0 software (Tamura

et al., 2007). The origin of the reference strains and their GenBank accession numbers are as follows: Fukui, Japan –AB090073, AB090082, AF202972; Okinawa, Japan –AB190940–AB190942, AB190944, AB190948, AB190950, AB190951, AB190956, AB246733-AB246735; Vietnam –FJ798952, FJ798953, FJ798955, FJ798956, FJ798960, FJ798962, FJ798967–FJ798969; Thailand –GU173873–GU173879; China –AF247651, AF249275, AF367250, EU681369; Australia –AF202973, AF282853; Sweden –AY330664; selleckchem UK –AE000511; and United States –AB015414–AB015415. For the aligned cagA gene sequences, genetic distances were estimated using the Kimura 2-parameter method (Kimura, 1980), and for the translated full amino acid sequences of the CagA protein, the JTT (Jones–Taylor–Thornton) matrix-based method (Jones et al., 1992) was used. Phylogenetic trees were constructed using the neighbor-joining TSA HDAC molecular weight method (Saitou & Nei, 1987), and a bootstrap test (1000 replicates) for phylogeny was performed also using mega 4.0 (Tamura et al., 2007). It has been demonstrated previously that CagA can be divided into Western and East Asian types by the kind of amino acid at a tyrosine phosphorylation site (Higashi et

al., 2002a). Strains that possess WSS (Western CagA-specific, SHP-2-binding sequence) are classified as Western type CagA, whereas strains that possess ESS (East either Asian CagA-specific, SHP-2-binding sequence) are classified as East Asian type CagA (Higashi et al., 2002a). Tyrosine phosphorylation of CagA occurs at unique Glu–Pro–Ile–Try–Ala (EPIYA) motifs repeated several times in the C-terminal region. These

EPIYA motifs are involved in the interaction of CagA with SHP-2. The first and second EPIYA motifs (designated as ‘EPIYA-A’ and ‘EPIYA-B’, respectively) are present in almost all Western and East Asian CagA proteins, although the subsequent amino acid sequence is quite different between Western and East Asian type CagA. The third EPIYA motifs included in WSS or ESS were designated as ‘EPIYA-C’ or ‘EPIYA-D’ (Higashi et al., 2002a), respectively. A total of 19 H. pylori strains from 19 patients was used in this study: eight patients with gastritis, three patients with duodenal ulcer, six with gastric ulcer, and two with gastric cancer. There were ten males and nine females, with a mean age of 52.89±11.55 years (range from 30 to 67 years). All Philippine strains examined were cagA-positive and the CagA genotypes of the 19 Philippine strains are shown in Table 2. The Philippine strains can be divided into East Asian (five strains) or Western (14 strains) types. Sequencing of the cagA gene showed a variable size of 3504–3651 bp full-length encoding region, and the predicted size of CagA in 19 strains ranged from 1168 to 1217 amino acids.