AU3659099A

AU3659099A - Chlamydia proteins and their uses

Info

Publication number: AU3659099A
Application number: AU36590/99A
Authority: AU
Inventors: John P. Bannantine; Daniel D. Rockey
Original assignee: Oregon State Board of Higher Education
Current assignee: Oregon State Board of Higher Education
Priority date: 1998-04-20
Filing date: 1999-04-20
Publication date: 1999-11-08
Anticipated expiration: 2019-04-20
Also published as: AU754122B2; CA2326002A1; EP1073458A1; EP1073458A4; WO1999053948A1

Description

WO 99/53948 PCT/US99/08744 CHLAMYDIA PROTEINS AND THEIR USES I. FIELD OF THE INVENTION The present invention relates to the detection of Chlamydia and to the diagnosis, treatment 5 and prevention of Chlamydia infections in animals. II. BACKGROUND Chlamydiae are obligate intracellular bacterial pathogens with a unique biphasic life cycle. They appear as two distinct cellular types, a small dense cell or elementary body (EB) that is 10 enclosed in a rigid bacterial cell wall, and a larger metabolically active reticulate body (RB). The EB is resistant to physical disruption and is infectious, whereas the RB is more fragile and only exists inside cells. The Chlamydia life cycle begins with the attachment of the EB form to the host cell which is followed by endocytosis into a nascent vacuole, also called an "inclusion membrane." After EB attachment and entry, replication of the EB form produces RB forms that continue to 15 grow within the vacuole. By 72 hour post-infection, this growth phase is terminated when the RBs condense, and reorganize back to EBs. The lysis of the host cell results in release of EBs to infect new host cells. The difficulties in working with Chlamydiae center on the obligate intracellular requirement for growth and the fact that no adequate genetic engineering methods have been developed for this organism. 20 The genus Chlamydia includes two species that are primarily associated with human disease: C. trachomatis and C. pneumoniae. C. trachomatis causes trachoma, an eye disease that is the leading cause of preventable infectious blindness worldwide with an estimated 500 million cases of active trachoma worldwide. C. trachomatis also causes a sexually transmitted chlamydial disease which is very common worldwide. C. trachomatis also causes lymphogranuloma 25 venereum, a debilitating systemic disease characterized by lymphatic gland swelling. The most serious sequelae of chlamydial genital infections of females include salpingitis, pelvic inflammatory disease, and ectopic pregnancy. In the US alone, it is estimated that over 4 million new sexually transmitted C. trachomatis infections occurred in 1990, leading to over four billion dollars in direct and indirect medical expenses. The World Health Organization estimates that 89 30 million new cases of genital Chlamydia occurred worldwide in 1995 (Peeling and Brunham, 1996). C. pneumoniae causes respiratory diseases including so called walking pneumonia, a low grade disease such that the infected person frequently fails to obtain treatment and remains in the community as an active, infectious carrier. C. pneumoniae is currently of interest because of its strong epidemiological association with coronary artery disease, and there is also some evidence to 35 link it with multiple sclerosis. Of the other disease-causing species of Chlamydia, Chlamydia psittaci and Chlamydia pecorum are primarily pathogens of wild and domestic animals, but these species may infect WO 99/53948 PCT/US99/08744 -2 humans accidentally. C. psittaci is acquired through respiratory droplet infection and is considered an occupational health hazard for bird fanciers and poultry workers. There is tremendous interest in the identification of candidate antigens for protection against chlamydial disease. While a prior infection with C. trachomatis will protect against a 5 subsequent challenge by the same strain, indicating a protective component that stimulates the host immune response, most serious chlamydial diseases are exacerbated by an overaggressive anti-chlamydial immune response. Antigens recognized in the context of an infection appear to elicit a protective response whereas immunization with purified, killed (EB form) Chlamydia results in an immunopathological response. Therefore for the purposes of vaccine development, 10 one needs to find epitopes that confer protection, but do not contribute to pathology. It is an object of this invention to provide Chlamydia polypeptides for use as vaccines that induce a protective immune response without inducing the pathological response caused by the antigens associated with the EB form of Chlamydia. Such immunostimulatory peptides will be useful in the treatment, as well as in the diagnosis, detection and prevention of Chlamydial infections. 15 III. SUMMARY OF THE INVENTION The present invention includes the use of Chlamydia proteins that show enhanced expression in the reticulate body (RB) stage relative to the elementary body (EB) stage of the Chlamydia life cycle. These proteins are not present at detectable levels in the EB form using 20 current immunological techniques and are thus said to be "infection-specific." Certain of these infection-specific proteins are found in the inclusion membrane of the infected cell, and so have been termed "Inc" proteins. These include the IncA, IncB, and IncC proteins of Chlamydia as described in the present disclosure. The genes that encode the IncA, IncB and IncC proteins are referred to as incA, incB and incC respectively. Other proteins of Chlamydia described herein 25 have also been shown by the inventors to be infection-specific, but are not known to be incorporated into the inclusion membrane; these include the p242, TroA, and TroB proteins. The TroA and TroB proteins have been so named because they resemble the Tro proteins of Treponema pallidum, which are thought to form part of an ABC transport system. The inventors have shown that the infection-specific Chlamydia proteins of the disclosure 30 are recognized by convalescent antisera (i.e., antisera taken from an animal that has recovered from a Chlamydia infection) but are not recognized by antisera against the killed EB form of Chlamydia. Thus, the proteins are expressed only during active chlamydial infection and are therefore useful as protective antigens. These infection-specific proteins may be used to confer a protective immune response without inducing a pathological effect. Additionally, immuno 35 fluorescence microscopy and immunoblotting with antisera demonstrated that the infection-specific proteins are present in Chlamydia-infected HeLa cells, but are undetectable in purified EBs and absent in uninfected HeLa cells.

WO 99/53948 PCT/US99/08744 -3 Immunofluorescense microscopy reveals that IncA, IncB and IncC are localized to the inclusion membrane of infected HeLa cells. Reverse-transcription polymerase chain reactions (RT-PCR), northern hybridization data, and restriction analysis revealed that the incB and incC genes are closely linked and transcribed in an operon. RT-PCR, restriction analysis and sequential 5 Southern hybridizations of incA then incC to the same filter provided evidence that incA is separated from the incB and incC operon by about 110 kb. The C. trachomatis Tro genes are not closely linked with the p242 gene. The present invention includes the nucleotide and amino acid sequences for certain infection-specific proteins from Chlamydia. These proteins are p242, TroA, and TroB from C. 10 trachomatis, and the IncB, and IncC proteins from C. psittaci. The scope of the invention includes fragments of these proteins that may be used in a vaccine preparation or that may be used in a method of detecting Chlamydia antibodies. Such fragments may be, for example, 5, 10, 15, 20, 25, or 30 contiguous amino acids in length. They may even encompass the entire protein. More specifically, the present invention encompasses the purified infection-specific 15 proteins having amino acid sequences as shown in SEQ ID NOS: 2, 4, 6, 10, and 12, amino acid sequences that differ from such sequences by one or more conservative amino acid substitutions, and amino acid sequences that show at least 75 % sequence identity with such amino acid sequences. Then invention also includes isolated nucleic acid molecules that encode a protein as 20 described in the above paragraph, including isolated nucleic acid molecules with nucleotide sequences as shown in SEQ ID NOS: 1,3, 5, 9, and 11. The present invention also includes a vaccine or immunostimulatory preparation directed against the reticulate body (RB) form of Chlamydia comprising one or more purified infection specific peptides (or portions or fragments thereof, or peptides showing sequence similarity to a 25 portion of such a peptide). Such peptide fragments may be, for example, 5, 10, 15, 20, 25, or 30 contiguous amino acids in length, of the sequence shown in SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, 16, or 18. Peptides used in such a vaccine may even encompass the entire purified peptide of SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, 16, or 18, a peptide that differs from such a peptide by one or more conservative amino acid substitutions, or a peptide having at least 75% sequence identity 30 with such a peptide. Such vaccine preparations may contain one or more pharmaceutically acceptable excipients, adjuvants or diluents. The invention additionally encompasses methods for making a vaccine, comprising combining a pharmaceutically acceptable excipient with a peptide described herein. Also included is a method of vaccination comprising administering a vaccine as described herein to a mammal. 35 The present invention also provides a method for the diagnostic use of the disclosed purified infection-specific peptides, for instance by use in a diagnostic assay to detect the presence of infection-specific antibodies in a medical specimen, in which antibodies bind to the Chlamydia peptide and indicate that the subject from which the specimen was removed was previously WO 99/53948 PCT/US99/08744 -4 exposed to Chlamydia. Such a method may comprise: (i) supplying a biological sample, such as blood from an animal, that is suspected to contain infection-specific anti-Chlamydia antibody, (ii) contacting the sample with at least one infection-specific Chlamydia peptide described herein, such that a reaction between the peptide and the infection-specific anti-Chlamydia antibody gives rise to 5 a detectable effect, such as a chromogenic conversion; and (iii) detecting this detectable effect. The present invention also provides a method of using antibodies that bind specifically with the disclosed proteins for detection of infection-specific Chlamydia antigen, indicating the presence of Chlamydia in the RB stage as distinct from the EB stage. For instance, the relevant infection-specific antibodies may be used to provide specific binding in an Enzyme Linked 10 Immunosorbant Assay (ELISA) or other immunological assay wherein the antibody F, portion is linked to a chromogenic, fluorescent or radioactive molecule and the Fab portion specifically interacts with, and binds to, an infection-specific protein. Such a method may comprise: (i) supplying a biological sample from an animal suspected to contain an infection-specific Chlamydia antigen, and (ii) contacting the sample with at least one infection-specific anti-Chlamydia antibody, 15 such that a reaction between the antibody and the infection-specific Chlamydia protein gives rise to a detectable effect; and (iii) detecting this detectable effect. Other aspects of the present invention include the use of probes and primers derived from the nucleotide sequences that encode infection-specific peptides, to detect the presence of Chlamydia nucleic acids in medical specimens. Such probes and primers may be nucleotide 20 fragments, of, for example, 15, 20, 25, 30 or 40 contiguous nucleotides of the sequence shown in SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13, 15, or 17. An additional aspect of the invention is a method of treating a Chlamydia infection by directing a therapeutic agent against a specific target, where the target is chosen from an infection specific protein of Chlamydia, a gene that encodes an infection-specific protein of Chlamydia, and 25 an RNA transcript that encodes an infection-specific protein of Chlamydia, wherein the therapeutic agent interacts with said target to affect a reduction in pathology. These and other aspects of the invention will become more apparent from the following description. 30 IV. SEQUENCE LISTING SEQ ID NO: 1 shows a nucleic acid sequence encoding the p242 C. trachomatis protein, with deduced primary amino acid sequence also shown. SEQ ID NO:2 shows the amino acid sequence of the p242 C. trachomatis protein. SEQ ID NO:3 shows a nucleic acid sequence encoding the TroA C. trachomatis protein, 35 with deduced primary amino acid sequence also shown. SEQ ID NO:4 shows the amino acid sequence of the TroA C. trachomatis protein. SEQ ID NO:5 shows a nucleic acid sequence encoding the TroB C. trachomatis protein, with deduced primary amino acid sequence also shown.

