Genome sequence of Helicobacter suis supports its role in gastric pathology.

Helicobacter (H.) suis has been associated with chronic gastritis and ulcers of the pars oesophagea in pigs, and with gastritis, peptic ulcer disease and gastric mucosa-associated lymphoid tissue lymphoma in humans. In order to obtain better insight into the genes involved in pathogenicity and in the specific adaptation to the gastric environment of H. suis, a genome analysis was performed of two H. suis strains isolated from the gastric mucosa of swine. Homologs of the vast majority of genes shown to be important for gastric colonization of the human pathogen H. pylori were detected in the H. suis genome. H. suis encodes several putative outer membrane proteins, of which two similar to the H. pylori adhesins HpaA and HorB. H. suis harbours an almost complete comB type IV secretion system and members of the type IV secretion system 3, but lacks most of the genes present in the cag pathogenicity island of H. pylori. Homologs of genes encoding the H. pylori neutrophil-activating protein and γ-glutamyl transpeptidase were identified in H. suis. H. suis also possesses several other presumptive virulence-associated genes, including homologs for mviN, the H. pylori flavodoxin gene, and a homolog of the H. pylori vacuolating cytotoxin A gene. It was concluded that although genes coding for some important virulence factors in H. pylori, such as the cytotoxin-associated protein (CagA), are not detected in the H. suis genome, homologs of other genes associated with colonization and virulence of H. pylori and other bacteria are present.

Introduction

Helicobacter (H.) suis is a very fastidious, spiral-shaped, Gram-negative bacterium requiring a biphasic culture medium at pH 5 enriched with fetal calf serum, and a microaerobic atmosphere for in vitro growth [1]. H. suis colonizes the stomach of more than 60% of slaughter pigs [1,2]. Although the exact role of H. suis in gastric disease in pigs is still unclear, it has been associated with chronic gastritis [3,4] and ulcers of the pars oesophagea of the stomach [5-7]. This may result in significant economic losses due to sudden death, decreased feed intake and reduced daily weight gain [8]. A reduction of approximately 20 g/day in weight gain was observed in animals experimentally infected with H. suis, compared to the non-infected control animals [9].

Bacterial gastric disorders in humans are mainly caused by Helicobacter pylori [10]. However, non-Helicobacter pylori helicobacters (NHPH) have also been associated with human gastric disease with a prevalence ranging between 0.2 and 6% [5]. H. suis is the most frequent NHPH species found in humans, where it was originally named "H. heilmannii" type 1 [11]. There are strong indications that pigs may serve as a source of infection for humans [5,12]. In the human host, H. suis has been associated with peptic ulcer disease [13], gastric mucosa-associated lymphoid tissue (MALT) lymphoma [14] and chronic gastritis [15]. In rodent models of human gastric disease, the bacterium causes severe inflammation and MALT lymphoma-like lesions [16].

Up to now, little is known about the pathogenesis of H. suis infections. To improve understanding in the genes playing a role in pathogenicity, gastric colonization and persistence of H. suis, a genome-wide comparison with the well-investigated H. pylori genome was performed. Some virulence factors may indeed be similar for both bacteria. As there may also be differences, ab initio annotations of the H. suis genome were performed as well.

Materials and methods

Genome sequencing

A pyrosequencing (454 Life Sciences Corporation, Branford, CT, USA) assay was applied to the genome of the type strain of H. suis (HS1T = LMG 23995T = DSM 19735T) and H. suis strain 5 (HS5), isolated from the gastric mucosa of two different swine, according to the method described by Baele et al. [1]. Quality filtered sequences were assembled into contigs using a 454 Newbler assembler (Roche, Branford, CT, USA).

Functional annotation

In order to maximize the number of quality gene annotations, two different annotating approaches were followed: cross-mapping with three Helicobacter pylori strains (26695, Shi470, and G27 with NCBI accession numbers NC_000915, NC_010698, and NC_011333, respectively), and ab initio annotation.

