies every year in the United States alone, these devices greatly benefit lifesaving diagnosis and treatment.

With the increasing use of these reusable medical devices, however, there are also adverse effects. During an endoscopy, endoscopes can be contaminated with tissues and microorganisms from patients. When reprocessed improperly, this can lead to false diagnosis or infections in subsequent patients. Despite all the guidelines on reprocessing flexible endoscopes, many publications and reports have described the transmission of microorganisms, infections and even outbreaks related to failures in cleaning and disinfection of flexible endoscopes.

Guidelines are continuously revised and translated in local work procedures and quality protocols. Many control mechanisms, audits and quality checks are performed on the process of cleaning and disinfection of flexible endoscopes.

The fact that endoscope related infections still occur in spite of these quality improvements, however, triggers us to have a look at the process of reprocessing flexible episodes again and the need for new improvements.

Endoscopy related infections

Infections related to flexible endoscopic procedures and the related use of flexible endoscopes can be caused by either the patient’s own microorganisms or by microorganisms introduced into the patient via the flexible endoscope or its accessories. Many publications and reports on contamination, infections, and outbreaks due to improper reprocessed flexible endoscopes were published over the last decades. It’s bizarre that with no other reusable medical devices are these kinds of problems described. This implies that despite all the measures taken to clean and disinfect flexible endoscopes as detailed in international and nationwide guidelines, that there are well-known risks when using reprocessed flexible endoscopes.

The incidence of infections caused by transmission of microorganisms between patients or from the environment is estimated at approximately one infection per 1.8 million procedures. This indicates a negligible risk, which presumes that the use of flexible endoscopes – and therefore also their reprocessing – is highly safe. In fact, infection risks range from less than 1% in simple upper up to 11% for endoscopic retrograde cholangio pancreatography (ERCP).

Due to manipulation of the bile and pancreatic ducts during diagnostic and therapeutic procedures, ERCP is reported with the highest risk of infectious complications. There is a difference between diagnostic and therapeutic ERCP. Diagnostic ERCP is a safe procedure with a 1% rate of complications such as inflammation of the pancreas. Although therapeutic ERCP can also be regarded as a relatively safe procedure, about 3% of the patients may experience complications, including infections, bleeding and pancreatitis. Palabiyikoglu et alconcluded that at least 1.8% of all patients undergoing ERCP had an ERCP related sepsis, with a mortality rate of approximately 26%.

It’s assumed that, besides reported publications on outbreaks, infection rates related to flexible endoscopes are underestimated because infections after endoscopy may be under-recognised: they are easily masked by the primary signs and symptoms, and a good registration of infectious complications after endoscopy is often missing.

The design of modern flexible endoscopes, with their long narrow lumens, cross connections, springs, valves, occluded dead ends and the presence of rough or pitted surfaces could be mitigating factors in cleaning and disinfection.

Reprocessing flexible endoscopes

In today’s practice flexible endoscopes are regarded as semi critical instruments, as they contact mucous membranes and non-intact skin. The infection risks are also regarded as semi-critical. To conform to the Spaulding schedule these instruments require disinfection or a high-level disinfection.

The whole process of cleaning and disinfection is described in many nationwide and local guidelines and consists of the following steps: a pre-cleaning followed by a manual cleaning, finally automated cleaning and disinfection in an automated endoscope reprocessor using a chemical or thermal-chemical disinfection phase, followed by a thorough drying.

It’s remarkable that despite thorough reprocessing guidelines some flexible endoscopes aren’t clean at the end of reprocessing. Are there other factors at play than simply issues related to design that could have an adverse event on the outcome of reprocessing?

Important steps in reprocessing flexible endoscopes are yet to be automated, meaning the whole process is very time consuming and labour intensive, especially with today’s pressure on endoscope programmes, the number of flexible endoscopes, the capacity of endoscope reprocessors and the personnel available for reprocessing flexible endoscopes.

While time consuming, meticulous manual cleaning – with extensive brushing of all channels and components – prior to automated cleaning and disinfection is an essential step in reprocessing flexible endoscopes, eliminating more than 90% of debris, biofilms and microorganisms.

Routine sampling could be a worthwhile additional step that gives us information on not only the final reprocessing results, but could also provide an early detection of possible damages and niches in endoscope channels.

According to the earlier mentioned aspects as time and costs, we are also now studying the use of the ATP-method as a quick scan of cleanliness of endoscopes after reprocessing. Additional microbiologic controls can have an added value in the detection of early damages or niches in endoscopes.

Sheaths and sterilisation

Today there are some interesting alternatives that can be used to acquire really clean flexible endoscopes for using them more safely in tissues and organs, like sheaths or additional methods of cleaning and disinfection.

