Version October 2024
INTRODUCTION — Gastrointestinal endoscopy is a commonly performed diagnostic and/or therapeutic procedure, while endoscopy-related transmission of infection occurs very rarely. However, duodenoscopes have been implicated in transmission of multidrug-resistant organisms, resulting in evolving strategies for endoscope reprocessing and general infection control. This topic will review risk factors for infections transmitted by endoscopy and preventive measures, including a general overview of endoscope reprocessing. For specific reprocessing instructions, we rely on technical standards developed by national and local regulatory agencies, professional societies, and the manufacturers of endoscopes and reprocessing equipment [1-4].
Specific endoscopic procedures are discussed separately:
●(See "Overview of upper gastrointestinal endoscopy (esophagogastroduodenoscopy)".)
●(See "Overview of colonoscopy in adults".)
●(See "Overview of endoscopic retrograde cholangiopancreatography (ERCP) in adults".)
●(See "Therapeutic endoscopic ultrasound".)
ENDOSCOPY-RELATED INFECTIONS
Mode of transmission — Endoscopy-related transmission of infection may occur if microorganisms are spread from patient to patient by contaminated equipment. During an endoscopic procedure, the surface and internal channels of the endoscope are exposed to body fluids, and disinfection of these reusable instruments presents challenges [5]. For example, flexible endoscopes are heat-labile devices, and thus, steam sterilization cannot be performed routinely. In addition, ethylene oxide gas sterilization is not a feasible long-term strategy because of process duration, toxicity of chemical vapor, and cost [6,7]. Thus, endoscope reprocessing includes mechanical and detergent cleaning followed by high-level disinfection (HLD). Endoscopy-related infections occur rarely with adherence to these protocols [8]. Historically, outbreaks of infection transmitted by endoscopes occurred when reprocessing protocols were not followed. (See 'Overview of endoscope reprocessing' below.)
Risk factors
Duodenoscopes — Overall, the risk of infection from duodenoscopes (the endoscope used for endoscopic retrograde cholangiopancreatography [ERCP]) is very low (approximately 1 per 20,000 ERCPs performed) [8]. However, some endoscopy centers have reported transmission of multidrug-resistant organisms (MDROs) such as carbapenem-resistant Enterobacteriaceae (CRE; including Escherichia coli, Klebsiella pneumoniae) despite adherence to established reprocessing protocols [9-11]. The source of infection was traced to duodenoscopes, and it was theorized that the complex design of the elevator mechanism, the elevator cable, and the cable channel was a risk for persistent contamination, despite reprocessing [10,12]. The elevator mechanism is located at the distal tip of the duodenoscope, and it facilitates the insertion of a catheter into the biliary ducts to perform interventions such as stone removal [13]. (See 'Elevator channel endoscopes' below and "Carbapenem-resistant E. coli, K. pneumoniae, and other Enterobacterales (CRE)".)
Surveillance studies have shown that duodenoscopes may remain contaminated with microorganisms despite adherence to the manufacturer's instructions for reprocessing [14-17]. In a report of a surveillance study including 33 samples collected in sterile fashion from reprocessed duodenoscopes, one of 33 samples (3 percent) was positive for high-concern organisms often associated with disease (eg, E. coli, Pseudomonas aeruginosa).
Linear array echoendoscopes — Linear array echoendoscopes that are used for endoscopic ultrasound procedures contain an elevator mechanism; however, data regarding the risk of transmitting infection from echoendoscopes are limited [18,19]. Surveillance studies have reported that linear array echoendoscopes may remain contaminated following HLD; however, no cases of endoscope-related transmission of MDROs to patients have been reported [18]. (See 'Duodenoscopes' above.)
Other factors — Other potential factors for endoscopy-related infection include:
●Bioburden – Standard reprocessing and HLD of endoscopes provide a lower margin of safety. On average, the internal channel of post-procedure endoscopes may contain 8 to 10 log10 enteric organisms; reprocessing and HLD reduce the bioburden 8 to 12 log10. Thus, the margin of safety for this process is 0 to 2 log10 [12]. This low margin of safety is in contrast with 17 log10 margin of safety associated with sterilization of surgical instruments [20].
●Biofilm – Biofilms on endoscopes are difficult to remove with reprocessing methods, and they typically form on defects in the biopsy channels [21]. Unlike free-floating bacteria, a biofilm is a community of bacteria attached to one another and to a surface by a polysaccharide matrix. This matrix limits the diffusion of disinfectants used during cleaning protocols, thus preventing the elimination of bacteria in the biofilm.
Moisture buildup is critical for the development and persistence of biofilm. In one study using a borescope to photograph residual fluid despite reprocessing, most endoscopes retained some moisture when they were stored in the absence of continuous, forced dried air [22]. (See 'Storage and reuse' below.)
