Healthcare professionals / Gastroenterology / EXALTTM Model D Single-Use DuodenoscopeClinical / Whitepaper

The ERCP Patient: Risk Factors for Infection

Grace Thornhill, PhD
Infection Prevention Fellow
Boston Scientific – Endoscopy
Brian Dunkin, MD
Chief Medical Officer
Boston Scientific – Endoscopy

“Every infection prevented is one that needs no treatment.”

(World Health Organization)



In September of 2013 the Center for Disease Control and Prevention alerted the Food and Drug Administration (FDA) about a duodenoscope-associated NDM-E.coli outbreak (1). Since that time numerous outbreaks involving multidrug-resistant organisms (MDRO) have been reported worldwide, some resulting in patient deaths (2-4). The FDA has been diligent in its efforts to understand their etiology including a requirement for post-market surveillance studies aimed at assessing the burden of endoscope contamination following reprocessing by high-level disinfection (HLD). From this effort, and that of other investigators, three important learnings have emerged.

1. Despite using best practices in reprocessing duodenoscopes with high level disinfection (HLD), there remains >5% risk that duodenoscopes continue to harbor pathogenic organisms thus increasing the risk of patient infection due to cross-contamination (5).
2. A key factor in the resilience of microorganisms, including MDROs, to withstand reprocessing is their ability to form biofilm. Biofilm, once established, is extremely difficult to remove compromising the effectiveness of manual cleaning that is essential to successful disinfection or sterilization (6, 7). While the complexity of the elevator mechanism in the distal tip of a duodenoscope makes it particularly vulnerable to inadequate cleaning practices, the entire scope, including accessories and the irrigation system, are also at risk (8).
3. The use of “enhanced” reprocessing methods recommended by the FDA (e.g. double HLD or sterilization with ethylene oxide) has been shown to be unreliable in producing an endoscope that is free from contamination (9-12).

As a result, the FDA recommends that “Hospitals and endoscopy facilities should transition to innovative duodenoscope designs that include disposable components such as disposable endcaps, or to fully disposable duodenoscopes when they become available.” (5).


Although the risk for infection following an ERCP procedure is rare (13) it is important to acknowledge that some patients are more vulnerable to infection than others (14). The goal of this white paper is to describe those factors that affect an ERCP patient's risk for infection.

Identifying risk factors for infection: The ERCP patient.

Understanding the risk factors that facilitate the transmission of infectious agents is important for preventing their spread and can also be used to identify those patients most vulnerable to infection. This white paper provides a list of risk factors that may cause a patient who is undergoing ERCP to be more susceptible to infection or colonization or may put a reusable duodenoscope inventory at risk. This list is based on general principles of infection prevention, outbreak investigation literature, and professional association guidelines. This list is not a risk index or risk calculator. Actual post-ERCP infection and colonization rates in clinical practice are unknown (15) therefore not all risk factors are identified and thus this list is not comprehensive.

Infection risk depends on the complex interplay of patient status, the infectious agent, and the environment of care (Table 1). Some factors can be controlled, whereas others require the implementation of interventions to mitigate their effect. Because of this complexity, assessment of infection risk is best performed on a case by case basis (14).

Table 1: General Factors Contributing to Risk of Infection (14)

