VacA s/i/d/m region subtyping was accomplished by three single PCR amplification assays. The signal-sequence (SS) region was amplified using primer M13-SeqS.se and SeqS.as; the intermediate and deletion region (IR and DR) using primer M13-SeqVac.se and SeqVac.as; the midregion (MR) using primer M13-SeqM.se and VAG-R (Figure  2; Table  2), respectively Amplification conditions used were identical in all assays as described previously [45]. Prior to sequencing, amplicons were analysed

by automated capillary gel electrophoresis using a QIAxcel system and a QIAxcel DNA High Resolution kit (Qiagen, Hilden, Germany). cagA EPIYA motif and vacA s/i/d/m-region sequence analysis M13-tagged cagA EPIYA and vacA TSA HDAC datasheet amplicons were sequenced using M13 uni (−21) sequencing primer and a customer sequencing service (Eurofins MWG Operon, Ebersberg, Germany). The obtained GS-4997 in vitro cagA and vacA sequences were aligned and compared

with catalogued H. pylori 26695 [GenBank:AE000511, H. pylori J99 [GenBank:AE001439], H. pylori P12 [GeneBank:CP001217], H. pylori G27 [GenBank:CP001173], and H. pylori Shi470 [GeneBank:CP001072] sequences using the CLC DNA Workbench version 5.5 [55]. Sequences were retrieved from the NCBI nucleotide database [56]. CagE and cag-PAI (empty-site) amplicon sizes were analysed by capillary gel electrophoresis only. Statistical analysis Selleckchem A-1210477 Binary logistic regression analysis of data was performed using Minitab 15 software. Statistical significance was assumed at P < 0.05. All statistical analyses presented here were significant according to Hosmer-Lemeshow

(HL) goodness-of-fit test, with HL p values >0.05. In the logistic regression analysis and the GLM analysis, a 95% confidence interval including 1.0 was next regarded as non-significant. Odds ratios with 95% confidence intervals (CI) were calculated to explore possible associations of individual genotypes to peptic ulcer or gastric atrophy. Age and sex were included as covariates. With regard to atrophy, data from duodenal biopsies were not included in the statistical analysis. Acknowledgements The study was supported by grants from the Research Council in the South-East of Sweden (FORSS, the ALF program, the committee for medical R&D, and the Molecular Biology program at Clinical Microbiology, Laboratory Medicine Centre-DC, University Hospital, Linköping, Sweden. We are grateful to Statistician Olle Eriksson, PhD, for statistical calculations and advice. Electronic supplementary material Additional file 1: Results from cagA and vacA genotyping, including clinical data. (PDF 18 KB) References 1. Marshall BJ, Warren JR: Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet 1984,1(8390):1311–1315.PubMedCrossRef 2. Cover TL, Blaser MJ: Helicobacter pylori and gastroduodenal disease. Annu Rev Med 1992, 43:135–145.PubMedCrossRef 3.