# Patent

## Title
Vaccines for immunization against helicobacter

## Abstract

The invention relates to the immunization of pigs against Candidatus Helicobacter suis using antigens of species related to Candidatus Helicobacter suis.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of U.S. patent application Ser. No. 11/453,170 filed Jun. 14, 2006, which in turn claims benefit of U.S. Provisional Application Ser. No. 60/691,394 filed Jun. 16, 2005 and U.S. Provisional Application Ser. No. 60/695,995, filed Jul. 1, 2005, the disclosures of which are incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to tools and methods for the immunization of animals against infection by Helicobacter species.
BACKGROUND OF THE INVENTION
Helicobacter (H.) pylori infections in humans are a major cause of gastric and duodenal ulceration as well as gastric cancer. Triple therapies with proton pump inhibitors and clarithromycin and amoxicillin are recommended as first line treatment. These standard therapies increasingly face problems with antibiotic resistance and recurrence of infection, especially in areas where H. pylori is endemic. Various studies in animal models have shown the feasibility of both prophylactic and therapeutic vaccination against H. pylori (Del Guidice (2001) Annu. Rev. Immunol. 19, 523-563; Sanchez et al. (2001) FEMS Immunol Med. Microbiol. 30, 157-165). H. pylori proteins expressed in infected mice and hence exposed to the mouse immune system, appear similar to those detected in human infections, suggesting that the mouse model is suitable for the preclinical screening of antigen candidates (Bumann et al. (2002) Inf. Imm. 70, 6494-6498). Immunizations with recombinant urease was found to induce local and serum immune responses in mice and protect against Helicobacter pylori infection (Kleanthous et al. (1998) Inf. Imm. 66, 2879-2886).
H. pylori is not the only bacterial pathogen capable of colonizing the human gastric mucosa. “H. heilmannii” indeed has been found in approximately 0.96% of gastric biopsies. This organism is strongly associated with gastritis, but also with peptic ulceration, gastric adenocarcinoma and mucosa associated lymphoid tissue (MALT) lymphoma.
Some studies revealed sufficient antigenic cross-reactivity between H. felis and H. pylori to generate protection to H. felis challenge following immunization with a H. pylori sonicated antigen solution (Lee & Chen (1994) Inf. Imm. 62, 3594-3597; Michettti et al. (1994) Gastroenterology 107, 1002-1011). One study shows that H. heilmannii infection can be prevented by vaccination both with H. heilmannii UreB and H. pylori UreAB, confirming that protective immunity against Helicobacter infections can be elicited by homologous as well as heterologous Helicobacter urease (Dieterich et al. (1999) Inf. Imm. 67, 6206-6209).
Recently it has been shown that H. heilmannii does not represent a single species, but a group of different bacterial species with a similar spiral morphology, most of which are probably zoonotic in origin. On the basis of 16S rRNA sequences, “H. heilmannii” has been classified into two types (Solnick et al. (1993) J. Infect. Dis. 168, 379-385). ‘H. heilmannii’type 2 organisms are closely related, if not identical, to the canine and feline Helicobacter spp., namely H. felis, H. bizzozeronii and H. salomonis. More than 50% of the “H. heilmannii” infections in humans however are due to “H. heilmannii” type I. It is now accepted that “H. heilmannii” type 1 is identical to “Candidatus H. suis” (O'Rourke et al. (2004) Int J Syst Evol Microbiol. 54, 2203-2212; De Groote et al. (1999) Int. J. Syst. Bacteriol. 49, 1769-1777), a spirally shaped bacterium that colonizes the stomach of more than 60% of slaughterpigs.
Little information is available in the literature on the potential of vaccine-induced protection against non-pylori helicobacter strains, such as “Candidatus H. suis”. In vitro cultivation of “Candidatus H. suis” currently is not possible, but mouse inoculation can be used to grow and maintain this bacterium viable for more than two years starting from infected pig stomach mucosa (Mendes et al., (1991) cited above; Dick et al. (1989) J. Med. Microbiol. 29, 55-62; Park et al., (2003) J. Comp. Pathol. 129:154-160).
SUMMARY OF THE INVENTION
The present invention relates to the use of an antigen preparation of a species related to a Candidatus Helicobacter suis for vaccination of animals against Helicobacter species, more particularly against Candidatus H. suis. 
A first aspect of the invention thus relates to the use of a composition comprising one or more antigen preparations of one or more species related to Candidatus H. suis for the manufacture of a vaccine against Helicobacter species, more particularly against Candidatus H. suis. More particularly, the bacterial species related to Candidatus Helicobacter suis envisaged within the context of the present invention is/are species of bacteria having a 16S rRNA sequence having at least 93% sequence identity to the sequence of Candidatus Helicobacter suis. According to a particular embodiment the composition used comprises one or more antigen preparations of one or more species related to Candidatus Helicobacter suis selected from the group consisting of Helicobacter felis, Helicobacter salomonis, Helicobacter heilmannii (type II), H. baculiformis, Helicobacter cynogastricus, Helicobacter pylori or Helicobacter bizzozeronii. 
According to particular embodiments of the invention the species related to Candidatus Helicobacter suis is/are selected from H. felis, H. bizzozeronii, H. baculiformis or H. cynogastricus. A further embodiment of the invention relates to the use of an antigen preparation of H. cynogastricus in the preparation of a vaccine against Helicobacter species, more particularly against Candidatus H. suis. Another further embodiment of the invention relates to the use of an antigen preparation of H. baculiformis in the preparation of a vaccine against Helicobacter species, more particularly against Candidatus H. suis. 
A further aspect of the invention thus provides vaccines for use in the vaccination of animals against Helicobacter spp. (species), more particularly against Candidatus H. suis. More particularly, the vaccines of the present invention comprise one or more antigen preparations of one or more bacterial species related to Candidatus Helicobacter suis envisaged within the context of the present invention is/are species of bacteria having a 16S rRNA sequence having at least 93% sequence identity to the sequence of Candidatus Helicobacter suis. According to a particular embodiment the vaccines comprise one or more antigen preparations of one or more species related to Candidatus Helicobacter suis selected from the group consisting of Helicobacter felis, Helicobacter salomonis, Helicobacter heilmannii (type II), Helicobacter cynogastricus, Helicobacter baculiformis, Helicobacter pylori or Helicobacter bizzozeronii. The vaccines can further optionally comprise an adjuvant and/or a pharmaceutically acceptable carrier.
The vaccines of the present invention can be used for either prophylactic or therapeutic immunization and suitable vaccination routes include, but are not limited to, intranasal, subcutaneous, oral, and intramuscular immunization. Suitable vaccination routes also comprise combination administrations (e.g. oral/intramuscular administration).
According to particular embodiments, the antigen preparation used in the preparation of a vaccine comprises a lysate of bacteria. Alternative embodiments include vaccines wherein the antigen preparation comprises whole-killed bacteria or live-attenuated bacteria. Additionally or alternatively the vaccine according to the invention comprises an antigen preparation which comprises a processed and/or artificial bacterial preparation.
A further aspect of the invention relates to methods of vaccinating an animal against Helicobacter spp. infection, more particularly against a Candidatus H. suis infection comprising the step of administering a composition comprising one or more antigen preparations of one or more species related to a Candidatus H. suis to the animal, either before infection (for prophylactic vaccination) or after infection has been identified (as therapeutic vaccination). Optionally the antigen preparation is administered together with an adjuvant and/or a pharmaceutically acceptable carrier. Specific embodiments of the method of the invention relate to antigen preparations comprising preparations of H. felis and/or H. bizzozeronii and/or and/or H. baculiformis, and/or H. cynogastricus. More specifically, the antigen preparation used comprises a lysate of one or more of these bacteria, but alternative embodiments include antigen preparations comprising live-attenuated bacteria or processed and/or artificial bacterial preparations. The methods of the invention may comprise intranasal or subcutaneous administration of the vaccine of the invention.
Yet a further aspect of the invention relates to an animal model for Candidatus Helicobacter suis infection, more particularly a mouse model. This model allows the in vivo propagation of Candidatus Helicobacter suis in an animal other than its natural host. This model is obtained according to the invention by infecting a mouse with Candidatus Helicobacter suis-infected material. More particularly this comprises isolating cells from the stomach wall of a pig infected with Candidatus Helicobacter suis, optionally making a homogenate thereof, and intragastrically infecting mice with the cells or homogenate. The infection in the mice and the effect of vaccination can be followed up by faecal PCR.
A further aspect of the invention relates to an isolated bacterium of the species Helicobacter cynogastricus deposited under Accession Number LMG P-23100. The invention further relates to the use of Helicobacter cynogastricus in the production of a vaccine.
A further aspect of the invention relates to an isolated bacterium of the species Helicobacter baculiformis deposited under Accession Number LMG 23839 at the BCCM/LMG bacteria collection of the University of Ghent—Laboratorium for Microbiolgy, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium. This strain was deposited by M. Baele of the Dept. of Pathology, Bacteriology and Avian diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium, on Oct. 17, 2006.
Details on the isolation and characterization of H. baculiformis are published in Baele et al. (2008) Int. J. Syst. Evol. Microbiol. 58, 357-364 “Helicobacter baculiformis sp. nov., isolated from feline stomach mucosa”, which is incorporated by reference herein.
The invention further relates to the use of Helicobacter baculiformis in the production of a vaccine.
DETAILED DESCRIPTION OF THE INVENTION
The present invention will be described with reference to certain embodiments and to certain Figures, but the present invention is not limited thereto, but only by the claims.
The present invention demonstrates that administration of an antigen preparation of a strain related to Candidatus H. suis, more particularly phylogenetically related to Candidatus H. suis to an animal is capable of eliciting an immune response protecting the animal against infection by Candidatus H. suis. Based on the observations it is contemplated that a relatedness of the species at the DNA level for 16S rRNA of at least 93% (i.e. less than 7% difference) ensures cross-immunity. Additionally or alternatively, the species envisaged to be suitable in the context of the present invention have at least 70% sequence identity with the partial ureAB of Candidatus H. suis. 
The present invention relates to the vaccines and vaccination methods against Helicobacter spp., more particularly against Candidatus Helicobacter suis. The present invention relates to the use of antigens and antigen preparations of certain Helicobacter species for vaccinating animals, especially livestock (cows, sheep, horses, . . . ), more particularly swine, most particularly cultivated pigs, which are infected with susceptible to infection with Helicobacter spp., more particularly with Candidatus Helicobacter suis. Also other animals, such as, but not limited to humans, monkeys, rabbits, rodents, cats and dogs which are suspected to be infected with Helicobacter spp., more particularly with Candidatus Helicobacter suis can be vaccinated with the antigen preparation of the present invention.
“Candidatus Helicobacter suis” as referred to herein is a bacterium which was previously known as “H. heilmannii” type I (Trebesius et al. (2001) J Clin Microbiol. 39, 1510-1516. It is now accepted that “H. heilmannii” type 1 is identical to “Candidatus H. suis” (O'Rourke et al. (2004) Int J Syst Evol Microbiol. 54, 2203-2211; De Groote et al. (1999) Int. J. Syst. Bacteriol. 49, 1769-1777), a spirally shaped bacterium that colonizes the stomach of more than 60% of slaughterpigs. Candidatus Helicobacter suis is also defined at the molecular level as the Helicobacter species having a 16S rRNA sequence Genbank Accession AF 127028 (SEQ ID NO:16) (D. De Groote et al. (1999) cited above) and AF506788-92 (O'Rourke et al. (2004) cited above) and a urease gene sequence as depicted in Genbank Accession AF508013-AF508014 (O'Rourke et al. (2004) Int J Syst Evol Microbiol. 54, 2203-2211).
The bacterial species suitable for the purpose of the invention are bacteria other than Candidatus Helicobacter suis of the Helicobacter genus, most particularly species that are related to but not identical to Candidatus Helicobacter suis. The phrase “related to” in the context of bacterial species is used herein to indicate a phylogenetic relation, preferably expressed by molecular biology parameters. More generally the bacteria related to Candidatus Helicobacter suis have a 16S rRNA sequence which is at least 75%, 80%, 85%, 90%, 93%, 95%, or 96% identical with the 16S rRNA sequence of Candidatus Helicobacter suis. Particular embodiments of the invention relate to strains which are maximally 96.9% identical with the 16S rRNA sequence of Candidatus Helicobacter suis. 
In this context it is noted that bacterial strains having a sequence of the 16S rRNA reference gene which is between 97 and 99% identical at the DNA level are generally considered as belonging to the same species, bacterial strains having a sequence of the 16S rRNA reference gene which is between 95 and 97% identical at the DNA level are generally considered as belonging to the same genus) and strains having a sequence of this reference gene which is between or between 93 and 95% identical at the DNA level are generally considered as belonging to a different genus. The reference sequence of 16S rRNA of Candidatus Helicobacter suis corresponds to that of Genbank Accession AF 127028 (SEQ ID NO:16).
Species that are identified as ‘closely related to Candidatus Helicobacter suis’, based on the above criteria (e.g. with a 16S rRNA sequence having at least about 97% to 99%, sequence identity with Candidatus Helicobacter suis), can nevertheless be identified as a different species based on other criteria such as, but not limited to, whole-cell protein profiles, or sequence differences in other reference genes. The sequences of the urease genes ureA and ureB are an alternative tool for phylogenetic analysis of gastric Helicobacter species (O'Rourke et al., 2004, above). Accordingly, particular embodiments of bacteria related to Candidatus Helicobacter suis are bacteria comprising a partial urease (ureAB) coding sequence which is at least 60,70%, 75%, 80%, 85%, 90%, or up to 93% identical at the DNA level with the urease sequence of Candidatus Helicobacter suis. Particular embodiments of bacterial species related to Candidatus Helicobacter suis are bacterial species which comprise a partial urease (ureAB) gene sequence having a sequence which is between 70 and 93% identical, more particularly is between 73 and 93% identical, or between 73 and 84% identical or between 73 and 82% identical at the DNA level with the partial urease DNA sequence of Candidatus Helicobacter suis. Conserved partial 60 kDa heat-shock protein (HSP60) gene sequences have also been shown to give additional phylogenetic information useful for differentiating Helicobacter species (Mikkonen et al., 2004, Int J Syst Evol Microbiol 54, 753-758). It is nevertheless demonstrated that while the differences with Candidatus H. suis may vary, depending on the phylogenitic analysis used, the organisms considered as related thereto based on their 16S rRNA, are similarly related using other methods. Accordingly, the reference gene for determining relatedness is not critical.
“Antigen preparation” as used in the context of the present invention relates to a composition comprising at least one protein or fragment thereof which provokes an immune response (hereafter referred to as ‘antigen’) when administered to an animal. For use as a vaccine in the context of the present invention the antigen preparation may comprise whole-killed (inactive) bacteria, live-attenuated (weakened) bacteria or processed and/or artificial bacterial preparations or combinations thereof. Processed bacterial preparations included preparations of bacterial proteins which are partially or completely purified and/or pretreated. Methods of obtaining antigen preparations are well known in the art. Generally such methods involve extracting proteins from bacterial preparations using techniques such as sonication, proteolytic digestion, heat treatment, freeze-thaw treatment, osmotic shock treatment etc. . . . Examples of artificial bacterial preparations include protein preparations either in part or entirely obtained by synthetic or recombinant methods. Oligonucleotides can probes can be devised based on the sequences of the bacterial genome and can be used to probe genomic or cDNA libraries for genes encoding antigens useful in the context of the invention. Genes can be isolated using standard techniques.
According to certain embodiments the antigen preparations used for vaccination according to the present invention comprise one or more antigens obtained from different Helicobacter species which are related to Candidatus Helicobacter suis. Examples of suitable antigens include but are not limited to the urease enzyme, heat shock proteins (Hsp60), cagA and VacA, adhesins, haemagglutinins (such as HpaA), epitopes derived from flagellins (Fla). It is to be understood that the antigen preparations can also include other immunogens not specifically described herein.
A “vaccine” as used herein refers to a composition such as the antigen preparation described herein which is administered to stimulate an immune response that will protect a person from illness due to that agent. The vaccine of the present invention is intended for use both as a therapeutic (treatment) vaccine, i.e. for administration to the animal after infection with the intention to reduce or arrest disease progression and as a preventive (prophylactic) vaccine, for administration to the animal prior to infection, with the intent to prevent initial (and/or recurrent) infection.
The vaccination protecting against one species using antigens from another species is referred to as “cross-vaccination” or “heterologous vaccination”.
The present invention is based on the observation that mucosal and parenteral vaccination with heterologous antigens from H. pylori SS1, H. felis CS1, H. bizzozeroni, or H. cynogastricus elicited a significant reduction in bacterial burden but not sterilizing immunity upon “Candidatus H. suis” challenge. Phylogenetically, H. felis is more closely related to “Candidatus H. suis” than H. pylori (De Groote et al. (1999) cited above), therefore one could expect to obtain better results with heterologous H. felis immunization. The present invention demonstrates that only minor non-significant differences in the level of protection between these two groups are found.
The invention thus relates to heterologous vaccination, i.e. the use of an antigen preparation of a species related to Candidatus H. suis, to obtain protection against infection by Helicobacter spp., more particularly by Candidatus H. suis. 
The object of the vaccine and vaccination therewith according to the present invention includes obtaining complete protection (sterilizing immunity) against Helicobacter spp., more particularly against Candidatus Helicobacter suis in an animal but also reducing the bacterial burden of Helicobacter spp., more particularly of Candidatus Helicobacter suis by at least 25, 40, 60, 80% compared to prior to vaccination and/or compared to animals which have not received the vaccine of the present invention and are/have been subjected to the same infectious agent. Most particularly, the present invention relates to vaccines and vaccination strategies which ensure a protective effect or reduced bacterial burden for a prolonged period of time, such as during at least 4, 6, 10, 12 or more than 12 weeks.
Identification and quantification of such infection and/or bacterial burden in an animal can be done in a number of ways. Classically, this is done by determining the presence of the infectious agent, or a protein or DNA sequence thereof in a sample of body fluid or in urine or faeces. Alternatively, the reaction of the immune system, e.g. the presence of antibodies to the infectious agent, can be measured. According to a particular embodiment of the invention accurate diagnosis and quantification of Helicobacter infection is obtained by identification of Candidatus H. suis DNA, e.g. by PCR as described in the art (Fox and Lee (1997) Lab. Anim. Sci. 47, 222-255). Since “Candidatus H. suis” is hitherto uncultivable, a quantitative urease test is use to quantify this species. This assay has been used in the prior art to quantify H. heilmannii, H. felis and H. pylori infection in mouse immunization studies (Michetti et al. (1994) Gastroenterology 107: 1002-1011; Kleanthous (2001) Vaccine 19, 4883-4895; Saldinger et al. (1998) Gastroenterology 115, 891-897). This urease test was found to be less sensitive than determining the number of bacteria after cultivation.
According to a first aspect, an antigen preparation of one or more species related to Candidatus H. suis is used to obtain prophylactic or therapeutic immunity to Candidatus H. suis. More particularly, the invention relates to antigen preparations of one or more species, different from Candidatus H. Suis, having at least 93% sequence identity in the 16S rRNA or urease protein sequence to Candidatus H. suis. Additionally or alternatively, the one or more species used for the antigen preparation according to the invention are characterized by the fact that they comprise a partial urease (ureAB) gene sequence having a sequence which is between 70 and 93% identical, more particularly is between 73 and 93% identical, or between 73 and 84% identical or between 73 and 82% identical at the DNA level with the partial urease DNA sequence of Candidatus Helicobacter suis. According to particular embodiments of the present invention the species related to Candidatus Helicobacter suis is a/are species selected from the group of H. pyloris, H. bizzozeronii, H. felis, H. baculiformis and H. salomonii. Other suitable Helicobacter species are H. bilis, H. fenelliae, H. pametensis, H. nemestrinae, H. nemestrinae, H. pametensis, H. acinonychis, H. pullorum, H. mustelae, H. hepaticus, H. cinaedi and H. canis. Other species have been described as being related to Candidatus Helicobacter suis, such as H. cerdo (WO2004069184).
The present invention further provides a particular embodiment of a strain useful for the vaccination against Candidatus H. suis, i.e. H. cynogastricus, as described in the Examples herein.
The present invention further provides another particular embodiment of a strain useful for the vaccination against Candidatus H. suis, i.e. H. baculiformis, as described in the Examples herein.
According to a particular embodiment, the antigen preparation is a cell lysate, i.e. a mixture obtained upon lysis of bacterial cells. A particular example of a bacterial cell lysate is the soluble fraction of a sonicated bacterial culture, e.g. obtained after filtration. Alternatively or in addition, bacteria can be fragmented using a high-pressure homogenizer (e.g. Avestin model EmulsiFlexC5) Optionally, the cell lysate is further inactivated by treatment with formalin, or a comparable agent. Generally not all proteins in a lysate will provoke an immune response. Alternatively, the antigen preparation according to the present invention is obtained by fractionation and/or purification of one or more proteins from a lysate or bacterial culture medium to obtain a composition of enriched or purified antigens. Also falling within the concept of the present invention are recombinant proteins or fragments thereof used as antigen preparation. Most particular examples of isolated, purified and/or recombinant bacterial proteins suitable in the context of the present invention are heat shock proteins and/or urease proteins.
The vaccine of the present invention optionally contains only the antigen preparation of the invention. Alternatively, the vaccine can comprise, in addition to the antigen preparation of the present invention, a suitable adjuvant. The type of adjuvant will vary, depending on the type of antigen preparation and rout of administration used. According to a particular embodiment of the present invention the antigen preparation which is a sonicated antigen solution is administered intranasally with Cholera toxin (CT) or subcutaneously with saponine as adjuvant. Any adjuvant known in the art may be used in the vaccine composition, including oil-based adjuvants such as Freund's Complete Adjuvant and Freund's Incomplete Adjuvant, mycolate-based adjuvants (e.g., trehalose dimycolate), bacterial lipopolysaccharide (LPS), peptidoglycans (i.e., mureins, mucopeptides, or glycoproteins such as N-Opaca, muramyl dipeptide [MDP], or MDP analogs), proteoglycans (e.g., extracted from Klebsiella pneumoniae), streptococcal preparations (e.g., OK432), BiostimTM (e.g., 01K2), the “Iscoms” of EP 109 942, EP 180 564 and EP 231 039, aluminum hydroxide, saponin, DEAE-dextran, neutral oils (such as miglyol), vegetable oils (such as arachis oil), liposomes, Pluronic® polyols. Adjuvants include, but are not limited to, the RIBI adjuvant system (Ribi Inc.), alum, aluminum hydroxide gel, cholesterol, oil-in water emulsions, water-in-oil emulsions such as, e.g., Freund's complete and incomplete adjuvants, Block co-polymer (CytRx, Atlanta Ga.), SAF-M (Chiron, Emeryville Calif.), AMPHIGEN® adjuvant, saponin, Quil A, QS-21 (Cambridge Biotech Inc., Cambridge Mass.), GPI-0100 (Galenica Pharmaceuticals, Inc., Birmingham, Ala.) or other saponin fractions, monophosphoryl lipid A, Avridine lipid-amine adjuvant, heat-labile enterotoxin from E. coli (recombinant or otherwise), cholera toxin, or muramyl dipeptide, among many others. According to a particular embodiment recombinant mutant of Escherichia coli heat-labile toxin is added to the antigen preparation prior to injection into the animal.
According to another aspect, the present invention relates to the use of the vaccines of the present invention to obtain prophylactic or therapeutic immunity to Helicobacter spp. such as those referred to herein, more particularly to Candidatus H. suis. 
According to a first embodiment the invention provides antigen preparations for use in prophylactic vaccination which ensure protection against Helicobacter spp., more particularly against Candidatus H. suis which is more than transient. Transient infection of prophylactically immunized mice has only been reported once in the H. pylori model (Garhart et al. 2002, Infect. Immun. 70:3529-3538). The present invention shows the evolution of protection over time. This is performed by a method for detection of infection in faecal samples, particularly developed for this purpose. A PCR is carried out on faecal samples collected at subsequent time points, which gives an impression of the colonization in the stomach with “Candidatus H. suis”. The PCR reaction is performed on a small fragment of the 16S rRNA gene. Typically, this fragment has a length of less than 400 by (e.g. a fragment between 200 and 400 bp, a fragment between 200 and 100 by or a fragment between 100 and 50 bp), more particularly a fragment which comprises sequences for PCR amplification that are species-specific. This allows the detection of degraded 16S rRNA of a specific Helicobacter species in faecal samples. Larger fragments or full length 16S rRNA, such as detected in gastric samples (De Grootte et al. (2000) cited above), could not be detected in faecal samples of pigs. It is demonstrated herein that there is a decrease in excretion of Helicobacter DNA from one week after infection in the immunized mice compared to the non-immunized mice, and that colonization in immunized mice never reaches the same level as in non-immunized mice.
In another aspect the present invention relates to methods for therapeutic immunization, when the organisms have already orientated the host immune response to their benefit.
The antigen preparations or vaccines of the present invention can be administered via any suitable route, such as by mucosal (intranasal), parenteral, or intramuscular administration, oral, intradermal, intraperitoneal, intravenous, or subcutaneous administration. Suitable vaccination routes also comprise combination administrations (e.g. oral/intramuscular administration). According to a specific embodiment of the invention therapeutic immunization is performed by parenteral administration of the antigen preparation of the invention. Parenteral immunization can mobilize cells from systemic origin that have not been already primed in one given direction by a Helicobacter infection (Guy et al. (1999) Vaccine 17, 1130-1135). According to another specific embodiment of the invention, intramuscular administration is used for efficient vaccination.
The antigens the present invention can be administered alone or with suitable pharmaceutical carriers, and can be in solid or liquid form such as, tablets, capsules, powders, solutions, suspensions, or emulsions.
The solid unit dosage forms can be of the conventional type. The solid form can be a capsule, such as an ordinary gelatin type containing the proteins or peptides of the present invention or the antibodies or binding portions thereof of the present invention and a carrier, for example, lubricants and inert fillers such as, lactose, sucrose, or cornstarch. In another embodiment, these compounds are tableted with conventional tablet bases such as lactose, sucrose, or corn starch in combination with binders like acacia, corn starch, or gelatin, disintegrating agents such as, corn starch, potato starch, or alginic acid, and a lubricant like stearic acid or magnesium stearate.
The antigens of the present invention may also be administered in injectable dosages by solution or suspension of these materials in a physiologically acceptable diluent with a pharmaceutical carrier. Such carriers include sterile liquids such as water and oils, with or without the addition of a surfactant and other pharmaceutically acceptable adjuvants. Illustrative oils are those of petroleum, animal, vegetable, or synthetic origin, for example, peanut oil, soybean oil, or mineral oil. In general, water, saline, aqueous dextrose and related sugar solution, and glycols such as, propylene glycol or polyethylene glycol, are preferred liquid carriers, particularly for injectable solutions.
For use as aerosols, the antigens of the present invention in solution or suspension may be packaged in a pressurized aerosol container together with suitable propellants, for example, hydrocarbon propellants like propane, butane, or isobutane with conventional adjuvants. The materials of the present invention also may be administered in a non-pressurized form such as in a nebulizer or atomizer.
According to yet another aspect of the invention, an in vivo animal model is provided for infection with Candidatus H. suis. The invention provides a method of obtaining Candidatus H. suis infection in a laboratory or model animal, such as mice, which method comprises intragastrically inoculating the laboratory or model animal with homogenates of cells obtained from the stomach wall of infected animals, more particularly infected pigs. According to a specific embodiment the upper cell layers and mucus are scraped from the antrum and homogenized. According to yet a further particular embodiment the material from the stomach wall of infected animals is homogenized in lyophilization medium (2 volumes of horse serum, 1 volume of BHI broth and 10% glucose) (LYM). Optionally, larger particles are removed by centrifugation. According to a particular embodiment the stomach from infected laboratory animal or model animal so obtained is again dissected and homogenized for at least two additional passages in the same animal. The infection is optionally followed up by faecal PCR as described herein.



