Pathogens of Concern:

Keeping Our Patients Safe in Endoscopy

Faculty: Donna Girard, BSN RN CGRN


Guide to Study

eLearning Activity

Flexible endoscope reprocessing has long been recognized as a challenging and complex process.  Successfully completing each step in the process is critically dependent on all previous steps being meticulously completed and documented.  This module reviews the called-out steps in reprocessing and provides information identifying where lapses in best practice can provide an opportunity for cross contamination, exposure to microorganisms for both patients and staff, and transmission of pathogenic organisms to patients.

The completion of each step is considered critical and is dependent on all previous steps in the process. Additionally, these steps must be meticulously done and documented.  After the scope has been cleaned and high level disinfected there is opportunity for the scope to become recontaminated even though it has not yet been used on a patient.  This education session will explore those steps and opportunities for contamination, decontamination and recontamination of the scope.  Following manufacturers’ instructions for use, utilizing current guidelines and using your policies and procedures will help you participate in the complete circle of protection for flexible endoscope reprocessing.

Note: It should be noted that endoscopes are the medical devices most often involved in infection outbreaks. In the absence of defective equipment, every reported case of infection associated with a contaminated endoscope has been linked to a breech or violation of at least one requisite reprocessing.

Everything we do in relation to infection prevention in endoscopy leads us one way or another back to microbiology. Although invisible to us, every day we are exposed to a multitude of different microorganisms. For the most part they cause no harm but a disease-causing microorganism contaminating an endoscope can cause serious illness and death.

Microorganisms are minute life forms essential to the cycling of nutrients in the eco system of the planet. They have evolved over millions of years and can adapt to a wide range of environments. The basic requirements for microbial growth are an energy source and water. Pathogen is a term used to describe a microbe that produces a disease.

It is estimated that 90% of the cells on or in the human body are viruses, bacteria, fungi, worms and insects which make up our normal flora. Most of these microbes live on external body surfaces, such as the skin and conjunctivae or on internal body surfaces that communicate with the exterior, such as the mouth, gastrointestinal tract, urethra and vagina. The blood and organs such as the brain, liver and the respiratory tract below the vocal cords are normally sterile. Microbes found in those areas usually indicate infection.

Bacteria make up the largest part of our normal flora. One half the weight of feces is made up of bacteria (there are approximately 1 million (106) bacteria per gram of feces. Some bacteria can cause disease if they move from their normal colonization sites. For example, 50% of us carry Neisseria meningitis in our throats. If it moves to the bloodstream or brain, it can cause septicemia or meningitis.

Viruses can be found in the absence of infection. Retroviruses make up 3% of our chromosomes and play a role in gene activation. Once infected with any of the eight human herpes viruses, that virus will stay in our cells for life.

The gastrointestinal tract is the major site for colonization and there are an estimated 2-4 pounds of bacteria in this part of the adult body. There is also great diversity, particularly in the colon. This normal bacterial flora is important in the proper development of the gut and also in synthesizing some vitamins (K and B complex). It is estimated that 500-1000 different species live in the gut. The metabolic activity of the bacteria in our intestines greatly exceeds our own metabolism. The genetic diversity of these bacteria is immense.

And now for a Pop Quiz to test your knowledge. Try to answer the question before clicking on the bar to reveal the answer.

Pop Quiz

What is a pathogen?

A pathogen is a micro-organism that has the potential to cause disease

What is an infection?

An infection is the invasion and multiplication of pathogenic microbes in an individual.

Most reported healthcare outbreaks ae linked to what instrument?



Did you know: Normal skin flora serve useful roles in killing exogenous bacteria picked up by touching. However the hands are relatively deficient in normal flora and are an important means of transfer of bacteria. That is why hand washing is so important to prevent infection.

Bacteria are small “prokaryotes”; they do not possess nuclei or intracellular organelles. Most bacteria are free living and can grow in humans, other animals and in the environment. They are the smallest living cell with an average size of one micron (1/1000 of a millimeter). Bacteria make up the major component of our normal body flora. Bacteria are found all over the earth and are thought to be one of the first life forms. They can survive in the deepest oceans, the highest mountains and even in the arctic ice. They can colonize in any environment; acid/alkali, boiling/freezing and with/without oxygen. Their survival lies in their ability to go dormant for extended periods.

Bacteria divide by asexual binary fission. Under ideal conditions, bacteria divide every 20 minutes and it is estimated that the mutation rate is, at the lowest, one in every 100 million cells. It follows that in the colon, at normal growth, one million mutant bacteria will be produced every 20 minutes. It is clear that the intestinal bacteria have a great capacity to react to any adverse conditions to which they are exposed. This includes the administration of antibiotics to fight infections. It is no coincidence that the intestinal bacteria are a major reservoir of antibiotic resistant genes.

