Determination of bacterial species present in biofilm contaminating the channels of clinical endoscopes

Background: Outbreaks of endoscopy-related Carbapenem-resistant Enterobacteriaceae has highlighted failures in endoscope decontamination resulting in biofilm formation. Biofilms are tolerant to detergents and disinfectants. We evaluated decontaminated endoscope channels for residual bacterial contamination and biofilm presence. Methods: 64 channels were collected from 12 gastroscopes and 11 colonoscopes. Aerobic bacteria were isolated from inside the endoscope tubing by scrapping, sonication, and aerobic plate culture. Total number of contaminating bacteria was determined by quantitative real-time PCR with 16s rRNA eubacterial universal primers. Microbial diversity was assessed using next generation DNA sequencing. Biofilm presence was visually confirmed by confocal laser scanning and scanning electron microscopy. Results: 47% of channels were culture positive, with α-haemolytic Streptococci from gastroscopes and coliforms from colonoscopes the most frequently isolated species. Sphingomonas spp., Staphylococcus spp., Streptococcus spp., and Pseudomonas aeruginosa were also isolated. An average of 1.2 × 10³ bacteria/cm contaminated air-water channels, 2.8 × 10² and 6.6 × 10² bacteria/cm contaminated gastroscope and colonoscope working channels, respectively. Biofilm was on all 39 channels examined and was principally composed of environmental bacteria, although all samples contained potential pathogens. Conclusion: Biofilm is present on many endoscope channels obtained from Australian hospitals. Any soil including biofilm can compromise disinfectant action.