# Patent

## Title
Bacterial vaccine

## Abstract

The disclosure relates to a composition comprising one, two or more immunogenic bacterial polypeptides and multivalent and monovalent vaccine compositions comprising the immunogenic bacterial polypeptides.

## Background
REFERENCE TO RELATED APPLICATIONS
This application is a US national phase entry of International Patent Application No. PCT/GB2013/050910, filed Apr. 9, 2013, which claims priority to GB Patent Application No. 1206366.5, filed Apr. 11, 2012.
FIELD OF THE INVENTION
The disclosure relates to a composition comprising one, two, or more immunogenic bacterial polypeptides and a vaccine composition, typically a multivalent vaccine, comprising the immunogenic bacterial polypeptides in the prevention or treatment of bacterial infections in humans and animals.
BACKGROUND TO THE INVENTION
Vaccines protect against a wide variety of infectious diseases. Many modern vaccines are therefore made from protective antigens of the pathogen, which are isolated by molecular cloning and purified. These vaccines are known as ‘subunit vaccines’. The development of subunit vaccines has been the focus of considerable research in recent years. The emergence of new pathogens and the growth of antibiotic resistance have created a need to develop new vaccines and to identify further candidate molecules useful in the development of subunit vaccines. Likewise the discovery of novel vaccine antigens from genomic and proteomic studies is enabling the development of new subunit vaccine candidates, particularly against bacterial pathogens. However, although subunit vaccines tend to avoid the side effects of killed or attenuated pathogen vaccines, their ‘pure’ status means that subunit vaccines do not always have adequate immunogenicity to confer protection.
An approach to improve the efficacy of vaccine compositions is to provide multivalent vaccines comprising dominant antigens that provoke both a B cell and T cell response thereby mounting a more rigorous immune response in the subject receiving the vaccine. A typical multivalent vaccine might be a whole cell vaccine comprising multiple antigenic molecules. For example the Bacillus Calmette Guerin [“BCG”] vaccine includes an attenuated Mycobacterium bovis strain that provokes protective immunity in humans. For many pathogens chemical or heat inactivation while it may give rise to vaccine immunogens that confer protective immunity also gives rise to side effects such as fever and injection site reactions. In the case of bacteria, inactivated organisms tend to be so toxic that side effects have limited the application of such crude vaccine immunogens and therefore vaccine development has lagged behind drug-development. Moreover, effective vaccine development using whole cell inactivated organisms suffers from problems of epitope masking, immunodominance, low antigen concentration and antigen redundancy.
There is therefore a continuing need to identify antigens that are protective and can be used in multivalent vaccines of bacterial pathogens. The combinations may be used in combination with non-protein immunogenic molecules such as polysaccharide antigens and anti-bacterial agents to provide a treatment regimen for control of bacterial infection. It is also within the scope of this disclosure to modify the treatment regimen to immunize subjects with a series of temporally separated administrations as an alternative to the administration of a single vaccine comprising multiple antigens.
This disclosure therefore relates to immunogenic compositions and vaccines, typically multivalent vaccines but also monovalent vaccines and their use in the prophylaxis and treatment of bacterial infections. We disclose polypeptides that are typically membrane spanning proteins that include an extracellular domain. For example DivlB is an integral membrane protein comprising an intracellular domain, an intermembrane domain and an extracellular domain. The related gene DivlC is also an integral membrane protein the extracellular domain. This disclosure also relates to antigens encoded by the genes PheP, YdiE and FtsL each of which has an extramembranous domain. Typically, it would be desirable to develop vaccines against Gram positive bacterial pathogens which include, by example: Bacillus anthracis, Clostridium botulinum, Clostridium difficile, Enterococcus faecalis, Mycobacterium tuberculosis, Staphylococcus spp, Streptococcus group A, Streptococcus group B, Streptococcus pneumonia. Moreover the development of vaccines against Gram negative bacterial pathogens such as, Helicobacter pylori, Neisseria gonorrhoea, Neisseria meningitidis type B, Shigella flexneri, Escherichia coli, Haemophilus influenzae, Chlamydia trachomatis, Pseudomonas aeruginosa, Yersinia pestis, Burkholderia mallei or B. pseudomallei would also be desirable.
STATEMENTS OF INVENTION
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Bacillus spp genes selected from the group consisting of:

    i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 1, 2, 3, 4, 5, 6 or 7; or
    ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 112; or
    i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 144 or 145; or
    ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 158 or 159; or
    iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 168 or 169; or
    iv) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 112, 144, 145, 158, 159, 168 or 169, wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 112, 144, 145, 158, 159, 168 or 169.


A modified polypeptide or variant polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions, truncations that may be present in any combination. Among preferred variants are those that vary from a reference polypeptide by conservative amino acid substitutions. Such substitutions are those that substitute a given amino acid by another amino acid of like characteristics. The following non-limiting list of amino acids are considered conservative replacements (similar): a) alanine, serine, and threonine; b) glutamic acid and aspartic acid; c) asparagine and glutamine d) arginine and lysine; e) isoleucine, leucine, methionine and valine and f) phenylalanine, tyrosine and tryptophan. Most highly preferred are variants that retain or enhance the immunogenecity and/or activity as the reference polypeptide from which it varies.
In one embodiment, the variant polypeptides have at least 80-89% sequence identity, more preferably at least 90% identity, even more preferably at least 95% identity, still more preferably at least 97% identity, and most preferably at least 99% identity with the full length amino acid sequences illustrated herein.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Bukholderia spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 8, 9, 10, 11, 12, 13 or 14; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 113 or 114; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 8, 9, 10, 11, 12, 13, 14 or 113 wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 8, 9, 10, 11, 12, 13, 14, 113 or 114.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Bukholderia spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 15, 16, 17, 18, 19, 20 or 21; or
iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 115 or 116; or
iv) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 15, 16, 17, 18, 19, 20, 21, 115 or 116; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 15, 16, 17, 18, 19, 20, 21, 115 or 116.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Clostridium spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 22, 23, 24, 25, 26, 27 or 28; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 118; or
iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO:146 or 147; or
iv) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO:160 or 161; or
v) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 22, 23, 24, 25, 26, 27, 28, 118, 146, 147, 160 or 161 wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 22, 23, 24, 25, 26, 27, 28, 118, 146, 147, 160 or 161.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Clostridium spp genes selected from the group consisting of

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 29, 30, 31, 32, 33, 34 or 35; or
        ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 119; or
        iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO:148 or 149; or
        iv) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 29, 30, 31, 32, 33, 34, 35, 119, 148 or 149; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 29, 30, 31, 32, 33, 34, 35, 119, 148 or 149.
    
    


According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Enterococcus spp genes selected from the group consisting of
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 36, 37, 38, 39, 40, 41 or 42;
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 120 or 121; or
iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 150 or 151; or
iv) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO:162 or 163; or
v) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO:170 or 171; or
vi) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 36, 37, 38, 39, 40, 41, 42, 120, 121, 150, 151, 162, 163, 170 or 171; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 36, 37, 38, 39, 40, 41, 42, 120, 121, 150, 151, 162, 163, 170 or 171.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Escherchia spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 43, 44, 45, 46, 47, 48 or 49; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 122 or 123; or 25; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 43, 44, 45, 46, 47, 48, 49, 122 or 123; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 43, 44, 45, 46, 47, 48, 49, 122 or 123.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Haemophilus spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 50, 51, 52, 53, 54, 55 or 56; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 124 or 125; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 50, 51, 52, 53, 54, 55, 56, 124 or 125; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 50, 51, 52, 53, 54, 55, 56, 124 or 125.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Heliobacter spp genes selected from the group consisting of
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 57, 58, 59, 60, 61, 62 or 63; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 126; or
iv) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 57, 58, 59, 60, 61, 62, 63 or 126; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 57, 58, 59, 60, 61, 62, 63 or 126.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Mycobacterium spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 64, 65, 66, 67, 68, 69 or 70; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 127 or 128; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 64, 65, 66, 67, 68, 69, 70, 127 or 128; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 64, 65, 66, 67, 68, 69, 70, 127 or 128.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Shigella spp genes selected from the group consisting of
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 78, 79, 80, 81, 82, 83 or 84; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 134 or 135; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 78, 79, 80, 81, 82, 83, 84, 134 or 135; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 78, 79, 80, 81, 82, 83, 84, 134 or 135.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Streptococcus spp genes selected from the group consisting of

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 85, 86, 87, 88, 89 or 90; or
        ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO 136 or 137; or
        iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO 152 or 153; or
        iv) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO 174 ore 175; or
        v) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 85, 86, 87, 88, 89, 90, 136, 137, 152, 153, 174 or 175; wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO 85, 86, 87, 88, 89, 90, 136, 137, 152, 153, 174 or 175.
    