For some types of endoscopes like bronchoscopes or cystoscopies, sterile, disposable single-use sheaths are available, even with an integrated biopsy channel. These sheaths can have advantages if ‘sterile’ structures are passed or part of the diagnosis or treatment. Using these, the endoscope and its internal channels are kept clean. The use of sheaths can also have an advantage if there is a limited availability of flexible endoscopes. Sheath use provides a fast turnaround time, with a simple wipe down disinfection in-between patient use. To the author’s knowledge, as yet there are no cases of transmission of infections reported by using endoscopes with sheaths, but this may also be caused by underreporting and identifying infections related to endoscopy.

There might be some discussion about image quality when using sheaths. The costs of sheaths could be another point of discussion, but should be compared with other costs in the whole process of endoscope use and reprocessing including staff, time, logistics, and number of endoscopes.

In the Netherlands, Hilgers concluded in 2005 that, based on the results of bacteriological culturing and leakage tests that the use of a sterile sheath, in combination with applied operational protocols, can sufficiently guarantee safe and clean use of flexible endoscopes without an instrument channel.

In 2009, Alvarado concluded that the use of high quality, single-use, disposable sterile sheaths on nasopharyngoscopes with an in between enzymatic cleaning and disinfection with 70% ethanol can provide a reliably decontaminated instrument. Despite all this positive data, sheaths still are not regarded as a replacement for high-level disinfection. It is important to remember that even when using sheaths, guidelines must be strictly followed.

In our hospital we recently used sheaths on some flexible endoscopes used for intubation in the operating room. It was necessary to obtain some new endoscopes, suitable for the use of sheaths. Sheaths are only used with strict protocols, with a wipe off between disinfection and daily mechanical cleaning and disinfection. As yet the process has not been evaluated.

We stopped the use of sheaths, however, for flexible ear nose and throat (ENT) endoscopes without internal channels. Here ENT scopes were used with a new sheath for each patient and an in between wipe-down disinfection with isopropyl alcohol 70%. At the end of each day, these endoscopes were additionally reprocessed by using automated cleaning and disinfection on the reprocessing unit of the endoscopy department, using the same process as all other flexible endoscopes.

We noticed that the use of sheaths was expensive – approximately 70,000 Euros per year – and had additional costs for the daily cleaning and disinfection on the endoscopy department of around 20,000 Euros per year, as well as costs to repair ENT scopes. We also noticed that disinfection with alcohol 70% (as defined in working guidelines) between changing sheaths wasn’t always performed correctly. This also frequently resulted in sheaths getting stuck on the distal end of the endoscope, resulting in damaging these when removing sheaths.

In 2012 our ENT department built a new reprocessor for ENT scopes and other reusable ENT devices, which resulted in a new vision of using sheaths and reprocessing these ENT endoscopes. A new, special reprocessor for ENT endoscopes was installed. It was also necessary to increase the amount of flexible ENT scopes. Well-educated and experienced staff for reprocessing these endoscopes and other ENT devices were employed. The whole process on reprocessing these flexible ENT endoscopes was validated and controlled by microbiological sampling and ATP controls before and after reprocessing.

We concluded that this process was effective and safe. Nowadays after every patient use, each flexible ENT endoscope is manually cleaned and leak tested, and mechanically cleaned and disinfected. Flexible endoscopes are then packed and sealed as ‘ready for use’ and stored for usage. Although investigations into endoscopes, equipment and staff were carried out, this process is even more cost effective than the older method with sheaths. Of more importance, this process for ENT endoscopes is more guaranteed and is a qualitative and safe improvement for patients undergoing ENT endoscopy.

Especially therapeutic ERCP can be indicated as a surgical procedure, potentially shifting duodenoscopes used for this from semi critical to critical devices. This reinforces the need for an alternative in achieving cleaner, and therefore safer, flexible endoscopes. This could be achieved by an additional sterilisation of these, for example using a low temperature sterilisation with hydrogen peroxide plasma.

At a congress of the Dutch Steering Group for Flexible Endoscope Cleaning and Disinfection (SFERD), we presented data from two university hospitals in the Netherlands on possible episodes of sepsis related to ERCP with duodenoscopes. We concluded that 0.4-0.9% of all patients (n=492) who had had an ERCP could be marked as an post-ERCP sepsis.

Although these results were based on a retrospective quick search and we couldn’t relate the outcome to the contaminated duodenoscopes, based on literature we concluded that more efforts should be made to achieve clean duodenoscopes and thus a safe use of these devices, such as using low temperatures when sterilising.

Following our hospital protocol that spanned a 30 month period, 12 times duodenoscopes were indicated for low temperature hydrogen peroxide plasma sterilisation because they cultured positive with the same bacteria after two rounds of reprocessing (first initial sample after patient use followed by manual cleaning and automated reprocessing. Second sample after again automated reprocessing).

