WO2018162428A1 - Pentavalent streptococcus suis vaccine composition - Google Patents

Abstract

This invention relates to vaccine compositions for use against Streptococcus suis that comprise one or more isolated immunogenic polypeptide(s) selected from SSU0185, SSU1215, SSU1355, SSU1773 and SSU1915. Vaccine compositions and methods for their production and use in treating S. suis infection, for example in pig and human populations, are provided.

Description

PENTAVALENT STREPTOCOCCUS SUIS VACCINE COMPOSITION

Field

This invention relates to vaccine compositions and methods for the treatment of

Streptococcus suis infection.

Background

Streptococcus suis is a Gram positive, encapsulated bacterium which is a global zoonotic pathogen carried in the upper respiratory tract and on the tonsils of pigs [1 ]. S. suis was first reported in the 1950s after outbreaks of meningitis and arthritis occurred in piglets [2].

Infection of pigs with S. suis significantly impacts productivity and animal welfare in the pig industry worldwide. This is of particular concern in regions of high-intensity pig production, including South-East Asia, Europe and North America.

Streptococcus suis is also a zoonotic pathogen of humans. Human disease caused by S. suis was first reported in the 1960s in Denmark [3], but current concern lies in the role of S. suis in large, fatal outbreaks of toxic shock-like syndrome and meningitis in Asian countries including China [4-6] and Thailand [7,8]. Notably, S. suis was reported to be the most frequent cause of adult bacterial meningitis in Vietnam [9,10].

Identification of S. suis is by serotyping and this has distinguished 35 serotypes, all of which are associated with disease. Serotypesl through 9 plus 14 (including serotype 1 -2) are those most frequently isolated from diseased pigs globally [1 ], with serotypes 2,3,7 and 9 being responsible for most disease - although there are variations in prevalence between countries around the world [1 ]. Serotype 2 is most frequently reported in human cases [1 ,1 1 ]. Several (n=15) complete genome sequences of S. suis are available, including that of P1/7, a well-characterized strain [37; Table 4] which show that there is a high level of conservation amongst S. suis isolates across the different serotypes and from different countries.

In order to understand the population structure of S. suis, we have performed an analysis of the genomes of 459 S. suis strains. This is the largest comparison of strains to date of 29 different serotypes isolated from diseased and healthy pigs from the UK (184 strains), Vietnam (191 strains) and published and draft genome sequences from North America, South America, Europe and Asia. We have defined the core genome (i.e. the complete set of genes encoded by all strains analysed) and shown that there is conservation of virulence factors in strains from different parts of the world and in strains that were isolated from cases of disease or from healthy pigs (genomic analysis of 375 of these strains has been published by Weinert et al. 2015 [72] and the authors have added to this collection and continued the analysis to cover a total of 459 strains). A wide range of virulence-related factors from S. suis has been described, including capsular polysaccharide, extracellular protein factor (EF), muramidase-released protein (MRP), sortase A and suilysin. Some, but not all, of these have been shown to be required for virulence in pig challenge models [12]. Much literature addresses the complex

pathogenicity of S. suis and its implication for vaccine development [12,13 and references therein]. Various approaches have been used to develop vaccines for S. suis, including the use of killed whole-cell vaccines [14-16], live attenuated strains [17] and in recent years no less than 15 surface-associated immunogenic antigens have been identified and tested in different animal models [reviewed in 18]. However, the level of protection achieved has been variable and in many cases is serotype- or strain-dependent [18-21 ]. In the absence of effective commercial vaccines, control of disease caused by S. suis is reliant on

antimicrobial medication. New strategies for S. suis control are needed to reduce the dependence of pig production on antimicrobials and to protect human health. Colonization of the upper respiratory tract is a crucial step that could lead to subsequent infection by S. suis. Once the bacteria have colonized, they may breach mucosal epithelium barriers and access the bloodstream to invade various organs and cause exaggerated inflammation in pigs [1]. Identification of genes required for colonization could lead to a better understanding of the pathogenesis of S. suis and may provide valuable candidates for more efficient vaccine development. In vitro organ culture (IVOC), an air-liquid interface model using respiratory organ explants, provides a physiological, naturally mixed-cell population with a functional, mucus-producing ciliated surface that can be maintained for up to 72 hours [22-24]. The use of IVOC systems to study pathogenesis could dramatically reduce the use of human and animal models for in vivo studies while overcoming the limitation of in vitro cell culture systems [25-27]. IVOC systems have been established previously for colonization and host-pathogen interaction studies of veterinary respiratory pathogens such as Bordetella bronchiseptica [22], bovine herpesvirus-1 [24] and swine influenza and herpes viruses [28,29].

Functional screens have been conducted for the identification of various putative virulence factors of S. suis [30-33]. However the fitness mechanisms and genetic requirements for colonization of the upper respiratory tract of S. suis are still largely unknown.

Surface-associated proteins and immunogenic antigens involved in fitness and virulence of bacteria are promising candidates for vaccine development [52]. Various approaches have been used to identify surface-associated proteins from S. suis resulting in a large number of published protein vaccine candidates [12,18, 53]. For example, Huang et al. report the identification and characterisation of a surface-associated arginine peptidase in S. suis serotype 2, which is protective in mice against challenge with virulent S. suis [49]. Gomez- Gascon et al. report identified surface proteins using proteomics, that are present in a range of serotypes of S. suis from Spain and the Netherlands [19]. Two of these proteins, encoded by ssu0253 and ssu1760, were also protective against challenge with virulent S. suis but again this has only been shown in mice to date [73, 74].

Summary

The present inventors have developed improved vaccine compositions for use against Streptococcus suis.

An aspect of the invention provides a vaccine composition comprising one or more isolated immunogenic polypeptide(s) selected from SSU0185, SSU 1215, SSU1355, SSU1773 and SSU 1915.

A vaccine composition of the invention may for example comprise isolated SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 polypeptides.

Another aspect of the invention provides a vaccine composition of the invention for use in a method of treating S. suis infection in an individual or a population of individuals.

Another aspect of the invention provides a method of treating S. suis infection comprising administering a vaccine composition of the invention to an individual or a population of individuals in need thereof.

Another aspect of the invention provides the use of a vaccine composition of the invention in the manufacture of a medicament for treating S. suis infection in an individual or a population of individuals. Another aspect of the invention provides a method of producing a vaccine composition comprising admixing one or more isolated immunogenic polypeptides selected from

SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 with an excipient and/or an adjuvant. Description of Figures

Figure 1 shows the survival of pigs immunised with the cassette of five components and adjuvant after intra-nasal challenge with S. suis (P1/7, serotype 2) from day 0 (challenge) to day 15. Ag = 5 subunit vaccine; adj C/P = Carbopol 971 (Lubrizol) and Addavax (Invivogen) / polyethylene-imine (PEI); adj E/P = emulsigen D (MVP Technologies) / polyethylene-imine (PEI).

Figure 2 shows the survival of immunised pigs, condensed into immunised (Ag+adj) or non- immunised (No Ag) groups, after intra-nasal challenge with S. suis (P1/7, serotype 2) from day 0 (challenge) to day 15.

Figure 3 shows antibody responses (IgG), measured as reciprocal logio titre using indirect ELISA, against the 5 subunits, in serum samples collected from immunised pigs in Group 1 (adjuvant combination 1 ) and Group 2 (adjuvant combination 2) at 14, 21 and 28 days after first date of immunisation.

Figure 4 shows antibody responses (IgG), measured as reciprocal logio titre using indirect ELISA, against heat killed S. suis P1/7, in pooled serum samples collected from immunised pigs in Group 2 (adjuvant combination 2) collected at 0 and 21 days after first date of immunisation.

Figure 5 shows antigen-responsive interferon-gamma secreting cells in the peripheral blood mononuclear cell population of pigs at 14, 21 and 28 days after immunisation with 5 subunit proteins of S. suis, or sham immunisation. Adj1 +SsAg = groupl (adjuvant combination 1 with 5 subunits), Adj2+SsAg = group 2 (adjuvant combination 2 with 5 subunits), No Ag (Adj 1 ) = group 3 (pigs received adjuvant combination 1 but no subunits), No Ag (Adj2) = group 4 (pigs received adjuvant combination 2 but no subunits), PBS = group 5 (pigs received no adjuvant and no subunits, only PBS). Figure 6 shows cytokine production from peripheral blood mononuclear cells in response to restimulation using the pool of 5 subunits. The responses are shown for PBMC harvested from the 5 groups of pigs as follows, Adj1 +SsAg = groupl (adjuvant combination 1 with 5 subunits), Adj2+SsAg = group 2 (adjuvant combination 2 with 5 subunits), No Ag (Adj 1 ) = group 3 (pigs received adjuvant combination 1 but no subunits), No Ag (Adj2) = group 4 (pigs received adjuvant combination 2 but no subunits), PBS = group 5 (pigs received no adjuvant and no subunits, only PBS). Figure 7 shows antibody responses (IgG) amongst immunised pigs from Group 1 (Addavax combination) and Group 2 (Emulsigen D combination) at day 0 and day 28 after

immunisation, measured as OD450 using an indirect ELISA, against whole cell killed antigen extracted from a range of isolates of S. suis. These isolates represent a range of disease- associated serotypes of UK origin (serotypes 1 , 2, 1 -2, 3, 14) and also isolates of US origin. Strains; 478 Nasal: unknown serotype, non-virulent; SU1606 and ISU2606: USA origin P1/7: virulent serotype 2; SS021 and SS045: serotype 1 ; SS043 and SS100: serotype1/2 SS002 and SS008: serotype 2; SS053 and SS084: serotype 3; SS063 and SS077: serotype 14; All SS strains: UK origin and virulent.

Figure 8 shows the survival of immunised pigs, condensed into IN/IM80, IN, IM80, IN/IM20 and adjuvant only groups (see Table 7), after intra-nasal challenge with S. suis (P1/7, serotype 2) from day 0 (challenge) to day 16.

Figure 9 shows antibody responses (IgG), measured as reciprocal logio titre using indirect ELISA, against the 5 subunits, in serum samples collected from pigs immunised with the ssAg formulated with IN/IM80, IN, IM80 and IN/IM20 adjuvant (Groups 1 , 3, and 4; Table 7) at 14, 21 and 28 days after first date of immunisation.

Figure 10 shows IFN-gamma (IFN-γ) production from peripheral blood mononuclear cells after stimulation with media alone (NoStim), heat-killed P1/7 S. suis (hkP1/7) or all 5 S. suis subunit proteins (protein pool). The responses are shown for PBMCs harvested from the 5 groups of pigs shown in Table 7 and expressed as the average +/- SEM for the group.

Figure 1 1 shows IFN-gamma (IFN-γ) production from peripheral blood mononuclear cells after stimulation with media alone (NoStim), or with each of the subunit proteins individually (SSU0185, SSU1215, SSU1355, SSU1773, and SSU1915). The responses are shown for PBMCs harvested from single pigs in 3 of the 5 groups shown in Table 7 (IN/IM80, IM80 and IN/IM20) with the mean for the group shown with a line.

Detailed Description

This invention provides vaccine compositions useful in the treatment of S. suis infection in mammals, such as pigs and humans. The vaccine compositions may comprise one, two, three, four or all five immunogenic polypeptides selected from SSU0185, SSU1215, SSU 1355, SSU1773 and SSU1915 A vaccine composition is a formulation comprising one or more immunogenic components that is capable of generating protective immune responses in an individual to the one or more immunogenic components. Where the immunogenic components are derived from a pathogen, an individual to whom the vaccine composition has been administered may display acquired and/or adaptive immune responses against the pathogen when

subsequently exposed to it. These responses may confer protection against morbidity caused by infection with the pathogen. The vaccine composition may for example, reduce the likelihood of infection with the pathogen, reduce the severity or duration of the clinical signs of infection in the individual, prevent or delay the onset of clinical signs of infection or prevent or reduce the risk of the death of the individual following infection with the pathogen.

The incidence of morbidity caused by infection within a population to which a vaccine composition has been administered may be reduced relative to unimmunised populations. For example, the proportion of individuals in the immunised population that display clinical signs of infection following exposure to a pathogen may be reduced compared to

unimmunised populations. In some embodiments, immunisation of a population with a vaccine composition as described herein may reduce the number of individuals in the population showing clinical signs of infection by 50% or more, 66% or more or 75% or more following exposure to the pathogen.

Individuals suitable for treatment with a vaccine composition described herein may include humans or non-human mammals, preferably mammals susceptible to S. suis infection, such as pigs. In some embodiments, a population of individuals may be treated, for example a herd of pigs.

The vaccine compositions described herein comprise one or more immunogenic

polypeptides derived from S. suis that are capable of eliciting an immune response against S. suis in an individual. The immunogenic polypeptides may, for example, be

immunoreactive against S. st//s-exposed serum, such as S. st//s-exposed pig or human serum.

The one or more immunogenic polypeptides are preferably in isolated form i.e. they exist in a physical environment that is distinct from the S. suis cell in which they occur in nature and are free or substantially free of S. suis cells or material, such as other proteins or factors, from S. suis cells. Multiple isolated immunogenic polypeptides from S. suis may be formulated together in the vaccine compositions described herein.

The vaccine compositions described herein comprise one or more isolated immunogenic polypeptides from S. suis. The immunogenic polypeptides may be derived from S. suis of any serotype or strain and the genes encoding the immunogenic peptides have been detected in different serotypes of S. suis isolated from clinical (as well as non-clinical) cases in the UK, China, Vietnam, Canada, Denmark and the Netherlands. In some embodiments, the immunogenic polypeptides may be derived from serotype 2, for example serotype 2 strain P1/7. The genome sequence of S. suis P1/7 is available in public databases (see

Genbank entry: AM946016.1 Gl: 251819067). GenBank® is the recognized US-NIH genetic sequence database, comprising an annotated collection of publicly available DNA sequences, and which further incorporates submissions from the European Molecular Biology Laboratory (EMBL) and the DNA DataBank of Japan (DDBJ), see Nucleic Acids Research, January 2013,v 41 (D1 ) D36-42 for discussion.

