Antimicrobial Resistance (AMR)
Introduction
Antimicrobial resistance (AMR) has become an increasingly critical concern in healthcare settings worldwide since 2019. The widespread use and misuse of antibiotics, along with a stagnation in the development of new antimicrobial agents, have contributed significantly to the rise of multidrug-resistant (MDR) organisms [1]. Furthermore, the exchange of sophisticated resistance mechanisms among pathogens has severely limited treatment options [6]. To support healthcare professionals (HCPs) in developing effective strategies for antibiotic susceptibility testing (AST) and whole-genome sequencing (WGS), Tables A and B present recent data [1][2][3] highlighting AMR trends in hospital systems, with a focus on microbial surveillance of gastrointestinal (GI) endoscopes and the care environment.
Table A: Honed-In lens on emerging AMR in GI endoscopy*
High Concern Organism | Reservoir | Relevance to S&C of endoscopes | Prevelance rates |
|---|---|---|---|
Eschericha coli | Natural colonizer of human GI tract and frequently recovered from water outlets (e.g. faucets and drains). | Can indicate lapses in manual cleaning or disinfection, or possibly device damage. | ERCP: high Upper GI (non-ERCP): medium Lower GI: low |
Klebsiella pneumoniae | Natual colonizer of human GI tract and rarely recovered from inanimate surfaces. | Can indicate lapses in manual cleaning or disinfection, or possibly device damage. | ERCP: high Upper GI (non-ERCP): medium Lower GI: low |
Pseudomonas aeruginosa | Frequently recovered from water or inanimate surfaces and fomites (e.g. drains, bed rails, sinks) and occasionally colonizes human GI tract. | Can indicate water contamination or lapses in disinfection, drying, or storage and handling. | ERCP: medium Upper GI (non-ERCP): medium Lower GI: low |
Acinetobacter baumanii | Skin, surfaces and fomites. Very common colonizer on hospital surfaces. Rarely recovered from human GI tract. | Can indicate inadequacies with storage or drying, or sample contamination. | ERCP: medium Upper GI (non-ERCP): medium Lower GI: low |
*Data as of 2022
Tabel B: Rapidly Gaining AMR in Hospital Settings
Organism | Resistance | Relevance to S&C of endoscopes | Reservoir |
|---|---|---|---|
Enterobacterales | Carbapenem-resistance and Extended-spectrum beta-lactamase (ESBL)-producing | Can indicate lapses in manual cleaning or disinfection, or possibly device damage. | Enterobacterales is a large grouping of bacteria, recoverable from water, soil, and environmental surfaces. Clinical specimens have isolated Enterobacterales from the nasopharynx, skin, mucous membranes, and GI tract. |
Acinetobacter spp. (Particularly A. baumanii) | Carbapenem-resistance | Can indicate inadequacies with storage or drying, or sample contamination. | Skin, surfaces and fomites. Very common colonizer on hospital surfaces. Rarely recovered from human GI tract. |
Candidozyma (Candida) auris | Multi-drug resistance (MDR) | Can indicate lapses in manual cleaning or disinfection, or possibly device damage. Candida spp. have also been rarely recovered from hospital water systems. | Candidozyma (Candida) auris can be recovered from water and soil. Candida is also a common commensal organism found on skin, the GI tract, and female genital tract. |
Staphylococcus aureus | Methicillin-resistance | Can indicate inadequacies with storage or drying, or sample contamination. | Skin, surfaces and fomites. Very common colonizer on hospital surfaces. Rarely recovered from human GI tract. |
Enterococcus spp. | Vancomycin-resistance | Can indicate lapses in endoscope drying, handling, and or storage. Potentially lapses in manual cleaning or possibly indicative of device damage. | Enterococci greatly colonize the GI and Biliary tracts, and to a lesser extent skin, oral cavity, groin and genetical tracts. They can also be recovered in water and soil. |
Pseudomonas aeruginosa | Multi-drug resistance (MDR) | Can indicate water contamination or lapses in disinfection, drying, or storage and handling. | Frequently recovered from water or inanimate surfaces and fomites (e.g. drains, bed rails, sinks) and occasionally colonizes human GI tract. |
The Role of Microbial Surveillance
Sampling and culturing remain the gold standard for assessing the microbial profile of flexible endoscopes. Pure isolates obtained from cultured samples can be analyzed for AST and WGS, enabling precise identification of resistance patterns. Infection preventionists can use Table A to evaluate which types of GI procedures and associated endoscopes are at higher risk for AMR contamination or transmission. This information supports targeted epidemiological investigations and informed antibiotic stewardship decisions.
Environmental Reservoirs and Biofilm Formation
Pathogenic microorganisms recovered from clinical specimens are often traced back to environmental sources such as water, surfaces, and soils. Medical devices, including endoscopes, can serve as vectors for transmission. The ability of bacteria, such as Pseudomonas or Acinetobacter, to produce biofilms enhances their survival in harsh conditions, including exposure to detergents, disinfectants, desiccation, and extreme temperatures. Biofilms protect microbes, allowing them to survive, exchange genetic material, and spread. Identifying the origin of bacteria is crucial for guiding decontamination efforts and understanding potential lapses in reprocessing practices. Table B summarizes common resistance mechanisms and reservoirs based on the CDC’s 2022 Antimicrobial Threats Report [4][5]. Infection preventionists can leverage this information to refine cleaning and disinfection protocols in endoscopy units and enhance audits in reprocessing spaces.
Sources and further readings
Antimicrobial Resistance Collaborators. “Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis.” Lancet (London, England) vol. 399,10325 (2022): 629-655. doi:10.1016/S0140-6736(21)02724-0.
Deb, Anasua et al. “Gastrointestinal Endoscopy-Associated Infections: Update on an Emerging Issue.” Digestive diseases and sciences vol. 67,5 (2022): 1718-1732. doi:10.1007/s10620-022-07441-8.
Balan, Gheorghe G et al. “Duodenoscope-associated infections: a review.” European journal of clinical microbiology & infectious diseases: official publication of the European Society of Clinical Microbiology vol. 38,12 (2019): 2205-2213. doi:10.1007/s10096-019-03671-3.
CDC. “Antimicrobial Resistance Threats in the United States, 2021-2022.” Antimicrobial Resistance, 16 July 2024, www.cdc.gov/antimicrobial-resistance/data-research/threats/update-2022.html. Accessed January 2026.
CDC. “Antimicrobial Resistance Facts and Stats.” Antimicrobial Resistance, 22 Apr. 2024, www.cdc.gov/antimicrobial-resistance/data-research/facts-stats/index.html. Accessed Jauary 2026.
Peri AM et al. Antimicrobial treatment challenges in the era of carbapenem resistance. Diagnostic Microbiology and Infectious Disease vol 94, 4 (2019): 413-425. https://doi.org/10.1016/j.diagmicrobio.2019.01.020. Accessed January 2026.