Part II: Infection Prevention and Control Guideline for Flexible Gastrointestinal Endoscopy and Flexible Bronchoscopy – Transmission of infection by flexible endoscopy


1. Background

1.1 Spaulding Classification for Medical Devices

In the 1960s, Spaulding developed a system to classify the cleaning, disinfection and sterilization requirements for equipment used in patient/client careFootnote 14. The system divides medical devices into three categories based on the invasiveness of the procedure that the device will be used for. The three categories are non-critical, semi-critical, and critical. This classification system is widely accepted and used by professional organizationsFootnote 1, Footnote 4, Footnote 6, Footnote 7, Footnote 15 to help determine the level of disinfection or sterilization required for various medical devices. Refer to Appendix C for the Spaulding Classification System and to Appendix B, Glossary of Terms, for definitions. The recommendations for reprocessing of endoscopes presented here are based on and consistent with the principles of Spaulding’s classification.

2. Overview

Flexible endoscopic procedures are used for diagnostic (i.e., visualization and sample collection) as well as therapeutic purposes. The endoscopes that will be discussed in these guidelines are used for medical conditions involving the lungs (bronchoscopy), the esophagus, stomach and small intestine (gastroscopy and enteroscopy), the biliary tract and pancreas (duodenoscopy with endoscopic retrograde cholangiopancreatography (ERCP)), or the large bowel (colonoscopy). Also included are new modalities that continue to develop and evolve such as combined ultrasound transduodenoscopy, which provides endoscopic ultrasound to endoscopy (EUS).

Infections related to flexible endoscopic procedures are caused by either endogenous flora (the patient’s own microorganisms) or exogenous microbes (microorganisms introduced into the patient via the flexible endoscope and/or its accessories). Microbial sources of infection and modes of acquisition of exogenous microorganisms causing infection are discussed in detail in Section 3 of this guideline. The post-procedure infection rate related to inadequate reprocessing is difficult to determine, as there are no prospective studies that differentiate endogenous from exogenous infections.

The incidence of infections caused by transmission of microorganisms between patients or from the environment following endoscopy is estimated to be very low. Twenty-eight reported cases of endoscopy-related transmission of infection were reported in the United States between 1988 and 1992Footnote 16. During that period, approximately 40 million procedures were performed nationally, with the estimated incidence of transmission therefore in the order of approximately 1 infection per 1.8 million proceduresFootnote 3, Footnote 4, Footnote 8, Footnote 16,.The risk of infection from endogenous sources ranges from close to 0% with simple upper endoscopy or sigmoidoscopy to slightly greater than 1% in complicated ERCPFootnote 17. Although rarely associated with clinical infection, bacteremia with various gastrointestinal endoscopic procedures is not uncommon. The mean frequency of post-procedure bacteremia has been reported to range from 0.5% for flexible sigmoidoscopy to 2.2% for colonoscopy, 4.2% for esophagogastroduodenoscopy (EGD) and 5.6% to 11% for ERCP. Performance of biopsy or polypectomy does not change the associated rates of bacteremia. Esophageal dilatation and sclerotherapy in conjunction with EGD have been reported to raise the incidence to 45% and 31% respectivelyFootnote 18 Footnote 19, although recent prospective studies estimate that bacteremia rates for esophageal dilatation and sclerotherapy may be significantly lower than that, ranging between 12% and 22%Footnote 20.

There is even less information available on infection post-bronchoscopy. The apparent low incidence might reflect a truly uncommon occurrence, or infections may be under-recognized because they are easily masked by the primary signs and symptoms for which bronchoscopy is performedFootnote 9. Although pneumonia appears to be a rare complication of bronchoscopy (<1%)Footnote 21, this procedure has been identified as an independent risk factor for healthcare-associated pneumoniaFootnote 22. Infections after bronchoscopies are commonly due to mechanical or structural defects in the device that lead to its inadequate reprocessingFootnote 23, Footnote 24, Footnote 25.

3. Microbial Sources

3.1 Endogenous

Endogenous infections after flexible endoscopic procedures arise when the patient’s own microbial flora gain entry to the bloodstream or other normally sterile body sites as a result of mucosal trauma or instrumentation and are not related to instrument reprocessing problems. Examples of endogenous infections include pneumonia resulting from aspiration of oral secretions in a sedated patient or bacteremia resulting from microscopic tissue trauma occurring during endoscope insertion or removal.