The vaccine compositions may comprise any combination of isolated immunogenic polypeptides selected from SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915. For example, the vaccine composition may comprise any one, two, three or four of these immunogenic polypeptides or all five. For example, a vaccine composition may comprise one of the following combinations of isolated immunogenic polypeptides;

(1 ) SSU0185,

(2) SSU 1215,

(3) SSU1355,

(4) SSU1773,

(5) SSU1915,

(6) SSU0185 and SSU1215,

(7) SSU0185 and SSU 1355

(8) SSU0185 and SSU1773

(9) SSU0185 and SSU1915,

(10) SSU1215 and SSU 1355

(1 1 ) SSU1215 and SSU 1773

(12) SSU1215 and SSU1915

(13) SSU1355 and SSU1773

(14) SSU1355 and SSU1915

(15) SSU1773 and SSU1915 (16) SSU0185, SSU1215 and SSU 1355

(17) SSU0185, SSU1215 and SSU 1773

(18) SSU0185, SSU1215 and SSU1915

(19) SSU0185, SSU1355 and SSU1773

(20) SSU0185, SSU1355 and SSU1915

(21 ) SSU0185, SSU1773 and SSU1915

(22) SSU 1215, SSU1355 and SSU1773

(23) SSU 1215, SSU1355 and SSU1915

(24) SSU1215, SSU1773 and SSU1915

(25) SSU1355, SSU1773 and SSU1915

(26) SSU0185, SSU 1215, SSU1355, and SSU1773

(27) SSU0185, SSU 1215, SSU1355, and SSU1915

(28) SSU0185, SSU1355, SSU1773, and SSU1915

(29) SSU0185, SSU1355, SSU1773, and SSU1915

(30) SSU 1215, SSU1355, SSU1773, and SSU1915

(31 ) SSU0185, SSU 1215, SSU1355, SSU1773, and SSU1915

In some embodiments, the one or more isolated immunogenic polypeptides (for example any one of combinations (1 ) to (31 ) above) are the only immunogenic factors in the vaccine composition i.e. the vaccine composition may lack any other peptidyl or non-peptidyl antigens which elicit an immune response in an individual and may not elicit immune responses other than responses to the one or more immunogenic polypeptides.

An isolated SSU0185 polypeptide may comprise the amino acid sequence of SEQ ID NO: 1 or may be a variant or fragment thereof.

An isolated SSU1215 polypeptide may comprise the amino acid sequence of SEQ ID NO: 2 or may be a variant or fragment thereof. An isolated SSU1355 polypeptide may comprise the amino acid sequence of residues 28- 607 of SEQ ID NO: 3 or may be a variant or fragment thereof.

An isolated SSU1773 polypeptide may comprise the amino acid sequence of residues 31 - 674 of SEQ ID NO: 4 or may be a variant or fragment thereof. An isolated SSU1915 polypeptide may comprise the amino acid sequence of residues 41 - 1692 of SEQ ID NO: 5 or may be a variant or fragment thereof.

Reference sequences for SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 from S. suis serotype 2 strain P1/7 are provided in SEQ ID NOs: 1 to 5. The sequences of SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 from other serotypes and strains of S. suis are readily available from public databases.

In some embodiments, sequences from S. suis serotype 2 strain P1/7 may be preferred because they are shown herein to be conserved with a high degree of sequence identity across the core genome of S. suis (i.e. shared by all strains), and across the great majority of clinical isolates.

A variant of a reference polypeptide sequence, such as one of SEQ ID NOs: 1 to 5, may comprise an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or at least 98% sequence identity to the reference polypeptide sequence.

Nucleotide and amino acid sequence identity is generally defined with reference to the algorithm GAP (GCG Wisconsin Package™, Accelrys, San Diego CA). GAP uses the Needleman & Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. Generally, the default parameters are used, with a gap creation penalty = 12 and gap extension penalty = 4. Use of GAP may be preferred but other algorithms may be used, e.g. BLAST, BLASTP or BLASTN (which use the method of Altschul et al., FASTA (which uses the method of Pearson and Lipman, or PSI-Search which uses the Smith-Waterman algorithm), generally employing default parameters [54-56, 75].

An isolated immunogenic polypeptide may, for example, comprise an amino acid sequence which differs from a reference polypeptide sequence, such as one of SEQ ID NOs: 1 to 5, by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5-10, 10-20, 20-30, or 30- 40 or more amino acids.

An isolated immunogenic polypeptide may be a fragment of a reference polypeptide sequence, such as one of SEQ ID NOs: 1 to 5, or a variant of a reference polypeptide sequence. A fragment is a truncated polypeptide consisting of fewer amino acids than the full-length sequence that comprises at least one immunogenic determinant of the full-length sequence and retains immunogenicity. Suitable fragments may comprise at least 100, at least 150, at least 200, at least 250 or at least 300 amino acids of the full-length sequence. A fragment of a full-length immunogenic polypeptide is capable of raising an immune response (if necessary, when suitably adjuvanted) that recognises the full-length immunogenic polypeptide as well as the S. suis serotype or strain from which the immunogenic protein was derived. Suitable fragments may for example be identified by in silico modelling of potential immunogenic sites, followed by the generation of panels of fragments, and in vivo testing in pig protection models.

Suitable immunogenic polypeptides for use in vaccine compositions may lack a signal peptide sequence.

An isolated immunogenic polypeptide in a vaccine composition described herein may be comprised within a fusion protein. One or more heterologous amino acids, such as a heterologous peptide or heterologous polypeptide sequence, may be joined or fused to an immunogenic polypeptide sequence described herein. For example, an isolated

immunogenic polypeptide may comprise immunogenic polypeptide sequence as described above linked or fused to one or more heterologous amino acids. The one or more heterologous amino acids may include sequences from a source other than the

immunogenic polypeptide.

In some embodiments, an immunogenic polypeptide may be fused to a carrier or moiety, which can for example be any macromolecule that enhances the immunogenicity of the polypeptide. Examples of carriers include keyhole limpet hemocyanin (KLH), recombinant exoprotein A (rEPA), diphtheria protein CRM9 and tetanus toxin (TT).

Isolated immunogenic polypeptides may be produced by any convenient technique and a range of suitable approaches is available.

Isolated immunogenic polypeptides may be generated wholly or partly by chemical synthesis. For example, polypeptides may be synthesised using liquid or solid-phase synthesis methods; in solution; or by any combination of solid-phase, liquid phase and solution chemistry, e.g. by first completing the respective peptide portion and then, if desired and appropriate, after removal of any protecting groups being present, by introduction of the residue X by reaction of the respective carbonic or sulfonic acid or a reactive derivative thereof. Chemical synthesis of polypeptides is well-known in the art [57-62].

More preferably, isolated immunogenic polypeptides may be generated wholly or partly by recombinant techniques. For example, a nucleic acid encoding an immunogenic polypeptide described herein may be expressed in a host cell and the expressed polypeptide isolated and/or purified from the cell culture. In some embodiments, a nucleic acid encoding the one or more immunogenic polypeptides used in the vaccine compositions described herein may be expressed in the host cell and the expressed polypeptides isolated and/or purified from the cell culture.

Another aspect of the invention provides a set of nucleic acids encoding one or more isolated immunogenic polypeptides as defined above (for example any one of combinations (1 ) to (31 ) above).

For the production of a recombinant immunogenic polypeptide, nucleic acid sequences encoding the immunogenic polypeptide may be comprised within an expression vector. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. Preferably, the vector contains appropriate regulatory sequences to drive the expression of the encoding nucleic acid in a host cell. Suitable regulatory sequences to drive the expression of heterologous nucleic acid coding sequences in a range of expression systems are well-known in the art and include tac, lac and T7 p promoters for expression in E. coli and the CMV or SV40 promoters, for expression in eukaryotic systems.

A vector may also comprise sequences, such as origins of replication and selectable markers, which allow for its selection and replication and expression in bacterial hosts such as E. coli and/or in eukaryotic cells, such as yeast, insect or mammalian cells. Suitable vectors are well known in the art include pET30 vectors, such as pET-30 Ek/LIC. pET-30 Ek/LIC is designed for cloning and high-level expression of target proteins fused with His tag and S tag coding sequences that are cleavable with enterokinase (Ek) protease. pET-30 Ek/LIC contains a llac promoter, an optimized RBS, the coding sequence for the Ek protease cleavage site (AspAspAspAspLys), and a multiple cloning site to facilitate insert transfer. Vectors suitable for use in expressing nucleic acids that encode immunogenic polypeptides may include plasmids and viral vectors e.g. 'phage, or phagemid, and the precise choice of vector will depend on the particular expression system which is employed. In some embodiments, the pET30 Ek LIC vector (Novagen) may be used. Immunogenic polypeptides may be expressed in any convenient expression system, and numerous suitable systems are available in the art, including bacterial, yeast, insect or mammalian cell expression systems. For further details see, for example, Molecular Cloning: a Laboratory Manual [63]. Techniques and protocols for expression of recombinant polypeptides in cell culture and their subsequent isolation and purification are well known in the art (see for example Protocols in Molecular Biology and Recombinant Gene Expression Protocols [64,65]).

Another aspect of the invention provides a set of recombinant cells comprising heterologous nucleic acids encoding said one or more isolated immunogenic polypeptides as defined above (for example any one of combinations (1 ) to (31 ) above).

The heterologous nucleic acids may be incorporated into one or more expression vectors.

In some embodiments, the one or more immunogenic polypeptides may be expressed and purified individually, and then formulated together in the vaccine composition. In other embodiments, any two, three, four or all five of the immunogenic polypeptides may be expressed and purified together in the same expression system.

An immunogenic polypeptide may be expressed in an expression system as a fusion protein comprising the immunogenic polypeptide sequence and a purification tag. Preferably, a protease recognition site is located between the immunogenic polypeptide and the purification tag. Following expression, the fusion protein may be isolated by affinity chromatography using an immobilised agent which binds to the purification tag. After isolation, the fusion protein may be proteolytically cleaved at the protease recognition site, for example using thrombin, factor Xa or enterokinase protease (Ek), to remove the purification tag and produce the immunogenic polypeptide.

A purification tag is a heterologous amino acid sequence which forms one member of a specific binding pair. Polypeptides containing the purification tag may be detected, isolated and/or purified through the binding of the other member of the specific binding pair to the polypeptide. For example, the purification tag may form an epitope which is bound by an antibody molecule. Various suitable purification tags are known in the art, including, for example, MRGS(H)6, DYKDDDDK (FLAG™), T7-, S- (KETAAAKFERQHMDS), poly-Arg (R₅-₆), poly-His (H₆-io), poly-Cys (C₄) poly-Phe(Fn ) poly-Asp(D₅-i₆), Strept-tag II (WSHPQFEK), c-myc

(EQKLISEEDL), Influenza-HA tag [66], Glu-Glu-Phe tag [67], Tag.100 (Qiagen; 12 aa tag derived from mammalian MAP kinase 2), Cruz tag 09™ (MKAEFRRQESDR, Santa Cruz Biotechnology Inc.) and Cruz tag 22™ (MRDALDRLDRLA, Santa Cruz Biotechnology Inc.). Known tag sequences are reviewed in Terpe [68]. In some preferred embodiments, a poly-His purification tag may be employed. Following expression, a fusion protein comprising the immunogenic polypeptide and poly-His may be isolated by affinity chromatography using an affinity resin containing bound bivalent nickel or cobalt ions. The purification of poly-His fusion proteins using affinity resins is well known in the art. Optionally, the poly-His tag may be removed by proteolytic cleavage after purification to produce the immunogenic polypeptide.

In addition to the one or more isolated immunogenic polypeptides, a vaccine composition described herein may further comprise an adjuvant. An adjuvant is one or more non-immunogenic agents that increases or enhances the immune response to an antigen in an individual (for a review, see, e.g., Montomoli et al. [69], and Vaccine Adjuvants: adjuvants: preparation methods and research protocols [70]).

Any suitable adjuvant may be used in the vaccine compositions described herein. Suitable adjuvants include the RIBI adjuvant system (Ribi Inc.; Hamilton, MT); alum; aluminum hydroxide gel; aluminum phosphate; oil-in water emulsions including squalene-water emulsions, such as emulsigen™ (MVP Technologies Inc), Addavax™ and MF59™ (see, for example WO 90/14837; water-in-oil emulsions such as Freund's complete and incomplete adjuvants; Block copolymer (CytRx; Atlanta, GA); SAF-M (Chiron; Emeryville, CA);

AMPHIGEN® adjuvant; killed Bordetella; monophosphoryl lipid A (MPL-A); avridine; lipid- amine adjuvant; heat-labile enterotoxin from Escherichia coli (recombinant or otherwise); cholera toxin; and muramyl dipeptide. Also suitable is MPL™ (3-O-deacylated

monophosphoryl lipid A; Corixa, Hamilton, MT; US4, 912,094) Other suitable adjuvants include synthetic lipid A analogs or aminoalkyl glucosamine phosphate (AGP) compounds, or derivatives or analogs thereof, which are available from Corixa (Hamilton, MT; US 6,1 13,918); L121/squalene; D-lactide-polylactide/glycoside;

pluronic polyols; muramyl dipeptide; extracts of Mycobacterium tuberculosis; bacterial lipopolysaccharides generally; pertussis toxin (PT); and an E. coli heat-labile toxin (LT), particularly LT-K63, LT-R72, PT-K9/G129 (see for example WO 93/13302 and WO

92/19265).

Other suitable adjuvants include synthetic polynucleotides, such as oligonucleotides containing CpG motifs (see for example US 6,207,646). CpG oligonucleotides, such as P- class immunostimulatory oligonucleotides, may be suitable useful, including E-modified P- class immunostimulatory oligonucleotides.

