April 9, 2015 - Laboratory Practices Committee Prepares Endoscopy Document

On The Question of Culturing of Duodenoscopes

A recent report details an investigation of a hospital cluster of NDM-Escherichia coli infections associated with gastrointestinal endoscopy.  Nine patients with positive cultures for NDM-E. coli were identified and each had undergone an endoscopic procedure at this hospital.  Cultures obtained from the duodenoscope used on 5 of the 9 cases grew NDM-E. coli which were all highly related (1). Subsequent reports of similar outbreaks with CRE (carbapenem-resistant Enterobacteriaceae) strains have impacted healthcare facilities across the U.S.

These reports have raised concerns over the appropriate reprocessing (including cleaning and disinfection/sterilization) of these devices and the suggestion that microbial culturing of these duodenoscopes should be considered prior to reuse.  As pointed out in the editorial note by Rutala and Weber (2), one must have an understanding of duodenoscope reprocessing to address these concerns.  These concerns include:

  1. The most common method of duodenoscope reprocessing in the U.S. is by cleaning (the physical removal of gross soil) followed by microbial inactivation using high level disinfection.  High level disinfection is expected to inactivate most pathogenic organisms with the exception of bacterial spores, and is required to be validated as part of the FDA clearance process. Because flexible gastrointestinal endoscopic instruments are heat labile, only high-level disinfection or sterilization with chemical agents is FDA approved in the U.S.  The FDA recently highlighted that these devices should be sterilized, but can be high level disinfected if sterilization is not available (http://www.fda.gov/downloads/medicaldevices/deviceregulationsandguidance/guidancedocuments/ucm253010.pdf)
  2. Some previous outbreaks have been traced to deficient disinfection practices, or damaged/flawed duodenoscopes or automated duodenoscope reprocessors (AERs). 
  3. Although duodenoscope reprocessing guidelines exist and show that rigorous adherence to these guidelines will result in a patient-safe duodenoscope, others have demonstrated that manual duodenoscope reprocessing is rarely performed properly.  Duodenoscope reprocessing has improved with the use of AERs, but these systems do not replace the need for appropriate manual cleaning and routine maintenance. 

One of the duodenoscopes in question is manufactured by Olympus America, Inc. (OAI).  In March of 2015, OAI released a new updated protocol for reprocessing their leading duodenoscope (http://www.fda.gov/MedicalDevices/Safety/AlertsandNotices/ucm439999.htm).  OAI Technical Support has verbally stated that they do not now, nor have they ever recommended any routine microbiology culturing on their reprocessed duodenoscopes.  Nowhere in their revised protocol does it state to perform bacteriology cultures after reprocessing (http://medical.olympusamerica.com/sites/default/files/pdf/150326_TJF-Q180V_Customer_letter.pdf). 

An example of a duodenoscope culturing protocol, recently published by the CDC (http://www.cdc.gov/hai/pdfs/cre/interim-duodenoscope-surveillance-Protocol.pdf), was written by scientists who oversee the environmental laboratory at the CDC for the purposes of outbreak investigations.  The original protocol was published in the first edition of the Clinical Microbiology Procedures Handbook to assist in finding a source for an ongoing outbreak. This original protocol was adapted to the one recently released by the CDC and posted on their website. These culture and sampling protocols are part of a much larger document for use in outbreak surveillance. There are little to no data that document the performance of this culture method for either routine practice, or periodic validation of duodenoscope reprocessing practices. Furthermore, concern exists that residual aldehyde biocide that is used to reprocess duodenoscope is toxic to bacteria, and may result in falsely negative cultures (Benjamin Tanner, Antimicrobial Test Laboratories, personal communication), even when following the CDC protocol.

Several additional questions must be evaluated prior to deciding to culture reprocessed duodenoscopes (Rutala and Weber): 1) What level of detectable bacteria should be used to indicate proper disinfection?  2) What level would indicate an alert or necessitate action by the facility?  3) What actions should be taken if an alert level is reached (i.e. patient notification with an offer of blood-borne pathogen testing, ethylene oxide sterilization of positive duodenoscopes, or ethylene oxide sterilization of all duodenoscopes)?

Rutala and Weber end their editorial by stating that real-time monitoring methods need to be developed and validated to assess the risk of infection.  They further state that enforcement of best practices including equipment maintenance and routine audits with at least yearly competency testing of staff who perform reprocessing is imperative.  It is evident that routine best practices should be correctly employed before microbiological testing is even considered. 

At this time, it seems that clinical microbiology laboratories should not perform routine cultures of reprocessed duodenoscopes due to lack of data on the utility of such culturing.  Additionally, routine cultures of duodenoscopes should not be performed by clinical diagnostic laboratories because the techniques, equipment, and expertise for surveillance are more appropriate for a reference laboratory.  If such cultures are performed in the clinical laboratory in an outbreak situation, the limitations of such culturing and interpretation must be thoroughly understood. 

Considering further that culturing of reprocessed duodenoscopes does not detect all bacteria, does not detect any viruses or parasites, does not substantiate cleanliness nor any level of disinfection or sterility, the American Society for Microbiology recommends the following:

  1. Use the latest approved cleaning, high level disinfection or chemical sterilization protocols from manufacturers for duodenoscope reprocessing.
  1. Enforce strict adherence to both manual and automated reprocessing protocols.
  1. Do not perform routine duodenoscope cultures in the clinical diagnostic laboratory.  If culturing is deemed necessary as part of an outbreak investigation, consider sending to an appropriate reference laboratory. 


  1. Epstein L, JC Hunter, MA Arwady, et al. New Delhi metallo-β-lactamase–producing carbapenem-resistant Escherichia coli associated with exposure to duodenoscopes. JAMA. 2014:312(14):1447-1455
  2. William A. Rutala, David J. Weber, MD, MPH; 1Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill
    2Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill  Gastrointestinal Duodenoscopes. : A Need to Shift from Disinfection to Sterilization? William A. Rutala, David J. Weber, MD, MPH; 1Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill
    2Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill JAMA. 2014;312(14):1405-1406)


Acknowledgements: ASM Public and Scientific Affairs Board Committee on Laboratory Practices, Susan E. Sharp, Ph.D., DABMM, FAAM, Chair.  April 2015