The pathogenesis of other infections involving production of biofilm is discussed separately. (See "Prosthetic joint infection: Epidemiology, microbiology, clinical manifestations, and diagnosis", section on 'Biofilm' and "Infection due to coagulase-negative staphylococci: Epidemiology, microbiology, and pathogenesis", section on 'Biofilm'.)
●Simethicone and other insoluble agents – Through-the-scope use of simethicone may result in residue and persistent contamination in the endoscopic channels despite utilizing HLD and adherence to reprocessing methods [23,24]. The practice of using intraprocedural simethicone or other insoluble agents has raised concerns about transmitting infection through contaminated endoscopes, although there have been no confirmed cases of infection related to simethicone use. Simethicone is a nonabsorbable oral agent that is commonly used to eliminate bubbles in the intestinal lumen because it reduces the surface tension of gas bubbles [25]. (See "Overview of intestinal gas and bloating", section on 'Management'.)
Infection response — In general, a suspected endoscopy-related infection should prompt process review and evaluation to identify areas for improved adherence [26]. Implicated endoscopes should be removed from use until closely inspected for damage. Outbreaks or clusters of infection related to endoscopy should be evaluated in collaboration with the local or state health departments. If a breach in reprocessing is discovered, exposed patients should be notified and, in some instances, observed for subsequent outcomes related to the exposure [5,27].
Principles of infection control and management of specific health care-associated infections including those with multidrug-resistant organisms are discussed separately:
●(See "Infection prevention: General principles".)
●(See "Carbapenem-resistant E. coli, K. pneumoniae, and other Enterobacterales (CRE)".)
●(See "Clinical features, diagnosis, and treatment of Klebsiella pneumoniae infection".)
OVERVIEW OF ENDOSCOPE REPROCESSING
Goals — Gastrointestinal endoscopes are semi-critical devices (ie, devices that contact the mucous membranes), and these devices require high-level disinfection (HLD) to destroy microorganisms and prevent transmission of endoscopy-related infection [28]. Endoscope reprocessing is a multistage process including manual initial cleaning, HLD, rinsing, drying, and storage.
Regulatory and manufacturer guidance — Protocols for endoscope reprocessing are informed by regulatory agencies, manufacturers, professional societies, and local health care institutions including:
●US Food and Drug Administration (FDA) [29]
●American Society for Gastrointestinal Endoscopy [4,5]
●European Society of Gastrointestinal Endoscopy [1]
●Society of Gastroenterology Nurses and Associates [30]
●World Gastroenterology Organization [2]
Initial cleaning — The initial step in endoscope reprocessing is cleaning prior to HLD [2,31] (see 'High-level disinfection' below):
Precleaning — Manual cleaning of the endoscope with detergent solution and brushes is performed promptly after procedure completion to prevent drying of debris on or within the endoscope [5]. The exterior of the insertion tube is wiped, and the endoscope's channels are flushed with detergent according to the manufacturer's instructions [2]. The air/water channel is purged to clear debris from the channel. This action prevents debris from drying on surfaces and removes microorganisms. After these steps have been completed, the endoscope is ready to be transferred to the processing area in an enclosed container.
Leak testing — Leak testing is performed according to the manufacturer's instructions to check the integrity of all channels [2]. The repair process is informed by the manufacturer's instructions if a leak is detected or the scope appears to be damaged.
Manual cleaning — Manual cleaning is performed prior to HLD [32]. The scope is immersed in detergent and all debris is washed from its exterior by wiping and brushing. A low-foaming medical grade detergent is used and is diluted according to the manufacturer's instructions. The scope remains immersed during the cleaning process. The suction and air/water valves, the biopsy channel cover, the distal end hood (if present), and all other removable parts are detached, while parts not intended for reuse are discarded. Brushing continues until there is no debris visible on the brush or the instrument. For elevator channel endoscopes (eg, duodenoscopes), it is important to ensure that the elevator mechanism located at the distal tip of the duodenoscope is thoroughly cleaned and free of all visible debris by examining both sides of the elevator. (See 'Elevator channel endoscopes' below.)
Single-use brushes are discarded after use. Reusable brushes are cleaned using high-level disinfectant and are inspected after each use [3]. Reusable brushes are replaced when worn, bent, or otherwise damaged. Worn bristles are ineffective for cleaning, while damaged brushes can damage endoscope channels.
Cleaning adapters are used for the suction, biopsy, air/water channels, and all channels are flushed with detergent solution to remove debris [3]. Automated pumps to eliminate the need for manual flushing are also available.
