Understanding the Differences in Sampling and Culturing of Flexible Endoscopes: Why we Need a Unified Approach

What is sampling and culturing?

Microbiological sampling and culturing (S&C) is a multi-step surveillance testing technique used to prevent the transmission of infectious agents through endoscopy [1]. The process involves sampling endoscope channels and critical areas of the endoscope such as the distal end of duodenoscopes, then culturing the collected samples to detect any contamination still present after reprocessing [2].

Why is S&C important in infection prevention and control?

Post-endoscopy infection in patients can occur as a result of the examination (endogenous infection caused by translocation of the patient´s own bacteria to other sites in the body) or as a result of entry during the use of contaminated medical devices (exogenous infection). In the latter case, deviations from the manufacturer´s IFU or from recommended processing protocols might play a role.

With the implementation of an early S&C program within a healthcare facility, such reprocessing errors can be prevented, helping to mitigate the risks involved with the reprocessing of reusable medical devices [4]. Furthermore, when data obtained from S&C endoscopes is used to its full potential, it can provide insight into potential device, equipment (e.g., endoscope washer-disinfector [EWD]) or environmental (e.g., water quality) deficiencies, and eventually result in additional staff training [3]. It is important to remember, however, the efficacy of the sample collection approach itself, to ensure effective detection of microbial contamination in patient-ready endoscope channels [3].

Current guidelines in Europe

The 2007 combined European Society of Gastrointestinal Endoscopy (ESGE) and European Society of Gastroenterology Nurses and Associates (ESGENA) guidelines recommend that a quality assurance program with regular microbiological surveillance must be established within all clinical facilities – based on the duty of care owed to patients. A three-month interval between routine testing is recommended [1].

Differences in S&C methods

Although the S&C of endoscopes is commonplace in many countries, national guidelines and laws on hygiene and infection control vary and are based on historic regional/national level evidence (see table below). Consequently, a baseline S&C standard could therefore help minimize the risk of infections and make it easier to compare results from different countries [3].

Example differences in S&C practice between countries

Country Sampling

Netherlands [5]

France [6][7]

US [2]

Australia [8]

Sampling fluid

Sterile saline


Sterile DI or RO water

Sterile water or saline


Instrument/ suction channel

All channels

Instrument channel (duodenoscopes only)

All channels

Sampling method for channel(s)


F or FSF


FBF or F

Sampling method for distal ends



Swab or FBF













Netherlands [5]

France [6][7]

US [2]

Australia [8]

Lab method

Membrane filtration (0.45µm)

Membrane filtration

Filtration or centrifugation of entire sample

Centrifugation of entire pooled sample to 1 mL

Agar plates

Blood, R2A



Blood, MacConkey

Incubation conditions

35°C for 72hrs

30°C up to 5 days

35-37°C for 72hrs

- 35°C for 48hrs up to 5 days

- 28°C for 48 hrs up to 5 days

DI=deionized; RO=reverse osmosis; F=flush; FB=flush & brush; FBF=flush & brush & flush; FSF=flush-suction-flush; R2A=Reasoner´s 2A agar; PCA=plate count agar; TSA=trypticase soy agar

Why is a unified approach important?

In the last decade, studies on the transmission of pathogens from endoscopes to patients have generated evidence and insights that inform best practice [4]. However, the differences in S&C methods make it difficult to compare data generated in outbreak situations and determine the respective core and critical principles [3].

Creating a unified standard, will enable outcomes and contamination levels to be compared across countries. This will help establish a global benchmark for standard of care and patient safety and hopefully optimize patient outcomes.

For further information about the implementation and management of an endoscope S&C program, additional Olympus publications are available such as a white paper on the practical implementation of a S&C program: Tips, Tricks and Insights for Implementation and Management of an Endoscope Sampling and Culturing Program.

Sources and further readings

  1. Beilenhoff U, Neumann CS, Rey JF, Biering, et al. ESGE-ESGENA guideline for quality assurance in reprocessing: microbiological surveillance testing in endoscopy. Endoscopy. 2007;39(2):175-81.

  2. FDA/CDC/ASM. Duodenoscope Surveillance Sampling and Culturing. Reducing the Risks of Infection. Available at: https://www.fda.gov/media/111081/download. Accessed September 2022.

  3. Alfa, M., & Singh, H. Contaminated flexible endoscopes: Review of impact of channel sampling methods on culture results and recommendations for root-cause analysis. Infection Control & Hospital Epidemiology. 2022;43(5):623-638.

  4. Olympus. Tips, Tricks and Insights for Implementation and Management of an Endoscope Sampling and Culturing Program. Available at: https://infectionprevention.olympus.com/en-us/scientific-evidence/publications/sampling-and-culturing. Accessed December 2022.

  5. Rauwers, A. W., Voor In 't Holt, A. F., Buijs, J. G., et al. High prevalence rate of digestive tract bacteria in duodenoscopes: a nationwide study. Gut. 2018;67(9):1637–1645.

  6. INSTRUCTION N° DGOS/PF2/DGS/VVS1/PP3/2018/195 du 2 août 2018 relative à l’actualisation du traitement des endoscopes souples thermosensibles à canaux de type duodénoscope au sein des structures de soins. Available at: INSTRUCTION N°. DGOS/PF2/DGS/VVS1/PP3/2018/195 du 2 août 2018 relative à l’actualisation du traitement des endoscopes souples thermosensibles à canaux de type duodénoscope au sein des structures de soins - Légifrance (legifrance.gouv.fr). Accessed September 2022.

  7. Ministere des Affaires Sociales et de la Sante: Guide Technique. Traitement des endoscopes souples thermosensibles a canaux. 2016. Available at: https://www.preventioninfection.fr/document/guide-technique-traitement-des-endoscopes-souples-thermosensibles-a-canaux/. Accessed October 2022.

  8. Gastroenterological Society of Australia (GESA): Clinical Update - Infection Prevention and Control in Endoscopy 2021. Available at: https://www.genca.org/public/5/files/Nurses%20info/IPCE%202021_Feb2022update.pdf Accessed October 2022.