WO 99/53948 PCT/US99/08744 -5 SEQ ID NO:6 shows the amino acid sequence of the TroB C. trachomatis protein. SEQ ID NO:7 shows a nucleic acid sequence encoding the IncA C. psittaci protein, with deduced primary amino acid sequence also shown. SEQ ID NO:8 shows the amino acid sequence of the IncA C. psittaci protein. 5 SEQ ID NO:9 shows a nucleic acid sequence encoding the IncB C. psittaci protein, with deduced primary amino acid sequence also shown. SEQ ID NO: 10 shows the amino acid sequence of the IncB C. psittaci protein. SEQ ID NO: 11 shows a nucleic acid sequence encoding the IncC C. psittaci protein, with deduced primary amino acid sequence also shown. 10 SEQ ID NO: 12 shows the amino acid sequence of the IncC C. psittaci protein. SEQ ID NO:13 shows a nucleic acid sequence encoding the IncA C. trachomatis protein, with deduced primary amino acid sequence also shown. SEQ ID NO: 14 shows the amino acid sequence of the IncA C. trachomatis protein. SEQ ID NO: 15 shows a nucleic acid sequence encoding the IncB C. trachomatis protein, 15 with deduced primary amino acid sequence also shown. SEQ ID NO: 16 shows the amino acid sequence of the IncB C. trachomatis protein. SEQ ID NO: 17 shows a nucleic acid sequence encoding the IncC C. trachomatis protein, with deduced primary amino acid sequence also shown. SEQ ID NO: 18 shows the amino acid sequence of the IncC C. trachomatis protein. 20 SEQ ID NO: 19 shows the upstream oligonucleotide used to amplify the C. psittaci incC ORF. SEQ ID NO:20 shows the downstream oligonucleotide used to amplify the C. psittaci incC ORF. SEQ ID NO:21 shows the upstream oligonucleotide used to amplify the C. psittaci incB 25 ORF. SEQ ID NO:22 shows the downstream oligonucleotide used to amplify the C. psittaci incB ORF. SEQ ID NO:23 shows the upstream oligonucleotide used to amplify the C. psittaci incA ORF. 30 SEQ ID NO:24 shows the downstream oligonucleotide used to amplify the C. psittaci incA ORF. V. DESCRIPTION OF THE INVENTION A. DEFINITIONS 35 Particular terms and phrases used herein have the meanings set forth below.

WO 99/53948 PCT/US99/08744 -6 "EB" refers to the Elementary Body, an environmentally refractile and largely metabolically dormant form of Chlamydia that is infectious and is presented as a small dense body enclosed by a bacterial cell wall. "RB" refers to the Reticulate Body, a metabolically active form of Chlamydia that is not 5 infectious, and exists only within a host cell, being very fragile, often branched, and appearing larger and less dense that the EB. "Infection-specific" refers to a protein that shows enhanced expression in the RB form of Chlamydia compared to the EB form. Infection-specific proteins are not necessarily absent from the EB form, but they are significantly more common in the RB form than in the EB form. 10 "infection-specific antibody" is an antibody that binds specifically to an infection-specific protein. "Biological sample" refers to any sample of biological origin including, but not limited to a blood sample, a plasma sample, a mucosal smear or a tissue sample. "Isolated" An isolated nucleic acid has been substantially separated or purified away 15 from other nucleic acid sequences in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA. The term "isolated" thus encompasses nucleic acids purified by standard nucleic acid purification methods. The term also embraces nucleic acids prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids. 20 "Probes" and "primers." Nucleic acid probes and primers may readily be prepared based on the nucleic acid sequences provided by this invention. A "probe" comprises an isolated nucleic acid attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes. "Primers" are short nucleic acids, typically DNA oligonucleotides 15 nucleotides or more 25 in length, which are annealed to a complementary target DNA strand by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand, then extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR) or other nucleic-acid amplification methods known in the art. 30 Probes and primers as used in the present invention typically comprise at least 15 nucleotides of the nucleic acid sequences that are shown to encode infection-specific proteins. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30 or 40 consecutive nucleotides of the disclosed nucleic acid sequences. 35 Methods for preparing and using probes and primers are well known in the art and are described in, for example Sambrook et al. (1989); Ausubel et al., (1987); and Innis et al., (1990). PCR primer pairs can be derived from a known sequence, for example, by using computer WO 99/53948 PCT/US99/08744 -7 programs intended for that purpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge, MA). "Conservative amino acid substitutions" are those substitutions that, least interfere with the properties of the original protein, i.e., the structure and especially the function of the protein is 5 conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions. Original Residue Conservative Substitution Ala Ser Arg Lys Asn gln, his Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His asn, gln Ile leu, val Leu ile, val Lys arg, gin, glu Met leu, ile Phe met, leu, tyr Ser Thr Thr Ser Trp Tyr Tyr trp, phe Val ile, leu Conservative substitutions generally maintain (a) the structure of the polypeptide 10 backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in protein properties will be non-conservative, for instance changes in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, 15 phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histadyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine. "Sequence identity" The similarity between two nucleic acid sequences, or two amino 20 acid sequences is expressed in terms of the level of sequence identity shared between the sequences. Sequence identity is typically expressed in terms of percentage identity; the higher the percentage, the more similar the two sequences are. Variants of naturally occurring infection specific peptides useful in the present invention are typically characterized by possession of at least 50% sequence identity counted over the full length alignment with the amino acid sequence of a WO 99/53948 PCT/US99/08744 -8 naturally occurring infection-specific peptide when aligned using BLAST 2.0.1 (Altschul et al., 1997). For comparisons of amino acid sequences of greater than about 30 amino acids, the BLAST 2 analysis is employed using the blastp program set to default perameters (open gap = 11, extension gap = 1 penalty, gap x dropoff = 50, expect = 10, word size = 3, filter on), and using 5 the default BLOSUM62 matrix (gap existence cost = 11, per residue gap cost = 1, lambda ratio = 0.85). When aligning short peptides (fewer than around 30 amino acids), the alignment should be performed using the Blast 2 sequences function, employing the PAM30 matrix (gap existence cost = 9, per residue gap cost = 1, lambda ratio = 0.87). Proteins with even greater similarity to the reference sequences will show increasing percentage identities when assessed by this method, 10 such as at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, or at least 95% sequence identity. The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., 1990) is available from several sources, including the National Center for Biotechnology Information (NCBI, Bethesda, MD) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. It can be accessed at 15 http//www.ncbi.nlm.nih.gov/BLAST/. A description of how to determine sequence identity using this program is available at http://www.ncbi.nlm.nih.gov/BLAST/blast help.html. Similarly, when comparing nucleotides, blastn may be used with default settings (rewards for match = 1, penalty for mismatch = -2, open gap = 5, extension gap = 2 penalty, gap x dropoff = 50, expect = 10, word size = 11, filter on), with the default BLOSUM62 matrix (as 20 above). Variants of naturally occurring infection-specific nucleic acid sequences useful in the present invention are typically characterized by possession of at least 50% sequence identity counted over the full length alignment with the nucleic acid sequence of a naturally occurring infection-specific ORF when aligned using BLAST 2.0.1. Useful nucleic acids may show even greater percentage identity, and may, for example, possess at least 55%, at least 65%, at least 25 75%, at least 80%, at least 85%, at least 90%, or at least 95% sequence identity naturally occurring infection-specific ORF. "Operably linked" A first nucleic acid sequence is "operably" linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence 30 if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in the same reading frame. "Recombinant" A recombinant nucleic acid is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated 35 segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.

WO 99/53948 PCT/US99/08744 -9 "Stringent Conditions" Stringent conditions, in the context of nucleic acid hybridization, are sequence-dependent and are different under different environmental parameters. Generally, stringent conditions are selected to be about 5 degrees to 20 degrees lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the 5 temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Conditions for nucleic acid hybridization and calculation of stringencies can be found in Sambrook et al. (1989), pages 9.49-9.55. Typical high stringency hybridization conditions (using radiolabeled probes to hybridize to nucleic acids immobilized on a nitrocellulose filter) may include, for example, wash conditions of 0.1 X SSC, 0.5% SDS at a 10 wash temperature of 68 0 C. When referring to a probe or primer, the term "specific for (a target sequence)" indicates that the probe or primer hybridizes under high-stringency conditions substantially only to the target sequence in a given sample comprising the target sequence. "Purified" A purified peptide is a peptide that has been extracted from the cellular 15 environment and separated from substantially all other cellular peptides. As used herein, the term peptide includes peptides, polypeptides and proteins. In certain embodiments, a purified peptide is a preparation in which the subject peptide comprises 50% or more of the protein content of the preparation. For certain uses, such as vaccine preparations, even greater purity may be preferable. 20 "Immunostimulatory peptide" as used herein refers to a peptide that is capable of stimulating a humoral or antibody-mediated immune response when inoculated into an animal. "Vaccine" A vaccine is a composition containing at least one immunostimulatory peptide which may be inoculated into an animal with the intention of producing a protective immunological reaction against a certain antigen. The antigen to be protected against may be, for instance, an 25 infectio-specific antigen of Chlamydia. B. ISOLATION OF INFECTION SPECIFIC CHLAMYDIA POLPEPTIDES AND IDENTIFICATION OF GENES ENCODING THESE POLYPEPTIDES 30 1. ISOLATION OF IncA, IncB AND IncC Bacterial strains. Chlamydia (C. psittaci strain GPIC or C. trachomatis LGV-434, ser. L2) was cultivated in HeLa 229 cells using standard methods (Caldwell et al., 1981). Purified Chlamydiae were obtained using Renografin (E. R. Squibb & Sons, Inc., Princeton, N.J.) density 35 gradient centrifugation. Escherichia coli DH50 (Bethesda Research Laboratories, Inc., Gaithersburg, Md.) was used as the host strain for transformations with recombinant DNA. E. coli XL1-Blue MRF' (Stratagene, La Jolla, Calif.) was used as the host strain for infection with lambda ZAPII phage vector. E. coli SOLR (Stratagene) was used as the host strain for infection with in vivo excised filamentous lambda ZAPII.

WO 99/53948 PCT/US99/08744 -10 Antisera. MBP (Maltose Binding Protein)-Inc fusion proteins were used as antigens for the production of mono-specific antibody reagents in Hartley strain guinea-pigs. The protein was diluted to 100 pg/m 1 -' sterile saline and mixed with the Ribi Trivalent Adjuvant (Ribi Immunochem.). The antigen/adjuvant emulsion was administered to anaesthetized guinea-pigs 5 using a procedure provided by the manufacturer. Sera were collected 14 days after secondary and tertiary immunizations. Control antisera were produced by immunizing guinea-pigs with adjuvant alone, or with adjuvant plus purified maltose-binding protein. Convalescent guinea-pig antisera, antisera against live EBs, and antisera against formalin fixed EBs were produced using standard methods (Rockey and Rosquist, 1994 and Rockey et al., 10 1995). C. psittaci library construction and screening. For the incB and incC genes, C. psittaci strain GPIC DNA was extracted using a genomic DNA extraction kit (Qiagen) with one modification; dithiothreitol (5mM) was added to the suspension buffer to assist EB lysis. DNA was partially digested with Tsp509I and ligated to EcoRI digested X-ZAPII phage arms 15 (Stratagene). The ligation was packaged in vitro with Gigapack extracts according to the manufacturer's instructions (Stratagene). Recombinant phage were plated on E. coli XL-1 Blue at densities of approximately 104 PFU/150-mm (diameter) plate. Following a nine hour incubation to allow development of the plaques, the plates were sequentially overlaid with nitrocellulose disks and the resulting lifts were processed for immunoblotting with convalescent antisera and antisera to 20 fixed EBs. Of approximately 8,000 plaques, 18 had reactivity with the convalescent sera but not sera generated against EBs. One of these was subcloned into pBluescript SK(-) phagmid by in vitro excision in the E. coli SOLR strain (Stratagene) and designated pBS200-7. For the incA gene, genomic DNA from C. psittaci strain GPIC was partially digested with Sau3A, size-selected (2-8 kb) by electrophoresis through low-melting-temperature agarose, 25 and blunt-ended with T4 DNA polymerase. This DNA was ligated to an EcoR1/ INotl adapter (Life Technologies), kinased, and ligated to EcoRl-digested Lambda ZAP II vector (Stratagene Cloning Systems). Recombinants were packaged (Lambda Gigapack Gold, Stratagene) and used to infect E. coli XL1-Blue (Stratagene). Plaques were allowed to develop for 4 h at 37 0 C. Nitrocellulose filters laden with 10 mM IPTG (US Biochemical Corp.) were placed onto the plaques and 30 incubated for an additional 4 h at 37oC. These filters were removed and placed into a blocking solution consisting of PBS (150 mM NaC1, 10 mM NaPO4, pH7.2) plus 0.1% Tween-20 (TPBS) and 2% BSA-TPBS. Filters were incubated for 1 h, rinsed twice in TPBS, and incubated overnight in convalescent-guinea-pig sera diluted 1:100 in BSA-TPBS. After three washes in TPBS, the filters were incubated for 1 h in 1 25 1-staphylococcal protein A (New England Nuclear) 35 diluted to approx. 124 nCiml

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' in BSA-TPBS. Filters were again washed three times in TPBS and positive plaques were detected by exposure of the dried filters to autoradiography film overnight at room temperature. Positive clones were picked and plaque-purified. pBluescript-SK- plasmids WO 99/53948 PCT/US99/08744 -11 containing the chlamydial genes of interest were recovered from the purified bacteriophage using ExAssist filamentous bacteriophages (Stratagene). Identification of antigens recognized by convalescent antisera. Recombinant plaques were identified that showed reactivity with convalescent (anti-RB) antisera, but not with anti-EB 5 serum. The purified recombinant phage were converted into pBluescriptlI SK plasmid by in vivo excision and recircularization and these recombinant DNAs were used to transform E. coli. SDS PAGE and immunoblot analysis of lysates of these recombinant E. coli showed that each expressed one or more proteins that reacted with convalescent antisera but not with the EB serum. DNA Cloning and fusion protein production. The plasmid pJC2 contains a 5.0 kb 10 EcoRI GPIC genomic fragment cloned into the pZEro2.1 vector (Invitrogen). To construct pJC2, the incC ORF sequence was 32 P-radiolabeled using random priming (Gibco-BRL) and used to probe EcoRI cut GPIC genomic DNA fragments separated by agarose gel electrophoresis. Fragments in the size range of the positive signal were excised from the gel and purified by Gene Clean (Biol01). The gel-purified fragments were used in a ligation along with EcoRI-digested 15 pZEro2.1. Kanamycin resistant colonies were screened by colony hybridization with radiolabeled incC. MBP fusions of the five ORFs present in pJC2 were produced using the pMAL-C2 vector (New England Biolabs). The reading frame of incC, with the exception of the first four codons, was amplified using Pwo polymerase (Boehringer Mannheim) and pBS200-7 as the template. The 20 upstream and downstream oligonucleotides for this amplification were 5'-AGAACCGATTTAACTCCAGGCG-3' (SEQ ID NO: 19) and 5'-GCGCGGATCCTTAATGTCCGGTAGGCCTAG-3' (SEQ ID NO: 20), respectively. The vector was digested with XmnI and BamHI, and the amplication product was digested with BamHI. Ligation of these products resulted in an in-frame fusion between the malE gene in the 25 vector and the incC reading frame from pBS200-7. The stop codon for this construction is provided by the insert. Following ligation, the products were transformed into E.coli strain HD50. The resulting fusion protein (MBP/IncC) was overexpressed and purified by maltose affinity chromatography using an amylose resin supplied by New England Biolabs. The same approach was used for production of the MBP/IncB fusion protein. The 30 sequence encoding the N-terminal 101 amino acids of the IncB ORF was PCR amplified using the oligonucleotides 5'-ATGTCAACAACACCAGCATCTTC-3' (SEQ ID NO: 21) and 5'-GCGCGGATCCTTAATTAGTGCCTTCTGGATTAGG-3' (SEQ ID NO: 22). The purified MBP/IncB and MBP/IncC fusion proteins were used as antigen for the 35 production of monospecific antibody in Hartley strain guinea-pigs by standard methods (Rockey et al., 1995). Inserts in each construct were confirmed by DNA sequencing.

