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This chapter focuses on the application of molecular subtyping methods for identifying and tracing sources of microbial pathogens in food and food-borne human diseases. It should be noted, however, that in addition to the food-borne pathogens, harmless or nonpathogenic microorganisms can also contaminate the food supply and contribute to spoilage. These microbes are generally part of the natural microbiota of raw foods and food products, which serves as an ideal growth medium for many organisms with nearly neutral pH, high water activity, and richness in nutrients. If left unchecked, growth of these harmless microorganisms on foods results in off odors and flavors and, ultimately, in an inedible food product. Many of the methods developed to inhibit the growth of nonpathogenic microbes in foods also restrict the growth of food-borne pathogens. The major advantage of pulsed-field gel electrophoresis (PFGE) profiling is that the technique can be widely applied to different bacterial species and is relatively simple and straightforward to perform in the laboratory. Outbreak investigation and epidemiological tracing have been the primary incentives encouraging the development of the PulseNet and FoodNet national systems for food-borne disease surveillance. In the future, the authors expect to see the application of new molecular genotyping systems with rapid throughput, such as those based on single-nucleotide polymorphisms, to generate high-quality genotypic data for microbial source tracking.

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.