In silico Analysis of Virulence, Resistance Genes and Phylogeny of Helicobacter pylori Strains from Different Continents

Year 2021, Volume: 11 Issue: 3, 170 - 178, 08.12.2021

Mehmet Demirci , Özge Ünlü , Bekir Kocazeybek

https://doi.org/10.26650/experimed.2021.970580

Abstract

Objective:Helicobacter pylori (H. pylori) is a bacterium that infects the gastric mucosa of 50% of the world population. It is known that different regional treatment practices used against the infections of H. pylori affect both the expression of virulence and antimicrobial resistance genes, giving the bacteria geographic differentiation. The aim of this study was to perform in silico analysis of virulence, resistance genes and phylogeny of H. pylori strains obtained from people living in different continents.

Material and Method: Complete gene sequences of 18 H. pylori strains from six continents were downloaded from the National Center for Biotechnology Information (NCBI) database. The phylogeny of the strains, resistance and virulence genes were analyzed by CSI phylogeny, CARD and VFanalyzer, respectively.

Results: African strains were the most distant identity to European strains. A2147G single nucleotide polymorphism associated with clarithromycin resistance was detected in South American and Asian origin. It was determined that strains were differentiated by a total of 95 related virulence genes under eight headings. The cagA, cagE, cagL and vacA genes were found in all strains in Asia.

Conclusion: In conclusion, our study demonstrated that H. pylori strains, whose data were collected in different continents, differ from each other in terms of similarities and there is a serious differ-ence especially in terms of virulence genes.

Keywords

Helicobacter pylori, virulence genes, in silico analysis, geographic phylogeny

Farklı Kıtalardaki Helicobacter pylori Suşlarının Virülans, Direnç Genleri ve Filogenisinin in silico Analizi

Abstract

Amaç:Helicobacter pylori (H. pylori), tüm dünya popülasyonunun %50’sinin mide mukozasını enfekte eden bir bakteridir ve bölgesel farklı tedavi uygulamaları, hem virülans genleri, hemde antimikrobiyal direnç genlerini etkileyerek, bakteriye coğrafik olarak farklılaşma kazandırdığı bilinmektedir. Çalışmamızda, dünyanın farklı kıtalarında yaşayan insanlardan elde edilen H. pylori kökenlerinin filogeni, virülans ve antimikrobiyal direnç genleri açısından in silicoanalizinin yapılması amaçlanmıştır.

Gereç ve Yöntem: Altı kıtadan, toplam 18 H. pylori kökenine ait tüm genom dizileri NCBI veritabanından indirilerek çalışmamıza dahil edildi. Kökenlerin evrimsel yakınlıkları, direnç gen belirteçleri ve virülans genleri, sırasıyla CSI filogeni, CARD ve VFanalyzer online yazılımları ile gerçekleştirildi.

Bulgular: Avrupa kökenine göre en uzak benzerlik Afrika kökenleriydi. Klaritromisin direnci ile ilişkili A2147G tek nokta polimorfizmi Güney Amerika ve Asya kökeninde saptandı. Suşların 8 başlık altın-da toplam 95 ilişkili virülans geni taşıdığı belirlendi. Asya'daki tüm suşlarda cagA, cagE, cagL ve vacA genleri bulundu.

Sonuç: Sonuç olarak, çalışmamızın verileri, farklı kıtalarda tespit edilen H. pylori kökenlerinin birbirinden farklılıklar gösterdiği ve özellikle virülans genleri açısından ciddi farklılık içerdiğini ortaya koymuştur.

