Development of phylogenetic oligonucleotide probes for screening foodborne bacteria

The aim of this study was to develop phylogenetic oligonucleotide probes for screening common foodborne bacteria. Twenty oligonucleotide probes were designed by aligning representative 16S ribosomal DNA (rDNA) sequences from 64 species of common foodborne bacteria and other bacteria. To confirm the specificity of each probe simultaneously, a DNA microarray that the 20 probes were immobilized on a glass slide was prepared. RNAs extracted from 13 species of foodborne bacteria were fluorescently labeled and hybridized on the DNA microarray. The 16S rRNAs showed a unique hybridization pattern in combination with the designed oligonucleotide probes, leading to 16S rDNA phylogenetic analysis of their sequences. Probe EC001 for Escherichia coli spp. and Shigella spp., probe SSP003-L for Salmonella enterica subsp. enterica serovar Enteritidis and Salmonella enterica subsp. enterica serovar Typhimurium, probe YE002 for Yersinia enterocolitica and probe BC001 for Bacillus cereus group were particularly useful for screening these foodborne bacteria. DNA microarray is useful as a procedure for evaluating the multiple designed probes. The selected probes can be readily applied to screening of foodborne bacteria using hybridization methods, such as fluorescent in situ hybridization (FISH), bead array hybridization and so on.