The population genetics of Escherichia coli.

E. coli is a successful and diverse group of organisms, well defined by DNA hybridization within the Enterobacteriacae and including the closely related organisms Shigella and the Alkalescens-Dispar biogroup. The primary habitat of E. coli is the lower intestinal tract of warm-blooded animals, which is colonized shortly after birth. At any one time, most normal individuals carry several strains of E. coli in their intestinal tract, including a small number of resident clones exhibiting a rate of replacement measured in weeks or months and a much larger number of transient clones that are replaced in a matter of days or weeks. The secondary habitats of E. coli are soil, sediment, and water, where its half life is thought to be only a few days. Pathogenic forms of E. coli are associated with diarrheal diseases, urinary tract infections, neonatal meningitis, nosocomial infections, and in infections of domesticated animals. E. coli populations contain much genetic diversity, more than is found in most eukaryotes. Genetic diversity has been studied from the standpoint of (a) serology with respect to surface antigens, (b) biogrouping with respect to variable characters such as nutritional versatility, antibiotic resistance, and bacteriophage susceptibility, (c) electrophoresis of enzymes of intermediary metabolism or outer membrane proteins, (d) DNA hybridization, (e) restriction-fragment length polymorphisms, (f) DNA sequences, (g) insertion sequences, and (h) plasmids. However identified, strains of E. coli appear to have a wide, but not totally indiscriminate, host range. Aside from genes directly associated with virulence, genetic divergence between pathogenic and nonpathogenic strains, although statistically significant, is not pronounced. Electrophoretic studies indicate that, while some serotypes may represent a single genetic clone almost exclusively, other serotypes may represent two or more genetically unrelated clones. Unrelated clones may therefore converge to the same or very similar serotypes. Electrophoresis has also been used to define three groups of clones among natural isolates, perhaps corresponding to subspecies of E. coli. These groups are worldwide in distribution and have a wide host range. E. coli populations exhibit great linkage disequilibrium, which occurs as highly nonrandom combinations of alleles at different loci. Reproduction is evidently largely asexual, with insufficient genetic recombination to dissipate linkage disequilibrium.(ABSTRACT TRUNCATED AT 400 WORDS)