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Background   Helicobacter pylori  is a Gram-negative bacterium which mainly causes peptic ulcer disease in human, but is also the predominant cause of stomach cancer. It has been coevolving with human since 120,000 years and, according to Multi-locus sequence typing (MLST),  H. pylori  can be classified into seven major population types, namely, hpAfrica1, hpAfrica2, hpNEAfrica, hpEastAsia, hpAsia2, hpEurope and hpSahul.  Helicobacter pylori  harbours a large number of restriction-modification (R-M) systems. The methyltransferase (MTase) unit plays a significant role in gene regulation and also possibly modulates pathogenicity. The diversity in MTase can act as geomarkers to correlate strains with the phylogeographic origins. This paper describes the complete genome sequence and methylome of gastric pathogen  H. pylori  belonging to the population hpNEAfrica.    Results  In this paper, we present the complete genome sequence and the methylome profile of  H. pylori  hpNEAfrica strain HP14039, isolated from a patient who was born in Somalia and likely to be infected locally during early childhood prior to migration. The genome of HP14039 consists of 1,678,260 bp with 1574 coding genes and 38.7% GC content. The sequence analysis showed that this strain lacks the cag pathogenicity island. The  vacA  gene is of S2M2 type. We have also identified 15 methylation motifs, including WCANHNNNNTG and CTATAYG that were not previously described.    Conclusions  We have described the complete genome of  H. pylori  strain HP14039. The information regarding phylo-geography, methylome and associated metadata would help scientific community to study more about hpNEAfrica population type.    Electronic supplementary material  The online version of this article (10.1186/s13099-019-0284-y) contains supplementary material, which is available to authorized users.

The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039