You will be having an upper endoscopy (EGD) and/or a colonoscopy. As you may have heard, The Centers for Disease Control have reported rare cases of antibiotic resistant bacterial infections that were transmitted to patients at UCLA Medical Center. Similar cases have occurred in Seattle Washington. They have been transmitted by a special instrument, called a duodenoscope, that is used for a procedure that treats conditions of the bile duct, known as an ERCP.
You should be reassured that no cases of this infection have been linked to EGD or colonoscopy. A duodenoscope is not used in either procedure. You should be reassured that the risk of an infection from endoscopy or colonoscopy is vanishingly rare, and we have never had a case of an infectious agent being transmitted to a patient from an instrument. We take great care to make certain that our instruments exceed every industry standard for cleaning and proper use.
For more information on this topic, read this recent CNN article addressing carbapenem-resistant Enterobacteriaceae (CRE).