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Journal of Bacteriology, November 2008, p. 6948-6960, Vol. 190, No. 21
0021-9193/08/$08.00+0     doi:10.1128/JB.00625-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Systematic Identification and Sequence Analysis of the Genomic Islands of the Enteropathogenic Escherichia coli Strain B171-8 by the Combined Use of Whole-Genome PCR Scanning and Fosmid Mapping ^,

Yoshitoshi Ogura,^1,2 Hiroyuki Abe,^3,4 Keisuke Katsura,² Ken Kurokawa,⁵ Md Asadulghani,² Atsushi Iguchi,² Tadasuke Ooka,² Keisuke Nakayama,² Atsushi Yamashita,⁶ Masahira Hattori,^6,7,8 Toru Tobe,⁴ and Tetsuya Hayashi^1,2*

Division of Bioenvironmental Science, Frontier Science Research Center,¹ Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan,² Division of Applied Bacteriology, Graduate School of Medicine,³ Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan,⁴ Department of Biological Information, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan,⁵ Kitasato Institute for Life Science, Kitasato University, Kanagawa, Japan,⁶ RIKEN Genomic Sciences Center, Kanagawa, Japan,⁷ Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan⁸

Received 6 May 2008/ Accepted 18 August 2008

Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) are diarrheagenic pathogens that colonize the intestinal tract through the formation of attaching and effacing lesions, induced by effectors translocated via a type III secretion system (T3SS) encoded on the locus of enterocyte effacement (LEE). In EHEC O157, numerous virulence factors, including around 40 T3SS effectors, have been identified. Most of them are encoded on genomic islands (GEIs) such as prophages and integrative elements. For EPEC, however, no systematic search of GEIs and virulence-related genes carried therein has been done, and only a limited number of virulence factors have been identified so far. In this study, we performed a systemic and genome-wide survey of the GEIs in strain B171-8, one of the prototype strains of EPEC, by the combined use of whole-genome PCR scanning and fosmid mapping and identified 22 large GEIs, including nine lambda-like prophages, three P2-like prophages, the LEE, and three additional integrative elements. On these prophages and integrative elements, we found genes for a set of T3SS proteins, a total of 33 T3SS effectors or effector homologues, and 12 other virulence factors which include five nonfimbrial adhesins. Most of the T3SS effector families identified are also present in EHEC O157, but B171-8 possesses a significantly smaller number of effectors. Not only the presence or absence of Shiga toxin genes but also the difference in the T3SS effector repertoire should be considered in analyzing the pathogenicity of EPEC and EHEC strains.

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* Corresponding author. Mailing address: Division of Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 899-1692, Japan. Phone: 81-985-85-0871. Fax: 81-985-85-6475. E-mail: thayash{at}med.miyazaki-u.ac.jp

Published ahead of print on 29 August 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

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Journal of Bacteriology, November 2008, p. 6948-6960, Vol. 190, No. 21
0021-9193/08/$08.00+0     doi:10.1128/JB.00625-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

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