WO 99/53948 PCT/US99/08744 -12 For IncA, a maltose-binding protein/IncA fusion protein was produced using the pMAL C2 vector system from New England Biolabs. The reading frame of incA shown in Fig. 1, with the exception of the initiator ATG, the incA ORF was amplified using Vent DNA polymerase (New England Biolabs) and plasmid pGP17 as template. The upstream and downstream oligo 5 nucleotides for this amplification were 5'-CGCAGTACTGTATCCACAGACAAC-3' (SEQ ID NO: 23) and 5'-GTCGGATCCGAGAAACTCTCCATGCC-3' (SEQ ID NO: 24), respectively. The vector was digested with Xmnl and BamHl, and the amplification product was digested with Scal and BamHl. Ligation of these products resulted in an in-frame fusion between the malE gene in 10 the vector and the incA reading frame from pGP17. The stop codon for this construction is provided by the insert. Following ligation, the products were transformed into E. coli strain DH50. The resulting fusion protein (MBP/IncA) was overexpressed and purified by maltose affinity chromatography using amylose resin (New England Biolabs). MBP/IncA was used as antigen for the production of mono-specific antibody reagents in 15 Hartley strain guinea-pigs. DNA sequencing and sequence analysis. The pBS200-7 and pJC2 genomic clones as well as the MBP fusions were sequenced with the Taq DyeDeoxy Terminator Cycle Sequencing Kit (Perkin Elmer/Applied Biosystems Division). Several internal primers were designed to sequence further into the cloned inserts. Sequence assembly was performed using AssemblyLIGN 20 software and sequence analysis was performed with MacVector software (International Biotechnologies Incorporated). Hydrophilicity profiles were determined using the Kyte-Doolittle scale (Kyte and Doolittle, 1982) with a window of 7. Deduced amino acid sequences were compared with the database using the BLAST program (on default settings) available from the National Center for Biotechnology Information on the world wide web. The entire nucleotide 25 sequence of the pJC2 insert was deposited in the GenBank/EMBL Nucleotide Sequence Data Library, under accession number AF017105. For incA, nucleotide sequencing was conducted using the Sequences system (US Biochemical) with the M13 forward and reverse primers, and internal primers synthesized on an Milligen/Biosearch Cyclone Plus DNA synthesizer. Computer analyses were conducted using the 30 MacVector Sequence Analysis Software (International Biotechnologies Incorporated). Hydrophilicity profiles were determined using the Kyte-Doolittle scale (Kyte and Doolittle, 1982) with a window of 7. Secondary-structure predictions were generated using a combination of the Chou-Fasman and Robson-Garnier methods (Robson and Suzuki, 1976; Chou and Fasman, 1978). Deduced amino acid sequences were compared with those in the EMBL and GenBank databases 35 using the BLASTP program available from the National Center for Biotechnology Information.

WO 99/53948 PCT/US99/08744 -13 Electrophoresis and immunoblotting. Polyacrylamide gel electrophoresis (PAGE) was conducted using standard methods (Rockey and Rosquist, 1994). Immunoblotting was performed using standard methods (Rockey et al., 1995). Immunofluorescence studies. Chlamydiae grown in HeLa cells on sterile glass 5 coverslips were fixed for microscopy one of two ways. Cells were either incubated in methanol for 5 minutes, or in the combination fixative periodate-lysine-paraformaldephyde (PLP) for three hours at room temperature followed by permeabilization with 0.05% saponin (Brown and Farquhar, 1989). Immunostaining of the fixed coverslips was performed according to standard methods (Rockey et al., 1995) and visualized under a Nikon Microphot FXA microscope using the 10 63x objective and oil immersion. RT-PCR analysis. RNA for RT-PCR analysis was extracted from approximately 2 x 1014 C. psittaci-infected cells. A Qiagen column was used for extraction and purification according to the manufacturer s instructions (Qiagen). RQ1 RNase DNase (Promega) was used to ensure removal of contaminating genomic DNA. cDNA was prepared by incubating 1.5 Pg of RNA, 2.5 15 pM of the reverse oligonucleotide primer, and AMV reverse transcriptase (Promega) for 1 hour at 42 0 C in sodium pyrophosphate buffer, according to the manufacturer's instructions. PCR reactions were carried out using 1 pl of the cDNA reaction, 1.25 1iM of each oligonucleotide primer, and Pwo polymerase (Boehringer Mannheim). Each RT-PCR reaction was accompanied by a positive control reaction that utilized the same primer set and 10 ng of C. psittaci genomic 20 DNA, and a negative control reaction in which 1 pl of the same RNA preparation was used as template in the PCR reaction. A control primer set located within the incC gene was also used as an RT-PCR control. Identification of incA, incB and incC genes of C. trachomatis. The nucleotide sequence information obtained for the incA, incB and incC of C. psittaci (above) was used, with standard 25 methods, to identify the inc gene orthologues of C. trachomatis. Probes were made that corresponded to the 3' and 5' ends of the C. psittaci inc open reading frames. Standard PCR amplification (as above) was used, with the C. trachomatis genome as a template, to amplify the corresponding C. trachomatis nucleotide sequence. The amplified DNA was then sequenced, using standard methods. 30 2. ISOLATION OF p 2 4 2 , TroA AND TroB Bacterial strains. C. trachomatis LGV-434, serotype L2, was cultivated in HeLa 229 cells using standard methods (Caldwell et al., 1981). Purified chlamydiae were obtained using Renografin (E. R. Squibb & Sons, Inc., Princton, N.J.) density gradient centrifugation (Hackstadt 35 et al., 1992). Escherichia coli DH50 (Bethesda Research Laboratories, Inc., Gaithersburg, Md.) was used as the host strain for transformations with recombinant DNA. E. coli XL1-Blue MRF' (Stratagene, La Jolla, Calif.) was used as the host strain for infection with lambda ZAPII phage WO 99/53948 PCT/US99/08744 -14 vector. E. coli SOLR (Stratagene) was used as the host strain for infection with in vivo excised filamentous lambda ZAPII. Antisera. Two Cynomolgus monkeys (Macaca fasicularis) were anaesthetized and infected urethrally with C. trachomatis EBs. Each monkey was infected twice and allowed to 5 recover between infections. Symptoms of infection were monitored over time. Antisera from infected monkeys were tested for reactivity to Chlamydia by ELISA (Su et al., 1990). Sera were collected every two weeks and anti-chlamydial titers were determined. These animals showed mild clinical signs of disease which cleared spontaneously. A second challenge was then administered. Sera were collected from these animals and used to probe a C. trachomatis 10 expression library as discussed below. As a control, Guinea Pigs were immunized with killed C. trachomatis of the EB form. Sera from these animals were obtained and also used to probe the C. trachomatis expression library. C. trachomatis library construction and immunoscreening. A C. trachomatis genomic library was constructed with the lambda ZAPII vector as described above for C. psittaci. 15 Approximately 15,000 plaques were plated, transferred to nitrocellulose filters (Schleicher and Schuell, Keene, N.H.) in duplicate, and probed with the monkey convalescent antiserum and with Guinea Pig serum against killed EBs (Bannantine et al., 1998). Plaques that reacted only with the monkey convalescent antisera were selected for further study. Identification of antigens recognized by convalescent antisera. Four positive 20 recombinant plaques were identified that showed reactivity with convalescent antisera but not with anti-EB serum. The purified recombinant phage were converted into pBluescriptII SK plasmid by in vivo excision and recircularization and these recombinant DNAs (pCtl, pCt2, pCt3 and pCt4) were used to transform E. coli. SDS-PAGE and immunoblot analysis of lysates of these recombinant E. coli showed that each expressed one or more proteins that reacted with 25 convalescent (anti-RB) antisera but not with the anti-EB antiserum. Two of the recombinants clones, pCt2 and pCt3, expressed an identical 19.9 kDa protein (p242). The pCt4 recombinant expressed two different proteins of approximately 32 kDa each that are strongly recognized by convalescent antisera (TroA and TroB). 30 C. SEQUENCE ANALYSIS Sequence analysis of pCtl, 2, and 3 revealed overlapping inserts with only one open reading frame (ORF) common in all three. This ORF encodes an approximately 19.9 kDa protein (p242) that shows no similarity to other known proteins. The nucleotide sequence encoding C. trachomatis p242, and the amino acid sequence of the protein are shown in SEQ ID NOS: 1 and 2, 35 respectively. The insert in pCt4 contains two complete ORFs which code for two proteins, each of approximately 32kDa (TroA and TroB) that show some homology with proteins from Treponema WO 99/53948 PCT/US99/08744 -15 pallidum. The nucleotide sequences encoding the 32 kDa proteins (TroA and TroB) and the amino acid sequences of these proteins are shown in SEQ ID NOS: 3, 4, 5, and 6. D. EMBODIMENTS OF THE INVENTION 5 The present invention includes the nucleotide and amino acid sequences for certain infection-specific proteins from Chlamydia. These proteins are p242, TroA, and TroB from C. trachomatis, and the IncB, and IncC proteins from C. psittaci. The scope of the invention includes fragments of these proteins that may be used in a vaccine preparation or that may be used in a method of detecting Chlamydia antibodies. Such fragments may be, for example, 5, 10, 15, 10 20, 25, or 30 contiguous amino acids in length, or may even encompass the entire protein. The present invention also encompasses the use of infection-specific proteins of Chlamydia, and the use of nucleotides encoding such proteins. Infection-specific proteins include the IncA, IncB and IncC proteins of C. psittaci, the IncA, IncB and IncC proteins of C. trachomatis, and the TroA, TroB, and p242 proteins of C. trachomatis. The inventors have shown 15 that these proteins are infection-specific by using immunological techniques such as immuno fluorescence microscopy and immunoblotting. The present invention includes a vaccine against chlamydial infections comprising infection-specific proteins or fragments of these proteins or proteins that are homologous or show substantial sequence similarity to these proteins. In one embodiment, one or more purified 20 infection-specific proteins may be mixed with a pharmaceutically acceptable excipient to produce a vaccine that stimulates a protective immunological response in an animal. In one embodiment the vaccine may be administered intra-muscularly or sub-cutaneously or intravenously. In another embodiment, the vaccine may be administered by inoculation into or onto the mucous membranes of the subject animal. For example, the vaccine may be administered urethrally or genitally as a 25 liquid or in the form of a pessary. In another embodiment, it may be administered to the mucosa of the lungs as a spray or vapor suspension. Since at least three amino acids are required to produce an antigenic epitope, the vaccine should comprise at least three consecutive amino acids, preferably at least five consecutive amino acids, and may comprise at least 10, 15, 25, 30, 40, or 45 consecutive amino acids of the 30 infection-specific proteins as shown in SEQ ID NOS: 2, 4, 6, 8, 10, 12, 14, 16, and 18. The vaccine of the invention may be used to inoculate potential animal targets of any of the chlamydial diseases including those caused by C. psittaci, C. trachomatis, C. pneumoniae or C. pecorum. Indeed the vaccine of the invention may be used to inoculate animals against any disease that shows immunological cross-protection as a result of exposure to infection-specific 35 Chlamydia antigen. Vaccines of the present invention can include effective amounts of immunological adjuvants known to enhance an immune response (e.g., alum). The protein or polypeptide is present in the vaccine in an amount sufficient to induce a protective immune response whether WO 99/53948 PCT/US99/08744 -16 through humoral or cell mediated pathways or through both. Such a response protects the immunized animal against chlamydial infections specifically by raising an immune response against the Reticulate Body form of Chlamydia. Protective antibodies may be elicited by a series of two or three doses of the antigenic vaccine given about two weeks apart. 5 The present invention also teaches a method of making a vaccine against chlamydial infections. The method of making the vaccine comprises providing a pure (or substantially pure) infection-specific chlamydial peptide or portion thereof, and mixing the peptide with a pharmacologically acceptable excipient or adjuvant. Adjuvants may include commonly used compounds such as alum. Additionally, the vaccines may be formulated using a peptide according 10 to the present invention together with a pharmaceutically acceptable excipient such as water, saline, dextrose and glycerol. The vaccines may also include auxiliary substances such as emulsifying agents and pH buffers. Doses of the vaccine administered will vary depending on the antigenicity of the particular peptide or peptide combination employed in the vaccine and characteristics of the animal or human patient to be vaccinated. 15 The infection-specific vaccine of the invention is directed towards not only C. psittaci, but against all forms of Chlamydia including C. pneumoniae, C. trachomatis and C. pecorum, and the vaccine may comprise not just peptides derived from C. psittaci, but also orthologous peptides and fragments of such orthologous peptides from other species of Chlamydia and peptides that are substantially similar to such peptides. 20 The present invention also teaches a method of vaccination comprising administering a vaccine formulated as described above to an animal either intravenously, intramuscularly, subcutaneously, by inhalation of a vapor or mist, or by inoculation in the form of a liquid, spray, ointment, pessary or pill into or onto the mucous membranes of the mouth, nose, lungs or urogenital tract or colon. 25 The methods of the invention may be practiced equally with human or non-human animal subjects. The present invention also teaches a method of detecting Chlamydia infection-specific proteins produced by the Reticulate Body form of the organism. In this embodiment, antibodies raised to the infection-specific proteins are used in an immunological assay such as an Enzyme 30 Linked Immunosorbant Assay or Biotin-Avidin assay or a radioimmunoassay or any other assay wherein specific antibodies are used to recognize a specific protein. Such assays may be used to detect both the quantity of proteins present and also the specificity of binding of such proteins. In such an assay, antibodies have attached to them, usually at the Fc portion, a detectable label, such as an enzyme, fluorescent marker, a radioactive marker or a Biotin-Avidin system marker that 35 allows detection. A biological sample is provided from an animal that has been putatively exposed to Chlamydia. Such a sample may be, for example, whole blood, serum, tissue, saliva or a mucosal secretion. The sample is then contacted with the labeled antibody and specific binding, if any, is detected. Other methods of using infection-specific antibodies to detect infection-specific WO 99/53948 PCT/US99/08744 -17 antigens that are present in cells or tissues include immunofluorescense, indirect immunofluorescense and immunohistochemistry. In immunofluorescense, a fluorescent dye is bound directly to the antibody. In indirect-immunofluorescence, the dye is bound to an anti immunoglobulin. Specific binding occurs between antigen and bound antibody is detected by 5 virtue of flourescent emissions from the dye moiety. This technique would be particularly useful, for instance, for detection of Chlamydia antigen present on a urogenital mucosal smear. Other techniques, such as competitive inhibition assays may also be used to assay for antigen, and one of ordinary skill in the art will readily appreciate that the precise methods disclosed may be modified or varied without departing from the subject or spirit of the invention 10 taught herein. The present invention also teaches a method of detection of Chlamydia infection-specific antibodies made against the Reticulate Body. In this embodiment a sample is provided from an animal putatively exposed to Chlamydia to determine whether the sample contains infection specific antibodies. Such a sample may be, for example, whole blood, serum, tissue, saliva or a 15 mucosal secretion. This sample is contacted with infection-specific antigens such that the amount and specificity of binding of the antibody may be measured by its binding to a specific antigen. Many techniques are commonly known in the art for the detection and quantification of antigen. Most commonly, the purified antigen will be bound to a substrate, the antibody of the sample will bind via its Fab portion to this antigen, the substrate will then be washed and a second, labeled 20 antibody will then be added which will bind to the Fc portion of the antibody that is the subject of the assay. The second, labeled antibody will be species specific, i.e., if the serum is from a human, the second, labeled antibody will be anti-human-IgG antibody. The specimen will then be washed and the amount of the second, labeled antibody that has been bound will be detected and quantified by standard methods. 25 The present invention also teaches a method of treating a Chlamydial infection by directing a therapeutic agent against a specific target, such as: (i) an infection-specific protein of Chlamydia, (ii) a gene that encodes an infection-specific protein of Chlamydia and (iii) an RNA transcript that encodes an infection-specific protein of Chlamydia, wherein said therapeutic agent interacts with said target to affect a reduction in pathology. 30 For example, the present invention teaches a method of treating chlamydial infection wherein antisense technology is used to prevent the expression of infection-specific genes, thereby preventing the pathologies associated these proteins and preventing reproduction of the RB phase of Chlamydia. In this embodiment, RNA molecules complementary to transcripts of infection specific genes are introduced into the host cells that contain Chlamydia, and by binding to the 35 mRNA transcripts of the infection-specific genes, prevent translation and therefore expression of the infection-specific proteins that are associated with pathogenesis. The invention may be practiced to produce a vaccine against any species of Chlamydia, including C. psittaci, C. pecorum, C. trachomatis and C. pneumoniae.

