# Patent

## Title
Chlamydial antigens

## Abstract

The invention is in the field of immunology and vaccinology. In particular, it relates to antigens derived from Chlamydia trachomatis that are expressed on the cell surface and so are ideal for use in immunization as well as combinations of these antigens.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a 35 U.S.C. §371 filing of PCT/IB2006/004121, filed Dec. 19, 2006. PCT/IB2006/004121 claims the benefit of U.S. Provisional Patent Application No. 60/753,305, filed Dec. 22, 2005 and U.S. Provisional Patent Application No. 60/795,857, filed Apr. 28, 2006. The disclosures of the aforementioned applications are incorporated by reference in their entireties for all purposes.


All documents cited herein are incorporated by reference in their entirety.
TECHNICAL FIELD
This invention is in the fields of immunology and vaccinology. In particular, it relates to antigens derived from Chlamydia trachomatis and their use in immunisation.
BACKGROUND ART
The Chlamydiae are obligate intracellular parasites of eukaryotic cells which are responsible for endemic sexually transmitted infections and various other disease syndromes. They occupy an exclusive eubacterial phylogenic branch, having no close relationship to any other known organisms. A particular characteristic of the Chlamydiae is their unique life cycle, in which the bacterium alternates between two morphologically distinct forms: an extracellular infective form (elementary bodies, EB) and an intracellular non-infective form (reticulate bodies, RB). The life cycle is completed with the re-organization of RB into EB, which leave the disrupted host cell ready to infect further cells.
The genome sequences of at least five Chlamydia trachomatis or chlamydophila species are currently known—C. trachomatis, C. pneumoniae, C. muridarum, C. pecorum and C. psittaci [1, 7]. The various C. trachomatis strains, of which there are currently at least 18 serovariants (serovars), may be classified according to their serological reactivities with polyclonal or monoclonal antisera. These serological differences are typically detected due to differences in the MOMP (Major Outer Membrane Protein) of C. trachomatis. 
Although Chlamydia infection itself causes disease, it is thought that the severity of symptoms in some patients is actually due to an aberrant or an altered host immune response which may arise from either (i) the nature of the invading Chlamydia organism which may vary from serovar to serovar or (ii) the nature of the subject invaded (for example, the nature of the patient profile). The failure to clear the infection results in persistent immune stimulation and, rather than helping the host, this results in chronic infection with severe consequences, including sterility and blindness [8]. In addition, the protection conferred by natural Chlamydial infection is usually incomplete, transient, and strain-specific.
Unfortunately the major determinants of Chlamydia pathogenesis are complicated and at present still unclear, mostly due to the intrinsic difficulty in working with this pathogen and the lack of adequate methods for its genetic manipulation. In particular very little is known about the antigenic composition of elementary body surface, that is an essential compartment in pathogen-host interactions, and likely to carry antigens able to elicit a protective immune response.
Due to the serious nature of the disease, there is a desire to provide suitable immunogenic compositions, such as vaccines to deal with an aberrant or altered host cell immune response which may result from, for example, allelic variation in the invading Chlamydia strain and/or aberrant or altered forms of Chlamydia invading strain. These immunogenic compositions may be useful (a) for immunisation against Chlamydial infection or against Chlamydia-induced disease (prophylactic vaccination) or (b) for the eradication of an established chronic Chlamydia infection (therapeutic vaccination). Being an intracellular parasite, however, the bacterium can generally evade antibody-mediated immune responses.
Various antigenic proteins have been described for C. trachomatis, and the cell surface in particular has been the target of detailed research [9]. These include, for instance, Pgp3 [10, 11, and 12], MOMP [13], Hsp60 (GroEL) [14] and Hsp70 (DnaK-like) [15]. Not all of these have proved to be effective vaccines, however, and further candidates have been identified [16]. Compositions comprising combinations of C. trachomatis antigens are described in reference 17.
Vaccines against pathogens such as hepatitis B virus, diphtheria and tetanus typically contain a single protein antigen (e.g. the HBV surface antigen, or a tetanus toxoid). In contrast, acellular whooping cough vaccines typically have at least three B. pertussis proteins, and the PrevnarTM pneumococcal vaccine contains seven separate conjugated saccharide antigens. Other vaccines such as cellular pertussis vaccines, the measles vaccine, the inactivated polio vaccine (IPV) and meningococcal OMV vaccines are by their very nature complex mixtures of a large number of antigens. Whether protection can be elicited by a single antigen, a small number of defined antigens, or a complex mixture of undefined antigens, therefore depends on the pathogen in question.
It is an object of the invention to provide further and improved immunogenic compositions for providing immunity against Chlamydial disease and/or infection. In particular, it is an object of the invention to provide improved immunogenic compositions for providing immunity against aberrant or altered Chlamydia serovar strains (e.g. strains such as allelic variant strains).
It is an object of the invention to provide further and improved compositions for providing immunity against chlamydial disease and/or infection. The compositions are based on a newly discovered, surface-exposed C. trachomatis antigens.
DISCLOSURE OF THE INVENTION
Within the  ̃900 proteins described for the C. trachomatis genome of reference 4, the applicant has discovered a group of twenty Chlamydia trachomatis surface-exposed antigens, surface-associated antigens and fragments thereof that are particularly suitable for immunisation purposes, particularly when used in combinations. These antigens which are exposed on the surface of Chlamydia trachomatis have been identified using “surface shaving” techniques. Until now, surface proteins of Chlamydia trachomatis have been detected by indirect methods [18], but here we describe the use of a method which identifies one or more surface-exposed and/or surface associated antigens from the surface of a Chlamydia Elementary Body (EB) and fragments of these antigens. The invention therefore provides a composition comprising a combination of Chlamydia trachomatis antigens, said combination consisting of two or more (i.e. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or all 20) Chlamydia trachomatis antigens of a first antigen group, said first antigen group consisting of: (1) a GroEL-1 antigen, (2) a DnaK antigen, (3) an Ef-Tu antigen, (4) a Mip-like protein antigen, (5) a Major outer membrane protein (MOMP) antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (10) a Tarp antigen, (11) a Rs10 antigen, (12) an OmpH-like protein antigen, (13) a Rs13 antigen, (14) a R11 antigen, (15) a CT875 antigen, (16) a HtrA antigen, (17) a RpoA antigen, (18) a PepA antigen, (19) an Alanyl tRNA synthetase antigen, (20) a RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and (26) a CT814 antigen. These antigens are referred to herein as the ‘first antigen group’.
A preferred subgroup of the first antigen group consists of: (1) a GroEL-1 antigen, (2) a DnaK antigen, (3) an Ef-Tu antigen, (4) a Mip-like protein antigen, (5) a Major outer membrane protein (MOMP) antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (10) a Tarp antigen, (11) a Rs10 antigen, (12) an OmpH-like protein antigen, (13) a Rs13 antigen, (14) a R11 antigen, (15) a CT875 antigen, (16) a HtrA antigen, (17) a RpoA antigen, (18) a PepA antigen, (19) an Alanyl tRNA synthetase antigen and (20) a RpoC antigen.
A further preferred subgroup of the first antigen group consists of: (1) a GroEL-1 antigen, (3) an Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) a Rs10 antigen, (13) a Rs13 antigen, (14) a R11 antigen, (15) a CT875 antigen, (17) a RpoA antigen, (19) an Alanyl tRNA synthetase antigen and (20) a RpoC antigen.
A further preferred subgroup of the first antigen group consists of (1) a GroEL-1 antigen, (3) an Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) a Rs10 antigen, (13) a Rs13 antigen, (14) a R11 antigen, (15) a CT875 antigen, (17) a RpoA antigen, (19) an Alanyl tRNA synthetase antigen, (20) a RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and (26) a CT814 antigen.
A further preferred subgroup consists of (7) a CT577 antigen, (8) a CT223 antigen, (15) a CT875 antigen, (9) a GroeS antigen and (13) a Rs13 antigen.
A further preferred subgroup of the first antigen group consists of (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and (26) a CT814 antigen.
Reference to the ‘first antigen group’ herein includes reference to the first antigen group itself as well as the preferred subgroups.
The efficacy of a composition of Chlamydia trachomatis antigens may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other known Chlamydia trachomatis antigens include a second antigen group consisting of: (1) a LcrE antigen; (2) an ArtJ antigen; and (3) a CT398 antigen. These antigens are referred to herein as the ‘second antigen group’.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and one, two or three Chlamydia trachomatis antigens of the second antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other known Chlamydia trachomatis antigens include a third antigen group consisting of: (1) a L7/L12 antigen; (2) an OmcA antigen; (3) an AtoS antigen; (4) a CT547 antigen; (5) an Eno antigen; and (6) a MurG antigen. These antigens are referred to herein as the ‘third antigen group’.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and one, two, three, four, five or six Chlamydia trachomatis antigens of the third antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other known Chlamydia trachomatis antigens include a fourth antigen group consisting of: (1) a PGP3 antigen, (2) one or more PMP antigens, (3) a Cap1 antigen (CT529); (4) a GroEL-like hsp60 protein (Omp2) antigen; and (5) a 60 kDa Cysteine rich protein (omcB) antigen. These antigens are referred to herein as the ‘fourth antigen group’.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and one, two, three, four or five Chlamydia trachomatis antigens of the fourth antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens of known and unknown biological function may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other Chlamydia trachomatis antigens of known and unknown biological function include a fifth antigen group consisting of: (1) a YscJ antigen; (2) a Pal antigen; (3) a CHLPN 76 kDA homologue antigen; (4) a CT700 antigen; (5) a CT266 antigen; (6) a CT077 antigen; (7) a CT165 antigen and (8) a PorB antigen. These antigens are referred to as the “fifth antigen group”.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and one, two, three, four, five, six, seven or eight Chlamydia trachomatis antigens of the fifth antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens of known and unknown biological function may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other Chlamydia trachomatis antigens of known and unknown biological function include a sixth antigen group consisting of: (1) a CT082 antigen; (2) a CT181 antigen; (3) a CT050 antigen; (4) a Phospholipase D superfamily antigen; and (5) an AdK adenylate cyclase antigen. These antigens are referred to as the “sixth antigen group”.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and one, two, three, four or five Chlamydia trachomatis antigens of the sixth antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens of known and unknown biological function may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other Chlamydia trachomatis antigens of known and unknown biological function include a seventh antigen group consisting of (1) a CT153 antigen; (2) a CT262 antigen; (3) a CT276 antigen; (4) a CT296 antigen; (5) a CT372 antigen; (6) a PmpA antigen; (7) an OligoPeptide Binding Protein antigen; (8) a CT548 antigen; (9) a CT043 antigen; (10) a CT635 antigen; (11) a CT859 (Metalloprotease) antigen; (12) a CT671 antigen; (13) a CT016 antigen; (14) a CT017 antigen; (15) a PmpD antigen and (16) a PmpE antigen. These antigens are referred to as the “seventh antigen group”. The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all 16) Chlamydia trachomatis antigens of the seventh antigen group.
The efficacy of a composition of Chlamydia trachomatis antigens of known and unknown biological function may be improved by combination with one or more Chlamydia trachomatis antigens from the first antigen group. Such other Chlamydia trachomatis antigens of known and unknown biological function include a eighth antigen group consisting of (1) a GatA antigen, (2) a GatB antigen, (3) a CT005 antigen, (4) a CT042 antigen, (5) a sucB1 antigen, (6) a CT113 antigen, (7) an Rs9 antigen, (8) a DhnA antigen, (9) an AcpP antigen, (10) a HimD antigen, (11) a Tal antigen, (12) a DksA antigen, (13) a CT425 antigen, (14) a Ym74 antigen, (15) a Rl15 antigen, (16) a Rs5 antigen, (17) a Rl6 antigen, (18) a Rl24 antigen, (19) a Rl22 antigen, (20) a Rl2 antigen, (21) a Rl4 antigen, (22) a LerH1 antigen, (23) an AhpC antigen, (24) a CT610 antigen, (25) a CT622 antigen, (26) a CT664 antigen, (27) a FliN antigen, (28) a PyrH antigen, (29) a CT741 antigen, (30) a Efp2 antigen, (31) a CT768 antigen, (32) a CT771 antigen, (33) a Ldh antigen, (34) a Rl35 antigen, (35) a FtsH antigen and (36) a Pnp antigen. These antigens are referred to as the “eighth antigen group”.
The invention thus includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group and of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or all 36) Chlamydia trachomatis antigens of the eighth antigen group.
The invention includes a composition comprising a combination of Chlamydia trachomatis antigens, said combination selected from the group consisting of one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) antigens of the first antigen group and “A” antigens from the second antigen group, “B” antigens from the third antigen group, “C” antigens from the fourth antigen group, “D” antigens from the fifth antigen group, “E” antigens from the sixth antigen group and “F” antigens from the seventh antigen group, wherein

    
    
        A=0-3, B=0-6, C=0-5, D=0-8, E=0-5 and F=0-16, and A+B+C+D+E+F>1 (i.e. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42 or 43).
    
    


Such a composition may optionally comprise “G” antigens from the eighth antigen group, wherein G=0-36, and A+B+C+D+E+F+G>1 (i.e. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78 or 79).
Thus the compositions comprise at least one antigen from the first antigen group and at least one antigen from any one or more of the second to seventh groups. The compositions may comprise more than one antigen from a given group or no antigens from one or more of the second to seventh groups. However, where the composition only contains a single antigen from the first group, it must also contain at least one antigen from one or more of the second to seventh, or eighth groups. Preferably, the compositions comprise two, three, four or five Chlamydia trachomatis antigens of the first antigen group. Still more preferably, the composition comprises of five Chlamydia trachomatis antigens of the first antigen group. Preferably, the composition consists of five Chlamydia trachomatis antigens of the first antigen group.
There is an upper limit to the number of Chlamydia trachomatis antigens which will be in the compositions of the invention. Preferably, the number of Chlamydia trachomatis antigens in a composition of the invention is less than 20, less than 19, less than 18, less than 17, less than 16, less than 15, less than 14, less than 13, less than 12, less than 11, less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, or less than 3. Still more preferably, the number of Chlamydia trachomatis antigens in a composition of the invention is less than 6, less than 5, or less than 4. The Chlamydia trachomatis antigens used in the invention are preferably isolated, i.e., separate and discrete, from the whole organism with which the molecule is found in nature or, when the polynucleotide or polypeptide is not found in nature, is sufficiently free of other biological macromolecules so that the polynucleotide or polypeptide can be used for its intended purpose.
First Antigen Group
(1) GroEL-1 One example of “GroEL-1” is disclosed as CT110 in reference 19 (GenBank accession number: AAC67701, GenInfo Identifier: 3328508; Hsp-60; SEQ ID NO: 1 herein). GroEL is a chaparone of the Hsp-60 class, known as chaperonins. GroEL is able to catalyse the unfolding of small proteins.
Preferred GroEL proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 1; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 1, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These GroEL-1 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 1. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 1. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 1. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 2-8 and 130-136, which consist of amino acids 85-105, 182-197, 287-308, 309-319, 328-339, 381-390, 485-500, 59-75, 106-117, 143-168, 172-181, 352-362, 463-474 and 475-484 of CT110 respectively.
(2) DnaK One example of a DnaK protein is disclosed as SEQ ID NOs: 107 & 108 in reference 16 (GenBank accession number: AAC67993, GenInfo Identifier:3328822; CT396; Hsp-70; SEQ ID NO: 9 herein). Other DnaK sequences are disclosed in references 20, 21 and 22.
Preferred DnaK proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 9; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 9, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These DnaK proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 9. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 9. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 9. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The DnaK may be phosphorylated e.g. at a threonine or a tyrosine. Particularly preferred fragments are those recited in SEQ ID NOs: 10-13 and 149-151, which consist of amino acids 112-125, 269-292, 327-343, 362-385, 81-90, 82-90 and 171-186 of DnaK respectively.
(3) Ef-Tu One example of a “Ef-Tu” protein is disclosed as CT322 in reference 19 (Genbank accession number AAC67915, GenInfo Identifier:3328740; SEQ ID NO: 14 in the attached sequence listing). It is an elongation factor protein that assists aa-tRNAs during protein synthesis.
Preferred Ef-Tu proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 14; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 14, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Ef-Tu proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 14. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 14. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 14. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 15, 16 and 143-148, which consist of amino acids 178-188, 191-205, 46-57, 60-75, 137-162, 206-224, 253-263 and 271-280 of CT322 respectively.
(4) Mip-like One example of a “Mip-like” protein is disclosed as SEQ ID NOs: 149 & 150 in reference 16 (GenBank accession number: AAC68143, GenInfo Identifier:3328979; CT541; SEQ ID NO: 17 herein).
Preferred Mip-like proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 17; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 17, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Mip proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 17. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 17. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 17. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 18, 19 and 160, which consist of amino acids 34-46, 62-74 and 75-94 of CT541 respectively.
(5) Major Outer Membrane Protein—MOMP One example of a MOMP sequence is disclosed as SEQ ID Nos: 155 and 156 in reference 16 (GenBank accession number AAC68276, GenInfo Identifier:3329133; CT681; SEQ ID NO: 20 herein). This protein is thought to function in vivo as a porin [23], and to be present during the whole life cycle of the bacteria [24]. MOMP displays four variable domains (VD) surrounded by five constant regions that are highly conserved among serovars [25, 26]. In vitro and in vivo neutralizing B-cell epitopes have been mapped on VDs [27-31]. T-cell epitopes have been identified in both variable and constant domains [32, 33].
Preferred MOMP proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 20; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 20, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These MOMP proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 20. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 20, preferably one or more of the B cell or T cell epitopes identified above. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 20. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Other preferred fragments include one or more of the conserved constant regions identified above. A particularly preferred fragment is that recited in SEQ ID NO: 21, which consists of amino acids 309-330 of CT681.
(6) HctA One example of a Histone-like developmental protein is disclosed in reference 4 (GenBank accession number AAC68338, Geninfo Identifier:3329202; CT743; SEQ ID NO: 22 herein).
Preferred HctA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 22; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 22, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These HctA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 22. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 22. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 22. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 23, which consists of amino acids 10-23 of CT743.
(7) CT577 CT577 protein is disclosed in reference 7 (GenBank accession number AAC68179, GenInfo Identifier:3329019; SEQ ID NO: 24 herein). A biological function for CT577 has not previously been described. However, it is postulated that CT577 forms part of a Type Three Secretion System (TTSS).
Preferred CT577 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 24; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 24, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT577 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 24. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 24. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 24. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 25 and 163, which consist of amino acids 63-81 and 89-105 of CT577 respectively.
(8) CT223 CT223 protein is disclosed in reference 7 (GenBank accession number AAC67815, GenInfo:3328632; SEQ ID NO: 26 herein). A biological function for CT223 has not previously been described.
Preferred CT223 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 26; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 26, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT223 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 26. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 26. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 26. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 27, which consists of amino acids 113-124 of CT223.
(9) GroES One example of a GroES chaperonin protein is disclosed in reference 4 (GenBank accession number AAC67702, GenInfo Identifier:3328509; CT111; SEQ ID NO: 28 herein).
Preferred GroES proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 28; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 28, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT111 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 28. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 28. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 28. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 29, which consists of amino acids 59-76 of CT111.
(10) Tarp One example of a Tarp protein is disclosed as SEQ ID NOs: 255 & 256 in [16] (GenBank accession number AAC68056, GenInfo Identifier:3328889; CT456; SEQ ID NO: 30 herein). Tarp is also known as CT456 [34].
Preferred Tarp proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 30; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 30, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Tarp proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 30. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 30. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 30. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 31, 155 and 156, which consist of amino acids 166-178, 179-197 and 279-298 of Tarp respectively.
(11) Rs10 One example of an “RS10” protein (a S10 Ribosomal Protein) is disclosed in reference 4 (GenBank accession number AAC68035, GenInfo Identifier:3328867; CT436; SEQ ID NO: 32 herein).
Preferred Rs10 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 32; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 32, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Rs10 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 32. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 32. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 32. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 33, which consists of amino acids 14-32 of Rs10.
(12) OmpH-like One example of ‘OmpH-like’ protein is disclosed as SEQ ID NOs: 57 & 58 in reference 16 (GenBank accession number: AAC67835, GenInfo Identifier:3328652; CT242; SEQ ID NO: 34 herein).
Preferred OmpH-like proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 34; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 34, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These OmpH-like proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 34. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 34. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more; preferably 19 or more, to remove the signal peptide) from the N-terminus of SEQ ID NO: 34. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide as described above, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 35 and 138, which consist of amino acids 62-72 and 73-91 of OmpH respectively.
(13) Rs13 One example of an “Rs13” protein (S13 Ribosomal Protein) is disclosed in reference 4 (GenBank accession number AAC68110, Geninfo Identifier:3328946; CT509; SEQ ID NO: 36 herein).
Preferred Rs13 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 36; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 36, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Rs13 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 36. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 36. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 36. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 37, which consists of amino acids 45-55 of Rs13.
(14) R11 One example of an “R11” protein is disclosed in reference 4 (GenBank accession number AAC67911, GenInfo Identifier:3328735; CT318; SEQ ID NO: 38 herein).
Preferred R11 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 38; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 38, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These R11 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 38. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 38. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 38. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 39 and 142, which consist of amino acids 38-47 and 20-31 of R11 respectively.
(15) CT875 CT875 is disclosed in reference 4 (GenBank accession number AAC68473, GenInfo Identifier:3329351; SEQ ID NO: 40 herein). A biological function for CT875 has not previously been described.
Preferred CT875 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 40; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 40, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT875 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 40. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 40. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 40. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 41 and 167-172, which consist of amino acids 52-75, 159-176, 293-308, 336-346, 433-447, 556-567 and 521-567 of CT875 respectively.
(16) HtrA One example of an ‘HtrA’ protein is disclosed as SEQ ID NOs: 229 & 230 in reference 16 (GenBank accession number: AAC68420, GenInfo Identifier:3329293; CT823; DO Serine protease; SEQ ID NO: 42 herein).
Preferred HtrA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 42; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 42, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These HtrA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 42. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 42. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more; preferably at least 16 to remove the signal peptide) from the N-terminus of SEQ ID NO: 42. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide as described above, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 43, which consists of amino acids 475-489 of HtrA. The preferred fragment recited in SEQ ID NO: 43 is predicted to comprise two CD4+ Th1 epitopes. These epitopes are NVLLMVSQG (SEQ ID NO: 261) and DVVRFIVLK (SEQ ID NO: 262). See also the examples and FIG. 10.
(17) RpoA (RNA polymerase alpha) One example of an ‘RpoA’ protein is disclosed as spot 24 in reference 19 (GenBank accession number: AAC68108, GenInfo Identifier:3328944; CT507; SEQ ID NO: 44 herein).
Preferred RpoA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 44; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 44, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These RpoA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 44. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 44. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more; preferably at least 16 to remove the signal peptide) from the N-terminus of SEQ ID NO: 44. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide as described above, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 45 and 157-159, which consist of amino acids 21-33, 216-224, 225-235 and 342-359 of RpoA respectively.
(18) PepA (Leucyl aminopeptidase) One example of a ‘PepA’ protein is disclosed as SEQ ID NOs: 71 & 72 in reference 16 (GenBank accession number: AAC67636, GenInfo Identifier:3328437; CT045; SEQ ID NO: 46 herein). It is believed to catalyse the removal of unsubstituted N-terminal amino acids from various polypeptides.
Preferred PepA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 46; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 46, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These PepA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 46. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 46. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 46. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 47 and 129, which consists of amino acids 184-197 and 399-413 of PepA respectively.
The PepA protein may contain manganese ions.
(19) Alanyl tRNA synthetase One example of an alanyl tRNA synthetase is disclosed in reference 4 (GenBank accession number AAC68344, GenInfo Identifier:6578113; CT749; SEQ ID NO: 48 herein).
Preferred Alanyl tRNA synthetase proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 48; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 48, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT749 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 48. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 48. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 48. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 49, which consists of amino acids 600-616 of CT749.
(20) RpoC (RNA polymerase beta) One example of an ‘RpoC’ protein is disclosed in reference 4 (GenBank accession number AAC67907, GenInfo Identifier:3328731; CT314; SEQ ID NO: 50 herein).
Preferred RpoC proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 50; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 50, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT314 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 50. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 50. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 50. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 51, 139 and 140, which consist of amino acids 407-420, 263-273 and 347-362 of CT314 respectively.
(21) YaeL (Metalloprotease) One example of a ‘YaeL’ protein is disclosed in reference 4 (GenBank accession number: AAC67663, GenInfo Identifier: 3328467; CT072; SEQ ID NO: 105 herein).
Preferred YaeL proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 105; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 105, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YaeL proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 105. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 105. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6; 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 105. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 106, which consists of amino acids 232-244 of YaeL.
(22) EF-G (Elongation factor G) One example of an ‘EF-G’ protein is disclosed in reference 4 (GenBank accession number: AAC68036, GenInfo Identifier: 3328868; CT437; SEQ ID NO: 107 herein).
Preferred EF-G proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 107; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 107, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These EF-G proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 107. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 107. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 107. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 108, 109, 110 and 111, which consist of amino acids 141-153, 300-310, 428-443 and 234-251 of EF-G respectively.
(23) CT578 CT578 is disclosed in reference 4 (GenBank accession number AAC68180, GenInfo Identifier: 3329020; SEQ ID NO: 112 herein). A biological function for CT578 has not previously been described. However, it is postulated that CT576 forms part of a Type Three Secretion System (TTSS).
Preferred CT578 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%; 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 112; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 112, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT578 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 112. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 112. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 112. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 113, 114, 115 and 116, which consists of amino acids 70-91, 92-107, 108-120 and 454-467 of CT578 respectively.
(24) CT579 CT579 is disclosed in reference 4 (GenBank accession number AAC68181, GenInfo Identifier: 3329021; SEQ ID NO: 117 herein). A biological function for CT579 has not previously been described. However, it is postulated that CT576 forms part of a Type Three Secretion System.
Preferred CT579 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 117; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 117, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT579 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 117. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 117. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 117. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 118, 119, 120, 121, 122 and 123, which consists of amino acids 108-133, 231-251, 271-285, 252-270, 286-296 and 305-322 of CT579 respectively.
(25) Rs2 (S2 ribosomal protein) One example of an ‘Rs2’ protein is disclosed in reference 4 (GenBank accession number: AAC68275, GenInfo Identifier: 3329132; CT680; SEQ ID NO: 124 herein).
Preferred Rs2 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 124; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 124, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Rs2 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 124. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 124. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 124. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 125, which consists of amino acids 120-133 of Rs2.
(26) CT814 CT814 is disclosed in reference 4 (GenBank accession number AAC68410, GenInfo Identifier: 3329282; SEQ ID NO: 126 herein). A biological function for CT814 has not previously been described.
Preferred CT814 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 126; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 126, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT814 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 126. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 126. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 126. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 127, which consists of amino acids 118-131 of CT814.
Second Antigen Group
(1) LcrE low calcium response E protein (CT089) One example of a ‘LcrE’ protein is disclosed as SEQ ID NOs: 61 & 62 in WO 03/049762 (GenBank accession number: AAC67680, GenInfo Identifier:3328485; ‘CT089’; SEQ ID NO: 52 herein). Preferred LcrE proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 52; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 52, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These LcrE proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 52. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 52. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 52. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(2) ArtJ arginine-binding protein (CT381) One example of an ‘ArtJ’ protein is disclosed as SEQ ID NOs: 105 & 106 in WO 03/049762 (GenBank accession number: AAC67977, GenInfo Identifier:3328806; ‘CT381’; SEQ ID NO: 53 herein). Preferred ArtJ proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 53; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 53, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These ArtJ proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 53. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 53. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 53. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The ArtJ protein may be bound to a small molecule like arginine or another amino acid.
(3) CT398 protein One example of a ‘CT398’ protein is disclosed as SEQ ID NOS: 111 & 112 in WO 03/049762 (GenBank accession number: AAC67995, GenInfo Identifier:3328825; SEQ ID NO: 54 herein). A biological function for CT398 has not previously been described.
Preferred CT398 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 54; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 54, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT398 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 54. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 54. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 54. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 152, which consists of amino acids 130-151 of CT398.
Third Antigen Group
(1) L7/L12 ribosomal protein (CT316) One example of an ‘L7/L12’ protein is deposited in GenBank under accession number AAC67909 (GenInfo Identifier:3328733; ‘CT316’; SEQ ID NO: 55 herein).
Preferred L7/L12 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 55; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 55, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These L7/L12 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 55. Preferred fragments of (b) comprise an epitope from SEQ ID NO 55. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 55. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The L7/L12 protein may be N-terminally modified. A particularly preferred fragment is that recited in SEQ ID NO: 141, which consists of amino acids 32-73 of CT316.
(2) OmcA cysteine-rich lipoprotein (CT444) One example of an ‘OmcA’ protein is disclosed as SEQ ID NOs: 127 & 128 in WO 03/049762 (GenBank accession number: AAC68043, GenInfo Identifier:3328876; ‘CT444’, ‘Omp2A’, ‘Omp3’; SEQ ID NO: 56 herein). A variant sequence is disclosed in reference 35.
Preferred OmcA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 56; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 56, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These OmcA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 56. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 8. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more; preferably 18 or more to remove the signal peptide) from the N-terminus of SEQ ID NO: 56. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide as described above, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The protein may be lipidated (e.g. by a N-acyl diglyceride), and may thus have a N-terminal cysteine.
(3) AtoS two-component regulatory system sensor histidine kinase protein (CT467) One example of an ‘AtoS’ protein is disclosed as SEQ ID NOs: 129 & 130 in reference 36 (GenBank accession number: AAC68067, GenInfo Identifier:3328901; ‘CT467’; SEQ ID NO: 57 herein).
Preferred AtoS proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 57; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 57, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These AtoS proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 57. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 57. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 57. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(4) CT547 protein (Hypothetical Protein) One example of ‘CT547’ protein is disclosed as SEQ ID NOs: 151 & 152 in reference 36 (GenBank accession number: AAC68149, GenInfo Identifier:3328986; SEQ ID NO: 58 herein).
Preferred CT547 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 58; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 58, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT547 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 58. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 58. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 58. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(5) Enolase (2-phosphoglycerate dehydratase) protein (CT587) One example of an ‘Eno’ protein is disclosed as SEQ ID NOs: 189 & 190 in reference 36 (GenBank accession number: AAC68189, GenInfo Identifier:3329030; ‘CT587’; SEQ ID NO: 59 herein).
Preferred Eno proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 59; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 59, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Eno proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 59. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 59. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15; 20, 25 or more) from the N-terminus of SEQ ID NO: 59. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The Eno protein may contain magnesium ions, and may be in the form of a homodimer. Particularly preferred fragments are those recited in SEQ ID NOs: 164 and 165, which consist of amino acids 365-386 and 402-423 of CT587 respectively.
The preferred fragments recited in SEQ ID NOs: 164 and 165 are predicted to comprise seven and two CD4+ Th1 epitopes respectively. These epitopes are LSHRSGETE (SEQ ID NO: 263), SGETEDTTI (SEQ ID NO: 264), IADLAVAFN (SEQ ID NO: 265), LAVAFNTGQ (SEQ ID NO: 266), VAFNTGQIK (SEQ ID NO: 267), FNTGQIKTG (SEQ ID NO: 268) and TGQIKTGSL (SEQ ID NO: 269) for SEQ ID NO: 164 and YNRLMAIEE (SEQ ID NO: 270) and RIAKYNRLM (SEQ ID NO: 271) for SEQ ID NO: 165. See also the examples and FIG. 10.
(6) MurG peptidoglycan transferase protein (CT761) One example of a ‘MurG’ protein is disclosed as SEQ ID NOs: 217 & 218 in reference 36 (GenBank accession number: AAC68356, GenInfo Identifier:3329223; ‘CT761’; SEQ ID NO: 60 herein). It is a UDP-N-acetylglucosamine-N-acetylmuramyl(pentapeptide)pyrophosphoryl undecaprenol-N-acetylglucosamine transferase.
Preferred MurG proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 60; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 60, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These MurG proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 60. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 60. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 60. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide as described above, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). The MurG may be lipidated e.g. with undecaprenyl.
Fourth Antigen Group
(1) Plasmid Encoded Protein (PGP3, P-glycoprotein) One example of PGP3 sequence is disclosed in, for example, at Genbank entry GenInfo Identifier: 121541. Immunization with PGP3 is discussed in [37] and [38]. One example of a PGP3 protein is described herein as SEQ ID NO: 61.
Preferred PGP3 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 61; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 61, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These PGP3 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 61. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 61. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 61. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(2) Polymorphic Membrane Proteins (PMP) A family of nine Chlamydia trachomatis genes encoding predicted polymorphic membrane proteins (PMP) have been identified (pmpA to pmpI). See reference 4, specifically FIG. 1. Examples of amino acid sequences of the PMP genes are set forth as SEQ ID NOS: 62-70. (These sequences can also be found in Genbank—GenInfo Identifier nos. 15605137 (pmpA), 15605138 (pmpB—CT413), 15605139 (pmpC—CT414), 15605546 (pmpD), 15605605 (pmpE), 15605606 (pmpF), 15605607 (pmpG), 15605608 (pmpH), and 15605610 (pmpI)). These PMP genes encode relatively large proteins (90 to 187 kDa in mass). The majority of these PMP proteins are predicted to be outer membrane proteins, and are thus also referred to as Predicted Outer Membrane Proteins. As used herein, PMP refers to one or more of the Chlamydia trachomatis pmp proteins (pmpA to pmpI) or an immunogenic fragment thereof. Preferably, the PMP protein used in the invention is pmpE or pmpI. Preferably, the PMP protein used in the invention comprises one or more of the fragments of pmpE or pmpI identified in International Patent Application PCT/US01/30345 (WO 02/28998) in Table 1 on page 20 (preferred fragments of pmpE) or Table 2 on page 21 (preferred fragments of pmpI).
Preferred PMP proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to one of the polypeptide sequences set forth as SEQ ID NOS: 62-70; and/or (b) which is a fragment of at least n consecutive amino acids of one of the polypeptide sequences set forth as SEQ ID NOS: 62-70, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These PMP proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of the polypeptide sequences set forth as SEQ ID NOS: 62-70. Preferred fragments of (b) comprise an epitope from one of the polypeptide sequences set forth as SEQ ID NOS: 62-70. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of one of the polypeptide sequences set forth as SEQ ID NOS: 62-70. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 257 and 258, which consist of amino acids 208-233 of CT413 and 1377-1392 of CT414 respectively.
(3) Cap1 (CT529) The Chlamydia trachomatis Cap1 protein corresponds with the hypothetical open reading frame CT529 and refers to Class I Accessible Protein-1 [39] (see also GenBank accession number NP—220044; GI:15605258. One example of a Cap1 protein is referred to herein as SEQ ID NO: 71. Predicted T-cell epitopes of Cap1 are identified in this reference as SEQ ID NO: 72 CSFIGGITYL, preferably SEQ ID NO: 73 SFIGGITYL, and SEQ ID NO: 74 SIIGGITYL.
Preferred Cap1 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 71; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 71, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Cap1 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 71. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 71. Preferred T-cell epitopes include one or more of the T-cell epitopes identified above. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 71. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(4) GroEL-like hsp60 protein One example of a Chlamydia trachomatis GroEL-like hsp60 protein is set forth herein as SEQ ID NO: 75 (see also GenBank accession number NP—219613; GenInfo Identifier: 15604829). The role of Hsp60 in chlamydial infection is further described in, for example, [40-44]. Immunization of guinea pig models with recombinant Hsp60 is described in reference 45. B-cell epitopes of Hsp60 are identified in reference 46.
Preferred hsp60 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 75; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 75, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These hsp60 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 75. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 75, including one or more of the epitopes identified in the references discussed above. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 75. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Other preferred fragments comprise a polypeptide sequence which does not cross-react with related human proteins.
(5) 60 kDa Cysteine rich protein (OmcB) (CT443) One example of a Chlamydia trachomatis 60 kDa Cysteine rich protein is referred to herein as SEQ ID NO: 76 (see also GenBank accession number CAA39396; GenInfo Identifier: 40725). This protein is also generally referred to as OmcB, Omp2 or CT 443. The role of OmcB in chlamydial infection is further described in, for example, references 47-51.
Preferred OmcB proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 76; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 76, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These OmcB proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 76. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 76, including one or more of the epitopes identified in the references discussed above. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 76. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 153 and 154, which consist of amino acids 77-85 and 155-166 of OmcB respectively.
Fifth Antigen Group
(1) YscJ (CT559) One example of a ‘YscJ’ protein is disclosed as SEQ ID NOs: 199 & 200 in reference 36 (GenBank accession number: AAC68161.1; GenInfo Identifier:3329000; ‘CT559’; SEQ ID NO: 77 herein).
Preferred YscJ proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 77; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 77, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These YscJ proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 77. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 77. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 77. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 161 and 162, which consist of amino acids 118-131 and 294-313 of CT559 respectively.
(2) Pal (CT600) One example of a ‘Pal’ protein is disclosed as SEQ ID NOs: 173 & 174 in reference 36 (GenBank accession number: AAC68202.1; GenInfo Identifier:3329044 ‘CT600’; SEQ ID NO: 78 herein).
Preferred Pal proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 78; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 78, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Pal proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 78. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 78. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 78. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(3) CHLPN (76 kDa) (CT623) One example of a CHLPN (76 kDa protein) is disclosed as SEQ ID NOs: 163 & 164 in reference 36 (GenBank accession number: AAC68227.2; GenInfo Identifier:6578109 ‘CT623’; SEQ ID NO: 79 herein).
Preferred CHLPN (76 kDa protein proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 79; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 79, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CHLPN (76 kDa protein) proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 79. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 79. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 79. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(4) CT700 One example of a CT700 Hypothetical Protein is disclosed as SEQ ID NOs 261 & 262 in reference 36 (GenBank accession number: AAC68295.1; Geninfo Identifier:3329154 ‘CT700’; SEQ ID NO: 80 herein). A biological function for CT700 has not previously been described.
Preferred CT700 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 80; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 80, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT700 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 80. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 80. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 80. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(5) CT266 One example of a CT266 Hypothetical Protein is disclosed as SEQ ID NOs 77 & 78 in reference 36 (GenBank accession number: AAC67859.1; Geninfo Identifier:3328678 ‘CT266’; SEQ ID NO: 81 herein). A biological function for CT266 has not previously been described.
Preferred CT266 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 81; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 81, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT266 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 81. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 81. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 81. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(6) CT077 One example of a CT077 Hypothetical Protein is disclosed as SEQ ID NOs 65 & 66 in reference 36 (GenBank accession number: AAC67668.1; GenInfo Identifier:3328472 ‘CT077’; SEQ ID NO: 82 herein). A biological function for CT077 has not previously been described.
Preferred CT077 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 82; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 82, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT077 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 82. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 82. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 82. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(7) CT165 One example of a CT165 protein is disclosed in [4] (GenBank accession number: AAC67756.1; GenInfo Identifier:3328568; ‘CT165’; SEQ ID NO: 83 herein). A biological function for CT165 has not previously been described.
Preferred CT165 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 83; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 83, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT165 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 83. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 83. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 83. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(8) PorB (CT713) One example of a PorB protein is disclosed as SEQ ID NOs 201 & 202 in reference 36 (GenBank accession number: AAC68308.1; GenInfo Identifier:3329169; ‘CT713’; SEQ ID NO: 84 herein).
Preferred PorB proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 84; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 84, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These PorB proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 84. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 84. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 84. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
Sixth Antigen Group
(1) CT082 One example of a CT082 protein is disclosed in reference 4 (GenBank accession number: AAC67673.1; GenInfo Identifier:3328477; ‘CT082’; SEQ ID NO: 85 herein): A biological function for CT082 has not previously been described.
Preferred CT082 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 85; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 85, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT082 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 85. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 85. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 85. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(2) CT181 One example of a CT181 protein is disclosed as SEQ ID NOs 245 & 246 in reference 36 (GenBank accession number: AAC67772.1; GenInfo Identifier:3328585; ‘CT181’; SEQ ID NO: 86 herein). A biological function for CT181 proteins has not previously been described.
Preferred CT181 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 86; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 86, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT181 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 86. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 86. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 86. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(3) CT050 One example of a CT050 protein is disclosed in reference 4 (GenBank accession number: AAC67641.1; GenInfo Identifier:3328442; ‘CT050’; SEQ ID NO: 87 herein). A biological function for CT050 proteins has not previously been described.
Preferred CT050 hypothetical proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 87; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 87, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT050 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 87. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 87. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 87. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(4) Phospholipase D SuperFamily (CT157) One example of a Phospholipase D SuperFamily Protein is disclosed as (GenBank accession number: AAC67748.1; GenInfo Identifier:3328559; ‘CT157’; SEQ ID NO: 88 herein).
Preferred Phospholipase D SuperFamily proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 88; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 88, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Phospholipase D SuperFamily proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 88. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 88. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 88. Other fragments omit one or more domains of the protein (e.g. omission of, a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(5) AdK (Adenylate Kinase) (CT128) One example of an Adenylate Kinase Protein is disclosed as (GenBank accession number: AAC67719.1 GenInfo Identifier:3328527; ‘CT128’; SEQ ID NO: 89 herein).
Preferred Adenylate Kinase proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 89; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 89, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Adenylate Kinase proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 89. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 89. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 89. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
Seventh Antigen Group
(1) CT153 One example of a CT153 Protein is disclosed in reference 4 (GenBank accession number: AAC67744.1; GenInfo Identifier:3328555; ‘CT153’; SEQ ID NO: 90 herein). A biological function for CT153 proteins has not previously been described.
Preferred CT153 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 90; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 90, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT153 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 90. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 90. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 90. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 137, which consists of amino acids 23-36 of CT153.
(2) CT262 One example of a CT262 protein is disclosed in reference 4 (GenBank accession number: AAC67855.1; GenInfo Identifier: 3328674; CT262′; SEQ ID NO: 91 herein). A biological function for CT262 proteins has not previously been described.
Preferred CT262 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 91; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 91, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT262 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 91. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 91. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 91. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(3) CT276 One example of a CT276 protein is disclosed in reference 4 (GenBank accession number: AAC67869.1; GenInfo Identifier:3328689; ‘CT276’; SEQ ID NO: 92 herein). A biological function for CT276 proteins has not previously been described.
Preferred CT276 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 92; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 92, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT276 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 92. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 92. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 92. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(4) CT296 One example of a CT296 protein is disclosed in reference 4 (GenBank accession number: AAC67889.1; GenInfo Identifier:3328711; ‘CT296’; SEQ ID NO: 93 herein). A biological function for CT296 proteins has not previously been described.
Preferred CT296 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 93; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 93, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT296 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 93. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 93. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 93. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(5) CT372 One example of a CT372 protein is disclosed as SEQ ID NOs 187 & 188 in reference 36 (GenBank accession number: AAC67968.1; GenInfo Identifier:3328796; ‘CT372’; SEQ ID NO: 94 herein). A biological function for CT372 proteins has not previously been described.
Preferred CT372 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 94; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 94, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT372 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 94. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 94. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 94. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(6) Putative Outer Membrane Protein A (PmpA) (CT412) One example of a PmpA protein is disclosed as SEQ ID NOs 89 & 90 in reference 36 (GenBank accession number: AAC68009.1; GenInfo Identifier:3328840; ‘CT412’; SEQ ID NO: 95 herein and also SEQ ID NO: 61 above).
Preferred PmpA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 95; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 95, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These PmpA proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 95. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 95. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 95. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(7) Oligopeptide Binding Lipoprotein (CT480) One example of an Oligopeptide binding lipoprotein is disclosed as SEQ ID NOs 141 & 142 in reference 36 (GenBank accession number: AAC68080.1; GenInfo Identifier:3328915; ‘CT480’; SEQ ID NO: 96 herein).
Preferred Oligopeptide Binding Lipoproteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 96; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 96, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These OligoPeptide Binding proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 96. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 96. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 96. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(8) CT548 One example of a CT548 protein is disclosed as SEQ ID NOs 153 & 154 in reference 36 (GenBank accession number: AAC68150.1; GenInfo Identifier:3328987; ‘CT548’; SEQ ID NO: 97 herein). A biological function for CT548 proteins has not previously been described.
Preferred CT548 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 97; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 97, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT548 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 97. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 97. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 97. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(9) CT043 One example of a CT043 protein is disclosed in reference 4 (GenBank accession number: AAC67634.1; GenInfo Identifier:3328435; ‘CT043’; SEQ ID NO: 98 herein). A biological function for CT043 proteins has not previously been described. It is postulated here that CT043 is a type three secretion system (TTSS) chaperone.
Preferred CT043 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 98; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 98, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT043 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 98. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 98. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 98. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 128, which consists of amino acids 75-95 of CT043.
The preferred fragment recited in SEQ ID NO: 128 is predicted to comprise three CD4+ Th1 epitopes. These epitopes are LYEKLLEGS (SEQ ID NO: 272), GSMLGGQMA (SEQ ID NO: 273) and GGGVGVATK (SEQ ID NO: 274). An optional variant of the third epitope is GGVGVATKE (SEQ ID NO: 275). See also the examples and FIG. 10.
(10) CT635 One example of a CT635 protein is disclosed in reference 4 (GenBank accession number: AAC68239.1; GenInfo Identifier:3329083; ‘CT635’; SEQ ID NO: 99 herein). A biological function for CT635 proteins has not previously been described.
Preferred CT635 Hypothetical proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 99; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 99, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT635 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 99. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 99. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 99. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 166, which consists of amino acids 70-88 of CT635 respectively.
(11) Metalloprotease (CT859) One example of a Metalloproease Protein is disclosed in reference 4 (GenBank accession number: AAC68457.1; GenInfo Identifier:3329333; ‘CT859’; SEQ ID NO: 100 herein).
Preferred Metalloprotease proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 100; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 100, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These Metalloprotease proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 100. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 100. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 100. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(12) CT671 One example of a CT671 protein is disclosed in reference 4 (GenBank accession number: AAC68266.1; GenInfo Identifier:3329122; ‘CT671’; SEQ ID NO: 101 herein). A biological function for CT671 proteins has not previously been described.
Preferred CT671 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 101; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 101, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT671 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 101. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 101. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 101. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(13) CT016 One example of a CT016 protein is disclosed in reference 4 (GenBank accession number: AAC67606.1; GenInfo Identifier:3328405; ‘CT016’; SEQ ID NO: 102 herein). A biological function for CT016 proteins has not previously been described.
