Computer identification of Escherichia coli rRNA gene restriction patterns

Abstract

A total of 191 strains of Escherichia coli comprising 164 serovar reference strains and 28 clinical strains were characterized by rRNA gene restriction patterns (ribotypes) generated after cleavage of total DNA with Mlul, Clal or Hindlll restriction endonucleases and hybridization of fragments with acetylaminofluorene-labelled 16+23S rRNA. A wide diversity of ribotypes was observed with endonucleases Mlul (104 patterns), Clal (90 patterns) and Hindlll (98 patterns). When Mlul was used, 85% of patterns (11 to 15 fragments) shared five fragments 17.09, 3.94, 3.06, 2.23 and 1.76 kb in size. When these fragments were used as internal standards, the percent errors in fragment length determination was half of that obtained with an external standard. Two fragment size databases of Mlul and Clal ribotypes were built. Automatic identification was obtained after setting the percent fragment size variation tolerance (error) at 5%. Mlul ribotyping is recommended as a primary epidemiological marker. Strains with similar Mlul ribotype should then be submitted to Clal ribotyping. Ribotyping with Hindlll can only be the third choice, since the patterns were often uncertain due to the frequent occurrence of faint bands. Most of the studied serovars gave discrete patterns and these data provide the basis for a molecular typing system for E. coli which could possibly substitute for serotyping when the latter is not available.