Risks associated with improper cleaning of flexible endoscopes

A single inadequately cleaned channel within a flexible endoscope can harbor millions of bacteria, representing a significant risk for the transmission of infection to multiple patients.

Flexible endoscopes are indispensable tools in modern medicine, enabling direct visualization of internal body structures. These devices play a crucial role in early diagnosis, targeted therapies, and life-saving interventions on a daily basis. However, while they facilitate healing, they can also pose a serious risk of infection if not properly cleaned and disinfected. Risks associated with improper cleaning of flexible endoscopes include microbial contamination, biofilm formation, and transmission of infections to patients.

Doctors examine the contamination risks associated with improper cleaning of flexible endoscopes under a microscope.

Challenges of cleaning flexible endoscopes

Flexible endoscopes are highly complex instruments, featuring long, flexible channels, valves, and intricate internal components that are difficult to access. These internal cavities and bends provide ideal hiding places for microorganisms. Even a single missed step or improperly performed cleaning procedure can leave residual contamination and sustain the risk of infection, a problem that can occur even in well-equipped healthcare facilities.

To understand why cleaning these devices is so important, it helps to know their infection risk classification. Medical devices are categorized by the Spaulding system based on how likely they are to cause infections. Most flexible endoscopes are considered “semi-critical,” as they contact mucous membranes and require thorough cleaning and high-level disinfection. Some therapeutic endoscopes and their accessories are classified as “critical” because they enter sterile body areas and must be sterilized after each use. This classification means that flexible endoscopes require strict, careful cleaning and disinfection processes, making their reprocessing especially challenging (1 2).

Consequences of inadequate reprocessing

Cross-Contamination

Hospital ward showing multiple patient rooms, highlighting risks of cross-contamination from improperly cleaned flexible endoscopes.

During use, endoscopes come into direct contact with a patient’s mucous membranes and body orifices such as the mouth, rectum, or urethra. These areas naturally harbor a wide range of microorganisms, including bacteria, viruses, fungi, and other potential pathogens. If the instrument is not properly decontaminated, these microorganisms may remain on its surfaces or within internal channels, potentially being transmitted to the next patient.

This process is known as cross-contamination, one of the most serious risks associated with diagnostic and surgical endoscopic procedures. A single

inadequately reprocessed endoscope can transmit infections to multiple patients, including infections caused by antibiotic-resistant bacteria.

Biofilm Formation

Another, less visible but equally dangerous source of infection is the formation of biofilm. Biofilm is a thin, mucus-like layer produced by microorganisms that adheres to the internal surfaces of endoscopes. This layer protects microbes from disinfectants, meaning that viable pathogens can persist even after thorough cleaning. In the presence of biofilm, the effectiveness of disinfection is significantly reduced, leading to the potential development of an infection chain: microorganisms may survive within the device for extended periods and infect multiple patients (3).

Microscopic images of biofilm growth in the water channel, air/water junction, and air channel of a flexible gastroscope.

Additional Risks of Improper Cleaning

Beyond biofilm formation and cross-contamination, additional hidden risks must also be considered. Below are three additional, often overlooked risk factors associated with inadequate endoscope reprocessing:

1. Irritation and Allergic Reactions: If the cleaning or rinsing process is incomplete, residual detergents, enzymes, or organic debris may remain on the instrument. These residues can cause mucosal irritation, a burning sensation, or even allergic reactions in patients.

   
   

2. Diagnostic Errors and Technical Malfunctions: Improper cleaning may result in foggy or contaminated lenses, or in clogged channels within the endoscope. This can compromise image quality or hinder procedures such as biopsies, potentially leading to misdiagnosis or incomplete examinations.

   
   

3. Hidden Infection Transmission: Some pathogens, such as Hepatitis B or human papillomavirus (HPV), can remain asymptomatic for long periods. Neither the patient nor the physician may be aware that the infection originated from an improperly cleaned endoscope, allowing the issue to go unnoticed and unaddressed. In fact, infections related to endoscopic procedures often remain hidden due to inadequate surveillance, low incidence rates, or the absence of clinical symptoms. This is particularly concerning because even if a patient shows no symptoms, they can still carry and transmit the infection to others, or develop health problems later without knowing the source of the contamination. (3)

The Solution: Standardized, evidence-based decontamination

Proper endoscope decontamination is not optional but a fundamental element of patient safety. Cleaning, disinfection, and drying must be performed meticulously after every use, in line with the latest guidelines and supported by modern technological solutions.

Automated endoscope reprocessing systems are playing an increasingly important role. They are more efficient and faster than manual methods, enabling significant time savings. These systems offer a cost-effective solution by reducing the need for disposable items and supporting more sustainable operations. Their ease of use minimizes the risk of human error and ensures consistent, reproducible cleaning outcomes. Furthermore, they reduce the physical and mental burden on staff, improving workplace ergonomics and increasing staff efficiency. As such, these systems are key to advancing modern endoscope decontamination practices.

The Khamsin automatic flexible endoscope cleaning and reprocessing machine, designed for efficient and thorough decontamination of flexible endoscopes. Click here and learn more.

A Shared Responsibility

Preventing infection is a collective responsibility. Collaboration between manufacturers, healthcare professionals, infection prevention experts, and hospital leadership is essential to ensure that endoscope reprocessing is truly safe and effective. The objective is not merely regulatory compliance, but the assurance of patient safety.

1/4 Kovaleva, J., Peters, F.T.M., van der Mei, H.C. and Degener, J.E. (2013). Transmission of Infection by Flexible Gastrointestinal Endoscopy and Bronchoscopy. Clinical Microbiology Reviews, 26(2), pp.231–254. doi:https://doi.org/10.1128/cmr.00085-12.

3 Pajkos, A., Vickery, K. and Cossart, Y. (2004). Is biofilm accumulation on endoscope tubing a contributor to the failure of cleaning and decontamination? Journal of Hospital Infection, 58(3), pp.224–229. doi:https://doi.org/10.1016/j.jhin.2004.06.023.

2 Nih.gov. (2025). Preparing to download ... [online] Available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC7962740/pdf/nihms-1672672.pdf [Accessed 16 May 2025].