Antibody-antigen complex. The third and final line of defence is the immune response. The invading microbe or pathogen is called an antigen. It is regarded as a threat by the immune system and is capable of stimulating an immune response. Antigens are proteins that are found on the surface of the pathogen.Antigens are unique to that pathogen.The whooping cough bacterium, for example, will have different antigens on its surface from the TB bacterium. When an antigen enters the body, the immune system produces antibodies against it.t is regarded as a threat by the immune system and is capable of stimulating an immune response. Antigens are proteins that are found on the surface of the pathogen. Antigens are unique to that pathogen. The whooping cough bacterium, for example, will have different antigens on its surface from the TB bacterium.