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Background  Persistent colonization of the human stomach by  Helicobacter pylori  is associated with asymptomatic gastric inflammation (gastritis) and an increased risk of duodenal ulceration, gastric ulceration, and non-cardia gastric cancer. In previous studies, the genome sequences of  H. pylori  strains from patients with gastritis or duodenal ulcer disease have been analyzed. In this study, we analyzed the genome sequences of an  H. pylori  strain (98-10) isolated from a patient with gastric cancer and an  H. pylori  strain (B128) isolated from a patient with gastric ulcer disease.    Results  Based on multilocus sequence typing, strain 98-10 was most closely related to  H. pylori  strains of East Asian origin and strain B128 was most closely related to strains of European origin. Strain 98-10 contained multiple features characteristic of East Asian strains, including a type s1c  vacA  allele and a  cagA  allele encoding an EPIYA-D tyrosine phosphorylation motif. A core genome of 1237 genes was present in all five strains for which genome sequences were available. Among the 1237 core genes, a subset of alleles was highly divergent in the East Asian strain 98-10, encoding proteins that exhibited <90% amino acid sequence identity compared to corresponding proteins in the other four strains. Unique strain-specific genes were identified in each of the newly sequenced strains, and a set of strain-specific genes was shared among  H. pylori  strains associated with gastric cancer or premalignant gastric lesions.    Conclusion  These data provide insight into the diversity that exists among  H. pylori  strains from diverse clinical and geographic origins. Highly divergent alleles and strain-specific genes identified in this study may represent useful biomarkers for analyzing geographic partitioning of  H. pylori  and for identifying strains capable of inducing malignant or premalignant gastric lesions.

Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer