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

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

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