Genotypes and phylogenetic relationships of Salmonella typhimurium are defined by molecular fingerprinting of IS200 and 16S rrn loci.

Molecular fingerprints of chromosomal genotypes in Salmonella typhimurium were generated by analysis of variation at the 16S rrn gene loci and the sites of the insertion sequence IS200. Genetic and reference strains of S. typhimurium were compared with clinical phage type strains from cases of human salmonellosis. Three 16S rrn profiles, one of which was predominant, were found. The copy number of the Salmonella-specific insertion sequence IS200 varied from 6 to 12, and all insertions were chromosomal. Three of the insertion sites shared by all strains were serovar-specific for S. typhimurium. Thirteen distinct profiles of IS200 were detected, providing a high level of intraserovar strain discrimination. Profiles were generally more conserved among genetic and reference strains; representatives of clinical phage type strains, which are recent human isolates, showed much greater diversity of IS200 profiles. Irrespective of their origin, strains could be assigned to IS200 profile groups, phylogenetically related lines identified by combinations of conserved insertion sites. Hybridization profiles of this mobile element are markers of intermediate and short-term evolution in S. typhimurium. They provide a fingerprinting scheme for the purposes of genetics, and delineate a molecular typing scheme for the purposes of epidemiology.