Yes and No. The immune system fights everything that does not belong to the body and has potential to harm it. This includes bacteria and virus from the surrounding environment, as well as the body's own cells (which are altered in cases of cancer but unchanged in autoimmune diseases). The potential of the immune system to protect the body is limited, so when a cancerous overgrowth exists in the body, the immune system fights against the cancer cells in order to destroy them. It's possible then that the bacteria and/or virus might invade the body. These conditions are visible in patients who developed cancer after prolonged or severe illnesses.