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Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia., We thank the entities that financially supported the development of this work. A.B.M. is a recipient of a scholarship from the Centro de Estudios Interdisciplinarios Básicos y Aplicados (CEIBA) Foundation, Colombia; and A.B.M., C.A., J.S., and A.A.T.-R. are recipients of a project grant (120380763025/2018) from MinCiencias, Colombia. The work is partially supported by Research Vice-Rectory, Pontificia Universidad Javeriana (PPTA_7676) and F.P.I.T. BanRepCultural (project 3956). F.F.V. is financed by national funds from the Fundação para a Ciência e a Tecnologia (FCT) through an assistant researcher grant (CEECIND/03023/2017), a project grant (PTDC/BTM-SAL/28978/2017), and projects UIDB/04138/2020 and UIDP/04138/2020; these funds partially supported this work. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

We present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from children. This will be important for future studies of comparative genomics in order to better understand the virulence determinants underlying peptic ulcer disease. This work was supported by the FCT-PTDC/BIM-MEC/1051/2012 grant from the Fundação para a Ciência e a Tecnologia (FCT) (to M.O.). A.N. and F.F.V. are recipients of postdoctoral fellowships (SFRH/BPD/75295/2010 and SFRH/BPD/95125/2013, respectively) from FCT, and R.R. is a recipient of a fellowship (BRJ-DDI/2012) from the National Institute of Health.

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., IMPORTANCE 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.