Identification of strain-specific DNA of Actinobacillus actinomycetemcomitans by representational difference analysis

Abstract

A genomic subtraction method, the representational difference analysis (RDA), was tested for its use in identifying strain-specific DNA in Actinobacillus actinomycetemcomitans. Subtraction of strain D7S with strain HK1651 yielded D7S-specific 2.3-kilobase (kb) islet-A and 5.3-kb islet-B. Islet-A contains a 1.5-kb region that is homologous to a region found in the A. actinomycetemcomitans plasmid pVT745. Islet-B contains a 2.1-kb homolog of vgr, a component of a DNA repeat element rhs. The distribution of these islets among A. actinomycetemcomitans strains was further examined by polymerase chain reaction. Islet-A was found in nine serotype a and two serotype b strains but was missing from 34 strains. Islet-B was found in one serotype a strain, four serotype d strains and two serotype e strains, but was missing from 34 strains.