There are three main ways that an invading pathogen can result in disease:

Damage or destroy host cells

This is host specific and ligands on the pathogen must fit host receptor proteins on the host cell. This is commonly seen in viral infections as the virus takes over cells to be able to function. An example of this is seen in HIV infection. HIV invades and destroys a type of T cell (white blood cell), resulting in an immunocompromised patient (low immune system).

Produce toxins

Some bacteria/viruses produce toxins, which result in damage to the host.

An example of this is Vibrio cholerae which release harmful exotoxins that destroys chloride and hydrogencarbonate ions.

Overt immune response

Sometimes the body produces an inflammatory response, which results in damage to cells. During infection with Mycobacterium turberculosis , the body tries to destroy the bacteria with a proinflammatory response this causes damage to cells in the lungs leaving cavities in the lung and sometimes blood vessels.

Some bacteria may cause disease using all 3 methods, the ability for a bacteria/virus to do this relies on its location, specificity and pathogenicity.

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