FIGURE LEGENDS
The following Figures represent illustrative embodiments of the invention.
FIG. 1: Quantitative urease assay on gastric stomach tissue of different sites (cardia, fundus, antrum) from pigs infected with Candidatus Helicobacter suis from mice (n=5) and controls (n=5) according to one embodiment of the invention.
FIG. 2: Excretion of “Candidatus Helicobacter suis” DNA in faeces of BALB/c mice immunized intranasally with H. pylori antigens (♦) or H. felis antigens (⋄) compared to non-immunized mice (▴), 1 to 16 weeks after infection with “Candidatus Helicobacter suis”, according to one embodiment of the invention. The excretion is expressed as percentage of mice positive in PCR per group.
FIG. 3: Excretion of “Candidatus Helicobacter suis” DNA in faeces of BALB/c mice immunized subcutaneously with H. pylori (♦) or H. felis (⋄) antigens, compared to non-immunized (▴) animals, 1 to 16 weeks after infection with “Candidatus Helicobacter suis”, according to one embodiment of the invention. The excretion is expressed as percentage of mice positive in PCR per group.
FIG. 4: Quantitative urease activity of gastric stomach tissue, represented as OD value (550 nm), from mice intranasally immunized with H. pylori or H. felis antigens according to one embodiment of the invention. Solid lines represent the geometric mean for each group studied. (Cs) animals challenge infected with “Candidatus Helicobacter suis”; (Cp) animals challenge infected with H. pylori; (Cf) animals challenge infected with H. felis; (IN,p) intranasal immunization with H. pylori antigens; (IN,f) intranasal immunization with H. felis antigens.
FIG. 5: Quantitative urease activity of gastric stomach tissue, represented as OD value (550 nm), from mice subcutaneously immunized with H. pylori (SCp) or H. felis (SCf) antigens according to one embodiment of the invention. Solid lines represent the geometric mean for each group studied. Significant differences (P<0.05) between immunized and non-immunized challenged animals, for each Helicobacter sp., are indicated with letter a. (Cs) animals challenge infected with “Candidatus Helicobacter suis”. 
FIG. 6: Excretion of “Candidatus Helicobacter suis” DNA in the faeces of BALB/c mice immunized intranasally with H. felis CS1 or H. bizzozeronii antigens three weeks post “Candidatus Helicobacter suis” challenge according to particular embodiments of the invention. The excretion is expressed as percentage of mice positive in PCR. The differences between the experimental conditions are explained in detail in Table 1.
FIG. 7: Quantitative urease activity of gastric stomach tissue, represented as OD value (550 nm). Solid lines represent geometric mean for each group studied. A significant (P<0.05) decrease in urease activity between non-immunized, challenged (group 9) and immunized animals was found for group 1 and group 2, both representing intranasal immunization with H. felis CS1 sonicated antigen solution or H. bizzozeronii respectively (a), according to particular embodiments of the invention. The differences between the experimental conditions are explained in detail in Table 1.
FIG. 8A: Serumconversion (s/p values) against H. felis antigens after vaccination with H. felis antigens (serology data in swine) (group 1: ▪; group 2: ♦; group 3: ▴) and H. bizzozeronii antigens (group 4: ●) (adjuvants only: _) Pre: pre-immunization; 1×: 3 weeks after the first immunization; 2×: two weeks after the second immunization.
FIG. 8B: Serumconversion (s/p values) against H. bizzozeronii antigens after vaccination with H. felis antigens (group 3: ▴) and H. bizzozeronii antigens (group 4: ●) (adjuvants only: _) Pre: pre-immunization; 1×: 3 weeks after the first immunization; 2×: two weeks after the second immunization.
FIG. 9A: Dendrogram (A) derived from the numerical analysis of the whole-cell protein profiles (B) of H. cynogastricus, H. pylori, H. bizzozeronii, H. salomonis and H. felis reference strains.
FIG. 9B: Similarity matrix based on 16S rRNA sequence comparison.
FIG. 10: Phylogenetic tree for 25 strains of Helicobacter species based on 16S rRNA sequence similarity. The scale bar represents a 10% difference in nucleotide sequences as determined by measuring the lengths of the horizontal lines connecting any two species.
FIG. 11: Genomic sequence of 16S rRNA gene of Helicobacter cynogastricus. 
FIG. 12: Similarity matrix based on UreAB sequence comparison.
FIG. 13: Whole-cell protein analysis of Helicobacter species, including H. baculiformis strain M50T.



