Endoscopic Disinfection

Publication Date: April 1, 2019
Last Updated: March 14, 2022


Recommended changes to reprocessing and storage


— Precleaning must be carried out immediately after use.


— Cleaning (manual or using an automatic flexible endoscope reprocessor (AFER) with an FDA or nationally approved cleaning cycle) must be carried out promptly* within 30 minutes after precleaning.
* “Promptly” in these guidelines means within 30 minutes.


— After manual cleaning of the endoscope, machine or manual high-level disinfection must be undertaken promptly.
— Endoscopes should be thoroughly rinsed with bacteria-free water after disinfection.

Alcohol flush and forced-air drying

— After disinfection by any means, the endoscope must have a prompt initial alcohol flush and forced-air drying for 10 minutes and storage in an approved forced-air storage/drying cabinet.
The endoscope may be used on another patient after the initial forced-air drying, but it must be placed in the storage cabinet if not immediately used for another patient procedure.
See below on drying cabinets.

Recommended changes for duodenoscopes

Endoscopy units performing endoscopic retrograde cholangiopancreatography (ERCP) should…

Volume of procedures

— Consider if the number of ERCP procedures performed is sufficient to continue offering this clinical service.

Dedicated staff and training

— Have dedicated staff to reprocess duodenoscopes who are aware of, and have undertaken specific training in, the particular problems associated with cleaning and disinfecting the instruments and obtaining endoscope samples for bacteriological surveillance.

Bacteriological surveillance

Perform monthly bacteriological surveillance cultures of duodenoscopes, using sample collection protocols that include samples from the distal lever cavity.*

Duodenoscopes with positive surveillance bacterial cultures in which organisms of concern are detected should be sent for service (unless there is an alternative explanation — e.g., staff error).

Include appropriate risk notification of possible multidrug-resistant organism (MDRO) transmission in the informed consent information.
* Consideration should be given to using the recently published FDA/CDC/ASM duodenoscope sample collection and culture protocol, which has been validated by duodenoscope manufacturers.

Endoscope drying

It is critical that drying is performed after manual or AFER reprocessing — regardless of AFER manufacturer claims.
  • Initial drying — All endoscopes should have a preliminary alcohol flush and forced-air channel drying for 10 minutes.
  • Storing/drying cabinet — After initial drying, endoscopes should be promptly transferred to an approved endoscope forced-air storage/drying cabinet and channel-purge air drying should be started.
    • This should continue until the endoscope is used again, or the safe storage period has elapsed.
    • Storage/drying cabinets should comply with the relevant national standard or with European Standard EN 16442, “Controlled Environment Storage Cabinet for Processed Thermolabile Endoscopes.” Note: If needed, the duodenoscope can be used for another patient procedure after the initial forced-air drying, or before the drying cycle in the cabinet is completed.
Note: If needed, the duodenoscope can be used for another patient procedure after the initial forced-air drying, or before the drying cycle in the cabinet is completed.

Interventions to control carbapenem-producing Enterobacteriaceae (CPE) transmission in the facility

CPE status — Be aware of the CPE status of your hospital.

CPE-infected patients

— Ensure that known CPE-positive patients are notified to the endoscopy unit before they arrive at the unit.
— CPE-infected patients, or those at high risk who have yet to have cultures taken, should be examined last on the list and managed in isolation from other patients, with use of a separate toilet or a commode.
— Clean and decontaminate the procedure room after the endoscopy procedure as per specific protocols for terminal cleaning of contaminated areas.

Plumbing standards

— Sinks, taps, and plumbing should comply with the national standards to minimize the risks of spray from drains in sinks or overflow of waste water from blocked pipes.

Infection control procedures

— The emergence of CPE is another compelling reason to meticulously follow standard infection control procedures including hand hygiene and the use of appropriate personal protective equipment (i.e., gloves and impervious gowns for each procedure).
— Endoscopy units should provide regular education and should assess compliance with hand hygiene and environmental cleaning and decontamination.

AFER maintenance

  • Ensure that the water quality is appropriate for the AFER.
  • Ensure that a schedule of replacement for external water filters is established and that the internal submicron filters are replaced in accordance with the manufacturer’s instructions for use.

Recommendation Grading




Endoscopic Disinfection

Authoring Organization

Endorsing Organizations

Publication Month/Year

April 1, 2019

Last Updated Month/Year

June 12, 2023

Supplemental Implementation Tools

Document Type


External Publication Status


Country of Publication


Inclusion Criteria

Female, Male, Adult, Older adult

Health Care Settings


Intended Users

Healthcare business administration, nurse, nurse practitioner, physician, physician assistant


Prevention, Management

Diseases/Conditions (MeSH)

D004203 - Disinfection


Disinfection, Endoscopic, Gastrointerology Endoscope