The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

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

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 antimicrobi- al 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 phy- logeny 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 Europe- an 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.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 antimik- robiyal direnç genlerini etkileyerek, bakteriye coğrafik olarak fark- lılaşma kazandırdığı bilinmektedir. Çalışmamızda, dünyanın farklı kıtalarında yaşayan insanlardan elde edilen H. pylori kökenlerinin filogeni, virülans ve antimikrobiyal direnç genleri açısından in silico analizinin 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 kökenle- riydi. 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 vi

Resuscitation of the Helicobacter pylori Coccoid Forms by Resuscitation Promoter Factor Obtained from Micrococcus Luteus

Helicobacter pylori is a gram negative, spiral-shaped, and microaerophilic bacteria which can cause life-threatening diseases. It is known that more than 55% of the human population in the world is already infected by this bacterium. The traditional treatment of H. pylori infection consists of a combination of two or more antibiotics. However, H. pylori has evolved to turning its shape from spiral to coccoid form in the presence of antibiotics and this decreases the therapeutic efficacies of conventional antibiotic applications. Resuscitation promoter factor (RPF) is a protein secreted by Micrococcus luteus have significant resuscitation effects on some bacteria especially in the group of viable but non-culturable (VBNC) pathogens. However, there is no study in the literature investigating the resuscitation effects of RPF derived from M. luteus on H. pylori in order to change its form from coccoid to spiral. The purpose of this study is to investigate the resuscitation effect of RPF-containing metabolites isolated from M. luteus on the morphological transformation of H. pylori coccoid forms to spiral forms in order to increase their susceptibilities to antibiotic treatments. Rpf-containing metabolites were primarily obtained from M. luteus culture supernatants. H. pylori was exposed to five different conditions such as prolonged culture, incubation at + 4 degrees C, incubation at + 22 degrees C, cultivation in PBS and treatment with kanamycin in order to induce transformations of bacteria to coccoid forms. Induced H.pylori coccoids were characterized by inverted microscope, UV spectrophotometer, SEM imaging, and flow-cytometer. As a result, it was found that the most suitable condition for inducing coccoid forms was cultivation of bacteria with kanamycin. Followingly, different concentrations of RPF-containing metabolites were applied on H. pylori coccoids induced by kanamycin. For the first time in this study, it was determined that the Rpf-containing metabolites obtained from M. luteus demonstrated very high resuscitation effect on kanamycin-induced H. pylori coccoid forms. This new approach for resuscitation of H. pylori coccoids is thought to play an important role in increasing the treatment effectiveness of the conventional antibiotics against the infection