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

Cover Page

Cite item

Abstract

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.

About the authors

V. M. Sorokin

Rostov-on-Don Research Institute for Plague Control

Email: soroka53@mail.ru

PhD (Biology), Senior Researcher, Tularemia Laboratory 

Rostov-on-Don

Russian Federation

A. V. Svarval

St. Petersburg Pasteur Institute

Author for correspondence.
Email: alenasvar@rambler.ru

Alena V. Svarval,  PhD (Medicine), Senior Researcher, Laboratory of Pathogenes Identification 

197101, St. Petersburg, Mira str., 14

Phone: +7 911 223-14-11 

Russian Federation

A. S. Vodop'janov

Rostov-on-Don Research Institute for Plague Control

Email: alexvod@gmail.com

PhD (Medicine), Head of the Virology Group 

Rostov-on-Don

Russian Federation

R. V. Pisanov

Rostov-on-Don Research Institute for Plague Control

Email: pisanov.ruslan@yandex.ru

PhD (Biology), Head of the Laboratory for Diagnostics of Especially Dangerous Infections 

Rostov-on-Don

Russian Federation

References

  1. Момыналиев К.Т., Челышева В.В., Акопиан Т.А., Селезнева О.В., Линц Б., Ахтман М., Говорун В.М. Популяционная идентификация российских изолятов Helicobacter pylori // Генетика. 2005. Т. 41, № 10. С. 1434–1437. [Momynaliev K.T., Chelysheva V.V., Akopian T.A., Selezneva O.V., Lints B., Akhtman M., Govorun V.M. Population identification of Russian Helicobacter pylori isolates. Genetika = Genetics, 2005, vol. 41, no. 10, pp. 1434–1437. (In Russ.)]
  2. Патент RU 2688434C1. Российская Федерация, МПК C12Q 1/68 (2006.01), C12N 15/10 (2006.01), G01N 33/53 (2006.01), A61K 39/02 (2006.01). Способ дифференциации штаммов Helicobacter pylori путем молекулярно-генетического типирования: № 2011154058/10; заявлено 28.12.2011: опубликовано: 20.05.2013 / Сорокин В.М., Писанов Р.В. Патентообладатель: ФКУЗ «Ростовский-на-Дону ордена Трудового Красного Знамени научно-исследовательский противочумный институт» Федеральной службы по надзору в сфере защиты прав потребителей и благополучия человека. 7 с. [Patent No. 2688434C1 Russian Federation, Int. Cl. C12Q 1/68 (2006.01), C12N 15/10 (2006.01), G01N 33/53 (2006.01), A61K 39/02 (2006.01). Method for differentiation of strains Helicobacter pylori by multilocal VNTR-typing: No. 2011154058/10; application: 2011.12.28: date of publication 2013.05.20 / Sorokin V.M., Pisanov R.V. Proprietors: Federal’noe kazennoe uchrezhdenie zdravookhranenija “Rostovskij-na-Donu ordena Trudovogo Krasnogo Znameni nauchnoissledovatel’skij protivochumnyj institut” Federal’noj sluzhby po nadzoru v sfere zashchity prav potrebitelej i blagopoluchija cheloveka. 7 p.]
  3. Achtman M., Azuma T., Berg D.E., Ito Y., Morelli G., Pan Z.J., Suerbaum S., Thompson S.A., van der Ende A., van Doorn L.J. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol. Microbiol., 1999, vol. 32, pp. 459–470. doi: 10.1046/j.1365-2958.1999.01382.x
  4. Björkholm B., Sjölund M., Falk P.G., Berg O.G., Engstrand L., Andersson D.I. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc. Natl. Acad. Sci. USA, 2001, vol. 98, pp. 14607–14612. doi: 10.1073/pnas.241517298
  5. Delport W., Cunningham M., Olivier B., Preisig O., Van Der Merwe S.W. A population genetics pedigree perspective on the transmission of Helicobacter pylori. Genetics, 2006, vol. 174, pp. 2107–2118. doi: 10.1534/genetics.106.057703
