A system for providing medical device with anti-microbial properties to prevent infections. The system includes a medical device having a portion for insertion into the body of a patient, a lumen, and a substrate comprising an anti-microbial agent to be inserted into the lumen of the medical device. To protect the substrate from anti-microbial agents during insertion into the lumen, the system further includes a collapsible cover connected to the substrate. A connector can be used for attaching the substrate to the cover. The substrate may be an iodine-based rod. A guidewire may be attached to the connector to further facilitate insertion of the substrate into the lumen.