WO2007131292A1

WO2007131292A1 - Methods of diagnosis and treatment of m. tuberculosis infection and reagents therefor xi

Info

Publication number: WO2007131292A1
Application number: PCT/AU2007/000663
Authority: WO
Inventors: Robert Cole; Susanne Pedersen
Original assignee: Proteome Systems Limited
Priority date: 2006-05-16
Filing date: 2007-05-16
Publication date: 2007-11-22

Abstract

The present invention provides isolated M. tuberculosis protein that is a putative transcriptional regulatory protein of the Tet repressor family (hereinafter 'TetR'; SEQ ID NO: 1) and immunogenic peptide fragments thereof (any one of SEQ ID NOs: 2-13), and antibodies produced against the full-length protein and immunogenic peptide fragments for the diagnosis of M. tuberculosis infection in humans, for example using an antigen-based sandwich ELISA format. The present invention also provides multi-analyte assays in which the TetR-based diagnostic assays of the present invention are multiplexed with the detection of immunogenic epitopes from other proteins from M. tuberculosis e.g., epitopes of the BSX protein (any one of SEQ ID NOs: 14-24) and/or glutamine synthetase protein (any one of SEQ ID NOs: 25-28).

Description

Methods of diagnosis and treatment of M. tuberculosis infection and reagents therefor XI

Related application data This application claims priority from Australian Patent Application No. 2006902607 filed on May 16, 2006, the contents of which are incorporated herein in their entirety.

Field of the invention

The present invention relates to novel diagnostic, prognostic and therapeutic reagents for infection of an animal subject such as a human by M. tuberculosis, and conditions associated with such infections, such as, for example, tuberculosis. More particularly, the present invention provides the first enabling disclosure of the expression in an infected subject of a putative transcriptional regulatory protein of the TetR family of proteins from M. tuberculosis (designated herein as "TetR"; SEQ ID NO: 1), and immunogenic epitopes thereof suitable for the preparation of immunological reagents, such as, for example, antigenic proteins/peptides and/or antibodies, for the diagnosis, prognosis and therapy of infection, and vaccine development.

Background of the invention Description of the related art

Tuberculosis is a chronic, infectious disease that is generally caused by infection with Mycobacterium tuberculosis. It is a major disease in developing countries, as well as an increasing problem in developed areas of the world, with about eight million new cases and three million deaths each year. Although the infection may be asymptomatic for a considerable period of time, the disease is most commonly manifested as an acute inflammation of the lungs, resulting in fever and a productive cough. If left untreated, M. tuberculosis infection may progress beyond the primary infection site in the lungs to any organ in the body and generally results in serious complications and death.

The problems of the rapidly growing global incidence of tuberculosis and microbial resistance have been often described by many workers in the health care industry and are well known to skilled artisans in that field. In particular there is a growing recognition that new diagnostics, drugs and vaccines are urgently needed.

The immunological mechanisms by which M. tuberculosis maintains and multiplies within the host are poorly^" understood. Consequently, any new information regarding the immunological relationship between tuberculosis and the host could clearly be used in many different ways to improve diagnosis, therapy and treatment of that disease.

The incidence of tuberculosis is especially common in late-staging AIDS patients, a majority of whom suffer from it. In fact, HIV infection is a most important risk factor for the development of active tuberculosis in purified protein derivative (PPD)- tuberculin-positive subjects, and the risk of acquisition of tuberculosis infection in HIV-infected immune-suppressed individuals may be markedly enhanced compared to those individuals that are not HIV-infected. It is also likely that co-infections with HIV-I, and M. tuberculosis mediate a shortened HIV symptom-free period and shortened survival time in subjects, possibly by triggering increased viral replication and virus load that results in depletion of CD4+ T-cells and immune deficiency or immune suppression (Corbett et al 2003; Ho, Mem. Inst. Oswaldo Cruz, 91, 385-387, 1996).