Cross-mapping annotation

A custom BLAST [17] database was created from the HS1T and HS5 genomic contigs. The H. pylori proteome and non-coding RNAs were aligned (tblastn program of the BLAST suite, e threshold set to 10-3) to the H. suis database. For each BLAST hit the following additional information was analysed: 1) (secretion) signal peptide cleavage site if present, as assessed by the SignalP 3.0 program [18,19]; 2) specifications of transmembrane helices (number, start and end positions, presumed topology with regard to the cytoplasmic membrane) if present, as assessed by the TMHMM program [20]; 3) an estimate of the ribosome binding strength of the mRNA region preceding the most probable start codon. Ribosome binding strength was estimated by applying two established facts: i) on an mRNA strand, usually within 20 nucleotides before the actual start codon, the reverse complement of 5 to 7 nucleotides near the 16S rRNA 3' end acts as an attractor and positioner for the ribosomal small subunit; this region is known as the Shine-Dalgarno sequence [21,22]; ii) in Gram-negative bacteria an AU-rich mRNA region some 16 nucleotides long and immediately preceding the Shine-Dalgarno sequence may also attract and position ribosomes to help initiate translation of the correct, biologically active gene product [23,24]. For H. suis, the Shine-Dalgarno sequence was determined to be a subsequence of AGGAGGU (which is the reverse complement of the 3' end of the 16S rRNA), and the minimum AU-richness (equivalent to ribosome binding capacity) of the preceding region was arbitrarily set to 10/16. For each theoretical ORF a range of possible start codons was scored; the higher the similarity to the ideal Shine-Dalgarno sequence, or the AU-richer the preceding region, or the better a combination of both, the more likely the potential start codon is to be the actual start codon.

Ab initio annotation

For ab initio annotation, theoretical open reading frames (ORFs) were first determined using the EMBOSS getorf tool (with minimum ORF length set to 90 nucleotides, and taking all alternative start codons into account) [25]. All ORFs were translated subsequently, and BLAST (blastp program) was performed with an e threshold of 10-15 against the Uniprot-KB universal protein database. The generalist algorithm of getorf yielded roughly a tenfold of the expected natural ORFs, reducing the risk of false negatives. In order to keep the false positive rate low, extra parameters were considered: 1) percentage alignment between query and hit ORFs; 2) percentage similarity or conservation between aligned portions of query and hit ORFs; 3) ribosome binding strength (for more details see above). To determine the presence of one or more conserved domains a rpsblast search (with default parameter values) was carried out for every single theoretical ORF against the compiled Conserved Domain Database which holds protein domain alignments from several other database sources [26].

Results

General features of the H. suis genome

In the HS1T genome a total of 1 635 292 base pairs and in the HS5 genome 1 669 960 bp were sequenced, both with an average GC content of 40%. In contrast to H. pylori, only one copy of both the 16S and 23S rRNA genes was detected, but like H. pylori, H. suis has three copies of the 5S rRNA gene. Thirty-eight transfer RNAs were identified. On the whole, 1266 ORFs from HS1T and 1257 from HS5 were detected, of which 194 and 191 encoded hypothetical proteins respectively. In 98 and 92 ORFs a signal peptide cleavage site was detected, demonstrating predicted secreted proteins of HS1T and HS5 respectively. The TMHMM program predicted 210 and 206 proteins with at least one transmembrane helix for HS1T and HS5 respectively. The sequence fraction identical for HS1T and HS5 is henceforward described together as the "H. suis genome".

Genes possibly involved in gastric colonization and persistence

Homologs of H. pylori genes involved in acid acclimation, chemotaxis, adhesion to gastric epithelial cells, oxidative stress resistance (Table 1), and motility were detected in the H. suis genome. The latter were identified as a flagellar biosystem similar to that of H. pylori [27]. Moreover, H. suis contains a fibrinonectin/fibrinogen-binding protein coding gene, but the corresponding protein lacks a transmembrane helix or signal peptide cleavage site according to the bioinformatics tools mentioned earlier. Homologs coding for CMP-N-acetylneuraminic acid synthetase (NeuA) (HSUHS1_0474, HSUHS5_0481), sialic acid synthase (NeuB) (HSUHS1_0477, HSUHS5_0478), and UDP-N-acetylglucosamine-2-epimerase (WecB) (HSUHS1_1107, HSUHS5_0784) were observed as well.

