WO2009158240A1

WO2009158240A1 - Salmonella vectored vaccines against chlamydia and methods of use

Info

Publication number: WO2009158240A1
Application number: PCT/US2009/047542
Authority: WO
Inventors: Jonathan Lewis Telfer; Mark Richard Redfern; Michael Joseph Lacy
Original assignee: Emergent Product Development Uk Limited
Priority date: 2008-06-16
Filing date: 2009-06-16
Publication date: 2009-12-30
Also published as: US8703153B2; US20110268760A1; EP2326344A1; EP2326344A4

Abstract

The invention provides an attenuated Salmonella vaccine vector comprising one or more heterologous polynucleotides that encode immunogenic Chlamydial peptides. In one embodiment, the attenuated Salmonella vaccine vector comprises aroC and ssaV attenuating mutations. The heterologous polynucleotides encoding the immunogenic Chlamydial peptides can be under the control of an inducible promoter such as a Salmonella ssaG promoter. In one embodiment of the invention, the immunogenic Chlamydial peptide is a PmpG peptide, for instance, a CT110, CT84 or CT40 peptide.

Description

SALMONELLA VECTORED VACCINES AGAINST CHLAMYDIA AND METHODS OF USE

[001] This application claims priority to U.S. Provisional Application No. 61/1 18,204 filed November 26, 2008 and PCT/US2008/007490 filed June 16, 2008; both of which are herein encorporated by reference in their entireties.

FIELD OF THE INVENTION

[002] The present invention relates to live Salmonella vectors expressing Chlamydia antigens for vaccination against Chlamydia infection, and methods of vaccination using the same.

BACKGROUND

[003] Chlamydial organisms cause a wide spectrum of diseases in humans, other mammals and birds and have an enormous economic impact on both human and animal health and on agricultural industries worldwide. The two principal pathogens of humans are Chlamydia trachomatis and Chlamydophila pneumoniae. Chlamydia trachomatis is a cause of chronic conjunctivitis and is also the most common cause of sexually transmitted disease in humans. Chlamydophila pneumoniae causes acute respiratory disease and is responsible for 5 to 10 % of the cases of community-acquired pneumonia, bronchitis and sinusitis. The organism has also been associated with chronic obstructive pulmonary disease, asthma, reactive airway disease, Reiter's syndrome, sarcoidosis and atherosclerosis.

[004] Although antibiotics are available to Chlamydial infections, C. trachomatis infection remains asymptomatic in approximately 50% of infected men and approximately 70% of infected women. The major clinical manifestations of genital chlamydial infection in women include mucopurulent cervicitis, endometritis and pelvic inflammatory disease. Genital infection with C. trachomatis markedly enhances the risk for reproductive tract sequelae in women, including tubal factor infertility, chronic pain and ectopic pregnancy. Babies born to mothers with infection of their genital tract frequently present with chlamydial eye infection within a week of birth (chlamydial ophthalmia neonatorum), and may subsequently develop pneumonia.

[005] In addition to the complications of genital chlamydia infection, C. trachomatis remains the leading cause of preventable blindness worldwide. Chronic ocular infections, referred to as trachoma, predominate in developing countries. It is estimated that 12 million people with trachoma will develop blindness by the year 2020, which has placed trachoma on the WHO priority list for intervention. Since 2001 , the WHO has promoted control strategies including, for example, antibiotics, improved hygiene, and environmental measures, with limited success.

[006] C. trachomatis infection is also a known co-factor for HIV/AIDS transmission.

Epidemiological studies have linked genital chlamydial infection to an increased risk for acquisition of HIV disease. See, for instance, Brunham, R. C. et al., 1996, J. Infect. D/s.173: 950-956 and Ghys, P. D. et al., 1997, AIDS 1 1 : F85-F93. Immunosuppression due to HIV may lead to more aggressive chlamydial disease conditions like pelvic inflammatory disease in those who are infected with C. trachomatis. See, Thomas, K. et al., 2002, Hum. Reprod. 17:1431-1436.

[007] Attempts in the 1950s and 1960s to develop a C. trachomatis vaccine capable of preventing infection and disease focused on immunization with crude formalin- killed whole chlamydia elementary body (EB) preparations or detergent extracts of EBs. Overall, the results of these trials demonstrated that a whole cell or detergent extract vaccine, while relatively safe, provided only a marginal benefit that was short-lived.

[008] Following the identification of MOMP as the major protein component

(approximately 60%) of the outer membrane in the early 1980s and the discovery that strong antibody responses are raised to that protein in infected animals and humans, vaccine studies focused on this protein. In the early 1990s, attention was turned to the development of recombinant MOMP vaccines. See, Longbottom, D., 2003, J. Med. Microbiol. 52:537-540. Although MOMP is highly immunogenic and can elicit a local neutralizing anti-Chlamydia antibody, most MOMP-specific neutralizing epitopes that have been mapped are located within the VD regions and thus give rise only to serovar-specific antibody. Attempts to combine serovar-specific epitopes in various vaccine vectors (e.g., poliovirus) to generate broadly cross-reactive neutralizing antibodies have been only marginally successful. See, for instance, Murdin, A. D. et al., 1993, Infect. Immun., 61 :4406-4414 and Murdin, A.D. et al., 1995, Infect. Immun., 63:11 16-1 121 ).

[009] Despite efforts to better understand the immune response in Chlamydial infections and efforts to develop an effective Chlamydial vaccine, a C. trachomatis vaccine has not been advanced into a Phase I clinical trial in over 40 years. Accordingly, a need exists for an effective vaccine to prevent and/or ameliorate Chlamydial infections and associated conditions such as trachoma.

SUMMARY OF THE INVENTION [0010] The present invention provides attenuated Salmonella microorganism comprising: i) an attenuating mutation in a Salmonella Pathogenicity Island 2 (SPI-2) gene; ii) an attenuating mutation in a second gene; and iii) one or more gene expression cassettes, each gene expression cassette comprising a heterologous nucleic acid under the control of an inducible promoter, wherein at least one of said heterologous nucleic acids encodes an immunogenic Chlamydial peptide. In one embodiment, the immunogenic Chlamydial peptide is one or more of a Chlamydial PmpG, Pmpl, PmpE, MOMP, PmpD, PmpH, OmcB, OmpH or HtrA protein (full length or mature) or an immunogenic fragment or variant thereof. For instance, the invention includes an attenuated Salmonella capable of expressing PmpG peptides CT1 10, CT84 or CT40. In one embodiment of the invention, the attenuated Salmonella microorganism induces an effective immune response when administered to a human patient. In one embodiment, the effective immune response is to C. trachomatis or C. pneumoniae.

[0011] The attenuated Salmonella of the invention comprises at least one attenuating mutation in a SPI-2 gene (e.g., ssa, sse, sse and/or ssr gene). In one embodiment, the SPI- 2 gene is an ssa gene. For instance, the invention includes an attenuated Salmonella with an attenuating mutation in one or more of ssaV, ssaJ, ssaU, ssaK, ssaL, ssaM, ssaO, ssaP, ssaQ, ssaR, ssaS, ssaT, ssaU, ssaD, ssaE, ssaG, ssal, ssaC {spiA) and ssaH. In one embodiment the attenuating mutation in an ssa V gene or ssaJ gene.

[0012] In another embodiment, the SPI-2 is an sse gene. For instance, the invention includes an attenuated Salmonella with an attenuating mutation in one or more of sseA sseB, sseC, sseD, sseE, sseF, sseG, sseL and spiC {ssaB).

[0013] The attenuated Salmonella of the invention comprises an attenuating mutation in a second gene that may or may not be in the SPI-2 region. In one embodiment of the invention, the second gene is outside of the SPI-2 region. In one embodiment of the invention, the second gene is involved in the biosynthesis of aromatic compounds. For instance, the invention includes an attenuating mutation in an aro gene. In one embodiment of the invention, the aro gene is aroA or aroC.

[0014] The attenuating mutations in the SPI-2 gene and second gene can be accomplished using methods known in the art. In one embodiment of the invention, the attenuating mutation is the result of a deletion or inactivation of the gene. If the attenuating mutation is a deletion mutation, the mutation results in a deletion site. In one embodiment of the invention, the attenuated Salmonella cell is derived from Salmonella enterica serovar Typhi ZH9 comprising deletion sites in the aroC and ssa V genes.

[0015] The attenuated Salmonella of the invention comprises one or more gene expression cassettes. In one embodiment of the invention, the gene expression cassette comprises a heterologous polynucleotide encoding a Chlamydial peptide under the control of an inducible promoter. In one embodiment, the inducible promoter is a prokaryotic promoter. In one embodiment, the inducible promoter is induced under acidic conditions. In another embodiment, the inducible promoter is induced under oxidative conditions. In yet another embodiment, the inducible promoter is induced in macrophages. An in vivo inducible promoter may be used in one embodiement of the invention. For instance, in one embodiment of the invention, the inducible promoter is a Salmonella ssaG promoter. [0016] Although not necessary to induce a cell-mediated immune response, in one embodiment of the invention, the gene expression cassette comprises a secretion signal that acts to secrete the Chlamydial peptide from the cell or display the Chlamydial peptide on the surface of the cell. For instance, a secretion signal such as CIyA secretion signal or E. coli CS3 signal sequence can be used in the construct of the attenuated Salmonella of the invention. By expressing an immunogenic Chlamydial peptide on the surface of the Salmonella cell or exporting a Chlamydial peptide out of the Salmonella cell, a humoral immune response can be elicited.

[0017] The invention includes compositions comprising the attenuated microorganism of the invention and a pharmaceutically acceptable carrier and/or diluent. In one embodiment of the invention, the composition comprises a plurality of different attenuated Salmonella cells. For instance, the plurality of Salmonella cells may comprise more than one populations of cells with each population capable of expressing a different Chlamydial antigen(s) (e.g., one population within the plurality may express PmpG peptides such as CT1 10 and/or CT84 and a second population within the plurality may express HtrA, Pmpl, PmpE, PmpD, PmpH, MOMP, OmcB and/or OmpH peptides). The plurality of Salmonella cells may also comprise a population of cells that is capable of exporting the Chlamydial peptides out of the cell and/or are capable of expression the Chlamydial peptides on the cell surface (e.g., population secretes via a secretion signal) and a second population of cells that is not capable of exporting the Chlamydial peptides (e.g., population lacks a secretion signal).

[0018] In one embodiment of the invention, the composition comprises an isolated recombinant antigen of the invention and a pharmaceutically acceptable carrier and/or diluent. For instance, the invention includes a composition comprising an isolated recombinant antigen comprising a secretion tag and an immunogenic Chlamydial peptide. In another embodiment, the invention includes a composition comprising an isolated recombinant antigen comprising two or more immunogenic Chlamydial peptides fused together. The recombinant antigens of the invention may further be fused to linker peptides and/or immunostimulatory therapeutic antigens (e.g., cytokine or chemokine). [0019] The compositions of the invention may contain an adjuvant, for instance, a CpG oligodeoxynucleotide adjuvant, aluminium salt (e.g., aluminium hydroxide, aluminum oxide and aluminum phosphate), oil-based adjuvant (e.g., Freund's Complete Adjuvant and Freund's Incomplete Adjuvant), mycolate-based adjuvant (e.g., trehalose dimycolate), bacterial lipopolysaccharide (LPS), peptidoglycan (e.g., murein, mucopeptide or glycoproteins such as N-Opaca, muramyl dipeptide [MDP], or MDP analog), proteoglycan (e.g., extracted from Klebsiella pneumoniae), streptococcal preparation (e.g., OK432), muramyldipeptide, Immune Stimulating Comlex, saponin, DEAE-dextran, neutral oil (e.g., miglyol), vegetable oil (e.g., arachis oil), liposome, polyol, Ribi adjuvant, vitamin E, Carbopol or interleukin.

[0020] The invention includes methods for vaccinating a subject against a Chlamydial infection by administering an attenuated microorganism or recombinant antigen to a subject. In one embodiment, the invention includes methods for preventing or ameliorating a condition associated with a Chlamydial infection by administering an attenuated microorganism or recombinant antigen to a subject. For instance, the invention includes a method of preventing or ameliorating a condition associated with C. trachomatis such as urethritis, prostatis, proctitis, epididymitis, cervicitis, salpingitis, endometritis, pelvic inflammatory disease, tubal factor infertility, chronic pelvic pain, cervical dysplasia, ectopic pregnancy, lymphogranuloma venereum (LGV), newborn eye infection, newborn lung infection, trachoma or reactive arthritis. The invention also includes a method of preventing or ameliorating a condition associated with C. pneumoniae such as pneumonia, acute respiratory disease, atherosclerosis, coronary artery disease, myocardial infarction, carotid artery disease, cerebrovascular disease, coronary heart disease, carotid artery stenosis, aortic aneurysm, claudication, stroke, chronic obstructive pulmonary disease, asthma, reactive airway disease, Reiter's syndrome or sarcoidosis. Accordingly the invention is useful as a vaccine and in the treatment of conditions associated with a Chlamydial infection. [0021] The invention further provides methods of eliciting an immune response in a subject by administering an attenuated Salmonella or composition of the invention to a subject. In one embodiment, the immune response is cell-mediated immunity. In another embodiment, the immune response is a mucosal IgA response.

[0022] The invention includes antisera and antibodies to the attenuated Salmonella of the invention. In another embodiment, the invention includes antisera and antibodies to a composition of the invention. Antisera and antibodies can be raised by methods known in the art. In one embodiment of the invention, the antibodies are isolated and substantially purified.

DESCRIPTION OF THE FIGURES [0023] Figure 1 shows a vector map of the pMBS vector map (with CT84 insert) and the nucleic acid sequence around the cloning site.

[0024] Figure 2 shows a vector map of suicide vector pCVD (with CT84 insert) and the nucleic acid sequence around the cloning site.

[0025] Figure 3 shows a vector map of suicide vector pCVD (with CT1 10 insert) and the nucleic acid sequence around the cloning site.

[0026] Figure 4 is an E. coli codon optimized nucleic acid sequence encoding CT1 10.

[0027] Figure 5 is the coding region of an E. coli codon optimized nucleic acid sequence encoding CT110.

[0028] Figure 6 is an immunogenic Chlamydia CT1 10 peptide.

[0029] Figure 7 is an E. coli codon optimized nucleic acid sequence encoding CT84.

[0030] Figure 8 is the coding region of an E. coli codon optimized nucleic acid sequence encoding CT84.

[0031] Figure 9 is an immunogenic Chlamydia CT84 peptide.

[0032] Figure 10 is a nucleic acid sequence encoding C. trachomatis serovar L2 PmpG.

[0033] Figure 11 is an immunogenic C. trachomatis serovar L2 PmpG protein.

[0034] Figure 12 is a nucleic acid sequence encoding C. trachomatis serovar B PmpG.

[0035] Figure 13 is an immunogenic C. trachomatis serovar B PmpG protein.

[0036] Figure 14 is a nucleic acid sequence encoding C. trachomatis serovar F PmpG.

[0037] Figure 15 is an immunogenic C. trachomatis serovar F PmpG protein.

[0038] Figure 16 is a nucleic acid sequence encoding C. trachomatis CT40 and the corresponding peptide sequence.

[0039] Figure 17 is a Salmonella ssaG promoter nucleic acid sequence.

[0040] Figure 18 is a CIyA secretion signal sequence.

[0041] Figure 19 is a CT84-ssaG promoter construct.

[0042] Figure 20 is a CT110-ssaG promoter construct.

[0043] Figure 21 is a amino acid sequence of C. muridarum CT1 10.

[0044] Figure 22 is a nucleotide sequence of C. muridarum CT110. DETAILED DESCRIPTION OF THE INVENTION

[0045] General Description

[0046] The invention provides live attenuated Salmonella microorganisms capable of expressing Chlamydial antigens, vaccine compositions, and methods of preventing and treating Chlamydial infection and related conditions. In particular, the live attenuated Salmonella of the invention are capable of expressing Chlamydial PmpG, Pmpl, PmpE, MOMP, PmpD, PmpH, OmcB, OmpH and HtrA proteins or fragments thereof that when administered to a subject, elicit an effective immune response. The vaccine compositions of the present invention are suitable for inducing an effective immune response, e.g., including cellular immune response, against Chlaymdial infection such as a C. trachomatis, C. pneumoniae or C. muridarum infection or a C. trachomatis or C. pneumoniae related condition.

[0047] In one aspect, the invention provides an attenuated Salmonella expressing an immunogenic peptide that comprises an immunogenic portion of a Chlamydia peptide. The Salmonella is capable of presenting the C. trachomatis antigen(s) to the host immune system in a manner that generates an effective immune response, e.g., when administered orally to, or to a mucosal surface of, a human or non-human animal patient.

[0048] Definitions

[0049] As used herein, the term "attenuated" refers to a bacterium that has been genetically modified so as to not cause illness in a human or animal model. The terms "attenuated" and "avirulent" are used interchangeably herein.

[0050] As used herein, the term "bacterial vaccine vector" refers to an avirulent bacterium that is used to express a heterologous antigen in a host for the purpose of eliciting a protective immune response to the heterologous antigen. The attenuated microorganisms, including attenuated Salmonella enterica serovars, provided herein are suitable bacterial vaccine vectors. Bacterial vaccine vectors and compositions comprising the same disclosed can be administered to a subject to prevent or treat a Chlamydial infection or Chlamydial- related condition. Bacterial vaccine vectors and compositions comprising the same can also be administered to a subject to induce an immune response. In one embodiment, the bacterial vaccine vector is the sp/-VEC™ live attenuated bacterial vaccine vector (Emergent Product Development UK Limited, UK).

[0051] As used herein, the term "effective immune response" refers to an immune response that confers protective immunity. For instance, an immune response can be considered to be an "effective immune response" if it is sufficient to prevent a subject from developing a Chlamydial infection (e.g., C. trachomatis infection, C. pneumoniae or C. muridarum infection) after administration of a challenge of dose of C. trachomatis, C. pneumoniae or C. muridarum. An effective immune response may comprise a cell mediated immune response and/or humoral immune response. In one embodiment, an effective immune response is an MHC class ll-restricted, CD4+ T-helper type 1 (TH1 ) response. In one embodiment, the TH1 response is mediated by IFN-gamma or IFN-alpha. In another embodiment, an effective immune response is an MHC class l-restricted cytotoxic CD8+ T cell response. In one embodiment, the effective immune response refers to the ability of the vaccine of the invention to elicit the production of antibodies. An effective immune response may give rise to mucosal immunity. For instance, in one embodiment, an effective immune response is a mucosal IgA response.

[0052] As used herein, the term "gene expression cassette" refers to a nucleic acid construct comprising a heterologous nucleic acid under the control of an inducible promoter. In one embodiment, the heterologous nucleic acids encode one or more C. trachomatis C. pneumoniae peptides and/or C. muridarum. For instance, in one embodiment, the heterologous nucleic acid encodes a PmpG peptide. The Chlamydial peptide may lack an N-terminus (e.g., PmpG peptides CT84 and CT110) and, optionally, may lack a transmembrane domain (e.g., PmpG peptide CT84). In another embodiment, the heterologous nucleic acid encodes one or more of a chemokine and/or cytokine. In one embodiment, the non-Salmonella polynucleotide or polynucleotide regions of the gene expression cassette is codon-optimized for expression in a gram negative bacterium such as Salmonella or E. coli. In one embodiment, the inducible promoter is an in vivo inducible promoter. The gene expressing cassette may additionally comprise, for instance, one or more of a nucleic acid encoding a secretion tag and a nucleic acid encoding a peptide linker. A gene expression cassette may be contained on a plasmid or may be chromosomally integrated, for instance, at a gene deletion site. An attenuated Salmonella cell may be constructed to contain more than one gene expression cassette. For instance, a Salmonella cell can be constructed to express a first gene expression cassette in an am gene deletion site (e.g., aroC deletion site) and a second gene expression cassette in a Salmonella Pathogenicity Island 2 gene deletion site (e.g., ssaV deletion site).

[0053] As used herein, the term "immunogenic peptide" refers to a portion of a Chlamydial protein capable of eliciting an immunogenic response when administered to a subject. An immunogenic peptide can be a full length protein, a mature protein or a protein fragment. The immunogenic peptide can be a recombinant peptide. The invention includes immunogenic peptides comprising at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to Chlamydial PmpG, Pmpl, PmpE, MOMP, PmpD, PmpH, OmcB, OmpH or HtrA peptides and variants and fragments thereof capable of eliciting an immunogenic response. For instance, the invention includes immunogenic Chlamydia peptides disclosed in PCT/US08/006656, filed May 23, 2008; PCT/US08/007490, filed June 16, 2008; allowed US Application 10/398,248, filed August 1 , 2003; US application 11/781 ,203, filed July 20, 2007; US application 1 1/781 ,199, filed July 20, 2007; US application 09/677,752, filed October 2, 2000; allowed US application 08/942,596, filed October 2, 1997; US application 10/766,711 , filed January 27, 2004; PCT/US98/20737 (WO 99/17741 ), filed October 1 , 1998; US patent 6,887,843, filed April 3, 2000; US patent 6,642,023, filed July 6, 2000; US patent 7,419,807, filed November 4, 2004; and US application 10/931 ,779, filed September 1 , 2004, each of which is herein incorporated by reference in its entirety. In one embodiment of the invention, an immunogenic peptide comprises at least 10, 15, 20, 25, 30, 35, 40, 45 or 50 or more contiguous amino acids of a PmpG, Pmpl, PmpE, MOMP, PmpD, OmcB, OmpH or HtrA peptide.

[0054] In one embodiment of the invention, the immunogenic peptide lacks an N-terminus domain. For instance, the invention includes Chlamydial proteins that lack at least about 5, 10, 15, 20, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 125, 150, 175, 200, 225, 250, 275 or 300 or more amino acids at the N-terminus. In another embodiment of the invention, the immunogenic peptide lacks a transmembrane region. In yet another embodiment of the invention, the immunogenic peptide lacks at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70 80, 90, 100, 125, 150, 175, 200, 225, 250, 275 or 300 or more amino acids at the C-terminus.

[0055] In yet another embodiment of the invention, the immunogenic peptide lacks regions greater than 10 amino acids in length that share greater than 90% identity to eukaryotic peptides. For instance, in one embodiment of the invention, the immunogenic peptide is an HtrA peptide that consists essentially of a polypeptide with at least 70% identity to amino acids 1-151 or 1-169 of SEQ ID NOS: 2, 6 or 8 of PCT/US08/006656, filed May 23, 2008, or an immunogenic fragment thereof.

[0056] Chlamydial immunogenic peptide and Chlamydial antigen are used interchangeably herein.

[0057] The term "pharmaceutically acceptable" means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.

[0058] As used herein, the term "promoter" refers to a region of DNA involved in binding RNA polymerase to initiate transcription. In one embodiment of the invention, the promoter is a prokaryotic promoter such as a Salmonella ssaG promoter (Figure 17). In one embodiment of the invention, the promoter is a eukaryotic promoter.

[0059] As used herein, the terms "nucleic acid," "nucleic acid molecule," or "polynucleotide" refer to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the terms encompass nucleic acids containing analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed- base and/or deoxyinosine residues (Batzer et al. (1991 ) Nucleic Acid Res. 19:5081 ; Ohtsuka et al. (1985) J. Biol. Chem. 260:2605-2608; Cassol et al. (1992); Rossolini et al. (1994) MoI. Cell. Probes 8:91-98). The term nucleic acid is used interchangeably with gene, cDNA, and mRNA encoded by a gene. As used herein, the terms "nucleic acid," "nucleic acid molecule," or "polynucleotide" are intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof.

[0060] As used herein, the term "sequence identity" refers to a relationship between two or more polynucleotide sequences or between two or more polypeptide sequences. When a position in one sequence is occupied by the same nucleic acid base or amino acid residue in the corresponding position of the comparator sequence, the sequences are said to be "identical" at that position. The percentage "sequence identity" is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of "identical" positions. The number of "identical" positions is then divided by the total number of positions in the comparison window and multiplied by 100 to yield the percentage of "sequence identity." Percentage of "sequence identity" is determined by comparing two optimally aligned sequences over a comparison window. In order to optimally align sequences for comparison, the portion of a polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions termed gaps while the reference sequence is kept constant. An optimal alignment is that alignment which, even with gaps, produces the greatest possible number of "identical" positions between the reference and comparator sequences. Percentage "sequence identity" between two sequences can be determined using the version of the program "BLAST 2 Sequences" which was available from the National Center for Biotechnology Information as of September 1 , 2004, which program incorporates the programs BLASTN (for nucleotide sequence comparison) and BLASTP (for polypeptide sequence comparison), which programs are based on the algorithm of Karlin and Altschul {Proc. Natl. Acad. Sci. USA 90(12):5873-5877, 1993). When utilizing "BLAST 2 Sequences," parameters that were default parameters as of September 1 , 2004, can be used for word size (3), open gap penalty (1 1 ), extension gap penalty (1 ), gap dropoff (50), expect value (10) and any other required parameter including but not limited to matrix option. [0061] As used herein, the term "transformation" refers to the transfer of nucleic acid (Ae., a nucleotide polymer) into a cell. As used herein, the term "genetic transformation" refers to the transfer and incorporation of DNA, especially recombinant DNA, into a cell.

[0062] "Variants or variant" refers to a nucleic acid or polypeptide differing from a reference nucleic acid or polypeptide, but retaining essential properties thereof. Generally, variants are overall closely similar, and, in many regions, identical to the reference nucleic acid or polypeptide. In one embodiment, "variant" refers to a C. trachomatis, C. pneumoniae or C. muridarum nucleic acids or peptides. In one embodiment, variants refers to C. trachomatis PmpG peptide variants.

[0063] In one embodiment of the invention, the immunogenic portions of the Chlamydial peptides, as described below, are presented to the host immune system via a live, attenuated bacterial vaccine vector, such as an attenuated Salmonella vaccine vector. In various embodiments, the bacterial vector is an attenuated Salmonella enterica serovar, for instance, S. enterica serovar Typhi, S. enterica serovar Typhimurium, S. enterica serovar Paratyphi, S. enterica serovar Enteritidis, S. enterica serovar Choleraesuis, S. enterica serovar Gallinarum, S. enterica serovar Dublin, S. enterica serovar Hadar, S. enterica serovar lnfantis and S. enterica serovar Pullorum.

[0064] Generally, the Salmonella vector carries one or more gene deletions or inactivations, rendering the microorganism attenuated. In certain embodiments, the Salmonella vector is attenuated by deletion of all or a portion of a gene(s) associated with pathogenicity. The site of the deleted nucleic acids is referred to herein as the deletion site. In one embodiment of the invention, a gene expression cassette is inserted in a deletion site of a mutated gene. For instance, a gene expression cassette comprising nucleic acids encoding one or more of Chlamydia proteins PmpG, Pmpl, PmpE, PmpH, MOMP, PmpD, OmcB, OmpH, HtrA or a variant or fragment thereof may be inserted into a deletion site.

[0065] Alternatively, the gene(s) may be inactivated, for example, by mutation in an upstream regulatory region or upstream gene so as to disrupt expression of the pathogenesis-associated gene, thereby leading to attenuation. For instance, such a gene may be inactivated by an insertional mutation.

[0066] In certain embodiments, the attenuated microorganism may be an attenuated gram negative bacterium as described in U.S. Patents 6,342,215; 6,756,042 and 6,936,425, each of which is hereby incorporated by reference in its entirety. For example, the microorganism may be an attenuated Salmonella spp. {e.g., S. enterica Typhi, S. enterica Typhimurium or S. enterica Enteritidis) comprising at least one deletion or inactivation in a gene located within the Salmonella pathogenicity island 2 (SPI2). The present invention includes an attenuated Salmonella spp. with more than one deleted or inactivated SPI2 genes.

[0067] SPI2 is one of more than two pathogenicity islands located on the Salmonella chromosome. SPI2 comprises several genes that encode a type III secretion system involved in transporting virulence-associated proteins, including SPI2 so-called effector proteins, outside of the Salmonella bacteria and potentially directly into target host cells such as macrophages. SPI2 apparatus genes encode the secretion apparatus of the type III system. SPI2 is essential for the pathogenesis and virulence of Salmonella in the mouse. S. typhimurium SPI2 mutants are highly attenuated in mice challenged by the oral, intravenous and intraperitoneal routes of administration.

[0068] Infection of macrophages by Salmonella activates the SPI2 virulence locus, which allows Salmonella to establish a replicative vacuole inside macrophages, referred to as the Sa/mone//a-containing vacuole (SCV). SPI2-dependent activities are responsible for SCV maturation along the endosomal pathway to prevent bacterial degradation in phagolysosomes, for interfering with trafficking of NADPH oxidase-containing vesicles to the SCV, and remodeling of host cell microfilaments and microtubule networks. See, for instance, Vazquez-Torres et al., Science 287:1655-1658 (2000), Meresse et al., Cell Microbiol. 3:567-577 (2001 ) and Guignot et al., J. Cell ScL 1 17:1033-1045 (2004), each of which is herein incorporated by reference in its entirety. Salmonella SPI2 mutants are attenuated in cultured macrophages (see, for instance, Deiwick et al., J. Bacteriol. 180(18):4775-4780 (1998) and Klein and Jones, Infect. Immun. 69(2):737-743 (2001 ), each of which is herein incorporated by reference in its entirety). Specifically, Salmonella enterica SPI2 mutants generally have a reduced ability to invade macrophages as well as survive and replicate within macrophages.

[0069] The deleted or inactivated SPI2 gene may be, for instance, an apparatus gene {ssa), effector gene {sse), chaperone gene {ssc) or regulatory gene {ssή. In certain embodiments, the attenuated Salmonella microorganism is attenuated via a deletion or inactivation of a SPI2 apparatus gene, such as those described in Hensel et al., Molecular Microbiology 24(1 ):155-167 (1997) and US 6,936,425, each of which is herein incorporated by reference in its entirety. In certain embodiments, the attenuated Salmonella carries a deletion or inactivation of at least one gene associated with pathogenesis selected from ssaV, ssaJ, ssaU, ssaK, ssaL, ssaM, ssaO, ssaP, ssaQ, ssaR, ssaS, ssaT, ssaU, ssaD, ssaE, ssaG, ssal, ssaC {spiA) and ssaH. For example, the attenuated Salmonella may carry a deletion and/or inactivation of the ssa V gene. Alternatively, or in addition, the microorganism carries a mutation within an intergenic region of ssaJ and ssaK. The attenuated Salmonella may of course carry additional deletions or inactivations of the foregoing genes, such as two, three, or four genes.

[0070] In certain embodiments, the attenuated Salmonella microorganism comprises a deletion or inactivation of a SPI2 effector gene. For instance, in certain embodiments, the attenuated Salmonella comprises a deletion or inactivation of at least one gene selected from sseA, sseB, sseC, sseD, sseE, sseF, sseG, sseL and spiC {ssaB). SseB is necessary is necessary to prevent NADPH oxidase localization and oxyradical formation at the phagosomal membrane of macrophages. SseD is involved in NADPH oxidase assembly. SpiC is an effector protein that is translocated into SalmonellaA nfected macrophages and interferes with normal membrane trafficking, including phagosome-lysosome fusion. See, for instance, Hensel et al., MoI. Microbiol., 30:163-174 (1998); Uchiya et al., EMBO J., 18:3924- 3933 (1999); and Klein and Jones, Infect. Immun., 69(2):737-743 (2001 ), each of which is herein incorporated by reference in its entirety. The attenuated Salmonella may of course carry additional deletions or inactivations of the foregoing genes, such as two, three, or four genes.

[0071] In certain embodiments, the attenuated Salmonella microorganism comprises a deleted or inactivated ssr gene. For instance, in certain embodiments, the attenuated Salmonella comprises a deletion or inactivation of at least one gene selected from ssrA {spiR) and ssrB. ssrA encodes a membrane-bound sensor kinase (SsrA), and ssrB encodes a cognate response regulator (SsrB). SsrB is responsible for activating transcription of the SPI2 type III secretion system and effector substrates located outside of SPI2. See, for instance, Coombes et al., Infect. Immun., 75(2):574-580 (2007), which is herein incorporated by reference in its entirety.

[0072] In other embodiments, the attenuated Salmonella comprises an inactivated SPI2 gene encoding a chaperone (ssc). For instance, in certain embodiments, the attenuated Salmonella comprises a deletion or inactivation of one or more from sscA and sseB. See, for instance, US Patent 6,936,425, which is herein incorporated by reference in its entirety. [0073] The invention includes an attenuated Salmonella comprising a first attenuating mutation in the SPI2 region and a second attenuating mutation outside of SPI2 region. The attenuated Salmonella may comprise additional attenuating mutations, for instance, a third, fourth or fifth attenuating mutation.

[0074] In one embodiment of the invention, the attenuated Salmonella may carry an "auxotrophic mutation," for example, a mutation that is essential to a biosynthetic pathway. The biosynthetic pathway is generally one present in the microorganism, but not present in mammals, such that the mutants cannot depend on metabolites present in the treated patient to circumvent the effect of the mutation. For instance, the present invention includes an attenuated Salmonella with a deleted or inactivated gene necessary for the biosynthesis of aromatic amino acids. Exemplary genes for the auxotrophic mutation in Salmonella, include an am gene such as aroA, aroC, aroD and aroE. In one embodiment, the invention comprises a Salmonella SPI2 mutant (e.g., Salmonella with an attenuating mutation in ssaV, ssaJ, sseB, sseC, etc.) comprising a second attenuating mutation in the aroA gene. In one embodiment of the invention, the invention comprises a Salmonella SPI2 mutant (e.g., Salmonella with an attenuating mutation in ssaV, ssaJ, sseB, sseC, etc.) and a second attenuating mutation in an aroC gene.

[0075] In addition to am gene mutations, the present invention includes an attenuated Salmonella with a deletion or inactivation of a purA, purE, asd, cya and/or crp gene. For instance, the invention includes an attenuated Salmonella with a first attenuating mutation in a SPI2 gene (e.g., ssaV, ssaJ, sseB, sseC) and a second mutation in a purA, purE, asd, cya and/or crp gene.

[0076] In another embodiment, the attenuated Salmonella SPI2 mutant also comprises at least one additional deletion or inactivation of a gene in the Salmonella Pathogenicity Island I region (SPH ). In yet another embodiment, the Salmonella SPI2 mutant comprises at least one additional deletion or inactivation of a gene outside of the SPI2 region which reduces the ability of Salmonella to invade a host cell and/or survive within macrophages. For instance, the second mutation may be the deletion or inactivation of a rec or sod gene. In yet another embodiment, the Salmonella spp. comprises the deletion or inactivation of transcriptional regulator that regulates the expression of one or more virulence genes (including, for instance, genes necessary for surviving and replicating within macrophages). For instance, the Salmonella SPI2 mutant may further comprise the deletion or inactivation of one or more genes selected from the group consisting of phoP, phoQ, rpoS and slyA.

[0077] In certain embodiments, the attenuated microorganism is a Salmonella microorganism having attenuating mutations in a SPI2 gene (e.g., ssa, sse, ssr or ssc gene) and an auxotrophic gene located outside of the SPI2 region. In one embodiment, the attenuated microorganism is a Salmonella enterica serovar comprising a deletion or inactivation of an ssa, sse and/or ssr gene and an auxotrophic gene. For instance, the invention includes an attenuated Salmonella enterica serovar with deletion or inactivating mutations in the ssaV and aroC genes (for example, a microorganism derived from Salmonella enterica Typhi ZH9, as described in U.S. Patent No. 6,756,042, which description is hereby incorporated by reference) or ssaJ and aroC genes.

[0078] In yet another embodiment, the attenuated Salmonella is a LPS mutant strain of Salmonella.

[0079] Where the attenuated microorganism is a Salmonella bacterium, the nucleic acids that encode Chlamydial peptides (for instance, PmpG, Pmpl, PmpE, PmpH, MOMP, PmpD, OmcB and OmpH peptides) may be codon-optimized for expression in a gram negative pathogen such as a Salmonella enterica serovar. Expression of the antigens may be improved if the G+C content and codon usage are adjusted closer to that of S. enterica serovar host. In another embodiment, Chlamydial peptides may be codon-optimized for expression in E. coli. Nucleic acids may be codon-optimized by methods known in the art.

[0080] In one embodiment of the invention, the Chlamydial peptides are PmpG peptides such as CT1 10 (Figures 6 and 21 ), CT84 (Figure 9) or CT40 (Figure 16). The peptides can be encoded by E. coli codon-optimized nucleic acids, see, for instance, Figures 4 and 7 which provide codon-optimized nucleic acid sequences for CT1 10 and CT84, respectively, and Figure 22 which provides the nucleic acid sequence for C. muridarum CT1 10, which can be expressed by the attenuated Salmonella of the invention.

[0081] The polynucleotide encoding the immunogenic peptide, e.g., as a recombinant Chlamydia peptide under the control of an inducible promoter, may be contained on an extrachromosomal plasmid, or may be integrated into the bacterial chromosome by methods known in the art. In certain embodiments, the microorganism is an attenuated Salmonella comprising an integrated gene expression cassette that directs the expression of the immunogenic peptide from an inducible promoter. In one embodiment, the expression of the immunogenic peptide comprising a C. trachomatis, C. pneumoniae or C. muridarum peptide (e.g., PmpG peptide such as CT1 10 or CT84), is controlled by a Salmonella in vivo promoter (e.g., ssaG promoter) (Figures 19 and 20).

[0082] In certain embodiments, for example, where the attenuated microorganism is derived from Salmonella enterica serovar Typhi ZH9, the gene expression cassette comprising a heterologous antigen is inserted at the aroC and/or ssaV gene deletion site. In one embodiment of the invention, an attenuated Salmonella enterica serovar with at least one deletion mutation in a SPI-2 gene (e.g., ssa, sse, ssr or ssc gene) comprises a gene expression cassette in the SPI-2 gene deletion site. In another embodiment, an attenuated Salmonella enterica serovar with at least one deletion mutation in a gene involved in the biosynthesis of aromatic compounds comprises a gene expression cassette in the deletion site. In yet another embodiment, the attenuated Salmonella enterica serovar with at least one deletion mutation comprises a deletion mutation in a gene involved in the production of lipopolysaccharide and a gene expression cassette inserted in the site of deletion. Attenuated Salmonella enterica serovars with one or more attenuating gene deletion mutations (Ae., deletion sites) may comprise one or more gene expression cassettes on extrachromosomal plasmids.

[0083] In one embodiment of the invention, the gene expression cassette of the invention, either integrated in a Salmonella chromosome or located on a plasmid, comprises at least one heterologous polynucleotide encoding a Chlamydia immunogenic peptide. In one embodiment, the gene expression cassette comprises multiple heterologous nucleic acids encoding Chlamydia immunogenic peptides. The expressed Chlamydia immunogenic peptides may be expressed as a fusion protein. In one embodiment, the expressed Chlamydia immunogenic peptides are expressed as a fusion protein comprising one or more linker peptides separating one or more of the Chlamydia immunogenic peptides from other peptides (for instance, other Chlamydia immunogenic peptides).

[0084] In some embodiments, the gene expression cassette comprising the heterologous polynucleotide encoding a Chlamydia peptide additionally comprises nucleic acids encoding an export sequence such as a Salmonella CIyA (Figure 18) or E. coli CS3 export signal. For instance, in one embodiment, the gene expression cassette comprises, in a 5' to 3' direction, an inducible promoter followed by a nucleic acid encoding the export signal, optionally followed by a nucleic acid encoding a linker peptide, followed by the heterologous nucleic acid encoding one or more Chlamydia peptides. In one embodiment of the invention, the gene expression cassette does not include a nucleic acid encoding an export sequence and/or linker sequence.

[0085] The invention also includes a gene expression cassette comprising one or more polynucleotides encoding immunostimulatory therapeutic antigens such as a chemokine or cytokine (e.g., IFN-alpha, IFN-beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11 , IL-12, IL-13, IL-14, IL-15 or IL-16). The gene expression cassette comprising the immunostimulatory therapeutic polynucleotide may further comprise a heterologous polynucleotide encoding a Chlamydia immunogenic peptide (e.g., PmpG such as CT110, CT84 or CT40). Such a construct may further comprise a nucleic acid encoding a linker peptide to separate an expressed immunostimulatory therapeutic antigen from other antigens (e.g., to separate from other immunostimulatory therapeutic antigens and/or Chlamydia immunogenic peptides).

[0086] In one embodiment of the invention, the gene expression cassette comprising a polynucleotide encoding one or more immunostimulatory therapeutic antigens does not comprise a heterologous polynucleotide encoding a Chlamydial antigen. In this embodiment, the attenuated bacterial cell comprising the gene expression cassette may be pooled with an attenuated Salmonella cell comprising a Chlamydial antigen. In another embodiment, the attenuated Salmonella cell of the invention comprises multiple gene expression cassettes such that at least one gene expression cassette may be capable of expressing the immunostimulatory therapeutic antigen or antigens and at least one gene expression cassette may be capable of expression a Chlamydial antigen. In one embodiment of the invention, the multiple gene expression cassettes are located in gene deletion sites within the Salmonella genome. For instance, in one embodiment, the gene expression cassettes are located within aroC and ssaV deletion sites. In another embodiment, one or more of the gene expression cassettes are located on extrachromosomal plasmids.

[0087] The immunogenic peptide, optionally fused to a secretion tag and/or linker peptide and/or immunostimulatory therapeutic antigen, may be expressed by the live, attenuated bacterial vaccine vector via an inducible promoter, such as a promoter inducible under particular physiological conditions. In certain embodiments, the inducible promoter is a prokaryotic inducible promoter. For instance, the inducible promoter of the invention includes a gram negative bacterium promoter, including, but not limited to, a Salmonella promoter. In certain embodiments, the inducible promoter is an in vivo inducible promoter. In certain embodiments, the inducible promoter directs expression of an immunogenic peptide and, optionally, a fused secretion tag and/or linker peptide and/or immunostimulatory therapeutic antigen, within the gastrointestinal tract of the host. In certain embodiments, the inducible promoter directs expression of the immunogenic peptide and, optionally, fused secretion tag and/or linker peptide and/or immunostimulatory therapeutic antigen, within the gastrointestinal tract and immune cells (for instance, macrophages) of the host.

[0088] In certain embodiments, the inducible promoter directs expression of an immunogenic peptide (optionally, fused to a secretion tag and/or linker peptide and/or immunostimulatory therapeutic antigen) under acidic conditions. For instance, in certain embodiments, the inducible promoter directs expression of an immunogenic peptide at a pH of less than or about pH 7, including, for instance, at a pH of less than or about pH 6, pH 5, pH 4, pH 3 or pH 2. [0089] The promoter of the invention can also be induced under conditions of low phosphate concentrations. In one embodiment, the promoter is induced in the presence of low pH and low phosphate concentration such as the conditions that exist within macrophages. In certain embodiments, the promoter of the invention is induced under highly oxidative conditions such as those associated with macrophages.

[0090] The promoter of the invention can be a Salmonella SPI2 promoter. In one embodiment, the microorganism is engineered such that the SPI2 promoter that directs expression of the immunogenic peptide is located in a gene cassette outside of the SPI2 region or within a SPI2 region that is different from the normal location of the specified SPI2 promoter. Examples of SPI2 promoters include the ssaG promoter, ssrA promoter, sseA promoter and promoters disclosed, for instance, in US Patent 6,936,425.

[0091] In certain embodiments, the promoter directs the expression of the immunogenic peptide under conditions and/or locations in the host so as to induce systemic and/or mucosal immunity against the antigen, including the ssaG, ssrA, sseA, pagC, nirB and katG promoters of Salmonella. The in vivo inducible promoter may be as described in WO 02/072845, which is hereby incorporated by reference in its entirety.

[0092] In certain embodiments, the expression of the immunogenic peptide and, optionally, fused secretion tag and/or linker peptide and/or immunostimulatory therapeutic antigen, by the attenuated microorganism may be controlled by a Salmonella ssaG promoter. The ssaG promoter is normally located upstream of the start codon for the ssaG gene, and may comprise the nucleotide sequence of Figure 17. In this context, the term "ssaG promoter" includes promoters having similar or modified sequences, and similar or substantially identical promoter activity, as the wild-type ssaG promoter, and particularly with respect to its ability to induce expression in vivo. Similar or modified sequences may include nucleotide sequences with high identity to the nucleic acid sequence of Figure 17 such as nucleic acid sequences having at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the nucleic acid sequence of Figure 17, as well as functional fragments, including functional fragments with high identity to corresponding functional fragments of the nucleic acid sequence of Figure 17. In certain embodiments, the functional ssaG promoter fragment comprises at least about 30 nucleotides, at least about 40 nucleotides, or at least about 60 nucleotides.

[0093] Levels of identity between coding or promoter sequences may be calculated using known methods. Publicly available computer-based methods for determining identity include the BLASTP, BLASTN and FASTA (Atschul et al., J. Molec. Biol., 215: 403-410, (1990)), the BLASTX programme available from NCBI, and the Gap programme from Genetics Computer Group (Madison Wl). Levels of identity may be obtained using the Gap programme, with a Gap penalty of 50 and a Gap length penalty of 3 for the polynucleotide sequence comparisons.

[0094] Thus, the present invention provides vaccines, and particularly, live attenuated bacterial vectors, capable of expressing immunogenic portions of one or more Chlamydial antigens. In one embodiment of the invention, one or more Chlamydial antigens expressed by the attenuated Salmonella of the invention are Chlamydia outer surface membrane proteins or immunogenic fragments thereof. In another embodiment of the invention, the one or more Chlamydial peptides (Ae., antigens) are selected from the group consisting of PmpG, Pmpl, PmpE, MOMP, PmpD, PmpH, OmcB, OmpH and HtrA. In one embodiment of the invention, the Chlamydial antigens are mature antigens (Ae., lacking a signal sequence). The invention includes one or more Chlamydial antigens lacking 5, 10, 15, 20, 25, 26, 27, 28, 29 or 30 or more amino acids from the N-terminus. In another embodiment of the invention, the invention includes Chlamydial antigens lacking a transmembrane domain.

[0095] The invention further includes a Chlamydial antigen that is protease resistant. In one embodiment of the invention the Chlamydial antigen is modified to express reduced or no protease activity.

[0096] In one embodiment of the invention, the Chlamydial antigen is a PmpG protein or fragment thereof. The PmpG protein can be full length or mature. In one embodiment of the invention, the PmpG protein is missing at least about 5 amino acids at the N-termus. In one embodiment of the invention, the PmpG peptide lacks about 5, 10, 15, 20, 25, 26, 27, 28, 29 or 30 or more amino acids at the N-terminus. In one embodiment, the PmpG peptide lacks one or more amino acids in the transmembrane domain. In one embodiment of the invention, the PmpG peptide lacks a transmembrane domain. In one embodiment of the invention, the PmpG peptide comprises a heparin binding domain. In one embodiment of the invention, the PmpG peptide comprises a porin-like domain.

[0097] PmpG peptides included in the invention are CT110, CT84 and CT40. The present invention includes PmpG peptides from all C. trachomatis serovars, C. pneumoniae serovars or C. muridarum. In one embodiment of the invention, the PmpG peptides are capable of eliciting an immune response across C. trachomatis serovars. C. trachomatis PmpG peptides of the invention include peptides with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to peptides comprising or consisting essentially of SEQ ID NO: 2 (serovar L₂₆), SEQ ID NO: 15 (serovar B) and SEQ ID NO: 16 (serovar F) of US Patents 7,459,524; 7,419,807; 6,887,843; and 6,642,023, each of which is herein incorporated by reference in its entirety. These peptides are reproduced in Figures 1 1 , 13 and 15 herein. The invention includes PmpG proteins encoded by nucleic acids with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to nucleic acids comprising or consisting essentially of SEQ ID NOS: 1 (serovar L_2B), 23 (serovar B) and 24 (serovar F) of US Patents 7,459,524; 7,419,807; 6,887,843; and 6,642,023. These nucleic acid sequences are reproduced as Figures 12, 14 and 16 herein. The invention includes polynucleotides that encode PmpG that are codon-optimized for expression in Salmonella or E. coli.

[0098] CT110 peptide is a PmpG fragment that corresponds to methionine plus amino acids 29 to 1012 of SEQ ID NO: 2 and methionine plus amino acids 29 to 1013 of SEQ ID NOS: 15 and 16 of US Patents 7,459,524; 7,419,807; 6,887,843; and 6,642,023. In one embodiment of the invention, the CT1 10 peptide consists essentially of a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the peptide of Figure 6. In another embodiment of the invention, the CT110 peptide consists essentially of a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the peptide of Figure 21. The invention includes CT1 10 encoded by a polynucleotide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the polynucleotide comprising the sequence of Figure 4 or 5. In another embodiment the invention includes CT110 encoded by a polynucleotide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the polynucleotide comprising the sequence of Figure 22. In one embodiment of the invention, CT1 10 is encoded by a polynucleotide codon-optimized for expression in E. coli or Salmonella comprising the nucleic acid sequence of Figure 4.

[0099] CT84 peptide is a PmpG fragment that lacks both an N-terminus and a transmembrane domain. In one embodiment of the invention, CT84 consists essentially of a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the peptide of Figure 9. The invention includes CT84 encoded by a polynucleotide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the polynucleotide comprising the nucleic acid of Figure 7 or 8. In one embodiment of the invention, CT1 10 is encoded by a polynucleotide codon-optimized for expression in E. coli or Salmonella comprising the nucleic acid of Figure 7.

[00100] CT40 peptide is a PmpG fragment that lacks both an N-terminus and a transmembrane domain. In one embodiment of the invention, CT40 consists essentially of a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the peptide of Figure 16. The invention includes CT40 encoded by a polynucleotide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the polynucleotide comprising the nucleic acid of Figure 16. In one embodiment of the invention, CT40 is encoded by a polynucleotide codon-optimized for expression in E. coli or Salmonella.

[00101] The invention includes additional PmpG peptides, for instance, protein fragments corresponding to SEQ ID NOS: 3, 17, 25 and 27 of US Patents 7,459,524; 7,419,807; 6,887,843; and 6,642,023. In one embodiment, the attenuated Salmonella of the invention is capable of expressing a PmpG peptide comprising or consisting essentially of a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the peptide of SEQ ID NOS: 3, 17, 25 and 27 of US Patents 7,459,524; 7,419,807; 6,887,843; and 6,642,023.

[00102] In one embodiment of the invention, the PmpG peptide comprises a peptide with at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to at least about 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 1 10, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390 or 400 or more contiguous amino acids of the peptide of Figures 11 , 13 and 15.

[00103] In one embodiment of the invention, the immunogenic peptide is a PmpE peptide. For instance, the invention includes full length PmpE, mature PmpE and immunogenic PmpE protein fragments. In another embodiment of the invention, the immunogenic peptide is a Pmpl peptide. For instance, the invention includes full length Pmpl, mature Pmpl and immunogenic Pmpl protein fragments. PmpE and Pmpl peptides include, but are not limited to those peptides disclosed, for instance, in US application 09/677,752, filed October 2, 2000 and PCT/US01/30345, filed September 28, 2001.

[00104] In one embodiment of the invention, the immunogenic peptide is a PmpD,

PmpH, OmcB, OmpH or HtrA peptide. For instance, the invention includes PmpD, PmpH, OmcB, OmpH and HtrA peptides disclosed in PCT/US08/006656, filed May 23, 2008 and PCT/US08/007490, filed June 16, 2008;

[00105] In one embodiment of the invention, the Chlamydial antigen is a C. trachomatis antigen. In another embodiment of the invention, the Chlamydial antigen is a C. pneumoniae antigen. In another embodiment of the invention, the Chlamydial antigen is a C. muridarum antigen. In yet another embodiment, the Chlamydial antigen is both a C. trachomatis and C. pneumoniae antigen.

[00106] C. trachomatis antigens can be from any of the at least 18 known C. trachomatis serovars. In one embodiment of the invention, the C. trachomatis antigen is from a C. trachomatis serovar A, B, or C. C. trachomatis serovars A, B and C are most commonly associated with trachoma although other serovars may cause trachoma. In another embodiment of the invention, the C. trachomatis antigen is from a C. trachomatis serovar D, E, F, G, H, I or K. C. trachomatis serovars D, E, F, G, H, I and K are most commonly associated with genital infections.

[00107] In one embodiment, the attenuated microorganism and/or immunogenic peptide may be constructed so as to secrete or express on the surface of the attenuated Salmonella cell one or more immunogenic peptides, each immunogenic peptide comprising portions of one or more Chlamydia antigens, for instance, PmpG, PmpE, Pmpl, PmpD, PmpH, OmcB, OmpH and/or HtrA. By secretion of the immunogenic peptide, a strong antibody response to the antigen, e.g., systemic and/or mucosal, may be elicited. In one embodiment of the invention, a plurality of attenuated Salmonella cells of the invention are administered to a subject, wherein some of the attenuated Salmonella cells secrete or express on the cell surface one or more Chlamydia antigens (i.e., by a secretion tag) and some of the attenuated Salmonella cells do not secrete or express on the cell surface Chlamydia antigens (Ae., no secretion tag) so as to elicit both a cell mediated and humoral immune response.

[00108] In certain embodiments, the immunogenic peptide is designed for secretion or cell surface expression by a bacterial export system. In one embodiment, the immunogenic peptide is secreted by a CIyA export system, e.g., by engineering the expressed immunogenic peptide to include a CIyA secretion tag. CIyA and its use for secretion of proteins from host cells is described in U.S. Patent No. 7,056,700, which is hereby incorporated by reference in its entirety. Generally, the CIyA export system secretes the immunogenic peptide in close association with membranous vesicles, which may increase the potency of the immune response.

[00109] Other secretion systems that may find use with the invention include other members of the HIyE family of proteins. The HIyE family consists of HIyE and its close homologs from E. coli, Shigella flexneri, S. typhi, and other bacteria. E. coli HIyE is a functionally well characterized, pore-forming, chromosomally-encoded hemolysin. It consist of 303 amino acid residues (34 kDa). HIyE forms stable, moderately cation-selective transmembrane pores with a diameter of 2.5-3.0 nm in lipid bilayers. The crystal structure of E. coli HIyE has been solved to 2.0 angstrom resolution, and visualization of the lipid- associated form of the toxin at low resolution has been achieved by electron microscopy. The structure exhibits an elaborate helical bundle about 100 angstroms long. It oligomerizes in the presence of lipid to form transmembrane pores.

[00110] This haemolysin family of proteins (of which CIyA is a member), typically cause haemolysis in eukaryotic target cells. Thus, the tag may be modified in some embodiments so as to be non-hemolytic or have reduced hemolytic activity. Such modifications may include modifications at one or more, or all of, positions 180, 185, 187, and 193 of the CIyA encoding polynucleotide. In certain embodiments, the CIyA export tag has one or more or all the following modifications: G180V, V185S, A187S, and I193S. However, alternative modifications to the wild-type sequence may be made, so long as the CIyA tag is substantially non-hemolytic. Such modifications may be guided by the structure of the protein, reported in Wallace et al., E. coli Hemolysin E (HIvE, CIvA, SheA): X-Rav Crystal Structure of the Toxin and Observation of Membrane Pores by Electron Microscopy, Cell 100:265-276 (2000), which is hereby incorporated by reference in its entirety. For example, modifications may include modification of outward-facing hydrophobic amino acids in the head domain to amino acids having hydrophilic side chains.

[00111] CIyA sequences that may be used and/or modified to export the immunogenic peptide include S. typhi clyA (available under GENBANK Accession No. AJ313034); Salmonella paratyphi clyA (available under GENBANK Accession No. AJ313033); Shigella flexneri truncated HIyE {hlyE), the complete coding sequence available under GENBANK Accession No. AF200955; and the Escherichia coli hlyE, available under GENBANK Accession No. AJ001829.

[00112] Other secretion sequences may be used to secrete the immunogenic peptide(s) from the bacterial host cell or express the immunogenic peptide(s) on the Salmonella cell surface, including, but not limited to secretion sequences involved in the Sec-dependent (general secretory apparatus) and Tat-dependent (twin-arginine translocation) export systems. For instance, a leader sequence from S. typhi sufl can be used (msfsrrqflqasgialcagaiplranaagqqqplpvppllesrrgqplfm) to export the immunogenic peptide. Additional export system sequences comprising the consensus sequence s/strrxfl plus a hydrophobic domain can be used to export the immunogenic peptide from the bacterial host cell.

[00113] Another secretion sequence of the invention is E. coli CS3 as is disclosed in

US provisional application 61 ,107,113, filed October 21 , 2008, which is hereby incorporated by reference in its entirety. The invention includes an attenuated Salmonella cell wherein the Chlamydial peptide is secreted or expressed on the cell surface. This can be accomplished by cloning a CS3 export signal nucleic acid (atgttaaaaataaaatacttattaataggtctttcactgtcagctatgagttcatactcactagct) upstream and in frame with the heterologous polynucleotide encoding the Chlamydial peptide. The amino acid CS3 export signal sequence (MLKIKYLLIGLSLSAMSSYSLA) may be completely or partially removed during the cell surface expression or export of the Chlamydial peptide.

[00114] It is envisioned that signal sequences and secretion sequences known in the art can be used to export the immunogenic peptide out of the live, attenuated microorganism and into the host, including the host gastrointestinal tract. Such sequences can be derived, for instance, from virus, eukaryotic organisms and heterologous prokaryotic organisms. See, for instance, US Patents 5,037,743; 5,143,830 and 6,025,197 and US Patent Application 20040029281 , for disclosure of additional signal sequences and secretion sequences.

[00115] In one embodiment of the invention, the secretion sequence is cleaved from the exported immunogenic peptide. In other embodiment of the invention, the bacterial secretion sequence is not cleaved from the exported or cell surface expressed immunogenic peptide, but, rather, remains fused so as to create a secretion tag and immunogenic peptide fusion protein. For instance, the invention includes a fusion protein comprising a CIyA export peptide fused to one or more immunogenic peptides. In other embodiment of the invention, the bacterial export sequence maintains the conformation of the immunogenic peptide.

[00116] In another embodiment of the invention, the secretion sequence causes the exported immunogenic peptide to "bleb off" the bacterial cell, i.e., a bacterial outer- membrane vesicle containing the immunogenic peptide is released from the bacterial host cell. See Wai et al., Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial CIyA Cvtotoxin, Cell 115:25-35 (2003), which is hereby incorporated by reference in its entirety. The invention includes avirulent bacterial vesicles comprising one or more immunogenic peptides of the invention. In one embodiment, avirulent bacterial vesicles comprise a secretion sequence fused to the one or more immunogenic peptides and, optionally, one or more linker peptides. For instance, the invention includes a S. enterica vesicle comprising a CIyA export sequence fused to a C. trachomatis PmpG peptide (e.g., full length or mature PmpG, CT110, CT84 or CT40).

[00117] Secretion tag, export tag, export sequence and secretion sequence are used interchangeably herein and refer to a sequence that directs export of an immunogenic peptide out of a cell or express an immunogenic peptide on the surface of the attenuated Salmonella cell.

[00118] In one embodiment, a peptide linker is used to separate a secretion tag from an immunogenic peptide. In another embodiment, a peptide linker is used to separate two immunogenic peptides, for instance, a PmpG peptide and HtrA peptide. In yet another embodiment, the peptide linker is used to separate an immunogenic peptide from immunostimulatory therapeutic antigen such as a chemokine or cytokine (e.g., IFN-alpha, IFN-beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11 , IL-12, IL-13, IL- 14, IL-15 or IL-16).

[00119] Accordingly, the present invention includes an attenuated Salmonella bacterium capable of expressing (a) a fusion protein comprising a secretion tag + linker + Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof), (b) a fusion protein comprising a first Chlamydia immunogenic peptide + linker + a second Chlamydia immunogenic peptide, (c) a fusion protein comprising a Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof) + linker + an immunostimulatory therapeutic antigen (e.g., IFN-alpha, IFN-beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-1 1 , IL-12, IL-13, IL-14, IL-15 or IL-16) and (d) a fusion protein comprising an immunostimulatory therapeutic antigen (e.g., IFN-alpha, IFN-beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-1 1 , IL-12, IL-13, IL-14, IL-15 or IL-16) + linker + a Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof) .

[00120] In yet another embodiment, the invention includes a vaccine comprising or expressing (a) a fusion protein comprising a secretion tag + linker + Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof), (b) a fusion protein comprising a first Chlamydia immunogenic peptide + linker + a second Chlamydia immunogenic peptide, (c) a fusion protein comprising a Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT110 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof) + linker + an immunostimulatory therapeutic antigen (e.g., IFN-alpha, IFN- beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11 , IL-12, IL-13, IL-14, IL-15 or IL-16) and (d) a fusion protein comprising an immunostimulatory therapeutic antigen (e.g., IFN-alpha, IFN-beta, IFN-gamma, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL- 11 , IL-12, IL-13, IL-14, IL-15 or IL-16) + linker + a Chlamydia immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT110 peptide, CT84 peptide, CT40 peptide and fragments and variants thereof) . The vaccine can be a live, attenuated bacterial vector vaccine or a polypeptide vaccine. In one embodiment, the polypeptide is contained within a bacterial membrane that is lacking genomic DNA.

[00121] Without wishing to be bound by a particular theory, it is believed that the peptide linker allows the C. trachomatis, C. pneumoniae and/or C. muridarum immunogenic peptide to maintain correct folding. The linker peptide may also assist with the effective presentation of the Chlamydial immunogenic, in particular by providing spatial separation from the secretion tag and/or other C. trachomatis immunogenic peptide and/or immunostimulatory therapeutic antigen. For example, the peptide linker may allow for rotation of two C. trachomatis immunogenic peptides relative to each other.

[00122] In one embodiment of the invention, the live, attenuated Salmonella comprises a nucleic acid sequence encoding a peptide linker about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1 , 12, 13, 14 or 15 amino acids in length.

[00123] In one embodiment, the linker comprises or consists essentially of glycine, proline, serine, alanine, threonine, and/or asparagine amino acid residues. In one embodiment of the invention, the peptide linker comprises or consists essentially of glycine and/or proline amino acids. For instance, in one embodiment, the peptide linker comprises the amino acid sequence GC. In another embodiment, the peptide linker comprises the amino acid sequence CG.

[00124] In one embodiment, the peptide linker comprises or consists essentially of glycine and/or serine amino acids. In one embodiment, the peptide linker comprises or consists essentially of proline amino acids. In one embodiment, the peptide linker comprises or consists essentially of glycine amino acids.

[00125] In other aspects, the invention provides recombinant antigens and polynucleotides encoding the same. The recombinant antigens of the invention comprise immunogenic portions of C. trachomatis, C. pneumonia or C. muridarum peptides (as described herein), and may be designed for secretion from a bacterial vector such as Salmonella. The recombinant antigens of the invention are useful for inducing an effective immune response, such as a cell mediated immune response or a mucosal immune response, against C. trachomatis or C. pneumoniae in a human patient.

[00126] The recombinant antigens of the invention further comprise a CIyA export tag or CS3 export tag, as described. For example, the recombinant antigen may comprise a CIyA export tag fused to a Chlamydia peptide (e.g., PmpG full length protein, PmpG mature protein, CT110, CT84 or CT40). In another embodiment, the recombinant antigen may comprise a Chlamydia peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10, CT84 or CT40) fused to an immunostimulatory therapeutic peptide such as IL-2. Such recombinant antigens may further comprise a linker between the secretion signal and the Chlamydia peptide, between two Chlamydia peptides, and/or between the Chlamydia peptide and immunostimulatory therapeutic antigen.

[00127] The invention includes an isolated recombinant antigen. The recombinant antigen can be isolated by methods known in the art. An isolated recombinant antigen can purified, for instance, substantially purified. An isolated recombinant antigen can be purified by methods generally known in the art, for instance, by electrophoresis (e.g., SDS-PAGE), filtration, chromatography, centrifugation, and the like. A substantially purified recombinant antigen can be at least about 60% purified, 65% purified, 70% purified, 75% purified, 80% purified, 85% purified, 90% purified or 95% or greater purified.

[00128] The invention further provides a polynucleotide encoding the recombinant antigens of the invention. Such recombinant antigens may be under the control of an inducible promoter as described, such as a Salmonella ssaG promoter, for example. The polynucleotide may be designed for integration at, or integrated at, an aroC and/or ssaV gene deletion site of a Salmonella host cell. In some embodiments, the polynucleotide of the invention is a suicide vector for constructing a microorganism of the invention, as exemplified in Figures 2 and 3. The invention includes an isolated and/or purified polynucleotide. By "isolated," it is meant that the polynucleotide is substantially free of other nucleic acids, e.g., at least about 20% pure, preferably at least about 40% pure, more preferably about 60% pure, even more preferably about 80% pure, most preferably about 90% pure, and even most preferably about 95% pure, as determined by agarose gel electrophoresis. A polynucleotide can be isolated or purified by methods generally known in the art.

[00129] The invention includes antisera and antibodies to the recombinant antigens, attenuated microorganisms and compositions of the invention. Antisera and antibodies can be raised by methods known in the art. In one embodiment, the antibodies are isolated. In another embodiment, the antibodies are substantially purified using methods known in the art.

[00130] The microorganism may be formulated as a composition for delivery to a subject, such as for oral delivery to a human patient. In addition, the invention also includes the formulation of the recombinant antigen as a composition for delivery to a subject, such as oral delivery to a human patient. In one embodiment, the recombinant antigen may be contained within a bacterial outer membrane vesicle.

[00131] In one embodiment of the invention, the vaccine comprises an attenuated

Salmonella capable of expressing one or more C. trachomatis, C. pneumoniae or C. muridarum immunogenic peptides in a subject. In another embodiment, attenuated Salmonella is capable of expressing one or more immunogenic peptides from a second pathogenic organism. For instance, the Salmonella vaccine vector of the invention can be engineered to additionally express an immunogenic peptide from a second, third or fourth pathogen. In one embodiment, the second, third and/or fourth pathogen is a pathogen that is associated with a sexually transmitted disease such as syphilis, gonorrhea, human papilloma virus or herpes virus. In another embodiment of the invention, the second, third or fourth pathogen is a pathogen that is associated with diseases and conditions of the eyes. In another embodiment of the invention, the second, third or fourth pathogen is associated with a cardiac, vascular or lung disease or condition.

[00132] The composition may comprise the microorganism as described, and a pharmaceutically acceptable carrier, for instance, a pharmaceutically acceptable vehicle, excipient and/or diluent. The pharmaceutically acceptable carrier can be any solvent, solid or encapsulating material in which the vaccine can be suspended or dissolved. The pharmaceutically acceptable carrier is non-toxic to the inoculated individual and compatible with the live, attenuated microorganism.

[00133] Suitable pharmaceutical carriers are known in the art, and include, but are not limited to, liquid carriers such as saline and other non-toxic salts at or near physiological concentrations. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. Examples of suitable pharmaceutical vehicles, excipients and diluents are described in "Remington's Pharmaceutical Sciences" by E. W. Martin, which is hereby incorporated by reference in its entirety.

[00134] In one embodiment of the invention, the composition comprises one or more of the following carriers: disodium hydrogen phosphate, soya peptone, potassium dihydrogen phosphate, ammonium chloride, sodium chloride, magnesium sulphate, calcium chloride, sucrose, sterile saline and sterile water. In one embodiment of the invention, the composition comprises an attenuated Salmonella enterica serovar (e.g., Typhi or Typhimurium or Enteritidis) with deleted or inactivated SPI2 (e.g., ssaV) and aroC genes and one or more gene expression cassettes comprising a nucleic acid encoding a C. trachomatis C. pneumoniae and/or C. muridarum immunogenic peptide (e.g., PmpG full length protein, PmpG mature protein, CT110, CT84, CT40 and fragments and variants thereof) under the control of an in vivo inducible promoter (e.g., ssaG promoter) and a carrier comprising disodium hydrogen phosphate, soya peptone, potassium dihydrogen phosphate, ammonium chloride, sodium chloride, magnesium sulphate, calcium chloride, sucrose and sterile water.

[00135] In certain embodiments, the compositions further comprise at least one adjuvant or other substance useful for enhancing an immune response. For instance, the invention includes a composition comprising a live, attenuated Salmonella bacterium of the invention with a CpG oligodeoxynucleotide adjuvant. Adjuvants with a CpG motif are described, for instance, in US Patent Application 20060019239, which is herein incorporated by reference in its entirety.

[00136] Other adjuvants that can be used in a vaccine composition with the attenuated microorganism of the invention, include, but are not limited to, aluminium salts such as aluminium hydroxide, aluminum oxide and aluminium phosphate, oil-based adjuvants such as Freund's Complete Adjuvant and Freund's Incomplete Adjuvant, mycolate-based adjuvants (e.g., trehalose dimycolate), bacterial lipopolysaccharide (LPS), peptidoglycans (e.g., mureins, mucopeptides, or glycoproteins such as N-Opaca, muramyl dipeptide [MDP], or MDP analogs), proteoglycans (e.g., extracted from Klebsiella pneumoniae), streptococcal preparations (e.g., OK432), muramyldipeptides, Immune Stimulating Complexes (the "Iscoms" as disclosed in EP 109 942, EP 180 564 and EP 231 039), saponins, DEAE-dextran, neutral oils (such as miglyol), vegetable oils (such as arachis oil), liposomes, polyols, the Ribi adjuvant system (see, for instance, GB-A-2 189 141 ), vitamin E, Carbopol, interferons (e.g., IFN-alpha, IFN-gamma, or IFN-beta) or interleukins, particularly those that stimulate cell mediated immunity (e.g., IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-1 1 , IL-12, IL-13, IL-14, IL-15, IL-16 and IL-17).

[00137] In certain embodiments, the compositions may comprise a carrier useful for protecting the microorganism from the stomach acid or other chemicals, such as chlorine from tap water, that may be present at the time of administration. For example, the microorganism may be administered as a suspension in a solution containing sodium bicarbonate and ascorbic acid (plus aspartame as sweetener).

[00138] Suitable formulations for oral administration include hard or soft gelatin capsules, pills, tablets, including coated tablets, elixirs, suspensions, syrups or inhalations and controlled release forms thereof. Gelatin capsules can serve as carriers for lypholized vaccines.

[00139] The compositions of the present invention can be administered via parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, transdermal, mucosal and buccal routes. Alternatively, or concurrently, administration may be noninvasive by either the oral, inhalation, nasal, or pulmonary route. In one embodiment, the compositions are administered orally. In another embodiment, the compositions of the invention are administered to the eye. In another embodiment, the compositions of the invention are administered vaginally.

[00140] Suspensions of the active compounds as appropriate oily injection suspensions may be administered. Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, ethyl oleate or triglycerides. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension include, for example, sodium carboxymethyl cellulose, sorbitol and dextran. Optionally, the suspension may also contain stabilizers. Liposomes can also be used to encapsulate the agent for delivery into the cell.

[00141] In certain embodiments, the vaccine dosage is 1 .0 x 10⁵ to 1 .0 x 10¹⁵ CFU/ml or cells/ml. For instance, the invention includes a vaccine with about 1.0 x 10⁵, 1.5 x 10⁵, 1 .0 x 10⁶, 1.5 x 10⁶, 1.0 x 10⁷, 1 .5 x 10⁷, 1 .0 x 10⁸, 1.5 x 10⁸, 1 .0 x 10⁹, 1 .5 x 10⁹, 1.0 x 10¹⁰, 1 .5 x 10¹⁰, 1 .0 x 10¹¹, 1 .5 x 10¹¹, 1.0 x 10¹², 1.5 x 10¹², 1 .0 x 10¹³, 1 .5 x 10¹³, 1.0 x 10¹⁴, 1.5 x 10¹⁴ or about 1.0 x 10¹⁵ CFU/ml or cells/ml. In certain embodiments, the dosage administered will be dependent upon the age, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired.

[00142] In certain embodiments, the compositions of this invention may be coadministered along with other compounds typically prescribed for the prevention or treatment of a C. trachomatis or C. pneumoniae infection or related condition according to generally accepted medical practice.

[00143] Recent studies have indicated that a prime-boost protocol is often a suitable method of administering vaccines. In a prime-boost protocol, one or more compositions of the present invention can be utilized in a "prime boost" regimen. An example of a "prime boost" regimen may be found in Yang, Z. et al. J. Virol. 77:799-803 (2002), which is incorporated herein by reference in its entirety. In a non-limiting example, one or more vaccine compositions of the present invention are delivered to an animal, thereby priming the immune response of the animal to a Chlamydia polypeptide of the invention, and then a second immunogenic composition is utilized as a boost vaccination. One or more compositions of the present invention are used to prime immunity, and then a second immunogenic composition, e.g., an attenuated bacteria vectored Chlamydia vaccine or vaccines or one or more purified subunits of the immunogenic Chlamydia peptides or fragments, variants or derivatives thereof is used to boost the ant\-Chlamydia immune response.

[00144] In another embodiment, the priming composition may be administered simultaneously with the boosting composition, but in separate formulations where the priming component and the boosting component are separated.

[00145] In one aspect, the invention provides a method for vaccinating a subject against C. trachomatis by administering an attenuated Salmonella of the invention, or composition comprising the same, to a patient. For example, the microorganism may be orally administered to a patient, such as a patient at risk of acquiring a C. trachomatis infection, or a patient having a C. trachomatis infection, including a patient having a recurrent infection. Accordingly, the present invention includes methods of preventing and/or treating a C. trachomatis infection or related condition comprising administering a composition comprising an attenuated Salmonella of the invention. For instance, the invention includes methods of preventing and/or treating a C. trachomatis infection or related condition comprising administering a composition comprising an attenuated Salmonella capable of expressing a PmpG peptide (e.g., full length protein, mature protein, CT1 10, CT84, CT40 and fragments and variants thereof) to a subject.

[00146] The method of the invention induces an effective immune response in the patient, which may include a cell mediated immune response and/or a mucosal IgA immune response against a C. trachomatis peptide (e.g., PmpG full length protein, PmpG mature protein, CT110, CT84, CT40 and fragments and variants thereof). In certain embodiments, the method of the invention may reduce the incidence of (or probability of) recurrent C. trachomatis infection. In other embodiments, the vaccine or composition of the invention is administered to a patient post-infection, thereby ameliorating the symptoms and/or course of the illness, as well as preventing recurrence. Symptoms of C. trachomatis infection and/or C. frac/?omaf/s-related conditions that can be prevented, reduced or ameliorated by administering the composition of the invention include, for instance, urethritis, prostatis, proctitis, epididymitis, cervicitis, salpingitis, endometritis, pelvic inflammatory disease, tubal factor infertility, chronic pelvic pain, cervical dysplasia, ectopic pregnancy, lymphogranuloma venereum (LGV), newborn eye infection, newborn lung infection, trachoma and reactive arthritis.

[00147] In one embodiment of the invention, administration of an attenuated

Salmonella of the invention capable of expressing a C. trachomatis peptide (e.g., PmpG full length protein, PmpG mature protein, CT1 10, CT84, CT40 and fragments and variants thereof) reduces the risk of HIV infection.

[00148] In another aspect, the invention provides a method for vaccinating a subject against C. pneumoniae by administering an attenuated Salmonella of the invention, or composition comprising the same, to a patient. For example, the microorganism may be orally administered to a patient, such as a patient at risk of acquiring a C. pneumoniae infection, or a patient having a C. pneumoniae infection, including a patient having a recurrent infection. Accordingly, the present invention includes methods of preventing and treating a C. pneumoniae infection or related condition comprising administering a composition comprising an attenuated microorganism of the invention. [00149] The method of the invention induces an effective immune response in the patient, which may include a cell mediated immune response and/or a mucosal IgA immune response against a C. pneumoniae peptide (e.g., PmpG, PmpE, Pmpl, PmpH, PmpD, MOMP, OmcB, OmpH and HtrA full length proteins, mature proteins, fragments and variants thereof). In certain embodiments, the method of the invention may reduce the incidence of (or probability of) recurrent C. pneumoniae infection. In other embodiments, the vaccine or composition of the invention is administered to a patient post-infection, thereby ameliorating the symptoms and/or course of the illness, as well as preventing recurrence. Symptoms of C. pneumoniae infection and/or C. pneumon/ae-related conditions that can be prevented, reduced or ameliorated by administering the composition of the invention include, for instance, pneumonia, acute respiratory disease, atherosclerosis, coronary artery disease, myocardial infarction, carotid artery disease, cerebrovascular disease, coronary heart disease, carotid artery stenosis, aortic aneurysm, claudication, stroke, chronic obstructive pulmonary disease, asthma, reactive airway disease, Reiter's syndrome and sarcoidosis.

[00150] In another aspect, the invention provides a method for vaccinating a murine subject against C. muridarum by administering an attenuated Salmonella of the invention, or composition comprising the same, to a subject. For example, the microorganism may be orally administered to a subject. Accordingly, the present invention includes methods of preventing and treating a C. muridarum infection or related condition comprising administering a composition comprising an attenuated microorganism of the invention.

[00151] The method of the invention induces an effective immune response in the murine subject, which may include a cell mediated immune response and/or a mucosal IgA immune response against a C. muridarum peptide (e.g., PmpG, PmpE, Pmpl, PmpH, PmpD, MOMP, OmcB, OmpH and HtrA full length proteins, mature proteins, fragments and variants thereof). In certain embodiments, the method of the invention may reduce the incidence of (or probability of) recurrent C. muridarum infection. In other embodiments, the vaccine or composition of the invention is administered to a subject post-infection, thereby ameliorating the symptoms and/or course of the illness, as well as preventing recurrence.

[00152] The vaccine may be administered to the patient once, or may be administered a plurality of times, such as one, two, three, four or five times.

[00153] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., Sambrook ef al., ed., Cold Spring Harbor Laboratory Press: (1989); Molecular Cloning: A Laboratory Manual, Sambrook et al., ed., Cold Springs Harbor Laboratory, New York (1992), DNA Cloning, D. N. Glover ed., Volumes I and Il (1985); Oligonucleotide Synthesis, M. J. Gait ed., (1984); MuIMs et al. U.S. Pat. No: 4,683,195; Nucleic Acid Hybridization, B. D. Hames & S. J. Higgins eds. (1984); Transcription And Translation, B. D. Hames & S. J. Higgins eds. (1984); Culture Of Animal Cells, R. I. Freshney, Alan R. Liss, Inc., (1987); Immobilized Cells And Enzymes, IRL Press, (1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology, Academic Press, Inc., N.Y.; Gene Transfer Vectors For Mammalian Cells, J. H. Miller and M. P. Calos eds., Cold Spring Harbor Laboratory (1987); Methods In Enzymology, VoIs. 154 and 155 (Wu et al. eds.); Immunochemical Methods In Cell And Molecular Biology, Mayer and Walker, eds., Academic Press, London (1987); Handbook Of Experimental Immunology, Volumes I-IV, D. M. Weir and C. C. Blackwell, eds., (1986); Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1986); and in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1989).

[00154] General principles of antibody engineering are set forth in Antibody

Engineering, 2nd edition, C.A.K. Borrebaeck, Ed., Oxford Univ. Press (1995). General principles of protein engineering are set forth in Protein Engineering, A Practical Approach, Rickwood, D., et al., Eds., IRL Press at Oxford Univ. Press, Oxford, Eng. (1995). General principles of antibodies are set forth in: Nisonoff, A., Molecular Immunology, 2nd ed., Sinauer Associates, Sunderland, MA (1984); and Steward, M.W., Antibodies, Their Structure and Function, Chapman and Hall, New York, NY (1984). Additionally, standard methods in immunology known in the art and not specifically described are generally followed as in Current Protocols in Immunology, John Wiley & Sons, New York; Stites et al. (eds) , Basic and Clinical -Immunology (8th ed.), Appleton & Lange, Norwalk, CT (1994) and Mishell and Shiigi (eds), Selected Methods in Cellular Immunology, W.H. Freeman and Co., New York (1980).

[00155] Standard reference works setting forth general principles of immunology include Current Protocols in Immunology, John Wiley & Sons, New York; Klein, J., Immunology: The Science of Self-Nonself Discrimination, John Wiley & Sons, New York (1982); Kennett, R., et al., eds., Monoclonal Antibodies, Hybridoma: A New Dimension in Biological Analyses, Plenum Press, New York (1980); Campbell, A., "Monoclonal Antibody Technology" in Burden, R., et al., eds., Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 13, Elsevere, Amsterdam (1984), Kuby Immunology 4^th ed. Ed. Richard A. Goldsby, Thomas J. Kindt and Barbara A. Osborne, H. Freemand & Co. (2000); Roitt, I., Brostoff, J. and Male D., Immunology, 6^th ed. London: Mosby (2001 ); Abbas A., Abul, A. and Lichtman, A., Cellular and Molecular Immunology, Ed. 5, Elsevier Health Sciences Division (2005); Kontermann and Dubel, Antibody Engineering, Springer Verlan (2001 ); Sambrook and Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press (2001 ); Lewin, Genes VIII, Prentice Hall (2003); Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Press (1988); Dieffenbach and Dveksler, PCR Primer, Cold Spring Harbor Press (2003).

[00156] All publications, patents and patent applications herein are incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

EXAMPLES [00157] Example 1 : Construction of a Salmonella ssaV and aroC double mutant

[00158] A Salmonella ssaV and aroC double mutant was constructed as provided in

Hindle et al., Infect. Immun., 70(7):3457-3467 (2002). Briefly, wild type S. typhi Ty2 was originally isolated from an individual with typhoid fever in 1916 and has been used for the derivation of all licensed typhoid vaccines. The strain was obtained from the National Collection of Type Cultures (NCTC) (a part of the Public Health Laboratory Service (PHLS) at Colindale, UK). The NCTC prepared the freeze-dried culture in 1982 using nutrient broth as the culture medium. Emergent Product Development UK Limited (then Microscience Ltd) received the strain from NCTC on 3^rd July 1998 with a certificate of analysis. A vial was re- suspended in liquid broth and streaked onto an agar plate. Inoculum was taken from the plate and cultured in liquid medium overnight. The resulting culture was used for the first step in the construction of the parent strain S. typhi (Ty2 aroC^" ssa\/^~) ZH9.

[00159] The wild type aroC gene, derived from the mutant strain S. typhi (Ty2 aroA^" purf\^~) MD9, is contained on plasmid pTAC2. A defined deletion of 600 bp was created within the aroC gene in pTAC2 by amplifying DNA fragments, flanking the aroC gene, from the pTAC2 by PCR and cloning them into the vector pUC18 to give plasmid pMIAC23. The 4.8 kb fragment containing the mutated aroC gene was isolated from pMIAC23 and cloned into the suicide vector pCVD442 to give plasmid pYCVC21. The mutated aroC gene was then introduced into wild-type S. typhi Ty2 by transformation with the suicide construct pYCVC21. The plasmid was able to integrate into the S. typhi genome following recombination between homologous regions on the plasmid and the genome to give ampicillin resistant transformants. The transformants, termed merodiploids, contained in the genome a copy of both the original wild type aroC gene and the mutated aroC gene separated by vector DNA sequences. A merodiploid was grown in the absence of ampicillin to allow for a second recombination event to occur which would result in loss of the pCVD442 vector DNA sequences and one copy of the aroC gene, either the wild-type aroC or the mutated aroC. Plating onto sucrose-containing media allowed for the selection of derivatives of the merodiploids that had undergone the second recombination event and lost the vector DNA sequences, as pCVD442 (and therefore pYCVC21 ) carries the sacB gene that when expressed results in a sucrose sensitive phenotype. Loss of the vector sequences was confirmed by testing the ampicillin sensitive phenotype, strains that had lost the vector DNA sequences were also ampicillin sensitive as the ampicillin resistance gene is carried on pCVD442. The ampicillin sensitive strains were then tested to determine whether they had retained a copy of the wild-type or mutated aroC gene. Ampicillin sensitive colonies that were unable to grow in the absence of the supplement of aromatic compounds were identified as those that had undergone recombination to lose the vector DNA sequences plus the copy of the wild-type aroC gene. The aroC genotype was confirmed by colony PCR analysis using a primer pair that gives a product of 995 bp for the wild type aroC and 401 bp for the mutated aroC gene. Sequence analysis of the resulting PCR products confirmed the presence of the required deletion in 5 individual isolates DTY6, DTY7, DTY8, DTY9 and DTY10. These strains are stored in Microbank vials at -80⁰C for long-term storage. Strain DTY8 was selected for further use and was denoted S. typhi (Ty2 aroC^") DTY8.

[00160] The construct pTYSV21 carries the wild-type ssaV gene derived from the mutant strain S. typhi (aroA^~ purf\^~) MD9. A defined deletion of 1.909 kb was created within the cloned ssaV gene on plasmid pTYSV21 using inverse PCR to give the plasmid pYDSVL The 5.5 kb DNA fragment containing the mutated ssaV gene plus flanking regions was isolated from pYDSVI and cloned into the suicide plasmid pCVD422 to give plasmid pYDSV214. The mutated ssaV gene was then introduced into S. typhi (Ty2 aroC^") DTY8 by transformation with the suicide construct pYDSV214. A number of ampicillin resistant merodiploids were obtained and one, termed MD120, was selected for further manipulations. MD120 was grown in the absence of ampicillin to allow for loss of the pCVD442 DNA sequences and one copy of the ssaV gene, either the wild-type copy or the mutated copy, and then plated onto sucrose containing plates. Single colonies from these plates were assessed for sensitivity to ampicillin and derivatives of MD120 that had undergone a second recombination event were identified as sucrose resistant and ampicillin resistant. These strains were subjected to colony PCR analysis to identify those that had retained only the deleted ssaV gene, using primers that gave a product of 2486 bp for the wild type ssaV and 592 bp for the deleted ssaV gene. The resulting PCR products were sequenced and the presence of the desired deletion was confirmed in 5 individual isolates, ZH2, ZH4, ZH6, ZH7 and ZH9. Serological analysis was performed on each of the strains. Strain ZH9 tested positive for the 09 and Vi antigens and was chosen for further use. This strain was denoted S. typhi (Ty2 aroC^" ssaV^~) ZH9.

[00161] Example 2: Introduction of the ssaG-Chlamydia antigen Promoter-gene

Fusion into the aroC Deletion of S. typhi (Tv2 aroC ssaV) ZH9

[00162] A ssaG-Chlamydia antigen gene expression cassette was then inserted in the aroC deletion site. Although constructs were made comprising E. coli codon optimized polynucleotides encoding CT110 and CT84, the cloning strategy can be used with other polynucleotides disclosed herein that encode immunogenic Chlamydia peptides as well as the Chlamydia polynucleotides disclosed in PCT/US08/006656, filed May 23, 2008; PCT/US08/007490, filed June 16, 2008; allowed US Application 10/398,248, filed August 1 , 2003; US application 11/781 ,203, filed July 20, 2007; US application 11/781 ,199, filed July 20, 2007; US application 09/677,752, filed October 2, 2000; allowed US application 08/942,596, filed October 2, 1997; US application 10/766,71 1 , filed January 27, 2004; PCT/US98/20737 (WO 99/17741 ), filed October 1 , 1998; US patent 6,887,843, filed April 3, 2000; US patent 6,642,023, filed July 6, 2000; US patent 7,419,807, filed November 4, 2004; and US application 10/931 ,779, filed September 1 , 2004, each of which is herein incorporated by reference in its entirety.

[00163] E. coli codon optimized polynucleotides encoding CT84 and CT1 10 were cloned into a pMBS intermediate plasmid which contains the ssaG promoter (see for instance, Figure 1 which was used for cloning CT84). The antigen gene was cloned downstream of the promoter using Nde\ and AvrW restriction enzyme sites present in the vector.

[00164] In the case of CT110 and CT84, the gene had previously been cloned into a protein expression vector. The restriction enzyme sites in the vector needed to be modified to allow the gene to be cloned into pMBS. The available restriction sites at the 5' end of the gene required modifying to insert an Xba\ and AvrW restriction enzyme site. This was added by creating a piece of linker DNA from two custom synthesized oligonucleotides. The plasmid backbone was cut using a unique cutting enzyme (SamHI for CT1 10 and Sal\ for CT84) and the custom linker (carrying compatible cohesive ends and the sequence for the additional enzyme sites) was inserted, as shown below:

Addition of a linker (using CT1 10 as an example): Initial 5' layout

CT1 10 BamHI

Stop codons

TAATAAGGVA 7CC

ATTATTCCTΛGG

Linker

Final site layout - CT1 10

CT1 10 Xbal Avrll

O LU[J UUUUI Io

TAATAAGGA TCTCTAGACT AGCCTAGGG G ATCC

ATTATTCCT AGAG ATCTGA TCGGATCCCC TAGG

Inserted linker (bold face)

BamHI site (italics)

Final site layout - CT84

Sail Xbal Avrll

TTCA CCTAATCTAG AGTCGACTAG CCTAGG TCGA C AAGT GGATTAGATC TCΛ GCTGATC GGATCCAGCT G

Inserted linker (bold face)

Sail site (italics)

[00165] Following modification of the antigen source DNA, the antigens were able to be cut from the protein expression vector using Nde\ and Avή\. The resulting fragment was then purified and cloned downstream of the ssaG promoter in pMBS resulting in the constructs shown in Figures 19 and 20.

[00166] Once the promoter-antigen fusion was made the final step was to move the fusions into the suicide vector for insertion into the S. typhi chromosome. The promoter- antigen fusion was cut from the pMBS backbone using Xho\ and Avή\ restriction enzymes. This fragment was then cloned directly into the replicated aroC deletion site present in the pCVD-based suicide vector. The suicide vector used for cloning the CT84 construct is provided in Figure 2. The suicide vector used for cloning the CT1 10 construct is provided in Figure 3. [00167] The mutated aroC gene containing the promoter-antigen fusion was then introduced into wild-type S. typhi Ty2 by transformation with the suicide constructs. The plasmid was able to integrate into the S. typhi genome following recombination between homologous regions on the plasmid and the genome to give ampicillin resistant transformants. The transformants, termed merodiploids, contained in the genome a copy of both the original deleted aroC gene and the promoter-antigen construct flanked by the aroC gene separated by vector DNA sequences. A merodiploid was grown in the absence of ampicillin to allow for a second recombination event to occur which would result in loss of the pCVD442 vector DNA sequences and one copy of the aroC gene, either the deleted parental aroC or the deleted aroC containing the promoter-antigen. Plating onto sucrose-containing media allowed for the selection of derivatives of the merodiploids that had undergone the second recombination event and lost the vector DNA sequences, as pCVD442 (and therefore any pCVD derivative) carries the sacB gene that when expressed results in a sucrose sensitive phenotype. Loss of the vector sequences was confirmed by testing the ampicillin sensitive phenotype, strains that had lost the vector DNA sequences were also ampicillin sensitive as the ampicillin resistance gene is carried on pCVD442. The ampicillin sensitive strains were then tested using PCR to determine whether they had retained a copy of the parent mutated aroC gene or the mutated aroC gene carrying our promoter-antigen construct.

[00168] Although the present invention has been described in detail with reference to examples above, it is understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims. All cited patents, patent applications and publications referred to in this application are herein incorporated by reference in their entirety.

[00169] Example 3: Mouse Genital Infectivity Model

[00170] The modified Salmonella of the invention that express one or more Chlyamdia trachomatis antigens (e.g., CT84 or CT1 10) can be evaluated as immunogens and vaccinogens using the generally accepted mouse C. trachomatis genital infectivity model. For instance, the model can be used to evaluate the constructs as immunogens and for the ability to protect BALB/c mice against challenge with various C. trachomatis serovars (e.g., L₂, B, E). The modified Salmonella can be administered to groups of Chlamydia-ftee animals by three different immunization routes: oral, nasal or subcutaneous. For each route, the immunogenicity of the Salmonella can be determined, either alone or in combination with an appropriate adjuvant. After the first immunization, animals are periodically sacrified and serum IgG and mucosal (cervix/vagina and intestinal slgA levels determined using known methodologies.

[00171] Six to eight week old (sexually mature), specific-pathogen free, female mice can be administered the modified Salmonella as described below. For oral immunization, animals would be withdrawn from rations 4 hours before dosing. The modified Salmonella is administered intragastrically to unanesthatized mice, lntragastrically vaccinated mice are returned to solid rations approximately 3-4 hours after immunization. For nasal immunization, animals are sedated lightly, placed on their backs and administered modified Salmonella. For subcutaneous administration, modified Salmonella are administered subcutaneously to unanesthesized mice.

[00172] Beginning immediately after the first immunization and continuing at 7 day intervals thereafter, animals from each vaccination group can be anesthetized, the abdominal cavity opened, and the animal exasanguinated by cardiac punction. Immediately thereafter, the lower reproductive tract (cervix and vagina) and small intestine can be surgically removed. Mucosal secretions can be collected from the intestine and cervix/vagina by gently scrapping prewashed and dissected organs with a sterile scalpel blade. Sera and mucosal secretions can be stored in PBS at -70⁰C. until the end of the experiment and analyzed as a group.

[00173] Chlamydial IgG and secretory IgA levels in serum and mucosal secretions can be determined by ELISA. Titers to both whole EB lysates and Chlamydial protein can be determined. Briefly, intact purified C. trachomatis L₂ EBs or Chlamydial protein can be diluted in 0.05 M sodium carbonate buffer and used to coat lmmulon-3 (DynaTech) 96 well microtiter plates. After blocking with 1 % BSA/PBS/0.05% Tween-20 and extensive washing (3x; PBS/0/05% Tween-20) serum or mucosal secretion samples, serially diluted in PBS, can be added and the plate incubated at 37°C. for 1 hour. All samples can be tested in duplicate. Unbound material can be removed by washing. Affinity-purified HRP-conjugated to either goat anti-mouse IgA (alpha chain) or goat anti-mouse IgG (Vector Labs), diluted 1/5,000 in PBS, can then be added and the plate reincubated at 37°C. for 1 hour. Secondary antibody is removed, the plate washed again and substrate (TMB) added.

[00174] The color change can be measured in a microplate spectrophotometer at 450 nm after a 30 minute incubation at room temperature and quenching with H₂SO₄. Readings >2SD of 10 the mean negative control value (pooled prebleed sera, pooled mucosal secretions from unvaccinated animals) would be defined as positive. Reaction specificity can be monitored by preabsorbing the primary antibody with antigen (antibody-blocking) and the secondary antibody with purified mouse IgG/lgA (conjugate blocking). Antibody titers for each data point (e.g., 5 animals/point) can be presented as the geometric mean ± S. D. of the last positive dilution.

[00175] Two weeks after the last (e.g., third) immunization, animals can be challenged intravaginally, while under mild anesthesia, with a single dose of 0.1 ml endotoxin-free PBS containing 1081 FU of purified, pretitered C. trachomatis EBs. Progesterone can be administered (about 2.0 mg per dose, i.m.) one week prior to and the time of challenge to block estrous and ensure infection of mouse cervical epithelial cells with human C. trachomatis strains. The presence and persistence of C. trachomatis in the lower reproductive tract of vaccinated animals can be assessed using both a commercial C/7/amyc//a-specific ELISA (Chlamydiazyme, Abbott Diagnostics) and by in vitro cultivation.

[00176] At 7, 14 and 21 days post-challenge, animals can be sacrificed as above and their lower reproductive tracts (cervix/vagina) and small intestine surgically removed. Tissue homogenates can be prepared by macerating and homogenizing identical amounts of tissue in 1.0 ml SPG buffer. Clarified samples can be serially diluted and tested for Chlamydia- specific antigen by commercial ELISA and used to infect McCoy cells grown to about 90% confluency in 24-well tissue culture plates. Each dilution can be assayed in duplicate. After a 24 hour cultivation period, infected monolayers can be fixed with methanol and inclusion bodies visualized by indirect fluorescence antibody staining using an anti-Chlamydia LPS antibody. Fluorescent inclusions can be counted at 4Ox magnification and the resulting titer expressed as the mean number of inclusions per 20 fields. Chlamydia IgG and slgA levels in the serum and intestine can also be determined for these animals as detailed above. Protection is defined as the ability to eliminate or reduce the level of C. trachomatis in the lower genital tract.

[00177] To determine whether vaccination with modified Salmonella protect mice against heterotypic challenge, equivalent groups of mice can be immunized with the modified Salmonella expressing a L₂ serotype antigen (e.g., L₂ CT84 or L2 CT1 10) and subsequently challenged with either C. trachomatis serovar B or E.

[00178] Example 4: Mouse Model of Salpingitis and Fertility

[00179] The Tuffrey murine infertility model can be employed to evaluate the efficacy of the modified Salmonella of the invention to protect animals against Chlamydia trachomatis-^'mduced salpingitis and infertility. Groups of female C3H HeOuJ mice (about 6 weeks of age) can be employed for this evaluation. The test group of animals can be immunized at, for instance, weeks 0, 2, and 3 by intranasal administration of modified Salmonella. Prior to immunization mice can be sedated using an anesthesia cocktail consisting of, for instance, 16% Ketaject and 16% Xylaject in 68% pyrogen-free PBS (100 μl i.p./animal). Sedated animals can be placed on their backs and using a standard laboratory pipette administered the vaccine formulation; about 10 μl of the vaccine solution per nostril with a 5-10 minute wait period between applications.

[00180] Briefly at week 4, all animals can be administered a single i.p. dose of progesterone (2.5 mg in pyrogen-free PBS, Depo-Provera, Upjohn) to stabilize the uterine epithelium. At week 5, animals can be immunized and animals in the negative control group can be infected by bilateral intrauterine inoculation with about 5 x 10⁵ inclusion forming units (IFU) of C. trachomatis in 100 μl of sucrose phosphate glutamate buffer (SPG). To mimic the manipulations to the reproductive tract experienced by the other two groups, animals in the positive control can be bilaterally inoculated with 100 μl of a McCoy cell extract that contains no C. trachomatis. At week 7, animals from each group can be sacrificed by CO₂ asphyxiation and the complete genital tract (both upper and lower reproductive tracts) removed for histopathological analysis. At week 9, the remaining females from each group can be caged with 8-10 week old male C3H mice for a 2 month breeding period to assess fertility (1 male for every 2 females per cage with weekly rotation of the males within each group, animals from different experimental groups would not be mixed). Palpation and periodic weighing can be used to determine when animals in each pair became pregnant. The parameters used to estimate group fertility can be: F, the number of mice which littered at least once during the mating period divided by the total number of mice in that study group; M, the number of newborn mice (born dead or alive) divided by the number of litters produced in that group during the mating period; and N, the number of newborn mice (born dead or alive) divided by the total number of mice in that group.

[00181] Genital tracts can be treated for ≥24 hrs in Bouin's fixative, progressively dehydrated in 50%, 70%, and 100% methanol, soaked in toluol, and either paraffin embedded or directly embedded in OCT compound (Tissue-TEK, Miles) and subsequently snap frozen in liquid nitrogen. Tissue sections (about 6 μm) can be stained with hematoxylin and eosin (after deparaffinization of the Bouin fixed samples). Inflammatory changes in the oviducts and ovaries can be graded as follows: 0, no apparent inflammatory reaction; 1 , a few mononuclear cells infiltrating the periovarial space or the submucosa of the oviduct; 2, same as 1 but to a greater extent; 3, same as 2 but with a thickened oviductal submucosa and the presence of inflammatory cells in the oviductal lumen; 4, same as 3 but to a greater extent. Inflammation in the cervix/vagina can be scored based on the level of the intraepithelial infiltrate observed.

[00182] Blood samples can be collected periodically during the immunization and challenge phases by retroorbital bleeding and serum prepared by centrifugation. Vaginal secretions can be collected by repeated injection of 50 μl of sterile PBS into the vagina with a standard laboratory pipettor and immediately withdrawing the solution. Two-to-three injection/withdrawal cycles can be performed.

[00183] Quantitation of antibody (Ab) responses by ELISA can be performed as previously described. Microwell ELISA plates (Maxisorb, NUNC) for determining Ab levels can be coated overnight at 4° C. with about 0.5-1.0 μg of gel-purified antigen per well in 10 mM carbonate/bicarbonate buffer (pH 9.6), washed with PBS containing 0.1% Tween-20 (washing buffer) and blocked for about 1 hr at 37° C. with a PBS solution containing 3% BSA. For the determination of antigen-specific serum IgG levels, test sera can be serially diluted in washing buffer containing 0.5% BSA and aliquots (100 μl) incubated in the antigen-coated wells for about 2 hr at 37° C. The plates can then be washed and incubated for about 1 hr at 37° C. with a horseradish peroxidase (HRP)-conjugated goat anti-mouse IgG second antibody (Sigma). A HRP-conjugated goat anti-mouse IgA secondary antibody can be used to detect the presence of Chlamydial antigen-specific IgA in vaginal secretions. After incubation with the appropriate secondary Ab, the plates can be washed and incubated for about 20-30 minutes at room temperature with TMB substrate (Sigma). Reactions can be stopped by the addition of 2M H₂SO₄ and the absorbance determined at 450 nm on a spectrophotometer (Molecular Devices SpectroMax microplate reader). Titers can be determined as the reciprocal of the sample dilution corresponding to an optical density of 1.0 at 450 nm.

