DNA Research Advance Access originally published online on February 22, 2006
DNA Research 2006 13(1):3-14; doi:10.1093/dnares/dsi026
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Complexity of the Genomic Diversity in Enterohemorrhagic Escherichia coli O157 Revealed by the Combinational Use of the O157 Sakai OligoDNA Microarray and the Whole Genome PCR scanning
1 Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki Miyazaki, Japan
2 Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki Miyazaki, Japan
3 Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology Nara, Japan
4 Laboratory of Molecular Gene Technics, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
5 Division of Applied Bacteriology, Graduate School of Medicine, Osaka University Osaka, Japan
6 Department of Bacteriology, National Institute for Infectious Diseases Tokyo, Japan
Escherichia coli O157, an etiological agent of hemorrhagic colitis and hemolytic uremic syndrome, is one of the leading worldwide public health threats. Genome sequencing of two O157 strains have revealed that the chromosome is comprised of a 4.1 Mb backbone shared by K-12 and a total of 1.4 Mb O157-specific sequences. Most of the large O157-specific sequences are prophages and prophage-like elements, which have carried many virulence genes into the O157 genome. This suggests that bacteriophages have played the key roles in the emergence of O157. The Whole Genome PCR Scanning (WGPScanning) analysis of O157 strains, on the other hand, revealed a high level of genomic diversity in O157. Variation of prophages has also been suggested as a major factor generating such diversity. In this study, we analyzed the gene content of O157 strains, by an oligoDNA microarray, using the same set of strains as examined by the WGPScanning method. Although most of the strains were typical O157 : H7, they differed remarkably in gene composition, particularly in those on prophages, and we identified more than 400 ‘variably absent or present’ genes which included virulence-related genes. This confirms the role of prophages in generating the genomic diversity, and raises a possibility that some level of variation in potential virulence is present among O157 strains. Fine comparison of the two datasets obtained by microarray and WGPScanning provided much further details on the O157 genome diversity than illustrated by each method alone, indicating the usefulness of this combinational approach in the genomic comparison of closely related strains.
Key words: E. coli O157; genomic diversity; microarray; whole genome PCR scanning
*To whom correspondence should be addressed. Tel. +81-985-85-0871, Fax. +81-985-85-6475, E-mail: thayash{at}med.miyazaki-u.ac.jp
Communicated by Satoshi Tabata
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