Pathogens contain genes not found in their closely related counter parts
Genes specific to the pathogens are organized into islands, islet, atolls. That is, specific regions that are unique to the pathogens.
Pathogenicity islands encode those functions needed for the pathogen to causes a successful infection. It still needs the rest of the chromosome!
Pathogenicity islands have different G+C content than the backbone chromosome. Islands tend to be A+T rich, especially in Salmonella and E.coli.
PA’s can encode a specialized secretion apparatus designed to transfer effector proteins into the host. The proteins are specifically designed to alter host cell function. The proteins usually interact with a specific host protein or class of proteins.
Some but not all PA’s have inserted in a rare tRNA seltRNA. This insertion event does not interrupt the tRNA, but provides a powerful selection for the PA’s presence.