[00184] For determination of Chlamydial antigen-specific cellular responses, groups of female C3H HeOuJ mice (Jackson Labs) can be sedated and immunized at weeks 0, 2 and 3 by intranasal administration with the vaccine as described above. At weeks 4 and 5 immediately prior to progesterone treatment and intrauterine challenge, respectively, animals (e.g., 3) from each group can be sacrificed by CO₂ asphyxiation and spleens aseptically removed and single cell suspensions prepared using conventional methodologies. Spleen cells from immunized animals can be analyzed separately. For both the positive control group (sham immunized and sham infected) and the negative control group (sham immunized, infected) spleen cells can be pooled and tested for restimulation.

[00185] For the measurement of spleen cell proliferation, spleens can be ground (5 to

10 rounds) in 5 ml of RPMI 1640 Glutamax I supplemented with 10% fetal calf serum, 25 mM HEPES, 50 U/ml penicillin, 50 μg/ml streptomycin, 1 mm sodium pyruvate, nonessential amino acids, and 50 μM 2-mercaptoethanol (Gibco-BRL). Live cells can be counted by Trypan Blue staining and diluted in the same media to reach a density of 1.0-2.0 x 10⁶ cells/ml (Falcon 2063 polypropylene tubes). Triplicate cultures can be set-up in round bottom 96-well culture plates (Nunclon, Nunc) using about 5 x 10⁵ responder cells per well in 200 μl of media Cells were stimulated with either 1.0 μg/ml of antigen (antigen-specific proliferation) or with 4 μg/ml concanavalin A (Boerhinger Mannheim) as a positive stimulation control; unrestimulated cell cultures were used as a negative control of cellular activation. After 72- 96 hours of incubation at 37° C. in 5% CO₂ cells can be pulsed labelled for about 18 hrs with 1.0 μCi ³H-thymidine (Amersham) per well. Pulsed cells can be harvested onto glass-fiber sheets using a Tomtec Cell Harvester (Mk III) and counted for beta-emission in a 3-channel Wallac 1450 Trilux Liquid Scintillation Counter. The stimulation index (Sl) for a sample (individual or pooled) can be defined as the mean of the antigen or ConA-stimulated T-cell uptake of ³H-thymidine for triplicate wells divided by the mean of the unstimulated uptake for triplicate wells. SIs for both antigen-specific (rHMWP-specific) and ConA-specific proliferation can be determined.

[00186] Example 5: Mouse Pneumonitis Model

[00187] The modified Salmonella of the invention containing C. muridarum inserts

(e.g., CT84 and CT1 10 analogs) can be analyzed using a mouse pneumonitis model. Briefly, the mouse model of female urogenital tract infection with Chlamydia muridarum (the mouse pneumonitis strain of Chlamydia trachomatis, MoPn) has been used for some time to study immunological protection related to chlamydial infections (Barron AL, et ai, J Infect Dis. 1981 ; 143:63-66 and Rank RG, Stephens RS, editors. Chlamydia: Intracellular Biology, Pathogenesis, and Immunity, American Society for Microbiology. Washington, D. C: 1999. p. 295). More recently, it has been used to study pathological immune responses during chlamydia infection. Hydrosalpinx formation, infertility and fibrotic oviduct occlusion are routine consequences of infection following a single intravaginal inoculation of Chlamydia muridarum in susceptible mouse strains (Swenson CE, et ai, J Infect Dis. 1983; 148:1101 — 1107; Swenson CE and Schachter J., Sex Trans Dis. 1984; 11 :64-67; De La Maza LM et al., Infect Immun. 1994;62:2094-2097; Darville T et ai, Infect Immun. 1997;65:3065-3073 and Shah AA et ai, Sex Trans Dis. 2005;32:49-56). These sequelae also serve to make the mouse:MoPn infection model a legitimate model to study chlamydia-induced host response- mediated pathology.

[00188] Although the present invention has been described in detail with reference to exampes above, it is understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims. All cited patents, patent applications and publications referred to in this application are herein incorporated by reference in their entirety.

Claims

CLAIMS:

1. An attenuated Salmonella microorganism comprising i) an attenuating mutation in a Salmonella Pathogenicity Island 2 (SPI-2) gene; ii) an attenuating mutation in a second gene; and iii) one or more gene expression cassettes, each gene expression cassette comprising a heterologous nucleic acid under the control of an inducible promoter, wherein at least one of said heterologous nucleic acid encodes an immunogenic Chlamydial peptide.

2. The attenuated Salmonella microorganism of claim 1 , wherein said cell induces an effective immune response when administered to a human patient.

3. The attenuated Salmonella microorganism of any one of claims 1 to 2, wherein the second gene is a Salmonella gene involved in the biosynthesis of aromatic compounds.

4. The attenuated Salmonella microorganism of claim 3, wherein the gene involved in the biosynthesis of aromatic compounds is aroC.

5. The attenuated Salmonella microorganism of any one of claims 1 to 4, wherein the SPI-2 gene is selected from the group consisting of a ssa, sse, sse or ssr gene.

6. The attenuated Salmonella microorganism of claim 5, wherein said SPI-2 gene is an ssa gene.

7. The attenuated Salmonella microorganism of claim 6, wherein said ssa gene is selected from the group consisting of ssaV, ssaJ, ssaU, ssaK, ssaL, ssaM, ssaO, ssaP, ssaQ, ssaR, ssaS, ssaT, ssaU, ssaD, ssaE, ssaG, ssal, ssaC {spiA) and ssaH.

8. The attenuated Salmonella microorganism of claim 7, wherein said ssa gene is ssaV.

9. The attenuated Salmonella microorganism of claim 7, wherein said ssa gene is ssaJ.

10. The attenuated Salmonella microorganism of claim 5, wherein said SPI-2 gene is an sse gene.

11. The attenuated Salmonella microorganism of claim 10, wherein said sse gene is selected from the group consisting of sseA, sseB, sseC, sseD, sseE, sseF, sseG, sseL and spiC {ssaB).

12. The attenuated Salmonella microorganism of any one of claims 1 to 1 1 , wherein the attenuating mutation in the SPI-2 gene is a deletion or inactivation of the SPI-2 gene, and wherein the attenuating mutation in the second gene is a deletion or inactivation of the second gene.

13. The attenuated Salmonella microorganism of any one of claims 1 to 12, wherein the attenuated Salmonella cell is derived from Salmonella enterica serovar Typhi ZH9.

14. The attenuated Salmonella microorganism of claim 12, wherein the gene expression cassette is inserted at the SPI-2 gene deletion site and/or the second gene deletion site.

15. The attenuated Salmonella microorganism of claim 14, wherein the SPI-2 deletion site is an ssa V gene deletion site and the second gene deletion site is an aroC deletion site.

16. The attenuated Salmonella microorganism of any one of claims 1 to 15, wherein said inducible promoter is a prokaryotic promoter.

17. The attenuated Salmonella microorganism of any one of claims 1 to 16, wherein said inducible promoter is induced under acidic conditions.

18. The attenuated Salmonella microorganism of any one of claims 1 to 17, wherein said inducible promoter is induced under oxidative conditions.

19. The attenuated Salmonella microorganism of any one of claims 1 to 18, wherein said inducible promoter is induced in macrophages.

20. The attenuated Salmonella microorganism of any of one of claims 1 to 18, wherein said inducible promoter is an in vivo inducible promoter.

21. The attenuated Salmonella microorganism of any one of claims 1 to 20, wherein said inducible promoter is a Salmonella ssaG promoter.

22. The attenuated Salmonella microorganism of any one of claims 1 to 21 , wherein the Chlamydial peptide is secreted from the microorganism via a secretion signal.

23. The attenuated Salmonella microorganism of claim 22, wherein the secretion signal comprises a CIyA secretion signal or a non-hemolytic derivative thereof.

24. The attenuated Salmonella microorganism of claim 22, wherein the secretion signal comprises an E. coli CS3 secretion signal.

25. The attenuated Salmonella microorganism of any one of claims 1 to 24, wherein the heterologous nucleic acid encoding at least one immunogenic Chlamydial peptide is codon optimized for gene expression in Salmonella or E. coli.

26. The attenuated Salmonella microorganism of claim 25, wherein the heterologous nucleic acid has a G/C content of about 50%.

27. The attenuated Salmonella microorganism of any one of claims 1 to 26, wherein the immunogenic Chlamydial peptide is selected from the group consisting of PmpG, Pmpl, PmpE, MOMP, PmpD, PmpH, OmcB, OmpH and HtrA or an immunogenic fragment thereof.

28. The attenuated Salmonella microorganism of claim 27, wherein said immunogenic Chlamydial peptide is PmpG or a fragment thereof.

29. The attenuated Salmonella microorganism of claim 28, wherein said PmpG or a fragment thereof binds to an antibody to PmpG.

30. The attenuated Salmonella microorganism of claim 28, wherein said PmpG fragment comprises at least about 25 contiguous amino acids of PmpG.

31. The attenuated Salmonella microorganism of any one of claims 28 to 30, wherein said PmpG or fragment thereof is CT84, CT1 10 or CT40.

32. The attenuated Salmonella microorganism of any one of claims 1 to 31 , wherein the Chlamydial peptide is a C. trachomatis peptide, C. pneumoniae or a C. muridarum peptide.

33. The attenuated Salmonella microorganism of any one of claims 1 to 32, wherein the gene expression cassette further comprises a nucleic acid encoding a linker peptide.

34. The attenuated Salmonella microorganism of any of claims 1 to 31 , wherein said attenuated Salmonella microorganism is selected from the group consisting of S. enterica serovar Typhi, S. enterica serovar Typhimurium, S. enterica serovar Paratyphi, S. enterica serovar Enteritidis, S. enterica serovar Choleraesuis, S. enterica serovar Gallinarum, S. enterica serovar Dublin, S. enterica serovar Hadar, S. enterica serovar lnfantis and S. enterica serovar Pullorum.

35. The attenuated Salmonella microorganism of any one of claims 1 to 34, wherein said microorganism is modified to express reduced or no LPS.

36. The attenuated Salmonella microorganism of any one of claims 1 to 35, wherein said microorganism is further modified to express one or more cytokines or chemokines.

37. The attenuated Salmonella microorganism of claim 36 wherein the cytokine is an interferon.

38. A composition of the treatment or prevention of a Chlamydial infection or related condition comprising the attenuated Salmonella microorganism of any one of claims 1 to 37, and a pharmaceutically acceptable carrier and/or diluent.

39. The composition of claim 38, further comprising at least one adjuvant.

40. The composition of claim 39, wherein said adjuvant is selected from the group consisting of a CpG oligodeoxynucleotide adjuvant, aluminium salt (e.g., aluminium hydroxide, aluminum oxide and aluminium phosphate), oil-based adjuvant (e.g., Freund's Complete Adjuvant and Freund's Incomplete Adjuvant), mycolate-based adjuvant (e.g., trehalose dimycolate), bacterial lipopolysaccharide (LPS), peptidoglycan (e.g., murein, mucopeptide or glycoproteins such as N-Opaca, muramyl dipeptide [MDP], or MDP analog), proteoglycan (e.g., extracted from Klebsiella pneumoniae), streptococcal preparation (e.g., OK432), muramyldipeptide, Immune Stimulating Comlex, saponin, DEAE-dextran, neutral oil (e.g., miglyol), vegetable oil (e.g., arachis oil), liposome, polyol, Ribi adjuvant, vitamin E, Carbopol and interleukin.

41. A method for vaccinating a subject against a Chlamydial infection, comprising: administering the microorganism of any one of claims 1 to 37 or the composition of any one of claims 38 to 40 to said subject.

42. A method for preventing or ameliorating a condition associated with a Chlamydial infection, comprising: administering the microorganism of any one of claims 1 to 37 or the composition of any one of claims 38 to 40 to said subject.

43. A method of eliciting an immune response in a subject comprising administering the microorganism of any one of claims 1 to 37 or the composition of any one of claims 38 to 40 to said subject.

44. The method of any one of claims 41 to 43, wherein administering the microorganism or composition to said subject induces cell-mediated immunity.

45. The method of any one of claims 41 to 43, wherein administering the microorganism or composition to said subject induces a mucosal IgA response.

46. The method of claim 41 or 42, wherein said Chlamydial infection is a C. trachomatis, C. pneumoniae or C. muridarum infection.

47. The method of claim 46, wherein said condition associated with a Chlamydial infection is associated with a C. trachomatis infection and is selected from the group consisting of urethritis, prostatis, proctitis, epididymitis, cervicitis, salpingitis, endometritis, pelvic inflammatory disease, tubal factor infertility, chronic pelvic pain, cervical dysplasia, ectopic pregnancy, lymphogranuloma venereum (LGV), newborn eye infection, newborn lung infection, trachoma and reactive arthritis.

48. The method of claim 46, wherein said condition associated with a Chlamydial infection is associated with a C. pneumoniae infection and is selected from the group consisting of pneumonia, acute respiratory disease, atherosclerosis, coronary artery disease, myocardial infarction, carotid artery disease, cerebrovascular disease, coronary heart disease, carotid artery stenosis, aortic aneurysm, claudication, stroke, chronic obstructive pulmonary disease, asthma, reactive airway disease, Reiter's syndrome and sarcoidosis.

49. The method of claim 41 or 42, wherein the subject has or has had a C. trachomatis infection.

50. The method of claim 41 or 42, wherein the Chlamydial infection is recurrent.

51. The method of any one of claims 41 to 48, wherein the subject is at risk of a C. trachomatis, C. pneumoniae or C. muridarum infection.

52. A method of reducing the risk of human immunodeficiency virus-related AIDS in a subject comprising administering the microorganism of any one of claims 1 to 37 or the composition of any one of claims 38 to 40 to said subject.

53. The method of any one of claims 41 to 52, wherein the microorganism is orally administered.

54. The method of any one of claims 41 to 52, further comprising at least one booster immunization.

55. An antibody to an attenuated Salmonella microorganism of any one of claims 1 to 37.