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Chapter 2 : Population Geneticists Discover Bacteria and Their Genetic/Molecular Epidemiology
In this chapter, the author considers the origins and early history of the enterprise: population genetics, genetic epidemiology, evolutionary genetics, molecular epidemiology, molecular evolution, molecular phylogeny, or molecular forensics, to which Tom Whittam made his awesome contributions. Tom was one of the first to apply population genetics procedures and theory to the genetic epidemiology of bacteria from clinical and other natural sources. From a population genetics perspective, the result of our E. coli enzyme variation study and its interpretation had sufficient “man bites dog” appeal to appear in Science. On the other hand, neither the considerable variability nor the clonal population genetic structure would have been surprising to microbiologists studying the epidemiology of bacteria from clinical and natural sources. Similar observations were made for a number of different species of bacteria with serological as well as other phenotypic markers, like phage resistance patterns (phage typing), repertoires of fermentation capabilities (biotyping), and the distribution of plasmids carried (plasmid typing). By the early 1980s investigators studying the genetic epidemiology of bacteria were also beginning to use various kinds of restriction endonuclease cutting procedures for these epidemiological studies. The author believes that the single most important consequence of early- 1980s studies of genetic variation in E. coli was not direct genetic evidence for the clonal structure of E. coli, which the enzyme data provided, but rather the introduction of population genetics theory and approaches to the genetic epidemiology of bacteria.