Table 1

Genes associated with pH homeostasis, chemotaxis, adhesion to epithelial cells, and oxidative stress resistance in the genome of H. suis type strain 1 (HS1T) and H. suis strain 5 (HS5).

Group	Gene detected in HS1T	Gene detected in HS5	Description of homolog	Percentage of sequence aligned (of which % conserved) with described homolog1
pH homeostasis	HSUHS1_0708	HSUHS5_0286	Urease subunit alfa (ureA) of H. heilmannii	100 (94)
	HSUHS1_0707	HSUHS5_0285	Urease subunit beta (ureB) of H. heilmannii	100 (94)
	HSUHS1_0706	HSUHS5_0284	Urease transporter (ureI) of H. felis	100 (89)
	HSUHS1_0705	HSUHS5_0283	Urease accessory protein (ureE) of H. bizzozeronnii	100 (84)
	HSUHS1_0704	HSUHS5_0282	Urease accessory protein (ureF) of H. bizzozeronnii	100 (84)
	HSUHS1_0702	HSUHS5_0280	Urease accessory protein (ureH) of H. bizzozeronnii	96 (84)
	HSUHS1_0703	HSUHS5_0281	Urease accessory protein (ureG) of H. bizzozeronnii	100 (95)
	HSUHS1_0133	HSUHS5_0547	Hydrogenase expression/formation protein (hypA) of H. pylori	98 (83)
	HSUHS1_0615	HSUHS5_0817	Hydrogenase expression/formation protein (hypB) of H. pylori	99 (91)
	HSUHS1_0616	HSUHS5_0816	Hydrogenase expression/formation protein (hypC) of H. pylori	98 (89)
	HSUHS1_0617	HSUHS5_0815	Hydrogenase expression/formation protein (hypD) of H. achinonychis	98 (80)
	HSUHS1_0081	HSUHS5_1197	l-Asparaginase II (ansB) of H. pylori	98 (64)
	HSUHS1_0230	HSUHS5_1130	Arginase (rocF) of H. pylori	99 (75)
	HSUHS1_0888	HSUHS5_0231	Acylamide amidohydrolase (amiE) of H. pylori	100 (93)
	HSUHS1_0680	HSUHS5_0265	Formamidase (amiF) of H. pylori	100 (98)
	HSUHS1_0161	HSUHS5_1077	α-Carbonic anhydrase of H. pylori	92 (69)
	HSUHS1_0391	HSUHS5_0874	Aspartase (aspA) of H. acinonychis	100 (89)
Chemotaxis	HSUHS1_1004	HSUHS5_0649	CheA-MCP interaction modulator of H. pylori	99 (79)
	HSUHS1_1003	-	Bifunctional chemotaxis protein (cheF) of H. pylori	82 (86)
	HSUHS1_1002	HSUHS5_0775	Purine-binding chemotaxis portein (cheW) of H. pylori	98 (91)
	HSUHS1_0538	HSUHS5_0706	Chemotaxis protein (cheV) of H. pylori	100 (92)
	HSUHS1_0846	HSUHS5_0081	Putative chemotaxis protein of H. pylori	100 (79)
	HSUHS1_0299	HSUHS5_0250	Chemotaxis protein (cheY) of H. pylori	100 (95)
	HSUHS1_1001	HSUHS5_0774	Methyl-accepting chemotaxis protein (tlpA) of H. pylori	100 (60)
	HSUHS1_0286	HSUHS5_0256	Methyl-accepting chemotaxis protein ( tlpB) of H. pylori	98 (63)
	HSUHS1_0479	HSUHS5_0476	Methyl- accepting chemotaxis protein of H. acinonychis	100 (66)
	HSUHS1_0196	HSUHS5_0122	Methyl- accepting chemotaxis protein of Campylobacter upsaliensis 2	99 (53)
	HSUHS1_0141	HSUHS5_0641	Methyl- accepting chemotaxis protein of Campylobacter fetus subsp. fetus 2	99 (64)
	HSUHS1_0763	-	Methyl- accepting chemotaxis protein of Methylibium petroleiphilum 2	83 (52)
	HSUHS1_0944	HSUHS5_0990	Methyl-accepting chemotaxis sensory transducer Marinomonas sp.2	57 (59)
Adhesion	HSUHS1_0666	HSUHS5_1053	Outer membrane protein (horB) of H. pylori	100 (63)
	HSUHS1_0354	HSUHS5_0398	Neuraminyllactose-binding hemagglutinin (hpaA) of H. acinonychis	94 (77)
Oxidative stress resistance	HSUHS1_1147	HSUHS5_0608	Catalase (katA) of H. acinonychis	95 (82)
	HSUHS1_0549	HSUHS5_1206	Mismatch repair ATPase (mutS) of H. hepaticus	99 (60)
	HSUHS1_0163	HSUHS5_0495	Superoxide dismutase (sodB) of H. pylori	100 (90)
	HSUHS1_1186	HSUHS5_0005	Bacterioferritin co-migratory protein of H. hepaticus	99 (72)
	HSUHS1_0683	HSUHS5_0262	NAD(P)H quinone reductase (mdaB) of Campylobacter fetus subsp. fetus	97 (68)
	HSUHS1_0689	HSUHS5_0268	Peroxiredoxin of H. pylori 3	100 (92)

1 Resulting from tblastn-based cross-mapping of the H. pylori proteome to the H. suis HS1T and HS5 genomes and blastp-based ab initio analyses of the translated H. suis HS1T and HS5 ORFs against the Uniprot-KB universal protein database. Differences between HS1T and HS5 homologs ≤ 1%.

2 Lacking in other Helicobacter genomes available at GenBank.

3 Member of the 2-Cys peroxiredoxin superfamily.

Genes encoding putative outer membrane proteins (OMPs) in relation to H. pylori OMPs are presented in Additional file 1 Table S1. Genes coding for members of major H. pylori OMP families (Hop, Hor, Hof proteins, iron-regulated and efflux pump OMPs) could be aligned with the H. pylori genome. Both H. suis strains contain the hof genes hofA, C, E, F, the hop genes hopE, G-2 and H, and the hor genes horB, C, D, and J. Additionally, HS1T contains homologs of the hopW protein precursor and horE, whereas HS5 possesses additional homologs of horA, horF, and horL. No members of the Helicobacter outer membrane (hom) family were detected in H. suis. Besides the major H. pylori OMP family proteins, the H. suis genome contains some predicted OMPs based on their N-terminal pattern of alternating hydrophobic amino acids similar to porins, encompassing omp29 for HS1T and omp11 and omp29 for HS5. A 491 amino acids membrane-associated homolog of the virulence factor MviN, aligned for 92% with the MviN homolog of H. acinonychis (Hac_1250), was also present in H. suis.

Type IV secretion systems in H. suis

Of the H. pylori type IV secretion systems (T4SS), only two members of the cag pathogenicity island (cagPAI) were identified in the H. suis genome (cag23/E and cagX). Most members of the comB transport apparatus were present. These include comB2, B3, B6, B8 and a number of additional genes not classified as comB: recA, comE, comL and dprA. H. suis possesses genes encoding VirB- and VirD-type ATPases (virB4, B8, B9, B10, B11, and virD2, D4), all designated members of the H. pylori type IV secretion system 3 (tfs3). The HS1T and HS5 T4SS are presented in Table 2.

Table 2

H. suis strain 1 (HS1T) and strain 5 (HS5) homologs of H. pylori and other Helicobacter sp. type IV secretion system genes.