In the lungs there is normally no resident flora. However, the mucosal surface of the upper respiratory tract has a substantial load (~ 106 cfu/gm)of microorganismsFootnote 26 that can be carried down into the lower respiratory tract when the insertion tube of the bronchoscope is introduced into the lung through the mouth. Oropharyngeal microorganisms include a wide range of viridans streptococci, Moraxella and Neisseria species, and anaerobic bacteria such as Porphyromonas species, Fusobacterium species and oral anaerobic spirochetes. The stomach and small intestine have only low levels of resident normal flora (103-6 cfu/gm of tissue)Footnote 26, but again microorganisms from the oropharyngeal cavity and throat can be introduced when the insertion tube is passed through the mouth into the stomach or small intestine. The large bowel, on the other hand, has high numbers of normal flora (~ 1012 /gram of feces)Footnote 26. Microorganisms found in the colon include anaerobic bacteria such as Bacteroides fragilis , Porphyromonasspecies, and Clostridium species as well as high numbers of Enterobacteriaceae (Escherichia coli, Klebsiella species, Enterobacter species, Proteus species, etc.) and Enterococcus species. In most immunocompetent patients bacteremia, which may occur during or after procedures, is usually transient and asymptomaticFootnote 19. No published data demonstrate a conclusive link between procedures of the gastrointestinal (GI) tract and the development of infective endocarditis (IE) and there are no studies that demonstrate that the administration of antibiotic prophylaxis prevents IE in association with GI procedures. Therefore, antibiotic prophylaxis solely to prevent IE is no longer recommended for patients who undergo GI tract procedures, including diagnostic esophagogastroduodenoscopy or colonoscopy. However, patients with high risk cardiac conditions (prosthetic heart valve, previous infective endocarditis, certain types of congenital heart disease and cardiac transplant recipients who develop cardiac valvulopathy) are candidates for prophylaxis before bronchoscopy, only if the procedure involves incision of the respiratory tract mucosa. For further details, the reader is referred to Prevention of infective endocarditis: Guidelines from the American Heart AssociationFootnote 27.

3.2 Exogenous

Exogenous infections arise from microorganisms introduced into the patient’s body by the flexible endoscope or by the accessories used in the procedure and are the focus of this document. Such infections are preventable with strict adherence to accepted reprocessing guidelines. Exogenously acquired microorganisms may originate from a number of sources, which are outlined in Figure 1. These include:

  1. A previously used endoscope, followed by inadequate cleaning and/or improper reprocessing technique.
  2. Contamination of the endoscope, accessories, or automated endoscope reprocessor from the environment during reprocessing (e.g., environmental microorganisms, skin microorganisms, and water microorganisms).
  3. Post-reprocessing contamination of the endoscope and accessories with water, environmental and/or skin microorganisms during final handling and/or storage.

The reservoir for exogenous microorganisms within a flexible endoscope may be the suction/biopsy channel or any other channel in the flexible endoscope (e.g., elevator wire channel in side-viewing duodenoscopes, air/water channel in colonoscopes, or any auxiliary channels that may be present)Footnote 28, Footnote 29, Footnote 30, Footnote 31, Footnote 32. In addition, the water bottle and tubing used for endoscopy procedures may also form a reservoir for exogenous microorganisms if these accessories are not properly reprocessed)Footnote 333. Components of the reprocessing procedure itself may serve as a reservoir, such as cleaning brushes if not inspected, cleaned and high level disinfected after each use; tap water diluted enzymatic detergent and tap water rinse that are not changed after each use; or if the water filtration system is not maintained as per manufacturers’ instructions)Footnote 34. Enzymatic detergent and rinse water used during manual cleaning should be changed for each scope to ensure residual microorganisms are not introduced into the next endoscope that is immersed in the used solution. Diluted preparations of enzymatic detergents should never be stored overnight as tap water-derived microorganisms can multiply to unacceptably high levels.

Tap water used for the final rinse after disinfection/sterilization may result in water microorganisms being left in the channelsFootnote 30, Footnote 35, Footnote 36, Footnote 37,. Most guidelinesFootnote 1, Footnote 3, Footnote 4, Footnote 9, Footnote 38 now recommend that, preferably, the final rinse water be sterile, filtered or otherwise rendered free of bacteria. If tap water is used for the final rinse, flushing the channels with 70-90% alcohol after the rinse is critical, not only to facilitate drying, but also to help eliminate any residual water microorganisms introduced from the tap water rinseFootnote 37, Footnote 39.

