Gene sequencing and data acquisition

Genome sequence data of H. pylori strains were obtained using paired-end reads (2 × 150 or 2 × 300 bp) on HiSeq 2000 and MiSeq sequencers (Illumina, Inc., San Diego, CA, USA). Sample multiplexing was provided by using an Indexed DNA library, and manipulated using the Nextera XT Index Kit and the Nextera XT DNA Library Preparation Kit (Illumina, Inc., San Diego, CA, USA), following the manufacturer’s instructions. We performed de-novo assembly of the short read data using the CLC Genomics Workbench v. 7.0.4 commercial software (CLC QIAGEN), with automated word size and bubble size, and a minimum contig size 200 bp. ORFs were predicted by the same software, which identified CagA and VacA using the genes of Japanese strain F32 (Accession Number {"type":"entrez-nucleotide","attrs":{"text":"NC_017366","term_id":"385215269"}}NC_017366). We took top hit genes whose % identity and length coverage were at least 85 and 80%, respectively. In case cagA and vacA genes were not detected by next-generation sequencing, we used PCR and the Sanger method. Primers for PCR amplification and direct sequencing of the entire coding regions of cagA and vacA are shown in Table 1. The regions containing full-length cagA and vacA were amplified by PCR, and sequenced as previously described. We attached a list of accession numbers of the cagA and vacA sequences as Additional file 1.

Primers used for DNA sequencing of H. pylori cagA and vacA in this study