Genes possibly involved in gastric colonization and persistence
The results of the present study demonstrate that several H. pylori genes involved in acid acclimation, chemotaxis and motility, have counterparts in the H. suis genome. These genes are known to be essential for colonization of the human gastric mucosa [27–32].
Several OMP coding sequences were identified by comparative analyses with H. pylori and other bacterial species. H. suis contains some similar members of the major OMP families described in H. pylori . Some of these OMPs have been described to be involved in adhesion of H. pylori to the gastric mucosa, which is widely assumed to play an important role in the initial colonization and long-term persistence in the human stomach. These include the gastric epithelial cell adhesin HorB  and the surface lipoprotein, H. pylori adhesin A (HpaA). HpaA, also annotated as neuraminyllactose-binding hemagglutinin, is found exclusively in Helicobacter and binds to sialic acid-rich macromolecules present on the gastric epithelium . On the other hand, H. suis lacks homologs of several other H. pylori adhesion factors, including genes coding for the blood group antigen binding adhesins babA (hopS) and babB (hopT), the sialic acid binding adhesins sabA (hopP) and sabB (hopO), and the adherence-associated lipoproteins alpA (hopC) and alpB (hopB) .
H. suis contains a fibrinonectin/fibrinogen-binding protein coding gene, which may enhance its adherence to injured gastric tissue. Damage to host epithelial cells may indeed expose fibronectin and other extracellular matrix components. Strong homology was found with fibronectin-binding proteins of H. felis (YP_004072974), H. canadensis (ZP_048703091) and Wolinella succinogenes (NP_907753). To our knowledge, no exact function has been given to these proteins in these species. In Campylobacter jejuni, however, fibronectin-binding proteins CadF and FlpA have been shown to be involved in adherence to and/or invasion of host's intestinal epithelial cells [37, 38]. According to the bioinformatics tools used here, the H. suis fibronectin-binding protein lacks a transmembrane helix or signal peptidase cleavage site, indicating that it is not surface exposed or secreted. Its real role in colonization therefore remains to be elucidated.
Three genes involved in sialic acid biosynthesis (neuA, neuB, and wecB) were annotated in the H. suis genome, indicating that this bacterium may decorate its surface with sialic acid. The presence of surface sialylation has been studied extensively in pathogenic bacteria, where it contributes to evasion of the host complement defense system .
Additionally, H. suis possesses genes encoding enzymes involved in oxidative-stress resistance (napA, sodB, katA, mutS, mdaB, and peroxiredoxin coding sequence). This indicates that H. suis may harbour a defense mechanism against the host inflammatory response, contributing to the ability of chronic gastric colonization by this bacterium .
Type IV secretion systems in H. suis
Two partial T4SS were predicted in the H. suis genome, namely the comB cluster and the tfs3 system. The H. suis comB system probably plays a role in genetic transformation [41, 42]. Transformation of DNA can be responsible for the high degree of diversity among H. suis strains as has been recently demonstrated by multilocus sequence typing of available H. suis strains . The role of the H. pylori tfs3 secretion system in pathogenesis is not exactly known. Seven genes of the tfs3 cluster are homologs of genes involved in type IV secretion: virB4, virB11, and virD4 code for ATPases which move substrates to and through the pore. The latter is coded by transmembrane pore genes virB7, virB8, virB9, and virB10 . All these genes, except virB7 were identified in H. suis, indicating that the H. suis tfs3 can be important in transmembrane transport of substrates in H. suis.
The H. pylori cag pathogenicity island (cag PAI) region encodes a T4SS allowing H. pylori to insert the cytotoxin-associated antigen A (CagA) into the host cell. This process results in altered host cell structure, an increased inflammatory response, and a higher risk for gastric adenocarcinoma . Although H. suis possesses two members of the H. pylori cag PAI (cag23/E and cagX), the majority of genes, including the gene coding for pathology-causing protein (CagA), were not identified. This indicates that HS1T and HS5 lack a functional cag protein transporter secretion system.
Genes possibly involved in induction of gastric lesions
Genomic comparison of H. suis with H. pylori resulted in the identification of additional genes possibly associated with virulence in H. suis. A H. suis homolog of the H. pylori vacA was detected. VacA is both a cytotoxin of the gastric epithelial cell layer, and an immunomodulatory toxin of H. pylori . H. pylori contains either a functional or non-functional vacA. The H. suis vacA homolog exhibits no vacA signal sequence, indicating that it might encode a non-functional cytotoxin . In vitro and in vivo studies with a knockout mutant of the H. suis vacA could clarify the functionality of the vacA homolog in this Helicobacter species.
Strong homology was found with two H. pylori virulence-associated genes namely napA, encoding the HP-NapA and ggt, encoding HP-GGT. The H. pylori GGT has been identified as an apoptosis-inducing protein [48, 49]. The HP-NapA protein is designated as a proinflammatory and immunodominant protein by stimulating production of oxygen radicals and IL-12 from neutrophils and recruiting leukocytes in vivo [50, 51]. Moreover, HP-NapA also plays a role in protecting H. pylori from oxidative stress by binding free iron . H. suis contains homologs of two H. pylori genes coding for plasminogen-binding proteins, pgbA and pgbB. The corresponding proteins, PgbA and PgbB bind host plasminogen, which subsequently can be activated to plasmin and may contribute to obstructing the natural healing process of gastric ulcers [53, 54]. The biological role of the H. suis pgbA and B homologs in chronicity of gastric ulceration is uncertain, as no exact membrane association was found in the corresponding proteins.
The risk to develop MALT lymphomas in H. suis infected human patients is higher than after infection with H. pylori [5, 14]. Homologs encoding the H. pylori flavodoxin (fldA) and its electron donor, the POR enzyme complex (porA to D) were found in H. suis. The H. pylori flavodoxin protein (FldA) has been proposed to play a role in the pathogenesis of H. pylori-associated MALT lymphoma, as antibodies against the H. pylori FldA protein were more prevalent in patients with MALT lymphomas compared to patients with other H. pylori- related diseases . Besides, insertion mutagenesis of the fldA and the por complex has shown that these genes are essential for the survival of H. pylori . These observations indicate that fldA and its por complex may play a role in gastric colonization of H. suis and MALT lymphoma development in H. suis infected people.
Recently, the genomes of the carcinogenic H. pylori strain B38 and the carcinogenic and ulcerogenic Helicobacter mustelae have been sequenced [57, 58]. Both helicobacters lack homologs of major H. pylori virulence genes (e.g. cagA, babA/B, sabA/B), which are also absent in the H. suis genome. Additionally, H. mustelae lacks a vacA homolog. Despite this absence, infection with H. pylori strain B38 and H. mustelae has been associated with gastric MALT lymphomas and other gastric disorders. Whole genome sequencing data are also available from H. acinonychis strain Sheeba, a gastric pathogen of large felines. Similar to H. suis, H. acinonychis lacks a cag PAI as well as genes encoding BabA/B and SabA/B. Both species contain a vacA homolog, which for H. acinonychis has been described to be fragmented [59, 60].
H. suis contains a mviN homolog. This gene has been described to be a virulence factor of several bacterial species, such as Burkholderia pseudomallei and Vibrio alginolyticus [61, 62]. In addition to virulence, MviN has been described to be essential for in vitro growth of these and other bacteria [61–63]. The biological significance of mviN in the Helicobacter genus, however, remains to be elucidated.