A pathogen is an organism that causes disease.
Pathogens include micro organisms (some bacteria, some fungi and all viruses) and some larger organisms (such as tapeworms).
Pathogens need to enter the body to cause disease. They get in through an organism's surface of contact (interface) with the environment.
The gas-exchange system:
Most pathogens breathed in will be trapped by the mucus lining the lung epithelium.
These cells also have cilia that beat and move the mucus up the trachea to the mouth where it's removed.
Some pathogens are able to reach the alveoli where they can invade cells and cause damage.