Phylogenetic structure based on sequence analysis of 8 H. pylori core genes. H. pylori strains analyzed in this figure include strains 98-10, B128, three strains for which genome sequences were previously determined (26695, J99, HPAG1), and representative strains isolated from patients in diverse geographic locations . The figure lists the strain designations and the countries where strains were isolated. The nucleotide sequences of the concatenated MLST loci were aligned and compared, as described in Methods. All positions containing gaps and missing data were eliminated from the dataset. There were a total of 3041 positions in the final dataset. Neighbor-joining trees were constructed based on distances estimated by the Kimura 2-parameter model of nucleotide substitution [57, 58]. The bootstrap consensus tree inferred from 1000 replicates is taken to represent the evolutionary history of the strains analyzed . Branches corresponding to partitions reproduced in fewer than 50% bootstrap replicates are collapsed. The tree is drawn to scale, with the branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. Phylogenetic analyses were conducted in MEGA4 . Five H. pylori strains for which genome sequences were available are denoted by diamonds. Three main H. pylori population groups (East Asian, European, and West African) are identifiable.