Other suitable adjuvants include saponins. Suitable saponins include triterpenoid saponins. These triterpenoids a group of surface-active glycosides of plant origin and share common chemical core composed of a hydrophilic region (usually several sugar chains) in association with a hydrophobic region of either steroid or triterpenoid structure. Because of these similarities, the saponins sharing this chemical core are likely to have similar adjuvanting properties. Triterpenoids suitable for use in the adjuvant compositions can come from many sources, either plant derived or synthetic equivalents, including but not limited to, Quillaja saponaria, tomatine, ginseng extracts, mushrooms, and an alkaloid glycoside structurally similar to steroidal saponins. Suitable saponins may include Stimulon™ QS-21 (Antigenics, Framingham, MA; US5,057,540) and particles generated therefrom such as ISCOMS (immunostimulating complexes), GPI-0100 (Galenica Pharmaceuticals, Inc.; Birmingham, AL) or other saponin fractions If a saponin is used, an adjuvant generally contains an immunologically active saponin fraction from the bark of Quillaja saponaria. The saponin may be, for example, Quil A or another purified or partially purified saponin preparation, which can be obtained

commercially. Thus, saponin extracts can be used as mixtures or purified individual components such as QS-7, QS-17, QS-18, and QS-21. In one embodiment the Quil A is at least 85% pure. In other embodiments, the Quil A is at least 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% pure.

Other suitable adjuvants include sterols. Sterols share a common chemical core, which is a steroid ring structure^], having a hydroxyl (OH) group, usually attached to carbon-3. The hydrocarbon chain of the fatty-acid substituent varies in length, usually from 16 to 20 carbon atoms, and can be saturated or unsaturated. Sterols commonly contain one or more double bonds in the ring structure and also a variety of substituents attached to the rings. Sterols and their fatty-acid esters are essentially water insoluble. In view of these chemical similarities, it is thus likely that the sterols sharing this chemical core would have similar properties when used in the vaccine compositions of the instant invention. Sterols are well known in the art and can be purchased commercially. For example cholesterol is disclosed in the Merck Index, 12th Ed., p. 369. Suitable sterols include, without limitations, sitosterol, stigmasterol, ergosterol, ergocalciferol, and cholesterol.

Suitable adjuvants may comprise one or more polymers such as, for example, DEAE

Dextran, polyethylene glycol, polyacrylic acid, and polymethacrylic acid (e.g.,

CARBOPOL®). The adjuvants may further comprise one or more Th2 stimulants such as, for example, Bay R1005(R) and aluminum.

A suitable adjuvant may additionally or alternatively further comprise one or more

immunomodulatory agents, such as quaternary ammonium compounds (e.g., DDA), interleukins, interferons, or other cytokines. A number of cytokines or lymphokines have been shown to have immune-modulating activity, and thus may be used as adjuvants.

These can include, but are not limited to, the interleukins 1 -α, 1 -β, 2, 4, 5, 6, 7, 8, 10, 12 (see, e.g., US 5,723,127), 13, 14, 15, 16, 17 and 18 (and its mutant forms), the interferons-a, β and gamma, granulocyte-macrophage colony stimulating factor (see, for example, US 5,078,996, and ATCC Accession Number 39900), macrophage colony stimulating factor, granulocyte colony stimulating factor, GSF, and the tumor necrosis factors a and β

Other suitable adjuvants include chemokines, such as MCP-1 , MIP-1 a, MIP-1 β, and

RANTES and adhesion molecules, including a selectin, such as L-selectin, P-selectin, and E-selectin. Still other suitable adjuvants include a mucin-like molecule, e.g., CD34, GlyCAM- 1 and MadCAM-1 ; a member of the integrin family such as LFA-1 , VLA-1 , Mac-1 and p150.95; a member of the immunoglobulin superfamily such as PECAM, ICAMs (e.g., ICAM- 1 , ICAM-2 and ICAM-3), CD2 and LFA-3; co-stimulatory molecules such as CD40 and CD40L; growth factors including vascular growth factor, nerve growth factor, fibroblast growth factor, epidermal growth factor, B7.2, PDGF, BL-1 , vascular endothelial growth factor; receptor molecules including Fas, TNF receptor, Fit, Apo-1 , p55, WSL-1 , DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DR5, KILLER, TRAIL-R2, TRICK2, and DR6; and Caspase (ICE; see also W098/17799 and W099/43839). Suitable adjuvants also include monophosphoryl lipid (MPL-A) and MPL™ (3-O-deacylated monophosphoryl lipid A; Corixa, Hamilton, MT; US4912094. Other suitable adjuvants include synthetic lipid A analogs, aminoalkyi glucosamine phosphate compounds (AGP), and derivatives or analogs thereof, which are available from Corixa (Hamilton, MT; see for example US61 13918). Suitable analogs of MPL-A for use in the preparation of adjuvants include bacterial derived natural LPS altered or unaltered in structure or synthetic,

Glucopyranosyl Lipid Adjuvant (GLA), pertactin , varying substitutions at 3-O-position of the reducing sugar, and synthetic forms of lipid A analog with low endotoxicity. AGPs may include 2-[(R)-3-Tetradecanoyloxytetradecanoylamino] ethyl 2-Deoxy-4-0-phosphono-3-0- [(R)-3-tetradecanoyoxytetradecanoyl]-2-[(R)-3-tetradecanoyloxytetradecanoyl-amino]-b-D- glucopyranoside, which is also known as 529 (formerly known as RC529). An RC529 adjuvant may be formulated as an aqueous form or as a stable emulsion.

Other suitable adjuvants include cholera toxins (CT) and mutants thereof, including those described in WO00/18434 (wherein the glutamic acid at amino acid position 29 is replaced by another amino acid, other than aspartic acid, preferably a histidine). Similar CT toxins or mutants are described in WO02/098368 (wherein the isoleucine at amino acid position 16 is replaced by another amino acid, either alone or in combination with the replacement of the serine at amino acid position 68 by another amino acid; and/or wherein the valine at amino acid position 72 is replaced by another amino acid). Other CT toxins are described in

WO02/098369 (wherein the arginine at amino acid position 25 is replaced by another amino acid; and/or an amino acid is inserted at amino acid position 49; and/or two amino acids are inserted at amino acid positions 35 and 36). Said CT toxins or mutant can be included in the immunogenic compositions either as separate entities, or as fusion partners for the polypeptides described above.

Particularly preferred adjuvants for use in swine, which are both safe and effective, include the following, which generally comprise a combination of lecithin in light mineral oil (for example Amphigen®), and also an aluminum hydroxide component. Preferably, the oil used in the adjuvants is a light mineral oil. As used herein, the term "mineral oil" refers to a mixture of liquid hydrocarbons obtained from petrolatum via a distillation technique. The term is synonymous with "liquefied paraffin", "liquid petrolatum" and "white mineral oil." The term is also intended to include "light mineral oil," i.e., oil which is similarly obtained by distillation of petrolatum, but which has a slightly lower specific gravity than white mineral oil. See, e.g., Remington's Pharmaceutical Sciences, 18th Edition (Easton, Pa.: Mack Publishing

Company, 1990, at pages 788 and 1323). Mineral oil can be obtained from various commercial sources, for example, J. T. Baker (Phillipsburg, Pa.), USB Corporation

(Cleveland, Ohio). Preferred mineral oil is light mineral oil commercially available under the name DRAKEOL®. Amphigen® is generally described in U.S Patent 5,084,269 and provides de-oiled lecithin (preferably soy) dissolved in a light oil, which is then dispersed into an aqueous solution or suspension of the antigen as an oil-in-water emulsion.

In some embodiments, the only adjuvant component of the vaccine composition may be Amphigen.

Amphigen may be improved according to the protocols of U.S. Patent 6,814,971 (see columns 8-9 thereof) to provide a so-called "20% Amphigen" component for use in the vaccine compositions described herein. Thus, a stock mixture of 10% lecithin and 90% carrier oil (DRAKEOL®, Penreco, Karns City, PA) is diluted 1 : 4 with 0.63% phosphate buffered saline solution, thereby reducing the lecithin and DRAKEOL components to 2% and 18% respectively (i.e. 20% of their original concentrations). Tween 80 and Span 80 surfactants are added to the composition, with representative and preferable final amounts being 5.6% (v/v) Tween 80 and 2.4% (v/v) Span 80, wherein the Span is originally provided in the stock DRAKEOL component, and the Tween is originally provided from the buffered saline component, so that mixture of the saline and DRAKEOL components results in the finally desired surfactant concentrations. Mixture of the DRAKEOL/lecithin and saline solutions is accomplished using an In-Line Slim Emulsifier apparatus, model 405, Charles Ross and Son, Hauppauge, NY, USA, for example. The vaccine composition preferably also includes Rehydragel® LV (about 2% aluminum hydroxide content in the stock material), as additional adjuvant component (available from Reheis, NJ, USA, and ChemTrade Logistics, USA).

Typically, the oily phase is present in an amount from 50% to 95% by volume; preferably, in an amount of greater than 50% to 85%; more preferably, in an amount from greater than 50% to 60%, and more preferably in the amount of greater than 50-52% v/v of the vaccine composition. The oily phase preferably includes emulsifiers SPAN® 80 and TWEEN® 80, if any such emulsifiers are present. Non-natural, synthetic emulsifiers suitable for use in the adjuvant formulations of this example also include sorbitan-based non-ionic surfactants, e.g. fatty-acid-substituted sorbitan surfactants (commercially available under the name SPAN® or ARLACEL®), fatty acid esters of polyethoxylated sorbitol (TWEEN®), polyethylene glycol esters of fatty acids from sources such as castor oil (EMULFOR®); polyethoxylated fatty acid (e.g., stearic acid available under the name SIMULSOL® M-53), polyethoxylated isooctylphenol/formaldehyde polymer (TYLOXAPOL®), polyoxyethylene fatty alcohol ethers (BRIJ®); polyoxyethylene nonphenyl ethers (TRITON® N), polyoxyethylene isooctylphenyl ethers (TRITON® X). Preferred synthetic surfactants are the surfactants available under the name SPAN® and TWEEN®, such as TWEEN®-80 (Polyoxyethylene (20) sorbitan monooleate) and SPAN®-80 (sorbitan monooleate). Generally speaking, the emulsifier(s) may be present in the vaccine composition in an amount of 0.01 % to 40% by volume, preferably, 0.1 % to 15%, more preferably 2% to 10%.

Another preferred example of this type of adjuvant comprises SP-Oil® and Rehydragel® LV (or other Rehydragel® or Alhydrogel® products), with preferable amounts being about 5- 20% SP-Oil (v/v) and about 5-15% Rehydragel LV (v/v), and with 5% and 12%, respectively, being most preferred amounts. In this regard, it is understood that % Rehydragel refers to percent dilution from the stock commercial product. SP-Oil ® is a fluidized oil emulsion with includes a polyoxyethylene-polyoxypropylene block copolymer (Pluronic® L121 , BASF Corporation), squalene, polyoxyethylene sorbitan monooleate (Tween®80, ICI Americas) and a buffered salt solution. In some embodiments, a vaccine composition described herein may comprise TXO as an adjuvant; TXO is generally described in WO 2015/042369. All TXO compositions disclosed therein are useful in the preparation of vaccine compositions described herein. In TXO, the immunostimulatory oligonucleotide ("T"), preferably an ODN, preferably containing a palindromic sequence, and optionally with a modified backbone, is typically present in the amount of 0.1 to 5 μg per 50 μΙ of the vaccine composition (e.g., 0.5 - 3 μg per 50 μΙ of the composition, or more preferably 0.09-0.1 1 μg per 50 μΙ of the composition), although such can be varied. A preferred species thereof is SEQ ID NO: 8 as listed (page 17) in

WO2015/042369. In a representative example, the polycationic carrier ("X") is present in the amount of 1 -20 μg per 50 μΙ (e.g., 3-10 μg per 50 μΙ, or about 5 μg per 50 μΙ). Light mineral oil ("O") is also a component of the TXO adjuvant.

In certain embodiments, TXO adjuvants may be prepared as follows:

a) sorbitan monooleate, monophosphoryl lipid A (MPL-A) or analog thereof and cholesterol are dissolved in light mineral oil. The resulting oil solution is sterile filtered; b) the immunostimulatory oligonucleotide, Dextran DEAE ("X") and Polyoxyethylene (20) sorbitan monooleate are dissolved in aqueous phase, thus forming the aqueous solution; and

c) the aqueous solution is added to the oil solution ("O") under continuous

homogenization thus forming the adjuvant TXO.

TXO adjuvants with aluminum are referred to as "TXO-A", and may be preferred in some vaccine compositions described herein. Suitable adjuvants may comprise multiple oils, and one or more emulsifiers, wherein the oily phase comprises more that 50% of the adjuvant. The adjuvant may contain still further additional components. Multiple oils and combinations thereof are suitable for use in the vaccine compositions described herein. These oils include, without limitations, animal oils, vegetable oils, as well as non-metabolizable oils. Non-limiting examples of suitable vegetable oils are corn oil, peanut oil, soybean oil, coconut oil, and olive oil. Non-limiting example of animal oils is squalane. Suitable non-limiting examples of non-metabolizable oils include light mineral oil, straight chained or branched saturated oils, and the like.

As aforementioned, typically, the oily phase is present in an amount from 50% to 95% by volume; preferably, in an amount of greater than 50% to 85%; more preferably, in an amount from greater than 50% to 60%, and more preferably in the amount of greater than 50-52% v/v of the vaccine composition. The oily phase includes oil and emulsifiers (e.g., SPAN® 80, TWEEN® 80 etc), if any such emulsifiers are present. The volume of the oily phase is calculated as a sum of volumes of the oil and the emulsifier(s). Thus, for example, if the volume of the oil is 40% and the volume of the emulsifier(s) is 12% of a composition, then the oily phase would be present at 52% v/v of the composition. Similarly, if the oil is present in the amount of about 45% and the emulsifier(s) is present in the amount of about 6% of a composition, then the oily phase is present at about 51 % v/v of the composition. Since the adjuvants form only a part of the vaccine compositions described herein, oily phase is typically present in an amount from 50% to 95% by volume; preferably, in an amount of greater than 50% to 85%; more preferably, in an amount from 50% to 60%, and more preferably in the amount of 50-52% v/v of each of the adjuvants, although such can be varied. In some embodiments, applicable to all adjuvants and/or vaccine compositions described herein, the volume percentage of the oil and the oil-soluble emulsifier together is at least 50%, e.g., 50% to 95% by volume; preferably, in an amount of greater than 50% to 85%; more preferably, in an amount from 50% to 60%, and more preferably in the amount of 50- 52% v/v of the vaccine composition. Thus, for example and without limitations, the oil may be present in the amount of 45% and the lipid-soluble emulsifier would be present in the amount of greater than 5% v/v. Thus, the volume percentage of the oil and the oil-soluble emulsifier together would be at least 50%. In some embodiments, applicable to all vaccine compositions described herein, volume percentage of the oil is over 40%, e.g., 40% to 90% by volume; 40% to 85%; 43% to 60%, 44-50% v/v of the vaccine composition.

