Yersinia pestis was once called Pasturella pestis, a name that has persisted because it was used in much of the older, widely consulted, historical literature about European plagues. In 1971, the name was changed in part to honor Alexandre Yersin, a French microbiologist and student of Louis Pasteur, who, working in Southeast Asia during the late nineteenth century outbreak of plague, successfully cultured the microorganism.

Other members of the Pasturella family are rarely pathogenic in humans and do not provide cross-immunization with Y. pestis. Two organisms, however, have been added to the Yersinia group: Yersinia pseudotuberculosis, which causes a mild respiratory infection, and Yersinia enterocolitica, which causes a gastroenteritis that can be life-threatening in very young children. Infection with either of the other Yersinia species establishes some cross-immunity with Y. pestis, because they have shared antigens.

The antigens, or components of the organism, which stimulate an immune response, can vary in virulence, such that vaccines can be created that are very mild plague strains. Y. pestis causes severe human disease when it contains an envelope protein facilitating its entry into cells and other antigens that impede the body's white blood cells' attempt to kill infected cells. Y. pestis can liberate both endotoxins and exotoxins, leading to circulatory collapse. These combined activities stimulate, and can defeat, both cellular and humoral immunity to plague, and explain why the disease can carry extremely high-case fatality rates. With a typical virulent strain of the bacterium, over 60 percent of all infected humans untreated will die within 10 days of infection. If the organism reaches the lungs, there is even less chance the person will survive. A victim whose lungs become infected during the course of bubonic plague can cough out highly virulent, encapsulated organisms, which are rapidly absorbed on the mucous membranes of any nearby, susceptible person. This can lead to "primary" pneumonic plague in which the bubonic plague of disease is bypassed and spreads directly from human to human. When this has occurred, case fatality rates have been close to 100 percent.

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