COMPUTER IDENTIFICATION OF ESCHERICHIA-COLI RIBOSOMAL-RNA GENE RESTRICTION PATTERNS

A total of 191 strains of Escherichia coli comprising 164 serovar refe rence strains and 28 clinical strains were characterized by rRNA gene restriction patterns (ribotypes) generated after cleavage of total DNA with MluI, ClaI or HindIII restriction endonucleases and hybridizatio n of fragments with acetylaminofluorene-labelled 16+23S rRNA. A wide d iversity of ribotypes was observed with endonucleases MluI (104 patter ns), ClaI (90 patterns) and HindIII (98 patterns). When MluI was used, 85% of patterns (11 to 15 fragments) shared five fragments 17.09, 3.9 4, 3.06, 2.23 and 1.76 kb in size. When these fragments were used as i nternal standards, the percent errors in fragment length determination was half of that obtained with an external standard. Two fragment siz e databases of MluI and ClaI ribotypes were built. Automatic identific ation was obtained after setting the percent fragment size variation t olerance (error) at 5%. MluI ribotyping is recommended as a primary ep idemiological marker. Strains with similar MluI ribotype should then b e submitted to ClaI ribotyping. Ribotyping with HindIII can only be th e third choice, since the patterns were often uncertain due to the fre quent occurrence of faint bands. Most of the studied serovars gave dis crete patterns and these data provide the basis for a molecular typing system for E. coli which could possibly substitute for serotyping whe n the latter is not available.