Common Questions: Flexible Endoscope Reprocessing in Ambulatory Care

The following article was originally published in Preventing Infection in Ambulatory Care, the quarterly e-publication from the Association for Professionals in Infection Control and Epidemiology (APIC). To learn more about receiving this resource and joining APIC, visit To learn more about APIC, visit


Q. Should endoscopes be disinfected in the morning before the first patient?


A. The Association of periOperative Registered Nurses and several European organizations recommend disinfecting endoscopes before the first patient of the day. [1,2] However, evidence indicates that disinfecting (high-level) endoscopes before the first patient of the day is unnecessary when the endoscope at the end of the previous day was terminally dried after reprocessing using a 70% alcohol rinse followed by forced air. [2] Repeat reprocessing of flexible endoscopes prior to reuse, however, should be done whenever:


- The facility does not have in place a quality assurance program that ensures the endoscope was reprocessed, dried, and stored in accordance with published guidelines. [1,15-19]


- The facility's quality assurance program is imperfect and the endoscope is removed from storage and identified by staff to be contaminated or to have been improperly reprocessed, dried, or stored. For example:

  • The endoscope is observed to be wet
  • The endoscope's distal tip is touching the ground
  • The endoscope's valves had not been removed
  • The endoscope had been stored in an automated endoscope reprocessor (AER), automated "sterilizing" processor, or pillow or carrying case
  • The endoscope had been used during off hours and was not reprocessed by trained staff members prior to being placed back into storage


Q. Can liquid chemicals provide sterilization of flexible endoscopes?


A. Liquid chemical sterilants (LCSs), unlike other sterilizing agents such as pressurized steam and ethylene oxide (EtO) gas, have several salient shortcomings that limit them from achieving sterilization. For instance, LCSs and LCS-based AERs, among other limitations: (a) preclude instrument wrapping to maintain a shelf-life; (b) require a terminal water rinse that typically is not sterile (and therefore the processed instruments aren't sterile either) and may re-contaminate the instruments with microorganisms following chemical immersion (which is why it is essential to dry the endoscope before storage); and (c) pose challenges to routine biological monitoring. Additionally, when LCSs are used to reprocess complex instruments with narrow lumens, orifices, and connectors, their flow may be impeded, which limits their contact with every potentially contaminated surface. Due in part to the difficulty of microbiologically sampling all of a complex instruments internal channels and components, validation of the effectiveness of a LCS labeled for sterilization has proved elusive. Further, the survival curves of LCSs don't appear to exhibit log-linear kinetics; rather, their shapes are variable and depend on factors such as the LCS's stability and formulation.


Finally, available data suggest that LCSs are associated with a significantly higher, and potentially misleading, sterility assurance level (SAL) than achieved by, for example, sterilization processes that use pressurized steam or EtO gas. As the SAL increases, so too does the risk of sterilization failure, instrument contamination, and patient infection. In fact, there is a lack of independently published reports or data that show processes that use LCSs can be used reliably to sterilize complex instruments, such as flexible endoscopes.


Q. Our facility routinely uses high-level disinfectants on its flexible endoscopes. But if a patient is suspected of being infected with HIV or HBV, we instead sterilize the endoscope using ethylene oxide gas after patient use. Is this practice acceptable?


A. Although EtO is an acceptable alternative for reprocessing flexible endoscopes, high-level disinfectants destroy HIV, HBV, and virtually every other pathogen, including Clostridium difficile. Therefore, replacing high-level disinfection with EtO gas sterilization for an endoscope that may be contaminated with one of these viruses is unnecessary and superfluous. Employing a single (and effective) reprocessing procedure is important to maintain a consistent standard of care. Moreover, treating each patient as a potential carrier of a bloodborne pathogen is crucial to protect healthcare staff (standard precautions). Consequently, it is not recommended to alter a routine disinfection procedure for an endoscope that may be contaminated with HIV or HBV.


Q. Is it acceptable for our hospital endoscopy unit to use a liquid chemical sterilant instead of pressurized steam to disinfect/sterilize biopsy forceps after cleaning?


A. LCSs are convenient for reprocessing endoscopes near the patient procedure room. Similarly, using a LCS for point-of-use processing of (reusable) biopsy forceps would have its benefits, such as a reduction in instrument turn-around time and allowance for a smaller inventory of biopsy forceps to meet clinical needs. But biopsy forceps are critical instruments for which sterilization is recommended. Because these instruments are not damaged by heat, pressure, or moisture and are sufficiently complex in design to hinder direct contact of low temperature sterilizing agents with all of the instruments internal surfaces, steam sterilization is recommended; low-temperature sterilization is not. Steam autoclaved biopsy forceps have not been documented to transmit disease.