Bronchoscopic procedures involve substantial flushing of fluid through the biopsy-suction channel into the lung with subsequent aspiration from the lung back through the endoscope suction channel and into the side-trap. This “flushing process” through the endoscope channel, combined with the normally sterile lung environment, results in a higher likelihood of infection arising from any exogenously introduced microorganisms. This is not to say that upper and lower GI endoscopy have lower rates of exogenously introduced microorganisms; it simply reflects the higher likelihood that exogenous microorganisms introduced into the lung in combination with a certain degree of trauma will result in an infection compared to the same event occurring in the gut.

Figure 1. Acquisition of Exogenous Microorganisms Causing Endoscopy Related Infection

Figure 1. Acquisition of Exogenous Microorganisms Causing Endoscopy Related Infection
Text Equivalent - Figure 1

This figure represents the various sources of exogenously acquired microorganisms and how failure to properly clean, disinfect and sterilize reusable medical equipment may lead to the introduction of microorganisms into the flexible endoscope.  Possible sources of exogenously acquired microorganisms include:  Residual microorganisms from previous patient use; Residual environmental microorganisms acquired during reprocessing; Wet storage following appropriate disinfection/sterilization.

4. Specific Microorganisms Transmitted or Shown to Contaminate Flexible Endoscopes

Bacteria have caused the vast majority of exogenously acquired endoscope-related infections reported in the literature. The bacteria involved have been either true pathogens, which always have the potential to cause infection (e.g., Mycobacterium tuberculosis ), or opportunistic pathogens that cause infection if the microbial load is sufficient and/or host-factors are permissive (e.g., Pseudomonas aeruginosa ).

Transmission of viral pathogens via flexible endoscopic procedures is rare because these microorganisms are obligate intracellular microorganisms that cannot replicate outside viable human cells. This means that even if viral particles are present within a flexible endoscope channel after a patient procedure, the load of viruses cannot increase, as they are not capable of replication in vitro. Enveloped viruses (e.g., human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV)) die readily once dried but non-enveloped viruses (e.g., enteroviruses, rotavirus) can survive in dry conditions. Furthermore, enveloped viruses are more readily killed by high-level disinfectants and/or sterilants compared to non-enveloped viruses. Viruses can, however, survive longer in the presence of organic material than they can on dry surfaces. Published studies have demonstrated the efficient removal of HBV and HCV from endoscopes with standard reprocessing regimensFootnote 40, Footnote 41.

Although there is serious concern about the possibility of HIV transmission by flexible endoscopes, no cases have been identified. Thorough pre-cleaning has been shown to eliminate even high titres of HIV, and 2% alkaline glutaraldehyde has been found to inactivate the virus rapidly, even if the virus is dried in serum on a surfaceFootnote 41, Footnote 42, Footnote 43.

To date, only one case of clinically apparent HBV transmission, from an acutely viremic hepatitis B patient, via endoscopy has been documentedFootnote 31. A review of cleaning and disinfection procedures used at the time this case occurred revealed no breaches in reprocessing protocol. However, no disinfecting agent was being used to flush the air/water channel and standardized guidelines for reprocessing endoscopes were not yet available. These factors may have contributed to the hepatitis B transmission in this situation. A number of studies have followed patients who were exposed to endoscopes that had recently been used on HBsAg positive patients, without finding evidence of its transmission to othersFootnote 44, Footnote 45.

Eight cases of HCV transmission have now been attributed to gastrointestinal endoscopyFootnote 46. Thorough investigation with genotyping was performed in only three cases, in which transmission was firmly established by nucleotide sequencingFootnote 47, Footnote 48. While both reports implicate inadequate disinfection of the colonoscope, they each also raised the possibility of contamination of syringes or multidose vials as the actual source of transmission. A recent investigation of an outbreak of acute hepatitis C in patients who underwent procedures at the same endoscopy clinic revealed that transmission likely resulted from reuse of syringes on individual patients and use of single-use medication vials on multiple patients at the clinicFootnote 49. A multicentre cohort study by Ciancio et al.Footnote 50 followed 8260 HCV seronegative patients who were undergoing endoscopy. Follow-up serology was performed at 6 months, comparing them with a control population of healthy blood donors. There were no cases of seroconversion after endoscopy; in particular, none of the 912 patients who underwent endoscopy with the same instrument previously used on an HCV carrier showed anti-HCV seroconversion. There were four seroconversions in the control group (indicating a background seroconversion rate of 0.042 per 1000 patient-years). These results strongly suggest that when currently accepted guidelines are followed, transmission of HCV does not occur. Other recent studiesFootnote 51, Footnote 52 provide further evidence of the safety of reprocessing protocols based on current accepted standards.

