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Several outbreaks of foodborne and waterborne illness have directed the nation's attention to intestinal pathogens that are threats to public health. Among these pathogens are Cryptosporidium parvum and Escherichia coli O157:H7, which are known to infect and to be spread by not only humans, but also livestock and various species of wildlife. New regulations aimed at controlling these pathogens are being implemented, despite a shortage of scientific information about their ecology, how they contaminate food and water supplies, and how to detect and eliminate such contamination. Research is needed to address these issues and to develop better technologies for pathogen detection, water treatment and food processing.