Homolog	Gene detected in HS1T	Gene detected in HS5	Description of corresponding protein	Percentage of sequence fraction aligned (of which % conserved) with Helicobacter homolog1
cag pathogenicity island
cag23/E of H. pylori	HSUHS1_0731	HSUHS5_1234	DNA transfer protein	81 (42)
cagX of H. pylori	HSUHS1_0964	HSUHS5_0688	Conjugal plasmid transfer protein	92 (71)
comB system
comB2 of H. acinonychis	HSUHS1_1181	HSUHS5_0010	ComB2 protein	96 (64)
comB3 of H. acinonychis	HSUHS1_1182	HSUHS5_0009	ComB3 competence protein	95 (77)
comB6 of H. pylori	HSUHS1_0337	-	NADH-ubiquinone oxidoreductase	70 (85)
comB8 of H. pylori	HSUHS1_0747	Overlap with virB8	comB8 competence protein	93 (66)
trbL of H. pylori	HSUHS1_0755	HSUHS5_0054	TrbL protein	99 (77)
comE of H. acinonychis	HSUHS1_0314	HSUHS5_0381	Competence locus E	94 (55)
comL of H. pylori	HSUHS1_0722	HSUHS5_0300	Competence protein	99 (84)
dprA of H. acinonychis	HSUHS1_0096	HSUHS5_0824	DNA processing protein	99 (70)
recA of H. hepaticus	HSUHS1_0672	HSUHS5_1058	Recombinase A	97 (84)
virB -homologs
virB4 of H. pylori	HSUHS1_0960	HSUHS5_0692	DNA transfer protein	98 (68)
virB8 of H. pylori	HSUHS1_0963	HSUHS5_0689	DNA transfer protein	91 (61)
virB9 of H. cetorum	HSUHS1_0319	-	VirB9 protein	76 (69)
virB10 of H. cetorum	HSUHS1_0320	-	VirB10 protein	90 (77)
putative virB9 of H. pylori	-	HSUHS5_0372	Putative VirB9 protein	100 (86)
putative virB10 of H. pylori	-	HSUHS5_0371	Putative VirB10 protein	97 (87)
virB11 of H. pylori	HSUHS1_0750	HSUHS5_0368	VirB11 protein	100 (98)
virB11 of H. cetorum	HSUHS1_0965	-	VirB11 protein	95 (71)
virB11-like of H. pylori (HPSH_04565)	-	HSUHS5_0686	VirB11-like protein	98 (72)
virB11-like of H. pylori (HPSH_07250)	HSUHS1_0036	HSUHS5_0600	Type IV ATPase	100 (75)
virD - homologs
virD2 of H. cetorum	HSUHS1_0752	HSUHS5_0414	VirD2 protein (relaxase)	100 (90)
virD4 of H.pylori	HSUHS1_0870	HSUHS5_0257	VirD4 protein (conjugation protein)	82 (78)

1 Resulting from tblastn-based cross-mapping of the H. pylori proteome to the H. suis HS1T and HS5 genomes and blastp-based ab initio analyses of the translated H. suis HS1T and HS5 ORFs against the Uniprot-KB universal protein database. Differences between HS1T and HS5 homologs ≤ 1%.

Genes possibly involved in induction of gastric lesions

Homologs of H. pylori genes involved in induction of gastric lesions in the H. suis genome are summarized in Table 3. Homology searches with the H. pylori vacuolating cytotoxin A gene (vacA) identified HSUHS1_0989 in HS1T. The corresponding protein, which is exceptional in that it is one of the longest in the world of prokaryotes, possesses three small conserved VacA regions (residues 490-545, 941-995, and 1043-1351), followed by an autotransporter region (residues 2730-2983). The amino acid sequence of the HS5 homolog (HSUHS5_0761) could be aligned for 22% with the H. pylori strain HPAG1 sequence, and possesses only one conserved VacA region (residues 242-298), followed by an autotransporter region (1258-1510). In both vacA homologs, no signal sequence was determined. Additionally, an ulcer-associated adenine-specific DNA methyltransferase (HSUHS1_0375, HSUHS5_0957) coding sequence was identified, whereas a molecular homolog of the ulcer-associated restriction endonuclease (iceA) could not be discovered in H. suis. H. suis contains homologs of pgbA and pgbB encoding plasminogen-binding proteins, though both lacking a transmembrane helix or signal peptide cleavage site according to the bioinformatics tools mentioned earlier. H. suis harbours homologs of genes coding for the H. pylori neutrophil-activating protein (HP-NapA) and γ-glutamyl transpeptidase (HP-GGT). Homologs encoding the H. pylori flavodoxin fldA and the pyruvate-oxidoreductase complex (POR) members porA, porB, porC, and porD were also identified in H. suis.