    


According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Yersinia spp genes selected from the group consisting of
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 91, 92, 93, 94, 95, 96 or 97; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 138 or 139; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 91, 92, 93, 94, 95, 96, 97, 138 or 139 wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 91, 92, 93, 94, 95, 96, 97, 138 or 139.
According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Streptococcus spp genes selected from the group consisting of:

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 98, 99, 100, 101, 102, 103, or 104; or
        ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 140 or 141; or
        iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 154 or 155; or
        iv) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 164 or 165; or
        v) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO 172 or 173; or
        vi) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 98, 99, 100, 101, 102, 103, 104, 140, 141, 154, 155, 164, 165, 172 or 173 wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 98, 99, 100, 101, 102, 103, 104, 140, 141, 154, 155, 164, 165, 172 or 173.
    
    


According to an aspect of the invention there is provided an immunogenic composition comprising two or more different polypeptides wherein said polypeptides are encoded by different Streptococcus spp genes selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 105, 106, 107, 108, 109, 110 or 111; or
ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 142 or 143; or
iii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 156 or 157; or
iv) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 166 or 167; or
v) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO 176 or 177; or
vi) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequences presented in SEQ ID NO: 105, 106, 107, 108, 109, 110, 111, 142, 143 156, 157, 166, 167, 176, 177, wherein said sequences are modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 105, 106, 107, 108, 109, 110, 111, 142, 143 156, 157, 166, 167, 176, 177.
According to an aspect of the invention there is provided an immunogenic composition comprising at least one Pseudomonas spp polypeptide selected from the group consisting of:

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 71; or
        ii) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 72, 73, 74, 75, 76 or 77; or
        iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequence presented in SEQ ID NO: 71, 72, 73, 74, 75, 76 or 77, wherein said sequence is modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO: 71, 72, 73, 74, 75, 76 or 77.
    
    


According to an aspect of the invention there is provided an immunogenic composition comprising at least one Chlamydia spp polypeptide selected from the group consisting of:

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 117; or
        ii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequence presented in SEQ ID NO: 117, wherein said sequence is modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO 117.
    
    


According to an aspect of the invention there is provided an immunogenic composition comprising at least one Neisseria spp polypeptide selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 130; or
iii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequence presented in SEQ ID NO: 130, wherein said sequence is modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO 130.
According to an aspect of the invention there is provided an immunogenic composition comprising least one Neisseria spp polypeptide selected from the group consisting of:
i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 131; or
ii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequence presented in SEQ ID NO: 131, wherein said sequence is modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO 131.
According to an aspect of the invention there is provided an immunogenic composition comprising at least one Pseudomonas spp polypeptide selected from the group consisting of:

    
    
        i) a polypeptide, or immunogenic fragment thereof, comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 132 or 133; or
        ii) a modified polypeptide wherein said polypeptide is a polypeptide variant of the amino acid sequence presented in SEQ ID NO: 132 or 133, wherein said sequence is modified by addition, deletion or substitution of one or more amino acid residues which modified polypeptides have retained or enhanced immunogenicity when compared to the polypeptide as represented in SEQ ID NO 132 or 133.
    
