Different forms of chlamydia express different types of proteins, to form a chlamydia inclusion that provides protection from the immune system. Chlamydia pathogens may also express different types of abnormal proteins, during different phases of the life cycle. Other types of immortal pathogens are also capable of expressing abnormal proteins to create a membrane to encapsulate the pathogen, and protect the pathogen from the immune system. By definition, proteins expressed or generated by pathogens are abnormal proteins.

Chlamydia pathogens inside the inclusions continue to express abnormal proteins, creating clumps of abnormal proteins. As the pathogen spreads or dies, the abnormal proteins can be dispersed to aberrant locations in the body; generate an immune response and inflammation; and can attach to genes to create genetic abnormalities and abnormalities in gene expression.