The sequencing of the Mycobacterium tuberculosis genome has facilitated an enormous research effort to identify potential M. tuberculosis proteins that theoretically may be expressed by the organism. However, sequence data alone are insufficient to conclude that any particular protein is expressed in vivo by the organism, let alone during infection of a human or other animal subject. Nor does the elucidation of open reading frames in the genome of M tuberculosis indicate that any particular protein encoded or actually expressed by the bacterium comprises any immunodominant B-cell epitopes or T-cell epitopes that are required for the preparation of diagnostic, prognostic and therapeutic immunological reagents. For example, to conclude that a particular protein of M tuberculosis or a peptide fragment derived there from has efficacy as a diagnostic reagent in an immunoassay format, or is suitable for use in a vaccine preparation, it is necessary to show that the protein is expressed during infectious cycle of the bacterium, and that the host organism mounts an immune response to the protein, and/or to a peptide fragment that comprises a B cell epitope or T-cell epitope (e.g., CD8⁺-restricted CTL epitope).

The ability to grow M. tuberculosis in culture has provided a convenient model to identify expressed tuberculosis proteins in vitro. However, the culture environment is markedly different to the environment of a human macrophage, lung, or extrapulmonary site where M. tuberculosis is found in vivo. Recent evidence indicates that the protein expression profile of intracellular parasites, such as, for example, M. tuberculosis, varies markedly depending on environmental cues, such that the expression profile of the organism in vitro may not accurately reflect the expression profile of the organism in situ.

Infection with M. tuberculosis bacilli, or reactivation of a latent infection, induces a host response comprising the recruitment of monocytes and macrophages to the site of infection. As more immune cells accumulate a nodule of granulomata forms comprising immune cells and host tissue that have been destroyed by the cytotoxic products of macrophages. As the disease progresses, macrophage enzymes cause the hydrolysis of protein, lipid and nucleic acids resulting in liquefaction of surrounding tissue and granuloma formation. Eventually the lesion ruptures and the bacilli are released into the surrounding lung, blood or lymph system.

During this infection cycle, the bacilli are exposed to four distinct host environments, being alveoli macrophage, caseous granuloma, extracellular lung and extrapulmonary sites, such as, for example the kidneys or peritoneal cavities, lymph, bone, or spine.

It is thought that bacilli can replicate to varying degrees in all these environments, however, little is known about the environmental conditions at each site. All four host environments are distinct, suggesting that the expression profile of M. tuberculosis in each environment will be different.

Accordingly, the identification of M. tuberculosis proteins from logarithmic phase cultures does not necessarily suggest which proteins are expressed or highly immunogenic in each environment in vivo. Similarly, the identification of M. tuberculosis proteins in a macrophage grown in vitro will not necessarily emulate the protein expression profile of M. tuberculosis in caseous granuloma, highly aerated lung, or at an extrapulmonary site having a low oxygen content.

Furthermore, M. tuberculosis infection within the host can be seen as a dynamic event where the host immune system is continually trying to encapsulate and destroy bacilli through destruction of infected macrophages. Consequently, the M. tuberculosis bacilli progress through cycles of intracellular growth, destruction (where both intracellular and secreted bacterial proteins are exposed and destroyed), and rapid extracellular multiplication. Host and pathogen interaction is a result of many factors, which can not be replicated in vitro.

Accordingly, until the present invention, it was not clear which M. tuberculosis proteins were the most highly expressed and/or highly immunologically active or immunogenic proteins of M. tuberculosis in any particular environment in vivo.

There clearly remains a need for rapid and cost-effective diagnostic and prognostic reagents for determining infection by M. tuberculosis and/or disease conditions associated therewith.

Conventional techniques of molecular biology, microbiology, proteomics, virology, recombining DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology described, for example, in the following texts: 1. Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, New York, Second Edition (1989), whole of VoIs I, II, and III;

2. DNA Cloning: A Practical Approach, VoIs. I and II (D. N. Glover, ed., 1985), IRL Press, Oxford, whole of text;

3. Oligonucleotide Synthesis: A Practical Approach (M. J. Gait, ed., 1984) IRL Press, Oxford, whole of text, and particularly the papers therein by Gait, ppl-22; Atkinson et al, pp35-81; Sproat et al, pp 83-115; and Wu et al, pp 135-151;