The invention is illustrated by but not limited to the following examples.
EXAMPLES
General Methodology
Mice. All experiments involving animals were approved by the Animal Care and Ethics Committee of the Faculty of Veterinary Medicine, Ghent University. Five week-old male, SPF BALB/c mice were purchased from an authorized breeder (HARLAN, Horst, The Netherlands). The animals were housed individually in autoclaved filter top cages and provided with a commercial diet (TEKLAD, HARLAN) and water ad libitum. After an adaptation period of one week, the animals were used in the experiments.
Antigens for vaccination. H. pylori SS1, H. felis CS1 (ATCC 49179) and H. bizzozeronii (CCUG 35545) were grown on brain heart infusion (BHI, Oxoid, England) agar plates supplemented with 10% horse blood, 5 mg/ml amphotericin B, 10 mg/ml vancomycin, 5 mg/ml trimethoprim lactate and 2500 units/l polymyxin B (Skirrow, Campylobacter Selective Supplement, Oxoid) and Vitox supplement (Oxoid). Plates were incubated at 37° C. in micro aerobic conditions. The antigens used for immunization were prepared by harvesting 3-day old cultures in sterile phosphate buffered saline. The bacterial suspension was sonicated (8 times 30 seconds, 50% capacity; Misonix, Incorporated, USA). After centrifugation (5,000 g, 5 min., 4° C.) the supernatant was filtered through a 0.22-μm pore filter (Schleisser Schuell, Dassel, Germany) and stored at −70° C. Afterwards, protein concentration was determined by the Lowry assay (Lowry et al. (1951) J. Biol. Chem. 193, 265-275).
Formalin inactivated bacterial cultures were prepared by transferring bacterial cultures from agar plates to BHI broth supplemented with 0.2% Skirrow, 0.6% Vittox and 10% horse serum. After 24 h of incubation at 37° C. 0.5% formaldehyde was added and further incubated at 37° C. Twenty-four hours later the culture was cooled to 4° C. and checked microscopically for presence of intact bacteria. Twenty percent of sodiumbisulphite 0.166M was added to neutralize formaldehyde. Afterwards, protein concentration was determined by the Lowry assay.
Intranasal immunization. Forty-five mice were divided into seven groups of six animals (groups 1-7) and one group of three animals (group 8). All animals from groups 1 and 3 were immunized intranasally with H. felis CS1 and those of groups 2 and 4 with H. pylori SS1, twice with three weeks time interval. Intranasal immunization was done by applying about 100 μl with 100 μg of sonicated antigen solution mixed with 5 μg cholera toxin (List, Campbell, Calif., US) on the external nares of unanaesthetized mice. Mice from groups 5, 6, 7 and 8 were not immunized. Four weeks after the final immunization, all animals from groups 2 and 5 and all animals from group 1 and 6 were challenged with H. pylori or H. felis respectively, by intragastric inoculation with 0.3 ml of the bacterial suspension. This homologous vaccination experiment serves as a control. At the same time all animals from groups 3, 4 and 7 were inoculated intragastrically with “Candidatus H. suis”. For this purpose a frozen stock from “Candidatus H. suis” was placed at 37° C. for 15 minutes.
During 1, 2, 4, 5, 6, 7, 9, 11, 13 and 15 weeks after challenge, faecal material was collected for three consecutive days from each individual mouse inoculated with “Candidatus H. suis” to screen for the presence of bacterial DNA. PCR on faecal samples was performed as described below.
Sixteen weeks after challenge, all animals were euthanized by cervical dislocation following isoflurane anaesthesia (IsoFLo, Abbot, Ill., US). From all animals, half of the stomach was used for a quantitative urease-test (Corthésy-Theulaz et al. (1995) cited above) as described below. From the other half, 2 mm2 tissue samples from the fundic region were frozen (−20°) and used for PCR specific for “Candidatus H. suis” (samples from group 3, 4 and 7), H. felis (samples from groups 1 and 6) or H. pylori (samples from groups 2 and 5) as described below.
Subcutaneous immunization. Twenty-one mice were divided into three groups of six animals (groups 1-3) and one group of three animals (group 4). Animals from groups 1 and 2 were immunized with H. pylori or H. felis respectively, three times with three weeks time interval. For this purpose about 100 μl with 100 μg of the sonicated bacterial antigen solution was mixed in equal amounts with saponine adjuvant and injected subcutaneously at the lower back of the animals. Four weeks after the final immunization, animals from groups 1, 2 and 3 were infected with “Candidatus H. suis” as described in protocol 1. Animals from group 4 were not immunized or challenged. Sampling of faecal material, from groups 1, 2 and 3, during the experiment and sampling of stomach material from all animals, at the end of the study, was done as described in protocol 1.
Preparation of Candidatus H. suis in an in vivo system, for use in challenge experiments. Thirty pig stomachs were obtained from the slaughterhouse. The stomachs were opened and the remaining food was rinsed off with autoclaved tap water (37° C.). A small mucosal fragment from the antrum (1 cm from the torus pyloricus) was taken to screen for the presence of “Candidatus H. suis”. Half of this fragment was used for rapid urease test (CUT, Temmler Pharma, Marburg, Germany, 37° C. for 1 h). The other half was frozen (−20° C.) and used for specific detection of “Candidatus H. suis” by PCR (De Groote et al. (200) J. Clin. Microbiol. 38, 1131-1135) as confirmation for the urease test. Stomachs from which the urease test give the quickest positive results were processed in the first instance. Therefore upper cell layers and mucus from the antrum were scraped. Scrapings were homogenized in lyophilization medium (2 volumes of horse serum, 1 volume of BHI broth and 10% glucose) (LYM). The homogenate was then centrifuged (5000 g, 5 min) to remove large particles. Supernatant was diluted 1/10 in LYM and intragastrically inoculated in three BALB/c mice. Two weeks later, these mice were euthanized, the stomachs were emptied and a fundus tissue sample was taken for rapid urease test. Urease positive stomachs were homogenized in LYM (5 ml LYM/stomach). After this first passage, two extra mouse passages were performed. Finally, infected mouse stomach homogenate from 15 mice was frozen at −70° C.
Preparation of H. pylori and H. felis for use in challenge experiments. H. pylori SS1 or H. felis CS1 were grown on BHI agar plates, statically at 37° C. in micro-aerobic conditions. After 3 days, bacteria were harvested, transferred to BHI broth supplemented with 0.2% Skirrow, 0.6% Vittox and 10% horse serum, and incubated statically at 37° C. in micro-aerobic conditions for 24 h. A bacterial suspension with an absorbance of 1.5 (450 nm) and an absorbance of 1.5 (660 nm) for H. pylori and H. felis respectively were consequently prepared in BHI broth, corresponding to approximately 107 cfu/ml for H. pylori and 108 cfu/ml for H. felis as confirmed by titration.
Statistical analysis. The presence of bacteria in faeces, as determined by PCR, was compared between the treatment groups by a generalized mixed model with PCR-positivity as binary response variable, time and treatment as categorical fixed effects and mouse as random effect. Pairwise comparisons were performed between the non-immunized group and the H. pylori and H. felis immunized groups at a global significance level of 5%, and a comparison wise significance level of 1.3% (adjusted by Bonferroni's technique with 3 comparisons).
The quantitative urease tests were compared by a fixed effects model with “OD value” as response variable and “treatment group” as fixed effect. Pairwise comparisons were performed between the treatment groups at a global significance level of 5% with again using Bonferroni's technique for multiple comparisons.
The quantitative urease tests shown in FIG. 7 were compared between the treatment groups by a Students t-test.
Example 1
Experimental Infection of Pigs with Candidatus H. suis 
Five-week-old pigs (n=10) were purchased from a specific pathogen free (SPF) breeding unit negative for Candidatus H. suis and randomly divided in a control group (group A) and an infected group (group B) with 5 pigs in each group. After an adaptation period of 1 week the pigs were used in the experiment. Before inoculation with the pathogen, all pigs were treated intramuscularly with 60 mg/kg cimetidine to reduce stomach acid production and were anaesthetised. Group A was the control group and was sham inoculated (inoculum from urease negative stomachs from non-infected BALB/c mice) on day 7, day 14 and day 21. Group B was inoculated with Candidatus H. suis (a stomach homogenate of Candidatus H. suis infected mice) on day 7, day 14 and day 21. Immediately before and immediately after administration of the murine stomach homogenate, pigs were intragastrically inoculated with Brucella Broth (Becton Dickinson, Erembodegem, Belgium) supplemented with 10% fetal bovine serum and 0.75% agar, to delay the passage of the bacterial suspension through the duodenum. Prolonged exposure of the gastric mucosa to the bacteria is assumed to make the stomach more susceptible to colonization with Helicobacter bacteria.
All animals were euthanized 5 weeks after the third inoculation, and necropsied immediately. At necropsy, the stomachs were excised. The mucosal surface from the pars oesophagea was macroscopically examined and lesions were scored on a scale of 0-5 using the method of Hessing et al. (1992). (score 0=intact mucosa, score 1=mild hyperkeratosis (<50% surface area), score 2=severe hyperkeratosis (50% or more of surface area), score 3=hyperkeratosis and a few small erosions (less than 5 and shorter than 2.5 cm), score 4=hyperkeratosis and extensive erosions (more than 5 erosions and/or longer than 2.5 cm), score 5=hyperkeratosis and very large erosions (more than 10 erosions or longer than 5 cm) and/or ulcers.
In group B, inoculated with “Candidatus H. suis”, three animals had a lesion score of 3, one animal a score of 4 and one animal a score of 5. In the control group, lesion scores were 2 (one animal), 3 (two animals) and 4 (two animals). The difference in lesion scores between “Candidatus H. suis” infected animals and control animals was not significant (P=0.36).
After scoring, three sites from the glandular mucosa (0.5 cm2) from each stomach were sampled for PCR, quantitative urease test and histology. These three sites corresponded to the cardia (immediately adjacent to the margo plicatus), the fundus, and the antrum pyloricum (1 cm away from the torus pyloricus).
PCR for specific detection of “Candidatus H. suis” infection in gastric tissue. DNA was extracted with DNeasy Tissue Kit (Qiagen, Hilden, Germany). PCR for specific detection of “Candidatus H. suis” was performed as described by De Groote et al. (2000) cited above. The samples of all control animals were negative. All fundus and antrum samples and 3/5 cardia samples of group B were positive in PCR.
The Urease assay was performed as described by Corthésy-Theulaz et al. (1995) cited above. Mean OD-values for each sampling site are shown in FIG. 1. Significant differences (P<0.05) between control animals and animals infected with “Candidatus H. suis” were found for all tissue samples originating from the fundus and the antrum (cardia, P=0.0676; fundus, P=0.0038; antrum pyloricum P=0.0011). There was no significant difference in mean OD value for the different sampling sites in infected animals (cardia vs. fundus P=0.2280; cardia vs. antrum pyloricum P=0.1733 and fundus vs. antrum pyloricum P=0.7824).
Histological examination was performed using a polyclonal goat anti-H. pylori antibody as described by De Groote et al. (2000). Animals positive for “Candidatus H. suis” had lesions predominantly in the antral mucosa. In this stomach region, focal lymphoplasmacytic cellular infiltrates in the mucosa were present in all 5 animals. In 3/5 infected animals antral lymphoid follicles with germinal centers were present. Due to the size of the follicles, they were associated with displacement and loss of gastric glands. In 2/5 infected animals no follicles could be detected in the antral mucosa, but these animals did show aggregates of lymphocytes and plasma cells in the lamina propria. In the fundus of “Candidatus H. suis” infected animals, only mild scattered infiltration of lymphocytes was present. In the antrum, colonization was present in the mucus overlying the surface epithelium and in the surface foveola, but did not extend deep into the gastric pits. Colonization of the fundic mucosa with “Candidatus Helicobacter suis” was detected in the glandular foveola and extended down halfway the gastric pits. Bacteria were found in close contact with gastric epithelial cells i.e. mucus producing cells and parietal cells. No bacteria were demonstrated in the stomach of the control animals. Control animals are negative for “Candidatus H. suis” (Group A).
Example 2
Experimental Set-Up of Comparative Immunization with Species Related to Candidatus H. suis 
In a parallel experiment, the effect of immunization with H. felis or H. bizzozeronii sonicate, H. bizzozeronii or H. felis formaline inactivated and control adjuvants was tested using intra-nasal or subcutaneous immunization routes. Sixty mice were divided into ten groups of six animals as shown below (Table 1).