Pathogenic bacteria include Staphylococcus aureus which can produce toxins (toxic shock syndrome) and in its more resistant form becomes methicillin-resistant Staphylococcus aureus (MRSA). Methicillin-resistant Staphylococcus aureus has mutated over time to develop a resistance to most antibiotics, causing infections that can be life threatening and difficult to treat. Sixty percent of Staph infections are now drug resistant, up from 2% in 1974. MRSA occurs most frequently in patients with weakened immune systems undergoing invasive procedures in hospitals and nursing homes.

Streptococcus pyogenes, solely a pathogen of humans, is responsible for rheumatic fever, skin infections and necrotizing fasciitis (a rare but deadly skin and deep tissue infection).

Pseudomonas aeruginosa is the fourth most commonly isolated hospital acquired pathogen. Ubiquitous in any moist environment, it can rapidly contaminate a moist endoscope with biofilm. It has been found in endoscope irrigation systems, automated reprocessors and even in the hospital water supply. It can be quite virulent and produces many toxins. There have been more than 200 reported cases of Pseudomonas aeruginosa transmission from endoscopes. Patients having bronchoscopies and ERCP are especially at risk for this pathogen. These infections cause discomfort, lengthy hospital stays and may result in death in critically ill patients.

Escherichia coli is a member of the large and diverse family of gram negative rods known as enterobacteriaceae. Although part of the normal intestinal flora, some strains are more pathogenic and can cause meningitis and septicemia. Escherichia coli is one of the three most common causes of diarrheal disease worldwide. A number of different E. coli strains can release toxins that cause a secretory diarrhea and urinary infections. Other members of this genus include Salmonella, Klebsiella and Serratia.

Helicobacter pylori is another solely human pathogen that has adapted to living in the harsh acidic environment of the stomach. It is estimated that half of the world’s population is colonized or infected with H. pylori. It adapts to the acidic stomach environment by secreting an enzyme, urease, which converts urea into bicarbonate and ammonia, creating a cloud of neutralizing chemicals to support bacterial growth. It then initiates an inflammatory response causing gastritis. This infection may be passed to the health care worker if proper personal protection is not used. Peptic ulcer disease can develop and H. Pylori may cause two forms of cancer: carcinoma of the stomach and a lymphoid tumor called maltoma.

Mycobacterium tuberculosis is an especially resistant bacteria with a waxy cell wall that causes particular staining properties called acid fast. This cell wall makes it resistant to destruction by drying and many chemical agents. Tuberculosis germs coughed into the air (or on a contaminated instrument) can remain alive and viable for weeks or months, much longer than other bacteria. Although it does not form spores, the resting form of these bacteria can survive many years without food or water. Because Mycobacterium tuberculosis is found in the stomach as well as the lungs, the infection is easily spread by a contaminated instrument. Many high level disinfectants are tested for potency using Mycobacterium tuberculosis. More resistant forms of Mycobacterium tuberculosis have been discovered in the HIV/AIDS populations.

Pop Quiz

What is drug resistant bacteria?

This is bacteria that has mutated over time to develop a resistance to most antibiotics, causing infections that can be life threatening and difficult to treat.

Which bacteria can be found in the hospital water supply?

Pseudomonas aeruginosa

What is one of the common causes of diarrhea?

E. coli is one of the three most common causes of diarrheal disease worldwide

What makes Mycobacterium tuberculosis such a highly resistant organism?

The waxy cell wall makes it highly resistant to drying and many chemical agents.


Did you know: Bacteria are found all over the earth and are thought to be one of the first life forms.

Endospores are a resistant, dormant, survival form of bacteria. They are resistant to high temperatures, most disinfectants, low level radiation and drying. Endospores can survive thousands of years until environmental stimuli trigger germination. Most high level liquid disinfectants require a longer time and specific instructions to kill spores. However, many of the spores that are found in the body are in the vegetative state and are susceptible to high level disinfection. Examples of spore-producing organisms include those that cause anthrax, tetanus, botulism and gangrene.

Bacillus anthractis is a disease of domesticated and wild animals. There are three types of anthrax: skin (cutaneous), lungs (inhalation) and digestive (gastrointestinal). Humans become infected by the disease Anthrax through contact with infected animals, their hides or meat.

Humans can become infected with anthrax by handling hides, meat or products from infected animals or by breathing in anthrax spores from infected animal products (like wool, for example). People also can become infected with gastrointestinal anthrax by eating undercooked meat from infected animals. In most cases, early treatment with antibiotics can cure cutaneous anthrax. Even if untreated, 80 percent of people who become infected with cutaneous anthrax do not die. Gastrointestinal anthrax is more serious because between one-fourth and more than half of cases lead to death. Inhalation anthrax is much more severe. In 2001, about half of the cases of inhalation anthrax ended in death.