    


In a preferred embodiment of the invention said immunogenic composition comprises or consists essentially of 2, 3, 4 or 5 antigenic polypeptides.
In a preferred embodiment of the invention said composition is a vaccine composition and includes at least one carrier and/or adjuvant.
Adjuvants (immune potentiators or immunomodulators) have been used for decades to improve the immune response to vaccine antigens. The incorporation of adjuvants into vaccine formulations is aimed at enhancing, accelerating and prolonging the specific immune response to vaccine antigens. Advantages of adjuvants include the enhancement of the immunogenicity of weaker antigens, the reduction of the antigen amount needed for a successful immunisation, the reduction of the frequency of booster immunisations needed and an improved immune response in elderly and immunocompromised vaccinees. Selectively, adjuvants can also be employed to optimise a desired immune response, e.g. with respect to immunoglobulin classes and induction of cytotoxic or helper T lymphocyte responses. In addition, certain adjuvants can be used to promote antibody responses at mucosal surfaces. Aluminium hydroxide and aluminium or calcium phosphate has been used routinely in human vaccines.
Adjuvants can be classified according to their source, mechanism of action and physical or chemical properties. The most commonly described adjuvant classes are gel-type, microbial, oil-emulsion and emulsifier-based, particulate, synthetic and cytokines. More than one adjuvant may be present in the final vaccine product according to the invention. They may be combined together with a single antigen or all antigens present in the vaccine, or each adjuvant may be combined with one particular antigen. The origin and nature of the adjuvants currently being used or developed is highly diverse. For example, aluminium based adjuvants consist of simple inorganic compounds and PLG is a polymeric carbohydrate. MDP is derived from bacterial cell walls; saponins are of plant origin, squalene is derived from shark liver and recombinant endogenous immunomodulators are derived from recombinant bacterial, yeast or mammalian cells. There are several adjuvants licensed for veterinary vaccines, such as mineral oil emulsions that are too reactive for human use. Similarly, complete Freund's adjuvant, although being one of the most powerful adjuvants known, is not suitable for human use.
A carrier is an immunogenic molecule which, when bound to a second molecule augments immune responses to the latter. The term carrier is construed in the following manner. A carrier is an immunogenic molecule which, when bound to a second molecule augments immune responses to the latter. Some antigens are not intrinsically immunogenic yet may be capable of generating antibody responses when associated with a foreign protein molecule such as keyhole-limpet haemocyanin or tetanus toxoid. Such antigens contain B-cell epitopes but no T cell epitopes. The protein moiety of such a conjugate (the “carrier” protein) provides T-cell epitopes which stimulate helper T-cells that in turn stimulate antigen-specific B-cells to differentiate into plasma cells and produce antibody against the antigen.
The vaccine compositions of the invention can be administered by any conventional route, including injection, intranasal spray by inhalation of for example an aerosol or nasal drops. The administration may be, for example, intravenous, intraperitoneal, intramuscular, intracavity, subcutaneous, or intradermally. The vaccine compositions of the invention are administered in effective amounts. An “effective amount” is that amount of a vaccine composition that alone or together with further doses, produces the desired response. In the case of treating a particular bacterial disease the desired response is providing protection when challenged by an infective agent.
In a preferred embodiment of the invention said vaccine composition is adapted for administration as a nasal spray.
In a preferred embodiment of the invention said vaccine composition is provided in an inhaler and delivered as an aerosol.