TABLE 1







Experimental design












Antigen





Groupa
preparationb
Adjuvantc
Routed
Challenge














1
H. felis
CT
IN
“Candidatus H. suis”



sonicate


2
H. bizzozeronii
CT
IN
“Candidatus H. suis



sonicate


3
H. bizzozeronii
CT
IN
“Candidatus H. suis”



formaline



inactivated


4
H. felis
saponine
SC
“Candidatus H. suis”



sonicate


5
H. felis
saponine +
SC
“Candidatus H. suis”



sonicate
LT


6
H. felis
saponine +
SC
“Candidatus H. suis”



formaline
LT



inactivated


7
H. bizzozeronii
Saponine +
SC
“Candidatus H. suis”



sonicate
LT


8
/
saponine +
SC
“Candidatus H. suis”




LT


9
/
/
/
“Candidatus H. suis”


10
/
/
/
/





aMice were divided into 10 experimental groups (1-10).


bOne hundred micrograms of sonicated antigen solution or formol inactivated antigens were used for each immunization.


cFive μg of cholera toxin was used for the intranasal immunization. For the subcutaneous immunization, antigens in solution was mixed with equal amount of saponine adjuvant and 1 μg of LT.


dIN, intranasally; SC, subcutaneously.






Groups 1, 2 and 3 were immunized intranasally twice with three weeks interval. Therefore 100 μg of H. felis or H. bizzozeronii sonicated proteins, mixed with 5 μg of cholera toxin (List, Campbell, Calif., US), was applied on the external nares of unanaesthetized mice.
Groups 4-7 were immunized subcutaneously three times with three weeks time interval. For this purpose 100 μg of the sonicated antigen solution was mixed in equal amounts with saponine adjuvant. Immediately prior to injection 1 μg of recombinant mutant of Escherichia coli heat-labile toxin (LTR192G, donated by J. Clements) was added and then the antigen preparation was injected subcutaneously at the lower back of the animals.
Animals from group 8 were immunized subcutaneously with saponine adjuvant plus LTR192G only. Mice from groups 9 and 10 were not immunized.
Four weeks after the final immunization, a frozen stock from “Candidatus H. suis”, was placed at 37° C. for 15 minutes. All animals from groups 1-9 were challenged by intragastric inoculation with 0.3 ml of the “Candidatus H. suis” stock.
During the third week after challenge, faecal material was collected for four consecutive days from each individual mouse to screen for the presence of “Candidatus H. suis” DNA. PCR on faecal samples was performed as described below.
Six weeks after challenge, all animals were euthanized by cervical dislocation following isoflurane anaesthesia (IsoFLo, Abbot, Ill., US). From all animals, half of the stomach was used for a quantitative urease-test (Corthésy-Theulaz et al. 1995, above) as described below. From the other half, 2 mm2 tissue samples from the fundic region were frozen (−20°) and used for PCR specific for Candidatus H. suis as described below.
Example 3
Faecal Excretion of “Candidatus H. suis” DNA in Faeces of Non-Immunized and Immunized Mice
Detection of ‘Candidatus H. suis’ DNA in faecal samples.
PCR on faecal samples was performed to evaluate the excretion of “Candidatus Helicobacter suis” DNA. DNA was extracted using QIAamp® DNA Stool Mini Kit (Qiagen, Hilden, Germany). Primers HS 586 gggaggacaagtcaggtgtgaa [SEQ ID:1] and HS641 tctcccacactccagaaggatag [SEQ ID:2], complementary to the 16S rRNA genes from “Candidatus Helicobacter suis” were used to amplify a 79-bp fragment. The specificity of the primerset was tested on DNA extracts from 17 other Helicobacter species and from Campylobacter jejuni (table 2). The sensitivity was assayed by adding cloned 16S rRNA to a fecal control sample. After DNA isolation and PCR, a fragment was obtained when about 100,000 copies were added to a control sample.










TABLE 2





bStrain
Species
bStrain
Species







CCUG 38995
H. bilis
LMG 11759
H. fenelliae


CCUG 29260
H. pametensis
LMG 14378
H. nemestrinae


CCUG 32350
H. nemestrinae
LMG 12678
H. pametensis


NCTC 11961
H. pylori
LMG 12684
H. acinonychis


LMG 6444
C. jejuni
R 10t51
H. bizzozeronii


LMG 16318
H. pullorum
R 1053
H. salomonis


LMG 18044
H. mustelae
R 3647
H. felis


LMG 16316
H. hepaticus
LMG 7543
H. cinaedi


LMG 18086
H. canis





bBacterial strains used for the evaluation of the “Candidatus Helicobacter suis” specific PCR on faecal samples.






PCR reaction mixtures (25 μl) contained 50 pmole of each primer (Invitrogen Life Technologies, Merelbeke, Belgium), 200 μM of each deoxynucleoside triphosphate (Amersham Pharmacia Biotech, Puurs, Belgium), 0.03 U/μl Taq platinum, 1.5 mM MgCl2 and 1×PCR buffer (Invitrogen Life Technologies). PCR products were run on 1.5% agarose gels containing 50 ng/ml ethidium bromide. After 1 hour at 160V the products were visualized with an UV transilluminator. The Candidatus Helicobacter suis amplified fragment has a length of 80 bp. No PCR fragments are obtained using any of the other species presented in Table 2.
Statistical Analysis
The presence of bacteria in faeces, as determined by PCR, was compared between the treatment groups by a generalized mixed model with PCR-positivity as binary response variable, time and treatment as categorical fixed effects and mouse as random effect. Pairwise comparisons were performed between the non-immunized group and the H. pylori and H. felis immunized groups at a global significance level of 5%, and a comparison wise significance level of 1.3% (adjusted by Bonferroni's technique with 3 comparisons).
The presence of DNA in faecal samples as determined by PCR assay, per group, and calculated for each week of sampling is depicted in FIG. 2 and FIG. 3 for experiment 1 and experiment 2 respectively. There was an overall significant difference in faecal excretion between non-immunized and intranasally immunized animals both for H. pylori and for H. felis sonicated antigen solution (P<0.0001) in that the intranasally immunized mice excreted less “Candidatus Helicobacter suis” DNA in the faeces in comparison to the non-immunized “Candidatus H. suis” challenged animals. The difference in excretion between the two intranasally immunized groups was not significant (P=0.0241).
A significant difference was found between non-immunized mice and mice immunized subcutaneously with H. pylori sonicated antigen solution (P=0.0001). The difference between non-immunized mice and mice immunized subcutaneously with H. felis sonicated antigen solution was significant at P=0.0175. There was no significant difference between the two subcutaneously immunized groups (P=0.2445).
The results of the experiment, described in Table 1, on the number of mice excreting “Candidatus Helicobacter suis” DNA in the faeces three weeks post challenge are shown in FIG. 6. Intranasal immunization caused a lower excretion compared to the non-immunized “Candidatus Helicobacter suis” challenged animals. For the subcutaneously immunized groups an effect of immunization was only detectable in group 4, representing animals immunized with H. felis CS1 sonicated antigen solution.
Example 4
Quantitative Urease in Gastric Tissue
Quantitative Urease Test of Gastric Tissue.
The stomach sample was immersed in 500 μl of CUTest and incubated at 37° C. for 3 hours. After centrifugation (5 min, 100 g) the supernatant was used for spectrophotometric quantification at an OD of 550 nm. The assay was performed as described in Corthésy-Theulaz et al. (1995) Gastroenterol. 109, 115-121).
For the homologous intranasal immunization (FIG. 4) there was a significant difference (P<0.05) in urease activity between non-immunized and immunized animals both for H. pylori SS1 and H. felis CS1. Immunization of animals with H. pylori SS1 or H. felis CS1 sonicates antigen solution before “Candidatus H. suis” challenge resulted in a significant decrease (P<0.0001) in urease activity compared to the non-immunized challenged group. Subcutaneous immunization (FIG. 5) with H. pylori or H. felis antigens, resulted in a significant (P<0.0001) decrease in urease activity compared to the non-immunized challenged group.
In the experiment described in Table 1, the mean OD value from non-immunized non-challenged mice was 0.103. The mean OD value from non-immunized mice, challenged with “Candidatus Helicobacter suis” was 2.038. A significant (P<0.05) difference in urease activity between non-immunized, challenged (group 9) and immunized animals was found for group 1 and group 2, representing intranasal immunization with H. felis CS1 or H. bizzozeronii sonicated antigen solution respectively. None of the subcutaneously immunized groups showed a significant decrease in urease activity compared with group 9. In the statistical analysis, group 7, representing animals immunized subcutaneously with H. bizzozeronii sonicated antigen solution, showed the lowest P value (P=0.085).
None of the animals immunized intranasally with H. felis CS1 sonicated antigen solution, followed by H. felis CS1 challenge contained Candidatus Helicobacter suis DNA. In contrast, immunization with H. pylori SS1 and homologous challenge all showed the presence of Candidatus Helicobacter suis DNA in stomach samples. After heterologous intranasal and subcutaneous immunization of mice with H. pylori or H. felis antigens, and challenged with “Candidatus H. suis”, all stomach samples contained Candidatus Helicobacter suis DNA.
Example 5
PCR Analysis of Gastric Tissue
PCR Analysis of Gastric Tissue.
DNA of the stomach sample was extracted with DNeasy Tissue Kit (Qiagen). PCR for detection of “Candidatus H. suis”, H. felis or H. pylori were performed as described previously (De Groote et al. (2000) cited above and De Groote (2001) J. Clin. Microbiol. 39, 1197-1199).
None of the animals immunized intranasally with H. felis CS1 sonicated antigen solution, followed by H. felis CS1 challenge contained Candidatus Helicobacter suis DNA. In contrast, immunization with H. pylori SS1 and homologous challenge all showed the presence of Candidatus Helicobacter suis DNA in stomach samples. After heterologous intranasal and subcutaneous immunization of mice with H. pylori or H. felis antigens, and challenged with “Candidatus H. suis”, all stomach samples contained Candidatus Helicobacter suis DNA.
In the experiment described in Table 1, all animals from group 10 were negative in the PCR test specific for “Candidatus Helicobacter suis”. From the challenged animals only one animal from group 7 was negative in PCR test.
Example 6
Seroconversion in Pigs upon Immunization with H. felis or H. bizzozeronii. 
30 conventional pigs of 5 weeks old (Agrivet Merelbeke), were divided into groups of 6 animals. All groups were immunized twice intramuscularly, with a three week interval, using 0.5 mg of antigens (bacterial lysate) (group 1-4) or using adjuvants only (5). Preliminary experiments with 0.1, 0.5 and 1 mg of antigen preparation showed that a dosis of 0.5 mg provoked the largest immune response.







TABLE 3







Immunization scheme for serumconversion










Group
Antigen preparation
species
additives





1
0.5 mg sonicated bacterial
H. felis*




lysate


2
0.5 mg sonicated bacterial
H. felis
CT (Cholera



lysate

Toxin)


3
0.5 mg sonicated bacterial
H. felis
CT



lysate



(formol inactivated)


4
0.5 mg sonicated bacterial
H. bizzozeronii
CT



lysate


5
Adjuvans only

CT





*H felis strain ATCC 49179






Preserum was collected from all animals. Two weeks after the first immunization, prior to the second immunization, blood was collected. Blood was further collected after one, two and three weeks after the second immunization.
ELISA plates were coated with bacterial lysate and used for incubation with serum. Bound antigens were detected with Alkaline phoshate labelled polyclonal goat anti swine antibodies.
The results are depicted in FIGS. 8a and 8b wherein ELISA results are depicted for plates respectively coated with H. felis and H. bizzozeronii. 
Using ELISA plates coated with H. felis, serumconversion could only be demonstrated in swine immunized with H. felis antigens. With plates coated with H. bizzozeronii serumconversion could be demonstrated against H. bizzozeronii. 
Example 7
Identification of Helicobacter cynogastricus 
A Helicobacter species related to Candidatus H. suis and suitable for the preparation a vaccine is a novel Helicobacter species Helicobacter cynogastricus (also designated in the present invention as strain JKM4T), which is a Gram-negative, microaerophilic helical-shaped rod.
Isolation of JKM4T
A Helicobacter strain (JKM4T) was isolated from the antrum and fundus region of the stomach of a euthanized dog at the Faculty of Veterinary Medicine, Ghent University, Belgium. Samples were handled as described by Gruntar et al. (2003) Int J Med Microbiol 293, 65. Bacteria were grown on brain heart infusion agar (BHI; Oxoid, Ltd., Basingstoke, England), containing 10% (vol/vol) horse blood, 5 mg/l amphotericin B (Fungizone; Bristol-Myers Squibb, Epernon, France), Campylobacter selective supplement (Skirrow, Oxoid; containing 10 mg/l vancomycin, 5 mg/l trimethoprim lactate and 2500 U/l polymyxin B), and Vitox supplement (Oxoid). Plates were incubated with lids, uppermost at 37° C., under humidified micro-aerobic conditions in a closed circuit, created by evacuating 80% of the normal atmosphere and introducing a gas mixture of 8% CO2, 8% H2 and 84% N2.
Plates were checked every two days and BHI broth was added on the agar surface to ensure plates would not dry up. Primary growth occurred after 10 days of incubation as an oily aspect on the broth covering the agar medium. Light microscopical examination of the broth revealed the presence of spiral-shaped, motile organisms. Gram staining proved the Gram negativity and the helical shape of the isolate. Bacterial growth of subcultures occurred as a spreading layer on moist agar plates. Pinpoint colonies were observed when an abundant amount of bacteria was brought on a dry agar surface. Bacteria grown on a dry agar mostly lost their spiral morphology and transformed to coccoid forms.
Bacteria with typical spiral morphology were harvested in BHI broth and stored at −70° C. in a medium consisting of 7.5 g glucose, 25 ml BHI (Oxoid) and 75 ml sterile inactivated horse serum. The isolated strain JKM4T is a novel helicobacter species, Helicobacter cynogastricus (see below) and has been deposited on Jun. 6, 2005 with Accession Number LMG P23-100 at the Belgian Coordinated Collections of Micro-organisms (BCCMTM/LMG) [Laboratorium voor Microbiologie, Universiteit Gent (RUG), K. L. Ledeganckstraat 35, 9000 Gent, Belgium] by Katleen van den Bulck.
Phenotypic Studies
For scanning and transmission electron microscopic examination, bacterial cultures were fixed in 2.5% glutaraldehyde and 2% paraformaldehyde in cacodylate buffer (0.1 M, pH 7.3). They were postfixed in 1% (w/vol) osmium tetroxide in distilled water. Samples for scanning electron microscopy were dehydrated in alcohol and acetone for subsequent critical point drying in liquid carbon dioxide, glued with carbon cement on aluminium stubs, sputtered with a gold layer and examined with a Philips 501 SEM. Samples for transmission electron microscopy were block stained with 2% (wt/vol) uranyl acetate in distilled water and dehydrated in ethanol. They were embedded in Epon-Spurr's (1:1) medium. Ultrathin sections were cut from samples in which bacteria were demonstrated, stained with lead citrate and examined with a Philips EM 208S.
Biochemical and tolerance tests were carried out as recommended by Dewhirst et al. (2000) Int J Syst Evol Microbiol 50, 2231-2237, for the description of new species of the genus Helicobacter. The isolate was tested for oxidase, catalase (with 3% hydrogen peroxide) and rapid urease activity, and for hydrolysis of indoxyl acetate. The bacteria were also subjected to API Campy test strips (Biomerieux S A, Marcy-I'Etoile, France), which include tests for urease activity, nitrate reductase activity, esterase activity, hippurate hydrolysis, gamma-glutamyl transpeptidase activity, alkaline phosphatase activity, triphenyltetrazolium chloride (TTC) reduction, and pyrrolidonyl, L-arginine, and L-aspartate arylamidase activity. Tolerance to 1% glycine (Merck, Darmstadt, Germany) and 1.5% NaCl (Merck) was tested on tryptic blood agar base (Oxoid) supplemented with 10% horse blood, as recommended by the Cape Town protocol for Campylobacteriaceae and Helicobacters. Tolerance to ox bile was tested by plating the bacteria on unsalted MacConkey agar (Oxoid).
Susceptibility to metronidazole, ampicilline, clarithromycin, tetracyclin, enrofloxacin, lincomycin, tylosin, neomycin, spectinomycin and gentamicin was tested through the agar dilution method, using Mueller-Hinton agar (Oxoid) supplemented with 10% horse blood, as previously described (Van den Bulck et al (2005b) Antimicrob Agents Chemother 49, 2997-3000). All antibiotics were supplied by Sigma (St. Louis, Mo., USA) as standard powders with known potencies, except for enrofloxacin, purchased from Bayer (Brussels, Belgium).
All growth and tolerance test preparations were incubated for 7 days in a micro-aerobic atmosphere at 37° C.
Growth of the organism was tested on BHI blood agar, Brucella blood agar (Oxoid) and Mueller-Hinton blood agar. Growth at 25, 30, 37, and 42° C. was determined on BHI blood agar. These media were incubated for 7 days in a micro-aerobic atmosphere at 37° C. In addition, growth on blood-supplemented BHI agar was tested in an aerobic, aerobic with 5% CO2, micro-aerobic and an anaerobic environment.
For polyacrylamide gel electrophoresis (PAGE) of whole-cell proteins, strain JKM4T (Helicobacter cynogastricus) was grown on Mueller-Hinton agar (Oxoid) supplemented with 5% (vol/vol) horse blood and was incubated at 37° C. in a microaerobic atmosphere containing approximately 5% O2, 3.5% CO2, 7.5% H2, and 84% N2. A whole-cell protein extract was prepared and sodium dodecyl sulphate PAGE was performed as described previously (Pot, et al. (1994) J Appl Bacteriol 77, 362-369.). Whole-cell protein profiles of H. bizzozeronii, H. salomonis and H. felis reference strains and of type and reference strains of other Helicobacter species were available from previous studies. The densitometric analysis, normalization and interpolation of the protein profiles, and numerical analysis were performed using the GelCompar software package version 4.2 (Applied Maths, Sint Martens Latem, Belgium). The similarity between all pairs of traces was expressed by the Pearson product moment correlation coefficient presented as percentages of similarity.
Genotypic Analysis
Genomic DNA was extracted using the DNeasy Tissue kit (Qiagen, Venlo, The Netherlands) according to the instructions of the manufacturer.
The 16S rRNA gene was amplified using primers complementary to the conserved edges. Consensus primers alpha-beta-NOT (5′-TCA AAC TAG GAC CGA GTC) [SEQ ID NO:3] and omega-MB (5′-TAC CTT GTT ACT TCA CCC CA) [SEQ ID NO:4] were used, as previously described (Baele et al. (2001) J Appl Microbiol 91, 488-491). A 1500 bp amplicon [SEQ ID NO: 5] encoding a part of 16S rRNA (FIG. 11) was amplified and sequenced using primer pD (5′-GTA TTA CCG CGG CTG CTG-3′) [SEQ ID NO:6], primer gamma* (5′-CTC CTA CGG GAG GCA GCA GT-3′) [SEQ ID NO:7], primer 3 (5′-GTT GCG CTC GTT GCG GGA CT-3′) [SEQ ID NO:8] and primer O* (5′-AAC TCA AAG GAA TTG ACG G-3′) [SEQ ID NO:9], as described elsewhere (Coenye et al. (1999) Int J Syst Evol Microbiol 49, 405-413). Sequence analysis was performed using the ABI PrismTM 3100 Genetic Analyzer (Applied Biosystems, Lennik, Belgium) and sequences were compared with Genbank using the BLAST algorithm. Phylogenetic analysis was performed using KODON (Applied Maths, Sint-Martens-Latem, Belgium). Pairwise alignment homologies were calculated and a dendrogram was constructed using the neighbour-joining method.
For the detection of the urease gene, a PCR with primers U430f (5′-ckgawttgatgcaagaagg-3′) [SEQ ID NO:10] and U1735r (5′-cttcgtgrattttaarrccaat-3′) [SEQ ID NO:11] was performed. This PCR results in an amplicon of 1224 bp in H. felis, H. bizzozeronii, H. salomonis and “Candidatus H. heilmannii” (O'Rourke et al. (2004) Int J Syst Evol Microbiol 54, 2203-2211). A PCR with primers Hh2f and Hh2r which specifically amplifies a part of the urease gene of “Candidatus H. heilmannii” was also applied (O'Rourke et al. (2004) cited above). DNA from “Candidatus H. heilmannii” served as positive control, while highly purified water was included as negative control. PCR products were separated through gel electrophoresis as previously described (Baele et al. (2004) J Clin Microbiol 42, 1115-1122.). Additionally, obtained PCR products for “Candidatus H. heilmannii” and JKM4T (Helicobacter cynogastricus) were sequenced using the BigDye Terminator Cycle Sequencing Kit (Perkin Elmer, Applied Biosystems) on a ABI PrismTM 3100 Genetic Analyzer (Applied Biosystems). The electropherograms were exported and converted to Kodon (Applied Maths) and sequences were compared with Genbank using BLAST.
tRNA intergenic length polymorphism analysis (tDNA-PCR) was performed with a consensus primer T3B (5′-AGG TCG CGG GTT CGA ATC C-3′) [SEQ ID:12] (labeled with the fluorescent marker TET) and primer HT135R (5′-ACC AAC TGG GCT AAG CGA CC-3′) [SEQ ID NO:13], a specific primer complementary to the tRNA intergenic spacer of Helicobacter species, as described earlier (Baele et al., 2004 cited above). DNA extracted from pure cultures of H. felis, H. salomonis and H. bizzozeronii served as positive controls, while highly purified water was included as negative control. The PCR products were separated by means of capillary electrophoresis using the ABI PrismTM 3100 Genetic Analyzer (Applied Biosystems, Lennik, Belgium). Lengths were determined by interpolation with an internal size standard mixture of GeneScan 500 ROX (Applied Biosystems) and GeneScan 400-HD ROX (Applied Biosystems), using GeneMapper (Applied Biosystems). To determine the prevalence of the new Helicobacter species in cats and dogs, gastric samples were collected from the corpus region of 110 dogs (65 male, 45 female, age ranging from 1 day to 18 years) and 43 cats (25 male, 18 female, aged from 7 weeks to 18 years), from various breeds, which were presented for autopsy at the Department of Pathology (Faculty of Veterinary Medicine, Ghent University) between November 2001 and September 2003 with various pathology. DNA was extracted from the feline and canine samples using the DNeasy tissue kit (Qiagen), according to the instructions of the manufacturer. These DNA samples were subjected to tRNA intergenic length polymorphism analysis.
Phenotypic studies The salient tests that distinguish the new isolate from other canine gastric helicobacters are listed in Table 4.