Clostridium tetani spores are found in large concentrations in the environment. Clostridia are also anaerobes and Clostridium tetani can be part of the normal flora of the human colon. The disease caused by C. tetani is known as tetanus and is the result of the release of a toxin called tetanospasmin that causes intense muscle spasm. It generally occurs after a cut, puncture wound or scratch from an object contaminated with the bacteria. As little as 100 nanograms can kill an adult. A vaccine is available for prevention, but it is ineffective for treatment of an acute infection. Antiserum is the only antidote for tetanospasmin toxin.

Clostridium botulinum is a spore forming anaerobic bacterium that causes food poisoning. Food borne botulism occurs when the food is contaminated with either spores or toxin. Improperly preserved food and contaminated honey are associated with this disease. Botulism toxin is a neurotoxin which blocks the transmission of nerve impulses to muscle causing a flaccid paralysis.

Clostridium difficile is an opportunistic, spore-forming, gram-positive, anaerobic bacillus. It is transmitted from one patient to another through direct or indirect contact, through the oral ingestion of its vegetative cells or endospores (i.e. the fecal-oral route) or from a contaminated environment or medical device. C. difficile may be found as a part of the normal intestinal flora and approximately 3% of healthy adults carry C. difficile without evidence of disease. C. difficile poses a particular risk for hospitalized patients where environmental contamination with C. difficilespores has been found. In fact, the primary reservoirs of C. difficile are infected and colonized patients in hospitals and long-term care facilities. C. difficile produces two types of toxins that attack the colon wall causing ulcerations.

The setting of a contaminated environment coupled with the use of broad spectrum antibiotics can produce a situation that upsets the balance of normal colon bacteria. In the case of C. difficile, the patient may develop mild diarrhea or progress to the more serious and sometimes fatal pseudomembranous colitis. The treatment is long and difficult, using potent antibiotics and requiring lengthy hospital stays. This infection can leave the patient weak and debilitated for a long period, lengthening recovery from surgery or other medical conditions.

Click the "Thinking Cap" button for more to learn.

Pop Quiz

What is an endospore?

An endospore is a resistant, dormant, survival form of bacteria.

What causes the symptoms of tetanus?

The release of a toxin called tetanospasmin

What spore forming bacteria is used as a treatment for achalasia?

Clostridium botulinum (Botox)

Name a risk factor for contracting C. difficile

Contaminated hospital environment, broad spectrum antibiotics, immunosuppression


Did you know: Anthrax also can be used as a weapon. This happened in the United States in 2001. Anthrax was deliberately spread through the postal system by sending letters with powder containing anthrax, causing 22 cases of anthrax infection.

It is of interest that Botulism toxin is being used as a treatment for achalasia (an esophageal obstruction that develops due to failure of the esophagogastric sphincter to relax, causing the upper esophagus to fill with retained food). Botox blocks nerve impulses to the lower esophageal sphincter causing it to relax. Botox injections are also used to reduce the appearance of facial wrinkles.

All living things are cellular except viruses. A virus is a tiny, lifeless, totally inert particle which is incapable of existing without a host. Virus size varies from 20 to 250 nanometers (one nanometer is one billionth of a meter). Once inside a cell however, thousands of virus particles spread to other cells, killing the host cell in the process. All viruses consist of two parts: a nucleic acid core and a protein coat. In some cases there is a fatty envelope. The function of the protein coat and envelope (if present) is to attach the viral particle to the cell membrane and get the virus into the cell. Unlike other microbes, viral nucleic acid codes for proteins needed for replication, not for cellular proteins. In doing so, this obligate intracellular parasite forces the cell to churn out proteins that the virus needs to make more of itself.

The attachment is very specific and the viral coat must fit exactly into the receptor site. This is why most viruses are species specific and quite often are specific to particular types of cells within an organism. The hepatitis B virus targets liver cells and the HIV virus goes to markers on certain white blood cells. Viruses that cause the common cold bind to cells lining the respiratory tract. Antibiotics are not effective against viruses.

Viruses, though fragile and easily destroyed, can still be vectors of infection, as demonstrated by recent headlines warning patients of potential risks after endoscope reprocessing breaches. Fifty to ninety percent of HIV infected patients are also infected with Hepatitis C. Cytomegalovirus is the most frequent opportunistic infection seen with AIDS. Cryptosporidium may cause self limiting diarrheal illness in a healthy host but chronic diarrhea in immuno-suppressed patients. Human Papillomavirus (HPV) has been suspected of being transmitted during colonoscopy, causing condyloma infection (venereal warts). Can you imagine the horror of becoming infected with a sexually transmitted disease during a colonoscopy?

Pop Quiz

What is a virus?

A virus is a tiny lifeless totally inert particle and is incapable of existing without a host.

What type of infection can be caused by HPV?

HPV could cause condyloma infection.


Did you know: Viruses also have the ability to become latent after an initial infection and as such, can remain dormant in the host ganglia. Varicella-zoster can reappear years later producing the painful rash of shingles. Viruses can also cause cancer. Virtually all cervical cancers are associated with the papilloma virus.