  6. Devi S.M., Ahmed I., Francalacci P., Hussain M.A., Akhter Y., Alvi A., Sechi L.A., Mégraud F., Ahmed N. Ancestral European roots of Helicobacter pylori in India. BMC genomics, 2007, vol. 8, no. 1: 184. doi: 10.1186/1471-2164-8-184
  7. Eppinger M., Baar C., Linz B., Raddatz G., Lanz C., Keller H., Morelli G., Gressmann H., Achtman M., Schuster S.C. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet., 2006, vol. 2, no. 7: e120. doi: 10.1371/journal.pgen.0020120.eor
  8. Falush D., Kraft C., Taylor N.S., Correa P., Fox J.G., Achtman M., Suerbaum S. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad. Sci. USA, 2001, vol. 98, no. 26, pp. 15056–15061. doi: 10.1073/pnas.251396098
  9. Falush D., Wirth T., Linz B., Pritchard J.K., Stephens M., Kidd M., Blaser M.J., Graham D.Y., Vacher S., Perez-Perez G.I., Yamaoka Y. Traces of human migrations in Helicobacter pylori populations. Science, 2003, vol. 299, no. 5612, pp. 1582–1585. doi: 10.1126/science.1080857
  10. Go M.F., Kapur V., Graham D.Y., Musser J.M. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. J. Bacteriol., 1996, vol. 178, pp. 3934–3938. doi: 10.1128/jb.178.13.3934-3938.1996
  11. Guo C., Liao Y., Li Y., Duan J., Guo Y., Wu Y., Cui Y. Genotyping analysis of Helicobacter pylori using multiplelocus variable-number tandem-repeats analysis in five regions of China and Japan. BMC Microbiol., 2011, vol. 11: 197. doi: 10.1186/1471-2180-11-197
  12. Han S.R., Zschausch H.C., Meyer H.G., Schneider T., Loos M., Bhakdi S., Maeurer M.J. Helicobacter pylori: clonal population structure and restricted transmission within families revealed by molecular typing. J. Clin. Microbiol., 2000, vol. 38, pp. 3646– 3651. doi: 10.1128/JCM.38.10.3646-3651.2000
  13. Kang J., Blaser M.J. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori. Nat. Rev. Microbiol., 2006, vol. 4, pp. 826–836. doi: 10.1038/nrmicro1528
  14. Kersulyte D., Chalkauskas H., Berg D.E. Emergence of recombinant strains of Helicobacter pylori during human infection. Mol. Microbiol., 1999, vol. 31, pp. 31–43. doi: 10.1046/j.1365-2958.1999.01140.x
  15. Kivi M., Tindberg Y., Sörberg M., Casswall T.H., Befrits R., Hellström P.M., Bengtsson C., Engstrand L., Granström M. Concordance of Helicobacter pylori strains within families. J. Clin. Microbiol., 2003, vol. 41, no. 12, pp. 5604–5608. doi: 10.1128/jcm.41.12.5604-5608.2003
  16. Lamichhane B., Wise M.J., Chua E.G., Marshall B.J., Tay C.Y. A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia. Evol. Appl., 2020, vol. 13, no. 2, pp. 278–289. doi: 10.1111/eva.12864
  17. Linz B., Balloux F., Moodley Y., Manica A., Liu H., Roumagnac P., Falush D., Stamer C., Prugnolle F., van der Merwe S.W., Yamaoka Y. An African origin for the intimate association between humans and Helicobacter pylori. Nature, 2007, vol. 445, no. 7130, pp. 915–918. doi: 10.1038/nature05562
  18. Marshall B.J., Armstrong J.A., McGechie D.B., Glancy R.J. Attempt to fulfil Koch’s postulates for pyloric Campylobacter. Med. J. Aust., 1985, vol. 142, pp. 436–439.
  19. Marshall B.J., Warren J.R. Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet, 1984, vol. 1, pp. 1311–1315. doi: 10.1016/s0140-6736(84)91816-6
  20. Moodley Y., Linz B. Helicobacter pylori sequences reflect past human migrations. Genome Dyn., 2009, vol. 6, pp. 62–74. doi: 10.1159/000235763
