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Wild rodents, including rats, can carry many different zoonotic pathogens, such as Leptospira, Toxoplasma gondii, and Campylobacter.

The Black Death is traditionally believed to have been caused by the micro-organism Yersinia pestis, carried by the tropical rat flea ( Xenopsylla cheopis ) which preyed on black rats living in European cities during the epidemic outbreaks of the Middle Ages ; these rats were used as transport hosts.

Other zoonotic diseases linked to pest rodents include classical swine fever and foot-and-mouth disease.