Protozoa form a large kingdom of eukaryotes consisting of the most complex unicellular organisms, with a membrane around the nuclei and intracellular organelles but no cell wall. They have very complex life cycles, dividing by binary fission or budding. They may require a host for part of the cycle. Protozoa are quite fragile and those that are shed into the environment or host usually produce thick walled cysts that are similar to spores. These cysts are excreted in feces and may be ingested in contaminated water, causing diarrheal illnesses such as amebic dysentery and giardiasis. A patient seeking treatment for diarrhea after a camping trip could in fact be harboring giardia protozoa spores. The Giardia cyst can survive for weeks to months in cold water, and therefore can be present in contaminated wells and water systems, especially stagnant water sources such as naturally occurring ponds, storm water storage systems, and even clean-looking mountain streams.

Fungi are eukaryotes that have chromosomes, a nucleus and internal structures called organelles. Fungi exist in either yeast or mold forms. They reproduce sexually and by binary fission. Some form large branching networks called mycelia (as in Tinea pedis/athlete’s foot); others, such as Candida albicans (a yeast) remain as single cells. Candida is an opportunistic infection often found in HIV and immune-compromised patients. It can cause esophagitis and thrush, a painful fungal mouth infection.

Pop Quiz

How do protozoa spread disease?

Protozoa produce cysts that are excreted in feces and may be ingested in contaminated water

What type of organism is Candida?

The fungus Candida albicans is a yeast that remains as a single cell.


Did you know: Giardia lamblia is a flagellated protozoan parasite that colonizes and reproduces in the small intestine. Giardia infection can occur through ingestion of dormant cysts in contaminated water food, or by the fecal-oral route (through poor hygiene practices).

Simply put, biofilm is a collection of microorganisms surrounded by the slime they secrete, attached to either an inert or living surface. You are already familiar with some biofilm: the plaque on your teeth, the slippery slime on river stones and the gel-like film on the inside of a vase which held flowers for a week.

Biofilm exists wherever surfaces contact water. More than 99% of all bacteria live in biofilm communities. Some are beneficial. Sewage treatment plants, for instance, rely on biofilm to remove contaminants from water. But biofilm can also cause problems by corroding pipes, clogging water filters, causing rejection of medical implants, and harboring bacteria that contaminate drinking water.

Biofilm is composed of millions of micro organisms that accumulate on surfaces in aqueous environments. They adhere to surfaces by producing extra cellular polysaccharide. As nutrients accumulate, the pioneer cells proceed to reproduce. The daughter cells then produce their own glycocalyx, greatly increasing the volume of ion exchange surface. Pretty soon a thriving colony of bacteria is established. Pseudomonas aeruginosa is a common ‘pioneer’ bacteria and is used in a lot of biofilm research. In one experiment, researchers found that Pseudomonas cells adhere to stainless steel, even to electro polished surfaces, within 30 seconds of exposure. The adherent bacteria produce micro colonies which initially are composed of only one bacterial type but frequently develop to contain several different species of micro organism living in a complex community.

The ability of bacteria to form biofilm is an important factor in the pathogenesis of endoscopy related infections, since biofilm interferes with disinfection. Biofilm is highly resistant to the germicide. In order to destroy the cell responsible for forming the biofilm, the disinfectant must first react with the surrounding polysaccharide network. The cells themselves are not actually more resistant, rather they have surrounded themselves with a protective shield. The disinfectant’s oxidizing power may used up before it can reach the cell.

Studies with bacterial strains have shown that smooth surfaces are colonized as easily as rough surfaces. Once a biofilm has formed, the resultant structure is highly elastic and behaves in a rubbery manner; it is very difficult to remove. The structural characteristics of biofilm give the individual micro colonies the tendency to break off and/or detach. It is during this detachment of cells that the antibiotic-resistant biofilm phenotype may pose a risk of infection.

It is easy to see how the channels of an endoscope could become coated with biofilm. The smaller air water channels that cannot be brushed are especially susceptible and studies have found this to be the case. In a 2003 Australian study, samples of scope channels were removed from scopes sent for repair. Biofilm was present in five out of thirteen biopsy channels and twelve out of thirteen air water channels. However, any scope channel is at risk if it is not promptly reprocessed and thoroughly dried before storage. This same caveat applies to water bottles and accessory tubing used during endoscopy for irrigation and cleaning.

Pop Quiz

What is the purpose of biofilm?

The best way to prevent biofilm formation is immediate post procedure cleaning, brushing all accessible channels and thoroughly drying the endoscope after reprocessing.

How quickly can Pseudomonas biofilm begin to form?

Pseudomonas biofilm may form within 30 seconds of exposure.

What channels of an endoscope would be susceptible to biofilm formation?

All channels but especially those channels that cannot be mechanically cleaned (brushed).