Emulsifiers suitable for use in adjuvants and vaccine compositions described herein include natural biologically compatible emulsifiers and non-natural synthetic surfactants. Biologically compatible emulsifiers include phospholipid compounds or a mixture of phospholipids.

Preferred phospholipids are phosphatidylcholines (lecithin), such as soy or egg lecithin. Lecithin can be obtained as a mixture of phosphatides and triglycerides by water-washing crude vegetable oils, and separating and drying the resulting hydrated gums. A refined product can be obtained by fractionating the mixture for acetone insoluble phospholipids and glycolipids remaining after removal of the triglycerides and vegetable oil by acetone washing. Alternatively, lecithin can be obtained from various commercial sources. Other suitable phospholipids include phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, phosphatidic acid, cardiolipin, and phosphatidylethanolamine. The phospholipids may be isolated from natural sources or conventionally synthesized.

In some embodiments, the emulsifiers used in adjuvants and vaccine compositions described herein do not include lecithin, or use lecithin in an amount which is not

immunologically effective.

Non-natural, synthetic emulsifiers suitable for use in the adjuvant formulations described herein include sorbitan-based non-ionic surfactants, e.g. fatty-acid-substituted sorbitan surfactants (commercially available under the name SPAN® or ARLACEL®), fatty acid esters of polyethoxylated sorbitol (TWEEN®), polyethylene glycol esters of fatty acids from sources such as castor oil (EMULFOR®); polyethoxylated fatty acid (e.g., stearic acid available under the name SIMULSOL® M-53), polyethoxylated isooctylphenol/formaldehyde polymer (TYLOXAPOL®), polyoxyethylene fatty alcohol ethers (BRIJ®); polyoxyethylene nonphenyl ethers (TRITON® N), polyoxyethylene isooctylphenyl ethers (TRITON® X).

Preferred synthetic surfactants are the surfactants available under the name SPAN® and TWEEN®, such as TWEEN®-80 (Polyoxyethylene (20) sorbitan monooleate) and SPAN®- 80 (sorbitan monooleate).

Generally speaking, the emulsifier(s) may be present in the vaccine composition in an amount of 0.01 % to 40% by volume, preferably, 0.1 % to 15%, more preferably 2% to 10%. An adjuvant may comprise one or more of cationic carriers, immunostimulatory

oligonucleotides, monophospholipid A and analogs thereof (MPL-A),

Polyinosinic:polycytidylic acid (poly l:C), saponins, quaternary ammoniums, sterols, glycolipids, a source of aluminum (e.g., REHYDRAGEL® or VAC 20® wet gel) and combinations thereof.

Suitable cationic carriers include, without limitations, dextran, dextran DEAE (and derivatives thereof), PEGs, guar gums, chitosan derivatives, polycellulose derivatives like hydroxyethyl cellulose (HEC) polyethylenimene, poly aminos like polylysine and the like. Suitable immunostimulatory oligonucleotides include ODN (DNA-based), ORN (RNA-based) oligonucleotides, or chimeric ODN-ORN structures, which may have modified backbone including, without limitations, phosphorothioate modifications, halogenations, alkylation (e.g., ethyl- or methyl- modifications), and phosphodiester modifications. In some embodiments, poly inosinic -cytidylic acid or derivative thereof (poly l:C) may be used.

CpG oligonucleotides are a recently described class of pharmacotherapeutic agents that are characterized by the presence of an unmethylated CG dinucleotide in specific base- sequence contexts (CpG motif). (Hansel TT, Barnes PJ (eds): New Drugs for Asthma, Allergy and COPD. Prog Respir Res. Basel, Karger, 2001 , vol 31 , pp 229-232). These CpG motifs are not seen in eukaryotic DNA, in which CG dinucleotides are suppressed and, when present, usually methylated, but are present in bacterial DNA to which they confer immunostimulatory properties.

A suitable adjuvant may utilize a so-called P-class immunostimulatory oligonucleotide, more preferably, a modified P- class immunostimulatory oligonucleotide, even more preferably, a E-modified P-class oligonucleotide. P-class immunostimulatory oligonucleotides are CpG oligonucleotides characterized by the presence of palindromes, generally 6-20 nucleotides long. The P-Class oligonucleotides have the ability to spontaneously self-assemble into concatamers either in vitro and/or in vivo. These oligonucleotides are, in a strict sense, single-stranded, but the presence of palindromes allows for formation of concatamers or possibly stem-and-loop structures. The overall length of P- class immunostimulatory oligonucleotides is between 19 and 100 nucleotides, e.g., 19-30 nucleotides, 30-40 nucleotides, 40-50 nucleotides, 50-60 nucleotides, 60-70 nucleotides, 70-80 nucleotides, 80- 90 nucleotides, 90-100 nucleotides. In some embodiments, the immunostimulatory oligonucleotide may comprise a 5' TLR activation domain and at least two palindromic regions, one palindromic region being a 5' palindromic region of at least 6 nucleotides in length and connected to a 3' palindromic region of at least 8 nucleotides in length either directly or through a spacer. P-class immunostimulatory oligonucleotides may be modified according to techniques known in the art. For example, J-modification refers to iodo-modified nucleotides. E-modification refers to ethyl-modified nucleotide(s). Thus, E-modified P-class immunostimulatory oligonucleotides are P-class immunostimulatory oligonucleotides, wherein at least one nucleotide (preferably 5' nucleotide) is ethylated. Additional modifications include attachment of 6-nitro-benzimidazol, O-Methylation, modification with propynyl-dU, inosine modification, 2-bromovinyl attachment (preferably to uridine).

P-class immunostimulatory oligonucleotides may also contain a modified internucleotide linkage including, without limitations, phosphodiesther linkages and phosphorothioate linkages. The oligonucleotides may be synthesized or obtained from commercial sources. P-Class oligonucleotides and modified P-class oligonucleotides are further disclosed in WO2008/068638. Suitable examples of modified P-class immunostimulatory

oligonucleotides are provided below ("^*" refers to a phosphorothioate bond and "_" refers to a phosphodiester bond).

i) 5' T^*C-G^*T^*C-G^*A^*C-G^*A^*T^*C-G^*G^*C^*G^*C-G^*C^*G^*C^*C^*G 3'

ii) 5' T^*C-G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^*G 3'

iii) 5' T^*C^*G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^*G^*T 3'

iv) 5' JU^*C-G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^*G 3'

v) 5' JU^*C-G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^* G^*T 3'

vi) 5' JU^*C^*G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^* G^*T 3'

vii) 5' EU^*C-G^*A^*C^*G^*T^*C^*G^*A^*T^*C^*G^*G^*C^*G^*C^*G^*C^*G^*C^*C^*G 3' viii) 5' JU^*C-G^*T^*C^*G^*A^*C^*G^*A^*T^*C^*G^*G^*C^*G^*G^*C^*C^*G^*C^*C^* G^*T 3'

ix) 5' JU^*C^*G^*T^*C^*G^*A^*C^*G^*A^*T^*C^*G^*G^*C^*G^*G^*C^*C^*G^*C^*C^* G^*T 3'

x) 5' T^*C_G^*T^*C_G^*A^*C_G^*A^*T^*C_G^*G^*C^*G^*C_G^*C^*G^*C^*C^*G 3'

xi) 5'-UUGUUGUUGUUGUUGUUGUU-3'

xii) 5'-UUAUUAUUAUUAUUAUUAUU-3'

xiii) 5'-AAACGCUCAGCCAAAGCAG-3'

xiv) dTdCdGdTdCdGdTdTdTdTrGrUrUrGrUrGrUdTdTdTdT-3'

The amount of P-class immunostimulatory oligonucleotide for use in an adjuvant depends upon the nature of the P-class immunostimulatory oligonucleotide used and the intended species, as is recognized in the art.

Quaternary amine compounds are ammonium based compounds with four hydrocarbon groups. In practice, hydrocarbon groups are generally limited to alkyl or aryl groups. In a set of embodiments, the quaternary amine compounds are composed of four alkyl chains, two of which are C10-C20 alkyls and the remaining two are C1 -C4 alkyls. In one set of embodiments, the quaternary amine is dimethyldioctadecylammonium bromide, chloride or pharmaceutically acceptable counterion (DDA). Suitable glycolipids are generally those which activate the Th2 response. The glycolipids include, without limitations, those that are generally described in US20070196384

(Ramasamy et al). In some embodiments, the suitable glycolipid is N-(2-Deoxy-2-L- leucylamino-b-D-glucopyranosyl)-N-octadecyldodecanoylamide or an acetate thereof.

Aluminum is a known adjuvant or a component of adjuvant formulations and is commercially available in such forms as Reheis, Inc, Brentag alhydrogel REHYDRAGEL® or VAC 20® wet gel. REHYDRAGEL® is a crystalline aluminum oxyhydroxide, known mineralogically as boehmite. It is effective in vaccines when there is a need to bind negatively charged proteins. The content of AI203 ranges from 2% to 10% depending on grade, and its viscosity is 1000-1300 cP. Generally, it may be described as an adsorbent aluminum hydroxide gel. VAC® 20 wet gel is a white or almost white, translucent, viscous colloidal gel. In certain embodiments, the content of AI2O3 is about 2% w/v.

Thus, in a first set of complex adjuvants suitable for use as described herein, in addition to the oil and the optional one or more emulsifiers, the adjuvant also comprises (or consists essentially of, or consists of) a combination of monophosphoryl lipid A (MPL-A) or an analog thereof, a sterol, and an immunostimulatory oligonucleotide. The adjuvants containing these ingredients are referred to as "TCMO". The TCMO adjuvant formulation may also optionally include poly l:C ("TCMYO") and/or a saponin. Thus, adjuvant formulations comprising, or consisting essentially of, or consisting of a combination of monophosphoryl lipid A (MPL-A) or an analog thereof, a sterol, and an immunostimulatory oligonucleotide and saponin are referred to as "QTCMO." In addition, the adjuvant formulations may also include poly l:C. Such adjuvants are referred to as "QTCMYO".

"TCMO" adjuvants may comprise light mineral oil in the amount of 40% to 50% v/v of the total volume of the vaccine composition. The emulsifiers include TWEEN-80 and SPAN-80, total amount 0.1 % to 40% v/v of the total volume of the vaccine composition, provided that sorbitan monooleate and oil together comprise about 50.5% to 52% v/v of the composition. The immunostimulatory oligonucleotide is an ODN, preferably, a palindrome containing ODN, optionally, with a modified backbone.

One dose of TCMO may contain between about 1 ug and about 400 ug of the

immunostimulating oligonucleotide, between about 1 ug and about 1000 ug of the sterol, between about 0.1 ug and 500 ug MPL-A or the analog thereof. TCMO adjuvants may be prepared as follows:

a) sorbitan monoleate, MPL-A and cholesterol are dissolved in light mineral oil. The resulting oil solution is sterile filtered;

b) the immunostimulatory oligonucleotide and Polyoxyethylene (20) sorbitan

monooleate are dissolved in aqueous phase, thus forming the aqueous solution;

c) the aqueous solution is added to the oil solution under continuous homogenization thus forming the adjuvant formulation TCMO.

In complex "TCMYO" adjuvants, the cholesterol, oil, optional emulsifiers, MPL-A, and the immunostimulatory oligonucleotides are present as in the TCMO adjuvant formulation for the respective species. Poly l:C ("Y") may be present generally in the amount between about 1 μg and about 100 μg per dose.

More specifically, poly l:C may be present in the amount of 5-100 μg per dose (e.g., 5-50 μg, or 10-30 μg) in certain embodiments suitable for swine. In certain embodiments suitable for piglets, one dose of TCMYO contains between about 1 and about 50 μg (e.g., 5-50 μς, or 10-20 μg) of poly l:C. In certain embodiments suitable for swine generally, one dose of TCMYO contains between about 1 and about 10 (e.g., 1 -5 μς, or 3-5 μς) of poly l:C, although those skilled in the art will appreciate that these amounts can be varied as needed.

In certain embodiments, TCMYO adjuvants are prepared similarly to the TCMO adjuvants, and the poly l:C is added to the aqueous solution.

In a further set of complex "QTCMO" adjuvants suitable for use as described herein, the cholesterol, oil, optional emulsifiers, MPL-A, and the immunostimulatory oligonucleotides are present as in the TCMO adjuvant formulation for the respective species. A saponin ("Q") s preferably Quil A or a purified fraction thereof, and may be present in the amounts of between about 0.1 μg and about 1000 μg per dose.

More specifically the saponin may be present in the amount of 0.1 to 5 μg per 50 μΙ of the vaccine composition (e.g., 0.5 - 30 μg per 50 μΙ of the composition, or more preferably 1 - 10 μg) per dose. In certain embodiments suitable for applications in companion animals and piglets, the saponin, e.g., Quil A or a purified fraction thereof is present in the amounts between about 10 and about 100 μg per dose (e.g., 10-50 μg or 20-50 μg per dose). In certain embodiments suitable for swine, the saponin, such as Quil A or a purified fraction thereof, is present in the amount of between about 100 and about 1000 μg per dose (e.g., 200-800 pg, or 250-500 μg per dose).