TABLE 4







Characteristics of JKM4 (Helicobacter cynogastricus) and related


gastric Helicobacters












Characteristic
H. cynogastricus
H. felis
H. bizzozeronii
H. salomonis
H. pylori





Cell length (μm)
10-18
  5-7.5
 5-10
5-7
2.5-5  


Cell width (μm)
0.8-1.0
0.4
0.3
 0.8-0.12
0.5-1.0


Periplasmic fibrils
+
+
−
−
−


Location of the
bipolar
bipolar
bipolar
bipolar
polar


flagella


No. of flagella
 6-12
14-20
10-20
10-23
4-8


Flagellar sheath
+
+
+
+
+


Catalase activity
+
+
+
+
+


Oxidase activity
+
+
+
+
+


Urease activity
+
+
+
+
+


Nitrate reduction
+
+
+
+
−


Hippurate hydrolysis
−
−
−
−
−


Indoxyl acetate
−
−
+
+
−


hydrolysis


γ-Glutamyl
+
+
+
+
+


aminopeptidase


TTC reduction
+
−
+
+
+


Alkaline
+
+
+
+
+


phosphatase activity


Growth at


25° C.
−
−
−
−
−


37° C.
+
+
+
+
+


42° C.
−
−
+
−
−


Tolerance to


  1% ox bile
−
−
−
−
−


1.5% NaCl
−
−
−
−
−


  1% glycine
−
−
−
−
−









The ultrastructural studies of strain JKM4T (Helicobacter cynogastricus) revealed large spiral cells which were 10 to 18 μm long and approximately 1 μm wide, with three to eight spirals per cell. One periplasmic fibril was present at every bacterial cell, running along the external side of the helix. Up to 12 sheathed flagella were detected at both ends of each cell and these flagella were slightly off-centre. The flagellae were blunt-ended and the terminal diameter was wider than the average diameter of the flagellar body. Coccoid forms were observed in older cultures. The ultrastructural characteristics of the organisms were examined several times after several subcultures and were the same in all studies.
The isolate presented oxidase, urease and catalase activity, and did not hydrolyze indoxyl acetate. The organisms were able to reduce nitrate and TTC, and were positive in the esterase, gamma-glutamyl transpeptidase, L-arginine arylamidase, and alkaline phosphatase tests, but negative in the hippurate hydrolysis, pyrrolidonyl arylamidase, and L-aspartate arylamidase tests. The bacteria grew well on blood-supplemented BHI, brucella and Mueller-Hinton agar media.
The bacteria were sensitive to all antimicrobials tested, as indicated by low MIC values, ranging from 0.03 to 0.25 μg/ml. They did not grow on media containing 1.5% NaCl, 1% bile or 1% glycine. They were able to grow at 37° C. and 30° C., but not at 25° and 42° C. Growth was abled in both anaerobic and microaerobic environments, while atmospheres containing normal levels of oxygen or solely an increase of CO2 were not suitable to culture the bacteria.
The whole-cell protein profile of strain JKM4T (Helicobacter cynogastricus) differed considerably from those of reference strains of other Helicobacter species (FIG. 9A). Correlation levels towards the protein profiles of other Helicobacter reference strains were all below 0.80 indicating that strain JKM4T represents a novel Helicobacter species. FIG. 9B shows the result of the numerical analysis of the protein profiles of strain JKM4T (Helicobacter cynogastricus) and its nearest phylogenetic neighbours.
Genotypic Studies
Sequencing of the 16S rRNA gene of JKM4T (Helicobacter cynogastricus) revealed >97% homology with H. felis, H. bizzozeronii, H. salomonis and “Candidatus H. heilmannii”, while the sequence differed more than 3% of “Candidatus H. suis” (FIG. 9B). A phylogenetic tree revealed clustering of the new isolate within all these species (FIG. 10).
PCR on genomic DNA of JKM4T (Helicobacter cynogastricus) using primers U430f (5′-gckgawttgatgcaagaagg-3′) [SEQ ID NO:14 and U1735r (5′-cttcgtgrattttaarrccaat-3′) [SEQ ID NO:15] produced a series of aspecific fragments and not the expected fragment of 1224 bp. PCR with “Candidatus H. heilmannii” specific primers Hh2f and Hh2r resulted in the production of a 320 bp fragment, which consistently differed from the expected 380 bp produced from DNA of “Candidatus H. heilmannii”. Sequence analysis of the PCR product revealed a unique sequence, which did not match to any sequence in the Genbank.
Analysis of the PCR products produced from the DNA of the new isolate in the tDNA-PCR consistently revealed an amplicon of 136.6 bp, which differed from the tDNA-amplicon of H. felis (137 bp), H. bizzozeronii (136 bp) and H. salomonis (134 bp). A fragment of the same size was found in 1 cat (2.3%) and in 23 dogs (20.9%).
The present example demonstrates the existence of a fourth culturable Helicobacter species, able to colonize the canine stomach.
Analysis of the 16S rRNA gene revealed a high degree of homology with the three previously isolated carnivorous Helicobacter species.
The urease gene has recently been approved to be discriminative between these Helicobacter species. PCR on genomic DNA of isolate JKM4T (Helicobacter cynogastricus) using primers that detect the urease gene in H. felis, H. bizzozeronii and H. salomonis only produced aspecific fragments. A “Candidatus H. heilmannii” specific PCR did revealed a PCR fragment but with a sequence different to the one of Candidatus H. heilmannii”. 
In addition, the PCR amplicon of the novel species of the present invention by tDNA-PCR differs from the amplicons of other Helicobacters. These findings, together with the results of protein-profiling, which revealed a completely different pattern from the patterns of other Helicobacter species, demonstrate that isolate JKM4T is a distinct, novel Helicobacter species which we designate Helicobacter cynogastricus. 
Example 8
Identification of H. baculiformis 
This example describes the characterization of a Helicobacter strain with flexispira-like morphology, isolated from the stomach mucosa of a cat.
This strain, designated M50T, was isolated from the mucosa of the stomach of a cat as described by Baele et al. (2008) Int J. Syst. Evol. Microbiol. 58, 357-364 “Helicobacter baculiformis sp. nov., isolated from feline stomach mucosa”, which is incorporated by reference herein.
Genotypic Studies
Genomic DNA of M50T was extracted using the DNeasy Tissue kit (Qiagen, Venlo, The Netherlands) according to the instructions of the manufacturer.
The 16S rRNA gene was amplified using primers αβ-NOT (5′-AGTTTGATCCTGGCTCAG-3′) [SEQ ID. NO: 3] and ωMB (5′-TACCTTGTTACGACTTCGTCCCA-3′) [SEQ ID. NO: 4]. The PCR products were sequenced using primers pD [SEQ ID. NO: 6], γ* [SEQ ID. NO: 7], 3 [SEQ ID. NO: 8] and O* [SEQ ID. NO: 9] as described above. The sequences were compared with the NCBI GenBank by using the BLAST search tool. Phylogenetic analysis was performed using the Kodon software after including the consensus sequence in an alignment of small ribosomal subunit sequences collected from GenBank. The 16S rRNA gene of strain M50T (accession no. EF070342) showed 98-99% sequence identity with “H. heilmannii” type 2, H. felis, H. salomonis and H. bizzozeronii. 
Multiple alignment was calculated using an open gap penalty of 100% and a unit gap penalty of 0%. A tree was constructed using the neighbour-joining method showing that strain M50T was situated near the H. felis, H. bizzozeronii, H. salomonis, H. cynogastricus, and “Cand. H. heilmannii” cluster. These species have all been isolated from the stomachs of dogs (Hänninen et al., 1996, Int J Syst Evol Microbiol, 53, 425-433; Jalava et al., 1997, Int J Syst Bacteriol 47, 975-982; Van den Bulck et al., 2006, Int J Syst Evol Microbiol 56, 1559-1564), cats (Lee et al., 1988, Infect Immun 56, 2843-2850; O'Rourke et al., 2004) and/or humans (Andersen et al., 1999; Jalava et al., 2001, Emerg Infect Dis 7, 1036-1038; O'Rourke et al., 2004). Only 90.7% sequence identity was obtained with the 16S rRNA gene sequence of “Flexispira rappini” taxon 7, comprising a Helicobacter isolate from a dog stomach (Accession Number U51874).
For identification of strain M50T to the species level, a multiplex PCR was performed enabling discrimination between H. felis, H. bizzozeronii, and H. salomonis. This PCR is based on a part of the tRNA intergenic spacer of Helicobacter species, amplified with TET-labelled primers, and on the urease gene of H. felis (NED-labelled primers) and H. bizzozeronii (HEX-labelled primers), as described earlier (Baele et al., 2004). DNA extracted from pure cultures of H. felis, H. salomonis and H. bizzozeronii served as positive controls, while highly purified water was included as a negative control. Fluorescently labelled PCR products were separated by means of capillary electrophoresis. Strain M50T yielded an amplicon of 137 bp with the tRNA intergenic spacer-specific primers, which is the same as the amplicon obtained for H. felis strains. However, no H. felis-specific urease gene fragment was obtained with the NED-labelled primers.
A 1224 bp fragment of the ureAB genes was amplified and sequenced using primers U430F and U1735R and with conditions as described above. A sequence of 1072 bp (accession no. EF070343) was obtained and showed about 80% sequence identity with the urease sequence of H. felis strain INTO (AY368267). Multiple alignment was calculated using an open gap penalty of 100% and a unit gap penalty of 0%. Highest similarity (77-81%) was obtained with sequences from H. felis strains. With H. salomonis, H. bizzozeronii, “Cand. H. suis”, “Cand. H. heilmannii” and H. cynogastricus, 78-80%, 75-76%, 73-75%, 72-74% and 71% sequence identity was obtained, respectively. The results of comparison of urease sequences of strain M50T with other gastric Helicobacter species are shown in FIG. 12. A 515 bp sequence (accession no. EF070344) obtained from isolate M50T using the methodology described by Mikkonen et al. (2004) placed this taxon into the cluster of H. felis, H. bizzozeronii, H. salomonis and H. cynogastricus, confirming the results based on 16S rRNA gene and ureAB sequence analysis. Only 70-75% similarity was obtained with these species, yielding sufficient difference to consign isolate M50T into a new taxon.
Polyacrylamide gel electrophoresis (PAGE) of whole-cell proteins of strain M50T was performed, in order to confirm its distinct taxonomic status. For this purpose, strain M50T was grown on BHI agar supplemented with 5% (vol/vol) horse blood and was incubated at 37° C. in a micro-aerobic atmosphere as described above. A whole-cell protein extract was prepared and sodium dodecyl sulphate PAGE was performed as described previously (Pot et al., 1994, J Appl Bacteriol 77, 362-369). Whole-cell protein profiles of H. bizzozeronii, H. salomonis, H. felis and H. cynogastricus reference strains and of type and reference strains of other Helicobacter species were available from previous studies (Jalava et al., 1998, App Environ Microbiol 64, 3998-4006, Jalava et al. 2001, Emerg Infect Dis 7, 1036-1038; Van den Bulck et al., 2006, Int J Syst Evol Microbiol 56, 1559-1564). The densitometric analysis, normalization and interpolation of the protein profiles, and numerical analysis were performed using the GelCompar software package version 4.2 (Applied Maths). The similarity between all pairs of traces was expressed by the Pearson product moment correlation coefficient presented as percentages of similarity. FIG. 13 demonstrates that strain M50T can be clearly distinguished from all of its cultured closest relatives. Given the correlation between level of whole-cell protein electrophoretic similarity and DNA-DNA hybridization these results confirm that strain M50T represents a species distinct from its nearest phylogenetic neighbours.
In conclusion, the combined evidence derived from phylogenetic analysis of the 16S rRNA, ureAB, and HSP60 genes and whole-cell protein electrophoresis demonstrates that strain M50T represents a novel species within the phylogenetic lineage thus far consisting of H. felis, H. bizzozeronii, H. salomonis, H. cynogastricus and “Candidatus H. heilmannii”. 
Nucleotide Sequence Accession Numbers.
The 16S rRNA gene sequence of H. baculiformis M50T (=type strain=LMG 23839T=CCUG 53816T) is available from GenBank under accession numbers EF070342. The partial ureAB gene sequences of H. baculiformis M50T (=type strain=LMG 23839T=CCUG 53816T) is available from GenBank under accession number EF070343. The hsp60 gene sequence of H. baculiformis M50T (=type strain=LMG 23839T=CCUG 53816T) is available from GenBank under accession number EF070344.
Phenotypic Analysis
Table 5 shows the most important phenotypic characteristics of H. baculiformis compared with those of other Helicobacter species. Data were obtained from Bronsdon et al. (1991), Dewhirst et al. (2000a), Eaton et al. (1993), Fox et al. (1988, 1995), Hänninen et al. (1996, 2005), Jalava et al. (1997) Int J Syst Bacteriol 47, 975-982, Lee et al. (1988, Infect Immun 56, 2843-2850, 1992), Mendes et al. (1996); Patterson et al. (2000), Van den Buick et al. (2006, Int J Syst Evol Microbiol 56, 1559-1564).







TABLE 5





Differential characteristics of H. baculiformis M50T sp. nov. and other


Helicobacter species.

















Taxon















1
2
3
4
5
6
7





Cell length (μm)
10
10-18
 5-10
  5-7.5
5-7
2.5-5  
1.2-2  


Cell width (μm)
 1
0.8-1.0
0.3
0.4
0.8-1.2
0.5-1.0
0.3


Catalase production
+
+
+
+
+
+
+


Nitrate reduction
+
+
+
+
+
−
−


Urease
+
+
(+)
(+)
+
+
+


Alkaline phosphate
+
+
V
V
V
+
+


hydrolysis


γ-Glutamyl transpeptidase
+
+
+
+
+
+
+


Indoxyl acetate
−
−
(−)
(−)
(−)
(−)
(−)


hydrolysis


Growth at 42° C.
−
−
V
V
−
(−)
(−)


Growth on 1%
−
−
(−)
−
−
−
−


glycine


Susceptibility to


Nalidixic acid
I
ND
R
R
R
R
R


(30 μg)


Cephalothin
R
ND
S
S
S
S
S


(30 μg)


Periplasmic fibril
+
+
−
+
−
−
−


No. of flagella/cell
11
 6-12
10-20
14-20
10-23
4-8
2-5


Sheathed flagella
Yes
Yes
Yes
Yes
Yes
Yes
Yes


Distribution of
BP
BP
BP
BP
BP
MP
MP


flagella












Taxon














8
9
10
11
12
13





Cell length (μm)
4-5
4-6
2

3.5-5  
4-8


Cell width (μm)
0.5
0.6-0.7
0.5

0.5-0.6
0.6


Catalase production
+
+
+
+
+
+


Nitrate reduction
+
+
+
−
−
−


Urease
+
+
+
+
+
+


Alkaline phosphate
−
−
+
+
+
−


hydrolysis


γ-Glutamyl transpeptidase
+
+
+
ND
+
+


Indoxyl acetate
−
−
+
−
−
+


hydrolysis


Growth at 42° C.
+
+
V
+
−
+


Growth on 1%
+
ND
−
−
−
−


glycine


Susceptibility to


Nalidixic acid
R
R
S
R
R
S


(30 μg)


Cephalothin
R
R
R
S
R
R


(30 μg)


Periplasmic fibril
+
+
−
−
+
+


No. of flagella/cell
 3-14
5-7
4-8
4-8
10-14
 7-10


Sheathed flagella
Yes
Yes
Yes
Yes
Yes
Yes


Distribution of
BP
BP
LP
BP
BP
BP


flagella





Species:


1, H. baculiformis (this study);


2, H. cynogastricus


3, H. bizzozeronii;


4, H. felis;


5, H. salomonis;


6, H. pylori;


7, H. acinonychis;


8, H. bilis;


9, H. trogontum;


10, H. mustelae;


11, H. nemestrinae;


12, H. muridarum;


13, H. aurati.


*R, resistant; S, susceptible; I, intermediate


**BP, bipolar; MP, monopolar; LP, lateral polar






Example 9
In Vivo Immunogenicity of High Pressure Homogenized Filtrate Antigens and Sonicated Filtrates of Different Species Related to Candidatus H. Suis 
Three week old male SPF BALB/c mice (free from Helicobacter spp.) were housed in autoclaved filter top cages (5 animals/cage), fed with a commercial diet and provided water ad libitum for 2-3 weeks prior to initiation of the experiment. At the time of the allotment, mice were housed in individual cages.
Antigens were prepared by inactivating cultures of H. cynogastricus and H. bizzozeronii using a high pressure homogenizer (Avestin). For H. cynogastricus, the protein concentration was 100 μg/26 μl obtained from 9.2×107 cells (3.85 mg/ml), while 100 μg of protein was obtained in 21.76 μl from 7.81×107 cells of H. bizzozeronii (4.6 mg/ml).
H. bizzozeronii and H. cynogastricus antigens were prepared by sonicating bacterial suspensions and filtering them through a 0.22-μm pore filter. Protein concentrations were determined by the Lowry assay. The H. bizzozeronii preparation had a concentration of 5.224 mg/ml. The H. cynogastricus preparation contained 5.079 mg/ml of protein. The Candidatus H. suis preparation had a concentration of 1.838 mg/ml.
For each dose of vaccine, 100 μg of protein was used.
For intranasal (IN) administration of the antigens, 5 μg of cholera toxin (Sigma) was added per dose.
Swine stomachs were collected from the slaughterhouse and homogenized. These stomach homogenates were used to infect BALB/c mice for propagating Candidatus H. suis in vivo. Passaging in mice was performed every two weeks with whole urease-positive mouse stomachs homogenized in LYM (5 mL LYM/stomach) (LYM used in this example consists of 2 volumes of horse serum, 1 volume of Brain Heart Infusion broth and 10% glucose). PCR confirmed the presence of Candidatus H. suis in each passage. The fourth mouse passage was performed in 10 BALB/c mice. From these 10 mice the urease-positive stomachs were pooled and homogenized. The homogenate was frozen at −70° C.
The titre of the frozen stock was determined after thawing the frozen stock. Fifteen minutes after thawing at 37° C., serial dilutions of homogenate in LYM were made and intragastrically (IG) inoculated in mice to determine the 100% mouse infection dose level.
Groups of 5 mice were vaccinated and inoculated according to Table 6.







