New Tool for Phylogenetic Analysis of Helicobacter pylori: An Advanced Study | Chapter 7 | Recent Progress in Microbiology and Biotechnology Vol. 7

The goal of this study was to find canonical insertion/deletion (INDEL) markers in the Helicobacter pylori genome and develop an INDEL-typing approach for strain classification. A local database of nucleotide sequences of 69 H. pylori strains was established for comparative examination of the genomes of H. pylori published in the GenBank database. A pairwise analysis of more than 1500 open reading frames (ORF) in the genomes of local database strains was done to find all INDEL markers with a fixed size of 6-20 bp. Ten loci with INDEL markers were discovered. 21 strains with known geographical origin from the most prevalent populations of hpEurope, hspWAfrica, and hspEAsia were examined in silico with the five most variable loci. A total of fifteen genotypes with a high diversity index (DI=0.95) were discovered. The minimum spanning tree (MST) method was utilised for cluster analysis, which revealed a clear distribution of clusters based on the geographical origin of the strains examined. In vitro INDEL-typing was done on 21 regional strains from the Astrakhan region. It was discovered that the vast majority of them are from the hpEuropean population. Despite the fact that the primary target of research is completely different genes, the results show that the suggested INDEL-typing approach almost exactly reflects the geographical distribution of H. pylori strains established by the multilocus sequence typing (MLST) method. To determine the geographical origin of H. pylori strains in Russia, more research is needed.

Author (S) Details

Vladimir Mihajlovich Sorokin
Rostov-on-Don Research Institute for Plague Control, Rostov-on-Don 344002, Russia.

Ruslan Vjacheslavovich Pisanov
Rostov-on-Don Research Institute for Plague Control, Rostov-on-Don 344002, Russia.

Aleksej Sergeevich Vodop'janov
Rostov-on-Don Research Institute for Plague Control, Rostov-on-Don 344002, Russia.

Elena Vadimovna Golubkina
Astrakhan State Medical University, Astrakhan 414000, Russia.

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