The Distinction Between Antibiotic Resistance and Disinfectant Resistance in Endoscopy Procedures Involving the GI Tract

Published on:

June 4, 2025

Last updated on:

October 15, 2025

• Scientific Summary

Endoscopic procedures, especially those involving the gastrointestinal (GI) tract, are essential for diagnosing and managing a wide range of diseases. These procedures typically involve reusable medical devices and so require thorough infection prevention protocols to minimize the potential risk of microbial cross-contamination. A challenge in maintaining device hygiene and patient safety is addressing both antibiotic resistance and disinfectant resistance among microorganisms, as these are often mistakenly assumed to be the same when, in reality, each involves distinct mechanisms that allow pathogens to persist despite control efforts.

Antibiotic resistance occurs when bacteria acquire or develop mechanisms that allow them to withstand exposure to certain antibiotics, which can render standard patient treatments less effective. This resistance can arise through genetic mutations or horizontal gene transfer, allowing rapid adaptation among bacterial populations. Key mechanisms include the production of enzymes that deactivate antibiotics, modifications to bacterial target sites, and the use of efflux pumps, which are cellular transport proteins that remove toxic substances, including antibiotics, from bacterial cells. These adaptations present a growing clinical concern, particularly in healthcare settings where patients are more vulnerable to infection.

The rise of antibiotic resistance has emerged as a significant global health concern in the 21^[st] century. Over the past few decades, the overuse and misuse of antibiotics have accelerated the development of resistant bacterial strains. Antibiotics are often used in cases where they may not be necessary, such as for viral infections or as prophylaxis, and the misuse of antibiotics in agriculture and animal husbandry also contributes to the spread of resistance. Antibiotic resistance is a natural process, but human activities have contributed to the emergence of multidrug-resistant organisms (MDROs), making once-treatable infections more difficult to manage. For example, bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile are increasingly resistant to multiple antibiotics, limiting treatment options and leading to higher morbidity and mortality rates ^[10].

In contrast, disinfectant resistance refers to the ability of microorganisms to survive exposure to chemical disinfectants. While healthcare disinfectants are designed to destroy a wide range of pathogens through the disruption of cell membranes and proteins, some microorganisms develop resistance through the formation of biofilms, activation of efflux pumps, or the expression of enzymes that neutralize disinfectants.

Biofilms are a key player in disinfectant resistance during medical device reprocessing. Biofilms are structured communities of bacteria encased in a protective matrix that can adhere to the surfaces of medical devices, highlighting the importance of adhering to validated reprocessing protocols to ensure their effective removal. Biofilms on medical devices, such as endoscopes, can serve as reservoirs for microorganisms and potentially protect them from disinfectants. Notably, pathogens like Pseudomonas aeruginosa can form biofilms within 24 hours of colonizing an endoscope, potentially reducing the efficacy of high-level disinfection.

Biofilms are composed of bacteria embedded in an extracellular matrix of polysaccharides, proteins, and DNA, which creates a physical barrier against antimicrobial agents. This structure allows bacteria to better survive in hostile environments and makes them more difficult to eliminate during cleaning and disinfection procedures ^[6]. While biofilm-associated bacteria can present challenges, with appropriate cleaning protocols and validated reprocessing techniques, it is possible to effectively prevent biofilm-related contamination and reduce the risk of infection in healthcare settings.

Antibiotic and Disinfectant Resistance Mechanisms

Bacteria can adapt to antibiotics through genetic mutations or by acquiring resistance genes from other bacteria. Horizontal gene transfer is a key process in this adaptation, enabling bacteria to acquire antibiotic-resistant genes from their environment or other bacterial cells. Plasmids, transposons, and integrons are genetic elements that facilitate the spread of resistance, making it easier for resistance traits to propagate rapidly within bacterial populations. This helps contribute to the accelerated emergence of antibiotic resistance, particularly in healthcare settings where antibiotics are used extensively ^[8].

Similarly, bacteria can develop several mechanisms to resist disinfectants, which are distinct yet similar in function to those used to resist antibiotics. One mechanism involves the activation of efflux pumps, which expel disinfectants from the bacterial cell, reducing their effectiveness. Additionally, bacteria can produce enzymes that degrade or neutralize disinfectants or modify target sites to reduce the efficacy of these chemicals. And as mentioned earlier, biofilm formation is another critical factor in disinfectant resistance as the biofilm matrix can prevent disinfectants from reaching the bacterial cells, further complicating disinfection efforts ^[9].

Infection Prevention

Infection prevention in healthcare settings requires a multifaceted approach, especially as antibiotic and disinfectant resistance continue to grow. This includes implementing thorough reprocessing protocols and routine surveillance to ensure adherence. Given the increasing prevalence of antibiotic resistance and emerging concerns about disinfectant resistance, ongoing staff training and education are pivotal in maintaining patient safety. Healthcare workers must be equipped with up-to-date knowledge of the latest industry best practices and reprocessing technologies. Proper training on reprocessing protocols is important to help ensure staff can implement best practices effectively. Education around antibiotic and disinfectant resistance, as well as how biofilm formation can impede reprocessing efforts, is key for healthcare professionals responsible for endoscopes. Regularly updating training programs and offering refresher courses can support strict adherence to infection prevention protocols and help staff remain vigilant in their efforts to reduce contamination risks ^[5].

Antibiotic-Resistant Bacteria in GI Endoscopy

In the context of GI endoscopy, the potential for antibiotic-resistant bacteria to remain on inadequately reprocessed endoscopes highlights the importance of validated cleaning protocols to support patient safety. Resistant pathogens, such as Klebsiella pneumoniae and Escherichia coli, some strains of which are naturally present in the gastrointestinal tract, have been associated with outbreaks following endoscopic procedures. These pathogens can exhibit resistance to multiple antibiotic classes, limiting available treatment options. Studies emphasize that maintaining stringent reprocessing standards is essential to minimize the risk of MDRO exposure in healthcare settings ^[1].

Antibiotic-resistant strains of pathogens such as Klebsiella pneumoniae and Pseudomonas aeruginosa are relatively common in healthcare settings, with several mechanisms possibly enabling their survival on endoscopes, including the formation of biofilms. The following table outlines some of the most significant mechanisms of resistance among pathogens encountered in GI endoscopy procedures:

Table 1: Mechanisms of Antibiotic Resistance in GI Endoscopy-Related Pathogens ^[7]

Challenges of Antibiotic and Disinfectant Resistance in Endoscopy

The presence of antibiotic and disinfectant resistant microorganisms in healthcare settings can present challenges for patient safety in endoscopic procedures. Past outbreaks of Carbapenem-resistant Enterobacteriaceae (CRE) linked to contaminated duodenoscopes have contributed to heightened awareness of infection risks, and data from the Centers for Disease Control and Prevention (CDC) suggest that MDROs are a factor in a significant portion of healthcare-associated infections ^[2].

Similarly, the presence of biofilms on medical devices and the associated disinfectant resistance can complicate patient safety efforts. Biofilms have the ability to not only protect microorganisms from high-level disinfection but could also serve as reservoirs for resistant pathogens. Research has demonstrated that challenges in fully eliminating biofilms during reprocessing may be a factor in transmission of resistant organisms in endoscopy units^[3].This highlights the need for end-users to ensure staff adhere to manufacturer’s validated reprocessing instructions for every device, every time.

Conclusion

Antibiotic resistance and disinfectant resistance are important considerations in the effective reprocessing of reusable medical devices, including endoscopes used in gastrointestinal procedures. While these two forms of resistance involve distinct mechanisms, both have the potential to significantly impact infection control efforts. Antibiotic-resistant pathogens can lead to difficult-to-treat infections, while biofilms can protect bacteria from disinfectants, allowing them to persist on device surfaces. To mitigate these risks, healthcare providers must implement thorough cleaning and disinfection protocols, invest in ongoing staff training, and continuously monitor device reprocessing. As antibiotic and disinfectant resistance continue to evolve, the healthcare community must remain attentive to protect patients from risks associated with resistant microorganisms.