Identifying pathogens is a simple matter. Anything that causes an excess or deficiency of Qi or makes the flow other than smooth and unhindered is a pathogen - cause of disease. There are two types, internal and external. The external pathogens are the climatic or environmental Qi.
Internal pathogens are Qi that originates within us but is not flowing harmoniously for a variety of reasons. Very commonly emotional Qi will disrupt the flow of Qi. Worry and Anger are too important culprits of this type. Foods are classified according to the same properties as herbs. They have temperature, taste and direction and these shoud be in harmony with the overall flow of Qi in a person. Sleeping habits can cause Qi to flow poorly or be insufficient. You may recall from the pages on Yin & Yang that you cannot remin in a Yin or a Yang state indefinitely. Sleep is a Yin state that we must spend sufficient time in.
Finally, an identified pathology can cause other pathologies. Liver Qi Stagnation frequently affects other organs and body processes until more pathology - illness arises. It is physically close to the Stomach and the Heart. If the Liver's Qi stagnates and thus casuses Heat or Fire, the Stomach or Heart's functions can be affected by the Heat or start their own Fires.