title: Genome sequencing reveals a phage in Helicobacter pylori.
abstract: Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H. pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) of H. pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H. pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H. pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H. pylori.
  
  
  OBJECTIVE
  Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population, and while most of the infected individuals do not develop disease, H. pylori infection doubles the risk of developing gastric cancer. An abundance and diversity of viruses (phages) infect microbial populations in most environments and are important mediators of microbial diversity. Our finding of a 24.6-kb prophage integrated inside an H. pylori genome and the observation of circular integrase gene-containing DNA and phage-like particles inside cells upon UV treatment demonstrate that we have discovered a viable H. pylori phage. The additional finding of integrase genes in a large proportion of screened isolates of diverse geographic origins indicates that the prevalence of prophages may have been underestimated in H. pylori. Since phages are important drivers of microbial evolution, the discovery should be important for understanding and predicting genetic diversity in H. pylori.
authors.affiliation: INSERM U853, Bordeaux, France. philippe.lehours@u-bordeaux2.fr
authors.forename: Philippe
authors.initials: P
authors.lastname: Lehours
authors.forename: Filipa F
authors.initials: FF
authors.lastname: Vale
authors.forename: Magnus K
authors.initials: MK
authors.lastname: Bjursell
authors.forename: Ojar
authors.initials: O
authors.lastname: Melefors
authors.forename: Reza
authors.initials: R
authors.lastname: Advani
authors.forename: Steve
authors.initials: S
authors.lastname: Glavas
authors.forename: Julia
authors.initials: J
authors.lastname: Guegueniat
authors.forename: Etienne
authors.initials: E
authors.lastname: Gontier
authors.forename: Sabrina
authors.initials: S
authors.lastname: Lacomme
authors.forename: António
authors.initials: A
authors.lastname: Alves Matos
authors.forename: Armelle
authors.initials: A
authors.lastname: Menard
authors.forename: Francis
authors.initials: F
authors.lastname: Mégraud
authors.forename: Lars
authors.initials: L
authors.lastname: Engstrand
authors.forename: Anders F
authors.initials: AF
authors.lastname: Andersson
mesh_terms: D001435:Bacteriophages / Q000235:genetics* / Q000302:isolation & purification / Q000648:ultrastructure; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D005753:Gastric Mucosa / Q000382:microbiology; D016680:Genome, Bacterial; D016481:Helicobacter Infections / Q000150:complications / Q000382:microbiology; D016480:Helicobacter pylori / Q000235:genetics* / Q000302:isolation & purification / Q000528:radiation effects / Q000821:virology*; D006801:Humans; D008223:Lymphoma / Q000150:complications; D008242:Lysogeny; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014466:Ultraviolet Rays
chemical_list: D004269:DNA, Bacterial; D004279:DNA, Viral
references.citation: J Mol Evol. 1980 Dec;16(2):111-20
references.pmid: 7463489
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14240-5
references.pmid: 15377794
references.citation: Science. 2003 Mar 7;299(5612):1582-5
references.pmid: 12624269
references.citation: Proc Natl Acad Sci U S A. 2011 May 31;108(22):9238-43
references.pmid: 21562218
references.citation: BMC Genomics. 2010 Jun 10;11:368
references.pmid: 20537153
references.citation: Appl Environ Microbiol. 2007 May;73(10):3423-7
references.pmid: 17400788
references.citation: PLoS One. 2009 Sep 03;4(9):e6859
references.pmid: 19727398
references.citation: Nat Rev Microbiol. 2010 May;8(5):317-27
references.pmid: 20348932
references.citation: Nucleic Acids Res. 1988 Nov 25;16(22):10881-90
references.pmid: 2849754
references.citation: Nucleic Acids Res. 2002 Dec 15;30(24):5391-7
references.pmid: 12490707
references.citation: Mol Microbiol. 2000 Sep;37(5):1052-65
references.pmid: 10972824
references.citation: J Clin Microbiol. 2006 Mar;44(3):1049-58
references.pmid: 16517893
references.citation: Genome Res. 2004 Jun;14(6):1036-42
references.pmid: 15173110
references.citation: FEMS Microbiol Rev. 2006 May;30(3):321-81
references.pmid: 16594962
references.citation: Int J Med Microbiol. 2010 Aug;300(6):357-62
references.pmid: 20452280
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):2106-11
references.pmid: 14762173
references.citation: J Med Microbiol. 1993 Apr;38(4):245-9
references.pmid: 8474115
references.citation: Science. 2008 May 23;320(5879):1047-50
references.pmid: 18497291
references.citation: J Bacteriol. 2004 Mar;186(5):1503-17
references.pmid: 14973019
references.citation: PLoS Genet. 2005 Oct;1(4):e43
references.pmid: 16217547
references.citation: PLoS One. 2010 Mar 24;5(3):e9836
references.pmid: 20352091
references.citation: J Bacteriol. 2002 Feb;184(4):992-1002
references.pmid: 11807059
references.citation: Environ Microbiol. 2008 Jan;10(1):200-7
references.pmid: 17894817
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3723-6
references.pmid: 12824403
references.citation: Nat Rev Microbiol. 2010 Aug;8(8):541-51
references.pmid: 20634809
references.citation: BMC Microbiol. 2009 Sep 08;9:193
references.pmid: 19737407
references.citation: PLoS One. 2010 Feb 05;5(2):e9083
references.pmid: 20140207
references.citation: Helicobacter. 2007 Dec;12(6):616-7
references.pmid: 18001402
references.citation: Brief Bioinform. 2004 Jun;5(2):150-63
references.pmid: 15260895
references.citation: Microbiology (Reading). 2002 Nov;148(Pt 11):3671-3680
references.pmid: 12427957
references.citation: Curr Opin Gastroenterol. 2005 Nov;21(6):653-9
references.pmid: 16220040
references.citation: PLoS One. 2009 Oct 06;4(10):e7297
references.pmid: 19806222
references.citation: DNA Res. 2008 Jun 30;15(3):163-8
references.pmid: 18442984
references.citation: Curr Opin Microbiol. 2008 Oct;11(5):447-53
references.pmid: 18824125
references.citation: Nature. 1997 Aug 7;388(6642):539-47
references.pmid: 9252185
references.citation: PLoS Genet. 2006 Jul;2(7):e120
references.pmid: 16789826
references.citation: Microbiol Mol Biol Rev. 2004 Sep;68(3):560-602, table of contents
references.pmid: 15353570
references.citation: Bioinformatics. 2008 Feb 1;24(3):383-8
references.pmid: 18086685
references.citation: Annu Rev Biomed Eng. 2006;8:343-75
references.pmid: 16834560
references.citation: J Med Microbiol. 1990 Jun;32(2):101-4
references.pmid: 2355390
references.citation: Curr Top Microbiol Immunol. 2009;337:129-71
references.pmid: 19812982
references.citation: J Bacteriol. 2008 Apr;190(7):2434-40
references.pmid: 18223072
references.citation: Gut. 2006 Jun;55(6):775-81
references.pmid: 16322107
references.citation: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14648-53
references.pmid: 8962108
references.citation: Appl Environ Microbiol. 2010 Apr;76(7):2360-5
references.pmid: 20139312
references.citation: Nat Rev Microbiol. 2009 Nov;7(11):828-36
references.pmid: 19834481
references.citation: Nucleic Acids Res. 2001 Sep 15;29(18):3742-56
references.pmid: 11557807
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9999-10004
references.pmid: 16788065
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Nature. 1999 Jan 14;397(6715):176-80
references.pmid: 9923682
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: Nucleic Acids Res. 2010 Oct;38(18):6089-101
references.pmid: 20478826
references.citation: FEMS Microbiol Rev. 2009 Jul;33(4):801-19
references.pmid: 19416364
references.citation: J Biol Chem. 2002 Sep 13;277(37):34191-7
references.pmid: 12105196
references.citation: BMC Genomics. 2009 Jan 05;10:3
references.pmid: 19123947
references.citation: IARC Monogr Eval Carcinog Risks Hum. 1994;61:1-241
references.pmid: 7715068
references.citation: Nature. 2005 Sep 15;437(7057):356-61
references.pmid: 16163346
references.citation: Nat Rev Microbiol. 2007 Jun;5(6):441-52
references.pmid: 17505524
references.citation: Genome Biol Evol. 2011;3:302-8
references.pmid: 21402865
references.citation: Digestion. 1987;37 Suppl 2:16-30
references.pmid: 3622946
references.citation: J Bacteriol. 2000 Aug;182(16):4406-13
references.pmid: 10913072
references.citation: Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2192-7
references.pmid: 10051617
references.citation: Nature. 2007 Feb 22;445(7130):915-918
references.pmid: 17287725
references.citation: Int J Med Microbiol. 2005 Sep;295(5):317-24
references.pmid: 16173498
references.citation: Infect Immun. 2004 Feb;72(2):880-8
references.pmid: 14742532
references.citation: J Bacteriol. 2009 Jan;191(1):447-8
references.pmid: 18952803
references.citation: PLoS Pathog. 2010 May 13;6(5):e1000888
references.pmid: 20485515
references.citation: Methods Mol Biol. 2009;501:113-26
references.pmid: 19066816
references.citation: Mol Microbiol. 2001 Jan;39(2):213-22
references.pmid: 11136444