Patient Status General health, Co-morbidities, Immune status, Disease state, Anatomic/Physiologic factors, Medical history, Immigration/Travel history 
Infectious Agent Prevalence, Transmission route, Antibiotic use, Pathogen vs Opportunist, Duration of exposure, Infectious dose (ID50), Virulence factor, Antibiotic resistance, Species of microorganism 
Environment of Care Type of health-care facility (Critical, Long Term Health, Ambulatory Surgery Center), Number of procedures performed, Staffing ratios, Length of stay, Adherence to infection prevention protocols, Occupational exposure
All pathogenic organisms have a reservoir, a place where they can grow and reproduce and that facilitates transmission (14). With respect to patient infection/colonization associated with ERCP procedures, there are two significant pathogen reservoirs, the patient and the duodenoscope (4). A significant reservoir is the normal/endogenous flora of the gastrointestinal tract. Infections of endogenous origin are thought to be caused by translocation of normal flora into the blood stream during endoscopic procedures (19). It is currently unknown which fraction of ERCP-related infections are endogenous in origin (27, 35). It should be noted that single-use endcaps or single-use duodenoscopes may not impact the rate of endogenous infections. Infection prevention protocols are designed to prevent transmission from all reservoirs and include endoscope reprocessing as well as hand and environmental hygiene. Although there are likely additional reservoirs for those organisms involved in ERCP-related infections, at a minimum, infection risk assessments should consider patient risk factors and other factors that put endoscope inventory at risk for persistent contamination (2, 3, 16, 17).

Patient factors that contribute to infection risk: Increased Susceptibility to Infection

ImmunocompromisedCancer, Transplant, Bone Marrow Transplant, Disease of Immune System, Advanced hematologic cancers, Severe neutropenia (absolute neutrophil count <500 cells/ml)
The immuno compromised patient is a patient who has defects in the body’s normal defense mechanisms that predisposes them to life-threatening infections that may not otherwise occur (18). Along with immune system diseases there are numerous patient factors that increase the risk of infection. Examples include cancer, transplant, age, pregnancy, occupation, residence, and travel/immigration status. Co-morbidities also contribute to infection risk. Examples include, but are not limited to, diabetes, eating disorder/poor nutritional status, drug/alcohol/tobacco addiction, chronic liver disease, and disease of the cardio pulmonary system (18). Those patient risk factors of most concern for ERCP patients are those with malignancies and liver transplant candidates/recipients (13, 19).
MalignanciesCholangiocarcinoma, Pancreatic cancer, Liver cancer, Cytotoxic chemotherapy drugs, Radiation treatments
The risk of infection increases in patients with cancer due to two major concerns, the cancer itself and the effect of treatment. Treatment of malignancies may include use of cytotoxicchemotherapeutic drugs and/or radiation therapy which suppresses immune system function leading to a greater risk of infection (14). All cancer patients are fragile and therefore at risk, but all do not carry the same risk. Acute hematologic cancers are of greater concern than chronic because these patients are at increased risk of bacteremia and sepsis after endoscopy (19).
TransplantTransplant candidates, Transplant recipients, Anti-rejection drugs
All transplant recipients are at greater risk for infection because they are receiving drugs that suppress the immune system (14). For the first 6-12 months after transplantation patients are at the highest risk of infection as anti-rejection drugs are given at their highest dosage during this time. For patients on a transplant waiting list, development of an infection may rapidly change their suitability for a transplant (20-22). Transplant candidates may be temporarily suspended from the list until the infection is resolved or can be delisted if the infection is caused by a multi drug-resistant organism (MDRO) or results in multiple organ failure (20-22). Infection is the primary cause for delisting a transplant candidate therefore, infection prevention is critical.

Patient factors that contribute to infection risk: Risk of Post-procedure Infection

ObstructionCholangiocarcinoma with hilar stricture, Cholangitis, Malignant biliary stricture, Multiple Strictures, Acute cholecystitis, Choledocholithiasis with incomplete stone clearance
Obstruction or stricture of a body passage is a recognized risk factor for infection (14). Cholangitis and sepsis are known adverse events associated with ERCP procedures occurring in up to 3% of cases (19). Incomplete biliary drainage was predictive of 91% of all cases of sepsis associated with ERCP (19). In those cases where complete drainage is not expected, a contaminated endoscope effectively “inoculates” the area with bacteria during the procedure further increasing the risk for infection (4). 
Prior and/or
Multiple Concurrent

Prior procedures: ERCP, Prior stent placement, Stent replacement, Biliary sphincterotomy