4. Nucleic Acid Hybridization: A Practical Approach (B. D. Hames & S. J. Higgins, eds., 1985) IRL Press, Oxford, whole of text;

5. Immobilized Cells and Enzymes: A Practical Approach (1986) IRL Press, Oxford, whole of text;

6. Perbal, B., A Practical Guide to Molecular Cloning (1984);

7. Methods In Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.), whole of series;

8. J.F. Ramalho Ortigao, "The Chemistry of Peptide Synthesis" In: Knowledge database of Access to Virtual Laboratory website (Interactiva, Germany);

9. Sakakibara, D., Teichman, J., Lien, E. Land Fenichel, R.L. (1976). Biochem. Biophys. Res. Commun. 73 336-342 10. Merrifield, R.B. (1963). J. Am. Chem. Soc. 85, 2149-2154.

11. Barany, G. and Merrifield, R.B. (1979) in The Peptides (Gross, E. and Meienhofer, J. eds.), vol. 2, pp. 1-284, Academic Press, New York.

12. Wύnsch, E., ed. (1974) Synthese von Peptiden in Houben-Weyls Metoden der Organischen Chemie (Mϋler, E.₅ ed.), vol. 15, 4th edn., Parts 1 and 2, Thieme, Stuttgart.

13. Bodanszky, M. (1984) Principles of Peptide Synthesis, Springer- Verlag, Heidelberg.

14. Bodanszky, M. & Bodanszky, A. (1984) The Practice of Peptide Synthesis, Springer -Verlag, Heidelberg. 15. Bodanszky, M. (1985) Int. J. Peptide Protein Res. 25, 449-474. 16. Handbook of Diagnostic testal Immunology, VoIs. I-IV (D. M. Weir and C. C. Blackwell, eds., 1986, Blackwell Scientific Publications).

17. Willdns M. R., Williams K. L., Appel R. D. and Hochstrasser (Eds) 1997 Proteome Research: New Frontiers in Functional Genomics Springer, Berlin.

Summary of invention 1. Introduction

In work leading up to the present invention, the inventors sought to elucidate the range of proteins expressed by M. tuberculosis in a range of in vivo environments, to thereby identify highly expressed and/or highly immunogenic M. tuberculosis proteins.

The inventors used a proteomics approach to identify M. tuberculosis proteins expressed in vivo and present in the body fluids of a cohort of diseased patients, including sputum, pleural fluid, plasma and serum. An M. tuberculosis protein was identified in vivo by 2-dimensional electrophoresis of immunoglobulin-containing samples, in particular IgG, obtained previously from a cohort of M. tuberculosis- infected patients. Peptide fragments were identified in serum and sputum from TB + subjects, and the amino acid sequences of peptide fragments were determined by mass spectrometry of tryptic fragments, and shown to align to the amino acid sequence of the putative transcriptional regulatory protein ("TetR") protein postulated to be encoded by the M. tuberculosis Rv3160c gene (SEQ ID NO: 1). In particular, matched peptides aligned to amino acid residues 1-19 of TetR (SEQ ID NO: 2); amino acid residues 2-15 of TetR (SEQ ID NO: 3); amino acid residues 2-19 of TetR (SEQ ID NO: 4); amino acid residues 20-26 of TetR (SEQ ID NO: 5); amino acid residues 39-46 of TetR (SEQ ID NO: 6); amino acid residues 209-225 (SEQ ID NO:7); amino acid residues 2-23 (SEQ ID NO:8); amino acid residues 131-149 (SEQ ID NO: 9); amino acid residues 183-194 (SEQ ID NO:10); and amino acid residues 195-217 of TetR (SEQ ID NO:11).