Parasites (e.g., C ryptosporidium sp.) do not replicate in moist environments in the same manner as bacteria and fungi, but the cysts and eggs of parasites can survive in such environments. Although there is a theoretical risk of Cryptosporidium cysts and Clostridium difficile spores surviving high level disinfection (HLD), transmission of such pathogens via endoscopy has not been reportedFootnote 3, Footnote 44. The presence of fungi is associated with prolonged storage of flexible endoscopes, however, these microorganisms rarely cause infections in immunocompetent patients. Consequently, although transmission by a contaminated endoscope has occurredFootnote 32, Footnote 53, Footnote 54, outbreaks of fungal infection associated with contaminated flexible endoscopes have been infrequent.

A review article covering the years from 1966 to July 1992Footnote 44 reported 281 infections following gastrointestinal endoscopy and 96 infections following bronchoscopyFootnote 44. Microorganisms associated with transmission of infection from contaminated flexible endoscopes are summarized in Table 1. Microorganisms associated with transmission, without infection, attributed to contaminated flexible endoscopes are summarized in Table 2.

Table 1. Microorganisms Associated With Transmission of Infection Attributed to Contaminated Flexible Endoscopes
Organisms Endoscope Type Problem Identified
Helicobacter pylori DuodenoscopeFootnote 55 Footnote 56 Transmission of microorganism to subsequent patients. Failure to use appropriate disinfectant between patients.
Pseudomonas aeruginosa
  1. BronchoscopesFootnote 24 Footnote 25
  2. DuodenoscopesFootnote 30 Footnote 39 Footnote 44 Footnote 57
  1. Microorganisms isolated from loose biopsy port caps due to design flaw, resulting in disinfection failure - multiple cases of cross-transmission.
  2. Bacteremias/cholangitis post-ERCP caused by inadequate disinfection (e.g., endoscope flushed with tap water between patients and no disinfectant usedFootnote 39, contamination of inner channels, or incomplete drying).
Salmonella species ColonoscopesFootnote 44 Footnote 58 Inadequately disinfected colonic biopsy forceps in one outbreak; in most outbreaks, disinfectant used was not effective against Salmonella sp. N.B.: No reported cases since publication of cleaning/disinfection standards in 1988.
Enterobacteriaceae (range of genera including: Escherichia coli, Serratia sp. )
  1. Colonoscopes/DuodenoscopesFootnote 44
  2. BronchoscopeFootnote 24
  1. High levels of bacteria within channels - Transient bacteremia after ERCP.
  2. Serratia sp. sequestered in loose biopsy port due to design flaw –cross-transmission to multiple patients (one infection).
Mycobacterium tuberculosis
  1. BronchoscopeFootnote 59
  2. BronchoscopeFootnote 60
  1. Failure to disinfect contaminated suction valve -cross-transmission to four patients (one infection).
  2. Lack of routine Leak Testing- cross- transmission to eight patients.
  1. DuodenoscopeFootnote 32
  2. DuodenoscopeFootnote 53
  1. Trichosporon beigelii isolated from biopsy channel after disinfection failure –cross-transmission to nine patients.
  2. T. asahii isolated from tip of endoscopic forceps and resistant to disinfectant –cross-transmission to one patient.
Hepatitis C ColonoscopeFootnote 47 Failure to clean suction channel with brush and sterilize biopsy forceps- cross-transmission to two patients who subsequently developed hepatitis.
Hepatitis B DuodenoscopeFootnote 31 No disinfecting agent used to flush air/water channel; standard guidelines not available –cross- transmission to one patient who subsequently developed hepatitis.
Strongyloides stercoralis DuodenoscopesFootnote 61 Circumstantial evidence for four cases of cross-transmission of parasite. No further cases following ETO sterilization.
Table 2. Microorganisms Associated With Transmission Without Infection Attributed To Contaminated Flexible Endoscopes
Organisms Endoscope Type Problem Identified
Bacillus sp . BronchoscopeFootnote 62 Bacillus sp. isolated from suction valves. Contamination related to improper disinfection and storage –microorganism detected in bronchial washing cultures obtained from asymptomatic patients.
Pseudomonas aeruginosa BronchoscopesFootnote 63 Pseudomonas aeruginosa isolated from suction channel not cleaned prior to disinfection- microorganism detected in bronchoalveolar lavage fluid (BAL) samples from eight asymptomatic patients.
Mycobacterium sp .
  1. BronchoscopesFootnote 64
  2. BronchoscopeFootnote 65
  1. M. chelonae isolated from lidocaine sprayers used during bronchoscopy- acid-fast bacilli (AFB) detected in bronchial washings of asymptomatic patients.
  2. M. gordonae isolated from tap water related to failure in filter replacement and maintenance-AFB detected in bronchial aspirates of asymptomatic patients.
Serratia marcescens
Pseudomonas aeruginosa
BronchoscopeFootnote 66 Serratia marcescens and Pseudomonas aeruginosa isolated from saline used to rinse disinfected scope. Procedure changed to use filtered water rinse with scheduled in-line filter changes- microorganism detected in bronchoalveolar lavage fluid (BAL) samples from 41 asymptomatic patients.
  1. BronchoscopeFootnote 67
  2. BronchoscopeFootnote 54
  1. Aureobasidium sp. isolated from re-use of stopcocks meant for single use in outpatient bronchoscopy unit –microorganism detected in BAL cultures from nine asymptomatic patients.
  2. B. dermatitidis contamination related to ineffective mechanical cleaning-microorganism detected in samples from two asymptomatic patients.
Legionella pneumophila BronchoscopeFootnote 36 Contaminated tap water used to rinse scopes after disinfection. Problem recurred because of inadequate maintenance to filters –microorganism detected in BAL samples from three asymptomatic patients.