Multiple concurrent procedures: Choledochoscopy during ERCP, LAP-assisted ERCP, Tumor ablation, EUS with biopsy, Percutaneous hepatic stent placement, Percutaneous intervention in radiology + endoscopy procedures

Infection risk may be procedure related with an increased risk seen in those patients who have had select advanced, multiple, or concurrent procedures (2, 4, 13, 23, 24). Instrumentation and mechanical manipulation of tissues provides opportunities for the occurrence of transmission events (14). For example, biliary sphincterotomy is a risk factor for cholangitis (13). Placement of in-dwelling biliary stents to relieve obstruction from stones or malignancies increases the risk of infection. Biofilm formation on stents is also of concern as colonized stents provide a conduit for microbes to migrate to other ducts and tissues (13).

Antibiotic Prophylaxis for ERCP/EUS

ASGE recommendations and suggestions 

 - Known or suspected biliary obstruction, where there is a possibility of incomplete biliary drainage to include primary sclerosing cholangitis (PSC), hilar cholangiocarcinoma

- Biliary complications post liver transplant

- Patients with high-risk cardiac conditions and established GI tract infections (for prevention of infective endocarditis)

- EUS-FNA for pancreatic and mediastinal cysts/pseudocysts

Patients who already meet criteria for receiving pre-ERCP antibiotic prophylaxis should be considered at higher risk for infection overall. The American Society for Gastrointestinal Endoscopy (ASGE) recommendations for antibiotic prophylaxis relevant to patients undergoing ERCP are summarized above (25). Of note is the recommendation for antibiotic prophylaxis to prevent infectious endocarditis (IE) in those patients with high-risk cardiac conditions that also have active GI infections such as cholangitis. ERCP patients may be especially vulnerable because of the high rate of post-procedure bacteremia (19). 

Patient factors that contribute to infection risk: Risk of Post-procedure Infection

High-risk cardiac patients include those with a prosthetic valve, prior history of infectious endocarditis (IE), cardiac transplant recipients who develop valvulopathy, and patients with congenital heart disease (13). The prevalence of hospital-acquired IE may be increasing along with changes in the microbiology of the disease prompting a discussion on changing the strategies to prevent this disease (26). 

Protection of Endoscope Inventory

Protection of Endoscope Inventory: Active Patient Infection and Colonization

Re-usable duodenoscopes (with or without removable end caps) exposed to patients with active infections are at risk of becoming persistently contaminated with pathogenic organisms and thus increasing the risk of patient infection and colonization (4). The emphasis on protection of a duodenoscope inventory has evolved as the GI community has become aware of pathogen transmissions and outbreaks associated with ERCP procedures (17). Currently the focus is on the emerging MDROs involved in these outbreaks but there should also be concern for infections caused by pan-sensitive pathogens with a less remarkable profile as they also result in significant patient morbidity and mortality (27). Active infections such as cholangitis, cholecystitis,localized infection, and septicemia all present risk for contamination of a duodenoscope inventory (2-4, 28). Patients colonized with pathogenic organisms are of concern because they may be asymptomatic or present with sub-clinical symptoms making them undetectable unless active screening is performed (14, 27, 29). Colonization also poses a risk to the patient as conversion to active infection may happen over a period of weeks to years (27). Travel history and immigration status may be an important factor as well as there are many regions of the world where MDROs are endemic (14).

