New tool for phylogenetic analysis of Helicobacter pylori

The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of Helicobacter pylori and offer INDEL-typing method for differentiation of H. pylori strains. For comparative analysis of the genomes of H. pylori presented in the GenBank database, a local database of nucleotide sequences of 69 H. pylori strains was created. For detecting all INDEL markers with a preset size of 6-20 bp a pairwise comparison of more than 1500 open reading frames (ORF) in the genomes of local database strains was performed. Ten loci containing INDEL markers were founded. The five most variable loci were tested in silico with 21 strains with known geographical origin from the most common populations of hpEurope, hspWAfrica, and hspEAsia. Fifteen individual genotypes with a high diversity index (DI=0.95) were identified. For cluster analysis, the minimal spanning tree (MST) method was used, which demonstrated a clear distribution of clusters according to the geographical origin of the strains tested. INDEL-typing of 21 regional strains from the Astrakhan region was performed in vitro. It was shown that an extensive majority of them belong to the population hpEurope. The findings in this study indicate that the proposed INDEL-typing method almost perfectly reflects the geographical distribution of H. pylori strains determined by the multilocus sequence typing (MLST) method, despite the fact that the primary object of research is completely different genes. Further research is needed to determine the geographical origin of H. pylori strains in Russia.