Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation

The aim of the study was to identify INDEL markers and study geographical origin of regional H. pylori strains circulating in the European part of the Russian Federation. The study included 56 strains of H. pylori isolated in three regions of the Russian Federation: Saint Petersburg, Astrakhan and R...

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Autores principales:	V. M. Sorokin, A. V. Svarval, A. S. Vodop'janov, R. V. Pisanov
Formato:	article
Lenguaje:	RU
Publicado:	Sankt-Peterburg : NIIÈM imeni Pastera 2021
Materias:	helicobacter pylori pcr indel mst dendrogram vntr typing geographical origin Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/389c3d5a95584a198e06085b18904206
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spelling	oai:doaj.org-article:389c3d5a95584a198e06085b189042062021-11-22T07:09:55ZGeographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation2220-76192313-739810.15789/2220-7619-GDO-1590https://doaj.org/article/389c3d5a95584a198e06085b189042062021-09-01T00:00:00Zhttps://www.iimmun.ru/iimm/article/view/1590https://doaj.org/toc/2220-7619https://doaj.org/toc/2313-7398The aim of the study was to identify INDEL markers and study geographical origin of regional H. pylori strains circulating in the European part of the Russian Federation. The study included 56 strains of H. pylori isolated in three regions of the Russian Federation: Saint Petersburg, Astrakhan and Rostov Regions. Genomic DNA was isolated using a set of Probe NA (DNA Technology, Russia), according to the manufacturer’s instructions. Detection of INDEL markers hp5605, hp6405, hp340, hp1390, hp3660 was performed using PCR. Clustering of the identified INDEL genotypes and building a phylogenetic tree were performed using the BioNumerics 7.6 and GrapeTree software packages. 21 strains from the GenBank database with known geographical origin were used as reference strains. In 20 strains from Saint Petersburg, 13 individual genotypes were identified, while 17 strains belong to the European cluster (hpEurope), 2 strains belong to the hspEAsia cluster and one strain belongs to the hspWAfrica cluster. The most common genotype identified in the European cluster includes six strains from Saint Petersburg and two strains from the GenBank database. For further differentiation of these strains, the VNTR typing method was used, which allowed identifying eight individual genotypes in eight strains. Fifty-six studied russian strains are represented by thirty individual genotypes, which reflects the high heterogeneity of strains circulating in the European part of the Russian Federation. The most frequent genotype is represented by two hpEurope strains, one strain from the Astrakhan region, as well as 5 and 6 strains from the Rostov Region and Saint Petersburg, respectively. The vast majority of Russian strains (52/56) belong to the hpEurope population, while two strains from Saint Petersburg are included in the hspEAsia population, and one strain from Saint Petersburg and the Astrakhan Region is included in the hspWAfrica population. Total, 77 H. pylori strains are represented by 37 individual genotypes with a high diversity index (DI = 0.95), which allows us to consider the proposed INDEL typing method as an independent method for genotyping H. pylori strains. Taking into consideration the complexity of the problem of accurately determining the geographical origin of H. pylori strains, the proposed simple and convenient method of INDEL typing of H. pylori strains, based on an available PCR method becomes very relevant and allows us to conduct an adequate primary analysis of the geographical origin of Russian H. pylori strains.V. M. SorokinA. V. SvarvalA. S. Vodop'janovR. V. PisanovSankt-Peterburg : NIIÈM imeni Pasteraarticlehelicobacter pyloripcrindelmst dendrogramvntr typinggeographical originInfectious and parasitic diseasesRC109-216RUInfekciâ i Immunitet, Vol 11, Iss 4, Pp 701-706 (2021)
institution	DOAJ
collection	DOAJ
language	RU
topic	helicobacter pylori pcr indel mst dendrogram vntr typing geographical origin Infectious and parasitic diseases RC109-216
spellingShingle	helicobacter pylori pcr indel mst dendrogram vntr typing geographical origin Infectious and parasitic diseases RC109-216 V. M. Sorokin A. V. Svarval A. S. Vodop'janov R. V. Pisanov Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
description	The aim of the study was to identify INDEL markers and study geographical origin of regional H. pylori strains circulating in the European part of the Russian Federation. The study included 56 strains of H. pylori isolated in three regions of the Russian Federation: Saint Petersburg, Astrakhan and Rostov Regions. Genomic DNA was isolated using a set of Probe NA (DNA Technology, Russia), according to the manufacturer’s instructions. Detection of INDEL markers hp5605, hp6405, hp340, hp1390, hp3660 was performed using PCR. Clustering of the identified INDEL genotypes and building a phylogenetic tree were performed using the BioNumerics 7.6 and GrapeTree software packages. 21 strains from the GenBank database with known geographical origin were used as reference strains. In 20 strains from Saint Petersburg, 13 individual genotypes were identified, while 17 strains belong to the European cluster (hpEurope), 2 strains belong to the hspEAsia cluster and one strain belongs to the hspWAfrica cluster. The most common genotype identified in the European cluster includes six strains from Saint Petersburg and two strains from the GenBank database. For further differentiation of these strains, the VNTR typing method was used, which allowed identifying eight individual genotypes in eight strains. Fifty-six studied russian strains are represented by thirty individual genotypes, which reflects the high heterogeneity of strains circulating in the European part of the Russian Federation. The most frequent genotype is represented by two hpEurope strains, one strain from the Astrakhan region, as well as 5 and 6 strains from the Rostov Region and Saint Petersburg, respectively. The vast majority of Russian strains (52/56) belong to the hpEurope population, while two strains from Saint Petersburg are included in the hspEAsia population, and one strain from Saint Petersburg and the Astrakhan Region is included in the hspWAfrica population. Total, 77 H. pylori strains are represented by 37 individual genotypes with a high diversity index (DI = 0.95), which allows us to consider the proposed INDEL typing method as an independent method for genotyping H. pylori strains. Taking into consideration the complexity of the problem of accurately determining the geographical origin of H. pylori strains, the proposed simple and convenient method of INDEL typing of H. pylori strains, based on an available PCR method becomes very relevant and allows us to conduct an adequate primary analysis of the geographical origin of Russian H. pylori strains.
format	article
author	V. M. Sorokin A. V. Svarval A. S. Vodop'janov R. V. Pisanov
author_facet	V. M. Sorokin A. V. Svarval A. S. Vodop'janov R. V. Pisanov
author_sort	V. M. Sorokin
title	Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
title_short	Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
title_full	Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
title_fullStr	Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
title_full_unstemmed	Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation
title_sort	geographical diversity of helicobacter pylori strains circulating in the european part of the russian federation
publisher	Sankt-Peterburg : NIIÈM imeni Pastera
publishDate	2021
url	https://doaj.org/article/389c3d5a95584a198e06085b18904206
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Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation

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