Protection of Endoscope Inventory: Persistent Contamination of Endoscopes

Persistent contamination of a duodenoscope results from a complex interplay of events involving exposure to infected/colonized patients, ineffective reprocessing protocols, and complex duodenoscope design (2, 4, 17, 30). Despite best efforts to follow current reprocessing guidelines an endoscope that is known to be contaminated can remain contaminated despite multiple rounds of reprocessing (2, 4, 5, 16). Persistent contamination indicates that reprocessing is ineffective. The primary culprit that impedes effective reprocessing is the presence of biofilm which can be extremely difficult to remove even with adherence to best practice reprocessing protocols (6,7). The primary factors that contribute to persistent biofilm formation and microbial contamination are:

  • Normal use of an endoscope results in damage that may include luminal shredding, scratches, gouges, staining, persistent debris, all of which provide a “safe harbor” for biofilm (1, 32, 33)
  • Inadequate manual cleaning impedes high-level disinfection/sterilization (1)
  • Incomplete drying resulting in storage of wet endoscopes (1,6, 34)
  • Complex endoscope design impedes proper reprocessing (1).

Protection of Endoscope Inventory 

Based on interim data from FDA post-market surveillance studies, up to 1 in 20 patient-ready duodenoscopes may be contaminated with pathogenic organisms (5, 31). Due to this ongoing challenge, contaminated duodenoscopes are now recognized as a risk factor for transmission of infection to ERCP patients (13). 


A patient’s risk of developing an infection involves complex interactions involving patient factors, procedural factors, pathogen characteristics, and environmental factors (e.g. a contaminated duodenoscope) and therefore should be assessed on a case-by-case basis. Even though the infection rate associated with ERCP is considered low, the infections due to duodenoscope-associated transmissions and outbreaks are severe and life-threatening making infection prevention efforts critical to providing high quality patient care.