WO 99/53948 PCT/US99/08744 -18 The following examples illustrate various embodiments of the invention. EXAMPLE 1: Homologous Sequences The DNA and protein sequences discussed herein are shown in SEQ ID NOS: 1-18. 5 These sequences refer to infection-specific proteins and to the DNA sequences that encode these proteins. Although these sequences are from C. psittaci and C. trachomatis, it would be equally possible to substitute in the present invention, the orthologs of these sequences from other Chlamydia species such as C. pecorum and C. pneumoniae. Such orthologous sequences may be obtained from the appropriate organisms by isolation 10 of the genome of the organism, digestion with restriction enzymes, separation of restriction fragments by electrophoresis and purification of these fragments and selection of fragments of appropriate size. Identity of the fragments can be confirmed by dot-blot and by standard DNA sequencing techniques. The orthologous sequences in different Chlamydia species may also be found by selection of appropriate PCR primers (selected from appropriate regions flanking the 15 Chlamydia gene of interest), and the use of these primers in a PCR reaction, using the genome of the particular species of Chlamydia of interest as a template, to amplify the ortholog of interest. Such PCR primers would be selected from the flanking regions to allow specific amplification of the target gene. The fragments so obtained could then be run on a gel to check size and sequenced and compared against the known sequences to determine sequence identity. 20 The degree of sequence identity between the infection-specific genes of C. psittaci or C. trachomatis and their orthologs from C. pecorum and C. pneumoniae, may be determined by comparing sequences using the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) as described herein. Orthologues of interest infection-specific proteins are characterized by possession of at 25 least 50% or greater sequence identity counted over the full length alignment with one of the disclosed amino acid sequences of the C. psittaci or C. trachomatis infection-specific proteins using gapped blastp set to default parameters (described herein). EXAMPLE 2: Heterologous Expression of Infection-Specific Antigens 30 Methods for expressing large amounts of protein from a cloned gene introduced into Escherichia coli (E. coli) may be utilized for the purification of the Chlamydia peptides. Methods and plasmid vectors for producing fusion proteins and intact native proteins in bacteria are well known and are described in Sambrook et al. (1989). Such fusion proteins may be made in large amounts, are relatively simple to purify, and can be used to produce antibodies. Native proteins 35 can be produced in bacteria by placing a strong, regulated promoter and an efficient ribosome binding site upstream of the cloned gene. If low levels of protein are produced, additional steps WO 99/53948 PCT/US99/08744 -19 may be taken to increase protein production; if high levels of protein are produced, purification is relatively easy. Often, proteins expressed at high levels are found in insoluble inclusion bodies. Methods for extracting proteins from these aggregates are described in chapter 17 of Sambrook et al. 5 (1989). Vector systems suitable for the expression of lacZ fusion genes include the pUC series of vectors (Ruther et al. (1983)), pEX1-3 (Stanley and Luzio (1984)) and pMR100 (Gray et al. (1982)). Vectors suitable for the production of intact native proteins include pKC30 (Shimatake and Rosenberg (1981)), pKK177-3 (Amann and Brosius (1985)) and pET-3 (Studiar and Moffatt (1986)). 10 Fusion proteins may be isolated from protein gels, lyophilized, ground into a powder and used as antigen preparations. Mammalian or other eukaryotic host cells, such as those of yeast, filamentous fungi, plant, insect, amphibian or avian species, may also be used for protein expression, as is well known in the art. Examples of commonly used mammalian host cell lines are VERO and HeLa 15 cells, Chinese hamster ovary (CHO) cells, and WI38, BHK, and COS cell lines, although it will be appreciated by the skilled practitioner that other prokaryotic and eukaryotic cells and cell lines may be appropriate for a variety of purposes, e.g., to provide higher expression, post-translational modification, desirable glycosylation patterns, or other features. Additionally, peptides, particularly shorter peptides, may be chemically synthesized, 20 avoiding the need for purification from cells or culture media. It is known that peptides as short as 3 amino acids can act as an antigenic determinant and stimulate an immune response. Such peptides may be administered as vaccines in ISCOMs (Immune Stimulatory Complexes) as described by Janeway & Travers, Immunobiology: The Immune System In Health and Disease, 13.21 (Garland Publishing, Inc. New York, 1997). Accordingly, one aspect of the present 25 invention includes small peptides encoded by the nucleic acid molecules disclosed herein. Such peptides include at least 5, and may be at least 10, 15, 20, 25, or 30 or more contiguous amino acids of the polypeptide sequences described herein. EXAMPLE 3: Production of Antibodies Specific for 30 Infection-Specific Antigens Antibody against infection-specific antigen is encompassed by the present invention, particularly for the detection of Chlamydia infection-specific antigen. Such antibody may be produced by inoculation of an animal such as a guinea-pig or a monkey with infection-specific antigen produced as described above. Such antigen may be a polypeptide as disclosed herein, such 35 as a complete or partial polypeptide from C. psittaci, C. trachomatis, C. pneumoniae or C. pecorum. As discussed above, any molecule that can elicit a specific, protective immune response WO 99/53948 PCT/US99/08744 -20 may be used as a vaccine, but since a minimum of three amino acids are required to do this, a vaccine should comprise at least three amino acids. The peptide for use in the vaccine of the invention may be naturally derived or may be synthetic such as those synthesized on a commercially available peptide synthesizer. The peptide 5 may also comprise a complete or partial peptide derived from the C. pneumoniae or C. pecorum infection-specific orthologs of the C. trachomatis or C. psittaci proteins as set out herein. In one method of production, a polyclonal antibody is produced by providing a purified peptide which is diluted to 100 micrograms per milliliter in sterile saline and mixed with RiBi Trivalent Adjuvant (RiBi Immunochem Inc). The antigen/adjuvant emulsion is then administered 10 to an anaesthetized guinea pig using a procedure as provided by the manufacturer. Serum is collected 14 days after secondary and tertiary immunizations. Monoclonal antibody to epitopes of the Chlamydia peptides identified and isolated as described can be prepared from murine hybridomas according to the classical method of Kohler and Milstein (1975) or derivative methods thereof. Briefly, a mouse is repetitively inoculated with 15 a few micrograms of the selected purified protein over a period of a few weeks. The mouse is then sacrificed, and the antibody-producing cells of the spleen isolated. The spleen cells are fused by means of polyethylene glycol with mouse myeloma cells, and the excess unfused cells destroyed by growth of the system on selective media comprising aminopterin, e.g., Hypoxanthene, Aminopterin and Thymidine (HAT) medium. The successfully fused cells are diluted and aliquots 20 of the dilution placed in wells of a microtiter plate where growth of the culture is continued. Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall (1980), and derivative methods thereof. Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are 25 described in Harlow and Lane (1988). An alternative approach to raising antibodies against the Chlamydia peptides is to use synthetic peptides synthesized on a commercially available peptide synthesizer based upon the amino acid sequence of the peptides predicted from nucleotide sequence data. In another embodiment of the present invention, monoclonal antibodies that recognize a 30 specific Chlamydia peptide are produced. Optimally, monoclonal antibodies will be specific to each peptide, i.e., such antibodies recognize and bind one Chlamydia peptide and do not substantially recognize or bind to other proteins, including those found in uninfected human cells. The determination that an antibody specifically detects a particular Chlamydia peptide is made by any one of a number of standard immunoassay methods; for instance, the western blotting 35 technique (Sambrook et al., 1989). To determine that a given antibody preparation (for instance from a guinea pig) specifically detects one Chlamydia peptide by western blotting, total cellular protein is extracted from a sample of blood from an unexposed subject and from a sample of blood from an exposed subject. As a positive control, total cellular protein is also extracted from WO 99/53948 PCT/US99/08744 -21 Chlamydia cells grown in vitro. These protein preparations are then electrophoresed on a sodium dodecyl sulfate-polyacrylamide gel. Thereafter, the proteins are transferred to a membrane (for example, nitrocellulose) by western blotting, and the antibody preparation is incubated with the membrane. After washing the membrane to remove non-specifically bound antibodies, the 5 presence of specifically bound antibodies is detected by the use of an anti-guinea pig antibody conjugated to an enzyme such as alkaline phosphatase; application of the substrate 5-bromo-4 chloro-3-indolyl phosphate/nitro blue tetrazolium results in the production of a dense blue compound by immuno-localized alkaline phosphatase. Antibodies which specifically detect the Chlamydia protein will, by this technique, be shown to bind to the Chlamydia-extracted sample at 10 a particular protein band (which will be localized at a given position on the gel determined by its molecular weight) and to the proteins extracted from the blood of the exposed subject. No significant binding will be detected to proteins from the unexposed subject. EXAMPLE 4: Use of Infection-Specific Sequences and their Corresponding Peptides and 15 Antibodies in Diagnostic Assays Another aspect of the present invention is a method for detecting the presence of anti Chlamydia antibodies that react with infection-specific Chlamydia proteins, Chlamydia peptides and Chlamydia nucleic acid sequences in biological samples. These methods include detection of antigen and antibody by ELISA and similar techniques, the detection of proteins in a tissue sample 20 by immunofluorescence and related techniques and the detection of specific DNA sequences by specific hybridization and amplification. One aspect of the invention is an ELISA that detects anti-Chlamydia antibodies in a medical specimen. An immunostimulatory infection-specific Chlamydia peptide of the present invention is employed as an antigen and is preferably bound to a solid matrix such as a crosslinked 25 dextran such as SEPHADEX (Pharmacia, Piscataway, NJ), agarose, polystyrene, or the wells of a microtiter plate. The polypeptide is admixed with the specimen, such as blood, and the admixture is incubated for a sufficient time to allow antibodies present in the sample to immunoreact with the polypeptide. The presence of the positive immunoreaction is then determined using an ELISA assay, usually involving the use of an enzyme linked to an anti-immunoglobulin that catalyzes the 30 conversion of a chromogenic substrate. In one embodiment, the solid support to which the polypeptide is attached is the wall of a microtiter assay plate. After attachment of the polypeptide, any nonspecific binding sites on the microtiter well walls are blocked with a protein such as bovine serum albumin. Excess bovine serum albumin is removed by rinsing and the medical specimen is admixed with the polypeptide in 35 the microtiter wells. After a sufficient incubation time, the microtiter wells are rinsed to remove excess sample and then a solution of a second antibody, capable of detecting human antibodies is added to the wells. This second antibody is typically linked to an enzyme such as peroxidase, WO 99/53948 PCT/US99/08744 -22 alkaline phosphatase or glucose oxidase. For example, the second antibody may be a peroxidase labeled goat anti-human antibody. After further incubation, excess amounts of the second antibody are removed by rinsing and a solution containing a substrate for the enzyme label (such as hydrogen peroxide for the peroxidase enzyme) and a color-forming dye precursor, such as 5 o-phenylenediamine is added. The combination of Chlamydia peptide (bound to the wall of the well), the human anti-Chlamydia antibodies (from the specimen), the enzyme-conjugated anti human antibody and the color substrate will produce a color that can be read using an instrument that determines optical density, such as a spectrophotometer. These readings can be compared to a negative control such as a sample known to be free of anti-Chlamydia antibodies. Positive 10 readings indicate the presence of anti-Chlamydia antibodies in the specimen, which in turn indicate a prior exposure of the patient to Chlamydia. In another embodiment, antibodies that specifically recognize a Chlamydia peptide encoded by the nucleotide sequences disclosed herein are useful in diagnosing the presence of infection-specific Chlamydia antigens in a subject or sample. For example, detection of infection 15 specific antigens that are present in cells or tissues may be done by immunofluorescence, indirect immunofluorescense and immunohistochemistry. In immunofluorescense, a fluorescent dye is bound directly to the antibody. In indirect-immunofluorescence, the dye is bound to an anti immunoglobulin. Specific binding occurs between antigen and bound antibody is detected by virtue of fluorescent emissions from the dye moiety. This technique may be particularly useful, 20 for instance, for detection of Chlamydia antigen present on a urogenital mucosal smear. Chlamydia may be present in urogenital mucosa, and a smear on a glass slide may be fixed and bathed in a solution containing an antibody specific to the infection-specific antigen. The slide is then washed to remove the unbound antibody, and a fluorescent anti-immunoglobulin antibody is added. The slide is washed again, and viewed microscopically under an appropriate wavelength of 25 light to detect fluorescence. Fluorescence indicates the presence of Chlamydia antigen. Alternatively, a urogenital mucosal smear may be taken, the sample cultured with HeLa cells to produce large amounts of the RB form, and immunofluorescence may then be used to detect infection-specific Chlamydia antibodies. Another aspect of the invention includes the use of nucleic acid primers to detect the 30 presence of Chlamydia nucleic acids that encode infection-specific antigens in body samples and thus to diagnose infection. In other embodiments, these oligonucleotide primers will comprise at least 15 contiguous nucleotides of a DNA sequence as shown in SEQ ID NOS: 1, 3, 5, 7, 9, 11, 13, 15, or 17. In other embodiments, such oligonucleotides may comprise at least 20 or at least 25 or more contiguous nucleotides of the aforementioned sequences. 35 One skilled in the art will appreciate that PCR primers are not required to exactly match the target gene sequence to which they anneal. Therefore, in another embodiment, the oligonucleotides will comprise a sequence of at least 15 nucleotides and preferably at least 20 nucleotides, the oligonucleotide sequence being substantially similar to a DNA sequence set forth WO 99/53948 PCT/US99/08744 -23 in SEQ ID NOS:1, 3, 5, 7, 9, 11, 13, 15, and 17. Such oligonucleotides may share at least about 75%, 85%, 90% or greater sequence identity. The detection of specific nucleic acid sequences in a sample by polymerase chain reaction amplification (PCR) is discussed in detail in Innis et al., (1990). PCR Protocols: A Guide to 5 Methods and Applications, Academic Press: San Diego, part 4 in particular. To detect Chlamydia sequences, primers based on the sequences disclosed herein would be synthesized, such that PCR amplification of a sample containing Chlamydia DNA would result in an amplified fragment of a predicted size. If necessary, the presence of this fragment following amplification of the sample nucleic acid could be detected by dot blot analysis. PCR amplification employing primers based 10 on the sequences disclosed herein may also be employed to quantify the amounts of Chlamydia nucleic acid present in a particular sample (see chapters 8 and 9 of Innis et al., (1990)). Alternatively, probes based on the nucleic acid sequences described herein may be labeled with suitable labels (such a P 32 or biotin) and used in hybridization assays to detect the presence of Chlamydia nucleic acid in provided samples. 15 Reverse-transcription PCR using these primers may also be utilized to detect the presence of Chlamydia RNA which is indicative of an ongoing infection. EXAMPLE 5: Production of Chlamydia Vaccines The purified peptides of the present invention may be used directly as immunogens for 20 vaccination. Methods for using purified peptides as vaccines are well known in the art and are described in Yang et al. (1991), Andersen (1994) and Jardim et al. (1990). As is well known in the art, adjuvants such as alum, Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA) may be used in formulations of purified peptides as vaccines. Accordingly, one embodiment of the present invention is a vaccine comprising one or more immunostimulatory C. 25 trachomatis or C. psittaci peptides encoded by nucleotide sequences as shown in the attached sequence listing, together with a pharmaceutically acceptable adjuvant. Additionally a vaccine may comprise a defined fraction of the disclosed peptide of C. trachomatis or C. psittaci or may comprise a peptide wherein the gene coding for the peptide shows substantial similarity to the DNA sequences disclosed herein, such as for orthologous genes 30 of C. pneumoniae or C. pecorum. Additionally, the vaccines may be formulated using a peptide according to the present invention together with a pharmaceutically acceptable excipient such as water, saline, dextrose and glycerol. The vaccines may also include auxiliary substances such as emulsifying agents and pH buffers. 35 It will be appreciated by one of skill in the art that vaccines formulated as described above may be administered in a number of ways including subcutaneous, intra-muscular and intra-venous injection. Doses of the vaccine administered will vary depending on the antigenicity of the particular peptide or peptide combination employed in the vaccine, and characteristics of the WO 99/53948 PCT/US99/08744 -24 animal or human patient to be vaccinated. While the determination of individual doses will be within the skill of the administering physician, it is anticipated that doses of between 1 microgram and 1 milligram will be employed. As with many vaccines, the vaccines of the present invention may routinely be 5 administered several times over the course of a number of weeks to ensure that an effective immune response is triggered. Where such multiple doses are administered, they will normally be administered at from two to twelve week intervals, more usually from three to five week intervals. Periodic boosters at intervals of 1-5 years, usually three years, may be desirable to maintain the desired levels of protective immunity. 10 Alternatively, multiple immunostimulatory peptides may also be administered by expressing the nucleic acids encoding the peptides in a nonpathogenic microorganism, and using this transformed nonpathogenic microorganism as a vaccine. Finally, a recent development in the field of vaccines is the direct injection of nucleic acid molecules encoding peptide antigens, as described in Janeway & Travers, (1997). Thus, plasmids 15 which include nucleic acid molecules described herein, or which include nucleic acid sequences encoding peptides according to the present invention may be utilized in such DNA vaccination methods. The vaccine of the invention may be used to inoculate potential animal targets of any of the chlamydial diseases including those caused by C. trachomatis, C. psittaci, C. pneumoniae or 20 C. pecorum. Indeed the vaccine of the invention may be used to inoculate animals against any disease that shows immunological cross-protection as a result of exposure to infection-specific Chlamydia antigen. The protein or polypeptide is present in the vaccine in an amount sufficient to induce a protective immune response whether through humoral or cell mediated pathways or through both. Such a response protects the immunized animal against chlamydial infections 25 specifically by raising an immune response against the Reticulate Body form of Chlamydia. The above embodiments are set out only by way of example and are not intended to be exclusive, one skilled in the art will understand that the invention may be practiced in various additional ways without departing from the subject of the spirit of the invention.

WO 99/53948 PCT/US99/08744 -25 REFERENCES Akins, D. R., et al. (1997) J. Bacteriol. 179:5076-5086. Amann and Brosius (1985). Gene 40:183. Andersen (1994). Infection & Immunity 62:2536. 5 Ausubel et al. (1987). Current Protocols in Molecular Biology, ed. Greene Publishing and Wiley Interscience: New York (with periodic updates). Blanco, D. R., et al. (1995) J. Bacteriol. 177:3556-3562. Bannantine, J.P., et al. (1997) Abstr. Gen. Mtg. Amer. Soc. Microbiol. D-004. Miami, FL. Blanco, D. R., et al. (1996) J. Bacteriol. 178:6685-6692. 10 Brown, W.J., and Farquhar, M.G. (1989) Meth Cell Biol 31:553-569. Caldwell, H.D., et al. (1981) Infect. Immunol. 31:1161-1176. Chou, P.Y. and Fasman, G.D. (1978) Annu Rev Biochem 47:251-276. Engvall (1980). Enzymol. 70:419. Gray et al. (1982). Proc. Natl. Acad. Sci. USA 79:6598. 15 Hackstadt, T., R. et al. (1992) Infect. Immun. 60:159-165. Hardham, J.M., et al. (1977) Gene 197:47-64. Harlow and Lane (1988). Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, New York. Innis et al. (1990) PCR Protocols: A Guide to Methods and Applications, Academic Press: San 20 Diego. Janeway & Travers (1997) Immunobiology: The Immune System in Health and Disease 13.21. Garland Publishing, Inc. New York. Kohler and Milstein (1975) Nature 256:495. Kyte, J. and Doolittle, R.F. (1982) J Mol Biol 157:105-132. 25 Peeling, R. and Burnham, R. (1996) Emerging Infectious Diseases 2 (4) 307-317. Rockey, D.D., and Rosquist, J.L. (1994) Infect Immun 62:106-112. Rockey, D.D., et al. (1995) Mol Microbiol 15:617-626. Rockey, D.D., et al. (1996) Infect Immun 64:4269-4278. 30 Rockey, D.D., et al. (1997). Mol Microbiol 24:217-228. Robson, B. and Suzuki, E. (1976)J Mol Biol 107:327-356. Rockey, D.D., and Rosquist, J.L. (1994). Infect Immun 62:106-112. Rockey, D. D., et al. (1995) Mol. Microbiol. 15:617-626. Rockey, D.D., et al. (1997) Mol. Microbiol. 24:217-228. 35 Rothman, J.E., and F. T. Wieland (1996) Science 272:227-234. Ruther and Muller-Hill (1983). EMBO J. 2:1791. Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, ed. Cold Spring Harbor Lab. Press: Cold Spring Harbor, NY.

WO 99/53948 PCT/US99/08744 -26 Shimatake and Rosenberg (1981). Nature (London) 292:128. Stanley and Luzio (1984). EMBO J. 3:1429. Studiar and Moffatt (1986). J. Mol. Biol. 189:113. Su, H., et al. (1990) J. Exp. Med. 172:203-212. 5 Yang et al. (1990) J. Immunology 145:2281-2285. Yuan, Y., et al. (1992) Infect Immun 60: 2288-2296.

Claims

1. A purified infection-specific protein comprising an amino acid sequence selected from the group consisting of: 5 (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, (c) SEQ ID NO: 6, (d) SEQ ID NO: 10, (e) SEQ ID NO: 12, 10 (f) an amino acid sequence that differs from an amino acid sequence of (a) to (e) inclusive, by one or more conservative amino acid substitutions, and (g) an amino acid sequence having at least 60% sequence identity to an amino acid sequence of (a) to (e) inclusive.

2. An isolated nucleic acid molecule encoding a protein according to claim 1. 15

3. An isolated nucleic acid molecule according to claim 2 wherein the nucleic acid molecule comprises a nucleic acid sequence selected from the group consisting of: (a) SEQ ID NO: 1, (b) SEQ ID NO: 3, (c) SEQ ID NO: 5, 20 (d) SEQ ID NO: 9, and (e) SEQ ID NO: 11.

4. A recombinant nucleic acid molecule comprising a promoter sequence operably linked to a nucleotide molecule according to claim 2.

5. A vaccine preparation comprising at least one purified peptide comprising at least 25 5 contiguous amino acids selected from the group consisting of: (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, (c) SEQ ID NO: 6, (d) SEQ ID NO: 8, 30 (e) SEQ ID NO: 10, (f) SEQ ID NO: 12, (g) SEQ ID NO: 14, (h) SEQ ID NO: 16, and (i) SEQ ID NO: 18. 35

6. The vaccine preparation of claim 5 wherein the peptide comprises at least 10 contiguous amino acids of at least one of the specified sequences.

7. The vaccine preparation of claim 5 wherein the peptide comprises at least 15 contiguous amino acids of at least one of the specified sequences. WO 99/53948 PCT/US99/08744 -28

8. The vaccine preparation of claim 5 wherein the purified peptide comprises at least 20 contiguous amino acids of at least one of the specified sequences.

9. A vaccine preparation comprising an amino acid sequence selected from the 5 group consisting of: (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, (c) SEQ ID NO: 6, (d) SEQ ID NO: 8, 10 (e) SEQ ID NO: 10, (f) SEQ ID NO: 12, (g) SEQ ID NO: 14, (h) SEQ ID NO: 16, (i) SEQ ID NO: 18, 15 (j) an amino acid sequence that differs from an amino acid sequence of (a) to (i) inclusive, by one or more conservative amino acid substitutions, and (k) an amino acid sequence having at least 60% sequence identity to an amino acid sequence of (a) to (i) inclusive.

10. A method of making a vaccine comprising combining a pharmaceutically 20 acceptable excipient with a purified peptide having an amino acid sequence selected from the group consisting of: (a) SEQ ID NO:2, (b) SEQ ID NO:4, (c) SEQ ID NO:6, 25 (d) SEQ ID NO:8, (e) SEQ ID NO:10, (f) SEQ ID NO:12, (g) SEQ ID NO:14, (h) SEQ ID NO:16, 30 (i) SEQ ID NO:18, (j) an amino acid sequence that differs from an amino acid sequence of (a) to (i) inclusive, by one or more conservative amino acid substitutions, (k) an amino acid sequence having at least 60% sequence identity to an amino acid sequence of (a) to (i) inclusive, and 35 (1) at least 10 contiguous amino acids from an amino acid sequence of (a) to (i) inclusive.

11. A method of vaccination, comprising administering a vaccine preparation according to claim 5 to a mammal. WO 99/53948 PCT/US99/08744 -29

12. A method of vaccination, comprising administering a vaccine preparation according to claim 9 to a mammal.

13. A method of detecting an infection-specific Chlamydia protein in a biological sample comprising: contacting the biological sample with at least one anti-Chlamydia antibody, 5 which antibody is an infection-specific antibody, such that a reaction between the antibody and the infection-specific Chlamydia protein gives rise to a detectable effect, and detecting the detectable effect.

14. The method of claim 13 wherein the anti-Chlamydia antibody binds specifically to a peptide having an amino acid sequence selected from the group consisting of: 10 (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, (c) SEQ ID NO: 6, (d) SEQ ID NO: 8, (e) SEQ ID NO: 10, 15 (f) SEQ ID NO: 12, (g) SEQ ID NO: 14, (h) SEQ ID NO: 16, and (i) SEQ ID NO: 18.

15. A method of detecting an infection-specific anti-Chlamydia antibody in a 20 biological sample comprising: contacting the biological sample with at least one Chlamydia peptide, which peptide is an infection specific peptide, such that a reaction between the peptide and the infection-specific anti-Chlamydia antibody gives rise to a detectable effect, and detecting the detectable effect.

16. The method of claim 15 wherein the Chlamydia peptide comprises at least 5 25 contiguous amino acids of a sequence selected from the group consisting of: (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, (c) SEQ ID NO: 6, (d) SEQ ID NO: 8, 30 (e) SEQ ID NO: 10, (f) SEQ ID NO: 12, (g) SEQ ID NO: 14, (h) SEQ ID NO: 16, and (i) SEQ ID NO: 18. 35

17. The method of claim 15 wherein said Chlamydia peptide comprises an amino acid sequence selected from the group consisting of: (a) SEQ ID NO: 2, (b) SEQ ID NO: 4, WO 99/53948 PCT/US99/08744 -30 (c) SEQ ID NO: 6, (d) SEQ ID NO: 8, (e) SEQ ID NO: 10, (f) SEQ ID NO: 12, 5 (g) SEQ ID NO: 14, (h) SEQ ID NO: 16, and (i) SEQ ID NO: 18.

18. A method of treating a Chlamydial infection comprising directing a therapeutic agent against a specific target, said target chosen from the group consisting of: (i) an infection 10 specific protein of Chlamydia, (ii) a gene that encodes an infection-specific protein of Chlamydia and (iii) an RNA transcript that encodes an infection-specific protein of Chlamydia, wherein said therapeutic agent interacts with said target to affect a reduction in pathology.