5. Occupational Infection Related to Endoscopy

Although transmission of infection is rare, endoscopy staff, like the patient, can become infected as a result of endoscopic procedures. Several studies have examined the prevalence of antibodies to Helicobacter pylori in the serum of gastroenterologists. Lin et alFootnote 68 found that endoscopists had a 69% seropositivity rate compared to 40% among internists. Seroprevalence was similarly higher in two studies comparing endoscopists (about 52%) to blood donors (14-21%)Footnote 69, Footnote 70. It is unclear whether the subjects wore appropriate personal protective equipment. In contrast, another study reported no statistically significant difference in seropositivity between endoscopists and age-matched controlsFootnote 71. Although differences in methodology may explain some of the discrepant results, overall it appears that endoscopists do have higher seropositivity to H. pylori , suggesting that endoscopy can be a risk factor for acquiring H. pylori . Catanzaro described transmission of M. tuberculosis to 10/13 (77%) of healthcare workers present at the bronchoscopy of an individual with undiagnosed tuberculosisFootnote 72. The author calculated that during bronchoscopy and intubation of the patient, at least 249 infectious units/hour of mycobacteria were generated. One case of bacterial conjunctivitis from a splash during colonoscopy has been reported, highlighting the need for appropriate personal protective equipmentFootnote 73.

6. Classic and Variant Creutzfeldt-Jakob Disease

Transmissible spongiform encephalopathies (TSEs) are caused by prions, which are protein particles that contain no nucleic acid, yet are capable of causing a transmissible disease. All prions are hardy, remain infectious for years in a dried state, and resist all routine sterilization and disinfection procedures commonly used by healthcare facilitiesFootnote 74, Footnote 75, Footnote 76, Footnote 77, Footnote 78. Differences in the pathogenesis of classic (sporadic, familial and iatrogenic) Creutzfeldt-Jakob Disease(CJD) and variant Creutzfeldt-Jakob Disease (vCJD) are reflected in the different distribution of TSE-specific protein (PrPTSE) in the bodies of patients with CJD versus vCJD. This means that different infection prevention precautions may be required during endoscopic procedures in patients with vCJD as compared to patients with classic CJD.