1. United States Food and Drug Administration. Infections Associated with Reprocessed Duodenoscopes [Available from:
2. Wendorf K, Kay M, Baliga C, Weissman S, Gluck M, Verma P, et al. Endoscopic Retrograde Cholangiopancreatography - Associated Amp C Escherichia coli Outbreak. Infection Control and Hospital Epidemiology. 2015;36(6):634-42.
3. Epstein L, Hunter J, Arwady A, Tsai V, Stein L, Gribogiannis M, et al. New Dehli Metallo-B-Lactamase Producing Carbapenem-Resistant Escherichia coli Associated with Exposure to Duodenoscopes. New England Journal of Medicine. 2014;312(14):1447-55.
4. Kim S, Russell D, Mohamadnejad M, Makker J, Sedarat A, Watson RR, et al. Risk factors associatedwith the transmission of carbapenem-resistant Enterobacteriaceae via contaminatedduodenoscopes. Gastrointestinal Endoscopy. 2016;83:1121-9.
5. United States Food and Drug Administration. The FDA is recommending transition toduodenoscopes with innovative design to enhance safety: FDA Safety Communication. 2019.
6. Alfa MJ. Medical instrument reprocessing: current issues with cleaning and cleaning monitoring. American Journal of Infection Control. 2019;47:A10-A6.
7. Alfa MJ, Singh H, Nugent Z, Duerksen D, Schultz G, Reidy C, et al. Simulated-use polytetrafluoroethylene biofilm model: repeated rounds of complete reprocessing lead to accumulation of organic debrisand viable bacteria. Infection Control and Hospital Epidemiology. 2017;38(11):1284-90.
8. Kovaleva J, Peters FT, van der Mei HC, Degener JE. Transmission of infection by flexible gastrointestinal endoscopy and bronchoscopy. Clinical Microbiology Reviews. 2013;26(2):231-54.
9. Snyder GM, Wright SB, Smithey A, Mizrahi M, Sheppard M, Hirsch EB, et al. Randomized Comparisonof 3 High-Level Disinfection and Sterilization Procedures for Duodenoscopes. Gastroenterology.2017;153:1018-25.
10. Bartles RL, Leggett JE, Hove S, Kashork CD, Wang L, Oethinger M, et al. A randomized trial of single versus double high-level disinfection of duodenoscopes and linear echoendoscopes using standard automated reprocessing. Gastrointestinal Endoscopy. 2018;88:306-13.
11. Rex DK, Sieber M, Lehman GA, Webb D, Schmitt B, Kressel AB, et al. A double-reprocessing high level disinfection protocol does not eliminate positive cultures from the elevators of duodenoscopes. Endoscopy. 2018;50:588-96.
12. Ofstead CL, Heymann OL, Quick MR, Johnson EA, Eiland JE, Wetzler HP. The effectiveness ofsterilization for flexible ureteroscopes: A real-world study. American Journal of Infection Control. 2017;45(8):888-95.
13. ASGE. Adverse Events Associated with ERCP. Gastrointestinal Endoscopy. 2017;85(1):32-47.
14. Fiutem C. Risk Factors Facilitating Transmission of Infectious Agents 2014. Available from:
15. Ofstead CL, Langlay AMD, Mueller NJ, Tosh PK, Wetzler HP. Re-evaluating endoscopy-associated infection risk estimates and their implications. American Journal of Infection Control. 2013(41):734-6.
16. Humphries RM, Yang S, Kim S, Muthusamy VR, Russell D, Trout AM, et al. Duodenoscope-Related Outbreak of a Carbapenem-Resistant Klebsiella pneumoniae Identified Using Advanced Molecular Diagnostics. Clinical Infectious Diseases. 2017;65:1159-66.
17. Rubin ZA, Kim S, Thaker AM, Muthusamy VR. Safely reprocessing duodenoscopes: current evidence and future directions. Lancet Gastroenterology and Hepatology. 2018;13(3):499-508.
18. Flood A. The Immunocompromised Host 2019. Available from:
19. ASGE. Anitbiotic prophylaxis for GI endoscopy. Gastrointestinal Endoscopy. 2015;81(1):81-9.
20. Alferink LJM, Oey RC, Hansen BE, Polak WG, Buuren HRv, Man RAd, et al. The impact of infections ondelisting patients from the liver transplantation waiting list. Transplant International. 2017;30:807-16.
21. Fagiuoli S, Colli A, Bruno R, Craxì A, Gaeta GB, Grossi P, et al. Management of infections pre- and post-liver transplantation: Report of an AISF consensus conference. Journal of Hepatology.2014;60:1075-89.
22. Reddy KR, O’Leary JG, Kamath PS, Fallon MB, Biggins SW, Wong F, et al. High Risk of Delisting or Death in Liver Transplant Candidates Following Infections: Results From the North AmericanConsortium for the Study of End-Stage Liver Disease. Liver Transplantation. 2015;21:881-8.
23. Thosani N, Zubarick R, S., Kochar R, Kothari S, Sardana N, Nguyen T, et al. Prospecitive evaluation of bacteremia rates and infectious complications amoung patients undergoing single-operator choledochoscopy during ERCP. Endoscopy. 2016;48:424-31.
24. Wang P, Xu T, Ngamruengphong S, Makary MA, Kalloo A, Hutfless S. Rates of infection after colonoscopy and osophagogastroduodenoscopy in ambulatory surgery centres in the USA. Gut.2018;67:1626-36.
25. ASGE. Antibiotic prophylaxis for GI endoscopy. Gastrointestinal Endoscopy. 2015;81(1):81-9.
26. Moreyra AE, East S-a, Zinonos S, Trivedi M, Kostis JB, DPhill, et al. Trends in Hospitalization for Infective Endocarditis as a Reason for Admission or a Secondary Diagnosis. American Journal ofCardiology. 2019;124:430-4.
27. Thornhill G, David M. Endoscope-associated infections: A microbiologist’s perspective on current technologies. Techniques in Gastrointestinal Endoscopy. 2019.
28. Baggs J, Jernigan J, Laufer-Halpin A, Epstein L, Hatfield K, McDonald LC. Risk of Subsequent Sepsis within 90 days after a Hospital Stay by Type of Antibiotic Exposure. Clinical Infectious Diseases.2018;66:1004-12.
29. Lutgring JD, Limbago BM. The Problem of Carbapenemase-Producing-Carbapenem-Resistant Enterobacteriaceae Detection. Journal of Clinical Microbiology. 2016;54(3):529-34.
30. Ofstead CL, Wetzler HP, Heymann OL, Johnson EA, Eiland JE, Shaw MJ. Longitudinal assessment of reprocessing effectiveness for colonoscopes and gastroscopes: Results of visual inspections, biochemical markers, and microbial cultures. American Journal of Infection Control. 2017;45:e26-e33.
31. United States Food and Drug Administration. The FDA Continues to Remind Facilities of the Importance of Following Duodenoscope Reprocessing Instructions: FDA Safety Communication 2019 [Available from:
32. Ofstead CL, Hopkins KM, Eil and JE, Wetzler HP. Widespread clinical use of s**********, insolublelubricants, and tissue glue for endoscopy: A call to action for infection preventionists. American Journal of Infection Control. 2019
33. Thaker AM, Kim S, Sedarat A, Watson RR, Muthusamy VR. Inspection of endoscope instrument channels after reprocessing using a prototype borescope. Gastrointestinal Endoscopy. 2018;88:612-9.
34. Ofstead CL, Heymann OL, Quick MR, Eiland JE, Wetzler HP. Residual moisture and waterborne pathogens inside flexible endoscopes: Evidence from a multisite study of endoscope drying effectiveness. American Journal of Infection Control. 2018;46(6):689-96.
35. Rauwers AW, Voor in’t holt AF, Bujis JG, de Groot W, Hensen BE, Bruno MJ, et al. High prevalence rateof digestive tract bacteria in duodenoscopes: a nationwide study. Gut. 2018;67(9):1637-45.