TABLE 6







Study design of vaccination experiment




















*Fecal









Sample
Necropsy Blood


Group
IVP
Route
N
Vaccination
Challenge
Collection
Sample





T01
Saline
IN
5
D21, D42
D70
D88-D91
D119-120


T02
HP
IN
5
D21, D42
D70
NA
D119-120



H. cyno


T03
SF
IN
5
D21, D42
D70
NA
D119-120



H. cyno


T04
HP
IN
5
D21, D42
D70
NA
D119-120



H. bizzo


T05
SF
IN
5
D21, D42
D70
NA
D119-120



H. bizzo


T07
SF
SC
5
D0, D21, D42
D70
NA
D119-120



H. cyno


T08
SF
SC
5
D0, D21, D42
D70
NA
D119-120



H. bizzo


T10
—
NA
5
D0, D21, D42
D70
D88-D91
D119-120



NVNC





IVP = Investigated veterinary product


H cyno = H. cynogastricus;


H bizzo = H. bizzozeronii


HP = High pressure preparations;


SF = Sonicated filtrate preparations


SC = Subcutaneous injection;


IN = Intranasal administration


NVNC = Non-vaccinated, non-challenged mice;


NA = Not applicable






Urease activity in the stomach of mice is indicative of colonization of Helicobacter bacteria and was assessed using the method of Corthésy-Theulaz et al. (1995), cited above. One half of the stomach was immersed in 500 μl of CUTest (Temmler Pharma) and incubated at 37° C. for 3 h. After centrifugation (5 min, 100 g) the supernatant was used for spectrophotometric quantification at an OD of 550 nm. The cut-off value was calculated in each experiment and corresponded to the mean +5 S.D. of the absorbance values obtained with gastric samples of non-immunized, nonchallenged mice.
DNA from mucosal tissue samples was extracted with the Dneasy Tissue kit (Qiagen, Hilden, Germany). PCR for specific detection of Candidatus H. suis was performed as described previously (De Groote et al., 2000 cited before)
The mean urease values per stomach tissue of vaccinated mice were compared with these of non-vaccinated mice. The percentage of stomachs PCR positive for Candidatus H. suis were compared between non-vaccinated/challenged mice vs. vaccinated-challenged controls. The stomachs of nonchallenged mice are PCR and urease negative.
Blood samples for serological analyses were taken at necropsy.
Fecal samples of mice of group T01 were all positive at D (Day) 88-D91. Fecal samples of mice of group T10 were all negative at D88-D91.
The results of urease and PCR tests are summarized in Table 7.







TABLE 7







Results of the urease test and PCR test of mice vaccinated with


different antigens and challenged with Candidatus H. suis.













Mean






Urease


Group
IVP
values
PCR Antrum#
PCR Fundus#














T01
Saline
1.63
5/5
5/5


T02
H. cyno IN HP
0.098
2/5
2/5


T03
H. cyno IN SF
0.092
2/3
1/3


T04
H. bizzo IN HP
0.079
3/4
3/4


T05
H. bizzo IN SF
0.094
4/5
2/5


T07
H. cyno SC SF
0.122
5/5
5/5


T08
H. bizzo SC SF
0.829
4/4
4/4


T10
NVNC
0.118
0/5
0/5





#Number of PCR positive samples/total samples













TABLE 8







Results of ELISA to measure antibodies binding


to H. suis, H. bizzo or H. cyno













Candidatus H. suis

H. cyno


Group
IVP
ELISA*
H. bizzo ELISA*
ELISA*














T01
Saline
<100
<100
<100


T02
H. cyno IN HP
224.9
<100
308.3


T03
H. cyno IN SF
167.3
303.1
349


T04
H. cyno IN HP
470.9
133.8
65.74


T05
H. bizzo IN SF
557.2
370.7
123.3


T07
H. cyno SC SF
302.8
231.5
1097


T08
H. bizzo SC SF
211.6
2407
246.6


T10
NVNC
<100
<100
<100





*Geometric mean titers (by ELISA) to the specific Helicobacter spp. listed.






The above results show that intranasal and subcutaneous immunization caused a decrease in mean urease activity values in the stomachs of all vaccinated animals. The urease activity levels were lower in all intranasally vaccinated animals and in the animals vaccinated with the H. cynogastricus antigen compared to the animals subcutaneously vaccinated with antigens prepared from H. bizzozeronii. PCR testing on stomach samples showed a partial clearance of Candidatus H. suis DNA in all intranasally vaccinated groups. Subcutaneous immunization of mice showed no reduction in PCR detection of Candidatus H. suis, for all antigens tested. Since PCR on stomach tissue samples at 49 days after challenge infection could still detect Candidatus H. suis-DNA in all immunization-challenge groups, complete clearance of challenge bacteria was not achieved. Also, serologic responses in the mice vaccinated with either H. bizzozeronii or H. cynogastricus were also detected in a Candidatus H. suis ELISA (Table 8). Thus, these vaccines generated immune responses that recognized Candidatus H. suis antigens by ELISA, suggesting a possible mechanism of cross-protection.
An analogous experiment is performed wherein antigen preparations of H. baculiformis are prepared and used as a vaccine against Candidatus H. suis infection.
Example 10
Efficacy of H. Cynogastricus and H. Bizzozeronii Sonicate Vaccine in Pigs Challenged with Stomach Homogenates Containing Candidatus H. suis 
ANIMALS
Pigs
Five gestating sows from a herd were confirmed to be free of “Candidatus Helicobacter suis” infection by urease and PCR screening of stomachs of herd mates at slaughter. Sows farrowed in purpose built farrowing rooms (one sow per room) in the Department of Reproduction, Obstetrics and Herd Health at Ghent University. Fifty pigs from these sows were allotted to groups and the study initiated at the time of first vaccination.
Mice
Five week-old male SPF BALB/c mice (free from Helicobacter spp.) were purchased from an authorized breeder. The mice were housed in autoclaved filter top cages (5 animals/cage) and fed a commercial diet and water ad libitum. After an adaptation period of one week, the animals were used to confirm the viability and dose of the pig stomach homogenate challenge material.







TABLE 9







Study Design












Number
Age at




group
of pigs
vaccination
Vaccine
Treatment regimen














T01
14
1, 3, 5 weeks
Saline
3 doses






(IM injection) at






5, 6 and 7






weeks of age


T02
17
1, 3, 5 weeks
Filtered sonicate of





H. cynogastricus


T03
15
1, 3, 5 weeks
Filtered sonicate of





H. bizzozeronii


NTX
4

NA
NA









Antigens were produced by scraping organisms of agar plates. Antigen was sonicated and filtered using a 0.22 μm membrane and total protein content used to determine dose. Each antigen was mixed 1:1 with 10% AMPHIGEN®) prior to vaccination.
Challenge and Vaccination
On the day of challenge, 6 swine pig stomachs were obtained from the slaughterhouse and transported to the lab. The stomachs were opened and the remaining food was rinsed off with 37° C. autoclaved tap water. The upper cell layers and mucus were scraped off the antrum of stomachs yielding a positive urease test until 200 ml of scrapings were obtained. A small mucosal tissue sample from the antrum (approximately 1 cm from the torus pyloricus) was taken to screen for the presence of “Candidatus H. suis”. Half of this tissue sample was used for a rapid urease test (CUT, Temmler Pharma, Marburg, Germany):
Another portion of gastric mucosal tissue was frozen (−20° C.) and used for specific detection of “Candidatus H. suis” by PCR. From each of 10 stomachs that yielded a positive urease test, the upper cell layers and mucus from the antrum were scraped off. Scrapings were pooled and homogenized 1 part to 2 in lyophilization medium (LYM) consisting of 2 volumes of horse serum, 1 volume of Brain Heart Infusion broth, (Oxoid, Basingstoke, England) and 10% glucose. A 10 mL aliquot of the pooled supernatants from 10 pigs was used to inoculate pigs.
To confirm that the pig stomach homogenate contained viable Candidatus H. suis, an aliquot of each challenge homogenate preparation was diluted 1/20 in LYM, and a 0.3 mL aliquot was administered to isoflurane anesthetized mice by oral gavage. Mice were sacrificed 2 weeks later and the stomach contents screened by urease and PCR for the presence of H. suis. 
Pigs were vaccinated with 100 μg of sonicated filtrate of H. cynogastricus or H. bizzozeronii (adjuvanted with AMPHIGEN®) by intramuscular injection 1, 3, and 5 weeks of age. Control pigs were vaccinated at the same time with an equal volume of saline. Pigs were observed for clinical signs one (1) day before and two (2) days after vaccination and any abnormalities were noted on the daily health form.
The day before each inoculation pigs were feed restricted. Ninety minutes before inoculation, all pigs except the NTX group, were treated to reduce stomach acid production. Pigs were anaesthetized. All pigs were inoculated intragastrically after stomach intubation with a plastic cannula with an inner diameter of 6 mm and an outer diameter of 8 mm. Challenge was performed three times at weekly intervals. Pigs received 10 mL of pig stomach homogenate containing “Candidatus H. Suis”. Immediately before and immediately after administration of the stomach homogenate, pigs were intragastrically inoculated with respectively 15 mL and 5-10 mL of Brucella Broth (Becton Dickinson, Erembodegem, Belgium) supplemented with 10% fetal bovine serum and 0.75% agar (Agar Noble, Becton Dickinson, Erembodegem, Belgium). This was administered into the stomach to delay the passage of the bacterial suspension through the duodenum.
Blood Sampling
On the day of the first vaccination, 2 weeks after the third vaccination, and just prior to necropsy, a blood sample (approximately 5 to 10 mL in serum separator tubes) was collected from all pigs for Helicobacter spp. (H. cynogastricus or H. bizzozeronii) serology (ELISA). Following separation, the serum was placed in at least 2 cryogenic vials. Serum samples were frozen at −20° C. and stored.
Necropsy
At necropsy, the stomachs were excised and opened along the greater curvature from the diverticulum to the pyloric sphincter. The mucosal surface from the pars oesophagea was macroscopically examined and lesions scored on a scale of 0-5 using the method of Hessing et al. (1992). Briefly the scores were recorded as follows: score 0=intact mucosa, score 1=mild hyperkeratosis (<50% surface area), score 2=severe hyperkeratosis (≧50% of surface area), score 3=hyperkeratosis and a few small erosions (less than 5 and shorter than 2.5 cm), score 4=hyperkeratosis and extensive erosions (more than 5 erosions and/or longer than 2.5 cm), score 5=hyperkeratosis and very large erosions (more than 10 erosions or longer than 5 cm) and/or ulcers. Each stomach was also scored using a Visual Analog Scale from 0-100 mm where 0=no lesion and 100=perforating ulcer.
After scoring, several sites from the glandular mucosa (approximately 0.5 cm2) from each stomach were sampled by PCR, quantitative urease test, and histology.
PCR for Specific Detection of “Candidatus H. suis” Infection in Gastric Tissue.
DNA was extracted with DNeasy Tissue Kit (Qiagen, Hilden, Germany). PCR for specific detection of “Candidatus H. suis” was performed as described by De Groote et al. (2000).
Urease Test
To assess the bacterial load in the stomachs, mucosal tissue samples (approximately 0.5 cm2) were immersed in 1,000 μl of CUTest (Temmler Pharma, Marburg, Germany) and incubated at 37° C. for approximately 3 hours as described by Corthésy-Theulaz et al. (1995). After centrifugation, the supernatant was used for spectrophotometric quantification at an optical density (OD) of 550 nm.
Histological Examination
Gastric antrum mucosal tissue samples (4 per pig) were fixed in 10% phosphate buffered formalin, processed by routine methods and embedded in paraffin. A second section was stained with HE for scoring of gastritis. Histopathological changes were scored for 1) diffuse lymphocytes—a score for the infiltration of lymphocytes diffusely in the propria mucosae; 2) formation of lymphoid follicles in the propria mucosae; 3) formation of lymphoid follicles under the surface epithelium; 4) diffuse infiltration in the propria mucosae of plasma cells. The presence of lymphoid follicles under the surface epithelium and in the propria mucosae were very noteworthy and characteristic lesions. Each parameter was scored by severity with a score of 0-3 with 0=no lesion, 1=mild, 2=moderate, and 3=severe. They were also scored using a visual analog scale.
ELISA for Detection of Antibodies in Serum Samples from Pigs Vaccinated with Helicobacter bizzozeronii or Helicobacter cynogastricus. 
Ninety-six well flat-bottom microtiter plates were coated with 100 μl of carbonate coating-buffer pH 9.6 containing 200 ng/well of Helicobacter bizzozeronii or Helicobacter cynogastricus antigens derived from medium supplemented with horse serum.
Porcine sera samples were initially diluted 1:100 in 1% PVA/DPBS and further diluted on each antigen coated plate 4 fold up to 1:102400. On every plate the positive control serum (from pigs previously vaccinated with the appropriate Helicobacter sp.), negative control serum and blank control wells were included. The plates were incubated at 37° C. for 1 hour and were washed 3 times. One hundred microliters of a conjugate (goat anti-swine IgG H&L HRP) diluted 1:1000 were added to each well. After incubation for 1 hour at 37° C., each plate was washed 3 times and color was developed with 100 ul of ABTS. Color development was terminated with 100 ul of Stop Solution. Optical densities at 405/490 were measured with a plate reader interfaced with commercial software.
The exact titer of each serum sample was calculated and expressed as a value at which the optical density (O.D.) value of the sample crossed the cut-off value. The cut-off value was based on 50% of the value of the positive control O.D. The cut-off value was determined for the O.D. of the positive control at a dilution of 1:400 when the O.D. fell between an O.D. of 0.800 and 1.800.
Data Analysis
Urease by PCR: Urease levels from each region in the stomach were transformed with an appropriate log transformation prior to analyses. The transformed values from each region were analyzed separately using a general linear mixed model. Pairwise treatment comparisons were made when the overall treatment was significant (P≦0.10). Treatment least squares means and 90% confidence intervals were back-transformed for presentation.
Serology: Serum antibody titers were transformed with an appropriate log transformation prior to analyses. The transformed titers were analyzed using a general linear mixed model. Pairwise treatment comparisons were made when the overall treatment was significant (P≦0.10). Treatment least squares mean and 90% confidence intervals were back-transformed for presentation.
Tissue Samples: The presence of focal lymphoid follicles under the surface epithelium, lymphoid follicles in the propria mucosae, the presence of diffuse lymphocytes, and plasma cellular infiltrates in the antral part of the gastric mucosa was evaluated.
Gross Lesions: At necropsy, gross lesions were scored using two methods—the Hessing ulcer score using a 0-5 range, and an analog scale in mm for 0-100 mm. Frequency distributions of positive/negative were calculated for each treatment and site/tissue/organ. Positive/Negative samples were analyzed using a generalized linear mixed model. When the general linear mixed model did not converge, Fisher's Exact test was used to analyze the data. Pair-wise treatment comparisons were made when the treatment main effect was significant (P≦0.10). Hessing scores were summarized with descriptive statistics.
Body Weight: Descriptive statistics including the mean, minimum, maximum and number of animals were calculated for each treatment and time point data collected.
Models for Analyses: Tissue sample results and gross lesion results (positive/negative) were analyzed with a generalized linear mixed model with fixed effect: treatment and random effects: type of room type (Hepa filtered or non-Hepa filtered) and block within room type. Linear combinations of the parameter estimates were used in a priori contrasts after testing for a significant (P≦0.10) treatment effect. Comparisons were made between treatments. The 10% level of significance (P≦0.10) was used to assess statistical differences. Where the model (via the GLIMMIX macro) did not converge, then Fisher's Exact test was used to analyze that variable. Contrasts between treatment groups were conducted. All hypothesis tests were conducted at the 0.10 level of significance using two-sided tests. There was no effect of the presence/absence of Hepa filters in the rooms.
Results
Gross lesion scores of pars esophagosa of the stomach: There was no significant difference in the visual analog scores between Helicobacter vaccinates or between Helicobacter and saline vaccinates (Tables 10-11).







