Disease pathology is due to embolized eggs that induce inflammatory reactions in various body organs, from which arise the classic symptoms of chronic schistosomiasis. This pathology is, however, very variable and is generally related to the intensity of infection. There are also pathological differences among the various species and among strains of the same species.

In S. haematobium lesions occur in the bladder and ureter around the entrapped and calcifying eggs, with the eventual laying down of fibrous connective tissue. The symptoms include blood in the urine (hematuria), painful and excessive urination (dysuria), and various symptoms associated with obstructions of passages, such as distension of the ureters (hydroureter) and distension and atrophy of the kidneys through blockage of the urethras (hydronephrosis). In the intestinal schistosomes, the lesions occur in the gut wall and liver, leading to the deposition of fibrous connective tissue. The venous obstruction produced by these lesions results in a compensatory increased arterial flow that leads to portal hypertension and the classic enlargement of the liver and spleen (hepatosplenomegaly). Eggs of all three species may also become trapped in the lungs, and with S. japonicum, nervous disorders or "cerebral schistosomiasis" can also occur if egg aggregates come to rest in the brain.

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