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Applied and Environmental Microbiology, May 2002, p. 2316-2325, Vol. 68, No. 5
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.5.2316-2325.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Genomic Subtraction To Identify and Characterize Sequences of Shiga Toxin-Producing Escherichia coli O91:H21

Nathalie Pradel,1 Sabine Leroy-Setrin,2 Bernard Joly,1 and Valérie Livrelli1*

Groupe de Recherche Pathogénie Bactérienne Intestinale, Faculté de Pharmacie, Université d'Auvergne Clermont-1, Unité soutenue par l'INRA, Clermont-Ferrand,1 Station de Recherche sur la Viande, Microbiologie, Institut National de la Recherche Agronomique, St-Genès-Champanelle, France2

Received 7 September 2001/ Accepted 27 February 2002

To identify Shiga toxin-producing Escherichia coli genes associated with severe human disease, a genomic subtraction technique was used with hemolytic-uremic syndrome-associated O91:H21 strain CH014 and O6:H10 bovine strains. The method was adapted to the Shiga toxin-producing E. coli genome: three rounds of subtraction were used to isolate DNA fragments specific to strain CH014. The fragments were characterized by genetic support analysis, sequencing, and hybridization to the genome of a collection of Shiga toxin-producing E. coli strains. A total of 42 fragments were found, 19 of which correspond to previously identified unique DNA sequences in the enterohemorrhagic E. coli EDL933 reference strain, including 7 fragments corresponding to prophage sequences and others encoding candidate virulence factors, such a SepA homolog protein and a fimbrial usher protein. In addition, the subtraction procedure yielded plasmid-related sequences from Shigella flexneri and enteropathogenic and Shiga toxin-producing E. coli virulence plasmids. We found that lateral gene transfer is extensive in strain CH014, and we discuss the role of genomic mobile elements, especially bacteriophages, in the evolution and possible transfer of virulence determinants.

* Corresponding author. Mailing address: Groupe de Recherche Pathogénie Bactérienne Intestinale, Faculté de Pharmacie, Université d'Auvergne, 28 Place Henri-Dunant, 63 001 Clermont-Ferrand, France. Phone: (33) 473 608 019. Fax: (33) 473 277 494. E-mail: Valerie.Livrelli{at}u-clermont1.fr.

Applied and Environmental Microbiology, May 2002, p. 2316-2325, Vol. 68, No. 5
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.5.2316-2325.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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