Following manual cleaning, the endoscope and all removable parts are thoroughly rinsed with clean water to remove residual debris and detergent. Water is purged from the channels using forced air. In addition, endoscopes and reusable accessories are visually inspected after manual cleaning and before HLD.
High-level disinfection — HLD is the process of completely eliminating all microorganisms in or on a medical device, except for small numbers of bacterial spores [33]. At most endoscopy centers, HLD is performed with a liquid chemical germicide solution by using an automated endoscope reprocessor that meets the standards of the FDA (or other government agency), while some centers use a manual process for HLD [5,34].
FDA guidance on reprocessing medical devices, including a list of devices that have completed validation testing for HLD (or liquid chemical sterilization), can be found here.
The germicidal chemical used for HLD must be compatible with the manufacturer's instructions [3]. Refer to the FDA website for a complete list of approved HLDs. Best practices for safe use of specific high-level disinfectants (eg, glutaraldehyde) can be found on the Occupational Safety and Health Administration website.
Rinsing — Following HLD, the endoscope surface, channels, and removable parts must be rinsed with clean, bacteria-free water [32]. Rinsing prevents exposing skin or mucous membranes to chemical residue.
Drying — Endoscopes are dried by purging water from the channels with compressed air, then flushing the channels with alcohol, followed by a second forced-air drying [3,35]. Alcohol mixes with residual water in the channels and facilitates evaporation as air flows through the channels. (See 'Risk factors' above.)
The exterior of the endoscope is dried with a soft, clean, lint-free towel [36].
Storage and reuse — Drying cabinets have connectors that force air through each endoscope channel, and thus, endoscopes can be stored vertically or horizontally [4]. Endoscopes stored in a vertical position should be stored with the tip hanging freely in a well-ventilated, dust-free, forced-air drying cabinet [3,21].
The maximum duration of storage before the endoscope requires repeat reprocessing before use is unclear. Endoscopes can be stored for at least seven days and perhaps longer without increased risk of contamination [4,37]. Most endoscopy centers store endoscopes for a maximum of five to seven days, provided that reprocessing and storage protocols have been followed [3,38,39].
ELEVATOR CHANNEL ENDOSCOPES
Reprocessing — Elevator channel endoscopes (eg, duodenoscopes, linear array endoscopic ultrasound scopes) present challenges to cleaning and disinfection due to their complex design; thus, additional reprocessing steps include [3,4] (see 'Risk factors' above):
●Inspection and manual cleaning – Similar to other endoscopes, manual cleaning for elevator channel endoscopes is done immediately after the endoscopic procedure has been completed. The elevator mechanism located at the distal tip of the endoscope should be raised (ie, opened) and lowered (ie, closed) during the manual cleaning process to allow brushing and flushing of both sides of the elevator. Visual inspection is done with the elevator in the raised position as well as with the elevator in the lowered position to ensure that there is no visible debris above or below the elevator mechanism.
●Drying – The channels and elevator mechanism of the elevator channel endoscope are thoroughly dried prior to storage. If channels and the elevator mechanism are not completely dry, bacterial growth can occur, forming a biofilm that is difficult to remove and could result in persistent contamination [40]. (See 'Drying' above.)
Reprocessing protocols for reusable medical devices including elevator channel endoscopes have been updated by regulatory agencies and manufacturers, and guidance from the US Food and Drug Administration (FDA) can be found here.
Limited data comparing duodenoscope reprocessing methods are available, and the optimal method remains unclear. In a trial that analyzed over 500 cultures from the working channel and elevator mechanism of reprocessed duodenoscopes, there were no significant differences in bacterial growth rates among duodenoscopes that had undergone single high-level disinfection (HLD), double HLD, or single HLD followed by ethylene oxide gas sterilization [16]. Ethylene oxide sterilization may have a role during infectious outbreaks, but this method has not been indicated for routine use [4].
Surveillance sampling — In addition to adherence to reprocessing protocols for duodenoscopes, a surveillance sampling program has been implemented at some endoscopy centers as a quality control measure. Microbiologic sampling of duodenoscopes involves sampling duodenoscope channels and the distal end of the duodenoscope, followed by culturing those samples with the goal of detecting bacterial contamination despite reprocessing.
The FDA, in collaboration with the Centers for Disease Control and the American Society for Microbiology, have developed protocols for surveillance sampling and culturing of duodenoscopes that can be implemented by health care facilities. The protocols for conducting infection surveillance and action plans in response to positive culture results can be found on the FDA website [41]. However, multiple questions remain about the optimal method for sampling, timing for sampling, and cutoffs to define proper disinfection. As a result, surveillance sampling is not regarded as a routine component of endoscope processing.
Duodenoscopes with disposable designs — The FDA recommends that health care facilities and manufacturers transition from duodenoscopes with fixed endcaps to those with disposable endcaps or to fully disposable duodenoscopes because of the limitations of reprocessing and the risk of persistent contamination [42]. Fixed endcap duodenoscopes have a plastic or rubber cap that is glued to the metal edges around the scope's distal end to prevent tissue injury. However, the endcap limits access to the crevices at the distal end of the duodenoscope during the cleaning process. In addition to removable endcap components, the FDA has approved fully disposable duodenoscopes [43] and duodenoscopes with a sterile disposable elevator component [44]. In an analysis of infection surveillance studies, duodenoscopes with disposable designs were associated with lower rates of contamination with high-concern organisms (eg, E. coli, Pseudomonas aeruginosa) compared with older duodenoscope models (0.5 versus 6.6 percent) [42]. These data support the use of innovative duodenoscopes that reduce or eliminate the need for reprocessing. (See 'Endoscopy-related infections' above.)
Potential uses for fully disposable duodenoscopes include procedures performed during nights or weekends when an endoscopy technician may not be available, operating room procedures (ie, sterile field), and for patients who are immunocompromised or have a history of multidrug resistant organism infection [45].
RESUABLE ACCESSORIES — Sterilization is required for critical reusable accessories (eg, biopsy forceps, snares, sphincterotomes) that breach the mucosal barrier [4,5].
The water bottle and its connecting tube are typically changed at least daily, and the water bottle and tubing are sterilized after use (or discarded if it is single-use only) [46,47]. Water from the water bottle is used for cleaning the endoscope lens and for irrigating the gastrointestinal lumen during the procedure.
QUALITY ASSURANCE — Quality assurance is essential for the effectiveness and safety of endoscope reprocessing protocols. Documenting the monitoring process typically includes the following [3,4,48]:
●Procedure date and time
●Patient name and medical record number
●Endoscopist name
●Endoscope model and serial number
●Automatic endoscope reprocessor (if used) model and serial number
●Names of technicians who reprocessed the endoscope
SOCIETY GUIDELINE LINKS — Links to society and government-sponsored guidelines from selected countries and regions around the world are provided separately. (See "Society guideline links: Endoscopy preparation, sedation, and special considerations".)
SUMMARY AND RECOMMENDATIONS
●Endoscopy-related infections – Reprocessing methods eliminate the risk of most endoscopy-related infections. However, transmission of organisms, including multidrug-resistant organisms such as carbapenem-resistant Enterobacteriaceae, despite adherence to reprocessing protocols has been reported. The source of infection was traced to duodenoscopes, and it has been theorized that the complex design of the elevator mechanism, the elevator cable, and the cable channel itself was a risk for persistent contamination. This risk may be eliminated through increasing use of disposable components or endoscopes, if possible. (See 'Endoscopy-related infections' above.)
●Endoscope reprocessing – Gastrointestinal endoscopes are semi-critical devices (ie, devices that contact the mucous membranes), and these devices require high-level disinfection (HLD) to destroy microorganisms and prevent transmission of endoscopy-related infection. (See 'Goals' above.)
•Protocols for endoscope reprocessing are informed by regulatory agencies, manufacturers, professional societies, and local health care institutions. (See 'Regulatory and manufacturer guidance' above.)
•The initial endoscope cleaning is an important reprocessing step that is performed prior to HLD. Initial cleaning includes precleaning, leak testing, and manual cleaning. (See 'Initial cleaning' above.)
•HLD is the process of completely eliminating all microorganisms in or on a medical device, except for small numbers of bacterial spores. HLD is performed with a liquid chemical germicide solution using an automated endoscope reprocessor or using a manual process. (See 'High-level disinfection' above.)
●Elevator channel endoscopes – Elevator channel endoscopes (eg, duodenoscopes, linear array echoendoscopes) present challenges to cleaning and disinfection due to their complex design. Thus, additional reprocessing steps include manually cleaning and visually inspecting the elevator mechanism. The US Food and Drug Administration issued a recommendation that health care facilities transition from duodenoscopes with fixed endcaps to those with disposable endcaps or to fully disposable duodenoscopes because of the limitations of reprocessing and risk of persistent contamination. (See 'Elevator channel endoscopes' above.)
●Quality assurance – Quality assurance is essential for the effectiveness and safety of endoscope reprocessing protocols. Documenting the monitoring process typically includes the following (see 'Quality assurance' above):
•Procedure date and time
•Patient name and medical record number
•Endoscopist name
•Endoscope model and serial number
•Automatic endoscope reprocessor (if used) model and serial number
•Names of technicians who reprocessed the endoscope
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