The amounts of vaccine will depend, of course, on the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used sufficient to provoke immunity; that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.
The doses of vaccine administered to a subject can be chosen in accordance with different parameters, in particular in accordance with the mode of administration used and the state of the subject. In the event that a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits. In general, doses of vaccine are formulated and administered in effective immunizing doses according to any standard procedure in the art. Other protocols for the administration of the vaccine compositions will be known to one of ordinary skill in the art, in which the dose amount, schedule of injections, sites of injections, mode of administration and the like vary from the foregoing. Administration of the vaccine compositions to mammals other than humans, (e.g. for testing purposes or veterinary therapeutic purposes), is carried out under substantially the same conditions as described above. A subject, as used herein, is a mammal, preferably a human, and including a non-human primate, cow, horse, pig, sheep or goat.
In a preferred embodiment of the invention there is provided a vaccine composition according to the invention that includes at least one additional anti-bacterial agent.
In a preferred embodiment of the invention said agent is a second different vaccine and/or immunogenic agent (for example a bacterial polypeptide and/or polysaccharide antigen).
According to a further aspect of the invention there is provided a vaccine according to the invention for use in the protection or treatment of a subject animal to a microbial infection or condition that results from microbial infection.
In a preferred embodiment of the invention a bacterial pathogen that causes said microbial infection or condition is selected from the group consisting of: Bacillus anthracis, Clostridium botulinum, Clostridium difficile, Enterococcus faecalis, Mycobacterium tuberculosis, Streptococcus group A, Streptococcus group B, Streptococcus pneumonia. 
In an alternative preferred embodiment of the invention a bacterial pathogen that causes said microbial infection or condition is selected from the group consisting of: Helicobacter pylori, Neisseria gonorrhoea, Neisseria meningitidis type B, Shigella flexneri, Escherichia coli, Haemophilus influenzae, Chlamydia trachomatis, Pseudomonas aeruginosa, Yersinia pestis, Burkholderia mallei or B. pseudomallei. 
In a preferred embodiment of the invention said subject is a human.
In an alternative preferred embodiment of the invention said subject is a non-human animal, preferably a livestock animal, for example cattle.
Throughout the description and claims of this specification, the words “comprise” and “contain” and variations of the words, for example “comprising” and “comprises”, means “including but not limited to”, and is not intended to (and does not) exclude other moieties, additives, components, integers or steps
Throughout the description and claims of this specification, the singular encompasses the plural unless the context otherwise requires. In particular, where the indefinite article is used, the specification is to be understood as contemplating plurality as well as singularity, unless the context requires otherwise.
Features, integers, characteristics, compounds, chemical moieties or groups described in conjunction with a particular aspect, embodiment or example of the invention are to be understood to be applicable to any other aspect, embodiment or example described herein unless incompatible therewith.
An embodiment of the invention will now be described by example only and with reference to the following materials, methods and the sequences in Table 1.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the sequences of SEQ ID NOS.: 1-111.
FIG. 2 shows the sequences of SEQ ID NOS.: 112-143.
FIG. 3 shows the sequences of SEQ ID NOS.: 144-157.
FIG. 4 shows the sequences of SEQ ID NOS.: 158-177.



MATERIALS AND METHODS
Construction of Plasmids for the Overexpression in E. coli of the Extramembranous Fragments of the Proteins
The PheP selected peptides were synthesized and conjugated through a cysteine at its C terminal to the carrier protein KLH to undertake as a chimeric protein used in vaccinations. The extramembranous fragments of YdiE, DivlB, DivlC and FtsL were PCR amplified using oligonucleotide pairs indicated according to the following PCR reaction conditions: 1 initial denaturation cycle of 94° C. for 4 min; 30 amplification cycles of denaturation 94° C. for 30 seconds, annealing 45° C. for 30 seconds, and extension at 30 72° C. for up to 2.5 minutes; finally, ongoing amplification rounds were allow to complete at 72° C. for 4 min.
The restrictions sites were engineered within the oligonucleotides. The amplified fragments were digested with the corresponding restriction enzymes (NcoI for the 5′ end, 35 and XhoI for the 3′ end) and cloned into the equivalent sites of the pET-21d(+) expression vector from Novagen (Cat. No. 69743-3) and resulting in the overexpression plasmids generating a T7-tagged (partial, at the N-terminal) and 6xHis-tagged (at the C-terminal end) form of the extramembranous fragments. The over expression plasmids were transferred into E. coli BL21 for over expression of the recombinant protein fragment.
The cloning of the PCR amplified fragment indicated above into the recipient pET21d(+) recipient plasmid vector at the NcoI and XhoI sites entailed the addition of hinge amino acids between the T7-tag and the extramembranous fragment, and between the latter and the His-tag.
Over Expression of Polypeptide Sequences
SEQ IDs were over expressed from plasmids pGL597, pGL601, pALB26, and pALB27 in E. coli BL21 strain using Brain Heart Infusion Broth (CMO225, Oxoid, United Kingdom) in the presence of 100 ^g/ml ampicillin and the Plac promoter gratuitous inducer IPTG (Isopropyl p-D-1-thiogalactopyranoside, 1 mM) for 4 to 6 hours at 37° C. and vigorous shaking. Following harvesting of the cells by centrifugation (5,000×g for 15 minutes at 4° C.) and subsequent lysis with 1 mg/ml lysozyme in phosphate buffer (Buffer A; 0.1 M pH7.2) containing 0.5M NaCl) for one hour and subsequent sonication (3 cycles of 10 second pulses in sonicating water bath) the soluble and insoluble forms of the proteins of interest were separated by centrifugation at 13,000×g for 10 minutes. The precipitate was then resuspended in Buffer A containing 8M urea by freeze/thawing (3 cycles of freezing at −80° C. for 10 minutes and subsequent thawing to room temperature) and sonication (3 cycles of 10 second pulses in sonicating water bath), and subsequent centrifugation for 25 minutes at 18,000×g). The over expressed proteins of interest in the supernatant and the solubilised pellet were purified by initial specific binding (through their His-tag) to a nickel (NiSO4)-bound Sepharose chromatography column (Ni— Sepharose) and elution with an imidazole solution run through the column in the following stepwise manner: 5% for 5 minutes, 30% for 60 minutes, 35% for 60 minutes, 50% for 100 minutes and 55% for 100 minutes. Fractions from this stepwise elution were analysed in acrylamide denaturing gels with a 4% acrylamide/bis-acrilamide stacking layer and a 12% acrylamide/bis-acrylamide separating layer. The fractions containing the over expressed proteins of interest were pooled and dyalized against sterile phosphate buffer (8 g NaCl, 0.2 g KCl, 1.44 g Na2HPO, 0.24 g KH2PO4, per liter of distilled H2O, pH 7.4).
All the proteins of interest were successfully over expressed from the indicated strains and under the indicated conditions. They were also subsequently extracted from the total cellular protein content of the over expressing E. coli strains with more than 95% purity. Examples of the purification obtained for each of the proteins are indicated below.
Vaccination: Generic Protocol for Polyvalent Vaccines
Combination (or polyvalent) vaccines including variations of the antigens (conjugated selected PheP peptide, YdiE, DivlB, DivlC and FtsL) will follow an identical protocol with the following modifications. The vaccine priming and boost mixtures will contain rather than a single component 2 or more of the components. The total volume of mixed vaccine used for priming and boosting injections will fluctuate in a range of 50-100 microliters per animal. Similarly the total amount in each of those injections may vary between 50-100 micrograms. The amount of each antigen to contribute to the total amount of vaccine in the priming or boosting mix will vary between 20% to 80% of the total.
Vaccination: Generic Protocol for Monovalent Vaccines
The generic protocol followed for the vaccinations is as follows. Each animal was primed with 100 microliters of a solution made up of a mixture 50 micrograms of recombinant antigen in 50 microliters endotoxin-free PBS (Phosphate Buffer Saline pH 7.4) and 50 microliters of Complete Freund's adjuvant. Two weeks later the animals were boosted 25 with 100 microliters of a solution made up of a mixture 50 micrograms of recombinant protein in 50 microliters of endotoxin-free PBS and 50 microliters of Incomplete Freund's adjuvant. A week later the animals received an identical boost. In each experiment, a control group of 10 animals were treated following an identical protocol except for the fact that instead of the recombinant protein component the mixture contained commercially available KLH protein (Keyhole limpet hemocyanin). Priming and boost injections were performed intradermally in the scruff of the neck of the animals.




















Bacterial
PheP
PheP
GCP
GCP
Div1B
DIV1B
Div1C
Div1C
FtsL
FtsL


Species
FL
ECD
FL
ECD
FL
ECD
FL
ECD
FL
ECD

























Bacillus
1
2, 3, 4, 5, 6, 7
112

144
145
158
159
168
169


Anthracis












Burkholderia
8
9, 10, 11, 12,
113
114








Mallei

13, 14










Burkholderia
15
16, 17, 18, 19,
115
116








pseudomallei

20, 21










Chlamydia


117









trachomatis












Clostridium
22
23, 24, 25,
118

146
147
160
161




Botulinum

26, 27, 28










Clostridium
29
30, 31, 32,
119

148
149






Difficile

33, 34, 35










Enterococcus
36
37, 38, 39,
120
121
150
151
162
163
170
171


Faecalis

40, 41, 42










Escherichia
43
44, 45, 46,
122
123








Coli

47, 48, 49










Haemophilus
50
51, 52, 53, 54,
124
125








influenza

55, 56










Helicobacter
57
58, 59, 60,
126









Pylori

61, 62, 63










Mycobacterium
64
65, 66, 67, 68,
127
128








tuberculosis

69, 70










Pseudomonas
71
72, 73, 74,










Aeruginosa

75, 76, 77










Neisseria


130









gonorrhoeae












Neisseria


131









meningitidis












Pseudomonas


132
133








aeruginosa












Shigella
78
79, 80, 81,
134
135








flexneri

82, 83, 84










Streptococcus
85
86, 87, 88,
136
137
152
153


174
175


pneumonia

89, 90










Yersinia pestis
91
92, 93, 94, 95,
138
139










96, 97










Streptococcus
98
99, 100,
140
141
154
155
164
165
172
173


agalactiae

101, 102, 103,












104










Streptococcus
105
106, 107,
142
143
156
157
166
167
176
177


pyogenes

108, 109, 110,












111





Table 1 discloses SEQ ID NOs corresponding to antigenic polypeptides [FL = full length sequence; ECD = extracellular domain

## Claims

1. An immunogenic composition, comprising an effective amount of an adjuvant and two or more different isolated polypeptides selected from:
i) a polypeptide comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 119 or 149;
ii) an immunogenic polypeptide variant having at least 90% identity to the amino acid sequence represented in SEQ ID NO:119 or 149, which immunogenic polypeptide variants have retained immunogenicity as compared to the polypeptide having the amino acid sequence represented in SEQ ID NO: 119 or 149 respectively; and
iii) any combination of isolated polypeptides from (i) and/or (ii).

2. The immunogenic composition according to claim 1, wherein the immunogenic composition consists essentially of 3, 4 or 5 different polypeptides.

3. The immunogenic composition according to claim 1, wherein the composition further comprises at least one carrier.

4. The immunogenic composition according to claim 3, wherein the composition further comprises at least one additional anti-bacterial agent.

5. A method to immunize a subject from a Clostridium difficile infection comprising administering an effective amount of an immunogenic composition according to claim 1 to the subject.

6. An immunogenic composition, comprising (a) an effective amount of an adjuvant, (b) a first polypeptide comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 119, and (c) a second polypeptide comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 149.

7. An immunogenic composition of claim 6, wherein the first polypeptide consists of the amino acid sequence as represented in SEQ ID NO: 119, and the second polypeptide consists of the amino acid sequence as represented in SEQ ID NO: 149.

8. The immunogenic composition according to claim 6, wherein the immunogenic composition consists essentially of 3, 4, or 5 different polypeptides.

9. The immunogenic composition according to claim 1, wherein the adjuvant is a gel-type adjuvant.

10. The immunogenic composition according to claim 1, wherein the adjuvant is an aluminium based adjuvant.

11. The immunogenic composition according to claim 10, wherein the aluminium based adjuvant is aluminium hydroxide.

12. The immunogenic composition according to claim 10, wherein the aluminium based adjuvant is aluminium phosphate.

13. The immunogenic composition according to claim 6, wherein the adjuvant is a gel-type adjuvant.

14. The immunogenic composition according to claim 6, wherein the adjuvant is an aluminium based adjuvant.

15. The immunogenic composition according to claim 14, wherein the aluminium based adjuvant is aluminium hydroxide.

16. The immunogenic composition according to claim 14, wherein the aluminium based adjuvant is aluminium phosphate.

17. The immunogenic composition according to claim 1, wherein the immunogenic polypeptide variant has at least 95% identity to the amino acid sequence represented in SEQ ID NO: 119 or 149.

18. The immunogenic composition according to claim 1, wherein the immunogenic polypeptide variant has 99% identity to the amino acid sequence represented in SEQ ID NO: 119 or 149.

19. The method according to claim 5, wherein the immunogenic composition consists essentially of 3, 4, or 5 different polypeptides.

20. The method according to claim 5, wherein the two or more different isolated polypeptides of the immunogenic composition comprise a first polypeptide comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 119, and a second polypeptide comprising or consisting of the amino acid sequence as represented in SEQ ID NO: 149.