In classic CJD, prion infectivity is largely limited to the central nervous system (CNS) and only surgical instruments contaminated with prions from these high-risk tissues have resulted in iatrogenic transmission. In classic CJD, PrPTSE is found less often in organs outside the CNS, such as the lung, spleen, and lymph nodes and these tissues are considered to have low infectivity. Much of the evidence for this conclusion comes from studies of the distribution of the abnormal prion protein and/or associated prion infectivity in tissues of individuals with prion diseases. The agent responsible for vCJD is different from the agent that causes sporadic CJD. With vCJD, PrPTSE has been detected in a number of lymphoid tissues, as well as the intestinal tract and these tissues are considered to have a higher level of infectivity than similar tissues in patients with classic CJD. Experimental evidence suggests that the lymphoreticular system may contain significant levels of infectivity for most of the incubation period (mean 10-30 years). To support this, PrPTSE was found in the germinal centres of an appendix that was removed eight months before the onset of neurological disease in a patient with vCJD. Lymphoid follicles and germinal centres are widely distributed in the gastrointestinal tract and are often biopsied; it is therefore possible that endoscopy on patients who have or are incubating vCJD may result in contamination of the instrument (and particularly the biopsy forceps) with PrPTSEFootnote 179.

In a patient with vCJD, an endoscope can potentially be contaminated with PrPTSE at several points during an endoscopy procedure. During upper GI endoscopy and bronchoscopy, the first potential point of contamination is the tonsils if they are traumatized during insertion of the scope. If a small bowel biopsy deep enough to encounter lymphatic tissue is obtained, it is possible to contaminate the biopsy/suction channel as the biopsy forceps are withdrawn. The biopsy channel is an issue with lower GI tract endoscopies if biopsies are obtained. An ileal biopsy is a higher risk procedure than duodenum or jejunum biopsy because of the higher concentration of Peyer’s patches in the ileumFootnote 80.

With classic CJD, since PrPTSE has not been found in the GI tract, GI endoscopy alone is unlikely to be a vector for its transmission. Although lung and lymphoid tissues have been identified as low infectivity for CJD, the magnitude of infectivity is such that special precautions related to the procedure and reprocessing of equipment are not requiredFootnote 7 Footnote 75 Footnote 76.

Disinfection techniques to eliminate prion infectivity include prolonged steam sterilization, and extended soaks in concentrated sodium hydroxide, sodium hypochlorite, or formic acidFootnote 81 (Please refer to Public Health Agency of Canada Infection Prevention and Control Guideline: Classic Creutzfeldt-Jakob Disease in Canada, Quick Reference Guide-2007 Footnote 75 and Classic Creutzfeldt-Jakob Disease in CanadaFootnote 75, Footnote 76, Footnote 80,. Unfortunately, an endoscope cannot be reprocessed by any of these techniques without sustaining severe damageFootnote 81. Therefore, endoscopes used on patients with vCJD must be single use or destroyed after useFootnote 7.

The risk of transmission of any pathogen from an endoscope depends on many factors including the susceptibility of the exposed individual, the infectivity load of the tissues, the amount of contaminating tissue (in part related to the type of procedure done) and the effectiveness of the decontamination processesFootnote 82. The quantification of risk from asymptomatic individuals depends on the prevalence of disease. The total number of cases of vCJD reported in the UK, since 1990, was 166 as of December 31st , 2009 ( and 211 worldwideFootnote 81. The risk in Canada is much lower than in the UK as reflected by only a single case reported to dateFootnote 83. This case occurred in 2002 and infection was likely acquired while the individual was living for a period of time in the United Kingdom. The transmission of CJD and vCJD via an endoscopic procedure, remains only a theoretical risk at this time, as no cases of such transmission have been reportedFootnote 46, Footnote 80.

7. Factors That Contribute to Survival of Microorganisms in Reprocessed Flexible Endoscopes

7.1 Wet Storage

Bacteria may replicate to substantive levels even after overnight storage at room temperature if there is adequate moisture in the endoscope channels. Some bacteria can survive drying (e.g., M. tuberculosis and Gram positive bacteria) whereas others, like Gram negative bacteria (e.g., P. aeruginosa and E. coli ), die rapidly when dried. Gram negative bacteria replicate more easily in the presence of moisture and have been implicated in endoscope associated infections more frequently than have Gram positive bacteriaFootnote 29.

Moisture remaining in the channels of flexible endoscopes is a major contributing factor to exogenous microorganisms being transmitted by flexible endoscopes and outbreaks related to inadequate drying and improper storage have been reportedFootnote 30, Footnote 37. A survey by Kazmarek et al. in 1991Footnote 84 cfu/channel. Alfa & Sitter 1991Footnote 29 demonstrated that overgrowth of bacteria in flexible endoscope channels during storage was most commonly associated with Gram negative organisms, rather than Gram positive organisms. Ensuring the endoscope channels are thoroughly dried can prevent this overgrowth.

7.2 Biofilm Formation and Organic Debris

The ability of bacteria to form biofilms is an important factor in their potential to cause endoscopy-related infections. During clinical use blood, feces, mucus, and other biological substances can adhere to the endoscope and its channels. If the channels are not properly cleaned, there may be high residual levels of organic material and microorganismsFootnote 85, Footnote 86, Footnote 87, Footnote 88, Footnote 89. If the endoscope remains moist for extended periods, the residual bacteria can produce biofilm. Biofilms consist of colonies of microorganisms forming structures to maximize growth potential. Development of a biofilm begins when free-swimming bacteria attach to a surface. Substantial biofilm formation may result after overnight storageFootnote 90. Microorganisms embedded within this biofilm are sheltered from the cidal activity of the disinfectant/sterilant. This protection is further enhanced if there is residual organic material post-cleaning; subsequent exposure to aldehyde based disinfectants leads to fixation of the matrix, but the microorganisms within the matrix (i.e., biofilm and/or residual patient secretions) may or may not be adequately killedFootnote 4, Footnote 80, Footnote 91. Additionally, biofilm formation explains why flexible endoscopes should not be left soaking in enzymatic detergent overnight. Enzymatic detergents do not inhibit bacterial replication, and indeed, the microorganisms can use the enzyme proteins as an energy source. Therefore the most important step in endoscope reprocessing is bedside flushing, with subsequent manual cleaning and brushing of endoscope channels, as soon as possible after the procedure.This will reduce the likelihood that residual organic material or bioburden will be present during the disinfection/sterilization stage. The importance of timely flushing, and manual cleaning and brushing, cannot be overemphasizedFootnote 92.

7.3 Equipment Design Flaws

Two studiesFootnote 24, Footnote 25 confirm that design flaws can contribute to, if not promote, microbial contamination despite adherence to proper reprocessing protocols. In both reports, the documented design flaw was a faulty biopsy port in a bronchoscope that could loosen, allowing patient secretions and microorganisms to become sequestered in a moist environment, inaccessible to adequate cleaning and disinfection. The problem was identified when an abnormally high rate of P. aeruginosa was detected in bronchoalveolar lavage (BAL) specimens. This illustrates how periodic review of microbiology reports from BAL samples may be a useful audit tool for bronchoscopy services. Such audits would not be possible for duodenoscopy and colonoscopy as cultures are generally not done as a part of these procedures. Correcting design flaws is beyond the ability of most endoscopy units and primarily the responsibility of manufacturers of equipment and their regulatory bodies. However, endoscopy users may be able to identify flaws that manufacturers should address.

8. Errors in Reprocessing

Outbreaks associated with flexible endoscopy have most often been associated with breaks in the cleaning and/or disinfection/sterilization stage of flexible endoscope reprocessingFootnote 92 CowanFootnote 45 has described how the currently used reprocessing protocols provide a very narrow margin of safety and any slight deviation from the recommended steps may result in an increased risk of infection transmission by flexible endoscopes. Tables 1 and 2 show that errors in reprocessing of flexible endoscopes are the most common underlying problems associated with endoscopy-related transmission of infection. Some of the most common errors associated with reprocessing of flexible endoscopes have been identified by surveys of endoscopy unitsFootnote 84, Footnote 93 and include:

  • Failure to perform leak testing prior to cleaning,
  • Failure to completely immerse scope during cleaning,
  • Inadequate exposure time to enzymatic detergent during cleaning,
  • Inadequate amount of active ingredient used for disinfection,
  • Inadequate volume of water used for rinsing,
  • Inadequate time for scope drying prior to storage, and
  • Placement of the valves on the endoscope during storage.

In addition to these breaches in reprocessing, a Canadian survey reported that few healthcare facilities (30%) had written instructions for reprocessing of flexible endoscopes in their facilityFootnote 93. The introduction of Minimum Effective Concentration (MEC) testing of liquid chemicals (LC) has reduced the problem previously associated with an inadequate level of active ingredient due to inactivation or dilution.

Barriers to the proper reprocessing of flexible endoscopes are both the lack of appropriate initial training and of ongoing competency assessment for staff performing the reprocessing. A checklist that can be used to ensure competency of staff in the flexible endoscope reprocessing area has been included in Appendix G .

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