Dormant phages of Helicobacter pylori reveal distinct populations in Europe

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.University of Malaya-Ministry of Education (UM-MoE) High Impact Research (HIR) Grant UM.C/HIR/MOHE/13/5 (h-50001-00-A000033) and by the Fundação para a Ciência e a Tecnologia (FCT) project grant PTDC/EBB-EBI/119860/2010

Supplementary Material for: Appropriateness of Repeating <b><i>Helicobacter pylori</i></b> Culture and Susceptibility Testing Following Failure of Individualized Antibiotic Therapy

<b><i>Background:</i></b> Current guidelines recommend direct <i>Helicobacter pylori</i> culture and antibiotic susceptibility testing following 2 failed eradication attempts. If this process is followed and yet subsequent treatment is unsuccessful, it is unclear whether susceptibility testing should be repeated. This is the first study to examine the appropriateness of repeated <i>H. pylori</i> culture and susceptibility testing following failure of individualized treatment. <b><i>Methods:</i></b> Between 2007 and 2014, consecutive patients who underwent at least 2 upper gastrointestinal endoscopies with <i>H. pylori</i> culture and susceptibility testing at our institution following several treatment failures were retrospectively identified. Antibiotic susceptibility was recorded and linked to demographic data. <b><i>Results:</i></b> A total of 68 cultures from 34 patients were included (12 (35.3%) men, 41.4 ± 16.6 years), and 20 (58.8%) cultures had a different antibiotic susceptibility profile on repeat testing (8 (23.5%) with new susceptibility and 13 (38.2%) with new resistance). Acquired resistance to clarithromycin, levofloxacin and metronidazole was observed in 9 (26.5%), 2 (5.9%) and 10 (29.4%) cultures, respectively. Subjects with resistance to ≤1 antibiotic at baseline were more likely to develop resistance to at least 1 antibiotic on subsequent culture, compared to subjects with resistance to ≥2 antibiotics at baseline (13 (100%) vs. 5 (23.8%), p < 0.01). <b><i>Conclusion:</i></b> Repeating <i>H. pylori</i> culture and susceptibility testing usually yields new antimicrobial susceptibility data. However, the clinical usefulness of this approach remains unclear