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.

Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

“…The titer of the progeny phage reached 10 9 PFU/ml after several rounds of amplification using fresh cultures of strain NCTC 11637 with the supernatants from a previous lysate. This differs from the case of phage HP33, which was difficult to amplify (29). During storage, the 1961P phage in crude lysates was stable at 4°C, and no significant loss in infectivity was found after 3 months, as determined by monitoring at intervals of 10 days.…”

“…Vale et al (46) described the release of phage-like particles by H. pylori following UV induction. Lehours et al (29) discovered that temperate phage of the Siphoviridae family was released from H. pylori strain B45 following induction. Wan et al (49) isolated a virulent phage of H. pylori.…”

Complete Genome Sequences of Two Helicobacter pylori Bacteriophages Isolated from Japanese Patients

“…Several bacteriophages (phages) of H. pylori have been reported (4,5,9,12). In general, phages are considered to contribute to bacterial evolution and may affect host features, such as biological behavior, pathogenesis, or adaptation, via their possible roles in horizontal gene transfer and bacteria-phage antagonistic coevolution (4,5,7).…”

“…In general, phages are considered to contribute to bacterial evolution and may affect host features, such as biological behavior, pathogenesis, or adaptation, via their possible roles in horizontal gene transfer and bacteria-phage antagonistic coevolution (4,5,7). In this study, to extend our understanding not only of the H. pylori phages themselves but also of the process of coevolution of H. pylori and its phages, phages KHP30 and KHP40 were isolated from the culture supernatants of East Asian-type isolates from Japanese patients living in distinct geographic regions, and their complete genomic sequences were determined.…”

DNA transfer in the gastric pathogen Helicobacter pylori

“…This diversity can be attributed to altered DNA repair, elevated mutation rates, high frequency of intraspecific recombination, chromosomal DNA transfer events from other species, incorporation of naked DNA from the environment, plasmid mobilization, and integration of acquired DNA in the so-called plasticity zones [4,[8][9][10]. In addition, the presence of phages has been described for several H. pylori strains, acting as another source of bacterial diversity and evolution [11][12][13][14][15]. Using newly developed bioinformatics programs, recent comparative studies of 29 complete genome sequences of strains from different parts of the world revealed a high-resolution picture of the H. pylori population structure as well as the extent and direction of genetic flux between subgroups of the bacterium [16].…”