Did you know: The best way to prevent biofilm formation is immediate post procedure cleaning, brushing all accessible channels and thoroughly drying the endoscope after reprocessing.

There's an old public relations saying that bad publicity is better than no publicity, but that is certainly not the case when it comes to hospital-acquired infection; negative publicity does not endear us to our patients. Imagine the reaction of patients and staff upon seeing these headlines and news reports!

More Infection Control Problems at XX Medical Facilities: The problem began in March 2009 when XX revealed that more than 2,400 Miami-area patients were given colonoscopies with improperly cleaned equipment and might have been infected with diseases.

XCMC tells 2,600 patients device wasn't properly disinfected: About 2,600 patients at XYZ County Medical Center are being notified that they were treated with a medical device that wasn't properly disinfected, the hospital disclosed Tuesday. The risk associated with the ultrasound endoscope is low, the hospital said, but it informed those affected.

500 patients warned of possible infection from dirty endoscopes: A news release revealed that patients at VGH General Hospital who had ERCP procedures June 2008 to January 2010 received letters regarding investigation following detection of a problem with cleaning of endoscopes.

As previously mentioned, there has not been a definitive study of the incidence of infections during endoscopy since 1992. Often infections go unreported or unrecognized unless there is an outbreak involving several cases. Discovering an apparent lapse in procedure necessitating patient notification causes a great deal of stress for patients potentially exposed.

The majority of the outbreaks and pseudo-outbreaks linked to contaminated endoscopes are caused by opportunistic bacteria, not patient-borne organisms. A pseudo-infection occurs when a medical device is contaminated and specimens obtained using that device culture out a microorganism that is then attributed to the patient, even though the patient is not colonized or infected with the organism. Opportunistic bacteria such as P. aeruginosa typically originate in the environment (e.g., contaminated rinse water, sinks, water filters) - not from a colonized or infected patient.

Transmission of opportunistic bacteria by a contaminated endoscope is typically due to inadequate drying or improper storage of the endoscope, whereas transmission of a patient-borne pathogen, such as the hepatitis C virus or TB, is typically due to inadequate cleaning or ineffective high level disinfection of the endoscope.

Pop Quiz

When was the last study of infections in endoscopy done?

There has not been a definitive study of the incidence of infections during endoscopy since 1992.

What is a pseudo-infection?

A pseudo infection occurs when a medical device is contaminated and specimens obtained using that device culture out a microorganism that is attributed to the patient, even though the patient is not colonized or infected with the organism.

What is the susal source of an infection with P. aeruginosa?

An infection with P. aeruginosa usually originates from the environment.

How does the transmission of a patient borne pathogen usually occur?

This type of transmission is typically due to inadequate cleaning or ineffective high-level disinfection of the endoscope


Did you know: “Ripped from the Headlines”

1998 New York: 18 patients undergoing bronchoscopy infected

2000 New Jersey: Reprocessing machine malfunction

2001 Tennessee: outbreak

2002 Maryland: Pseudomonas aeruginosa outbreak at major medical center

2002 USA Today: Medical community debates scope cleaning procedures

2002 Good Morning America: Contamination Controversy: Are endoscopes being disinfected properly?

Factors Affecting High Level Disinfection and Sterilization Efficacy

In 1968, Dr. Earl Spaulding developed a classification system to determine what type of disinfection or sterilization process is appropriate for medical devices. These three classes: critical, semi-critical and non-critical, stratify the risk of infection associated with each device. Critical devices break the mucosal barrier and should be sterilized (e.g. reusable biopsy forceps). Semi-critical devices (e.g. endoscopes) come in contact with mucous membranes or non-intact skin and should be sterilized or receive high level disinfection. Blood pressure cuffs and stethoscopes come into contact with intact skin and fall into the non-critical category. These items can be cleaned with soap and water or disinfected with a germicide.

Endoscopes are considered semi-critical and should receive at a minimum, high level disinfection with a liquid sterilant/disinfectant approved by the FDA. Complex endoscope design features may allow organic debris and microorganisms to accumulate, making manual cleaning essential. Biofilm formation may harbor microorganisms, making strict and meticulous adherence to reprocessing guidelines imperative in order to prevent cross-contamination and hospital acquired infections.

If an object is not clean, it cannot be high level disinfected or sterilized. The bioburden on endoscopes is much greater than on surgical instruments. Colonoscopes carry a load of 6.6 logs on the scope and 9.5 logs in the scope. By comparison, surgical instruments have fewer than 3 logs per device. (Each “log” is 1000 micro organisms). Studies have shown that Mycobacteria in an inadequately cleaned bronchoscope persisted after a 60 minute soak in Glutaraldehyde and was still present after 10 sequential full disinfecting cycles.

Think sterilization is the ultimate absence of microbes? Think again. “Transmission of Serratia by an inadequately cleaned bronchoscope caused several deaths, despite ETO ‘sterilization’.” (Can J Gastroenterology May 2001).