QTCMO adjuvants may be prepared similarly to TCMO adjuvants, and the saponin is added to the aqueous solution. In "QTCMYO" adjuvants, the saponin ("Q") may be present as in QTCMO adjuvant, and the rest of the ingredients are present as in TCMYO, for the respective species. QTCMYO adjuvants may be prepared similarly to TCMYO adjuvants, and the saponin may be added to the aqueous solution. In further examples of complex adjuvants, in addition to the oil and the optional emulsifier(s), the adjuvant formulations also comprise a combination of monophosphoryl lipid A (MPL-A) or an analog thereof and a polycationic carrier. These adjuvants are referred to as "XOM".

In some embodiments, in addition to the oil and the emulsifier(s), an adjuvant may also comprise a combination of a quaternary amine, a glycolipid, MPL-A or an analog thereof, and poly l:C. These adjuvants are referred to as "ODYRM". In ODYRM adjuvants, the oil is generally a mixture of phospholipids such as phosphatidyl cholines. AMPHIGEN® is a suitable example of such oil, and would be present in the amount similar to the amount of oil, as described above. In ODYRM adjuvants, the quaternary amine, e.g., DDA, may be present in the amount of between about 1 μg and about 200 μg per dose, poly l:C may be present in the amount of between about 0.5 μg and 100 μg per dose, the glycolipid may be present in the amount of between about 0.5 μg and about 2000 μg per dose, and the MPL-A or the analog thereof may be present in the amount of between about 0.5 μg and 100 μg per dose. In other complex oil-based adjuvants, in addition to the oil and the emulsifier(s), the adjuvant may further comprise a combination of a saponin, a sterol, a quaternary amine, a

polycationic carrier. These adjuvants are referred to as "QCDXO". In QCDXO adjuvants, the saponin, e.g., Quil A may be present in the amounts of between about 0.1 μg and about 1000 μg per dose, the sterol, e.g., cholesterol, is present between about 1 μg and about 1000 μg per dose, the quaternary amine, e.g., DDA, is present in the amount of between about 1 μg and about 200 μg per dose, and the polycationic carrier may be present in the amount of 0.5-400 mg per dose.

Other adjuvants suitable for use in the vaccine compositions described herein include Present-A (see for example US2007/0298053); and "QCDCRT" or "QCDC"-type adjuvants (see for example US2009/0324641 ).

Cationic carriers may also be useful in adjuvants for use as described herein. Suitable cationic carriers include, dextran, dextran-DEAE (and derivatives thereof), PEG's, guar gums, chitosan derivatives, polycellulose derivatives like hydroxyethyl cellulose (HEC), polyethylenimene, poly aminos, like polylysine, and the like.

In some preferred embodiments, the adjuvant in the vaccine compositions described herein may be polyethylene-imine (PEI), an acrylic acid polymer and/or a squalene-water emulsion.

Preferred adjuvants are suitable for human ingestion and do not affect the taste or quality of meat obtained from pigs immunised with the vaccine composition.

In some embodiments, the vaccine formulation may also be formulated or co-administered with immunogenic polypeptides from further pathogens to provide a multi-valent vaccine for the treatment of S. suis and one or more further pathogens. For example, in addition to the one or more isolated immunogenic polypeptides from S. suis described above, a vaccine composition described herein may further comprise one or more immunogenic polypeptides from a second pathogen that are capable of eliciting an immune response against the second pathogen in an individual. Optionally, the vaccine composition may further comprise one or more immunogenic polypeptides from a third pathogen that are capable of eliciting an immune response against the third pathogen in an individual. Alternatively the immunogenic polypeptides from S. suis may be expressed in a bacterial vector that also functions as a live attenuated vaccine for a second bacterial pathogen of pigs (for example Actinobacillus pleuropneumoniae).

Further pathogens may include Erysipelothrix rhusiopathiae, E. coli, PRRS virus, PCV2 virus, Actinobacillus pleuropneumoniae, Pasteurella multocida, Mycoplasma hyopneumoniae and Haemophilus parasuis. Suitable immunogenic polypeptides that are capable of eliciting an immune response against further pathogens in an individual are well known in the art.

A vaccine composition described herein may further comprise one or more pharmaceutically acceptable carriers, adjuvants, excipients, diluents, fillers, buffers, stabilisers, preservatives, lubricants, or other materials well known to those skilled in the art and optionally other therapeutic or prophylactic agents.

Any contaminants, such as endotoxins or phage, which may be present in the vaccine compositions described herein are within acceptable limits and do not result in deleterious effects on the individual.

A method of producing a vaccine composition described herein may comprise admixing one or more isolated polypeptides selected from SSU0185, SSU1215, SSU1355, SSU1773 and SSU1915 with a pharmaceutically or veterinarily acceptable excipient or carrier and optionally an adjuvant, for example, an adjuvant described above.

The term "pharmaceutically acceptable" or "veterinarily acceptable" as used herein pertains to compounds, materials, compositions, and/or dosage forms which are, within the scope of sound veterinary or medical judgement, suitable for use in contact with the tissues of a subject (e.g. pig or other mammal) without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio. Each carrier, excipient, etc. must also be "acceptable" in the sense of being compatible with the other ingredients of the formulation. Suitable excipients and carriers include, without limitation, water, saline, buffered saline, phosphate buffer, alcoholic/aqueous solutions, emulsions or suspensions. Other

conventionally employed diluents, adjuvants, and excipients may be added in accordance with conventional techniques. Such carriers can include ethanol, polyols, and suitable mixtures thereof, vegetable oils, and injectable organic esters. Buffers and pH-adjusting agents may also be employed, and include, without limitation, salts prepared from an organic acid or base. Representative buffers include, without limitation, organic acid salts, such as salts of citric acid (e.g., citrates), ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, phthalic acid, Tris, trimethylamine hydrochloride, or phosphate buffers. Parenteral carriers can include sodium chloride solution, Ringer's dextrose, dextrose, trehalose, sucrose, lactated Ringer's, or fixed oils. Intravenous carriers can include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer's dextrose, and the like. Preservatives and other additives such as, for example,

antimicrobials, antioxidants, chelating agents (e.g., EGTA; EDTA), inert gases, and the like may also be provided in the pharmaceutical carriers. The vaccine compositions described herein are not limited by the selection of the carrier. The preparation of these

pharmaceutically-acceptable compositions, from the above-described components, having appropriate pH, isotonicity, stability and other conventional characteristics, is within the skill of the art.

Suitable carriers, excipients, etc. can be found in standard pharmaceutical texts, for example, Remington's Pharmaceutical Sciences [71 ] and The Handbook of Pharmaceutical Excipients, 4th edit., eds. R. C. Rowe et al, APhA Publications, 2003. A vaccine composition may conveniently be presented in unit dosage form and may be prepared by any methods well-known in the art of pharmacy. Such methods include the step of bringing the one or more isolated immunogenic polypeptides into association with a carrier or excipient as described above which may constitute one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association the active compound with liquid carriers or finely divided solid carriers or both.

Vaccine compositions described herein may be produced in various forms, depending upon the route of administration. For example, the vaccine compositions can be made in the form of sterile aqueous solutions or dispersions, suitable for injectable use, or made in lyophilized forms using freeze-drying techniques. Lyophilized vaccine compositions are typically maintained at about 4°C, and can be reconstituted in a stabilizing solution, e.g., saline or HEPES, with or without adjuvant. Vaccine compositions can also be made in the form of suspensions or emulsions.

These vaccine compositions may contain additives suitable for administration via any conventional route of administration. The vaccine compositions may be prepared for administration to subjects in the form of, for example, liquids, powders, aerosols, tablets, capsules, enteric-coated tablets or capsules, or suppositories. Thus, the immunogenic compositions may also be in the form of, but are not limited to, suspensions, solutions, emulsions in oily or aqueous vehicles, pastes, and implantable sustained-release or biodegradable formulations. Compositions for sustained release or implantation may comprise pharmaceutically acceptable polymeric or hydrophobic materials, such as an emulsion, an ion exchange resin, a sparingly soluble polymer, or a sparingly soluble salt.

Formulations suitable for parenteral administration (e.g. by injection, including

intramuscular), include aqueous and non-aqueous isotonic, pyrogen-free, sterile injection solutions which may contain anti-oxidants, buffers, preservatives, stabilisers, bacteriostats, and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. Examples of suitable isotonic vehicles for use in such formulations include Sodium Chloride Injection, Ringer's Solution, or Lactated Ringer's Injection.

Typically, the concentration of the active compound in the solution is from about 1 μg ml to about 100 mg/ml, for example, from about 10 μg/ml to about 50 mg/ml. In some formulations for parenteral administration, the active ingredient may be provided in dry (i.e., powder or granular) form for reconstitution with a suitable vehicle (e.g., sterile pyrogen free water) prior to parenteral administration of the reconstituted composition. Other useful parenterally- administrable formulations include those which comprise the active ingredient in

microcrystalline form, in a liposomal preparation, or as a component of a biodegradable polymer system. Formulations suitable for nasal administration, wherein the carrier is a solid, include a coarse powder having a particle size, for example, in the range of about 20 to about 500 microns which is administered in the manner in which snuff is taken, i.e. by rapid inhalation through the nasal passage from a container of the powder held close up to the nose. Suitable formulations wherein the carrier is a liquid for administration as, for example, nasal spray, nasal drops, or by aerosol administration by nebuliser, include aqueous or oily solutions of the active compound. Vaccine compositions may be presented in unit-dose or multi-dose sealed containers, for example, ampoules and vials, and may be stored in a freeze-dried (lyophilised) condition requiring only the addition of the sterile liquid carrier, for example water for injections immediately prior to use.

The vaccine composition may be administered to a subject by any convenient route of administration. In some embodiments, administration is by parenteral routes, such as intramuscular, intranasal, trans-dermal or sub-cutaneous routes. For example, the vaccine composition may be administered by injection, preferably intramuscular injection.

It will be appreciated that appropriate dosages of the vaccine compositions can vary from individual to individual, or population to population, depending on the circumstances.

Determining the optimal dosage will generally involve the balancing of the level of therapeutic benefit against any risk or deleterious side effects of the administration. The selected dosage level will depend on a variety of factors including, but not limited to, the route of administration, the time of administration, the rate of excretion of the vaccine composition, other drugs, compounds, and/or materials used in combination, and the species, breed, maturity, sex, weight, condition and general health of the individual. The amount of vaccine composition and route of administration will ultimately be at the discretion of the veterinary surgeon or physician, although generally the dosage will be to achieve serum concentrations of the vaccine composition which are sufficient to produce a beneficial effect without causing substantial harmful or deleterious side-effects.

Treatment may comprise the administration of a therapeutically effective amount of a vaccine composition to the individual. "Therapeutically effective amount" pertains to that amount of a vaccine composition that is effective for producing some desired therapeutic effect, commensurate with a reasonable benefit/risk ratio. For example, a suitable amount of a vaccine composition for administration to an individual may be an amount that generates a protective immune response against each immunogenic polypeptide present in the composition in the individual.

In some embodiments, a therapeutically-effective amount of a vaccine composition may include 750ng to 750μg of the 5 subunit cassette (150ng to 150μg of each immunogenic polypeptide) administered to a 4-6 week old pig, for example in a 2ml volume. This may be repeated as a booster after the initial administration. Administration in vivo can be effected in one dose, continuously or intermittently (e.g., in divided doses at appropriate intervals). In some embodiments, vaccine compositions may be administered more than once to the same individual with sufficient time interval to obtain a boosting effect in the individual, e.g., at least 1 week, 2 weeks, 3 weeks or 4 weeks, between administrations, preferably about 2 weeks. A prime dose of the vaccine compositions may be administered to the individual followed by a booster dose. For example, a prime dose may be administered to a piglet at 1-4 weeks old and a booster dose at 3-6 weeks old. Methods of determining the most effective means and dosage of administration are well known to those of skill in the art and will vary with the formulation and the subject being treated. For example, in some embodiments, the prime dose of the vaccine composition may be administered when the levels of maternal derived antibodies in the piglet have declined (e.g. after 2-4 weeks) followed by a booster dose two weeks later. Single or multiple

administrations may be carried out with the dose level and pattern being selected by the veterinary surgeon or physician.

A vaccine composition described herein may be for use in a method of treatment of the animal or human body. Aspects of the invention provide a vaccine composition described herein for use in the treatment of S. suis infection in an individual or population of individuals; the use of a vaccine composition described herein for the manufacture of a medicament for use in the treatment of S. suis infection in an individual or population of individuals; and a method of treating S. suis infection may comprise administering a vaccine composition as described herein to an individual or population of individuals in need thereof. S. suis infection includes infection with S. suis of any serotype or strain, for example S. suis serotype 2, as well as clinical signs of S. suis infection, and conditions associated with S. suis infection, including bacterial meningitis, septicaemia, endocarditis, toxic shock syndrome, permanent hearing loss and arthritis. Clinical signs of S. suis infection in pigs may include distended joints, tremors, abnormal gait, lethargy, anorexia, lameness, rough hair coat, dyspnoea and neurological symptoms.

S. suis infection may be identified or diagnosed using standard diagnostic criteria. Treatment as described herein may prime the immune system of the individual to generate an immune response upon exposure to S. suis. This may achieve a desired therapeutic effect, for example, increased protection against or resistance to morbidity caused by S. suis infection.

Treatment as described herein may be prophylactic or preventative treatment i.e. the individual may not be suffering from S. suis infection and/or may not be displaying clinical signs of S. suis infection at the time of treatment. In some embodiments, the individual may be susceptible to or at risk of S. suis infection.

For example, the vaccine composition may be useful in the vaccination or immunisation of an individual against S. suis. The treatment of S. suis infection as described herein may prevent subsequent S. suis infection in the individual or ameliorate its effects. Prophylactic or preventative treatment may reduce the susceptibility of the individual to S. suis infection, reduce the risk or likelihood of infection with S. suis, delay or reduce the severity or duration of lesions or other clinical signs of a S. suis infection, or prevent or delay the onset of clinical signs of S. suis in the individual, and/or reduce or prevent morbidity caused by a S. suis infection.