Table 3

Homologs of H. pylori genes involved in induction of gastric lesions in the H. suis type strain 1 (HS1T) and strain 5 (HS5) genome.

Gene detected in HS1T	Gene detected in HS5	Gene name	Protein annotation/function in H. pylori	Sequence fraction HS1T/HS5 aligned with H. pylori homolog (%)1	Aligned sequence fraction HS1T/HS5 conserved with H. pylori homolog (%)1	References
HSUHS1_0989	HSUHS5_0761	vacA	Vacuolating cytotoxin A: host cell vacuolation, apoptosis-inducing, immunosuppresive	63/22	45/72	[46]
HSUHS1_0265	HSUHS5_0449	ggt	γ-glutamyl transpeptidase: apoptosis-inducing, immunosuppresive	99/99	86/86	[48,49,64]
HSUHS1_1177	HSUHS5_0014	napA	Neutrophil-activating protein A: proinflammatory	99/99	83/83	[50,51]
HSUHS1_1067	HSUHS5_1177	fldA	Electron acceptor of the pyruvate oxidoreductase enzyme complex, associated with gastric MALT lymphoma in humans	96/98	84/83	[55,56]
HSUHS1_0403	HSUHS5_0887	pgbA	Plasminogen-binding protein	60/60	72/72	[53,54]
HSUHS1_1192	HSUHS5_0523	pgbB	Plasminogen-binding protein	70/70	72/72	[53,54]

1Resulting from tblastn-based cross-mapping of the H. pylori proteome to the H. suis HS1T and HS5 genomes.

Discussion

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 [33]. 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 [34] 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 [35]. 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) [36].

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 [39].

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 [40].

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 [43]. 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 [44]. 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 (cagPAI) 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 [45]. Although H. suis possesses two members of the H. pylori cagPAI (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.

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 [46]. 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 [47]. 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 [52]. 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 [55]. Besides, insertion mutagenesis of the fldA and the por complex has shown that these genes are essential for the survival of H. pylori [56]. 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 cagPAI 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.

Conclusion

Although H. suis lacks homologs of some major H. pylori virulence genes, other candidate virulence factors, such as napA, ggt, mviN, and fldA were detected. H. suis also possesses genes known to be essential for gastric colonization. Future in vitro and in vivo research of the currently presented genes of this porcine and human gastric pathogen should elucidate their precise role in colonization and virulence.

Nucleotide sequence accession numbers

The genome sequences have been deposited at GenBank/EMBL/DDBJ under the accession ADGY00000000 for HS1T and ADHO00000000 for HS5. The versions described in this paper are the first versions, ADGY1000000 and ADHO1000000.

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

MV designed the study, analysed the data and drafted the manuscript. TTMV carried out the sequence alignment and participated in the design of the study. BF, AS and DDG participated in the design of the study. FP, WVC, RD, and FH coordinated and participated in the design of the study. All authors read and approved the final manuscript.

Additional file 1

Table S1 Classification of ) and strain 5 (HS5) outer membrane proteins (OMPs) in relation to . Additional file Table S1 presents the classification of H. suis outer membrane proteins in relation to H. pylori outer membrane proteins. Although this table is not essential, we believe that it is both a relevant and interesting addition to the content of the article.

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