title: Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins.
abstract: Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3' end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.
authors.affiliation: Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal.|Université de Bordeaux, Centre National de Référence des Campylobacters et Hélicobacters, Bordeaux, France.
authors.forename: Filipa F
authors.initials: FF
authors.lastname: Vale
authors.affiliation: Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisboa, Portugal.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Nunes
authors.affiliation: National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisboa, Portugal.
authors.forename: Mónica
authors.initials: M
authors.lastname: Oleastro
authors.affiliation: Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisboa, Portugal.
authors.forename: João P
authors.initials: JP
authors.lastname: Gomes
authors.affiliation: Innovation and Tecnhology Unit, Department of Human Genetics, National Institute of Health, Lisboa, Portugal.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Sampaio
authors.affiliation: National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisboa, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Rocha
authors.affiliation: Department of Biochemistry and Human Biology, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
authors.forename: Jorge M B
authors.initials: JM
authors.lastname: Vítor
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
authors.forename: Lars
authors.initials: L
authors.lastname: Engstrand
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Pascoe
authors.affiliation: Institute of Life Science, Swansea University Medical School, Swansea, UK.
authors.forename: Elvire
authors.initials: E
authors.lastname: Berthenet
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
authors.affiliation: Institute of Life Science, Swansea University Medical School, Swansea, UK.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Hitchings
authors.affiliation: Université de Bordeaux, Centre National de Référence des Campylobacters et Hélicobacters, Bordeaux, France.
authors.forename: Francis
authors.initials: F
authors.lastname: Mégraud
authors.affiliation: UM Marshall Centre and Department of Medical Microbiology, University of Malaysia, Kuala Lumpur, Malaysia.
authors.forename: Jamuna
authors.initials: J
authors.lastname: Vadivelu
authors.affiliation: Université de Bordeaux, Centre National de Référence des Campylobacters et Hélicobacters, Bordeaux, France.|INSERM U1053, Bordeaux, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lehours
mesh_terms: D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D016480:Helicobacter pylori / Q000821:virology*; D009030:Mosaicism; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames; D010802:Phylogeny; D039002:Prophages / Q000235:genetics*; D017422:Sequence Analysis, DNA