pathogen: the causative agent of a communicable disease. For example, influenza (disease) is caused by influenza virus (pathogen); malaria (disease) is caused by species of Plasmodium (pathogen). It is a common mistake to use the term for the disease when you actually mean the pathogen, and vice versa:

He contracted measles     not     He contracted measles virus
The sample was tested for measles virus     not     The sample was tested for measles

pathology: the study of diseases; do not use to mean disease

Influenza is a disease     not     Influenza is a pathology