TABLE 10







Least squares mean visual analog scores by group for gross


lesions of the pars esophagosa of the stomachs of pigs.














Number

Stand-
Lower
Upper



Treat-
of

ard
0.9
0.9


ment
Animals
LSM
Error
Confidence
Confidence
Range
















T01
14
32.33
4.941
23.99
40.67
 0 to 74


T02
17
28.53
4.66
20.67
36.39
10 to 70


T03
16
28.77
4.775
20.72
36.83
 9 to 60





LSM = least squares mean


T01 = vaccinated with saline


T02 = vaccinated with H. cynogastricus sonicated filtrates


T03 = vaccinated with H. bizzozeronii sonicated filtrates













TABLE 11







Hessing scores by category 0-5(0 = normal; 5 = perforating ulcer).










Hessing Score
Total














0
1
2
3
4
Observations



















N
%
N
%
N
%
N
%
N
%
N






















NTX
5
100
0
0
0
0
0
0
0
0
5


T01
1
7.1
1
7.1
5
35.7
5
35.7
2
14.3
14


T02
0
0
1
5.9
8
47.1
7
41.2
1
5.9
17


T03
0
0
1
6.3
8
50
5
31.3
2
12.5
16





N: number






Urease Scores: There were significant differences between T01-T02 and T02-T03 for the fundus (Table 12). However, there were no statistically significant differences in urease values for any other sites in the stomach.







TABLE 12







Least squares mean urease OD values for groups T01-T03 and the


non-treated (NTX) group.









Geometric Least Squares mean
















Treatment
N
A1
A2
A3
A4
Cardia
Fundus



















T01
Saline
14
0.62
0.58
0.8
0.87
0.18
1.17a


T02
Hc
17
0.34
0.61
0.43
0.59
0.21
**1.05ab


T03
Hb
16
0.44
0.43
0.41
0.43
0.17
*0.5c





T01-T03 comparison p = 0.02;


T02-T03 comparison p = 0.03


Values with different letters within a column and one antigen type are statistically significant (p < 0.05).






PCR: Table 13 shows that all animals were confirmed to be exposed to Candidatus H. suis following challenge with stomach homogenates. This confirms that the urease values were most likely due to the presence of Candidatus H. suis in the stomach.







TABLE 13







Number of animals with specific regions of the stomach positive by


PCR.
















Treament
N
A1
A2
A3
A4
Fundus
Cardia



















T01
saline
14
13
12
14
13
14
13


T02
H. cynogastricus
17
17
16
17
17
17
16


T03
H. bizzozeronii
16
16
16
16
16
16
13









Histopathology Scores: Table 14 summarizes the percentage of each region of the antrum in which there were abnormal scores for histopathological scoring. Only Lymphoid Follicles under Surface Epithelium and stomach region A2 were abnormal, i.e., there was a statistically significant difference between the saline and H. cynogastricus groups and between H. cynogastricus and H. bizzozeronii with H. cynogastricus having a greater percentage of pigs with abnormal scores than either of the other 2 groups.







TABLE 14







Histopathological Scores - Percentage with Abnormal Score by


Region of Antrum













N
A1
A2
A3
A4











Lymphoid Follicles under Surface Epithelium
















NTx
5
40
0
0
0



saline
T01
14
78.6
64.3
50
50



Hc
T02
15
66.7
100
62.5
68.8



Hb
T03
14
64.3
71.4
78.6
57.1







Plasma Cells
















NTx
5
0
0
0
0



saline
T01
14
21.4
28.6
35.7
14.3



Hc
T02
17
25
29.4
41.2
29.4



Hb
T03
14
26.7
26.7
33.3
33.3







Lymphoid Follicles in Propria Mucosae
















NTx
5
100
100
40
20



saline
T01
14
85.7
100
78.6
57.1



Hc
T02
16
75
94.1
94.1
76.5



Hb
T03
15
100
80
86.7
66.7







Diffuse Lymphocytes
















NTx
5
100
100
40
40



saline
T01
14
100
100
92.9
100



Hc
T02
15
93.8
100
100
88.2



Hb
T03
15
100
100
100
100










Serology: Geometric least squares mean titers to H. cynogastricus and H. bizzozeronii for Days 0, 34 and 84 of the study are presented in Table 15 and 16. The statistical comparison of these values per each antigen and each day are shown in Table 17. In general pig serum reacted much better to the homologous antigen than the heterologous antigen in the ELISA, especially those vaccinated with H. bizzozeronii. Pigs vaccinated with H. cynogastricus had longer sustained antibody titers than pigs vaccinated with H. bizzozeronii. Immune responses dropped to both antigens by Day 84 despite being challenged by Candidatus H. suis 4 times and vaccinated twice from the time of the initial antibody titer (Day 0).







TABLE 15







Geometric least squares mean antibody titers to H. bizzozeronii of


groups of pigs vaccinated with either H. cynogastricus or H. bizzozeronii.

















Geometric









least


Lower 90%
Upper 90%



Day of
Number
squares
Standard

confidence
confidence



study
of obs.
mean
error
Range
bound
bound

















T01
Day 0
16
55.0
5.38
50 to 111
46.7
64.8


T01
Day
12
293.3
39.05
154 to 898 
234.4
367.0



34


T01
Day
14
486.5
50.62
193 to 946 
408.1
580.0



84


T02
Day 0
17
71.6
6.80
50 to 153
61.1
84.0


T02
Day
17
295.7
33.77
160 to 551 
243.8
358.7



34


T02
Day
16
836.9
81.83
398 to 1253
709.3
987.3



84


T03
Day 0
16
58.5
5.72
50 to 141
49.7
69.0


T03
Day
15
2285.9
275.29
846 to 4564
1865.4
2801.1



34


T03
Day
16
846.3
83.03
452 to 1560
716.9
999.1



84
















TABLE 16







Geometric least squares mean antibody titers to H. cynogastricus


of pigs vaccinated with either H. bizzozeronii or H. cynogastricus.

















Geometric


Lower 90%
Upper 90%



Day of
Number
least squares
Standard

confidence
confidence



study
of obs.
mean
error
Range
bound
bound


















T01
Day 0
16
192.3
34.45
50 to 259
134.6
274.8


T01
Day 34
12
173.0
34.17
50 to 442
119.7
250.0


T01
Day 84
14
169.2
31.49
50 to 289
118.2
242.0


T02
Day 0
17
97.2
17.15
50 to 285
68.0
139.1


T02
Day 34
17
1940.0
342.08
936 to 7780
1356.4
2774.6


T02
Day 84
16
890.9
159.68
361 to 2336
623.2
1273.7


T03
Day 0
16
147.6
26.80
50 to 288
102.7
212.1


T03
Day 34
15
712.5
131.63
232 to 1590
495.8
1023.9


T03
Day 84
16
377.4
68.53
164 to 920 
262.6
542.3
















TABLE 17







Statistical significance of comparisons of antibody titers


between groups vaccinated with H. bizzozeronii or


H. cynogastricus and assayed against both antigens.












Treatment number
Day 0
Day 34
Day 84
















To HB






T01
55.0a
293.3a
486.5a



T02
71.6b
295.7ac
836.9b



T03
58.5ac
2285.9b
846.3bc



To HC



T01
192.3a
173.0a
169.2a



T02
97.2b
1940.0b
890.9b



T03
147.6ac
712.5c
377.4c







Values with different letters within a column and one antigen type are statistically significant (p < 0.05).






CONCLUSIONS
Vaccination of pigs with filtrates of sonicated H. bizzozeronii (p=0.01) resulted in a significant reduction of urease in the stomach fundus and Antrum 3-Antrum 4, thus indicating a reduction in colonization. Protective immunity may be related to antibodies to the urease fraction. Western blots completed after the end of this study were indicative of bands consistent in size and cross reactive to the large subunit of urease of H. pylori (data not shown). Serology results show that there was cross reaction between pigs vaccinated with H. cynogastricus tested against H. bizzozeronii and vice versa although the titer to the homologous antigen was much greater than to the heterologous antigen.
In two subsequent swine studies, it was demonstrated that pigs vaccinated with H. cynogastricus and H. bizzozeronii also generated antibody responses that recognized Candidatus H. suis antigens by ELISA (data not shown).
The protocol called for three confirmed challenges verified by mouse inoculations. However, only one out of three was confirmed. Thus, the efficacy of vaccines used in this study was not assessed against multiple challenges.
All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.
Other embodiments are within the scope of the claims.

## Claims

1. A method of vaccinating an animal against a Candidatus Helicobacter suis infection comprising the step of administering to said animal a vaccine comprising one or more antigen preparations from one or more Helicobacter species, wherein said species has a 16S rRNA sequence with at least 93% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO: 16).

2. The method according to claim 1, wherein said Helicobacter species has a 16S rRNA sequence with between 93 and 99% sequence identity to the sequence of Candidatus Helicobacter suis.

3. The method according to claim 2, wherein said Helicobacter species has a 16S rRNA sequence with between 95 and 97% sequence identity to the sequence of Candidatus Helicobacter suis.

4. The method according to claim 1, wherein said Helicobacter species is selected from the group consisting of Helicobacter felis, Helicobacter salomonis, Helicobacter heilmannii (type II), Helicobacter cynogastricus, Helicobacter baculiformis, Helicobacter pylori, and Helicobacter bizzozeronii.

5. The method according to claim 1, wherein said antigen preparation comprises whole-killed bacteria.

6. The method according to claim 1, wherein said antigen preparation comprises live-attenuated bacteria.

7. The method according to claim 1, wherein said antigen preparation comprises a processed bacterial preparation and/or a protein preparation either in part or entirely obtained by synthetic or recombinant methods.

8. The method according to claim 1, wherein said antigen preparation comprises a bacterial lysate.

9. The method according to claim 8, wherein said lysate is obtained by sonication.

10. The method according to claim 1, wherein said vaccine further comprises an adjuvant.

11. The method according to claim 1, wherein said step of administering said vaccine comprises intranasal administration.

12. The method according to claim 1, wherein said step of administering said vaccine comprises subcutaneous administration.

13. The method according to claim 1, wherein said step of administering said vaccine comprises prophylactic administration.

14. The method according to claim 1, wherein said step of administering said vaccine comprises therapeutic administration.

15. The method to claim 1, wherein said Helicobacter species is selected from the group consisting of Helicobacter acinonychis, Helicobacter nemestrinae, Helicobacter cynogastricus, Helicobacter heilmannii (type II), Helicobacter salomonis, Helicobacter bizzozeronii, and Helicobacter baculiformis.

16. The method to claim 1, wherein said Helicobacter species is selected from the group consisting of Helicobacter cynogastricus, Helicobacter bizzozeronii, and Helicobacter baculiformis.

17. The method according to claim 1, wherein said species has a 16S rRNA sequence with at least 95% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO: 16).

18. The method according to claim 1, wherein said species has a 16S rRNA sequence with at least 98% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO: 16).

19. The method according to claim 1, wherein said species has a 16S rRNA sequence with at least 99% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO: 16).

20. A vaccine for immunization against Candidatus Helicobacter suis comprising a composition of one or more antigen preparations from one or more Helicobacter species, wherein said species has a 16S rRNA sequence with at least 97% sequence identity to the sequence of Candidatus Helicobacter suis with Genbank Accession Number AF127028 (SEQ ID NO: 16).

21. The vaccine according to claim 20, wherein said antigen preparation comprises whole-killed bacteria.

22. The vaccine according to claim 20, wherein said antigen preparation comprises live-attenuated bacteria.

23. The vaccine according to claim 20, wherein said antigen preparation comprises a processed bacterial preparation and/or a protein preparation either in part or entirely obtained by synthetic or recombinant methods.

24. The vaccine according to claim 20, wherein said antigen preparation comprises a bacterial lysate.

25. The vaccine according to claim 20, wherein said vaccine further comprises an adjuvant.

26. The vaccine according to claim 20, wherein the bacterial species is characterized by a 16S rRNA sequence with between 97 and 99% sequence identity to said sequence of Candidatus Helicobacter suis.

27. The vaccine according to claim 20, wherein said species has a 16S rRNA sequence with at least 98% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO:16).

28. The vaccine according to claim 20, wherein said species has a 16S rRNA sequence with at least 99% sequence identity to the 16S rRNA sequence of Candidatus Helicobacter suis with Genbank Accession Number AF 127028 (SEQ ID NO:16).