Identification of meat-isolated Enterobacteriaceae by an In silico-ARDRA approach

A collection of 20 complete and published sequences were obtained from the NCBI Genbank. Then, an « electronic PCR » was realised for the sequences using the universal primer set S-D-Bact-0008-a-S-20 and S-D-Bact-1495-a-A-20 which target the conserved regions of the 16S ribosomal DNA gene. The In silico enzymatic restriction of amplified products by 180 restriction enzymes allowed the selection of AluI, MspI, and RsaI as the most discriminative restriction enzymes. Sixty isolates were collected from 10 different meat samples (chicken, turkey hen, sheep, pig, dromedary, cow, horse, fish, and ostrich). Preliminary morphological identification delimited the range of the concerned genera. Thus, the studied strains were assigned to one of the following genera: Klebsiella, Enterobacter, Salmonella, Proteus, Escherichia, Yesinia and Shigella spp. Enzymatic restriction of the 16S rDNA gene of the isolated strains using the same enzymes chosen for the theoretical restriction gave 12 ARDRA groups. Comparison of theoretical and experimental ARDRA profiles, using length and number analyses of the restricted fragments, confirm and identify each strain at the genus level, and sometimes up to species level. Epidemiological investigations can optimally be performed by the ARDRA technique, employing restriction enzymes designed electronically through public databases.