Quick Reference Guide: ERCP Patient – Risk Factors for Infection

Understanding the risk factors that facilitate the transmission of infectious agents during ERCP procedures is important for preventing their spread and can also be used to identify those patients most vulnerable to infection. Risk factors may be grouped into two general categories: patient factors and those factors that increase the risk of contamination of the endoscope inventory. 

Patient factors that contribute to infection risk: Susceptibility to Infection

Immunocompromised (13,18,19)Cancer, Transplant, Bone Marrow Transplant, Disease of Immune System, Advanced hematologic cancers, Severe neutropenia (absolute neutrophil count <500 cells/ml)
Malignancies (14,19)Cholangiocarcinoma, Pancreatic cancer, Liver cancer, Cytotoxic chemotherapy drugs, Radiation treatments
Transplant (14, 20-22)Transplant candidates, Transplant recipients, Anti-rejection drug therapy

Patient factors that contribute to infection risk: Risk of Post-procedure Infection 

Obstruction (4,14,19)Cholangiocarcinoma with hilar stricture, Cholangitis, Malignant biliary stricture, Multiple Strictures, Acute cholecystitis, Choledocholithiasis with incomplete stone clearance
Prior Procedures (2,4,13,14,23,24)ERCP, Prior stent placement, Stent replacement, Biliary sphincterotomy 
Multiple Concurrent Procedures (2,4,13,14,23,24) Choledochoscopy during ERCP, LAP-assisted ERCP, Tumor ablation, EUS with biopsy, Percutaneous hepatic stent placement, Percutaneous intervention in radiology + endoscopy procedures
Antibiotic Prophylaxis - ASGE recommendations and suggestions (13,19, 25)

- Known or suspected biliary obstruction, where there is a possibility of incomplete biliary drainage to include primary sclerosing cholangitis (PSC), hilar cholangiocarcinoma

- Biliary complications post liver transplant

- Patients with high-risk cardiac conditions and established GI tract infections (for prevention of infective endocarditis)

- EUS-FNA for pancreatic and mediastinal cysts/pseudocysts


Protection of Endoscope Inventory 

Protection of Endoscope Inventory
(2-4, 5, 14, 17, 28-31)
 - Active patient infection and/or colonization with pathogenic organisms
 - Persistent contamination of endoscopes after reprocessing

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