After ingestion of S. typhi or S. paratyphi, the salmonellae adhere to and penetrate the intestinal mucosa. They thus gain access to the mesenteric glands and the bloodstream causing a primary bacteraemia. The salmonellae are then taken up by reticulo-endothelial tissues such as the liver, spleen and bone marrow, where they multiply for 7 to 21 days.
Following this initial incubation period there follows a secondary bacteraemia where large numbers of salmonellae are released in to the bloodstream. This corresponds with the onset of symptoms.
During this symptomatic phase the kidneys are affected, as is the gall bladder, probably due to the direct spread of salmonella from the liver. Involved Peyer's patches may also later ulcerate potentially causing haemorrhage or perforation. There is also a prolonged fever which probably results from a combination of the effects of endotoxin and released pyrogens.
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