Activity of germicides against microorganisms depends on a number of factors, some of which are intrinsic qualities of the organism. The remaining factors are the chemical and external physical environment. The larger the number of microbes, the more time a germicide needs to destroy all of them. Only surfaces that directly contact the germicide will be disinfected, so there must be no air pockets or portions of the scope that are not completely immersed.

Pop Quiz

According to Spalding, what classification is an endoscope?

An endoscope is a semi-critical device since it comes in contact with intact mucous membrane.

Why is cleaning the most important step?

If a device is not clean it cannot be high level disinfected or sterilized.

Tue or False - surgical instruments have more bioburden than colonoscopes?

False, colonoscopes have 2-3 times as much bioburden as surgical instruments.


Did you know: Solution... In a perfect world, each patient would be provided with a sterile instrument. Instrument design, cost and time constraints have made us settle for less. Emerging new organisms may pose future risks not covered in the current standards. It cannot be over-emphasized: Cleaning is the most important step!

Training and Safety

Training is an important factor in infection prevention and safety. All staff in any setting where gastrointestinal endoscopy is performed must adhere to infection control principles that will maintain a safe environment, free from the possibility of spreading disease to patients and co-workers. This is true regardless of setting, (hospital, clinic, ambulatory care center and office), relative to any and all types of endoscopy procedures performed. Flexible endoscope reprocessing has been shown to have a narrow margin of safety. Any slight deviation from recommended reprocessing protocol can lead to the survival of microorganisms and an increased risk of infection. Various organizations maintain comprehensive resources on the subject of infection prevention in the endoscopy setting. The information is available on line and is a valuable resource for training, policies and guidelines.

Infection prevention education should be an ongoing process with annual competency and updates as required. Any new instrument or reprocessing equipment change introduced should be reviewed with the entire staff. In addition to the reprocessing procedures to be discussed in this module, initial orientation should include standard precautions, personal protective equipment, mechanisms of disease transmission and safe handling of chemicals.

Personnel responsible for scope reprocessing must have the time and resources to perform their duties without interruption. Endoscopy nurses should have a thorough understanding of the steps in reprocessing to be able to precept and monitor the process. There must be a policy of invariable adherence to the reprocessing protocol.

Quality assurance standards should receive the highest priority and include; training, supervision, annual competency and procedures to report any adverse event. In 2003, a multi-society guideline was published which suggested that, as part of a quality control program, documentation of endoscope reprocessing should include but is not limited to the following:

  1. the procedure date and time
  2. the patient’s name and medical record number
  3. the endoscopist
  4. the endoscope's model and serial number or other identifier
  5. the automatedendoscope reprocessor (AER) model and serial number or other identifier (if used)
  6. the staff member(s) reprocessing the endoscope

Safety is equally important. Staff should be provided with and required to wear personal protective equipment commensurate with the task. These should include waterproof gowns, gloves, mask with eye protection and shoe covers.

There should also be a high-level disinfectant or sterilant spill containment plan specific for the high-level disinfectant or sterilant used. The information from the specific Material Safety Data Sheet should be incorporated into the plan. The plan should include written procedures for actions to contain the spill and deactivate the chemical, an intra- and inter-departmental communication plan and an evacuation plan. Upon assignment to the department and annually thereafter, all persons working in the setting must be trained in the safe handling of high-level disinfectants or sterilants and spill containment procedures.

Pop Quiz

Why is it important for supervisors and nurses to understand the reprocessing policies?

In order to maintain quality assurance and give proper supervision and training to those responsible for the reprocessing nurses and supervisors must understand the process.

Why is record keeping an important part of the quality assurance program?

Record keeping, knowing what scope was used on what patient, is important in the event of an outbreak. You may need to determine which patients may have been exposed and who did the reprocessing of that scope.


CDC: Guideline for Disinfection and Sterilization in Healthcare Facilities (

AORN: Recommended Practices for Cleaning & Processing Flexible Endoscopes and Accessories (

SGNA: Standards of Infection Control in Reprocessing of Flexible Gastrointestinal Endoscopes (

Reprocessing of contaminated patient equipment should be done in an area designated and dedicated for this function. This should be a room separate from where endoscopic procedures are performed. Considerations include adequate space for reprocessing activities, proper airflow and ventilation requirements, work flow patterns, work surfaces, lighting, adequate utilities such as electrical support and water, hand washing and eye washing facilities, air drying capability and storage.

There should be a clear delineation of clean and dirty space within the reprocessing area(s) and a failsafe mechanism to determine if a scope is clean or contaminated. One method of identification could be a tag, signed and dated, applied to each scope after reprocessing. That tag would be removed by the endoscopist at the start of each procedure. Tap water (suitable for drinking) and/or water that has been filtered by passage through a 0.2 micron filter should be available in the reprocessing area. Bottled sterile water may be used for rinsing.