Q. Is an alcohol flush of lumens essential as a final step to support the drying of endoscopes?


A. Reports indicate that endoscope drying is as important to the prevention of infection as cleaning and high-level disinfection. Whereas wet or inadequately dried endoscopes pose an increased risk of contamination and have been associated with transmission of waterborne microorganisms and infection, thoroughly dried (and properly cleaned and high-level disinfected) endoscopes have not been linked to infection.

As part of the reprocessing protocol, an endoscope's internal channels (and exterior) must be dried using 70% alcohol in accordance with published guidelines. [15, 16] This step must be performed between patient procedures and before storage. [15] The Society of Gastroenterology Nurses and Associates' all-inclusive, evidence-based recommendation is to dry the endoscope after every reprocessing cycle, whether between patient procedures or before storage, and irrespective of the water quality or label claim of the endoscope reprocessor. [23] According to the medical literature, adoption of this recommendation may reduce the importance of not only monitoring the microbial quality of the rinse water, but also reprocessing endoscopes before the first patient of the day. Both of these practices are costly and few guidelines recommend them. [22]


Q. How long can a scope safely be stored after it has been high-level disinfected?


A. If the environment or cabinet in which the endoscope was stored is monitored and controlled to promote drying and prevent the growth of microorganisms within the endoscope's internal channels, the literature suggests that GI scopes (with exception of ERCP scopes, which, like bronchoscopes, I recommend be reprocessed before each use) can be stored for as many as 7 days, apparently without having to reprocess the endoscope before its reuse. [17,18-20, 21]



1. Clinical Issues. AORN J 2000 Feb;71:398-403.

2. Muscarella LF. AORN J 2001 June;73:1159-63.

3. Botha SJ, Holzapfel WH. Int J Food Microbiol 1988 Oct;7(2):169-72.

4. Russell AD. Clin Microbiol Rev 1990 Apr;3(2):99-119.

5. Hachisuka Y. Jpn J Microbiol 1969 Jun;13(2):199-207.

6. Clinical Issues. AORN J 2002;75(1):194-8.

7. CDC guidelines. Am J Infect Control 1986;14:110-129.

8. Muscarella LF. AORN J 1998 May;67:966-76.

9. FDA. Content and format of premarket notification submissions for liquid chemical sterilants/high level disinfectants, dated 1-3-2000.

10. Muscarella LF. Gastroenterol Nurs 2001;24(5):253-60.

11. Bronowicki JP, et al. N Engl J Med 1997 Jul 24;337(4):237-40.

12. Dwyer DM, et al. Gastrointest Endosc 1987;33:84-7.

13. Rutala WA. APIC guideline. Am J Infect Control 1996;24(4):313-42.

14. Lee RM, et al. Gastrointest Endosc 1998;47(5): 377-81.

15. CDC. Draft Guideline for Disinfection and Sterilization in Health­care Facilities. Federal Register 2002, April 30;67(83):21252.

16. Muscarella LF. Leading a horse to water: Are crucial lessons in en­doscopy and outbreak investigations being learned? Infect Control Hosp Epidemiol 2002 July;23(7):358-60.

17. Muscarella LF. Labeling of Liquid Chemical Sterilants: Are Modifi­cations Needed? Infection Control Today. February 2002.

18. Muscarella LF. Are all sterilization processes alike? AORN J 1998 May;67(5):966-76.

19. Muscarella LF. Anticipated reliability of liquid chemical sterilants. Am J Infect Control 1998 Apr;26(2):155-6. Review.

20. Muscarella LF. Application of environmental sampling to flexible endoscope reprocessing: the importance of monitoring the rinse water. Infect Control Hosp Epidemiol 2002 May;23(5):285-9.

21. Bond WW. Biological indicators for a liquid chemical sterilizer: a solution to the instrument reprocessing problem. Infect Control Hosp Epidemiol 1993 Jun;14(6):309-12.

22. Muscarella L. "Inconsistencies in endoscope-reprocessing and infection-control guidelines: the importance of endoscope drying" Am J Gastroenterol 101:2147-54.

23. Society of Gastroenterology Nurses and Associates. Standards of Infection Control in Reprocessing of Flexible Gastrointestinal Endoscopes.­NAL1208_2.pdf Revised 2008.


Read more from APIC:


- Overview: Infection Prevention and Control for Computers in Patient Care Areas


- Moving to a Consolidated vs. Decentralized Model for Sterile Processing


- Patient Safety Tool: Central Line Test Questions

Copyright © 2023 Becker's Healthcare. All Rights Reserved. Privacy Policy. Cookie Policy. Linking and Reprinting Policy.


Featured Webinars

Featured Whitepapers

Featured Podcast