Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene.
Commonly, 16S ribosome RNA (16S rRNA) sequence analysis has been used for identifying enteric bacteria. However, it may not always be applicable for distinguishing closely related bacteria. Therefore, we selected gyrB genes that encode the subunit B protein of DNA gyrase (a topoisomerase type II protein) as target genes. The molecular evolution rate of gyrB genes is higher than that of 16S rRNA, and gyrB genes are distributed universally among bacterial species. Microarray technology includes the methods of arraying cDNA or oligonucleotides on substrates such as glass slides while acquiring a lot of information simultaneously. Thus, it is possible to identify the enteric bacteria easily using microarray technology. We devised a simple method of rapidly identifying bacterial species through the combined use of gyrB genes and microarrays. Closely related bacteria were not identified at the species level using 16S rRNA sequence analysis, whereas they were identified at the species level based on the reaction patterns of oligonucleotides on our microarrays using gyrB genes.
Kakinuma
Kenichi
K
Genomics Research Institute, SRL, Inc., 5-6-50 Shinmachi, Hino-shi, Tokyo 191-0002, Japan.
Fukushima
Masao
M
Kawaguchi
Ryuji
R
D001483:Base Sequence; D027081:DNA Gyrase / Q000235:genetics*; D004269:DNA, Bacterial / Q000032:analysis; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012475:Salmonella / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012760:Shigella / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D027081:DNA Gyrase