Preferred CT016 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 102; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 102, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT016 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 102. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 102. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 102. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(14) CT017 One example of a CT017 protein is disclosed in reference 4 (GenBank accession number: AAC67607.1; GenInfo Identifier:3328406; ‘CT017’; SEQ ID NO: 103 herein). A function for CT017 proteins has not previously been identified.
Preferred CT017 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 103; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 103, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT017 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 103. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 103. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 103. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(15) PmpD (CT812) This polymorphic membrane protein D is discussed above as SEQ ID NO: 64 (CT812).
(16) PmpE (CT869) This polymorphic membrane protein E is discussed above as SEQ ID NO: 65.
Eighth Antigen Group
(1) GatA One example of a GatA protein is disclosed in reference 4 (GenBank accession number: AAC67593; GenInfo Identifier: 3328391; ‘CT003’; SEQ ID NO: 173 herein).
Preferred GatA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 173; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 173, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 173. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 173. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 173. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 174, which consists of amino acids 148-163 of GatA.
(2) GatB One example of a GatB protein is disclosed in reference 4 (GenBank accession number: AAC67594; GenInfo Identifier: 3328392; ‘CT004’; SEQ ID NO: 175 herein).
Preferred GatB proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 175; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 175, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 175. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 175. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 175. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 176, which consists of amino acids 437-450 of GatB.
(3) CT005 One example of a CT005 protein is disclosed in reference 4 (GenBank accession number: AAC67595; GenInfo Identifier: 3328393; ‘CT005’; SEQ ID NO: 177 herein). A function for CT005 proteins has not previously been identified.
Preferred CT005 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 177; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 177, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT005 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 177. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 177. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 177. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 178, which consists of amino acids 340-357 of CT005.
(4) CT042 One example of a CT042 protein is disclosed in reference 4 (GenBank accession number: AAC67632; GenInfo Identifier: 3328433; ‘CT042’; SEQ ID NO: 179 herein). CT042 is predicted to be a metalloprotease protein.
Preferred CT042 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 179; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 179, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT042 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 179. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 179. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 179. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 180, which consists of amino acids 396-412 of CT042.
(5) SucB1 One example of a SucB1 protein is disclosed in reference 4 (GenBank accession number: AAC67646; GenInfo Identifier: 3328448; ‘CT055’; SEQ ID NO: 181 herein).
Preferred SucB 1 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 181; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 181, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 181. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 181. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 181. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 182, which consists of amino acids 213-225 of SucB1.
(6) ClpB One example of a ClpB protein is disclosed in reference 4 (GenBank accession number: AAC67704; GenInfo Identifier: 3328511; ‘CT113’; SEQ ID NO: 256 herein).
Preferred ClpB proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 256; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 256, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 256. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 256. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 256. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain).
(7) Rs9 One example of a Rs9 protein is disclosed in reference 4 (GenBank accession number: AAC67717; GenInfo Identifier: 3328525; ‘CT126’; SEQ ID NO: 183 herein).
Preferred Rs9 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 183; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 183, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 183. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 183. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 183. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 184, which consists of amino acids 66-79 of Rs9.
(8) DhnA One example of a DhnA protein is disclosed in reference 4 (GenBank accession number: AAC67807; GenInfo Identifier: 3328623; ‘CT215’; SEQ ID NO: 185 herein).
Preferred DhnA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 185; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 185, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 185. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 185. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 185. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 186, which consists of amino acids 283-302 of DhnA.
(9) AcpP One example of a AcpP protein is disclosed in reference 4 (GenBank accession number: AAC67828; GenInfo Identifier: 3328645; ‘CT236’; SEQ ID NO: 187 herein).
Preferred AcpP proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 187; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 187, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 187. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 187. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 187. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 188, which consists of amino acids 9-23 of AcpP.
(10) HimD One example of a HimD protein is disclosed in reference 4 (GenBank accession number: AAC67860; GenInfo Identifier: 3328679; ‘CT267’; SEQ ID NO: 189 herein).
Preferred HimD proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 189; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 189, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 189. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 189. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 189. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 190, which consists of amino acids 35-44 of HimD.
(11) Tal One example of a Tal (transaldolase) protein is disclosed in reference 4 (GenBank accession number: AAC67906; GenInfo Identifier: 3328729; ‘CT313’; SEQ ID NO: 191 herein).
Preferred Tal proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 191; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 191, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 191. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 191. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 191. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 192, which consists of amino acids 10-25 of Tal.
(12) DksA One example of a DksA protein is disclosed in reference 4 (GenBank accession number: AAC68004; GenInfo Identifier: 3328835; ‘CT407’; SEQ ID NO: 193 herein).
Preferred DksA proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 193; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 193, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 193. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 193. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 193. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 194, which consists of amino acids 2-12 of DksA.
(13) CT425 One example of a CT425 protein is disclosed in reference 4 (GenBank accession number: AAC68022; GenInfo Identifier: 3328855; ‘CT425’; SEQ ID NO: 195 herein). A biological function for CT425 proteins has not previously been described.
Preferred CT425 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 195; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 195, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT425 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 195. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 195. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 195. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 196, which consists of amino acids 143-156 of CT425.
(14) Ym74 One example of a Ym74 protein is disclosed in reference 4 (GenBank accession number: AAC68060; GenInfo Identifier: 3328894; ‘CT460’; SEQ ID NO: 197 herein).
Preferred Ym74 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 197; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 197, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 197. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 197. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 197. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 198, which consists of amino acids 44-53 of Ym74.
(15) Rl15 One example of a Rl15 protein is disclosed in reference 4 (GenBank accession number: AAC68112; GenInfo Identifier: 3328948; ‘CT511’; SEQ ID NO: 199 herein).
Preferred Rl15 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 199; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 199, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 199. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 199. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 199. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 200, which consists of amino acids 84-100 of Rl15.
(16) Rs5 One example of a Rs5 protein is disclosed in reference 4 (GenBank accession number: AAC68113; GenInfo Identifier: 3328949; ‘CT512’; SEQ ID NO: 201 herein).
Preferred Rs5 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 201; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 201, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 201. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 201. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 201. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 202, which consists of amino acids 130-141 of Rs5.
(17) Rl6 One example of a Rl6 protein is disclosed in reference 4 (GenBank accession number: AAC68115; GenInfo Identifier: 3328951; ‘CT514’; SEQ ID NO: 203 herein).
Preferred Rl6 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 203; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 203, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 203. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 203. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 203. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 204, which consists of amino acids 116-128 of Rl6.
(18) Rl24 One example of a Rl24 protein is disclosed in reference 4 (GenBank accession number: AAC68118; GenInfo Identifier: 3328954; ‘CT517’; SEQ ID NO: 205 herein).
Preferred Rl24 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 205; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 205, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80; 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 205. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 205. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 205. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 206, which consists of amino acids 95-104 of Rl24.
(19) Rl22 One example of a Rl22 protein is disclosed in reference 4 (GenBank accession number: AAC68124; GenInfo Identifier: 3328960; ‘CT523’; SEQ ID NO: 207 herein).
Preferred Rl22 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 207; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 207, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 207. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 207. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 207. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 208, which consists of amino acids 49-64 of Rl22.
(20) Rl2 One example of a Rl2 protein is disclosed in reference 4 (GenBank accession number: AAC68126; GenInfo Identifier: 3328962; ‘CT525’; SEQ ID NO: 209 herein).
Preferred Rl2 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 209; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 209, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 209. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 209. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 209. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 210, which consists of amino acids 233-249 of Rl2.
(21) Rl4 One example of a Rl4 protein is disclosed in reference 4 (GenBank accession number: AAC68128; GenInfo Identifier: 3328964; ‘CT527’; SEQ ID NO: 211 herein).
Preferred Rl4 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 211; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 211, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 211. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 211. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 211. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 212 and 213, which consist of amino acids 123-139 and 184-200 of Rl4 respectively.
(22) LcrH1 One example of a LcrH1 protein is disclosed in reference 4 (GenBank accession number: AAC68178; GenInfo Identifier: 3329018; ‘CT576’; SEQ ID NO: 214 herein). It is postulated that CT576 forms part of a Type Three Secretion System (TTSS).
Preferred LcrH1 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 214; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 214, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 214. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 214. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 214. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 215 and 216, which consist of amino acids 42-51 and 159-177 of LcrH1 respectively.
(23) AhpC One example of an AhpC protein is disclosed in reference 4 (GenBank accession number: AAC67809; GenInfo Identifier: 3328625; ‘CT603’; SEQ ID NO: 217 herein).
Preferred AhpC proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 217; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 217, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 217. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 217. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 217. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 218, 219 and 220, which consist of amino acids 89-107, 108-124 and 137-147 of AhpC respectively.
(24) CT610 One example of a CT610 protein is disclosed in reference 4 (GenBank accession number: AAC68213; GenInfo Identifier: 3329055; ‘CT610’; SEQ ID NO: 221 herein). A biological function for CT610 proteins has not previously been described.
Preferred CT610 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 221; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 221, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT610 Hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 221. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 221. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 221. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 222, which consists of amino acids 94-116 of CT610.
(25) CT622 One example of a CT622 protein is disclosed in reference 4 (GenBank accession number: AAS90241; GenInfo Identifier: 46370936; ‘CT622’; SEQ ID NO: 223 herein). CT622 is predicted to be a CHLPN 76 kD homologue.
Preferred CT622 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 223; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 223, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT622 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 223. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 223. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 223. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 224, 225 and 259, which consist of amino acids 70-91, 109-123 and 443-459 of CT622 respectively.
(26) CT664 One example of a CT664 protein is disclosed in reference 4 (GenBank accession number: AAC68259; GenInfo Identifier: 3329115; ‘CT664’; SEQ ID NO: 226 herein). CT664 is predicted to be a FHA domain with homology to adenylate cyclase.
Preferred CT664 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%; 98%, 99%, 99.5% or more) to SEQ ID NO: 226; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 226, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT664 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 226. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 226. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 226. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 227-231 and 232, which consist of amino acids 186-200, 343-356, 297-312, 313-330, 357-372 and 405-426 of CT664 respectively.
(27) FliN One example of a FliN protein is disclosed in reference 4 (GenBank accession number: AAC68267; GenInfo Identifier: 3329123; ‘CT672’; SEQ ID NO: 233 herein). This protein is a flagellar motor switch domain of the YscQ family.
Preferred FliN proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 233; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 233, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 233. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 233. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 233. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 234, which consists of amino acids 90-105 of FliN.
(28) PyrH One example of a PyrH protein is disclosed in reference 4 (GenBank accession number: AAC68273; GenInfo Identifier: 3329130; ‘CT678’; SEQ ID NO: 235 herein). This protein is a UMP kinase.
Preferred PyrH proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 235; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 235, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 235. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 235. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 235. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 236 and 237, which consist of amino acids 13-26 and 61-72 of PyrH.
(29) CT741 One example of a CT741 protein is disclosed in reference 4 (GenBank accession number: AAC68336; GenInfo Identifier: 3329200; ‘CT741’; SEQ ID NO: 238 herein). A biological function for CT741 proteins has not previously been described.
Preferred CT741 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 238; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 238, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT741 hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 238. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 238. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 238. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 239, which consists of amino acids 73-86 of CT741.
(30) Efp2 One example of an Efp2 (elongation factor P) protein is disclosed in reference 4 (GenBank accession number: AAC68347; GenInfo Identifier: 3329213; ‘CT752’; SEQ ID NO: 240 herein).
Preferred Efp2 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 240; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 240, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 240. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 240. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 240. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 241, which consists of amino acids 163-176 of Efp2.
(31) CT768 One example of a CT768 protein is disclosed in reference 4 (GenBank accession number: AAC68363; GenInfo Identifier: 3329231; ‘CT768’; SEQ ID NO: 242 herein). A biological function for CT768 proteins has not previously been described.
Preferred CT768 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 242; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 242, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT768 hypothetical proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 242. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 242. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 242. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 243, which consists of amino acids 461-472 of CT768.
(32) CT771 One example of a CT771 protein is disclosed in reference 4 (GenBank accession number: AAC68366; GenInfo Identifier: 3329234; ‘CT771’; SEQ ID NO: 244 herein). CT771 is predicted to be a hydrolase/phosphatase homologue.
Preferred CT771 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 244; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 244, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These CT771 proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 244. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 244. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10; 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 244. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 245, which consist of amino acids 59-74 of CT771 respectively.
(33) Ldh One example of a Ldh (leucine dehydrogenase) protein is disclosed in reference 4 (GenBank accession number: AAC68368; GenInfo Identifier: 3329236; ‘CT773’; SEQ ID NO: 246 herein).
Preferred Ldh proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 246; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 246, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 246. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 246. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 246. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 247, which consists of amino acids 253-269 of Ldh.
(34) Rl35 One example of a 8135 (L35 ribosomal) protein is disclosed in reference 4 (GenBank accession number: AAC68431; Geninfo Identifier: 3329305; ‘CT834’; SEQ ID NO: 248 herein).
Preferred Rl35 proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 248; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 248, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 248. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 248. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 248. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). A particularly preferred fragment is that recited in SEQ ID NO: 249, which consists of amino acids 47-59 of Rl35.
(35) FtsH One example of a FtsH (ATP-dependent zinc protease) protein is disclosed in reference 4 (GenBank accession number: AAC68438; GenInfo Identifier: 3329313; ‘CT841’; SEQ ID NO: 250 herein).
Preferred FtsH proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 250; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 250, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 250. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 250. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 250. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 251 and 252, which consist of amino acids 252-264 and 626-632 of FtsH.
(36) Pnp One example of a Pnp (polynucleotide transferase) protein is disclosed in reference 4 (GenBank accession number: AAC68439; GenInfo Identifier: 3329314; ‘CT842’; SEQ ID NO: 253 herein).
Preferred Pnp proteins for use with the invention comprise an amino acid sequence: (a) having 50% or more identity (e.g. 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or more) to SEQ ID NO: 253; and/or (b) which is a fragment of at least n consecutive amino acids of SEQ ID NO: 253, wherein n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more). These proteins include variants (e.g. allelic variants, homologs, orthologs, paralogs, mutants, etc.) of SEQ ID NO: 253. Preferred fragments of (b) comprise an epitope from SEQ ID NO: 253. Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the N-terminus of SEQ ID NO: 253. Other fragments omit one or more domains of the protein (e.g. omission of a signal peptide, of a cytoplasmic domain, of a transmembrane domain, or of an extracellular domain). Particularly preferred fragments are those recited in SEQ ID NOs: 254 and 255, which consist of amino acids 261-270 and 271-294 of Pnp.
Preferably, a composition according to the invention comprises one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or all 20) Chlamydia trachomatis antigens of the first antigen group combined with one of the following combinations of Chlamydia trachomatis antigens: (1) CT016 and CT128 and CT671 and CT262; (2) CT296 and CT372 and CT635 and CT859; (3) CT412 and CT480 and CT869 and CT871; (4) CT050 and CT153 and CT157 and CT165; (5) CT276 and CT296 and CT456 and CT480; (6) CT089 and CT381 and CT396 and CT548; (7) CT635 and CT700 and CT711 and CT859; (8) CT812 and CT869 and CT552 and CT671; (9) CT713 and CT017 and CT043 and CT082; (10)'CT266 and CT443 and CT559 a CT597; and (11) CT045 and CT089 and CT396 and CT398 and CT39 (12) CT681 and CT547; (13) CT623 and CT414.
Preferably, a composition according to the invention comprises or consists of a) CT587, CT823, CT043, CT396 and CT381; and/or b) CT467, CT153, CT398 and CT480.
Preferably, a composition according to the invention comprises one or more of the epitopes recited in SEQ ID NOs: 261-275.
Preferably a composition according to the invention comprises one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group combined with the Chlamydia pneumoniae polypeptide referred to as SEQ ID NO: 2 in WO01/75114 or the polypeptide referred to as SEQ ID NO: 2 in WO01/075113 or a fragment thereof or a polypeptide holmologous thereto. Such polypeptide fragments preferably are at least 12 amino acids in length. Advantageously, they are at least 15 amino acids, preferably at least 20, 25, 30, 35, 40, 45, 50 amino acids, more preferably at least 55, 60, 65, 70, 75 amino acids, and most preferably at least 80, 85, 90, 95, 100 amino acids in length. Preferably the fragment comprises a T- and/or B-cell epitope.
Alternatively, a composition according to the invention comprises one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or all 26) Chlamydia trachomatis antigens of the first antigen group combined with the Chlamydia pneumoniae polypeptide referred to as SEQ ID NO: 1 in U.S. Pat. No. 6,491,924 or a fragment thereof or a polypeptide holmologous thereto. Such polypeptide fragments preferably are at least 12 amino acids in length. Advantageously, they are at least 15 amino acids, preferably at least 20, 25, 30, 35, 40, 45, 50 amino acids, more preferably at least 55, 60, 65, 70, 75 amino acids, and most preferably at least 80, 85, 90, 95, 100 amino acids in length. Preferably the fragment comprises a T- and/or B-cell epitope.
Type Three Secretion System
CT576, CT577, CT578 and CT579 are postulated to form part of a Type Three Secretion System (TTSS). CT576 is predicted to be a low calcium responsive protein H (lcrH1) similar to the lcrH encoded in the lcrGVH-yopBD operon of Yersinia, in proximity to YopBD. It therefore appears that CT579 is the Chlamydial equivalent of LcrV. LcrV is known to be an important virulence determinant (the V antigen) in Yersinia [52], and antibodies against this protein have been shown to be protective in a mouse model of plague [53].
Thus particularly preferred compositions of the invention comprise one or more CT579 antigens.
Fusion Proteins
The Chlamydia trachomatis antigens used in the invention may be present in the composition as individual separate polypeptides. Generally, the recombinant fusion proteins of the present invention are prepared as a GST-fusion protein and/or a His-tagged fusion protein.
Where more than one antigen is used, however, they do not have to be present as separate polypeptides. Instead, at least two (i.e. 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) of the antigens can be expressed as a single polypeptide chain (a ‘hybrid’ polypeptide). Hybrid polypeptides offer two principal advantages: first, a polypeptide that may be unstable or poorly expressed on its own can be assisted by adding a suitable hybrid partner that overcomes the problem; second, commercial manufacture is simplified as only one expression and purification need be employed in order to produce two polypeptides which are both antigenically useful.
The hybrid polypeptide may comprise two or more polypeptide sequences from the first antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, wherein said first and second amino acid sequences are selected from a Chlamydia trachomatis antigen or a fragment thereof of the first antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the second antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the second antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the third antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the third antigen group.
Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the fourth antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the fourth antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the fifth antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the fifth antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the sixth antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the sixth antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the seventh antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the seventh antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
The hybrid polypeptide may comprise one or more polypeptide sequences from the first antigen group and one or more polypeptide sequences from the eighth antigen group. Accordingly, the invention includes a composition comprising a first amino acid sequence and a second amino acid sequence, said first amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group and said second amino acid sequence selected from a Chlamydia trachomatis antigen or a fragment thereof from the eighth antigen group. Preferably, the first and second amino acid sequences in the hybrid polypeptide comprise different epitopes.
Hybrids consisting of amino acid sequences from two, three, four, five, six, seven, eight, nine, or ten Chlamydia trachomatis antigens are preferred. In particular, hybrids consisting of amino acid sequences from two, three, four, or five Chlamydia trachomatis antigens are preferred. Particularly preferred are hybrids consisting of amino acid sequences from two or three Chlamydia trachomatis antigens.
Different hybrid polypeptides may be mixed together in a single formulation. Within such combinations, a Chlamydia trachomatis antigen may be present in more than one hybrid polypeptide and/or as a non-hybrid polypeptide. It is preferred, however, that an antigen is present either as a hybrid or as a non-hybrid, but not as both.
Two antigen hybrids for use in the present invention may also comprise combinations of antigens selected from the second, third, fourth, fifth, sixth, seventh and eighth antigen groups.
Hybrid polypeptides can be represented by the formula NH2-A-{-X-L-}n-B—COOH, wherein: X is an amino acid sequence of a Chlamydia trachomatis antigen or a fragment thereof from the first antigen group, the second antigen group, the third antigen group, the fourth antigen group, the fifth antigen group, the sixth antigen group or the seventh antigen group; L is an optional linker amino acid sequence; A is an optional N-terminal amino acid sequence; B is an optional C-terminal amino acid sequence; and n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15. At least one —X— moiety is from the first antigen group and (n-1) —X— moieties are from the first antigen group, the second antigen group, the third antigen group, the fourth antigen group, the fifth antigen group, the sixth antigen group or the seventh antigen group.
If a —X— moiety has a leader peptide sequence in its wild-type form, this may be included or omitted in the hybrid protein. In some embodiments, the leader peptides will be deleted except for that of the —X— moiety located at the N-terminus of the hybrid protein i.e. the leader peptide of X1 will be retained, but the leader peptides of X2 . . . Xn will be omitted. This is equivalent to deleting all leader peptides and using the leader peptide of X1 as moiety -A-.
For each n instances of {—X-L-}, linker amino acid sequence -L- may be present or absent. For instance, when n=2 the hybrid may be NH2—X1-L1-X2-L2-COOH, NH2—X1—X2—COOH, NH2—X1-L1-X2—COOH, NH2—X1—X2-L2-COOH, etc. Linker amino acid sequence(s) -L- will typically be short (e.g. 20 or fewer amino acids i.e. 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples comprise short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. comprising Glyn where n=2, 3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art. A useful linker is GSGGGG (SEQ ID NO: 104), with the Gly-Ser dipeptide being formed from a BamHI restriction site, thus aiding cloning and manipulation, and the (Gly)4 tetrapeptide being a typical poly-glycine linker. The same variants apply to {—Y-L-}. Therefore, for each m instances of {—Y-L-}, linker amino acid sequence -L- may be present or absent.
-A- is an optional N-terminal amino acid sequence. This will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct protein trafficking, or short peptide sequences which facilitate cloning or purification (e.g. histidine tags i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable N-terminal amino acid sequences will be apparent to those skilled in the art. If X1 lacks its own N-terminus methionine, -A- is preferably an oligopeptide (e.g. with 1, 2, 3, 4, 5, 6, 7 or 8 amino acids) which provides a N-terminus methionine.
—B— is an optional C-terminal amino acid sequence. This will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include sequences to direct protein trafficking, short peptide sequences which facilitate cloning or purification (e.g. comprising histidine tags i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more), or sequences which enhance protein stability. Other suitable C-terminal amino acid sequences will be apparent to those skilled in the art. Most preferably, n is 2 or 3.
Preferred fusion protein compositions of the invention comprise one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) of CT587, 587his, gst587, CT823, 823his, gst823, CT043, 043his, gst043, CT396, 396his, gst396, CT381, 381his, gst381, CT467, 467his, gst467, CT153, 153his, gst153, CT398, 398his, gst398, CT480, 480his and/or gst480. According to this nomenclature, each antigen may have a N-terminal GST tag or a C-terminal his tag. Therefore, for example, 587his is CT587 with a C-terminal his tag and gst587 is CT587 with a N-terminal gst tag.
Preferably, a fusion protein composition according to the invention comprises one or more of the epitopes recited in SEQ ID NOs: 261-275.
The invention also provides nucleic acid encoding hybrid polypeptides of the invention. Furthermore, the invention provides nucleic acid which can hybridize to this nucleic acid, preferably under “high stringency” conditions (e.g. 65° C. in a 0.1×SSC, 0.5% SDS solution).
Polypeptides of the invention can be prepared by various means (e.g. recombinant expression, purification from cell culture, chemical synthesis, etc.) and in various forms (e.g. native, fusions, non-glycosylated, lipidated, etc.). They are preferably prepared in substantially pure form (i.e. substantially free from other chlamydial or host cell proteins).
Nucleic acid according to the invention can be prepared in many ways (e.g. by chemical synthesis, from genomic or cDNA libraries, from the organism itself, etc.) and can take various forms (e.g. single stranded, double stranded, vectors, probes, etc.). They are preferably prepared in substantially pure form (i.e. substantially free from other chlamydial or host cell nucleic acids).
The term “nucleic acid” includes DNA and RNA, and also their analogues, such as those containing modified backbones (e.g. phosphorothioates, etc.), and also peptide nucleic acids (PNA), etc. The invention includes nucleic acid comprising sequences complementary to those described above (e.g. for antisense or probing purposes).
The invention also provides a process for producing a polypeptide of the invention, comprising the step of culturing a host cell transformed with nucleic acid of the invention under conditions which induce polypeptide expression.
The invention provides a process for producing a polypeptide of the invention, comprising the step of synthesizing at least part of the polypeptide by chemical means.
The invention provides a process for producing nucleic acid of the invention, comprising the step of amplifying nucleic acid using a primer-based amplification method (e.g. PCR).
The invention provides a process for producing nucleic acid of the invention, comprising the step of synthesizing at least part of the nucleic acid by chemical means.
Polypeptides Used With the Invention
Polypeptides used with the invention can take various forms (e.g. native, fusions, glycosylated, non-glycosylated, lipidated, non-lipidated, phosphorylated, non-phosphorylated, myristoylated, non-myristoylated, monomeric, multimeric, particulate, denatured, etc.). F1, for instance, is known to exist in various forms, including a multimeric glycoprotein form. Lipoproteins are particularly preferred for use as immunogens.
Polypeptides used with the invention can be prepared by various means (e.g. recombinant expression, purification from cell culture, chemical synthesis, etc.). Recombinantly-expressed proteins are preferred, particularly for hybrid polypeptides.
Polypeptides used with the invention are preferably provided in purified or substantially purified form i.e. substantially free from other polypeptides (e.g. free from naturally-occurring polypeptides), particularly from other Chlamydia or host cell polypeptides, and are generally at least about 50% pure (by weight), and usually at least about 90% pure i.e. less than about 50%, and more preferably less than about 10% (e.g. 5%) of a composition is made up of other expressed polypeptides. Thus the antigens in the compositions are separated from the whole organism with which the molecule is expressed.
Polypeptides used with the invention are preferably C. trachomatis polypeptides.
The term “polypeptide” refers to amino acid polymers of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art. Polypeptides can occur as single chains or associated chains.
The invention provides polypeptides comprising a sequence —P-Q- or -Q-P—, wherein: —P— is an amino acid sequence as defined above and -Q- is not a sequence as defined above i.e. the invention provides fusion proteins. Where the N-terminus codon of —P— is not ATG, but this codon is not present at the N-terminus of a polypeptide, it will be translated as the standard amino acid for that codon rather than as a Met. Where this codon is at the N-terminus of a polypeptide, however, it will be translated as Met. Polypeptides used with the invention may be prepared as a GST-fusion protein and/or a His-tagged fusion protein.
Strains
The human serovars of C. trachomatis are divided into two biovariants (“biovars”). Serovars L1, L2 and L3 are the agents of invasive lymphogranuloma venereum (LGV) which is a sexually transmitted systemic infection. LGV is uncommon in industrialized countries but frequent in Africa, Asia, Australian and South America. It predominantly affects lymphatic tissue but may also occur as an acute symptomatic infection without apparent lymph node involvement or tissue reaction at the point of infection. Acute LGV is reported over five times more frequent in men than in women. Other biotypes of C. trachomatis include serovars A, B, Ba, and C which are associated with trachoma, a transmissible condition of the eye.
Serovars A-K (D, E, F, G, H, I, J and K) are typically associated with genital tract disease.
In particular, Serovars D, E, F, H and K account for nearly 85% of genital tract infections (see, for example, reference 54). Serovars A-K elicit epithelial infections primarily in the ocular tissue (A-C) or urogenital tract (D-K). Research to date also indicates that the 4 Serovars (or serotypes) responsible for Sexually Transmitted Infections or Diseases (STIs or STDs) in the US and Europe are D-K, preferably D, E, F and I.
Preferred polypeptides of the invention comprise an amino acid sequence found in C. trachomatis serovar A, B, C, D, E, K, L1, L2 or L3 or in one or more of an epidemiologically prevalent serovar. More preferably, the polypeptides of the invention comprise an amino acid sequence found in C. trachomatis serovar D, E or K. More preferably, the polypeptides of the invention comprise an amino acid sequence found in C. trachomatis serovar D.
Preferably, polypeptides of the invention comprise an amino acid sequence from a trachoma biovar of C. trachomatis. 
Preferred polypeptides of the invention comprise an amino acid sequence found in C. trachomatis strains D/UW-3/CX or L2/434/BU [4].
The polypeptides of the invention may also be obtained from C. pneumoniae. 
Where hybrid polypeptides are used, the individual antigens within the hybrid (i.e. individual —X— moieties) may be from one or more strains. Where n=2, for instance, X2 may be from the same strain as X1 or from a different strain. Where n=3, the strains might be (i) X1═X2═X3 (ii) X1═X2≠X3 (iii) X1≠X2═X3 (iv) X1═X2≠X3 or (v) X1≠X3≠X2, etc.
Heterologous Hosts
Whilst expression of the polypeptides of the invention may take place in Chlamydia, the invention preferably utilizes a heterologous host. The heterologous host may be prokaryotic (e.g. a bacterium) or eukaryotic. It is preferably E. coli, but other suitable hosts include Bacillus subtilis, Vibrio cholerae, Salmonella typhi, Salmonella typhimurium, Neisseria lactamica, Neisseria cinerea, Mycobacteria (e.g. M. tuberculosis), yeasts, etc.
Immunogenic Compositions and Medicaments
Compositions of the invention are preferably immunogenic compositions, and are more preferably vaccine compositions. The pH of the composition is preferably between 6 and 8, preferably about 7. The pH may be maintained by the use of a buffer. A phosphate buffer is typical. The composition may be sterile and/or pyrogen-free. The composition may be isotonic with respect to humans.
Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat infection), but will typically be prophylactic. Accordingly, the invention includes a method for the therapeutic or prophylactic treatment of Chlamydia trachomatis infection in an animal susceptible to chlamydial infection comprising administering to said animal a therapeutic or prophylactic amount of the immunogenic compositions of the invention.
Compositions may include an antimicrobial, particularly if packaged in a multiple dose format.
Compositions may comprise detergent e.g. a Tween (polysorbate), such as Tween 80. Detergents are generally present at low levels e.g. <0.01%.
Compositions may include sodium salts (e.g. sodium chloride) to give tonicity. A concentration of 10±2 mg/ml NaCl is typical.
Compositions may comprise a sugar alcohol (e.g. mannitol) or a disaccharide (e.g. sucrose or trehalose) e.g. at around 15-30 mg/ml (e.g. 25 mg/ml), particularly if they are to be lyophilised or if they include material which has been reconstituted from lyophilised material. The pH of a composition for lyophilization may be adjusted to around 6.1 prior to lyophilization.
The compositions of the invention may also comprise one or more immunoregulatory agents. Preferably, one or more of the immunoregulatory agents include(s) an adjuvant. The adjuvant may be selected from one or more of the group consisting of a TH1 adjuvant and TH2 adjuvant, further discussed below.
Adjuvants which may be used in compositions of the invention include, but are not limited to:
A. Mineral-Containing Compositions
Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminium salts and calcium salts. The invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulphates, etc. [e.g. see chapters 8 & 9 of ref. 55], or mixtures of different mineral compounds, with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption being preferred. The mineral containing compositions may also be formulated as a particle of metal salt [56].
A typical aluminium phosphate adjuvant is amorphous aluminium hydroxyphosphate with PO4/Al molar ratio between 0.84 and 0.92, included at 0.6 mg Al3+/ml. Adsorption with a low dose of aluminium phosphate may be used e.g. between 50 and 100 μg Al3+ per conjugate per dose. Where an aluminium phosphate it used and it is desired not to adsorb an antigen to the adjuvant, this is favoured by including free phosphate ions in solution (e.g. by the use of a phosphate buffer).
B. Oil Emulsions
Oil emulsion compositions suitable for use as adjuvants in the invention include oil-in-water emulsions and water-in-oil emulsions.
A submicron oil-in-water emulsion may include squalene, Tween 80, and Span 85 e.g. with a composition by volume of about 5% squalene, about 0.5% polysorbate 80 and about 0.5% Span 85 (in weight terms, 4.3% squalene, 0.5% polysorbate 80 and 0.48% Span 85), known as ‘MF59’ [57-59 chapter 10 of ref. 55; chapter 12 of ref. 60]. The MF59 emulsion advantageously includes citrate ions e.g. 10 mM sodium citrate buffer.
An emulsion of squalene, a tocopherol, and Tween 80 can be used The emulsion may include phosphate buffered saline. It may also include Span 85 (e.g. at 1%) and/or lecithin. These emulsions may have from 2 to 10% squalene, from 2 to 10% tocopherol and from 0.3 to 3% Tween 80, and the weight ratio of squalene:tocopherol is preferably ≦1 as this provides a more stable emulsion. One such emulsion can be made by dissolving Tween 80 in PBS to give a 2% solution, then mixing 90 ml of this solution with a mixture of (5 g of DL-α-tocopherol and 5 ml squalene), then microfluidizing the mixture. The resulting emulsion may have submicron oil droplets e.g. with an average diameter of between 100 and 250 nm, preferably about 180 nm.
An emulsion of squalene, a tocopherol, and a Triton detergent (e.g. Triton X-100) can be used.
An emulsion of squalane, polysorbate 80 and poloxamer 401 (“PluronicTM L121”) can be used. The emulsion can be formulated in phosphate buffered saline, pH 7.4. This emulsion is a useful delivery vehicle for muramyl dipeptides, and has been used with threonyl-MDP in the “SAF-1” adjuvant [61] (0.05-1% Thr-MDP, 5% squalane, 2.5% Pluronic L121 and 0.2% polysorbate 80). It can also be used without the Thr-MDP, as in the “AF” adjuvant [62] (5% squalane, 1.25% Pluronic L121 and 0.2% polysorbate 80). Microfluidisation is preferred.
Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used.
C. Saponin Formulations [Chapter 22 of Ref 55]
Saponin formulations may also be used as adjuvants in the invention. Saponins are a heterologous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponin from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponin can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria officianalis (soap root). Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs. QS21 is marketed as StimulonTM.
Saponin compositions have been purified using HPLC and RP-HPLC. Specific purified fractions using these techniques have been identified, including QS7, QS17, QS18, QS21, QH-A, QH-B and QH-C. Preferably, the saponin is QS21. A method of production of QS21 is disclosed in ref. 63. Saponin formulations may also comprise a sterol, such as cholesterol [64].
Combinations of saponins and cholesterols can be used to form unique particles called immunostimulating complexs (ISCOMs) [chapter 23 of ref. 55]. ISCOMs typically also include a phospholipid such as phosphatidylethanolamine or phosphatidylcholine. Any known saponin can be used in ISCOMs. Preferably, the ISCOM includes one or more of QuilA, QHA and QHC. ISCOMs are further described in refs. 64-66]. Optionally, the ISCOMS may be devoid of additional detergent [67].
A review of the development of saponin based adjuvants can be found in refs. 68 & 69.
D. Virosomes and Virus-Like Particles
Virosomes and virus-like particles (VLPs) can also be used as adjuvants in the invention. These structures generally contain one or more proteins from a virus optionally combined or formulated with a phospholipid. They are generally non-pathogenic, non-replicating and generally do not contain any of the native viral genome. The viral proteins may be recombinantly produced or isolated from whole viruses. These viral proteins suitable for use in virosomes or VLPs include proteins derived from influenza virus (such as HA or NA), Hepatitis B virus (such as core or capsid proteins), Hepatitis E virus, measles virus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus, Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages, Qβ-phage (such as coat proteins), GA-phage, fr-phage, AP205 phage, and Ty (such as retrotransposon Ty protein p1). VLPs are discussed further in [70-75]. Virosomes are discussed further in, for example [76].
E. Bacterial or Microbial Derivatives
Adjuvants suitable for use in the invention include bacterial or microbial derivatives such as non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), Lipid A derivatives, immunostimulatory oligonucleotides and ADP-ribosylating toxins and detoxified derivatives thereof.
Non-toxic derivatives of LPS include monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL). 3dMPL is a mixture of 3 de-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains. A preferred “small particle” form of 3 De-O-acylated monophosphoryl lipid A is disclosed in ref. 77. Such “small particles” of 3dMPL are small enough to be sterile filtered through a 0.22 μm membrane [77]. Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529 [78,79].
Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174. OM-174 is described for example in refs. 80 & 81.
Immunostimulatory oligonucleotides suitable for use as adjuvants in the invention include nucleotide sequences containing a CpG motif (a dinucleotide sequence containing an unmethylated cytosine linked by a phosphate bond to a guanosine). Double-stranded RNAs and oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
The CpG's can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded. References 82, 83 and 84 disclose possible analog substitutions e.g. replacement of guanosine with 2′-deoxy-7-deazaguanosine. The adjuvant effect of CpG oligonucleotides is further discussed in refs. 85-90.
The CpG sequence may be directed to TLR9, such as the motif GTCGTT or TTCGTT [91]. The CpG sequence may be specific for inducing a Th1 immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN. CpG-A and CpG-B ODNs are discussed in refs. 92-94. Preferably, the CpG is a CpG-A ODN.
Preferably, the CpG oligonucleotide is constructed so that the 5′ end is accessible for receptor recognition. Optionally, two CpG oligonucleotide sequences may be attached at their 3′ ends to form “immunomers”. See, for example, refs. 91 & 95-97.
Other immunostimulatory oligonucleotides include a double-stranded RNA, or an oligonucleotide containing a palindromic sequence, or an oligonucleotide containing a poly(dG) sequence.
Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the invention. Preferably, the protein is derived from E. coli (E. coli heat labile enterotoxin “LT”), cholera (“CT”), or pertussis (“PT”). The use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in ref. 98 and as parenteral adjuvants in ref. 99. The toxin or toxoid is preferably in the form of a holotoxin, comprising both A and B subunits. Preferably, the A subunit contains a detoxifying mutation; preferably the B subunit is not mutated. Preferably, the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LT-G192. The use of ADP-ribosylating toxins and detoxified derivatives thereof, particularly LT-K63 and LT-R72, as adjuvants can be found in refs. 100-107. Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in ref. 108, specifically incorporated herein by reference in its entirety.
Compounds of formula I, II or III (FIGS. 11A, 11B and 11C, respectively), can also be used as adjuvants:
as defined in reference 109, such as ‘ER 803058’, ‘ER 803732’, ‘ER 804053’, ER 804058′, ‘ER 804059’, ‘ER 804442’, ‘ER 804680’, ‘ER 804764’, ER 803022 or ‘ER 804057’ e.g.:




F. Human Immunomodulators

Human immunomodulators suitable for use as adjuvants in the invention include cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 [110], IL-17, IL-18 [111], IL-23, IL27 [112] etc.) [113], interferons (e.g. interferon-γ), macrophage colony stimulating factor, tumor necrosis factor and macrophage inflammatory protein-1 alpha (MTP-1alpha) and MIP-1beta [114].
G. Bioadhesives and Mucoadhesives
Bioadhesives and mucoadhesives may also be used as adjuvants in the invention. Suitable bioadhesives include esterified hyaluronic acid microspheres [115] or mucoadhesives such as cross-linked derivatives of poly(acrylic acid), polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the invention [116].
H. Microparticles
Microparticles may also be used as adjuvants in the invention. Microparticles (i.e. a particle of  ̃100 nm to  ̃150 μm in diameter, more preferably  ̃200 nm to  ̃30 μm in diameter, and most preferably  ̃500 nm to  ̃10 μm in diameter) formed from materials that are biodegradable and non-toxic (e.g. a poly(α-hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.), with poly(lactide-co-glycolide) are preferred, optionally treated to have a negatively-charged surface (e.g. with SDS) or a positively-charged surface (e.g. with a cationic detergent, such as CTAB).
I. Liposomes (Chapters 13 & 14 of Ref 55)
Examples of liposome formulations suitable for use as adjuvants are described in refs. 117-119.
J. Polyoxyethylene Ether and Polyoxyethylene Ester Formulations
Adjuvants suitable for use in the invention include polyoxyethylene ethers and polyoxyethylene esters [120]. Such formulations further include polyoxyethylene sorbitan ester surfactants in combination with an octoxynol [121] as well as polyoxyethylene alkyl ethers or ester surfactants in combination with at least one additional non-ionic surfactant such as an octoxynol [122]. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether (laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.
K. Phosphazenes (e.g. PCPP)
Phosphazene adjuvants include poly[di(carboxylatophenoxy)phosphazene] (“PCPP”) as described, for example, in references 123 and 124.
L. Muramyl Peptides
Examples of muramyl peptides suitable for use as adjuvants in the invention include N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), and N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine MTP-PE).
M. Imidazoquinolines
Imidazoquinoline adjuvants include Imiquimod (“R-837”) [125,126], Resiquimod (“R-848”) [127], and their analogs; and salts thereof (e.g. the hydrochloride salts). Further details about immunostimulatory imidazoquinolines can be found in references 128 to 132.
N. Thiosemicarbazones
Thiosemicarbazone adjuvants include those disclosed in reference 133. Methods of formulating, manufacturing, and screening for active compounds are also described in reference 131. The thiosemicarbazones are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF-α.
O. Tryptanthrins
Tryptanthrin adjuvants include those disclosed in reference 134. Methods of formulating, manufacturing, and screening for active compounds are also described in reference 134. The thiosemicarbazones are particularly effective in the stimulation of human peripheral blood mononuclear cells for the production of cytokines, such as TNF-α.
P. Nucleoside Analogs
Various nucleoside analogs can be used as adjuvants, such as (a) Isatorabine (ANA-245; 7-thia-8-oxoguanosine):




and prodrugs thereof; (b) ANA975; (c) ANA-025-1; (d) ANA380; (e) the compounds disclosed in references 135 to 137; (f) a compound having the formula:





wherein:

    
    
        R1 and R2 are each independently H, halo, —NRaRb, —OH, C1-6 alkoxy, substituted C1-6 alkoxy, heterocyclyl, substituted heterocyclyl, C6-10 aryl, substituted C6-10 aryl, C1-6 alkyl, or substituted C1-6 alkyl;
        R3 is absent, H, C1-6 alkyl, substituted C1-6 alkyl, C6-10 aryl, substituted C6-10 heterocyclyl, or substituted heterocyclyl;
        R4 and R5 are each independently H, halo, heterocyclyl, substituted heterocyclyl, —C(O)—Rd, C1-6 alkyl, substituted C1-6 alkyl, or bound together to form a 5 membered ring as in R4-5:
    
    






    
    
        
        
            the binding being achieved at the bonds indicated by a 
        
        
        X1 and X2 are each independently N, C, O, or S;
        R8 is H, halo, —OH, C1-6 alkyl, C2-6 alkenyl, C2-6 alkynyl, —OH, —NRaRb, —(CH2)n—O—Rc, —O—(C1-6 alkyl), —S(O)pRe, or —C(O)—Rd;
        R9 is H, C1-6 alkyl, substituted C1-6 alkyl, heterocyclyl, substituted heterocyclyl or R9a, wherein R9a is:
    
    






    
    
        
        
            the binding being achieved at the bond indicated by a 
        
        
        R10 and R11 are each independently H, halo, C1-6 alkoxy, substituted C1-6 alkoxy, —NRaRb, or —OH;
        each Ra and Rb is independently H, C1-6 alkyl, substituted C1-6 alkyl, —C(O)Rd, C6-10 aryl;
        each Re is independently H, phosphate, diphosphate, triphosphate, C1-6 alkyl, or substituted C1-6 alkyl;
        each Rd is independently H, halo, C1-6 alkyl, substituted C1-6 alkyl, C1-6 alkoxy, substituted C1-6 alkoxy, —NH2, —NH(C1-6 alkyl), —NH(substituted C1-6 alkyl), —N(C1-6 alkyl)2, —N(substituted C1-6 alkyl)2, C6-10 aryl, or heterocyclyl;
        each Re is independently H, C1-6 alkyl, substituted C1-6 alkyl, C6-10 aryl, substituted C6-10 aryl, heterocyclyl, or substituted heterocyclyl;
        each Rf is independently H, C1-6 alkyl, substituted C1-6 alkyl, —C(O)Rd, phosphate, diphosphate, or triphosphate;
        each n is independently 0, 1, 2, or 3;
        each p is independently 0, 1, or 2; or

or (g) a pharmaceutically acceptable salt of any of (a) to (f), a tautomer of any of (a) to (f), or a pharmaceutically acceptable salt of the tautomer.

Q. Lipids Linked to a Phosphate-Containing Acyclic Backbone

    
    


Adjuvants containing lipids linked to a phosphate-containing acyclic backbone include the TLR4 antagonist E5564 [138,139]:




R. Small Molecule Immunopotentiators (SMIPs)

SMIPs include:

    
    
        N2-methyl-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2,N2-dimethyl-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-ethyl-N2-methyl-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-methyl-1-(2-methylpropyl)-N2-propyl-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        1-(2-methylpropyl)-N2-propyl-1H-imidazo [4,5-c]quinoline-2,4-diamine;
        N2-butyl-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-butyl-N2-methyl-1-(2-methylpropyl)-1H-imidazo [4,5-c]quinoline-2,4-diamine;
        N2-methyl-1-(2-methylpropyl)-N2-pentyl-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-methyl-1-(2-methylpropyl)-N2-prop-2-enyl-1H-imidazo [4,5-c] quinoline-2,4-diamine;
        1-(2-methylpropyl)-2-[(phenylmethyl)thio]-1H-imidazo[4,5-c]quinolin-4-amine;
        1-(2-methylpropyl)-2-(propylthio)-1H-imidazo[4,5-c]quinolin-4-amine;
        2-[[4-amino-1-(2-methylpropyl)-1H-imidazo[4,5-c]quinolin-2-yl](methyl)amino]ethanol;
        2-[[4-amino-1-(2-methylpropyl)-1H-imidazo [4,5-c]quinolin-2-yl](methyl)amino]ethyl acetate;
        4-amino-1-(2-methylpropyl)-1,3-dihydro-2H-imidazo[4,5-c]quinolin-2-one;
        N2-butyl-1-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-butyl-N2-methyl-1-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2-methyl-1-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        N2,N2-dimethyl-1-(2-methylpropyl)-N4,N4-bis(phenylmethyl)-1H-imidazo[4,5-c]quinoline-2,4-diamine;
        1-{4-amino-2-[methyl(propyl)amino]-1H-imidazo[4,5-c]quinolin-1-yl}-2-methylpropan-2-ol;
        1-[4-amino-2-(propylamino)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol;
        N4,N4-dibenzyl-1-(2-methoxy-2-methylpropyl)-N2-propyl-1H-imidazo[4,5-c]quinoline-2,4-diamine.

S. Proteosomes

    
    


One adjuvant is an outer membrane protein proteosome preparation prepared from a first Gram-negative bacterium in combination with a liposaccharide preparation derived from a second Gram-negative bacterium, wherein the outer membrane protein proteosome and liposaccharide preparations form a stable non-covalent adjuvant complex. Such complexes include “IVX-908”, a complex comprised of Neisseria meningitidis outer membrane and lipopolysaccharides. They have been used as adjuvants for influenza vaccines [140].
T. Other Adjuvants
Other substances that act as immunostimulating agents are disclosed in references 55 and 60. Further useful adjuvant substances include:

    
    
        Methyl inosine 5′-monophosphate (“MIMP”) [141].
        A polyhydroxlated pyrrolizidine compound [142], such as one having formula:
    
    






    
    
        where R is selected from the group comprising hydrogen, straight or branched, unsubstituted or substituted, saturated or unsaturated acyl, alkyl (e.g. cycloalkyl), alkenyl, alkynyl and aryl groups, or a pharmaceutically acceptable salt or derivative thereof. Examples include, but are not limited to: casuarine, casuarine-6-α-D-glucopyranose, 3-epi-casuarine, 7-epi-casuarine, 3,7-diepi-casuarine, etc.
        A gamma inulin [143] or derivative thereof, such as algammulin.
        Compounds disclosed in reference 144.
        Compounds disclosed in reference 145, including: Acylpiperazine compounds, Indoledione compounds, Tetrahydraisoquinoline (THIQ) compounds, Benzocyclodione compounds, Aminoazavinyl compounds, Aminobenzimidazole quinolinone (ABIQ) compounds [146,147], Hydrapthalamide compounds, Benzophenone compounds, Isoxazole compounds, Sterol compounds, Quinazilinone compounds, Pyrrole compounds [148], Anthraquinone compounds, Quinoxaline compounds, Triazine compounds, Pyrazalopyrimidine compounds, and Benzazole compounds [149].
        Loxoribine (7-allyl-8-oxoguanosine) [150].
        A formulation of a cationic lipid and a (usually neutral) co-lipid, such as aminopropyl-dimethyl-myristoleyloxy-propanaminium bromide-diphytanoylphosphatidyl-ethanolamine (“VaxfectinTM”) or aminopropyl-dimethyl-bis-dodecyloxy-propanaminium bromide-dioleoylphosphatidyl-ethanolamine (“GAP-DLRIE:DOPE”). Formulations containing (±)-N-(3-aminopropyl)-N,N-dimethyl-2,3-bis(syn-9-tetradeceneyloxy)-1-propanaminium salts are preferred [151].
    
    


The invention may also comprise combinations of aspects of one or more of the adjuvants identified above. For example, the following adjuvant compositions may be used in the invention: (1) a saponin and an oil-in-water emulsion [152]; (2) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL) [153]; (3) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) [154]; (5) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions [155]; (6) RibiTM adjuvant system (RAS), (Bibi Immunochem) containing 2% squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (DetoxTM); and (7) one or more mineral salts (such as an aluminum salt)+a non-toxic derivative of LPS (such as 3dMPL).
The compositions of the invention will preferably elicit both a cell mediated immune response as well as a humoral immune response in order to effectively address a Chlamydia intracellular infection. This immune response will preferably induce long lasting (e.g. neutralizing) antibodies and a cell mediated immunity that can quickly respond upon exposure to Chlamydia. 
Two types of T cells, CD4 and CD8 cells, are generally thought necessary to initiate and/or enhance cell mediated immunity and humoral immunity. CD8 T cells can express a CD8 co-receptor and are commonly referred to as Cytotoxic T lymphocytes (CTLs). CD8 T cells are able to recognized or interact with antigens displayed on MHC Class I molecules.
CD4 T cells can express a CD4 co-receptor and are commonly referred to as T helper cells. CD4 T cells are able to recognize antigenic peptides bound to MHC class II molecules. Upon interaction with a MHC class H molecule, the CD4 cells can secrete factors such as cytokines. These secreted cytokines can activate B cells, cytotoxic T cells, macrophages, and other cells that participate in an immune response. Helper T cells or CD4+ cells can be further divided into two functionally distinct subsets: TH1 phenotype and TH2 phenotypes which differ in their cytokine and effector function.
Activated TH1 cells enhance cellular immunity (including an increase in antigen-specific CTL production) and are therefore of particular value in responding to intracellular infections. Activated TH1 cells may secrete one or more of IL-2, IFN-gamma, and TNF-beta. A TH1 immune response may result in local inflammatory reactions by activating macrophages, NK (natural killer) cells, and CD8 cytotoxic T cells (CTLs). A TH1 immune response may also act to expand the immune response by stimulating growth of B and T cells with IL-12. TH1 stimulated B cells may secrete IgG2a.
Activated TH2 cells enhance antibody production and are therefore of value in responding to extracellular infections. Activated TH2 cells may secrete one or more of IL-4, IL-5, IL-6, and IL-10. A TH2 immune response may result in the production of IgG1, IgE, IgA and memory B cells for future protection.
An enhanced immune response may include one or more of an enhanced TI-11 immune response and a TH2 immune response.
An enhanced TH1 immune response may include one or more of an increase in CTLs, an increase in one or more of the cytokines associated with a TH1 immune response (such as IL-2, IFN-gamma, and TNF-beta), an increase in activated macrophages, an increase in NK activity, or an increase in the production of IgG2a. Preferably, the enhanced Till immune response will include an increase in IgG2a production.
A TH1 immune response may be elicited using a TH1 adjuvant. A TH1 adjuvant will generally elicit increased levels of IgG2a production relative to immunization of the antigen without adjuvant. TH1 adjuvants suitable for use in the invention may include for example saponin formulations, virosomes and virus like particles, non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), immunostimulatory oligonucleotides. Immunostimulatory oligonucleotides, such as oligonucleotides containing a CpG motif, are preferred TH1 adjuvants for use in the invention.
An enhanced TH2 immune response may include one or more of an increase in one or more of the cytokines associated with a TH2 immune response (such as IL-4, IL-5, IL-6 and IL-10), or an increase in the production of IgG1, IgE, IgA and memory B cells. Preferably, the enhanced TH2 immune response will include an increase in IgG1 production.
A TH2 immune response may be elicited using a TH2 adjuvant. A TH2 adjuvant will generally elicit increased levels of IgG1 production relative to immunization of the antigen without adjuvant. TH2 adjuvants suitable for use in the invention include, for example, mineral containing compositions, oil-emulsions, and ADP-ribosylating toxins and detoxified derivatives thereof. Mineral containing compositions, such as aluminium salts are preferred TH2 adjuvants for use in the invention.
Preferably, the invention includes a composition comprising a combination of a TH1 adjuvant and a TH2 adjuvant. Preferably, such a composition elicits an enhanced TH1 and an enhanced TH2 response, i.e., an increase in the production of both IgG1 and IgG2a production relative to immunization without an adjuvant. Still more preferably, the composition comprising a combination of a TH1 and a TH2 adjuvant elicits an increased TH1 and/or an increased TH2 immune response relative to immunization with a single adjuvant (i.e., relative to immunization with a TH1 adjuvant alone or immunization with a TH2 adjuvant alone).
The immune response may be one or both of a TH1 immune response and a TH2 response. Preferably, immune response provides for one or both of an enhanced TH1 response and an enhanced TH2 response. The TH1/TH2 response in mice may be measured by comparing IgG2a and IgG1 titers, while the TH1/TH2 response in man may be measured by comparing the levels of cytokines specific for the two types of response (e.g. the IFN-γ/IL-4 ratio).
The enhanced immune response may be one or both of a systemic and a mucosal immune response. Preferably, the immune response provides for one or both of an enhanced systemic and an enhanced mucosal immune response. Preferably the mucosal immune response is a TH2 immune response. Preferably, the mucosal immune response includes an increase in the production of IgA.
A mineral salt, such as an aluminium salt, and an oligonucleotide containing a CpG motif may be combined to provide for an enhanced immune response. The invention therefore includes an oligonucleotide containing a CpG motif, a mineral salt such as an aluminium salt, and an antigen associated with a sexually transmissible disease, such as a Chlamydia trachomatis antigen. Further examples of antigens associated with a sexually transmissible disease are discussed further below.
The use of an aluminium hydroxide and/or aluminium phosphate adjuvant is particularly preferred, and antigens are generally adsorbed to these salts. Calcium phosphate is another preferred adjuvant. Other preferred adjuvant combinations include combinations of TH1 and TH2 adjuvants such as CpG & alum or resiquimod & alum.
The adjuvant may be selected from the group consisting of a mineral salt, such as an aluminium salt and an oligonucleotide containing a CpG motif. Most preferably, the immunogenic composition includes both an aluminium salt and an oligonucleotide containing a CpG motif.
Alternatively, the immunogenic composition includes an ADP ribosylating toxin, such as a detoxified ADP ribosylating toxin and an oligonucleotide containing a CpG motif.
Methods of Treatment and Medical Uses
The invention also provides a composition of the invention for use as a medicament. The medicament is preferably able to raise an immune response in a mammal (i.e. it is an immunogenic composition) and is more preferably a vaccine. The invention also provides the use of the compositions of the invention in the manufacture of a medicament for raising an immune response in a mammal. The medicament is preferably a vaccine.
The invention also provides one or more of (1) a GroEL-1 antigen, (3) a Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) a Rs10 antigen, (13) a Rs13 antigen, (14) a Rl1 antigen, (15) a CT875 antigen, (17) a RpoA antigen, (19) an Alanyl tRNA synthetase antigen, (20) a RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and/or (26) a CT814 antigen for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of (1) a GroEL-1 antigen, (3) a Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) a Rs10 antigen, (13) a Rs13 antigen, (14) a Rl1 antigen, (15) a CT875 antigen, (17) a RpoA antigen, (19) an Alanyl tRNA synthetase antigen, (20) a RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and/or (26) a CT814 antigen in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of (1) a GroEL-1 antigen, (3) a Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) a Rs10 antigen, (13) a Rs13 antigen, (14) a Rl1 antigen, (15) a CT875 antigen, (17) a RpoA antigen, (19) an Alanyl tRNA synthetase antigen, (20) a RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen and/or (26) a CT814 antigen in the manufacture of a medicament for the treatment of chlamydial infection.
The invention also provides one or more of the polypeptides recited in SEQ ID NOs: 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 18, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 138, 139, 140, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 155, 156, 157, 158, 159, 160, 163, 167, 168, 169, 170, 171 and/or 172 for use (i) as an immunogen, (ii) in therapy, and/or (iii) in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of the polypeptides recited in SEQ ID NOs: 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 18, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 138, 139, 140, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 155, 156, 157, 158, 159, 160, 163, 167, 168, 169, 170, 171 and/or 172 in the manufacture of a medicament for raising an immune response in a mammal.
The invention also provides the use of one or more of the polypeptides recited in SEQ ID NOs: 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 18, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 130, 131, 132, 133, 134, 135, 136, 138, 139, 140, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 155, 156, 157, 158, 159, 160, 163, 167, 168, 169, 170, 171 and/or 172 in the manufacture of a medicament for the treatment of chlamydial infection.
The phrase “one or more” in these uses includes, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.
The medicaments are preferably vaccines.
The invention also provides for a kit comprising a first component comprising a combination of Chlamydia trachomatis antigens. The combination of Chlamydia trachomatis antigens may be one or more of the immunogenic compositions of the invention. The kit may further include a second component comprising one or more of the following: instructions, syringe or other delivery device, adjuvant, or pharmaceutically acceptable formulating solution.
The invention also provides a delivery device pre-filled with the immunogenic compositions of the invention.
The invention also provides a method for raising an immune response in a mammal comprising the step of administering an effective amount of a composition of the invention. The immune response is preferably protective (such as an immunoprotective response) and preferably involves antibodies and/or cell-mediated immunity. Preferably, the immune response includes one or both of a TH1 immune response and a TH2 immune response. The method may raise a booster response.
Compositions of the invention can preferably protect against C. trachomatis biovars including one or both of trachoma and/or LGV.
Compositions of the invention can preferably protect against C. trachomatis serovars including one or more of A, B, C, D, E and K.
Compositions of the invention can preferably protect against C. trachomatis strains including one or both of D/UW-3/CX and L2/434/BU.
The mammal is preferably a human. Where the vaccine is for prophylactic use, the human is preferably a child (e.g. a toddler or infant) or a teenager; where the vaccine is for therapeutic use, the human is preferably a teenager or an adult. A vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc.
One way of checking efficacy of therapeutic treatment involves monitoring C. trachomatis infection after administration of the compositions of the invention. One way of checking efficacy of prophylactic treatment involves monitoring immune responses both systemically (such as monitoring the level of IgG1 and IgG2a production) and mucosally (such as monitoring the level of IgA production) against the Chlamydia trachomatis antigens in the compositions of the invention after administration of the composition. Typically, serum Chlamydia specific antibody responses are determined post-immunization but pre-challenge whereas mucosal Chlamydia specific antibody body responses are determined post-immunization and post-challenge.
These uses and methods are preferably for the prevention and/or treatment of a disease caused by a Chlamydia (e.g. trachoma, pelvic inflammatory disease, epididymitis, infant pneumonia, etc.). The compositions may also be effective against C. pneumoniae. 
The vaccine compositions (or immunogenic/immunoprotective compositions) of the present invention can be evaluated in in vitro and in vivo animal models prior to host, e.g., human, administration. For example, in vitro neutralization is suitable for testing vaccine compositions (such as immunogenic/immunoprotective compositions) directed toward Chlamydia trachomatis [156].
One example of such an in vitro test is described as follows. Hyper-immune antisera is diluted in PBS containing 5% guinea pig serum, as a complement source. Chlamydia trachomatis (104 IFU; inclusion forming units) are added to the antisera dilutions. The antigen-antibody mixtures are incubated at 37° C. for 45 minutes and inoculated into duplicate confluent Hep-2 or HeLa cell monolayers contained in glass vials (e.g., 15 by 45 mm), which have been washed twice with PBS prior to inoculation. The monolayer cells are infected by centrifugation at 1000×g for 1 hour followed by stationary incubation at 37° C. for 1 hour. Infected monolayers are incubated for 48 or 72 hours, fixed and stained with Chlamydia specific antibody, such as anti-MOMP. Inclusion-bearing cells are counted in ten fields at a magnification of 200×. Neutralization titer is assigned on the dilution that gives 50% inhibition as compared to control monolayers/IFU.
The efficacy of vaccine compositions (such as immunogenic/immunoprotective compositions) can also be determined in vivo by challenging animal models of Chlamydia trachomatis infection, e.g., guinea pigs or mice, with the vaccine compositions. For example, in vivo vaccine composition challenge studies in the guinea pig model of Chlamydia trachomatis infection can be performed. A description of one example of this type of approach follows. Female guinea pigs weighing 450-500 g are housed in an environmentally controlled room with a 12 hour light-dark cycle and immunized with vaccine compositions via a variety of immunization routes. Post-vaccination, guinea pigs are infected in the genital tract with the agent of guinea pig inclusion conjunctivitis (GPIC), which has been grown in HeLa or McCoy cells [157]. Each animal receives approximately 1.4×107 inclusion forming units (IFU) contained in 0.05 ml of sucrose-phosphate-glutamate buffer, pH 7.4 (Schacter, 1980). The course of infection monitored by determining the percentage of inclusion-bearing cells by indirect immunofluorescence with GPIC specific antisera, or by Giemsa-stained smear from a scraping from the genital tract [157]. Antibody titers in the serum are determined by an enzyme-linked immunosorbent assay.
Alternatively, in vivo vaccine compositions (such as immunogenic/immunoprotective compositions) challenge studies can be performed in the murine model of Chlamydia trachomatis [158]. A description of one example of this type of approach is as follows. Female mice 7 to 12 weeks of age receive 2.5 mg of depoprovera subcutaneously at 10 and 3 days before vaginal infection. Post-vaccination, mice are infected in the genital tract with 1,500 inclusion-forming units of Chlamydia trachomatis contained in 5 ml of sucrose-phosphate-glutamate buffer, pH 7.4. The course of infection is monitored by determining the percentage of inclusion-bearing cells by indirect immunofluorescence with Chlamydia trachomatis specific antisera, or by a Giemsa-stained smear from a scraping from the genital tract of an infected mouse. The presence of antibody titers in the serum of a mouse is determined by an enzyme-linked immunosorbent assay.
Compositions of the invention will generally be administered directly to a patient. Direct delivery may be accomplished by parenteral injection (e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly, or to the interstitial space of a tissue), or mucosally, such as by rectal, oral (e.g. tablet, spray), vaginal, topical, transdermal (See e.g. reference 159) or transcutaneous (See e.g. references 160 and 161), intranasal (See e.g. reference 162), ocular, aural, pulmonary or other mucosal administration.
The invention may be used to elicit systemic and/or mucosal immunity, preferably to elicit an enhanced systemic and/or mucosal immunity.
Preferably the enhanced systemic and/or mucosal immunity is reflected in an enhanced TH1 and/or TH2 immune response. Preferably, the enhanced immune response includes an increase in the production of IgG1 and/or IgG2a and/or IgA and/or IFN-γ/IL-4 ratio.
Dosage treatment can be a single dose schedule or a multiple dose schedule. Multiple doses may be used in a primary immunization schedule and/or in a booster immunization schedule. In a multiple dose schedule the various doses may be given by the same or different routes e.g. a parenteral prime and mucosal boost, a mucosal prime and parenteral boost, etc.
Chlamydial infections affect various areas of the body and so the compositions of the invention may be prepared in various forms. For example, the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g. a lyophilised composition or a spray-freeze dried composition). The composition may be prepared for topical administration e.g. as an ointment, cream or powder. The composition may be prepared for oral administration e.g. as a tablet or capsule, as a spray, or as a syrup (optionally flavoured). The composition may be prepared for pulmonary administration e.g. as an inhaler, using a fine powder or a spray. The composition may be prepared as a suppository or pessary. The composition may be prepared for nasal, aural or ocular administration e.g. as drops. The composition may be in kit form, designed such that a combined composition is reconstituted just prior to administration to a patient. Such kits may comprise one or more antigens in liquid form and one or more lyophilised antigens.
Where a composition is to be prepared extemporaneously prior to use (e.g. where a component is presented in lyophilised form) and is presented as a kit, the kit may comprise two vials, or it may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reactivate the contents of the vial prior to injection.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of antigen(s), as well as any other components, as needed. By ‘immunologically effective amount’, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, age, the taxonomic group of individual to be treated (e.g. non-human primate, primate, etc.), the capacity of the individual's immune system to synthesize antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.
The invention further provides a method for preparing a pharmaceutical product, comprising the steps of: (a) preparing a composition as described above; (b) mixing the composition with one or more pharmaceutically acceptable carriers; and (c) packaging the composition/carrier mixture into a container, such as a vial or a syringe, to give a pharmaceutical product. Insertion into a syringe may be performed in a factory or in a surgery.
Methods of Activating Chlamydia-Specific T Cells
The polynucleotides and/or immunogenic polypeptides of the present invention can be used to activate Chlamydia-specific T cells either in vitro or in vivo. Activation of Chlamydia-specific T cells can be used, inter alia, to provide model systems to optimize CTL responses to Chlamydia and to provide prophylactic or therapeutic treatment against Chlamydia infection.
Polyclonal populations of T cells can be derived from the blood, and preferably from peripheral lymphoid organs, such as lymph nodes, spleen, or thymus, of mammals that have been infected with Chlamydia. Preferred mammals include mice, chimpanzees, baboons, and humans. Infection with Chlamydia serves to expand the number of activated Chlamydia-specific T cells in the mammal. The Chlamydia-specific T cells derived from the mammal can then be restimulated in vitro by adding, a Chlamydia immunogenic polypeptide, polyprotein, and/or multiepitope fusion protein. The Chlamydia-specific T cells can then be tested for, inter alia, proliferation, the production of IFN-γ, and the ability to lyse target cells displaying, for example, the polypeptides of the present invention.
In a lymphoproliferation assay, Chlamydia-activated CD4+ T cells proliferate when cultured with a Chlamydia immunogenic polypeptide, polyprotein, and/or multiepitope fusion protein, but not in the absence of such an immunogenic polypeptide. Thus, particular Chlamydia polypeptides and fusions of these polypeptides that are recognized by Chlamydia-specific CD4+ T cells can be identified using a lymphoproliferation assay.
Similarly, detection of IFN-γ in Chlamydia-specific CD4+ and/or CD8+ T cells after in vitro stimulation with the above-described immunogenic polypeptides, can be used to identify, for example, epitopes and fusions of these epitopes that are particularly effective at stimulating CD4+ and/or CD8+ T cells to produce IFN-γ.
Further, 51Cr release assays are useful for determining the level of CTL response to Chlamydia [163]. For example, Chlamydia-specific CD8+ T cells can be derived from a Chlamydia infected mammal. These T cells can be tested in 51Cr release assays against target cells displaying one or more of the polypeptides of the present invention. Several target cell populations expressing different polypeptides epitopes can be constructed so that each target cell population displays different epitopes and polypeptides. The Chlamydia-specific CD8+ cells can be assayed against each of these target cell populations. The results of the 51Cr release assays can be used to determine which epitopes and polypeptides are responsible for the strongest CTL response to Chlamydia. 
A composition of the invention comprising a Chlamydia immunogenic polypeptide, or polynucleotide encoding such a polypeptide is administered in a manner compatible with the particular composition used and in an amount which is effective to activate Chlamydia-specific T cells as measured by, inter alia, a 51Cr release assay, a lymphoproliferation assay, or by intracellular staining for IFN-γ. The proteins and/or polynucleotides can be administered either to a mammal which is not infected with Chlamydia or can be administered to a Chlamydia-infected mammal.
Immune responses of a mammal generated by the delivery of a composition of the invention, including activation of Chlamydia-specific T cells, can be enhanced by varying the dosage, route of administration, or boosting regimens. Compositions of the invention may be given in a single dose schedule, or preferably in a multiple dose schedule in which a primary course of vaccination includes 1-10 separate doses, followed by other doses given at subsequent time intervals required to maintain and/or reinforce an immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose or doses after several months.
Further Components of the Composition
Compositions of the invention can be combined with pharmaceutically acceptable carriers. Such carriers include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolised macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, sucrose, trehalose, lactose, and lipid aggregates (such as oil droplets or liposomes). Such carriers are well known to those of ordinary skill in the art. The vaccines may also contain diluents, such as water, saline, glycerol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present. Sterile pyrogen-free, phosphate-buffered physiologic saline is a typical carrier. A thorough discussion of pharmaceutically acceptable excipients is available in reference 164.
Preferred compositions may further contain one or more antigens from another sexually transmitted disease causing organism, other disease causing organisms or antibiotics used to treat Chlamydia infections.
Antigens which may be included in compositions of the invention include, but are not limited to:

    
    
        an outer-membrane vesicle (OMV) preparation from N. meningitidis serogroup B, such as those disclosed in refs. 165-168 etc.
        a saccharide antigen from N. meningitidis serogroup A, C, W135 and/or Y, such as the oligosaccharide disclosed in ref. 169 from serogroup C [see also ref. 170] or the oligosaccharides of ref. 171.
        a protein antigen from N. meningitidis serogroup B, such as those disclosed in refs. 172-180, etc.
        antigens from Helicobacter pylori such as CagA [181 to 184], VacA [185, 186], NAP [187, 188, 189], HopX [e.g. 190], HopY [e.g. 190] and/or urease.
        a saccharide antigen from Streptococcus pneumoniae [e.g. 191, 192, 193].
        an antigen from hepatitis A virus, such as inactivated virus [e.g. 194, 195].
        an antigen from hepatitis B virus, such as the surface and/or core antigens [e.g. 195, 196].
        an antigen from hepatitis C virus [e.g. 197].
        an antigen from HIV [198]
        a diphtheria antigen, such as a diphtheria toxoid [e.g. chapter 3 of ref. 199].
        a tetanus antigen, such as a tetanus toxoid [e.g. chapter 4 of ref. 199].
        an antigen from Bordetella pertussis, such as pertussis holotoxin (PT) and filamentous haemagglutinin (FHA) from B. pertussis, optionally also in combination with pertactin and/or agglutinogens 2 and 3 [e.g. refs. 200 & 201].
        a saccharide antigen from Haemophilus influenzae B [e.g. 170].
        polio antigen(s) [e.g. 202, 203] such as IPV.
        an antigen from N. gonorrhoeae [e.g. 204, 205, 206, 207].
        an antigen from Chlamydia pneumoniae [e.g. refs. 208 to 214].
        an antigen from Porphyromonas gingivalis [e.g. 215].
        rabies antigen(s) [e.g. 216] such as lyophilised inactivated virus [e.g. 217, RabAvertTM].
        measles, mumps and/or rubella antigens [e.g. chapters 9, 10 & 11 of ref. 199].
        influenza antigen(s) [e.g. chapter 19 of ref. 199], such as the haemagglutinin and/or neuraminidase surface proteins. The flu antigen may be selected from a pandemic strain.
        antigen(s) from a paramyxovirus such as respiratory syncytial virus (RSV [218, 219]) and/or parainfluenza virus (PIV3 [220]).
        an antigen from Moraxella catarrhalis [e.g. 221].
        an antigen from Streptococcus pyogenes (group A streptococcus) [e.g. 222, 223, 224].
        an antigen from Staphylococcus aureus [e.g. 225].
        an antigen from Bacillus anthracis [e.g. 226, 227, 228].
        an antigen from a virus in the flaviviridae family (genus flavivirus), such as from yellow fever virus, Japanese encephalitis virus, four serotypes of Dengue viruses, tick-borne encephalitis virus, West Nile virus.
        a pestivirus antigen, such as from classical porcine fever virus, bovine viral diarrhoea virus, and/or border disease virus.
        a parvovirus antigen e.g. from parvovirus B19.
        a prion protein (e.g. the CJD prion protein)
        an amyloid protein, such as a beta peptide [229]
        a cancer antigen, such as those listed in Table 1 of ref. 230 or in tables 3 & 4 of ref. 231
        an allergen that triggers an allergic or asthmatic response
        a Human Papilloma Virus (HPV) antigen (see WO 00/09699)
    
    


Preferred gonococcal antigens include ngs13 (OmpA), OmpH, ngs576 (peptidyl-prolyl cis/trans isomerase (PPIase) protein), ngs41 and ngs117.
Preferred HPV antigens include one or more of HPV 16, HPV 18, HPV 6 and HPV 11.
The composition may further comprise an antibiotic that is useful for the treatment of chlamydial infection. Preferred antibiotics for use in the compositions include the tetracyclines, azithromycin and erythromycin. A particular preferred antibiotic is rifalazil.
Nucleic Acid Immunisation
The immunogenic compositions described above include polypeptide antigens from C. trachomatis. In all cases, however, the polypeptide antigens can be replaced by nucleic acids (typically DNA) encoding those polypeptides, to give compositions, methods and uses based on nucleic acid immunisation. Nucleic acid immunisation is now a developed field (e.g. see references 232 to 239 etc.), and has been applied to C. trachomatis vaccines [240-245].
The nucleic acid encoding the immunogen is expressed in vivo after delivery to a patient and the expressed immunogen then stimulates the immune system. The active ingredient will typically take the form of a nucleic acid vector comprising: (i) a promoter; (ii) a sequence encoding the immunogen, operably linked to the promoter; and optionally (iii) a selectable marker. Preferred vectors may further comprise (iv) an origin of replication; and (v) a transcription terminator downstream of and operably linked to (ii). In general, (i) & (v) will be eukaryotic and (iii) & (iv) will be prokaryotic.
Preferred promoters are viral promoters e.g. from cytomegalovirus (CMV). The vector may also include transcriptional regulatory sequences (e.g. enhancers) in addition to the promoter and which interact functionally with the promoter. Preferred vectors include the immediate-early CMV enhancer/promoter, and more preferred vectors also include CMV intron A. The promoter is operably linked to a downstream sequence encoding an immunogen, such that expression of the immunogen-encoding sequence is under the promoter's control.
Where a marker is used, it preferably functions in a microbial host (e.g. in a prokaryote, in a bacteria, in a yeast). The marker is preferably a prokaryotic selectable marker (e.g. transcribed under the control of a prokaryotic promoter). For convenience, typical markers are antibiotic resistance genes.
The vector of the invention is preferably an autonomously replicating episomal or extrachromosomal vector, such as a plasmid.
The vector of the invention preferably comprises an origin of replication. It is preferred that the origin of replication is active in prokaryotes but not in eukaryotes.
Preferred vectors thus include a prokaryotic marker for selection of the vector, a prokaryotic origin of replication, but a eukaryotic promoter for driving transcription of the immunogen-encoding sequence. The vectors will therefore (a) be amplified and selected in prokaryotic hosts without polypeptide expression, but (b) be expressed in eukaryotic hosts without being amplified. This arrangement is ideal for nucleic acid immunization vectors.
The vector of the invention may comprise a eukaryotic transcriptional terminator sequence downstream of the coding sequence. This can enhance transcription levels. Where the coding sequence does not have its own, the vector of the invention preferably comprises a polyadenylation sequence. A preferred polyadenylation sequence is from bovine growth hormone.
The vector of the invention may comprise a multiple cloning site.
In addition to sequences encoding the immunogen and a marker, the vector may comprise a second eukaryotic coding sequence. The vector may also comprise an IRES upstream of said second sequence in order to permit translation of a second eukaryotic polypeptide from the same transcript as the immunogen. Alternatively, the immunogen-coding sequence may be downstream of an IRES.
The vector of the invention may comprise unmethylated CpG motifs e.g. unmethylated DNA sequences which have in common a cytosine preceding a guanosine, flanked by two 5′ purines and two 3′ pyrimidines. In their unmethylated form these DNA motifs have been demonstrated to be potent stimulators of several types of immune cell.
Vectors may be delivered in a targeted way. Receptor-mediated DNA therapy techniques are described in, for example, references 246 to 251. Therapeutic compositions containing a nucleic acid are administered in a range of about 100 ng to about 200 mg of DNA for local administration in a gene therapy protocol. Concentration ranges of about 500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg to about 100 μg of DNA can also be used during a gene therapy protocol. Factors such as method of action (e.g. for enhancing or inhibiting levels of the encoded gene product) and efficacy of transformation and expression are considerations which will affect the dosage required for ultimate efficacy. Where greater expression is desired over a larger area of tissue, larger amounts of vector or the same amounts re-administered in a successive protocol of administrations, or several administrations to different adjacent or close tissue portions may be required to effect a positive therapeutic outcome. In all cases, routine experimentation in clinical trials will determine specific ranges for optimal therapeutic effect.
Vectors can be delivered using gene delivery vehicles. The gene delivery vehicle can be of viral or non-viral origin (see generally references 252 to 255).
Viral-based vectors for delivery of a desired nucleic acid and expression in a desired cell are well known in the art. Exemplary viral-based vehicles include, but are not limited to, recombinant retroviruses (e.g. references 256 to 266), alphavirus-based vectors (e.g. Sindbis virus vectors, Semliki forest virus (ATCC VR-67; ATCC VR-1247), Ross River virus (ATCC VR-373; ATCC VR-1246) and Venezuelan equine encephalitis virus (ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532); hybrids or chimeras of these viruses may also be used), poxvirus vectors (e.g. vaccinia, fowlpox, canarypox, modified vaccinia Ankara, etc.), adenovirus vectors, and adeno-associated virus (AAV) vectors (e.g. see refs. 267 to 272). Administration of DNA linked to killed adenovirus [273] can also be employed.
Non-viral delivery vehicles and methods can also be employed, including, but not limited to, polycationic condensed DNA linked or unlinked to killed adenovirus alone [e.g. 273], ligand-linked DNA [274], eukaryotic cell delivery vehicles cells [e.g. refs. 275 to 279] and nucleic charge neutralization or fusion with cell membranes. Naked DNA can also be employed. Exemplary naked DNA introduction methods are described in refs. 280 and 281. Liposomes (e.g. immunoliposomes) that can act as gene delivery vehicles are described in refs. 282 to 286. Additional approaches are described in references 287 & 288.
Further non-viral delivery suitable for use includes mechanical delivery systems such as the approach described in ref. 288. Moreover, the coding sequence and the product of expression of such can be delivered through deposition of photopolymerized hydrogel materials or use of ionizing radiation [e.g. refs. 289 & 290]. Other conventional methods for gene delivery that can be used for delivery of the coding sequence include, for example, use of hand-held gene transfer particle gun [291] or use of ionizing radiation for activating transferred genes [289 & 292].
Delivery DNA using PLG {poly(lactide-co-glycolide)} microparticles is a particularly preferred method e.g. by adsorption to the microparticles, which are optionally treated to have a negatively-charged surface (e.g. treated with SDS) or a positively-charged surface (e.g. treated with a cationic detergent, such as CTAB).
Antibodies
Antibodies can be generated to bind specifically to a surface-exposed and/or surface-associated antigen of the invention. The invention therefore provides an antibody that is specific for (1) a GroEL-1 antigen, (3) an Ef-Tu antigen, (6) a HctA antigen, (7) a CT577 antigen, (8) a CT223 antigen, (9) a GroeS antigen, (11) an Rs10 antigen, (13) an Rs13 antigen, (14) an R11 antigen, (15) a CT875 antigen, (17) an RpoA antigen, (19) an Alanyl tRNA synthetase antigen, (20) an RpoC antigen, (21) a YaeL antigen, (22) an EF-G antigen, (23) a CT578 antigen, (24) a CT579 antigen, (25) a CT680 antigen or (26) a CT814 antigen. Preferably an antibody according to the invention binds one of these 20 antigens with substantially greater affinity than antibodies known in the art. Preferably, the affinity is at least 1.5-fold, 2-fold, 5-fold 10-fold, 100-fold, 103-fold, 104-fold, 105-fold, 106-fold stronger than antibodies known in the art or greater.
The term “antibody” includes intact immunoglobulin molecules, as well as fragments thereof which are capable of binding an antigen. These include hybrid (chimeric) antibody molecules [293, 294]; F(ab′)2 and F(ab) fragments and Fv molecules; non-covalent heterodimers [295, 296]; single-chain Fv molecules (sFv) [297]; dimeric and trimeric antibody fragment constructs; minibodies [298, 299]; humanized antibody molecules [300-302]; and any functional fragments obtained from such molecules, as well as antibodies obtained through non-conventional processes such as phage display. Preferably, the antibodies are monoclonal antibodies. Methods of obtaining monoclonal antibodies are well known in the art.
Typically, at least 6, 7, 8, 10, or 12 contiguous amino acids are required to form an epitope. However, epitopes which involve non-contiguous amino acids may require more, e.g., at least 15, 25, or 50 amino acids. Various immunoassays (e.g., Western blots, ELISAs, radioimmunoassays, immunohistochemical assays, immunoprecipitations, or other immunochemical assays known in the art) can be used to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays are well known in the art. Such immunoassays typically involve the measurement of complex formation between an immunogen and an antibody which specifically binds to the immunogen. A preparation of antibodies which specifically bind to a particular antigen typically provides a detection signal at least 5-, 10-, or 20-fold higher than a detection signal provided with other proteins when used in an immunochemical assay. Preferably, the antibodies do not detect other proteins in immunochemical assays and can immunoprecipitate the particular antigen from solution.
Generation of Antibodies
The surface-exposed antigens of the invention can be used to immunize a mammal, such as a mouse, rat, rabbit, guinea pig, monkey, or human, to produce polyclonal antibodies. If desired, an antigen can be conjugated to a carrier protein, such as bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin. Depending on the host species, various adjuvants can be used to increase the immunological response. Such adjuvants include those described above, as well as those not used in humans, for example, Freund's adjuvant.
Monoclonal antibodies which specifically bind to an antigen can be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These techniques include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique [303-306].
In addition, techniques developed for the production of “chimeric antibodies,” the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used [307-309]. Monoclonal and other antibodies also can be “humanized” to prevent a patient from mounting an immune response against the antibody when it is used therapeutically. Such antibodies may be sufficiently similar in sequence to human antibodies to be used directly in therapy or may require alteration of a few key residues. Sequence differences between rodent antibodies and human sequences can be minimized by replacing residues which differ from those in the human sequences by site directed mutagenesis of individual residues or by grating of entire complementarity determining regions.
Alternatively, humanized antibodies can be produced using recombinant methods, as described below. Antibodies which specifically bind to a particular antigen can contain antigen binding sites which are either partially or fully humanized, as disclosed in reference 310.
Alternatively, techniques described for the production of single chain antibodies can be adapted using methods known in the art to produce single chain antibodies which specifically bind to a particular antigen. Antibodies with related specificity, but of distinct idiotypic composition, can be generated by chain shuffling from random combinatorial immunoglobin libraries [311].
Single-chain antibodies also can be constructed using a DNA amplification method, such as PCR, using hybridoma cDNA as a template [312]. Single-chain antibodies can be mono- or bispecific, and can be bivalent or tetravalent. Construction of tetravalent, bispecific single-chain antibodies is taught, for example, in reference 313. Construction of bivalent, bispecific single-chain antibodies is taught in reference 314.
A nucleotide sequence encoding a single-chain antibody can be constructed using manual or automated nucleotide synthesis, cloned into an expression construct using standard recombinant DNA methods, and introduced into a cell to express the coding sequence, as described below. Alternatively, single-chain antibodies can be produced directly using, for example, filamentous phage technology [315, 316].
Antibodies which specifically bind to a particular antigen also can be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature [317, 293].
Chimeric antibodies can be constructed as disclosed in reference 318. Binding proteins which are derived from immunoglobulins and which are multivalent and multispecific, such as the “diabodies” described in reference 319, also can be prepared.
Antibodies can be purified by methods well known in the art. For example, antibodies can be affinity purified by passage over a column to which the relevant antigen is bound. The bound antibodies can then be eluted from the column using a buffer with a high salt concentration.
General
The term “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
The term “about” in relation to a numerical value x means, for example, x±10%.
References to a percentage sequence identity between two amino acid sequences means that, when aligned, that percentage of amino acids are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in section 7.7.18 of Current Protocols in Molecular Biology (F. M. Ausubel et al., eds., 1987) Supplement 30. A preferred alignment is determined by the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith-Waterman homology search algorithm is disclosed in Smith & Waterman (1981) Adv. Appl. Math. 2: 482-489
The CT nomenclature was first described in reference 4, though further work on the identification of genes has been carried out using the methods described in reference 320. It is now the standard way of referring to proteins from Chlamydia trachomatis. 



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the neutralizing titers of mouse sera against 11 CT recombinant antigens. To evaluate their neutralizing activity, sera of mice immunized with the recombinant proteins were pre-incubated with purified EBs before in vitro infection. Titers are determined as the serum dilution giving 50% neutralization of infection, as compared with the infection obtained after EBs incubation with the corresponding Pre-immune serum.
FIG. 2a shows the flow cytometric assessment of antigen-specific CD4+Th-cells in spleen cells of mice infected intravaginally with C. trachomatis. Splenocytes of infected mice were collected 10 days after infection and stimulated with EB (10 μg/ml). After 4 hours of stimulation, 5 μg/ml of Brefeldin A were added to the cells for the following 12 hrs, to block cytokines secretion. Afterwards cells were fixed, permeabilized and stained. The intracellular IFN-γ and IL-5 expression was analyzed versus CD4 and CD8 surface expression of the gated viable cells. The left panel shows the CD4+ T cell subset gated for analyses. The right panel shows the CD4+ T cells producing IFNγ and IL-5 upon EB stimulation.
FIG. 2b shows the identification of antigens capable of inducing CD4 Th1 cells in BALB/c mice after a primary CT infection. Splenocytes of primary infected mice and non infected controls were collected 10 days after infection and stimulated with EB (10 μg/ml) or rMOMP (20 μml). After 4 hours of stimulation, 5 μg/ml of Brefeldin A were added to the cells for the following 12 hrs, to block cytokines secretion. Afterwards cells were fixed, permeabilized and stained. The intracellular IFN-γ and IL-5 expression was analyzed versus CD4 and CD8 surface expression of the gated viable cells, and assessed by flow cytometry. The histogram shows the number of CD4+T cells that produce IFN-γ upon specific stimulation with Ct EB or rMOMP, every 105 CD4+T splenocytes of primary infected (red bars) and mock-infected (green bars) mice. Data are representative of three different experiments that showed similar results. Data show a high frequency of EB-specific IFN-γ producing CD4 T cells in primary infected mice. A relatively high frequency is also shown for the most abundant EB surface protein MOMP, so far the only single antigen known from peer reviewed journal publications to confer protection in mice.
FIG. 3 shows those antigens inducing C. trachomatis specific CD4+/IFNγ+ T cells in splenocytes of BALB/c mice infected with C. trachomatis EBs upon in vitro stimulation with recombinant antigens.
FIG. 4 shows the clustered analysis of 53 human sera. The profile of 53 human sera obtained on the 53-Ag array is shown. Protein specific mean fluorescence signals have been grouped into four ranges. White squares indicate non specific background fluorescence (<5000 Fluorescence Intensity Units above background); yellow, orange and red squares indicate low (>5000 and <15000), medium (>15000 and <30000) and strong signals (>30000), respectively. For each serum, MIF titer is reported nearby. Neutralizing antigens are highlighted in red.
FIG. 5 shows the mouse model of vaginal infection with C. muridarum. To determine the optimal infectious dose of C. muridarum BALB/c mice were infected with two doses infectious doses of MoPn EB (105, 106 IFU). Number of IFU (inclusion forming units=viable chlamydiae) recovered from vaginal swabs after infection were determined at different time points with increasing infectious doses of MoPn EB (105, 106 IFU). The experiment was performed twice using groups of 30 mice in each experiment, and showed that BALB/c mice can be infected in a high percentage both using 105 or 106 IFU as the infecting dose. The experiments also showed that mice can be assessed for up to 21-23 days post infection (p.i.) while they completely recover by day 25 to 30 p.i.
FIG. 6 shows the set up of positive control of protection with C. muridarum. Group of 30 BALB/c mice received a primary infection with 106 C. muridarum IFU and vaginal swabs were collected at time intervals up to for 45 days p.i., to assure a complete bacterial clearance in the lower genital tract. Mice were then re-challenged with 105 IFU of C. muridarum. Protection level was determined by measuring the mean IFU in vaginal swabs of mice that received only a primary infection and mice that were re-challenged at week intervals (left panel). Protection was also determined considering the percentage of mice with positive vaginal swabs at week intervals (right panel). Mice that received a secondary infection (red symbols) showed a complete clearance of infectious chlamydiae in the lower genital tract by day 14 p.i., as compared to mice that received only a primary infection (black symbols).
FIG. 7 shows the set up of the mouse model of vaginal infection with C. trachomatis serovar D. BALB/c mice received a primary infection with 106 C. trachomatis serovar D IFU and vaginal swabs were collected at time intervals up to for 28 days p.i., to assure a complete bacterial clearance in the lower genital tract. Mice were then re-challenged with 105 IFU of C. trachomatis. Protection level was determined by comparing, at week intervals, the mean IFU in the vaginal swabs of re-challenged mice (red bars) with those of mice that were immunized with PBS/alum CpG and subsequently infected with 105 IFU of C. trachomatis (dark bars). Statistical significance of reduction of the mean IFU counts was done using Student t-test. Absolute numbers of infected mice are reported. Mice that received a secondary infection (light bars) showed a significant reduction in the number of IFU counts in the lower genital tract by day 7 p.i., as compared to mice that received only a primary infection.
FIG. 8 shows the immunisation, challenge and read-out schedule for the protective antigen assay.
FIG. 9 shows the evaluation of the protective effect of the 5 antigen combo. A group of 10 BALB/c mice were immunized three times i.p. with a combination of 5 antigens, including CT089, CT045, CT381, CT398, CT396, with Alum+CpG as adjuvant. 10 days post last immunization the mice were hormone-treated with 2.5 mg of Medroxyprogesterone acetate and 5 days later were challenged intra-vaginally with 105 IFU of C. trachomatis. Vaginal swabs were collected at week-intervals and number of viable chlamydiae (IFU) were measured. Data show the mean IFU counts at day 14 post challenge in the 5 antigen-combo immunized mice (light bars) and adjuvant immunized control (dark bars) in four independent experiments. The statistical significance of each experiment (p) was determined by Student t-test.
FIG. 10 shows the PREDBALB/c system output for CT823, CT587 and CT043.
FIGS. 11A-11C show adjuvant compounds of formula I (FIG. 11A), formula II (FIG. 11B) and formula III (FIG. 11C) as described in the application.



MODES FOR CARRYING OUT THE INVENTION
Identifying Surface-Exposed and/or Surface-Associated Chlamydia Antigens
Surface-exposed and/or surface-associated Chlamydia antigens can be identified using any one or combination of several proteomics approaches as outlined below. These proteomics strategies have great potential for shortening the time needed for vaccine discovery when compared with other strategies, such as reverse vaccinology. Surface-exposed and/or surface-associated Chlamydia antigens identified by these methods can be used as active agents in compositions for preventing and for treating Chlamydia infections.
One method for identifying surface-exposed and/or surface-associated Chlamydia antigens is described as follows: the surface of Chlamydia Elementary bodies (EBs) is digested in vivo under physiological conditions using reagents which cleave proteins. Typically the reagents are proteases (e.g., trypsin, protease K, papain), although any protein cleavage reagent can be used. These reagents include, for example, formic acid, hydroxylamine, BNPS-skatole (3-bromo-3-methyl-2-(o-nitrophenylsulfenyl)-indolenine), which cleaves at Trp residues), cyanogen bromide (which cleaves polypeptides on the carboxyl side of methionine residues), metal chelate reagents such as Fe-EDTA, and the like. Proteases can be either free or anchored, this latter condition favoring the identification of surface extruding regions. Combinations of more than one protein cleavage regent can be used. The recovered peptides are then separated by liquid chromatography and identified by tandem mass spectrometry. The actual accessibility of identified proteins to the immune system can be assessed by fluorescence-activated cell sorting (FACS) analysis. This proteomic approach permits validation of software-based topology predictions and vice versa.
Another method for identifying surface-exposed and/or surface-associated Chlamydia antigens includes the production of cell wall and/or membrane fractions which are generated by chemical cell fractionation of bacterial cells using, for example, 6 M guanidinium, urea, or SDS. The cell wall is insoluble in these reagents. This property allows the isolation of the cell wall and identification of anchored cell wall proteins. Chlamydia proteins in these fractions can be separated and identified as described above.
A further method for identifying surface-exposed and/or surface-associated Chlamydia antigens involves labeling cell surface Chlamydia proteins (e.g., by biotinylation), lysing the cells, and isolating labeled proteins using affinity chromatography. The isolated proteins can be separated by electrophoresis and identified using mass spectrometry. Alternatively, the isolated proteins can be digested in solution, followed by isolation of labeled peptides by affinity chromatography, separation of the labeled peptides by liquid chromatography, and identification of the labeled peptides using tandem mass spectrometry. These methods selectively isolate the labeled peptides, therefore they allow identification of the truly exposed domains. In this case, the use of two affinity chromatography steps results in a reduction of complexity of the sample to be loaded on the chromatography column.
For all the above embodiments a mutant can be used which harbors a deleted gene for one of the more abundant known surface-exposed antigens. These mutants will increase the probability of spotting previously unidentified, less abundant surface proteins
Proteolysis of the Chlamydial Surface and Analysis of Resultant Peptides.
Infectious forms (Elementary bodies, EBs) of Chlamydia trachomatis were grown in cell cultures and purified by gradient centrifugation as described in the literature. Approximately, 107 IFU of purified EBs in SPG Chlamydia transport buffer were digested (“shaved”) with trypsin. Limited digestion was carried out with 20 μg trypsin (Promega, Madison, Wis., USA) for 30 min at 37° C.
The digestion mixture was centrifuged in an Eppendorf centrifuge at 14,000 g for 30 min at 4° C., in order to separate the chlamydial cells from the peptides released by the surface proteolysis. The supernatant, containing the peptides released by trypsin digestion, was filtered from residual chlamydial cells either (a) by centrifugation at 4° C. in Centricon tubes or (b) by filtration using 10 kDa pore-size filters. The filtrate was treated with formic acid (0.1% formic acid final concentration) and submitted to proteomic analysis for the identification of the released peptides and consequent identification of the proteins which were exposed on the chlamydial surface.
In an alternative method, which has been found to recover around 20× more chlamydial elementary bodies, a Renografin density gradient is used.
Monolayers of rhesus monkey kidney (LLCMK2) cells were grown on glass coverslips in Eagle minimal essential medium (with Earle salts, 5% fetal bovine serum, gentamicin at 50 mg/ml, and cycloheximide at 1.5 mg/ml) and infected with the elementary bodies. 48 hours post-inoculation, cells were harvested with a cell scraper and disrupted by sonication (3×10 seconds, maximal power Sonicator IKA LABSYSTEM mod. U50 with probe MS 3 of 3 mm). Broken cells were centrifuged at 1,000×g for 10 min. at 4° C. The supernatant was recovered and centrifuged at 22,000×g for 30 min. at 4° C. Pellet was resuspended with 42 ml total of SP (0.01 M sodium phosphate (pH 7.2), 0.25 M sucrose), and sonicated as previously described. Two factions, each of 21 ml of this suspension were layered over 15 ml of 30% (v/v) Renografin-60 solution (diatrizoate meglumine and diatrizoate sodium, 60% for injection; Bracco Diogniostics, Irvine, Calif.). After centrifugation at 40,000×g for 30 min at 4° C., the two pellets were recovered, pooled and resuspended with 4 ml total of SP and sonicated 4×2 seconds with maximal power (see above). Finally, two fractions of 2 ml of suspension were layered over 2 discontinuous Renografin gradients, formed by adding successively in the centrifuge tubes 8 ml, 12 ml and 5 ml of Renografin solution at 54, 44 and 40% (v/v), respectively. The gradients were centrifuged at 40,000×g for 45 min at 4° C. The EB bands, located at the 44/54% Renografin interface, were collected, pooled, diluted with 3 volumes of SP, and then centrifuged at 30,000×g for 30 min. Purified EB were suspended in 1.2 ml total of SP. The titer was about 5×106 IFU/μl.
So far 88 proteins have been identified from the EB purified from the sucrose (64 proteins) and the renografin gradient (47 proteins). From both preparations, the membrane associated proteins (outer membrane, periplasmic and inner membrane proteins) as defined by PSORT software, represent about 50% of the identified proteins (53 and 49% from EB purified from sucrose and renografin gradient, respectively). Of 20 proteins identified from the sucrose gradient purified-EB that were also selected from the genomic approach, only 9 (45%) of them have been demonstrated to be FACS positive (reported in bold in the table 1), while from the 15 proteins identified from the renografin gradient purified-EB and previously selected from the genomic approach (reported in bold or highlighted in table 1), 12 (80%) have been shown to be FACS positive proteins. The results indicate that a protein identified from the surfome of the renografin gradient purified-EB is highly likely to be a surface exposed protein, independently of its prediction by PSORT software. In fact, from these 12 proteins demonstrated to be FACS positive, 8 are predicted to be inner membrane or cytoplasmic proteins. Moreover, the proteins include 5 out of the 11 in vitro neutralizing antigens identified (CT045 (Leucyl Aminopeptidase A), CT242 (OmpH-Like Outer Membrane Protein), CT587 (enolase), and CT681 (Major Outer Membrane Protein), and CT396 (HSP70)) and they include antigens stimulating IFN-γ producing CD4 cells (CT043 (hypothetical protein), CT587 (enolase) and CT823 (DO Serine Protease)).
Proteins, mainly those identified from the surfome of the renografin gradient purified-EB and not previously selected from the genomic approach, or already selected but lost during the screening are selected, cloned, expressed, and purified to be tested as potential vaccine (see below study on the identified proteins and on the saved peptides, and table 2).














TABLE 1











Surfome
Surfome








sucrose
rinographin







predicted
gradient
gradient


TMD
ID
FACS_ctr
FACS_cpn
ctr_new_annotation
localization
purified -EB
purified -EB






















0
CT073

VEDI 6688
predicted OMP [leader (19) peptide]
periplasmic space
x



0
CT242

pos 6577
(OmpH-Like Outer Membrane Protein)
periplasmic space
x
x


0
CT550

VEDI 7139
hypothetical protein
periplasmic space
x



0
CT600
10.46
NEG 7090
Peptidoglycan-Associated Lipoprotein
periplasmic space
x



0
CT681
34.66
pos 6998
Major Outer Membrane Protein
periplasmic space
x
x


0
CT823
26.62
POS. 7306
DO Serine Protease
periplasmic space
x
x


0
CT456
pos
VEDI 6866
hypothetical protein
outer membrane
x
x


0
CT476

neg 6890
hypothelical protein
outer membrane
x



0
CT812
23.48
pos 7287
Putative Outer Membrane Protein D
outer membrane
x



1
CT011


hypothetical protein
inner membrane
x



1
CT045
16.81
pos 6664
Leucyl Aminopeptidase A
inner membrane
x
x


1
CT055


Dihydrolipoamide Succinyltransferase
inner membrane




1
CT067

neg
Solute Protein Binding Famity
inner membrane
x




CT072

VEDI 6618
Metalloprotease
inner membrane

x


1
CT102


hypothetical protein
inner membrane
x



2
CT223


hypothetical protein
inner membrane
x



8
CT230


Neutral Amino Acid (Glutamate) Transporter
inner membrane
x



0
CT253


hypothetical protein
inner membrane
x



2
CT270

VEDI 6700
transglycolase/transpeptidase
inner membrane
x



1
CT313


Transaldolase
inner membrane

x


1
CT316
 9.68
VEDI 6338
L7/L12 Ribosomal Protein
inner membrane

x


1
CT322

BEDI 6331
Elongation Factor Tu
inner membrane
x
x


1
CT396
34.5 
pos 6790
HSP-70
inner membrane
x
x


1
CT413

pos 6830
Putative outer membrane protein B
inner membrane

x


1
CT437


Elongation Factor G
inner membrane
x
x


1
CT443
21.28
pos 6849
60 kDa Cysteine-Rich OMP
inner membrane

x


10
CT448


Protein Export
inner membrane
x



2
CT507


RNA Polymerase Alpha
inner membrane
x
x


11
CT510


Translocase
inner membrane
x



0
CT541
43.36
pos 6960
FKBP-type pep-prol cis-trans isom. (MIP)
inner membrane
x
x


1
CT559
23.21
pos 7140
Yop proteins translocation lipoprotein J
inner membrane

x


1
CT578


hypothetical protein
inner membrane
x
x


2
CT579


hypothetical protein
inner membrane

x


1
CT592


Succinate Dehydrogenase
inner membrane
x



1
CT608


DNA Helicase
inner membrane
x



11
CT624

no data
Integral Membrane Protein
inner membrane
x



2
CT664

neg
(FHA domain; homology to adenylate cyclase)
inner membrane
x
x


1
CT680


S2 Ribosomal Protein
inner membrane

x


2
CT686


ABC Transporter Membrane Protein
inner membrane
x



1
CT714


Glycerol-3-P Dehydrogenase
inner membrane
x



1
CT816


Glucosamine-Fructose-6-P Aminotransferase
inner membrane
x



2
CT841


ATP-dependent zinc protease
inner membrane

x


2
CT842


Polyribonucleotide Nucleotidyltransferase
inner membrane

x


11
CT856


Sulfate Transporter
inner membrane
x



1
CT041


hypothetical protein
inner membrane
x




CT814


hypothetical protein
inner membrane




0
CT003


Glu tRNA Gln Amidotransferae (A subunit)
cytoplasm

x


0
CT043
25.29
VEDI 6666
hypothetical protein
cytoplasm

x


0
CT064


GTPase
cytoplasm
x



0
CT098


S1 Ribosomal Protein
cytoplasm
x



0
CT110


HSP-60
cytoplasm
x
x


0
CT111


10KDa Chaperonin
cytoplasm
x



0
CT113


Clp Protease ATPase
cytoplasm
x



0
CT125


L13 Ribosomal Protein
cytoplasm
x



0
CT126


S9 Ribosomal Protein
cytoplasm
x
x


0
CT153
13.33

hypothetical protein
cytoplasm

x


0
CT205


Fructose-6-P Phosphotransferase
cytoplasm

x


0
CT215


Predicted 1,6-Fructose biphosphate aldolase
cytoplasm
x
x


0
CT267

VEDI 6697
Integration Host Factor Alpha
cytoplasm
x



0
CT269


UDP-N-acetylmuramoylalanylglutamyl DAP Ligas
cytoplasm
x



0
CT314


RNA Polymerase Beta'
cytoplasm
x
x


0
CT315


RNA Polymerase Beta
cytoplasm
x
x


0
CT318


L1 Ribosomal Protein
cytoplasm
x



0
CT348


ABC Transporter Protein ATPase
cytoplasm
x



0
CT436


S10 Ribosomal Protein
cytoplasm
x



0
CT438

VEDI 6842
S7 Ribosomal Protein
cytoplasm
x



0
CT509


S13 Ribosomal Protein
cytoplasm
x



0
CT511


L15 Ribosomal Protein
cytoplasm
x
x


0
CT521


L16 Ribosomal Protein
cytoplasm
x



0
CT527


L4 Ribosomal Protein
cytoplasm
x
x


0
CT576


Low Calcium Response Protein H
cytoplasm

x


0
CT577


hypothetical protein
cytoplasm
x
x


0
CT587
20.85
pos7111
enolase
cytoplasm

x


0
CT603


Thio-specific Antioxidant (TSA) Peroxidase
cytoplasm

x


0
CT622

pos 7033
CHLPN 76kDa Homolog
cytoplasm

x


0
CT636


Transcription Elongation Factor G
cytoplasm
x
x


0
CT678


UMP Kinase
cytoplasm

x


0
CT707

VEDI 7163
Trigger Factor-peptidyl prolyl isomerase
cytoplasm
x



0
CT743


Histone-Like Developmental Protein
cytoplasm
x
x


0
CT748


Transcription-Repair Coupling
cytoplasm
x



0
CT768


hypothetical protein
cytoplasm
x
x


0
CT771


hydrolase/phosphatase homolog
cytoplasm
x
x


0
CT834


L35 Ribosomal Protein
cytoplasm
x



0
CT859
10.91
VEDI 7348
Metalloprotease
cytoplasm
x



0
CT875


hypothetical protein
cytoplasm
x
x


0
CT236


Acyl Carrier Protein
cytoplasm

x


0
CT523


L22 Ribosomal Protein
cytoplasm

x


0
CT514


L6 Ribosomal Protein 
cytoplasm































TABLE 2











Surfome sucrose
Surfome rinographin


Locus

Experimental


Predicted
gradient purified -
gradient purified -


Name
TIGR Annotation
evidence
Cloning in the past
Cloning
Localization
EB
EB







CT110
HSP-60
surfoma (tripsina)
Never done before
entire form
cytoplasm
x
x




and lecterature


CT113
Clp Protease
surfoma (tripsina)
Never done before
entire form
cytoplasm
x



ATPase
and lecterature


CT576
Low Calcium
TTSS?
Never done before
entire form
cytoplasm

x



Response Protein



H


CT577 . . .
hypothetical
TTSS?
Never done before
entire form
cytoplasm

x



protein


CT578
hypothetical
surfoma (tripsina)
Done before, but not
entire form
inner membrane

x



protein
and TTSS?
expression


CT579
hypothetical
surfoma (tripsina)
Never done before
entire form
inner membrane

x



protein
and TTSS?


CT045
Leucyl
immunogenic
Done
entire form
inner membrane
x
x



Aminopeptidase
(protein chip) and



A
surfoma (tripsina)


CT622
CHLPN 76 kDa
surfoma (tripsina)
Done
entire form
cytoplasm

x



Homolog


CT768
hypothetical
surfoma (tripsina)
Never done before
entire form
cytoplasm

x



protein


CT814
hypothetical
surfoma (tripsina)
Mever done before
entire form
cytoplasm

x



protein


CT841
ATP-dependent
surfoma (tripsina)
Never done before
entire form
inner membrane

x



zinc protease


CT859
Metalloprotease
immunogenic
Never done before
entire form
cytoplasm
x




(protein chip) and




surfoma (tripsina)


CT875
hypothetical
surfoma (tripsina)
Never done before
entire form
cytoplasm
x
x



protein


CT664
(FHA domain;
surfoma (tripsina)
Never done before
entire form
inner membrane
x
x



homology to



adenylate


CT242
(OmpH-Like Outer
surfoma (tripsina)
Done
domain
periplasmic space
x
x



Membrane



Protein)


CT812
Putative Outer
immunogenic
Done
domain
outer membrane
x



Membrane Protein
(protein chip) and



D
surfoma (ProK)


CT823
DO Serine
immunogenic
Done
domain
periplasmic space
x
x



Protease
(protein chip) and




surfoma (tripsina)


CT456
hypothetical
immunogenic
Done
domain
outer membrane
x
x



protein
(protein chip) and




surfoma (tripsina)









Protein Identification by Nano-LC/MS/MS.

Two different experimental platforms were used for the chromatographic separation of peptides and further identification was performed by tandem mass spectrometry (MS/MS).
In the first platform, prior to analysis salts were removed by off-line HPLC, with a 7-min gradient of 2-80% acetonitrile (ACN) in 0.1% formic acid. Peptide fractions were concentrated with a Speed-vac centrifuge (Savant, Holbrook, N.Y.), and kept at −20° C. until further analysis. Peptides were separated by two-dimensional (2-D) nano-liquid chromatography (Dionex, Amsterdam, The Netherlands). In the first dimension, peptides were loaded on a strong cation exchange (SCX) column (10 cm×320 μm i. d.) and eluted by 5 salt concentrations (0.01, 0.05, 0.1, 0.5 and 1 M NaCl). In the second dimension, peptides were separated by a reversed phase C18 analytical column (15 cm×75 μm i. d., C18 PepMap100TM, 3 μm, 100 Å) via a C18 trap column (PepMapTM C18 μ-precolumn, 300 μm i.d.×1 mm, Dionex). Peptides were eluted with a 45-min gradient from 5 to 50% of 80% ACN in 0.1% formic acid. The flow rate was 300 nl/min. Eluates were continuously spotted onto an Anchor-Chip® MALDI target (Bruker Daltoniks, Bremen, Germany), prepared with a thin layer of a saturated solution of α-cyano-4-hydroxycynnamic acid in acetone, every 60 s using a Proteineer FC robot (Bruker Daltoniks). After fraction collection, spots were recrystallized with 0.6 μl of ethanol/acetone/0.1% trifluoroacetic acid (6:3:1). Mass spectrometry analysis was performed automatically with an Ultraflex MALDI TOF-TOF instrument, under the control of the WARP LC software (Bruker Daltoniks).
In the second platform, peptides were separated by nano-LC on a CapLC HPLC system (Waters, Milford, Mass., USA) connected to a Q-ToF Micro ESI mass spectrometer equipped with a nanospray source (Waters). Samples were loaded onto an Atlantis C18 NanoEase column (100 μm i.d.×100 mm, Waters), via a C18 trap column (300 μm i.d.×5 mm, Dionex). Peptides were eluted with a 50-min gradient from 2% to 60% of 95% ACN, 0.1% formic acid at a flow of 400 nl/min. The eluted peptides were subjected to an automated data-dependent acquisition program, using the MassLynx software (Waters). For both platforms, searching and identification of peptides were performed in batch mode with a licensed version of MASCOT, in a local database.
Results
These experiments have demonstrated that (1) GroEL-1, (2) DnaK, (3) Ef-Tu, (4) Mip-like protein, (5) Major outer membrane protein (MOMP), (6) HctA, (7) CT577, (8) CT223, (9) GroeS, (10) Tarp, (11) Rs10, (12) OmpH-like protein, (13) Rs13, (14) R11, (15) CT875, (16) HtrA, (17) RpoA, (18) PepA, (19) Alanyl tRNA synthetase, (20) RpoC, (21) YaeL, (22) EF-G, (23) CT578, (24) CT579, (25) CT680 and (26) CT814 are surface exposed and/or surface-associated Chlamydial antigens which are useful in immunogenic/immunoprotective or vaccine compositions.
Immunisation Studies
Antigens are selected for combining to give a composition of the invention. BALB/c mice are divided into nine groups and immunized as follows:












Group
Immunizing Composition
Route of Delivery







1
Mixture of antigens (10-20 μg protein/
Intraperitoneal or



each) + CFA (Complete Freund's Adjuvant)
intranasal or




subcutaneous


2
Mixture of antigens (5 μg/each) +
Intraperitoneal or



Al-hydroxide (200 μg)
intranasal or




subcutaneous


3
Mixture of antigens (10-20 μg protein/
Intraperitoneal or



each) + CpG (10 μg)
intranasal or




subcutaneous


4
Mixture of antigens (10-20 μg protein/
Intraperitoneal or



each) + Al-hydroxide (200 μg) +
intranasal or



CpG (10 μg)
subcutaneous


5
CFA
Intraperitoneal or




intranasal or




subcutaneous


6
Mixture of antigens (10-20 μg protein/
Intraperitoneal or



each) + LTK63 (5 μg)
Intranasal or




subcutaneous


7
Al-hydroxide (200 μg) +
Intraperitoneal or



CpG (10 μg)
intranasal or




subcutaneous


8
CpG (10 μg)
Intraperitoneal or




intranasal or




subcutaneous


9
LTK63 (5 μg)
Intraperitoneal or




intranasal or




subcutaneous









Mice are immunized at two-week intervals. Two to three weeks after the last immunization, all mice are challenged with the appropriate Chlamydia serovar strain. When mucosal immunization (e.g. intranasal) is used, the animal model is also challenged mucosally to test the protective effect of the mucosal immunogen. Immediately prior to challenge, mice are bled to determine antibody titre to the antigens that were administered.
For the mouse challenge, virulent bacteria will be grown in appropriate media. Bacteria are harvested by centrifugation, re-suspended, and serially diluted for the challenge inoculum. BALB/c mice are challenged and observed daily for 30 days post-exposure.
Total IgG and IgG1/IgG2A subtypes can be measured in mouse sera resulting from the different immunization regimens by using an ELISA assay on whole bacteria and on purified recombinant proteins. Furthermore, assessment of antigen-specific CD4+ and CD8+Th-cells in spleen cells and/or PBMC isolated from immunized mice can be carried out by multi-parametric FACS analysis, to evaluate the cytokine expression profiles of antigen-specific T-cells. In particular production of IFN-γ and IL-5 can be measured after in vitro stimulation of T cells with purified antigens and/or whole Chlamydia Elementary bodies (EB). In addition, splenocytes and/or PBMC from mice immunized with each antigen/vaccine formulation may be collected 10-12 days after the last immunization dose and stimulated with whole Chlamydia bacteria. After 4 hours of stimulation, Brefeldin A is added to the cells for the following 12 hours, to block cytokines secretion. Afterwards cells are fixed and stained with antibodies to detect Chlamydia-specific T cells expressing IFN-γ and IL-5.
T cells can be isolated from peripheral blood lymphocytes (PBLs) by a variety of procedures known to those skilled in the art. For example, T cell populations can be “enriched” from a population of PBLs through the removal of accessory and B cells. In particular, T cell enrichment can be accomplished by the elimination of non-T cells using anti-MHC class II monoclonal antibodies. Similarly, other antibodies can be used to deplete specific populations of non-T cells. For example, anti-Ig antibody molecules can be used to deplete B cells and anti-MacI antibody molecules can be used to deplete macrophages.
T cells can be further fractionated into a number of different subpopulations by techniques known to those skilled in the art. Two major subpopulations can be isolated based on their differential expression of the cell surface markers CD4 and CD8. For example, following the enrichment of T cells as described above, CD4+ cells can be enriched using antibodies specific for CD4. The antibodies may be coupled to a solid support such as magnetic beads. Conversely, CD8+ cells can be enriched through the use of antibodies specific for CD4 (to remove CD4+ cells), or can be-isolated by the use of CD8 antibodies coupled to a solid support. CD4 lymphocytes from Chlamydia infected patients can be expanded ex vivo, before or after transduction as described by reference 321.
Following purification of T cells, the purified T cells are pre-stimulated with various cytokines including but not limited to rIL-2, IL-10, IL-12, and IL-15, which promote growth and activation of lymphocytes.
Chlamydia-specific T cells, may be activated by the above-described immunogenic polypeptides. Chlamydia-specific T cells can be CD8+ or CD4+. Chlamydia-specific CD8+ T cells can be cytotoxic T lymphocytes (CTL) which can kill Chlamydia-infected cells that display any of the above described polypeptides or fragments thereof complexed with an MHC class I molecule. Chlamydia-specific CD8+ T cells can be detected by, for example, 51Cr release assays. 51Cr release assays measure the ability of Chlamydia-specific CD8+ T cells to lyse target cells displaying one or more of these epitopes. Chlamydia-specific CD8+ T cells which express antiviral agents, such as IFN-γ, are also contemplated herein and can also be detected by immunological methods, preferably by intracellular staining for IFN-γ or like cytokine after in vitro stimulation with one or more of the above described Chlamydia polypeptides. Chlamydia-specific CD4+ T cells can be detected by a lymphoproliferation assay. Lymphoproliferation assays measure the ability of Chlamydia-specific CD4+ T cells to proliferate in response to one or more of the above described polypeptides.
Antigens Inducing an Ab-Mediated Reduction of Infection
Sera obtained by immunizing mice with 158 purified recombinant C. trachomatis (Ct) proteins have been tested in vitro for neutralization activity. In vitro neutralization assays were performed on LLC-MK2 (Rhesus monkey kidney) epithelial cell cultures. Serial four-fold dilutions of mouse immune and corresponding preimmune sera were prepared in sucrose-phosphate-glutamic acid buffer (SPG). Mouse polyclonal sera to whole EB were used as positive control of neutralization, whereas SPG buffer alone was used as negative control of neutralization (control of infection). Purified infectious EB from the serotype-D Ct strain GO/96 were diluted in SPG buffer to contain 3×105 IFU/ml, and 10 μl of EB suspension were added to each serum dilution in a final volume of 100 μl. Antibody-EB interaction was allowed to proceed for 30 min at 37° C. on a slowly rocking platform. The 100 μl of reaction mix from each sample was used to inoculate PBS-washed LLC-MK2 confluent monolayers (in triplicate for each serum dilution), in a 96-well tissue culture plate, and centrifuged at 805×g for 1 hour at 37° C. After centrifugation Eagle's minimal essential medium containing Earle's salts, 20% fetal bovine serum and 1 μg/ml cycloheximide was added. Infected cultures were incubated at 37° C. in 5% CO2 for 72 hours. The monolayers were fixed with methanol and the chlamydial inclusions were detected by staining with a mouse anti-Chlamydia fluorescein-conjugated monoclonal antibody (Merifluor Chlamydia, Meridian Diagnostics, Inc.) and quantified by counting 5 fields per well at a magnification of 40×. The inhibition of infectivity due to EB interaction with the immune sera was calculated as percentage reduction in mean IFU number as compared to the SPG (buffer only)/EB control. In this calculation the IFU counts obtained with immune sera were corrected for background inhibition of infection observed with the corresponding pre-immune mouse serum. According to common practice, the sera were considered as “neutralizing” if they reduce infectivity by at least 50%. The corresponding neutralizing titer was defined as the serum dilution at which a 50% reduction of infectivity was observed. Experimental variability was evaluated by calculating the standard error of measurement (SEM) of three titration experiments for each recombinant antigen.
This analysis revealed 11 antigens showing neutralizing capability (CT681, CT467, CT398, CT587, CT823, CT396, CT381, CT242, CT552, CT547 and CT045) (see FIG. 1). In particular 5 antigens (CT242, OmpH-like; CT381, ArtJ; CT467, AtoS; CT547; and CT587, Enolase) have neutralizing titer which is superior to the titer observed with the polyclonal Abs against total EB. The remaining 6 antigens induce neutralizing Abs at a titer similar to EB. Interestingly, the homologs of 5 of the neutralizing antigens were also neutralizing in C. pneumoniae. In addition and most importantly, the neutralization capacity of all 11 antigens had never been described before.
Screening of Antigen-Specific Antisera for Their Capability to Induce Lysis of C. trachomatis Infected Cells in the Presence of Complement
Confluent HeLa cells are infected with C. trachomatis EBs. 40 hours post infection, sera from mice is added in serial twofold dilutions. Following 2 h incubation, the cells are washed, overlaid with complement and then incubated at 37° C. for 3 h. The levels of cytotoxicity of both infected HeLa cell monolayers and matched, uninfected controls are assessed with a LDH cytotoxicity detection kit. This is a colorimetric assay for the quantification of cell death and cell lysis based on the measurement of lactate dehydrogenase (LDH) activity released from the cytosol of the damaged cells into the supernatant. The supernatants of both test and control samples are centrifuged at 250 g to remove cells and cell debris, and the cell-free supernatants are diluted and incubated with the kit reaction mixture. An increase in the amount of dead or plasma membrane damaged cells results in an increase in the LDH enzyme activity in the culture supernatant.
In Vitro Model for the Selection of Antigens Inducing a CD4 Th1 Response
Th1-type cytokines, such as IL-12 and IFN-γ, have been proposed to be important for resolution of chlamydial infection. Indeed, mice deficient in IFN-γ are unable to control chlamydial infection in the genital tract as Chlamydia disseminates to systemic sites [322, 323].
Two immunological screening approaches to identify Chlamydia antigens capable of inducing Chlamydia-specific IFNγ-producing CD4+ T cells have been devised: 1) after experimental mouse infection with Chlamydia trachomatis, and 2) following mouse immunization with Chlamydia recombinant proteins. These antigens would be the most promising candidates to confer CD4+-mediated protection.
In the first approach female BALB/c mice 6-7 weeks old were pretreated with 2.5 mg of medroxy-progesterone acetate (Depo-Provera) on day −5 and then infected intravaginally at day 0 by depositing 15 ml of SPG (250 mM Sucrose, 10 mM Sodium Phosphate, 5 mM L-Glutamic acid) containing 106 IFU of C. trachomatis serovar D. Seven days post infection the course of infection was monitored by swabbing the vaginal vault and determining the number of recovered IFUs on LL-CMK2 cell monolayers using indirect immunofluorescence.
Splenocytes were prepared from spleens of mice infected with Chlamydia trachomatis (10 days post infection) and non-infected controls. Spleens of each group of mice were pooled and dispersed manually. Splenocytes were cultured in RPMI 1640 medium supplemented with 25 mM HEPES buffer, 100 UI/ml penicillin, 100 mg/ml streptomycin, 50 mM 2-mercaptoethanol, 0.15 mM L-glutamine, sodium pyruvate, vitamins, a cocktail of non-essential amino acids and 2.5% heat inactivated fetal calf serum.
Freshly prepared splenocytes from infected mice and non infected controls were stimulated for 4 hours in round-bottom 96 well plates with 20 mg/ml of various Chlamydia trachomatis recombinant antigens in the presence of 1 mg/ml anti-CD28. As positive controls of stimulation 1 mg/ml of anti-CD3 and 10 mg/ml of heat inactivated whole C. trachomatis Elementary Bodies were used. For the analysis of antigen induced intracellular cytokine expression, 2.5 mg/ml Brefeldin-A (Sigma) was added overnight. At the end of the stimulation period cells were fixed with 2% paraformaldeide and subsequently permeabilized with PBS-1% BSA-0.5% saponin. Fixed cells were stained for 30 min at room temperature with the following antibodies: antiCD4-FITC, antiCD8-PerCp, antiIFNg-APC and antiIL5-PE (all BD Pharmingen).
Stained cells were analyzed for cytokine production on a LSRII cytometer with a DIVA software.
In the second approach, mice were immunized intramusculary on days 1, 14 and 28 with a panel of recombinant chlamydial proteins with proper adjuvants. A week after the last immunization, PBMC were isolated and assessed by spleen harvesting as described above, in the presence of syngeneic irradiated APC. Ex vivo stimulation was carried out for 24 hours using whole Chlamydia trachomatis EBs. Following stimulation the cells were analysed for cytokine production (IFN-γ and IL-5) as described above.
Both screening are carried out using multi-parametric FACS analysis to assess the cytokine expression profile of antigen-specific Th1-cells.
In the first assay, splenocytes from mice that had experienced and resolved a primary C. trachomatis infection were separately stimulated with EB and recombinant MOMP. Based on published data, a considerable proportion of spleen T lymphocytes from these mice should produce IFNγ upon EB stimulus. A similar cytokine production, although at a lower level, should be observed in lymphocytes stimulated with rMOMP, the only protective antigen in the mouse model so far described in peer reviewed journals. The data shown in FIGS. 2a and 2b confirmed the expected CD4-Th1 response. Splenocytes stimulated with EB show a poor frequency of IL5+ cells and a high frequency of IFNγ+ T cells. FIG. 3 shows that 7 of the 54 tested antigens were able to induce significant C. trachomatis-specific CD4-Th1 responses. These seven antigens were CT681 (Momp), CT043 (Hypo), CT711 (Hypo), CT587 (Enolase), CT823 (DO serine protease), CT396 (Hsp70) and CT480 (Oligopeptide Binding Lipoprotein).
Analysis of Antigens for MHCII Epitopes
CT823, CT587, CT043 and CT153 were analysed using the PREDBALB/c system for predicting peptide binding to H2d molecules [324]. All of the peptides were predicted to contain MHC II epitopes. This indicates that these epitopes would be useful in raising a CD4-Th1 response. The epitopes predicted to be found in these antigens are recited in SEQ ID NOs: 261-275. The results of the analysis using the PREDBALB/c system is shown in FIG. 10.
Identification of Human Immunogens by Protein Array Analysis of Human Sera
A prototype protein array has been prepared containing 53 selected antigens, including all FACS positive antigens (see above). Spotting was performed on nitrocellulose FAST slides using a Chipwriter spotter. Proteins were spotted in four replicates at 0.3-0.5 mg/ml in PBS buffer. As positive control, human IgG was spotted at concentrations ranging from 0 to 0.5 mg/ml. Antigen recognition by human sera was obtained after 1 h incubation with human sera (1:1000 dilution), followed by incubation with Phycoerytrin-labelled goat anti-human IgG (1:500). Slide scanning was performed using a Scanarray 5000 instrument and spot quantification was done with Imagene 6.0 software. Data were processed using in-house developed software. For each protein, the mean fluorescence signal was determined after background subtraction and data were normalized to the mean fluorescence signals of human IgG spots. Proteins that, after background subtraction, showed mean fluorescence signal lower than 5000 were considered negative.
The array is being used for screening of a panel of 100 human sera from Chlamydia trachomatis positive patients. Results on a first batch of 53 sera out of the 100 (FIG. 4), indicate that 13 antigens appeared immunogenic (recognized by more than 30% of the tested sera) (Table 3). 5 proteins were recognized by more than 50% of the tested sera. 5 of the 13 were previously reported as immunogens (highlighted in yellow), while 8 proteins were never described before. 10 proteins were not detected by any of the tested sera.









TABLE 3





Antigen ID
annotation
% of positive sera

















443
60 Kda Cys. Ric. Omp
100


456
Hypothetical Protein
66


859
Metalloprotease
55


372
Hypothetical Protein
51


050
Hypothetical Protein
43


823
DO Serine Protease
42


pgp3
pgp3
36


153
Hypothetical Protein
32


089
Low Ca Response E
30


045
Leucyl Aminopep. A
32


467
2-comp regul sys
30


017
Hypothetical Protein
38


559
Yop transl lipop
36









Setting-Up of the C. muridarum (Alias MoPn) and the C. trachomatis Serovar D Animal Models

This model uses a murine strain of C. trachomatis which is more virulent in mice, and causes evident pathology of the urogenital tract (UGT) in a high percentage of infected mice. Owing to the only partial conservation of ortholog genes in the murine vs human genomes, immunizations in this model need to be carried out with the MoPn protein homologs to those being tested in parallel in the model with the human strain.
To set-up a mouse model of vaginal infection with C. muridarum, the optimal infectious dose was determined. C. muridarum was obtained from the ATCC and grown in LLCMK2 cells. The number of IFU (inclusion forming units=viable chlamydiae) recovered from vaginal swabs after infection of 3 different mouse strains (C57BL/6; BALB/c, C3H/Ne) with increasing infectious doses of MoPn EB (104, 105, 106 IFU) was compared. The experiment was performed twice using groups of 30 mice in each experiment, and showed that BALB/c mice can be infected in a high percentage both using 105 or 106 IFU as the infecting dose (see FIG. 5), whereas vaginal infection with 104 IFU yielded a low percentage of infected mice (not shown). These experiments also showed that mice can be assessed for up to 21-23 days post infection (p.i.) while they completely recover by day 25 to 30 p.i.
The positive control of protection (gold standard) was then set up, which is represented by the extent of natural immunity induced by a resolved primary infection. BALB/c mice received a primary infection with 106 C. muridarum IFU and vaginal swabs were collected at time intervals up to for 45 days p.i., to assure a complete bacterial clearance in the lower genital tract. Mice were then challenged with 105 IFU of C. muridarum and the protection level was determined by comparing IFU in vaginal swabs of mice that received only a primary infection with those of mice that received also a secondary infection (see FIG. 6). Mice that received a secondary infection showed a complete clearance of infectious chlamydiae in the lower genital tract by day 14 p.i., as shown by negative vaginal swab cultures.
A second model was set up by using the human serovar D. This model adopts the same technical approach with the difference that a 1-log higher infection dose is used to achieve 100% level of infection. Data is shown in FIG. 7.
Identification of Protective Antigens
The FACS positive and neutralizing antigens were tested for their capacity to induce protection against C. trachomatis serovar D challenge in vivo. Considering the complexity of the model, antigens were grouped in combination of 5 with the intention to deconvolute the mixture(s) which showed protective activity.
The antigen combinations included 15 μg of each selected proteins, 200 μg Alum and 10 μg of 1826-CpG (5′ TCCATGACGTTCCTGACGTT 3′; SEQ ID NO: 260). Immunizations were carried out intra peritoneally by administering three doses every 14 days (see FIG. 8 for assay schedule). 10 days post last immunization mice were hormone-treated with 2.5 mg of Medroxyprogesterone acetate and 5 days later were challenged intra-vaginally with 105 of C. trachomatis IFU. Vaginal swabs were collected at week-intervals, and chlamydiae were detached from the swabs under agitation in 200 μl SPG buffer. Serial dilutions of the Chlamydia suspension were used to infect a monolayer of LLC-MK2 cells and IFU counts were determined 48 hours later by fluorescence microscopy, after cell fixation and staining of inclusion with a fluorescently labelled anti-Chlamydia MAb.
A combination of 5 antigens, including CT089, CT045, CT381, CT398, CT396, showed a trend of reduction of infection in the immunized mice, as compared to control mice immunised with adjuvant alone.
In particular, at day 14 post challenge an up to 1 log reduction in shed chlamydiae was observed in four independent experiments carried out in groups of 10 mice (FIG. 9). Furthermore, an average of 25% reduction in the number of infected mice was observed, suggesting the immunization with the combo not only reduced the number of shed chlamydiae but also accelerated the bacterial clearance.
It will be understood that the invention has been described by way of example only and modifications may be made whilst remaining within the scope and spirit of the invention.
REFERENCES
The Contents of Which are Hereby Incorporated in Full


    [1] Kalman et al. (1999) Nature Genetics 21:385-389.
    [2] Read et al. (2000) Nucleic Acids Res 28:1397-1406.
    [3] Shirai et al. (2000) Nucleic Acids Res 28:2311-2314.
    [4] Stephens et al. (1998) Science 282:754-759.
    [5] WO 99/27105.
    [6] WO 00/27994.
    [7] WO 99/28475.
    [8] Ward (1995) Apmis. 103:769-96.
    [9] Moulder (1991) Microbiol Rev 55(1):143-190.
    [10] Comanducci et al. (1994) Infect Immun 62(12):5491-5497.
    [11] EP-A-0499681.
    [12] WO 95/28487.
    [13] Murdin et al. (1993) Infect Immun 61:4406-4414.
    [14] Cerrone et al. (1991) Infect Immun 59(1):79-90.
    [15] Raulston et al. (1993) J. Biol. Chem. 268:23139-23147.
    [16] WO 03/049762.
    [17] WO 2005/002619.
    [18] Montigiani et al. (2002) Infect Immun 70(1):368-379.
    [19] WO 00/37494.
    [20] Birkelund et al. (1990) Infect Immun 58:2098-2104.
    [21] Danilition et al. (1990) Infect Immun 58:189-196.
    [22] Raulston et al. (1993) J. Biol Chem 268:23139-23147.
    [23] Bavoil et al. (1984) Infection and Immunity 44:479-485.
    [24] Hatch et al., (1986) J. Bacteriol. 165:379-385.
    [25] Stephens et al., (1987) J. Bacteriol. 169:3879-3885.
    [26] Yuan et al., (1989) Infection and Immunity 57: 1040-1049.
    [27] Baehr et al., (1988) PNAS USA 85:4000-4004.
    [28] Lucero et al., (1985) Infection and Immunity 50:595-597.
    [29] Zhang et al., (1987) J. Immunol. 138:575-581.
    [30] Peterson et al., (1988) Infection and Immunity 56:885-891.
    [31] Zhang et al., (1989) Infection and Immunity 57:636-638.
    [32] Allen et al., (1991) J. Immunol. 147:674-679.
    [33] Su et al. (1990) J. Exp. Med. 172:203-212.
    [34] Clifton et al. (2004) PNAS 101(27): 10166-71.
    [35] Allen et al. (1990) Mol. Microbiol. 4:1543-1550.
    [36] WO 03/049762.
    [37] Ghaem-Maghami et al., (2003) Clin. Exp. Immunol. 132: 436-442.
    [38] Donati et al., (2003) Vaccine 21:1089-1093.
    [39] Fling et al., (2001) PNAS 98(3): 1160-1165.
    [40] Hessel, et al., (2001) Infection and Immunity 69(8): 4996-5000.
    [41] Eckert, et al., (1997) J. Infectious Disease 175:1453-1458.
    [42] Domeika et al., (1998) J. Infectious Disease 177:714-719.
    [43] Deane et al., (1997) Clin. Exp. Immunol. 109(3): 439-445.
    [44] Peeling et al., (1997) J. Infect. Dis. 175(5):1153-1158.
    [45] Rank et al., (1995) Invest Ophthalmol. Vis. Sci. 36(7):1344-1351.
    [46] Yi et al., (1993) Infection & Immunity 61(3):1117-1120.
    [47] Stephens et al., (2001) Molecular Microbiology 40(3):691-699.
    [48] Millman, et al., (2001) J. of Bacteriology 183(20):5997-6008.
    [49] Mygind, et al., Journal of Bacteriology (1998) 180(21):5784-5787.
    [50] Bas, et al., (2001) Journal of Clinical Microbiology 39(11):4082-4085.
    [51] Goodall, et al., (2001) Clin. Exp. Immunol. 126:488-493.
    [52] Molloy (2006) Nature Reviews Microbiology 4:6-7.
    [53] Philipovskiy et al. (2005) Infect Immun.73(3):1532-42.
    [54] WO 02/065129.
    [55] Vaccine Design . . . (1995) eds. Powell & Newman. ISBN: 030644867X. Plenum.
    [56] WO00/23105.
    [57] WO90/14837.
    [58] Podda & Del Giudice (2003) Expert Rev Vaccines 2:197-203.
    [59] Podda (2001) Vaccine 19: 2673-2680.
    [60] Vaccine Adjuvants: Preparation Methods and Research Protocols (Volume 42 of Methods in Molecular Medicine series). ISBN: 1-59259-083-7. Ed. O'Hagan.
    [61] Allison & Byars (1992) Res Immunol 143:519-25.
    [62] Hariharan et al. (1995) Cancer Res 55:3486-9.
    [63] U.S. Pat. No. 5,057,540.
    [64] WO96/33739.
    [65] EP-A-0109942.
    [66] WO96/11711.
    [67] WO00/07621.
    [68] Barr et al. (1998) Advanced Drug Delivery Reviews 32:247-271.
    [69] Sjolanderet et al. (1998) Advanced Drug Delivery Reviews 32:321-338.
    [70] Niikura et al. (2002) Virology 293:273-280.
    [71] Lenz et al. (2001) J Immunol 166:5346-5355.
    [72] Pinto et al. (2003) J Infect Dis 188:327-338.
    [73] Gerber et al. (2001) Virol 75:4752-4760.
    [74] WO03/024480
    [75] WO03/024481
    [76] Gluck et al. (2002) Vaccine 20:B10-B16.
    [77] EP-A-0689454.
    [78] Johnson et al. (1999) Bioorg Med Chem Lett 9:2273-2278.
    [79] Evans et al. (2003) Expert Rev Vaccines 2:219-229.
    [80] Meraldi et al. (2003) Vaccine 21:2485-2491.
    [81] Pajak et al. (2003) Vaccine 21:836-842.
    [82] Kandimalla et al. (2003) Nucleic Acids Research 31:2393-2400.
    [83] WO02/26757.
    [84] WO99/62923.
    [85] Krieg (2003) Nature Medicine 9:831-835.
    [86] McCluskie et al. (2002) FEMS Immunology and Medical Microbiology 32:179-185.
    [87] WO98/40100.
    [88] U.S. Pat. No. 6,207,646.
    [89] U.S. Pat. No. 6,239,116.
    [90] U.S. Pat. No. 6,429,199.
    [91] Kandimalla et al. (2003) Biochemical Society Transactions 31 (part 3):654-658.
    [92] Blackwell et al. (2003) J Immunol 170:4061-4068.
    [93] Krieg (2002) Trends Immunol 23:64-65.
    [94] WO01/95935.
    [95] Kandimalla et al. (2003) BBRC 306:948-953.
    [96] Bhagat et al. (2003) BBRC 300:853-861.
    [97] WO03/035836.
    [98] WO95/17211.
    [99] WO98/42375.
    [100] Beignon et al. (2002) Infect Immun 70:3012-3019.
    [101] Pizza et al. (2001) Vaccine 19:2534-2541.
    [102] Pizza et al. (2000) Int J Med Microbiol 290:455-461.
    [103] Scharton-Kersten et al. (2000) Infect Immun 68:5306-5313.
    [104] Ryan et al. (1999) Infect Immun 67:6270-6280.
    [105] Partidos et al. (1999) Immunol Lett 67:209-216.
    [106] Peppoloni et al. (2003) Expert Rev Vaccines 2:285-293.
    [107] Pine et al. (2002) J Control Release 85:263-270.
    [108] Domenighini et al. (1995) Mol Microbiol 15:1165-1167.
    [109] WO03/011223.
    [110] WO99/40936.
    [111] Marshall et al. (2006) Vaccine 24:244-257.
    [112] Matsui M. et al. (2004) J. Virol 78: 9093.
    [113] WO99/44636.
    [114] Lillard J W et al., (2003) Blood 101(3):807-14. Epub 2002 Sep. 12.
    [115] Singh et al] (2001) J Cont Release 70:267-276.
    [116] WO99/27960.
    [117] U.S. Pat. No. 6,090,406
    [118] U.S. Pat. No. 5,916,588
    [119] EP-A-0626169.
    [120] WO99/52549.
    [121] WO01/21207.
    [122] WO01/21152.
    [123] Andrianov et al. (1998) Biomaterials 19:109-115.
    [124] Payne et al. (1998) Adv Drug Delivery Review 31:185-196.
    [125] U.S. Pat. No. 4,680,338.
    [126] U.S. Pat. No. 4,988,815.
    [127] WO92/15582.
    [128] Stanley (2002) Clin Exp Dermatol 27:571-577.
    [129] Wu et al. (2004) Antiviral Res. 64(2):79-83.
    [130] Vasilakos et al. (2000) Cell Immunol. 204(1):64-74.
    [131] U.S. Pat. Nos. 4,689,338, 4,929,624, 5,238,944, 5,266,575, 5,268,376, 5,346,905, 5,352,784, 5,389,640, 5,395,937, 5,482,936, 5,494,916, 5,525,612, 6,083,505, 6,440,992, 6,627,640, 6,656,938, 6,660,735, 6,660,747, 6,664,260, 6,664,264, 6,664,265, 6,667,312, 6,670,372, 6,677,347, 6,677,348, 6,677,349, 6,683,088, 6,703,402, 6,743,920, 6,800,624, 6,809,203, 6,888,000 and 6,924,293.
    [132] Jones (2003) Curr Opin Investig Drugs 4:214-218.
    [133] WO2004/060308.
    [134] WO2004/064759.
    [135] U.S. Pat. No. 6,924,271.
    [136] US2005/0070556.
    [137] U.S. Pat. No. 5,658,731.
    [138] Wong et al. (2003) J Clin Pharmacol 43(7):735-42.
    [139] US2005/0215517.
    [140] WO02/072012.
    [141] Signorelli & Hadden (2003) Int Immunopharmacol 3(8):1177-86.
    [142] WO2004/064715.
    [143] Cooper (1995) Pharm Biotechnol 6:559-80.
    [144] PCT/US2005/022769.
    [145] WO2004/87153.
    [146] U.S. Pat. No. 6,605,617.
    [147] WO02/18383.
    [148] WO2004/018455.
    [149] WO03/082272.
    [150] U.S. Pat. No. 5,011,828.
    [151] U.S. Pat. No. 6,586,409.
    [152] WO99/11241.
    [153] WO94/00153.
    [154] WO98/57659.
    [155] European patent applications 0835318, 0735898 and 0761231.
    [156] Peterson et al. (1988) Infect Immun. 56(4):885-91.
    [157] Rank et al. (1988) Infect Immun. 56(9):2243-9.
    [158] Morrison et al. (1995) Infect Immun. 63(12):4661-8.
    [159] WO 99/27961.
    [160] WO 02/074244.
    [161] WO 02/064162.
    [162] WO 03/028760.
    [163] Cooper et al. (1999) Immunity 10:439-449.
    [164] Gennaro (2000) Remington: The Science and Practice of Pharmacy. 20th edition, ISBN: 0683306472.
    [165] Bjune et al. (1991) Lancet 338(8775):1093-96.
    [166] WO 01/52885.
    [167] Fukasawa et al. (1999) Vaccine 17:2951-2958.
    [168] Rosenqvist et al. (1998) Dev. Biol. Stand 92:323-333.
    [169] Costantino et al. (1992) Vaccine 10:691-698.
    [170] Costantino et al. (1999) Vaccine 17:1251-1263.
    [171] WO 03/007985.
    [172] WO 99/24578.
    [173] WO 99/36544.
    [174] WO 99/57280.
    [175] WO 00/66791.
    [176] WO 01/64922.
    [177] WO 01/64920.
    [178] WO 03/020756.
    [179] WO 2004/032958.
    [180] WO 2004/048404.
    [181] Covacci & Rappuoli (2000) J. Exp. Med 19:587-592.
    [182] WO 93/18150.
    [183] Covacci et al. (1993) Proc. Natl. Acad. Sci. USA 90:5791-5795.
    [184] Tummuru et al. (1994) Infect. Immun. 61:1799-1809.
    [185] Marchetti et al. (1998) Vaccine 16:33-37.
    [186] Telford et al. (1994) J. Exp. Med. 179:1653-1658.
    [187] Evans et al. (1995) Gene 153:123-127.
    [188] WO 96/01272 & WO96/01273, especially SEQ ID NO:6.
    [189] WO 97/25429.
    [190] WO 98/04702.
    [191] Watson (2000) Pediatr Infect Dis J 19:331-332.
    [192] Rubin (2000) Pediatr Clin North Am 47:269-285.
    [193] Jedrzejas (2001) Microbiol Mol Biol Rev 65:187-207.
    [194] Bell (2000) Pediatr Infect Dis J 19:1187-1188.
    [195] Iwarson (1995) APMIS 103:321-326.
    [196] Gerlich et al. (1990) Vaccine 8 Suppl:S63-68 & 79-80.
    [197] Hsu et al. (1999) Clin Liver Dis 3:901-915.
    [198] Stratov et al. (2004) Curr Drug Tgts 5(1):71-88.
    [199] Vaccines (1988) eds. Plotkin & Mortimer. ISBN 0-7216-1946-0.
    [200] Gustafsson et al. (1996) N. Engl. J. Med. 334:349-355.
    [201] Rappuoli et al. (1991) TIBTECH 9:232-238.
    [202] Sutter et al. (2000) Pediatr Clin North Am 47:287-308.
    [203] Zimmerman & Spann (1999) Am Fam Physician 59:113-118, 125-126.
    [204] WO 99/24578.
    [205] WO 99/36544.
    [206] WO 99/57280.
    [207] WO 02/079243.
    [208] WO 02/02606.
    [209] Kalman et al. (1999) Nature Genetics 21:385-389.
    [210] Read et al. (2000) Nucleic Acids Res 28:1397-406.
    [211] Shirai et al. (2000) J. Infect. Dis. 181(Suppl 3):S524-S527.
    [212] WO 99/27105.
    [213] WO 00/27994.
    [214] WO 00/37494.
    [215] Ross et al. (2001) Vaccine 19:4135-4142.
    [216] Dreesen (1997) Vaccine 15 Suppl:S2-6.
    [217] MMWR Morb Mortal Wkly Rep 1998 Jan. 16; 47(1):12, 19.
    [218] Anderson (2000) Vaccine 19 Suppl 1:S59-65.
    [219] Kahn (2000) Curr Opin Pediatr 12:257-262.
    [220] Crowe (1995) Vaccine 13:415-421.
    [221] McMichael (2000) Vaccine 19 Suppl 1:S101-107.
    [222] WO 02/34771.
    [223] Dale (1999) Infect Dis Clin North Am 13:227-43, viii.
    [224] Ferretti et al. (2001) PNAS USA 98:4658-4663.
    [225] Kuroda et al. (2001) Lancet 357(9264):1225-1240; see also pages 1218-1219.
    [226] Modlin et al. (2001) J Toxicol Clin Toxicol 39:85-100.
    [227] Demicheli et al. (1998) Vaccine 16:880-884.
    [228] Stepanov et al. (1996) J Biotechnol 44:155-160.
    [229] Ingram (2001) Trends Neurosci 24:305-307.
    [230] Rosenberg (2001) Nature 411:380-384.
    [231] Moingeon (2001) Vaccine 19:1305-1326.
    [232] Donnelly et al. (1997) Annu Rev Immunol 15:617-648.
    [233] Strugnell et al. (1997) Immunol Cell Biol 75(4):364-369.
    [234] Cui (2005) Adv Genet 54:257-89.
    [235] Robinson & Tones (1997) Seminars in Immunol 9:271-283.
    [236] Brunham et al. (2000) J Infect Dis 181 Suppl 3:S538-43.
    [237] Svanholm et al. (2000) Scand J Immunol 51(4):345-53.
    [238] DNA Vaccination—Genetic Vaccination (1998) eds. Koprowski et al. (ISBN 3540633928).
    [239] Gene Vaccination: Theory and Practice (1998) ed. Raz (ISBN 3540644288).
    [240] Wang et al. (2004) Vaccine 22:3348-57.
    [241] Titball & Williamson (2004) Expert Opin Biol Ther 4:965-73.
    [242] Garmory et al. (2004) Vaccine 22:947-57.
    [243] Grosfeld et al. (2003) Infect Immun 71(1):374-83.
    [244] Williamson et al. (2002) Vaccine 20:2933-41.
    [245] Bennett et al. (1999) Vaccine 18(7-8):588-96.
    [246] Findeis et al., Trends Biotechnol. (1993) 11:202.
    [247] Chiou et al. (1994) Gene Therapeutics: Methods And Applications Of Direct Gene Transfer. ed. Wolff.
    [248] Wu et al., J. Biol. Chem. (1988) 263:621.
    [249] Wu et al., J. Biol. Chem. (1994) 269:542.
    [250] Zenke et al., Proc. Natl. Acad. Sci. (USA) (1990) 87:3655.
    [251] Wu et al., J. Biol. Chem. (1991) 266:338.
    [252] Jolly, Cancer Gene Therapy (1994) 1:51.
    [253] Kimura, Human Gene Therapy (1994) 5:845.
    [254] Connelly, Human Gene Therapy (1995) 1:185.
    [255] Kaplitt, Nature Genetics (1994) 6:148.
    [256] WO 90/07936.
    [257] WO 94/03622.
    [258] WO 93/25698.
    [259] WO 93/25234.
    [260] U.S. Pat. No. 5,219,740.
    [261] WO 93/11230.
    [262] WO 93/10218.
    [263] U.S. Pat. No. 4,777,127.
    [264] GB 2,200,651.
    [265] EP-A-0 345 242.
    [266] WO 91/02805.
    [267] WO 94/12649.
    [268] WO 93/03769.
    [269] WO 93/19191.
    [270] WO 94/28938.
    [271] WO 95/11984.
    [272] WO 95/00655.
    [273] Curiel, Hum. Gene Ther. (1992) 3:147.
    [274] Wu, J. Biol. Chem. (1989) 264:16985.
    [275] U.S. Pat. No. 5,814,482.
    [276] WO 95/07994.
    [277] WO 96/17072.
    [278] WO 95/30763.
    [279] WO 97/42338.
    [280] WO 90/11092.
    [281] U.S. Pat. No. 5,580,859.
    [282] U.S. Pat. No. 5,422,120.
    [283] WO 95/13796.
    [284] WO 94/23697.
    [285] WO 91/14445.
    [286] EP 0524968.
    [287] Philip, Mol. Cell Biol. (1994) 14:2411.
    [288] Woffendin, Proc. Natl. Acad. Sci. (1994) 91:11581.
    [289] U.S. Pat. No. 5,206,152.
    [290] WO 92/11033.
    [291] U.S. Pat. No. 5,149,655.
    [292] WO 92/11033.
    [293] Winter et al., (1991) Nature 349:293-99.
    [294] U.S. Pat. No. 4,816,567.
    [295] Inbar et al., (1972) Proc. Natl. Acad. Sci. U.S.A. 69:2659-62.
    [296] Ehrlich et al., (1980) Biochem 19:4091-96.
    [297] Huston et al., (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5897-83.
    [298] Pack et al., (1992) Biochem 31, 1579-84.
    [299] Cumber et al., (1992) J. Immunology 149B, 120-26.
    [300] Riechmann et al., (1988) Nature 332, 323-27.
    [301] Verhoeyan et al., (1988) Science 239, 1534-36.
    [302] GB 2,276,169.
    [303] Kohler et al., (1985) Nature 256, 495-497.
    [304] Kozbor et al., (1985) J. Immunol. Methods 81, 31-42.
    [305] Cote et al., (1983) Proc. Natl. Acad Sci. 80, 2026-2030.
    [306] Cole et al., (1984) Mol. Cell Biol. 62, 109-120.
    [307] Morrison et al., (1984) Proc. Natl. Acad. Sci. 81, 6851-6855.
    [308] Neuberger et al., (1984) Nature 312, 604-608.
    [309] Takeda et al., (1985) Nature 314, 452-454.
    [310] U.S. Pat. No. 5,565,332.
    [311] Burton, (1991) PNAS 88:11120-23.
    [312] Thirion et al., (1996) Eur. J Cancer Prev. 5, 507-11.
    [313] Coloma & Morrison, (1997) Nat. Biotechnol. 15:159-63.
    [314] Mallender & Voss, (1994) J. Biol. Chem. 269:199-206.
    [315] Verhaar et al., (1995) Int. J. Cancer 61, 497-501.
    [316] Nicholls et al., (1993) J. Immunol. Meth. 165, 81-91.
    [317] Orlandi et al., (1989) Proc. Natl. Acad. Sci. 86, 3833-3837.
    [318] WO 93/03151.
    [319] WO 94/13804.
    [320] Karp et al. (1999) Trends Biotechnol 17(7):275-81.
    [321] Wilson et al. (1995) J. Infect. Dis. 172:88.
    [322] Cotter et al. (1997) Infect. Immun. 65:2145-2152.
    [323] Perry et al. (1997) J. Immunol. 158(7):3344-3352.
    [324] Zhang et al. (2005) Nucleic Acids Res. 33:W180-183.

## Claims

1. An immunogenic composition comprising: (1) an antigen comprising the sequence of SEQ ID NO:43; and (2) an antigen comprising the sequence of SEQ ID NO:98.

2. The immunogenic composition of claim 1, wherein the composition comprises an antigen comprising the sequence of SEQ ID NO:42 and an antigen comprising the sequence of SEQ ID NO:98.

3. The immunogenic composition of claim 1, further comprising an immunoregulatory agent.

4. The immunogenic composition of claim 1, further comprising an adjuvant.

5. A method of raising an immune response in a mammal, the method comprising administering to the mammal the immunogenic composition of claim 1.