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PCR and dot blot showed inconsistent results (negative PCR but positive dot blot) for jhp0917 and jhp0918 in ten and seven cases, respectively. Positive results for PCR but negative for dot blot were not observed. Overall, the agreement between PCR and dot blot results was 95.9% (234/244) for jhp0917 and 97.1% (237/244) for jhp0918. On the basis of the combined results of PCR and dot blot, 72 strains (29.5%) were judged to have both jhp0917 and jhp0918, Epigenetics inhibitor whereas 166 (68.0%) possessed neither. The remaining six strains (2.5%) contained only jhp0917. These results indicate that jhp0917 and jhp0918 are strongly linked (p?E-64 H.?pylori strains possessing both jhp0917 and jhp0918, there is a 1-bp insertion (C or T) after position 1385, resulting in a frameshift leading to one continuous gene, named dupA, homologous to the complete virB4 [8]. Therefore, the presence of jhp0917, jhp0918 and the 1-bp insertion after position 1385 are all required for the formation of dupA. To investigate the status of dupA in the H.?pylori strains used in the present study, we analysed the sequence around position 1385 in the 72 strains that had both jhp0917 and jhp0918. We found that all of them contained the 1-bp insertion referred to above. Therefore, we conclude that these 72 strains are all dupA-positive, accounting for 29.5% buy R428 of the total strains analysed. Table?3 shows a comparison of the prevalence of dupA in H.?pylori isolates in different disease states observed in the present study with those reported in previous studies in a range of populations. Using BLAST, we collected a total of 89 sequences covering the intergenic region between jhp0917 and jhp0918 deposited in GenBank. We found that 95.5% (85/89) of them had the 1-bp insertion after position 1385, whereas 4.5% (4/89) did not. These results, when taken together with those obtained in the present study, indicate that most, but not all, strains possessing both jhp0917 and jhp0918 are dupA-positive. Previous studies have shown that several genes in the plasticity region are not expressed and can be regarded as pseudogenes [19]. Because dupA is also located in the plasticity region, we aimed to investigate whether it is a true gene. RT-PCR of ten randomly selected dupA-positive strains confirmed that dupA was always expressed under the conditions tested, and thus is a true gene. To investigate the association between dupA and clinical outcomes, five H.?pylori strains without cagE and/or cagA and six strains that had only jhp0917 were excluded from the analysis.