Keywords

Helicobacter pylori, virülans genleri, in silicoanaliz, coğrafik filogeni

References

• 1. Marshall BJ, Warren JR. Unidentified curved bacilli in the stom-ach of patients with gastritis and peptic ulceration. Lancet 1984; 1(8390): 1311-5. [CrossRef] google scholar
• 2. Keikha M, Karbalaei M. Correlation between the geographical or-igin of Helicobacter pylori homB-positive strains and their clinical outcomes: a systematic review and meta-analysis. BMC Gastroen-terol 2021; 21: 181. [CrossRef] google scholar
• 3. Kocazeybek B, Tokman HB. Prevalence of Primary Antimicrobial Resistance of H. pylori in Turkey: A Systematic Review. Helico-bacter 2016; 21: 251-60. [CrossRef] google scholar
• 4. Chang WL, Yeh YC, Sheu BS. The impacts of H. pylori virulence fac-tors on the development of gastroduodenal diseases. J Biomed Sci 2018; 25: 68. [CrossRef] google scholar
• 5. de Brito BB, da Silva FAF, Soares AS, Pereira VA, Santos MLC, Sam-paio MM, et al. Pathogenesis and clinical management of Heli-cobacter pylori gastric infection. World J Gastroenterol 2019; 25: 5578-89. [CrossRef] google scholar
• 6. Thyagarajan SP, Ray P, Das BK, Ayyagari A, Khan AA, Dharmalin-gam S, et al. Geographical difference in antimicrobial resistance pattern of Helicobacter pylori clinical isolates from Indian pa-tients: Multicentric study. J Gastroenterol Hepatol 2003; 18: 13738. [CrossRef] google scholar
• 7. Covacci A, Telford JL, Del Giudice G, Parsonnet J, Rappuoli R. He-licobacter pylori virulence and genetic geography. Science 1999; 284(5418): 1328-33. [CrossRef] google scholar
• 8. Gilchrist CA, Turner SD, Riley MF, Petri WA Jr, Hewlett EL. Whole-ge-nome sequencing in outbreak analysis. Clin Microbiol Rev. 2015; 28: 541-63. [CrossRef] google scholar
• 9. Kaas RS, Leekitcharoenphon P, Aarestrup FM, Lund O. Solving the problem of comparing whole bacterial genomes across different sequencing platforms. PLoS One 2014; 9: e104984. [CrossRef] google scholar
• 10. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalat-mand A, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48: D517-D525. [CrossRef] google scholar
• 11. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47(D1): D687-D692. [CrossRef] google scholar
• 12. Delahay RM, Croxall NJ, Stephens AD. Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and con-jugative elements. Mob DNA 2018; 9: 5. [CrossRef] google scholar
• 13. Ofori EG, Adinortey CA, Bockarie AS, Kyei F, Tagoe EA, Adinortey MB. Helicobacter pylori Infection, Virulence Genes' Distribution and Accompanying Clinical Outcomes: The West Africa Situation. Biomed Res Int 2019; 2019: 7312908. [CrossRef] google scholar
• 14. Phuc BH, Tuan VP, Dung HDQ, Binh TT, Tung PH, Tri TD, et al. Helico-bacter pylori type 4 secretion systems as gastroduodenal disease markers. Sci Rep 2021; 11: 4584. [CrossRef] google scholar
• 15. Qumar S, Nguyen TH, Nahar S, Sarker N, Baker S, Bulach D, et al. A comparative whole genome analysis of Helicobacter pylori from a human dense South Asian setting. Helicobacter 2021; 26: e12766. [CrossRef] google scholar
• 16. Saribasak H, Salih BA, Yamaoka Y, Sander E. Analysis of Helico-bacter pylori genotypes and correlation with clinical outcome in Turkey. J Clin Microbiol 2004; 42(4): 1648-51. [CrossRef] google scholar
• 17. Yamaoka Y, Kato M, Asaka M. Geographic differences in gastric cancer incidence can be explained by differences between Heli-cobacter pylori strains. Intern Med 2008; 47: 1077-1083. [CrossRef] google scholar
• 18. Erzin Y, Koksal V, Altun S, Dobrucali A, Aslan M, Erdamar S, et al. Prevalence of Helicobacter pylori vacA, cagA, cagE, iceA, babA2 genotypes and correlation with clinical outcome in Turkish pa-tients with dyspepsia. Helicobacter 2006; 11: 574-80. [CrossRef] google scholar
• 19. Erzin Y, Koksal V, Altun S, Dobrucali A, Aslan M, Erdamar S, et al. Role of host interleukin 1beta gene (IL-1B) and interleukin 1 re-ceptor antagonist gene (IL-1RN) polymorphisms in clinical out-comes in Helicobacter pylori-positive Turkish patients with dys-pepsia. J Gastroenterol 2008; 43(9): 705-10. [CrossRef] google scholar
• 20. Demiryas S, Caliskan R, Saribas S, Akkus S, Gareayaghi N, Kir-musaoglu S, et al. The association between cagL and cagA, va-cAs-m, babA genes in patients with gastric cancer, duodenal ul-cer, and non-ulcer dyspepsia related to Helicobacter pylori. Acta Gastroenterol Belg 2020; 83(3): 385-92. google scholar
• 21. Kocazeybek BS, Caliskan R, Erdamar Cetin S, Ergin S, Kuskucu M, Kepil N, et al. Patterns of EPIYA motifs among cagA-positive He-licobacter pylori strains: a case-control study in a Turkish popula-tion with Eurasian geographical features. J Med Microbiol 2015; 64(10): 1117-23. [CrossRef] google scholar
• 22. Saribas S, Demiryas S, Yilmaz E, Uysal O, Kepil N, Demirci M, et al. Association between human leukocyte antigen gene polymor-phisms and multiple EPIYA-C repeats in gastrointestinal disorders. World J Gastroenterol 2020; 26: 4817-32. [CrossRef] google scholar
• 23. Kocak BT, Saribas S, Demiryas S, Yilmaz E, Uysal O, Kepil N, et al. As-sociation between polymorphisms in HLA-A, HLA-B, HLA-DR, and DQ genes from gastric cancer and duodenal ulcer patients and cagL among cagA-positive Helicobacter pylori strains: The first study in a Turkish population. Infect Genet Evol 2020; 82: 104288. [CrossRef] google scholar
• 24. Sun DL, Gong ZH, Shao SL, Shi XL, Yuan XY, Luo H, et al. virB11 gene potentially involves in ATP metabolism to provide energy in H. pylori infection. Microb Pathog 2020; 142: 104067. [CrossRef] google scholar
• 25. Yamaoka Y. Roles of the plasticity regions of Helicobacter pylori in gastroduodenal pathogenesis. J Med Microbiol 2008; 57: 545-53. [CrossRef] google scholar
• 26. Mwangi C, Njoroge S, Tshibangu-Kabamba E, Moloo Z, Rajula A, Devani S, et al. Whole Genome Sequencing Reveals Virulence Po-tentials of Helicobacter pylori Strain KE21 Isolated from a Kenyan Patient with Gastric Signet Ring Cell Carcinoma. Toxins (Basel) 2020; 12: 556. [CrossRef] google scholar
• 27. Lamichhane B, Wise MJ, Chua EG, Marshall BJ, Tay CY. A novel tax-on selection method, aimed at minimizing recombination, clari-fies the discovery of a new sub-population of Helicobacter pylori from Australia. Evol Appl 2019; 13: 278-89. [CrossRef] google scholar
• 28. Suzuki R, Shiota S, Yamaoka Y. Molecular epidemiology, popula-tion genetics, and pathogenic role of Helicobacter pylori. Infect Genet Evol 2012; 12(2): 203-13. [CrossRef] google scholar
• 29. Boyanova L, Mitov I. Geographic map and evolution of primary Helicobacter pylori resistance to antibacterial agents. Expert Rev Anti Infect Ther 2010; 8(1): 59-70. [CrossRef] google scholar