  21. Moodley Y., Linz B., Yamaoka Y., Windsor H.M., Breurec S., Wu J.Y., Maady A., Bernhöft S., Thiberge J.M., Phuanukoonnon S., Jobb G. The peopling of the Pacific from a bacterial perspective. Science, 2009, vol. 323, no. 5913, pp. 527–530. doi: 10.1126/science.1166083
  22. Raymond J., Thiberge J.M., Chevalier C., Kalach N., Bergeret M., Labigne A., Dauga C. Genetic and transmission analysis of Helicobacter pylori strains within a family. Emerg. Infect. Dis., 2004, vol. 10, no. 10, pp. 1816–1821. doi: 10.3201/eid1010.040042
  23. Salaun L., Audibert C., Le Lay G., Burucoa C., Fauchere J.L., Picard B. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol. Lett., 1998, vol. 161, pp. 231–239. doi: 10.1111/j.1574-6968.1998.tb12953.x
  24. Schuster S.C., Wittekindt N.E., Linz B. Molecular mechanisms of host-adaptation in Helicobacter. In: Helicobacter pylori: molecular genetics and cellular biology. Ed. by Yamaoka Y. Wymondham: Horizon Scientific Press, 2008, pp. 193–204.
  25. Sorokin V., Pisanov R., Golubkina E., Bereznyak E., Prozorova L. Comparative multiple-locus variablenumber tandem repeat analysis of Helicobacter pylori Isolates from South of Russia. IJMB, 2017, vol. 2, no. 3, pp. 135–138. doi: 10.11648.j.ijmb.20170203.15
  26. Sorokin V.M., Pisanov R.V., Vodop’janov A.S. Improvement of multiple-locus VNTR analysis typing scheme for Helicobacter pylori. Asian J. Biochem. Genet. Mol. Biol., 2018, vol. 1, no. 4, pp. 1–7.
  27. Sorokin V.M., Pisanov R.V., Vodop’janov A.S., Golubkina E.V. New tool for phylogenetic analysis of Helicobacter pylori. WJARR, 2020, vol. 6, no. 2, pp. 60–67. doi: 10.30574/wjarr.2020.6.2.0128
  28. Suerbaum S., Smith J.M., Bapumia K., Morelli G., Smith N.H., Kunstmann E., Dyrek I., Achtman M. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA, 1998, vol. 95, no. 21, pp. 12619–12624. doi: 10.1073/pnas.95.21.12619
  29. Taylor N.S., Fox J.G., Akopyants N.S., Berg D.E., Thompson N., Shames B., Yan L., Fontham E., Janney F., Hunter F.M. Longterm colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting. J. Clin. Microbiol., 1995, vol. 33, no. 4, pp. 918–923. doi: 10.1128/JCM.33.4.918-923.1995
  30. Tindberg Y., Bengtsson C., Granath F., Blennow M., Nyren O., Granstrom M. Helicobacter pylori infection in Swedish school children: lack of evidence of child-to-child transmission outside the family. Gastroenterology, 2001, vol. 121, pp. 310–316. doi: 10.1053/gast.2001.26282
  31. Tsang A.K.L., Lee H.H., Yiu S.M., Lau S.K., Woo P.C. Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny. Sci. Rep., 2017, vol. 7, no. 1: 4536. doi: 10.1038/s41598-017-04707-4
  32. Vale F.F., Nunes A., Oleastro M., Gomes J.P., Sampaio D.A., Rocha R., Vítor J.M., Engstrand L., Pascoe B., Berthenet E., Sheppard S.K. Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins. Sci. Rep., 2017, vol. 7: 42471. doi: 10.1038/srep42471
  33. Zhou Z., Alikhan N.F., Sergeant M.J., Luhmann N., Vaz C., Francisco A.P., Carriço J.A., Achtman M. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res., 2018, vol. 28, no. 9, pp. 1395–1404. doi: 10.1101/gr.232397.117

Supplementary files

There are no supplementary files to display.


Copyright (c) 2021 Sorokin V.M., Svarval A.V., Vodop'janov A.S., Pisanov R.V.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies