A scientific paper presented at the Association for Professionals in Infection Control in June of 2013 analyzed 275 duodenoscopes, gastroscopes, and colonoscopes and found 15% were contaminated by "bio-dirt." The percentages with bio-dirt were 30% for duodenoscopes, 24% for gastroscopes, and 3% for colonoscopes. There are 17 million endoscopies in the US annually so it means that 500,000 colonoscopies have bio-dirt and put patients at risk for HIV, hepatitis B and C, C. diff, and MRSA. The risk for transmission would be increased as immunity of the gut lessens, such as with ulcertive colitis, Crohn's disease, diverticulitis, etc.
There are now new approaches to identifying this bio-dirt with laser spectroscopy, but this is not yet in the mainstream. Here is another factor that is rarely discussed when assessing the risks of colonoscopies and other endoscopic procedures.