Flexible Endoscope Reprocessing: Why It’s One of the Most Challenging Jobs in Healthcare
There is no piece of medical equipment in a healthcare facility that is harder to clean than a flexible endoscope. Not because staff aren’t trained. Not because facilities aren’t trying.
Because the device itself, with its narrow internal channels, articulating components, and heat-sensitive materials, was designed to reach places inside the human body that nothing else can reach, and that same design makes it extraordinarily difficult to make safe for the next patient.
The duodenoscope in particular has been at the center of some of the most serious healthcare-associated infection outbreaks in recent history, and the lesson those outbreaks keep delivering is the same one: flexible endoscope reprocessing demands a level of technical knowledge and precision that general instrument processing experience simply doesn’t prepare you for.
What Makes Flexible Endoscopes So Hard to Reprocess
Most surgical instruments are straightforward to reprocess. Stainless steel construction means you can disassemble them, clean them, and run them through a steam autoclave at high temperature. Flexible endoscopes work nothing like that.
Heat sensitivity rules out steam sterilization entirely. The long, narrow internal channels, elevator mechanisms, and articulating components create dozens of hard-to-reach surfaces where organic matter and biofilm collect. And staff use them repeatedly throughout the day on different patients, often with minimal turnaround time.
The duodenoscope, used for ERCP procedures, is the most complex to reprocess. Its elevator mechanism, a small movable component at the distal tip, is notoriously difficult to clean.
The FDA has documented that high-concern organisms, including carbapenem-resistant Enterobacteriaceae (CRE), turn up on duodenoscopes even after staff followed the reprocessing protocol exactly.[1] The problem isn’t always human error. Sometimes device design simply hasn’t kept pace with the demands of safe reprocessing.
The Reprocessing Sequence and Where Things Go Wrong
Flexible endoscope reprocessing follows a specific sequence: pre-cleaning at the point of use, transport, leak testing, manual cleaning, visual inspection, high-level disinfection (HLD), rinsing, drying, and storage. Each step is critical. Skipping or shortcutting any one of them compounds the risk at every step that follows.[6][7]
Pre-cleaning is where the process most often breaks down first. Bioburden that dries inside the channels of a scope becomes exponentially harder to remove during manual cleaning. If staff don’t flush and wipe the scope immediately after patient use, before soil has time to dry, the manual cleaning step faces a losing battle before it starts.[2]
Manual cleaning itself is demanding work. Technicians must brush every channel of the scope, paying particular attention to areas like the elevator mechanism on duodenoscopes, where the geometry of the device makes it nearly impossible to fully clear debris with standard brushes.
In 2013, a CRE outbreak at a Chicago hospital sickened 38 patients following endoscopic procedures, with 10 developing clinical infections, traced to a duodenoscope that staff had reprocessed following the manufacturer’s instructions.[3] Surveillance data has put contamination rates on reprocessed duodenoscopes as high as 15% even after compliant reprocessing.[1]
High-level disinfection kills most pathogens but doesn’t achieve sterilization. It works when the prior cleaning steps have been done correctly. When they haven’t, residual organic matter shields microorganisms from the disinfectant, and HLD fails regardless of contact time or concentration.[2]
Drying is one of the most underestimated steps. Moisture left inside scope channels after reprocessing creates conditions for bacterial growth during storage. A scope that clears HLD but doesn’t dry thoroughly before hanging can become contaminated between patient uses, not during the procedure itself.[4]
The Human Factors Problem
One analysis described GI technicians in larger hospitals as reprocessing up to 30 flexible endoscopes per shift, often in reprocessing areas smaller than a child’s bedroom.[5] The work is physically demanding, detail-intensive, and time-pressured. The margin for error is essentially zero.
This is a human factors problem as much as a technical one. When staff work in poorly designed spaces without adequate training, the steps they rush or skip are the ones with the least visible immediate consequence. Pre-cleaning. Drying. Thorough brushing of hard-to-reach components. These are exactly the steps that determine whether a scope is safe for the next patient.
What Proper Training Changes
Technicians who understand the why behind every step in the reprocessing sequence make better decisions when conditions aren’t ideal. They know why drying matters.
Understanding which components of a duodenoscope require extra brushing, and why, comes with that same foundation. What to look for during visual inspection that signals a scope may not be adequately clean — that knowledge doesn’t come from following a checklist. It comes from training.
That level of understanding comes from structured training grounded in current standards, including AAMI ST91, which governs flexible and semi-rigid endoscope reprocessing and has seen significant updates in recent years to reflect what outbreak investigations have taught the industry.
SPU, LLC’s endoscope reprocessing course covers every stage of the reprocessing cycle, from pre-cleaning through storage, built on current AAMI guidance and designed for the technicians who do this work every day. The course draws from The Basics of Flexible Endoscope Reprocessing Textbook, 3rd edition, also available in the SPU, LLC store for those who want a deeper reference alongside the course material.
The Bottom Line
Flexible endoscope reprocessing isn’t complicated because people aren’t paying attention. The devices themselves present genuine technical challenges that even compliant reprocessing protocols don’t fully solve in all cases.
The field has learned hard lessons through patient harm and high-profile outbreaks, and those lessons now sit inside current AAMI standards and manufacturer guidance for good reason. Technicians trained specifically on scope reprocessing, not just general instrument processing principles, are the ones best positioned to protect patients in one of healthcare’s most demanding reprocessing environments.
References
- Centers for Disease Control and Prevention. Duodenoscope Surveillance Sampling and Culturing. CDC, 2018. Available at: https://stacks.cdc.gov/view/cdc/104184
- Kovaleva J, et al. Transmission of infection by flexible gastrointestinal endoscopy and bronchoscopy. Clinical Microbiology Reviews. 2013;26(2):231-254. Available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC3623380/
- Epstein L, et al. NDM-Producing CRE Associated with Exposure to Duodenoscopes. JAMA. 2014;312(14):1447-1455. Available at: https://journals.asm.org/doi/10.1128/jcm.01394-15
- Rutala WA, Weber DJ. Gastrointestinal Flexible Endoscopes: Infection Control Risks. GI Endoscopy Clinics of North America. 2020. Available at: https://stacks.cdc.gov/view/cdc/104184
- Ambu USA. Infection Control in Endoscopy: Endoscope Reprocessing and Human Factors. Available at: https://www.ambuusa.com/infection-control/human-factors
- AAMI ST91:2021. Flexible and Semi-Rigid Endoscope Processing in Health Care Facilities. Available at: https://www.aami.org
- CDC. Guidelines for Disinfection and Sterilization in Healthcare Facilities, 2008. Available at: https://www.cdc.gov/infectioncontrol/guidelines/disinfection/healthcare-equipment.html