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Background   elicobacter pylori  infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach.    Results  A set of 254  H. pylori  genes was used to perform array-based comparative genomic hybridization among 120 French  H. pylori  strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with  cag PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released  H. pylori  genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest  H. pylori  genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the  vacA s2m2 allele and lacks the genes encoding the major virulence factors (absence of  cag PAI,  bab B,  bab C,  sab B, and  hom B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6  H. pylori  sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38.    Conclusion  These isolates are deprived of the main  H. pylori  virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma