The primary site targeted by Johne's disease is the lower part of the intestine known as the
ileum. The wall of the ileum contains a large number of pockets of lymphoid tissue known as
Peyer's patches that lie just beneath the interior surface of the intestine. Peyer's patches are clusters of
macrophages and
lymphocytes organized much like
lymph nodes. Covering Peyer's patches are a layer of cells called
M cells. These cells function to sample the content of the lumen of the intestines and pass antigens (bacteria) through to the underlying cells of the Peyer's patch to "show" these antigens to the macrophages and lymphocytes. This is a means of "educating" the cells in a young animal about its environment, and is a protective mechanism designed to help the animal become immune to pathogens in its environment. Unfortunately, when M cells bring
M. paratuberculosis to the Peyer's patch, the bacteria find an ideal place for growth. Macrophages in Peyer's patches engulf
M. paratuberculosis for the purpose of destroying the foreign invader, but for reasons yet unclear, these macrophages fail to do this. Inside a macrophage,
M. paratuberculosis multiplies until it eventually kills the cell, spreads, and infects other nearby cells. In time, other parts of the ileum and other regions of the body are teeming with millions of the mycobacteria. How
M. paratuberculosis neutralizes or evades the normally efficient bacterial killing mechanisms of the macrophages is unknown, although the unusually resistant cell wall of mycobacteria likely plays an important role. The animal's immune system reacts to the
M. paratuberculosis invasion by recruiting more macrophages and lymphocytes to the site of the infection. The lymphocytes release a variety of chemicals signals, called
cytokines, in an attempt to increase the bacterial killing power of the macrophages. Macrophages fuse together, forming large cells, called multinucleated giant cells, in an apparent attempt to kill the mycobacteria. Infiltration of infected tissues with millions of lymphocytes and macrophages leads to visible thickening of the intestines. This prevents nutrient absorption, and diarrhea results. Late in the infection, antibody production by the animal occurs to
M. paratuberculosis in serum of animals, and is an indicator that clinical signs of disease and death from the infection will soon follow. For goats infected with this disease, the most apparent sign of having it is their bodies wasting away, even with a sufficient diet. If a goat develops Johne's and it has diarrhea, it is most likely going to die. When it has diarrhea, the goat is at the last stages of the disease. Herds should be tested once or twice a year to maintain the health and keep out the disease. ==Morbidity and mortality==