Chemicals required for infection prevention in the endoscopy unit include:

  1. low-foaming, neutral pH detergent or an enzymatic detergent formulated for endoscopes
  2. Food and Drug Administration (FDA) cleared high-level disinfectant or sterilant
  3. 70% isopropyl alcohol for flushing the scope after reprocessing
  4. EPA-registered hospital-grade disinfectant for surface cleaning

Reprocessing equipment should be readily available:

  • personal protective equipment (gloves, eye protection, impervious gown, face shield or simple surgical mask that will not trap vapors)
  • leak-testing equipment
  • channel cleaning adapters (per manufacturer's instructions)
  • large basin or sink
  • endoscope detergent solution prepared according to manufacturer's instructions
  • channel cleaning brushes
  • sponge and/or lint-free cloth

Did you know: Personal protective equipment, affectionately known as PPE, should always be worn for reprocessing. It protects the health care worker from unexpected contamination from the patient and chemicals. Because these incidents are "unexpected" it is important to always protect ourselves.

The steps for properly cleaning and disinfecting an endoscope can be found in the original equipment manufacturer’s manual and these steps should be incorporated into each unit’s policy and procedure manual. The general requirements discussed here include recommendations from the guidelines and resources previously listed.

The initial reprocessing steps take place in the procedure room immediately after the removal of the scope from the patient. Appropriate personal protective equipment should be worn. This includes gown, gloves, mask and eye protection.

Procedure steps:

  • Wipe down the insertion tube with a detergent-soaked lint free cloth
  • Immerse distal tip in detergent and depress suction valve to aspirate detergent for 30 seconds
  • Remove distal tip from detergent solution and depress suction valve to aspirate air for 10 seconds; repeat till clear
  • Alternating air and suction will assist in removal of debris from channel; flush with clean water
  • Attach air/water channel cleaning adapter and set the light source airflow to HIGH
  • Immerse the distal tip in clean water; depress air/water channel cleaning adapter and feed water for 30 seconds, release the air/water channel cleaning adapterfor 10 seconds or more to let air through the channels
  • Use a syringe to flush the auxiliary water channel or ERCP elevator channel till clear
  • Turn OFF light source; attach protective video cap and transport endoscope to the reprocessing area in a covered container

Between patients, the procedure room, equipment (monitors, video processors, light sources) and all surfaces should be wiped clean and disinfected with a surface disinfectant designed for this purpose.

Pop Quiz

Why is the immediate post prcedure cleaning so important?

The immediate post procedure cleaning removes gross debris and clears the channels of large amounts of bioburden.



Leak testing detects damage to the interior or exterior of the endoscope. It is important to perform a leak test after every procedure. An undetected leak can not only cause extensive damage to the internal components of the endoscope but an undetected leak turns the endoscope into a vector of infection for every patient exposed. In order to prevent damage, leak testing must be performed before the scope is immersed in water.

Follow these steps for leak testing:

  • Remove all valves
  • Pressurize the instrument using a manual or automated pump
  • Identify that the distal tip is inflated
  • Submerge the scope in clear clean water and observe carefully for signs of a leak, gently turning control knobs to angulate tip
  • If bubbles are seen and a leak identified, keep scope pressurized for the remaining reprocessing steps to prevent damage (fluid invasion).
  • If bubbles are not seen, disconnect the leak tester from the device and allow air to escape and scope to deflate before disconnecting from the scope. If pressure is left in the scope (by disconnecting from scope first), the pressurized distal tip would be prone to a puncture or damage during reprocessing..

Manual Cleaning of endoscopes is necessary prior to automated or manual disinfection. While the bedside cleaning removes gross debris, this mechanical cleaning will assist in removing the microbial burden and prevent biofilm formation in the channels. Retained debris may inactivate or interfere with the capability of the high level disinfectant solution to effectively kill and/or inactivate microorganisms.

  • Fill a sink or basin with freshly-made solution of water low-foaming, neutral pH detergent or an enzymatic detergent formulated for endoscopes
  • Immerse the endoscope and wash all debris from the exterior of the endoscope by brushing and wiping the instrument while submerged in the detergent solution; whenever practical, leave the endoscope submerged in the detergent solution while performing all subsequent steps; note that the instrument should be left under water during the cleaning process to prevent splashing of contaminated fluid and aerosolization of bioburden
  • Use a small, soft brush to clean all removable parts, including inside and under the suction valve, air/water valve, biopsy port cover and openings; use non-abrasive and lint-free cleaning tools to prevent damage to the endoscope
  • Brush all accessible endoscope channels including the body, insertion tube and the umbilicus of the endoscope; use a brush size compatible with each channel
  • After each passage, rinse the brush in the detergent solution, removing any visible debris before retracting and reinserting it; continue brushing until there is no debris visible on the brush
  • Attach the endoscope manufacturer’s cleaning adapters for suction, biopsy, air and water channels; refer to manufacturer’s guidelines for the use of automated pumps available for this step
  • Attach the manufacturer’s cleaning adapters for special endoscope channels (e.g., elevator channel, auxiliary channel, and double-channel scopes); because the elevator channel of a duodenoscope has a very small lumen, this channel requires manual reprocessing (all steps) using a 2 to 5 milliliter syringe
  • Flush all channels with the detergent solution to remove debris
  • Soak the endoscope and its internal channels for the period of time specified by the label, if using an enzymatic detergent
  • Thoroughly rinse the endoscope and all removable parts with clean water to remove residual debris and detergent
  • Purge water from all channels using forced air
  • Dry the exterior of the endoscope with a soft, lint-free cloth to prevent dilution of the liquid chemical germicide used in subsequent steps if manually reprocessing