In some embodiments, a vaccine composition described herein may not affect the shedding of S. suis in a population of treated individuals.

Treatment as described herein may be metaphylactic treatment i.e. a population of individuals, such as a herd of pigs, may be treated to eliminate or minimise the incidence or severity of S. suis infection in the population. Most or all of the individuals in the population may be free of clinical signs of S. suis infection at the time of treatment. The population may be a population that is at risk of S. suis infection, for example because of the age of the individuals or the location of the population (e.g. populations in countries with high occurrence of S. suis infection, for example countries, such as Vietnam, Thailand and China). Treatment of a population of individuals as described herein may reduce the incidence of morbidity in the population relative to unimmunised populations upon exposure to S. suis. For example, the proportion of individuals in the immunised population which display clinical signs of S. suis infection may be reduced compared to unimmunised populations. In some embodiments, treatment as described herein may reduce the number of individuals in a population showing clinical signs of infection by 50% or more, 66% or more or 75% or more compared to an untreated population. Another aspect of the invention provides a method of reducing or preventing clinical signs of S. suis infection comprising administering an effective amount of a vaccine composition described herein to an individual or a population of individuals in need thereof, for example an individual or population at risk of S. suis infection.

An individual suitable for treatment may be a human or a non-human mammal, for example a non-human mammal susceptible to S. suis infection, such as horse, cattle, sheep, cat, dog and pig Preferably, the non-human mammal is pig.

Pigs may include domestic pigs (Sus scrofa domesticus) and other members of the Sus genus.

In some embodiments, the individual may be a piglet or the population of individuals may be piglets. For example, a vaccine composition described herein may be administered to the piglet or population of piglets at 1 day of age or older. Administration of the vaccine composition described herein may achieve protective immunity in the piglet from about 1 day old to about 20 weeks of age, preferably about 5 weeks to about 15 weeks of age. Any suitable dosage regimen may be employed to achieve protective immunity. For example, the piglet or population of piglets may receive a single dose of the vaccine composition or a prime dose followed by a booster dose. In some embodiments, the piglet or population of piglets may receive a prime dose at 1 day to 4 weeks old, preferably 1 to 4 weeks old, followed about two weeks later by a booster dose e.g. at 2-6 weeks old. In other embodiments, the individual may be a pregnant sow or the population of individuals may be pregnant sows. Administration of a vaccine composition described herein may achieve protective immunity in the piglets farrowed by the sow through maternally derived anti-S. suis antibodies. For example, a pregnant sow may receive a prime dose at farrowing date minus 4 weeks and boosted at farrowing minus 2 weeks.

In other embodiments, the individual may be an incoming pig which is to be introduced to an existing population (e.g. breeding stock, such as a replacement gilt or boar) or the population of individuals may be incoming pigs. Administration of a vaccine composition described herein may achieve protective immunity in the pig for example before it is introduced to the herd. For example, an incoming pig may receive a prime and booster dose during a 6 week isolation/acclimatisation period before introduction. In other embodiments, the individual may be a human, for example a human with exposure to pigs and pig meat products, in particular in countries where S. suis zoonosis occurs. For example, prime and booster doses of a vaccine composition may be administered to a human at about 2 week intervals.

Preferably, a vaccine composition described herein reduces the incidence of S. suis related morbidity in a population relative to unimmunised populations. For example, the incidence of lesions or other clinical signs of S. suis infection may be reduced in the immunised population relative to unimmunised populations, following exposure to S. suis. In some embodiments, immunisation of a population with a vaccine composition as described herein may reduce the number of individuals in the population showing clinical signs of S. suis infection by at least 50% more preferably at least 60%, at least 65%, at least 70%, or at least 75%, most preferably at least 80%.

Various further aspects and embodiments of the present invention will be apparent to those skilled in the art in view of the present disclosure. All documents mentioned in this specification are incorporated herein by reference in their entirety for all purposes. The sequences having the database (e.g. Genbank) accession numbers set out above at the filing date are also incorporated herein by reference in their entirety.

"and/or" where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example "A and/or B" is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein.

Unless context dictates otherwise, the descriptions and definitions of the features set out above are not limited to any particular aspect or embodiment of the invention and apply equally to all aspects and embodiments which are described.

Certain aspects and embodiments of the invention will now be illustrated by way of example and with reference to the figures described above. Table 1 shows the competitive indices of transposon mutants of S. suis identified by TraDIS. The range of TraDIS fitness scores is shown for each gene and the fraction of significantly attenuated mutants in each gene is shown in parentheses, using the parameters: input read ≥ 500, P-value < 0.05. Competition index (CI) = (Output mutant CFU/Output wild type CFU) / (Input mutant CFU/lnput wild type CFU), mean Cls are calculated based on 5-6 biological repeats, and P-values are shown in parentheses.

Table 2 shows the characteristics of the five immunogenic polypeptides. With the exception of the cytoplasmic SSU0185, the proteins are cell wall or surface-associated, based on the computer program and database, LocateP. The TraDIS fitness scores are presented as log2- fold change of Output:lnput determined by DESeq2 after normalisation. The fraction of significantly attenuated mutants in each gene is shown in parentheses, using the

parameters: input read≥ 500, P-value < 0.05. The genes encoding the surface proteins were cloned into pET30 Ek/LIC, without the N-terminal signal peptides, and the amino acid residues and molecular weights of fusion proteins were calculated including the protein tag generated from the vector (43 AA, 4.8KDa) and excluding the signal peptides if present in the native protein.

Table 3 shows the results of analysis of the presence of the five immunogenic polypeptides in 459 isolates of S. suis. Proteins were identified as being present by comparing sequences encoding the protein sequences from strain P1/7 against the 459 genome sequences using BlastX. A protein was classified as present in an isolate if a coding sequence with greater than 80% sequence identity over 80% of its length was identified by BlastX.

Table 4 shows the protein identities of the five immunogenic polypeptides in published genome sequences of disease-associated serotypes and isolates of S. suis. The genome sequences of the strains are available in GenBank. The protein sequences of the 5 candidates in these strains had greater than 91 % identity to those in P1/7. Strains in which the protein sequences of all 5 proteins in these strains are 100% identical to those in P1/7 are highlighted in red. Table 5 shows the groups of caesarean-derived colostrum-deprived (CDCD) pigs used in the in the first S. suis subunit candidate protection experiment.

Table 6 shows the results of the first S. suis subunit candidate protection experiment. "NCS" indicates no clinical signs were observed. "^*" Pig #562 was lame on its right front leg for 2 days with no other clinical signs and recovered uneventfully. Pig #574 was lame on its left rear leg throughout the experiment after challenge but did not show clinical signs otherwise. "?" indicates that there were too many contaminating bacteria to see whether or not S. suis colonies were present, "tntc" indicates too numerous to count. "^**" indicates that approx. 500 colonies of non-S. suis bacteria were cultured out of the BALF. "+" indicates that S. suis colonies were present but numbers could not be estimated because of contaminating bacteria, "np" not plated.

Table 7 shows the groups of caesarean-derived colostrum-deprived (CDCD) pigs used in the in the second S. suis subunit candidate protection experiment. Table 8 shows the results of the second S. suis subunit candidate protection experiment.

"NCS" indicates no clinical signs were observed. "^*"Pig # 977 was lame on RR leg for 2 days with lethargy but recovered uneventfully."^**" Pig 979 showed intermittent lethargy day 3 through day 10 but never severe and appeared normal by end of the study. "?" indicates that there were too many contaminating bacteria to see whether or not S. suis colonies were present, "tntc" indicates too numerous to count. "^**" indicates that approx. 500 colonies of non-S. suis bacteria were cultured out of the BALF. "+" indicates that S. suis colonies were present but numbers could not be estimated because of contaminating bacteria, "np" not plated. Experiments

1 . IVOC TraDIS Study

In this study, an in vitro organ culture (IVOC) system using pig respiratory epithelium explants was adapted, providing a new platform for studying survival and fitness of S. suis in pig upper respiratory tract. Transposon mutagenesis in S. suis has been developed previously in our laboratory to generate small mutant pools containing hundreds of mutants [36]. In this study, an improved strategy was introduced allowing construction of large transposon mutant libraries containing thousands of mutants in a disease-associated serotype 2 strain, P1/7, for which the complete genome sequence is publicly available [37]. TraDIS was then applied to assess the genotype and relative fitness of 8718 distinct transposon insertion mutants during infection of the IVOC model. To date, this report represents the most comprehensive functional genomic screen to identify genes required by S. suis for survival and fitness on porcine respiratory tract tissues.

2. Methods

A novel strategy for generating transposon mutant libraries in S. suis was applied for generating transposon mutant libraries capable of generating thousands of S. suis mutants in parallel. The improved transposon mutagenesis strategy, involving induction of transposition on plates using a sub-lethal concentration of erythromycin, was developed to construct a large Tn977 transposon mutant library in S. suis P1/7. Our initial attempts at doing so were performed in batch culture, but these were problematic as siblings (identical mutants derived from replication rather than independent transposon insertions) were generated from early transposition events and rapidly dominated the library. We

circumvented this problem by generating the mutants on plates, and by exploiting the inducible nature of the Tn977 transposon, which can be mobilized using sub-lethal concentrations of erythromycin. Using this approach we were able to generate thousands of S. suis transposon mutants simultaneously, opening up the possibility of performing genome-wide functional screens using TraDIS.

TraDIS analyses were performed to determine the randomness and complexity of the S. suis library using the TraDIS technique described previously [34,35]. A combined super-pool (A- M) of pools of mutants from the 13 plate induction experiments was used for the

identification of genes important for survival and fitness of S. suis in an IVOC model of the pig respiratory tract.

To prepare the inocula for IVOC (input), each of the 13 mutant pools was replicated into 2ml 96-well plates containing 1 ml THY broth and grown statically overnight at 37 °C. Overnight cultures were combined and bacterial cells were washed and resuspended in 1 ^χ PBS. 5 μΙ

_Q

bacteria cells containing approximately 10 CFU of the mutant library super-pool was applied onto pig nasal or tracheal explants and incubated at 37 °C, 5% C0₂, in a humidified atmosphere. Infected nasal or tracheal tissues harvested at 42 hours post-infection were homogenized and grown statically overnight in THY broth at 37 °C to isolate output bacteria. Five independent biological replicates were performed.

Genomic DNA prepared from the IVOC input and output pools was analyzed using TraDIS. The number of sequence reads corresponding to each transposon in the input pool, and the number of reads mapping to the equivalent position in the output pool were compared using DESeq2 [38], to determine a log₂-fold change (fitness score) and a false discovery rate

(FDR)-adjusted p value. A negative fitness score indicates a mutant with reduced fitness; a positive score indicates a mutant that was more abundant in the output pool than in the input pool. Individual transposon mutants were isolated from the mutant library and assessed in a co- infection competitive fitness assay with the wild-type P1/7 strain using IVOC. The ratios of mutant:wild-type bacteria from output isolates were compared with those in the inoculum using Student's t-test.

3. Results

3.1 TraDIS analysis of S. suis mutant pools

Thirteen Tn977 transposon mutant pools were generated in S. suis serotype 2 strain P1/7 using the improved strategy described in the Methods. The pools were combined and characterized using TraDIS. A total of 8,718 distinct transposon insertions were

unambiguously mapped at the level of the single nucleotide to the S. suis P1/7 genome. The insertions were distributed throughout the P1/7 genome, disrupting 1049 of the 201 1 genes. Tn977 insertions occurred preferentially in a -200 kb hotspot surrounding the terminus of replication, where 39.8% of the transposons had inserted. Pilot studies were performed in which selected pools were repeatedly screened through IVOC by infecting both nasal and tracheal tissues, with output pools harvested at both 18 and 42 hours post-infection. These indicated that infection of nasal tissue, with harvesting of output pools at 42 hours post-infection, maximized the ability to discriminate between attenuated and non-attenuated mutants. Therefore, these conditions were used for the full study, using five independent biological replicates of the transposon mutant library, grown-up as five individual input pools.

3.2 Assessment of mutant fitness by TraDIS

The insertion position, disrupted gene and fitness scores of the 8718 transposon insertions identified were determined using TraDIS. The raw TraDIS sequence data are available from the NCBI Short Read Archive. To identify genes potentially important for fitness, we adopted additional stringent criteria to reduce the possibility of false positives. We disregarded mutants with fewer than 500 reads in the input pool, as mutants present at a low level in the input are more likely to exhibit "random drop-out" i.e. stochastic loss, for reasons unrelated to their genotype.

3.3 Competitive fitness assays validated the findings of the primary screen

To validate the IVOC-TraDIS screen, six candidate fitness genes that represented a wide range of functional categories and which contained multiple significantly attenuated insertions were selected for further investigation (Table 1 ). The genes chosen included zmpC (SSU0879), encoding an lgA1 protease that has an established role in the pathogenicity of S. suis in pigs [39] and in the pathogenesis of other streptococcal species in other hosts [40]; clpL {SSU0352), which encodes the ATP-binding subunit of an ATP- dependent protease and is involved in stress responses and virulence in various

streptococcal species [41 -44]; SSU1915, encoding a putative maltose/maltodextrin-binding protein precursor that is critical for alpha-glucan metabolism in S. pneumoniae [45], is required for virulence in the lungs [46] and has been identified as an extracellular protein from clinical S. suis strains [19]; SSU1215, which encodes a surface-associated arginine dipeptidase (AbpB, amylase binding protein B) that is one of the immunogenic extracellular components of S. suis [47,48] and has been associated with virulence in a mouse model of S. suis infection [49] and with colonization of the oral cavity by S. gordonii [50,51 ]; SSU0185, which encodes a putative tagatose-6-phosphate aldose/ketose isomerase, a protein family often associated with utilization of N-acetyl-galactosamine and galactosamine, major components of peptidoglycan and capsular polysaccharides; and SSU0130, which encodes a membrane protein, and is located in a gene cluster which also encodes competence proteins (SSU0126-0131). One individual transposon mutant of each target gene was isolated and tested in competition with the wild-type P1/7 strain through IVOC co-infection experiments. All the mutants of the six candidate fitness genes showed negative competitive indices (CI) (Table 1 ), indicating that the mutants were outcompeted by the wild-type in the IVOC model and could thus be classed as attenuated.

