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This chapter identifies epidemiologic and ecologic factors within the animal reservoir that are insufficiently understood but which may offer potential for control of Escherichia coli O157:H7. O157:H7 has been isolated from a diverse set of animal host species, in which it generally is not associated with any clinical abnormalities. The chapter describes the role of the reservoir in the epidemiology of zoonotic O157:H7 infections, and discusses evolution of O157:H7 and the animal reservoir. Considerable emphasis has been placed on characterizing O157:H7 colonization of domestic ruminants, particularly cattle and sheep, compared to other host species due to their prominence as sources of human infection. This work has included prevalence; descriptive epidemiology of O157:H7 shedding; identifying farm management factors associated with high prevalence of animal infection; and investigating the effects of vaccines, probiotics, and other interventions. Seasonal variation of O157:H7 fecal shedding by cattle has been reported in geographically diverse regions. There is little evidence that O157:H7 is a ‘‘professional pathogen’’; rather, it is a well-adapted commensal of numerous animal hosts. It has considerable strain diversity within cattle, and only a subset of strains is strongly associated with human disease. As the agent first came to human attention due to the severity of disease, it is natural that research attention has been primarily focused on pathogenesis.

Tom Whittam's pioneering research into the structure of Escherichia coli populations not only advanced the field of microbial evolution and genetics, but it also provided a contextual framework for investigating variation in the epidemiology and virulence of bacterial populations. This chapter highlights the work of his laboratory involving the use of various population genetic strategies for characterizing E. coli pathotypes, particularly enterohemorrhagic E. coli (EHEC) O157:H7, while focusing on contributions to epidemiology and public health. To determine whether specific genotypes are associated with human enteric disease, multilocus enzyme electrophoresis (MLEE) was used to examine 1,300 E. coli strains representing 16 serotypes, including EHEC O157:H7 from patients with hemorrhagic colitis and hemolytic uremic syndrome (HUS). Similar to MLEE and multilocus sequence typing (MLST) data, systematic analysis of single nucleotide polymorphisms (SNPs) is amenable to both population genetic and phylogenetic analyses. SNPs data can also be used to examine epidemiological associations between bacterial genotypes and clinical disease. By using the SNP genotyping phylogeny as a framework, it is possible to investigate virulence gene diversity, allelic variation, and gene expression differences among genotypes to identify bacterial genomic determinants of colonization, pathogenesis, and transmissibility. The chapter describes differences in stress resistance properties among clades, nonrandom distribution of stx variants, variation in adherence to epithelial cells, and differential expression among shared genes.

This chapter presents an overview of the habitats where Escherichia coli can be isolated. It reviews some of the data that characterize the boundaries of its broad ecological niche. The genus Escherichia is not as genetically diverse as once thought and contains only three named species: E. albertii, E. fergusonii, and E. coli. The frequency of gene flow among the phylogenetic lineages and the phylogenetic scale at which it is occurring suggest that boundaries to gene flow among Escherichia species are minimal and also that clades may not occupy entirely different ecological niches. The chapter discusses the niche of E. coli . A human host typically harbors two or three genotypes, and together these genotypes represent the majority of the E. coli cells to be found in a sample. First, nine or more genotypes may be detected in a sample at a single point in time. Second, selective plating reveals the presence of genotypes that exist at very low frequencies. Finally, the number of samples that contain rare genotypes also indicates that there may be a rather large pool of genotypes. The high densities of E. coli in sand led many to speculate that, as in the tropics and subtropics, E. coli is an environmental organism even in some of the coldest temperate regions. E. coli is widespread among warm-blooded animals and humans, and the dynamics of its colonization of the gastrointestinal (GI) tract is dependent on a number of host and microbial determinants.