High level disinfectants must be tested to assure potency (Minimum Effective Concentration). This should be done in accordance with the manufacturer’s instructions, using their specific test strip. For quality assurance, a log of the test results should be maintained. The MEC may never be used to extend the reuse claim of the product beyond the date specified on activation of chemical.

Manual high level disinfection may be required for certain specialty scopes and accessories. Immerse scope with channel connectors attached and all removable parts, completely submerging endoscope in a basin with a tight fitting lid to contain chemical vapors. Using adaptors and syringe, fill all channels with high level disinfectant and soak for the prescribed time. Use a timer to verify soaking time.

Purge all channels with air and remove scope; place in clean basin and rinse thoroughly with fresh clean water for each rinse. Purge all channels with air and flush with alcohol to facilitate drying. Purge all channels with air and dry scope thoroughly before storage. Thoroughly rinse; dry accessories and valves.

Automated endoscope reprocessors provide standardization of the high level disinfection process and decrease personnel exposure to high-level disinfectants and sterilants. Even if the reprocessor has a wash cycle, it is necessary to follow all steps for the manual cleaning of the endoscope prior to using an automated reprocessor. No independent confirmatory data is currently available to show that automated reprocessors are able to provide cleaning of endoscopes that is comparable to that of manual washing and brushing.

The ideal automated endoscope reprocessor will possess these desirable features as suggested by SGNA:

  1. The machine should circulate fluids through all endoscope channels at an equal pressure without trapping air.
  2. The reprocessor should be capable of disinfecting all channels of each scope, especially the small lumen of the ERCP elevator channel. Channel flow sensors provide an added measure of compliance.
  3. Automated reprocessors must be validated to reprocess valves, tubings and accessories.
  4. The disinfectant should not be diluted with any fluids.
  5. The machine should be self-disinfecting.
  6. No residual water should remain in hoses and reservoirs.
  7. Cycles for alcohol flushing and forced air drying are desirable.
  8. The machine should feature a self-contained or external water filtration system.
  9. A method to automatically store or print data verification of cycle completion is desirable.

Place the endoscope in the reprocessor as indicated, using only the connections that are compatible with the endoscope, as the connections are scope specific. Having a diagram of each scope's connectors available for reference is helpful. Place valves in holder or soaking basin if provided, otherwise reprocess manually. Test MEC if indicated. Set the reprocessor for a complete cycle. If a cycle is interrupted for any reason, it must be repeated.

Drying is an important part of reprocessing. At end of the cycle, an alcohol flush is necessary; this may be part of the automated cycle or it may have to be done manually. The ERCP elevator wire channel must be manually flushed and dried. A scope must be dry before storage, or water-borne environmental pathogens will begin to populate the scope channels. Store the dry scope in a clean, dry, well ventilated cabinet. Record reprocessing data according to established policy. In the event of an outbreak it will be important to trace the use of a particular scope with patients.

Accessories such as water bottles and auxiliary water channel tubings, should be washed, dried and high-level disinfected or sterilized. Reusable accessories that break the mucosal barrier should be cleaned, dried and sterilized.

Pop Quiz

Why is manual cleaning necessary after the post procedure cleaning?

The manual cleaning removes additional microbial burden and with the mechanical action of brushing helps to prevent biofilm formation. Remember if a scope is not clean it cannot be high level disinfected.

Why does the ERCP elevator wire vhannel have to be processed separtely?

Most reprocessors do not have adequate pressure to flow this very narrow lumen. Pseudomonas colonized in this channel has been responsible for many infections.

Why is drying such an important part of reprocessing?

If a scope is not completely dry, waterborne bacteria will grow as biofilm in the scope channels.


Our patients are at risk for infection because of the nature and variety of autologous and environmental pathogens. We have an obligation to protect our patients by consistently adhering to guidelines and procedures related to scope reprocessing and environmental cleaning. To protect ourselves, proper personal protective equipment and frequent hand washing are essential.

Did you know: Leak testing should never be omitted in reprocessing! An undetected leak can cause extensive damage to the instrument. It can also cause the scope to become a vector of infection for subsequent patients. Yuck!



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