3.4 Identification, cloning, expression and purification of S. suis subunit candidates

Protein-based S. suis immunogenic polypeptides were identified that (i) were significantly attenuated in the IVOC-TraDIS screen (ii) were present in the core genome or in the majority of clinical strains tested (iii) were surface associated and (iv) lacked trans-membrane domains in the centre of the protein.

Five suitable candidates were identified from the IVOC-TraDIS screen; putative tagatose-6- phosphate aldose/ketose isomerase (SSU0185), putative surface-anchored dipeptide (SSU1215), putative surface-anchored 5'-nucleotidase (SSU1355), putative surface- anchored serine protease (SSU1773) and putative maltose/maltodextrin binding protein precursor (SSU1915) (see Tables 2 to 4). We have analyzed the genomes of 459 S. suis strains including representatives of 29 different serotypes [72]. Our comparative genome analysis revealed that the 5 vaccine proteins (SSU0185, SSU1215, SSU 1355, SSU1773 and SSU1915) were either present in the S. suis core genome or in the majority of the clinical strains tested (Table 3) and were present in each of the 29 serotypes in the collection, providing an indication that they are promising protein-based vaccine candidates with cross- protective potential against S. suis infection.

Genes encoding each of these five candidate surface-associated proteins were amplified from S. suis P1/7, cloned into the pET system vector and expressed in E. coli BL21 (DE3) with N-terminal His-tags. The five recombinant proteins were further purified using nickel and ion-exchange columns for use as a 5-subunit vaccine cassette in the protection study.

4. Protection of pigs against S. suis infection following vaccination with the 5 subunit cassette-1

4.1 Method

Caesarean-derived colostrum-deprived (CDCD) pigs were immunized at 5.5 weeks of age using the 5-subunit cassette by intramuscular and intranasal routes using two different adjuvant formulations (see Table 5). Intranasal adjuvant combination 1 was polyethylene- imine (PEI). Branched, 25kDa PEI (Sigma ref: 408727). Intramuscular combination 1 was a combination of Carbopol 971 (Lubrizol) and Addavax (Invivogen). Intranasal adjuvant combination 2 was polyethylene-imine (PEI). Branched, 25kDa PEI (Sigma ref: 408727). Intramuscular combination 2 was emulsigen D (MVP Technologies). A booster dose was administered at 7.5 weeks of age.

The pigs were challenged intranasally with 2x10⁹cfu/ml of virulent S. suis at 9.5 weeks of age and then monitored for 15 days after the challenge for clinical signs of severe disease, including lameness, lethargy and neurological symptoms. Nasal washes and samples of serum and PBMCs were obtained weekly and samples were obtained post-mortem for bacterial enumeration and immunological assays of responses to the sub-unit cassette.

4.2 Results

The results are shown in Table 6 (Group 1 corresponds to pigs 554-559, Group 2 corresponds to pigs 560-565, Group 3 corresponds to pigs 566-568, Group 4 corresponds to pigs 569-571 and Group 5 corresponds to pigs 572-575) and Figures 1 and 2. These results show that immunisation with the panel of candidate proteins exerts a large and statistically significant protective effect on pigs subsequently exposed to S. suis infection.

Antibody (IgG) responses against the 5 subunit proteins were assessed using an indirect ELISA method in serum samples collected from immunized pigs at 14 (day of boost), 21 , and 28 days following the day of first immunization. IgG responses were induced against all 5 subunits between 14 and 28 days after the priming dose, for both adjuvant combinations, with highest titres for all subunits being achieved at 28 days after the first immunization, using adjuvant combination 2 (Figure 3). Antibody (IgG) responses against whole heat-killed S. suis were demonstrated and titrated in serial dilutions using pooled serum collected from Group 2 (adjuvant combination 2; see Table 5) pigs at day 0 and at 21 days post- immunisation (Figure 4).

Cell-mediated immune responses were measured using a standard interferon-gamma (IFN- gamma) recall assay to quantify IFN-gamma-releasing cells (representing memory T cells) following incubation of fresh peripheral blood mononuclear cells (PBMCs) from pigs in groups 1-5 (see Table 5) with either fresh cell culture medium alone or with fresh culture medium supplemented with the 5 pooled subunits. Recall responses were detectable at 14, 21 , and 28 days after the date of first immunisation using adjuvant combination 2 (group 2) (Figure 5). Recall responses were also detectable for pigs in group 1 (adjuvant combination 1 ) at 14 days after first date of immunisation. In addition, the responsiveness of PBMCs collected from immunised pigs were compared by re-stimulating these cells in vitro and measuring the subsequent production by those cells of specific cytokines (IFN-gamma, TNF- alpha, IL-2, and IL-10). Notably, there was a significantly higher TNF-alpha and IL-2 response from PBMC harvested from pigs immunised using the subunit pool (Figure 6). Cross-reactive antibodies which bind to additional serotypes of S. suis beyond the serotype 2 strain P1/7 were detected by ELISA in the serum of immunised pigs particularly those immunised in the emulisgen D group (Figure 7).

5. Protection of pigs against S. suis infection following vaccination with the 5 subunit cassette - 2

5.1 Method

Fresh pooled stocks of the five subunits were prepared just prior to use to avoid potential problems due to the protease activity of SSU1773. Each 2ml intramuscular (IM) dose contained 50ug of each subunit (250ug in total) and each 2ml intranasal (IN) dose contained 100ug of each subunit (500ug in total). The adjuvant for IN doses was polyethylene-imine (PEI). Branched, 25kDa PEI (Sigma ref: 408727). The adjuvant for intramuscular doses was 20% or 80% emulsigen D (MVP Technologies).

Caesarean-derived colostrum-deprived (CDCD) pigs were immunized at 5.5 weeks of age (day 0) using the 5-subunit cassette by intramuscular and intranasal routes using three different adjuvant formulations (see Table 7).. A booster dose was administered at 7.5 weeks of age. The pigs were challenged intranasally with 2x10⁹cfu/ml of virulent S. suis P1/7 at 9.5 weeks of age and then monitored for 15 days after the challenge for clinical signs of severe disease, including lameness, lethargy and neurological symptoms. Nasal washes and samples of serum and PBMCs were obtained weekly and samples were obtained postmortem for bacterial enumeration and immunological assays of responses to the sub-unit cassette.

5.2 Results

The results are shown in Table 8 (Group 1 corresponds to pigs 958-965, Group 2 corresponds to pigs 966-973, Group 3 corresponds to pigs 974-981 , Group 4 corresponds to pigs 982-989 and Group 5 corresponds to pigs 990-997) and Figures 8 to 1 1. These results show that immunisation with the panel of candidate proteins exerts a large and statistically significant protective effect on pigs subsequently exposed to S. suis infection.

Antibody (IgG) responses against the 5 subunit proteins were assessed using an indirect ELISA method in serum samples collected from immunized pigs at 14 (day of boost), 21 , and 28 days following the day of first immunization. IgG responses were induced against all 5 subunits between 14 and 28 days after the priming dose, for the IN/IM-80, IM-80 and IN- IM-20 adjuvant combinations (Figure 9). Responses in the IN-only and control group

(adjuvant/no antigen) were not different than the day 0 serum IgG response for any protein (not shown).

Peripheral blood mononuclear cells were collected on day 14 and 28 post vaccination and evaluated for ability to produce IFN-gamma (IFN-γ) after stimulation with media alone

(NoStim) or recall antigen. The recall antigens used were either a preparation of heat-killed P1/7 S. suis (hkP1/7) or a pool of all 5 S. suis subunit proteins (protein pool; 5μg ml of each protein). PBMC were incubated with antigen for approximately 18h and the assay completed by enumerating the number of cells producing IFN-γ. The results expressed as the average +/- SEM for the group are shown in Figure 10. Results for PBMCs from single pigs in each vaccination group are shown in Figure 1 1 with the mean for the group shown with a line. PBMCs from pigs that were vaccinated with the IN/IM-80, IM-80 and IN-IM-20 adjuvant combinations were found to produce IFN-γ after stimulation with the recall antigens. 6 Conclusion

Applying the IVOC-TraDIS (Transposon directed insertion site sequencing) technique has led the inventors to the selection of five proteins from S. suis which are required for fitness in the IVOC model of infection: SSU0185, SSU1215, SSU1355, SSU1773 and SSU1915 (See Experiments and Tables 1 and 2).

Genes encoding two of the proteins (SSU0185 and SSU1355) are present in the core genome of S. suis i.e. are present in 459 clinical and non-clinical strains of S. suis from around the world [72, Table 3]. SSU1215, SSU1773 and SSU1915 are present in 450 or more of these strains [72, Table 3]. The proteins are also present in clinical strains of various serotypes from China, the Netherlands, Denmark and Canada (Table 4). We have detected the presence of the genes encoding the five proteins in clinical strains of S. suis from the USA and have shown that they are highly conserved with over 91 % identity at the nucleotide level.

SSU0185 is a putative tagatose-6-phosphate aldose/ketose isomerase, a protein family associated with utilization of N-acetyl-galactosamine and galactosamine which are major components of peptidoglycan and capsular polysaccharides. SSU1215 is a surface- associated arginine dipeptidase that is one of the immunogenic extracellular components of S. suis [47,48] and has been associated with virulence in a mouse model of S. suis infection [49] and with colonization of the oral cavity by S. gordonii [50,51]. SSU1915 is a putative maltose/maltodextrin-binding protein precursor that is critical for alpha-glucan metabolism in S. pneumoniae [45]. Both SSU1215 and SSU1915, together with SSU1355 (a putative surface-anchored 5'-nucleotidase) and SSU1773 (a putative surface-anchored serine protease) have been identified as surface proteins from clinical strains of a range of serotypes of S. suis [19].

Hence these proteins are widespread in S. suis strains that cause clinical disease, as well as being present in strains isolated from pigs that do not have clinical disease. The proteins are important for metabolism and pathogenicity of S. suis. A cassette of the five protein components has been shown to protect experimental pigs from challenge with a virulent strain of S. suis serotype 2 and given the presence of these proteins in other strains of S. suis, it is likely that general cross-protection could be present. Cross-reactive antibodies to a range disease-associated isolates of other serotypes of S. suis were detected in the sera of pigs immunised with these proteins (Figure 7). Sequences

SEQ ID NO: 1 (SSU0185). CAR44485.1 Gl: 251819240

1 mfrlakeele klgaiitate iyqqpglwke ayqlyfdqle kiesflksik ekhdfvh vf 61 tgagtsdfvg qsianylnqv ndlkhirfsa igtvelvsrp hdylqadvpt vlvsfarsgn

121 spesvaavev akqlvdklyq vtitcapegk lalaaegdae nllllqpags ndkgfamtgs

181 yscmaltall vfssasqeek aawveiiarl gqdvldredy vqdlinldfe rviylgsggf

241 yglaheaqlk ileltagkia tmyesplgfr hgpksfinek tliflfasnd aytrqydvdl

301 lnevhgdgia erivalsadk lvgteaanfv laeggadlpd vfltfpyilf aqtvsimaai 361 kcnnlpdtps ptgtvnr vq gviihplek

SEQ ID NO: 2 (SSU 1215) CAR46535.1 Gl:251820175

1 mkktfvriat flmlvclfpv qlvqacsgfi igkglttdgs ilygrtedyp yppnngahnk 61 nyi vpatay akgdmlvdes fgftaphlan efkytstpda argdgsngnf gahgfnekgv

121 smtatvtaip nkkvlavdpl vtagglgeai lidyvlprvt saregielia ktidekgsae

181 gniiviadkn evwymeilsg hqyvaikfpe dkyaifanty ylghvdftdt enviasakve

241 evakqaenym mvdgkfhiak sygpenyadg drsrtyagik lldpassvty edavydllrq

301 ptdpsrrfsl qdtfalqrnr fehlpefrpd deagkvkqgd ngandqaada tykyalgnen 361 vidahvyqin sslpsafggt vwlglaqtrn tpyvpfygiv tdtyeafknr sasydtnswy

421 wtvqnidkma ishpelfgts iqekwialek ewiasqaald aqyaglseda avalaptvte

481 atlarsaeif aqlkaveaem makieaattp sssstepsts tepsssgtet ststsqstsd

541 sntggatdts sssrtvvpsd kkvtptnkkg ksslpstgeq vslllvalgv agiltaiflh 601 rkksske

SEQ ID NO: 3 (SSU1355) CAR46815.1 Gl:251820308

1 mkknirlkss ilalvagfsv iatqavlade lavqimgvnd fhgaldmtgt arlegetvrn

61 agtaallday mddsqaefee taaetetpae sirvqagdmv gaspsnsgll qdeptvkvfn 121 kmdveygtlg nhefdeglde ynrimtgeap kkgqfneivd nytreaakqe ivianvidke

181 tgeipygwkp yaiktipvnd keakigfigv vtteipnlvl kknyeqytfl neaetiakya

241 relaekgvna ivvlahvpat skdgvaagea admiaklnei ypehsvdlvf aghnhvytng

301 ttgktlivqa tsqgkayadv ravydtdiad fkavptakii avapgqktps peiqaivdea

361 ntivkkvteq kiatasqatd isrevnefke savgnlvtsa qlaiakksgy dvdfamtndg 421 giradlkvqe dgtvtwgaaq avqpfgnilq vvqmtgeqiy talnqqydeg ekyflqmsgi

481 kyiytkadnp teenpykvvk afkedgteiv ptetytlvin dflfgggdgf sifkeaklig

541 ainpdtevfv eyltdlekag qtisatipgr kafvekyvee pkaeekedna gtttdvktpe

601 kandggdsvt nqkateqpap sgsmapisnk ktekasgnqt Ipntgqealg sllislgglv 661 slgmavsvrr kege SEQ ID NO: 4 (SSU 1773) CAR47467.1 Gl:251820705

1 mkqkwsqien kqrfsikkls vgvasvsigf fitgvpmvqa dtsgeglest vavatdmdsr

61 qnsavekked gplsddpvkt eqvdepvaee g veevvdte ageesglltd qaateietta

121 gkttdeskek edisgkeasa pqtipqesql epeevttgry ilqfseenrn lvldklkkid

181 gvkivheyke vltgasvevg keslsdvkai teltsleesr rirptlhtak qlvgalkass

241 kyqtdgrgmv iavidsgldi khkdmrlddg vipkikditp sttgtytlkv phgynyvsgn

301 dnlyddthep hgmhiagtla gnatdeevas kkgvdgiapn aqllvykifs ndpknykaet

361 edaayaaied aikhgadvis lsvgyydsgl pgnayytiak raaekgiiit aaignagass

421 sdtsfdlhtn nalgavdtat tvgvaatpav iavgsarnth lvqrefmlng qsfgyypigy

481 ttltegkyef vdagnghwee vqgldlagkv avikkdkfdl kdavrnlkfk dvagiivint

541 dqgwnkdyyr thqllvddkt llsyssiwgi slsgedgrrl levanqsqgn tglvlkptig

601 mkklievptv sgfsswgptv nlelkpeiva pgedvyatln dnrygsmsgt smaspivaga

661 salllprirq mtppegmtrm dllriilmnt atplvdvlds sghalenspr qqgagllqid

721 rafetdvilh hrlkggvelk eigretefev tlenlgnqqr sfaisagkvl tsqdvpvdri

781 grsgk vkei hateikgssi hlseqsiqlg pkekrtirlk ldageakdqf aegyiyfksl

841 tegqsdisip yfgfvgdwsk erivdapawe tssklkltsv lssykhnksg ryielgreki

901 qdnqsplnpd niaiqnqhsd sqignafvrf allrditnyd ldivkeated apvlrridtg

961 tmlsrvryvd yfeslseysk lrtpielhrw dgkvydasnd enipapegqy ffrlrvknke

1021 ngayqytylp vkidnqkpei vaidtnrlss hrelvvtakd nnkvwevran Ingedllvek

1081 vvddagqlhy hlkevelpld aknhlrvevm diagnvvave kdlmapviqf knledlmair

1141 skktveikan vsaqvsdvqa nldaqavnys lengqlslqi peqsdgrhsf elilkdkdgn

1201 liytktlnyl vdnekptidl diekdeedee viqigkngrf tlkgkvsdnv slpkdiklyy

1261 snldigkger kiidvkedgs feqdffksdf praimltavd ekgnklkdlr intspeslde

1321 eeetevpitv nnwlidpirf nkeslgreld sglvdfkkqe dgtylftfei eaeteqahsv

1381 ringgekryf edgkltypvt lieegnvvdi svyneadelt ytkkyqmlvd tenpvlqlen

1441 evlplerqvv dseededeen qyagvllada dghltltgsa kdngiywslk inedfvargg

1501 fwrqygnnek afryelhslk dgdtvkldls dsfgnavvkk ykvrlndkev seqvpekdlh

1561 versdkdqtp sipilkseah ipmpkeensl apqtgsteia lltgdtredg vehlgkltkh

1621 eeplgisder ievsvphref fersgigetg alaadtsgkl pqtgdslgsv fistllglfg

1681 gamalgnlkr ke

SEQ ID NO: 5 (SSU1915) CAR47605.1 Gl:251820839

1 mkhnllksva llaastavla acsnsgsste asksaegske ltvyvdqgye syindvkagf

61 ekengvsvtv ktgdaltgld nlsldnqsgs apdvmmapyd rvgslgsegq lseltladds

121 kaddtttalv tnggkvygsp avietlvlyy nkdllteapk tfaeletlak dskyafagee

181 gktsafladw tnfyytygll sgyggyvfge ngtnpkdigl anegaikaie yaktwyekwp

241 qglqdgtaan nlintqftdg kaaaiiegpw kaasykeagv nygvatiptl vngknysafg

301 ggkawvvpag aknqemaqkf vdfltatdqq kalydatnev panteareya vskkdeltta

361 vinqfasaqp mpnisemgsv wtpagnmlfe aasgskdakt aatdavkaia deiaqkhsn Table 1 Competitive indices of transposon mutants of S. suis in in vitro organ culture (IVOC)

a TraDIS fitness scores are presented as log2 fold change of Output.lnput determined by DESeq2 after normalisation. The fraction of significantly attenuated mutants in each gene is shown in parentheses, cut offs: input read > 500, p value < 0.05.

An individual transposon mutant of each gene was isolated from the mutant library and used for co-infection IVOC experiments. Competitive indices (CIs) were calculated as the ratio of mutant CFU to wild-type CFU in the output pool divided by the ratio of mutant CFU to wild-type CFU in the inocula. Data are presented as the mean CI from at least 5 biological repeats and the significance of any differences in mutant to wild-type ratio was tested using Student's t-test.

Table 2 Characteristics of the five immunogenic polypeptides

a TraDIS fitness scores were presented as log2 fold change of Output:lnput determined by DESeq2 after normalisation. The fraction of significantly attenuated mutants in each gene is shown in parentheses, using the parameters: input read > 500, P- value < 0.05.

Genes encoding the surface proteins were cloned without the N-terminal signal peptides.

c LocateP DataBase, http://www.cmbi.ru.nl/locatep-db/cgi-bin/locatepdb.py

d The amino acid residues and molecular weights of pET30 Ek/LIC fusion proteins were calculated including the protein tag generated from the vector (43 AA, 4.8KDa) and excluding the signal peptides if present.

Table 3 Presence³ of the five immunogenic polypeptides in 459 isolates of S.

a The presence of the protein was investigated by taking the sequence of the protein from P1/7 and using BlastX against the 459 genomes in our S. suis collection (375 of these genomes were genetically characterized as described by Weinert et al. 2015 [72]). If the protein had 80% identity over 80% of the length, it was classified as present.

b Present in the core genome.

c Isolates recovered from either systemic sites in pigs with clinical signs and/or gross pathology consistent with S. suis infection (including meningitis, septicaemia and arthritis) or respiratory sites in the presence of gross lesions of pneumonia from the lung were classified as clinical. d Isolates from the tonsils or tracheo-bronchus of healthy pigs or pigs without any typical signs of S. suis infection but diagnosed with disease unrelated to S. suis (such as enteric disease or trauma) were classified as non-clinical. e Isolates for which there was insufficient information about the pigs sampled were classified as not known.

Table 4 Protein identities of the five immunogenic polypeptides in representative serotypes of disease-associated S. suis strains with complete genomes in GenBank³

Disease-associated S. suis serotypes Five immunogenic polypeptides

Strain Serotype Source Country Host SSU0185 SSU1215 SSU1355 SSU1773 SSU1915

SS12 1/2 Resoiratorv China pig 100% 100% 100% 100% 100%

ST1 1 unknown China pig 99% 98% 98% 97% 100%

S735 2 Respiratory Netherlands Pig 99% 100% 100% 99% 100%

PI/7 2 Svstemic (Brain) UK pig 100% 100% 100% 100% 100%

A7 2 Systemic (Brain) China pig 100% 100%, 100% 100% 100%

89/1591 ^b 2 Systemic (other) Canada pig 98% 99% 99% 98% 100%

BM407 2 Svstemic (Brain) Vietnam Human 100% 100% 100% 100% 100%

SC84 2 Svstemic (Brain) China Human 100% 100% 100% 100% 100%

98HAH33 2 Svstemic (Brain) China Human 100% 100% 100% 99% 100%

05ZYH33 2 Systemic (Brain) China Human 95% 98% 98% 99% 100%

GZ1 2 Systemic (other) China Human 97% 100% 100% 100% 100%

ST3 3 Respiratory China pig 98% 99% 99% 98% 100%

6407 4 Systemic (other) Denmark pig 99% 99% 99% 98% 100%

D9 7 Systemic (other) China pig 98% 99% 99% 97% 100%

D12 9 Respiratory China pig 96% 91 % 91 % 97% 97%

JS14 14 Systemic (other) China pig 100% 99% 99% 100% 100%

^a S. suis strains for which a complete genome sequence is available in GenBank (15 isolates)

b Strain 89-1591 , a North American isolate, for which a draft genome is available in GenBank.

All 16 strains are disease-associated S. suis serotypes isolated from various regions around the world. The protein identities of the five immunogenic polypeptides were identified in these strains by taking the protein sequences from P1/7 and using BlastP against the 16 genomes.

Strains with underlined text: protein sequences of all five subunit candidates in these strains are 100% identical to those in P1/7.

Table 5

Group Vaccinate³ Challenge Pig numbers Pig IDs

Group 1 SS Ag IN+IM/Adj combol SS P1/7 6 554-559

Group 2 SS Ag IN+IM/Adj combo2 SS P1/7 6 560-565

Group 3 No Ag IN+IM/Adj combol SS P1/7 3 566-568

Group 4 No Ag IN+IM/Adj combo2 SS P1/7 3 569-571

Group 5 PBS control SS P1/7 4 572-575

S. suis; Ag: antigen; IN: intranasal; IM: intramuscular; Adj combol : PEI IN, Carbopol/Addavax IM; Adj combo2: PEI IN, Emulsigen D IM.

Table 6

"NCS" indicates no clinical signs were observed

"^*" Pig #562 was lame on right front leg for 2 days with no other clinical signs and recovered uneventfully. Pig #574 was lame on left rear leg throughout the experiment after challenge but did not show clinical signs otherwise.

"?" indicates that there were too many contaminating bacteria to see whether or not S. suis colonies were present

"tntc" indicates too numerous to count

"^**" indicates that approx. 500 colonies of non-S. suis bacteria were cultured out of the BALF

"+" indicates that S. suis colonies were present but numbers could not be estimated because of contaminating bacteria,

"np" not plated

Table 7

Table 8

NCS = no clinical signs

^* Pig # 977 was lame on RR leg for 2 days with lethargy but recovered uneventfully.

^** Pig 979 intermittent lethargy day 3 through day 10 but never severe and appeared normal by end of the study. ? = too many contaminating bacteria to see whether or not Strep colonies were present, plan to do PCR.

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Claims

Claims

1 . A vaccine composition comprising one or more isolated polypeptides selected from SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915.

2. A vaccine composition according to claim, 1 comprising an isolated SSU0185 polypeptide.

3. A vaccine composition according to claim 1 or claim 2 comprising an isolated SSU1215 polypeptide.

4. A vaccine composition according to any one of the preceding claims comprising an isolated SSU1355 polypeptide.

5. A vaccine composition according to any one of the preceding claims comprising an isolated SSU1773 polypeptide.

6. A vaccine composition according to any one of the preceding claims comprising an isolated SSU1915 polypeptide.

7. A vaccine composition comprising an isolated SSU0185 polypeptide and one or more isolated polypeptides selected from SSU1215, SSU1355, SSU1773 and SSU 1915.

8. A vaccine composition according to claim 7 comprising two or more isolated polypeptides selected from SSU1215, SSU1355, SSU1773 and SSU1915.

9. A vaccine composition according to any one of the preceding claims comprising isolated SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 polypeptides.

10. A vaccine composition according to any one of the preceding claims wherein said one or more isolated polypeptides are the only immunogenic factors in the formulation.

1 1 . A vaccine composition according to any one of the preceding claims wherein the isolated SSU0185 polypeptide comprises an amino acid sequence having at least 80% amino acid identity to SEQ ID NO: 1 or a fragment thereof.

12. A vaccine composition according to any one of the preceding claims wherein the isolated SSU1215 polypeptide comprises an amino acid sequence having at least 80% amino acid identity to SEQ ID NO: 2 or a fragment thereof.

13. A vaccine composition according to any one of the preceding claims wherein the isolated SSU1355 polypeptide comprises an amino acid sequence having at least 80% amino acid identity to SEQ ID NO: 3 or a fragment thereof.

14. A vaccine composition according to any one of the preceding claims wherein the isolated SSU1773 polypeptide comprises an amino acid sequence having at least 80% amino acid identity to SEQ ID NO: 4 or a fragment thereof.

15. A vaccine composition according to any one of the preceding claims wherein the isolated SSU1915 polypeptide comprises an amino acid sequence having at least 80% amino acid identity to SEQ ID NO: 5 or a fragment thereof.

16. A vaccine composition according to any one of the preceding claims further comprising an adjuvant.

17. A vaccine composition according to any one of the preceding claims further comprising a pharmaceutically acceptable excipient.

18. A vaccine composition according to any one of the preceding claims for use in a method of treatment of the human or animal body.

19. A vaccine composition according to any one of the preceding claims for use in a method for treating S. suis infection in an individual.

20. A vaccine composition for use according to claim 19 wherein the individual is a pig or a human.

21 . A vaccine composition for use according to claim 19 or claim 20 wherein the treatment is prophylactic treatment.

22. A method of treating S. suis infection comprising;

administering a vaccine composition according to any one of claims 1 to 17 to an individual in need thereof.

23. A method according to claim 22 wherein the individual is a pig or a human.

24. A method according to claim 22 or claim 23 wherein the treatment is prophylactic treatment.

25. Use of an vaccine composition according to any one of claims 1 to 17 in the manufacture of a medicament for treating S. suis infection in an individual.

26. Use according to claim 25 wherein the individual is a pig or a human.

27. Use according to claim 25 or claim 26 wherein the treatment is prophylactic treatment.

28. A method of producing a vaccine composition comprising;

admixing one or more isolated polypeptides selected from SSU0185, SSU 1215, SSU1355, SSU1773 and SSU1915 with an excipient and/or an adjuvant.

29. A set of nucleic acids encoding one or more isolated polypeptides as defined in any one of claims 1 to 15.

30. A set of expression vectors comprising nucleic acid sequences encoding one or more isolated polypeptides as defined in any one of claims 1 to 15.

31 . A set of recombinant cells comprising one or more heterologous nucleic acids encoding one or more isolated polypeptides as defined in any one of claims 1 to 15.