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Identification of strain-specific genes located outside the plasticity zone in nine clinical isolates of Helicobacter pylori^b

Laboratoire de Bactériologie, Université Victor Segalen Bordeaux 2 and Hôpital Pellegrin, Place Amélie Raba-Léon, 33076 Bordeaux Cedex, France¹
AstraZeneca R and D, Boston, Waltham, MA, USA²

Author for correspondence: Francis Mégraud. Tel: +33 5 56 79 59 10. Fax: +33 5 56 79 60 18. e-mail: francis.megraud{at}chu-bordeaux.fr

Helicobacter pylori is a Gram-negative bacterium that is associated with the development of peptic ulcers and gastric carcinoma in humans. This species appears to be one of the most genetically variable bacteria described to date. The overall level of heterogeneity within strains of this organism was determined by comparing the genome sequences of two reference strains, J99 and 26695. The aim of this study was to measure the genetic diversity within strains of H. pylori by looking for strain-specific genes in nine H. pylori strains isolated from patients suffering from chronic gastritis (n=3), duodenal ulcers (n=3) or gastric cancer (n=3). Seven loci that contained strain-specific genes in strains J99 and 26695 were studied. These regions were subsequently amplified from most of the clinical isolates studied and their sequences were determined. ORFs were predicted from the sequence data and were compared to sequences within the databases. The results showed that the genes flanking the ORFs specific to either strain J99 or strain 26695 were also present in a similar configuration in the genomes of the nine clinical isolates. Moreover, in most regions, ORFs homologous to those found in the corresponding loci in the two reference strains were detected. However, in 10 regions, genes similar to those located at another locus in the genome of J99 or 26695 were found. Finally, six strain-specific genes were identified in three regions of three of the H. pylori strains isolated from patients with duodenal ulcers (n=2) and gastric cancer (n=1). Of these six genes, five were putative genes and one was an orthologue of a gene encoding a transposase in Thermotoga maritima. However, no association with disease was found for these genes.

Keywords: diversity, genome, pathogenicity

^b The GenBank accession numbers for the H. pylori sequences reported in this paper are AF326599–AF326607 for region A, AF326608–AF326616 for region B, AF326617–AF326625 for region C, AF326626–AF326634 for region D, AF327212–AF327220 for region E, AF328909–AF328916 and AF328924 for region F, and AF32917–AF32923 for region G.

^a Present address: Laboratoire de Virologie, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique, Bordeaux, France.

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