Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli

Chromosomal DNA from 23 closely related, pathogenic strains of Escherichiacoli was digested and probed for the insertion sequences IS1, IS2, IS4,IS5, and IS30. Under the assumption that elements residing in DNArestriction fragments of the same apparent length are identical by descent,parsimony analysis of these characters yielded a unique phylogenetic tree.This analysis not only distinguished among bacterial strains that wereotherwise identical in their biochemical characteristics and enzymeelectrophoretic mobilities, but certain aspects of the topology of the treewere consistent across several unrelated insertion elements. Thedistribution of IS elements was then reexamined in light of the inferredphylogenetic relationships to investigate the biological properties of theelements, such as rates of insertion and deletion, and to discover apparentrecombinational events. The analysis shows that the pattern of distributionof insertion elements in the bacterial genome is sufficiently stable forepidemiological studies. Although the rate of recombination by conjugationhas been postulated to be low, at least two such events appear to havetaken place.