Samples were taken by a manual flushing of the biopsy/suction channel and air/water channel with sterile demineralised water from the distal (tip) to the proximal end of the endoscope (retrograde sampling). Bacteria varied from Candida parapsilosis to Enterobacter cloacae, Escherichia coli, Klebsiella pneumonia, Klebsiella oxytoca, Stenatrophomonas maltophilia or Pseudomonas aeruginosa. After noticing this, the endoscopes were blocked for patient use, again reprocessed and sampled. In 12 of these samples, the duodenoscopes were again positive with the same microorganism. According to our protocol these endoscopes were cleaned and disinfected again with additional decontamination (sterilised) using low temperature hydrogen peroxide plasma sterilisation.

After this process, again samples were taken. Comparing with the initial positive samples and outcome, all cultures after low temperature sterilisation with hydrogen peroxide were negative when sampled directly after this process.

Based on these experiences I appealed at the same Dutch congress of the SFERD not only for a continuously active surveillance of post-endoscopic infections after ERCP, but also for a standard procedure for low temperature sterilisation with hydrogen peroxide plasma of duodenoscopes after each use.

The success of this kind of sterilisation for flexible endoscopes was published in 2001 by Bäret al. In addition, last October Rutala wrote a very interesting editorial on this, titled ‘A need to shift from disinfection to sterilization?’ Of course, all alternatives to improve endoscope reprocessing and thus make safer the use of flexible endoscopes have both advantages and disadvantages. These are discussed in a lot of publications and important papers, always concluding that further investigations and studies should be performed.

On going investigation and debate is good, but in my opinion it’s also a factor for not taken decisions, knowing that ERCP related sepsis is a major complication with not only high mortality rates, but also leads to increased costs. The episode in February 2015 with contaminated duodenoscopes in the USA showed the urgency for real action to investigate in a reprocessing process and handling of flexible endoscopes that is much safer than today’s cleaning and disinfection. Of 179 patients exposed to carbapenem-resistant Enterobacteriaceae, seven became infected and two died.

The new Dutch guideline on reprocessing flexible endoscopes indicates that flexible endoscopes should be used that can be disinfected or sterilised following the most equivalent alternative for thermal disinfection when there is an infection risk that can be regarded as semi critical, or sterilisation when this infection risk is critical. They also state, however, that mechanical cleaning and disinfection of flexible endoscopes can be used as routine procedure when sterilisation, even with hydrogen peroxide plasma or Ethylene oxide (ETO), has too many logistic challenges – even if these endoscopes are to be used in an area regarded as critical.

Due to increased productivity and the legitimate argument for use regarding a limited amount of flexible endoscopes and other factors that could contribute to increasing costs, it will be a hard and thorough way to achieve a shift in patient safety, from semi safety to real safety.

Flexible endoscopes, especially duodenoscopes, are difficult to clean. Despite the availability of evidence-based and well-accepted guidelines for reprocessing, contaminated endoscopes can still result in clustered infections and outbreaks, even with multi-drug resistant microorganisms.

Although stringent conformity to all steps in these guidelines, especially those time consuming steps like manual cleaning and brushing, could be more effective in achieving cleaner endoscopes, today’s cleaning and disinfection should be completed by alternatives such as sterilisation.

This should at least be implemented for so called high-risk flexible endoscopes like duodenoscopes, especially when used for therapeutic ERCP as this can be regarded as a surgical procedure. Other flexible endoscopes can be regard as ‘critical’ instead of ‘semi critical’, not only because they really are contacting sterile tissues or organs, but also because more and more sterile devices like stents are implanted in situ permanently. When looking at patient safety in relation to the use of flexible endoscopes, therefore, there should be a shift from defining flexible endoscopes as semi-critical to critical devices, with a corresponding shift in the reprocessing processes.

Sterile disposable, single-use sheaths could be a good alternative in this, but may not be available for all endoscopes like duodenoscopes. Since alternatives for steam sterilisation are available to sterilise flexible endoscopes, like low-temperature hydrogen peroxide plasma sterilisation, this process could also be used to obtain safer flexible endoscopes than with today’s cleaning and disinfection. These additional steps could be very worthwhile, especially for endoscopes that are used in primary sterile tissues and organs, but the importance of the first steps in the cycle of reprocessing shouldn’t be neglected.

Sure it’s time consuming, but meticulous manual cleaning and brushing is the first and most essential step in reprocessing flexible endoscopes. It can’t be skipped or speeded up without adversely affecting the outcome of the whole process. There must be a continuous awareness on this first step, even on staff education and a strict adherence to existing reprocessing guidelines. These factors cannot be underestimated anymore and need serious time, staff and money.

Since there are good alternatives like sterile sheaths and low-temperature sterilisation with hydrogen peroxide plasma, there are no excuses not to obtain really safe flexible endoscopes. Time consuming and money driven factors should no longer inhibit patients from safe devices and safe care.