Genomic variation in Helicobacter pylori: application to identification of strains.

DNA digest analysis, ribopatterns, and plasmid profiling were used to determine genomic variation in 55 strains of Helicobacter pylori from patients with gastritis in the USA, Peru, Australia, and the U.K. HaeIII-ribopatterns and total DNA digest patterns showed a high degree of heterogeneity, with at least 33 different genomic types among strains, including some sequential isolates. Plasmids, present in 51% of strains, were less useful as epidemiologic markers. Investigation of 14 multiple isolate sets showed that genotypic variants were present in pre- and post-treatment gastric mucosa, that relapse in some patients was due to reinfection by a genotypically different strain, and that the same strain persisted in most treatment failures. We conclude that molecular methods were excellent for precise identification of H. pylori, but ribopatterns had the advantages of reproducibility, high discrimination, and visual simplicity.