The inventors have also made antibodies that bind to putative transcriptional regulatory protein TetR and TetR-derived peptides for the development of antigen-based diagnostic and prognostic assays. For example, six distinct monoclonal antibodies and two distinct polyclonal antibodies have been prepared against a recombinant TetR protein comprising SEQ ID NO:1, and two polyclonal antibodies have been prepared against a synthetic peptide comprising an immunogenic region of TetR comprising amino acid residues 147-174 of TetR (SEQ ID NO: 12). Antibodies are also prepared using a synthetic peptide comprising the sequence set forth in SEQ ID NO: 13 as an immunogen. The region of TetR comprising the sequence set forth in SEQ ID NO: 12 does not appear to cross-react with sera or plasma from non-infected subjects. Antibodies were prepared by immunization of chickens and mice with recombinant protein (SEQ ID NO:1), and in rabbits by immunization with SEQ ID NO: 12, using standard procedures for polyclonal and monoclonal antibody production. For determining quantitative titer of antibodies, the ability of antibodies to bind to recombinant TetR was determined. As exemplified herein, antibodies raised against recombinant protein or TetR peptides were shown to bind to recombinant TetR protein. Antibodies prepared in rabbits against SEQ ID NO: 12 are also shown to bind to SEQ ID NO: 12. The antibodies described herein are also shown to detect endogenous TetR protein expressed by clinical and laboratory strains of M. tuberculosis, and to have no cross-reactivity with other microorganisms including yeast, Bacillus subtilise, Escherichia coli, or Pseudomonas aeruginosa. Additional antibodies are also obtained with a view to selecting high-affinity antibodies capable of detecting M. tuberculosis TetR at sub-nanogram/ml or sub-picogram/ml levels in patient body fluids, such as sputum, saliva, pleural fluid, serum, plasma, etc.

In antigen-based assays, a high proportion of TB-positive subjects are able to be detected using an antibody that binds to the protein (i.e., the assay has high sensitivity). In contrast, a low proportion of TB-negative subjects are detectable in non-TB respiratory disease subjects e.g., having bronchitis or pneumonia, using an antibody that binds to the protein (i.e., the assay has high specificity). These data indicate that the presence of TetR is correlated with a TB diagnosis. In multianalyte assays, e.g., using an antibody that binds to TetR and antibodies that bind to one or more M. tuberculosis proteins e.g., S9 protein and/or Bsx protein and/or glutamine synthetase (GS) protein, high sensitivity and specificity are also achieved.

Antibodies that bind to the amino acid sequence set forth in SEQ ID NO: 1 or a B-cell epitope thereof e.g., SEQ ID NO: 12, have been shown to be present in subjects during extrapulmonary infection by M. tuberculosis. The detection of such antibodies is a suitable assay for the diagnosis of tuberculosis. Recombinant TetR comprising the sequence set forth in SEQ ID NO: 1, or a peptide comprising the immunodominant B- cell epitope set forth in any one of SEQ ID NOS: 2-13, is useful in antibody-based diagnostic tests for tuberculosis, including multianalyte tests, by virtue of the high sensitivity and specificity of the assays. Other peptides derived from the full-length sequence of TetR are also useful for such tests, e.g., as primary ligands or as secondary ligands in a multi-analyte assay format, by virtue of their high specificity.

These findings provide the means for producing novel diagnostics for the detection of M. tuberculosis infection in a subject, and novel prognostic indicators for the progression of infection or a disease state associated therewith. Preferably, TetR or a B-cell epitope thereof is useful for the early diagnosis of infection or disease. It will also be apparent to the skilled person that such prognostic indicators as described herein may be used in conjunction with therapeutic treatments for tuberculosis or an infection associated therewith.

Accordingly, the present invention provides the means for producing novel diagnostics for the detection of M. tuberculosis infection in a subject, and novel prognostic indicators for the progression of infection or a disease state associated therewith, either by detecting TetR solus or as part of a multi-analyte test. Preferably, TetR or a B-cell epitope thereof is useful for the early diagnosis of infection or disease. It will also be apparent to the skilled person that such prognostic indicators as described herein may be used in conjunction with therapeutic treatments for tuberculosis or an infection associated therewith. 2. Specific embodiments

The scope of the invention will be apparent from the claims as filed with the application that follow the examples. The claims as filed with the application are hereby incorporated into the description. The scope of the invention will also be apparent from the following description of specific embodiments.

In one example, the present invention provides an isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof.

Preferably, the isolated or recombinant immunogenic TetR of M. tuberculosis comprises the amino acid sequence set forth in SEQ ID NO: 1 or having an amino acid sequence that is at least about 95% identical to SEQ ID NO: 1.

Preferably, the immunogenic TetR peptide is a synthetic peptide. Preferably TetR peptide, fragment or epitope comprises at least about 5 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, more preferably at least about 10 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, even more preferably at least about 15 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1, and still more preferably at least about 5 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1 fused to about 1-5 additional amino acid residues at the N-terminus and/or the C-terminus.

In a particularly preferred embodiment, TetR peptide, fragment or epitope comprises an amino acid sequence set forth in any one of SEQ ID Nos: 2-13 and preferably, the sequence set forth in SEQ ID NO: 12, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto. It will be apparent from the disclosure that a preferred immunogenic TetR peptide, fragment or epitope comprises an amino acid sequence of at least about 5 consecutive amino acid residues positioned between about residue 125 to about residue 200 of SEQ ID NO: 1, more preferably at least about 5 consecutive amino acid residues positioned between about residue 125 to about residue 175 of SEQ ID NO: 1. Still more preferably, a preferred immunogenic TetR peptide, fragment or epitope comprises an amino acid sequence of at least about 5 consecutive amino acid residues positioned between residue 140 to residue 175 of SEQ ID NO: 1, more preferably at least 5 consecutive residues of the sequence set forth in SEQ ID NO: 12 including any peptides comprising an N-tenninal extension of up to about 5 amino acid residues in length and/or a C-terminal extension of up to about 5 amino acid residues in length relative to SEQ ID NO: 12.

It is clearly within the scope of the present invention for the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof to comprise one or more labels or detectable moieties e.g., to facilitate detection or isolation or immobilization. Preferred labels include, for example, biotin, glutathione- S-transferase (GST), FLAG epitope, hexa-histidine, β-galactosidase, horseradish peroxidase, streptavidin or gold.

The present invention also provides a fusion protein comprising one or more immunogenic TetR peptides, fragments or epitopes according to any embodiment described herein. For example, the N-terminal and C-terminal portions of TetR can be fused. The skilled artisan will be aware that it is preferred to include an internal linking residue e.g., cysteine in such compositions of matter. Alternatively, a preferred fusion protein comprises a linker separating an immunogenic TetR peptide from one or more other peptide moieties, such as, for example, a single amino acid residue (e.g., glycine, cysteine, lysine), a peptide linker (e.g., a non-immunogenic peptide such as a poly- lysine or poly-glycine), poly-carbon linker comprising up to about 6 or 8 or 10 or 12 carbon residues, or a chemical linker. Such linkers may facilitate antibody production or vaccine formulation e.g., by permitting linkage to a lipid or hapten, or to permit cross-linking or binding to a ligand. The expression of proteins as fusions may also enhance their solubility.

Preferred fusion proteins will comprise the putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope fused to a carrier protein, detectable label or reporter molecule e.g., glutathione-S -transferase (GST), FLAG epitope, hexa- histidine, β-galactosidase, thioredoxin (TRX) (La Vallie et al., Bio/Technology 11, 187-

193, 1993), maltose binding protein (MBP), Escherichia coli NusA protein (Fayard,

E.M.S., Thesis, University of Oklahoma, USA, 1999; Harrison, inNovations 11, 4-7, 2000), E. coli BFR (Harrison, inNovations 11, 4-7, 2000) and E. coli GrpE (Harrison, inNovations 11, A-I, 2000).

The present invention also provides an isolated protein aggregate comprising one or more immunogenic TetR peptides, fragments or epitopes according to any embodiment described herein. Preferred protein aggregates will comprise the protein, peptide, fragment or epitope complexed to an immunoglobulin e.g., IgA, IgM or IgG, such as, for example as a circulating immune complex (CIC). Exemplary protein aggregates may be derived, for example, derived from an antibody-containing biological sample of a subject.

The present invention also encompasses the use of the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein, or a combination or mixture of said peptides or epitopes or fragments, for detecting a past or present infection or latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of antibodies in a sample obtained from the subject to said isolated or recombinant immunogenic TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope.

The present invention also encompasses the use of the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein, or a combination or mixture of said peptides or epitopes or fragments, for eliciting the production of antibodies that bind to M. tuberculosis TetR .

The present invention also encompasses the use of the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments in the preparation of a medicament for immunizing a subject against infection by M. tuberculosis.

The present invention also provides a pharmaceutical composition comprising the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments in combination with a pharmaceutically acceptable diluent, e.g., an adjuvant.

The present invention also provides an isolated nucleic acid encoding the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic

TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or encoding a combination of said peptides or epitopes or fragments e.g., as a fusion porotein, such as for the preparation of nucleic acid based vaccines or for otherwise expressing the immunogenic polypeptide, protein, peptide, fragment or epitope.

The present invention also provides a cell expressing the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments. The cell may preferably consist of an antigen- presenting cell (APC) that expresses the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof e.g., on its surface.

The present invention also provides an isolated ligand, e.g., a small molecule, peptide, antibody, or immune reactive fragment of an antibody, that binds specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein, or to a combination or mixture of said peptides or epitopes or fragments, or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. Preferred ligands are peptides or antibodies. Preferred antibodies include, for example, a monoclonal or polyclonal antibody preparation. This extends to any isolated antibody-producing cell or antibody-producing cell population, e.g., a hybridoma or plasmacytoma producing antibodies that bind to a TetR or immunogenic fragment of a TetR or other immunogenic peptide comprising a sequence derived from the sequence of a putative transcriptional regulatory protein TetR, or TetR-derived peptide.

The present invention also provides for the use of the isolated ligand according to any embodiment described herein or a combination of said ligands, especially any peptide ligand, antibody or an immune-reactive fragment thereof in medicine.

The present invention also provides for the use of the isolated ligand according to any embodiment described herein or a combination of said ligands, especially any peptide ligand, antibody or an immune-reactive fragment thereof for detecting a past or present

(i.e., active) infection or a latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of the ligand to M. tuberculosis TetR or an immunogenic fragment or epitope thereof present in a biological sample obtained from the subject. The present invention also provides for the use of the isolated ligand according to any embodiment described herein or a combination of said ligands, especially any peptide ligand, antibody or an immune-reactive fragment thereof for identifying the bacterium M. tuberculosis or cells infected by M. tuberculosis or for sorting or counting of said bacterium or said cells.

The isolated ligand according to any embodiment described herein, or combination of said ligands, especially any peptide ligand, antibody or an immune-reactive fragment thereof, is also useful in therapeutic, diagnostic and research applications for detecting a past or present infection, or a latent infection, by M. tuberculosis as determined by the binding of the ligand to an M. tuberculosis TetR or an immunogenic fragment or epitope thereof present in a biological sample from a subject (i.e., an antigen-based immunoassay).

Other applications of the subject ligands include the purification and study of the diagnostic/prognostic TetR protein or TetR-derived peptide, identification of cells infected with M. tuberculosis, or for sorting or counting of such cells.

The ligands are also useful in therapy, including prophylaxis, diagnosis, or prognosis, and the use of such ligands for the manufacture of a medicament for use in treatment of infection by M. tuberculosis. For example, specific humanized antibodies or other ligands are produced that bind and neutralize a TetR or M. tuberculosis, especially in vivo. The humanized antibodies or other ligands are used as in the preparation of a medicament for treating TB-specific disease or M. tuberculosis infection in a human subject, such as, for example, in the treatment of an active or chronic M. tuberculosis infection.

The present invention also provides a composition comprising the isolated ligand according to any embodiment described herein or a combination thereof, especially any peptide ligand, antibody or an immune-reactive fragment thereof, and a pharmaceutically acceptable carrier, diluent or excipient. The present invention also provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject antibodies that bind to an immunogenic TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof, the presence of said antibodies in the sample is indicative of infection. In a related embodiment, the presence of said antibodies in the sample is indicative of infection. The infection may be a past or active infection, or a latent infection, however this assay format is particularly useful for detecting active infection and/or recent infection.

For example, the method may be an immunoassay, e.g., comprising contacting a biological sample derived from the subject with the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein (e.g., a peptide comprising an amino acid sequence set forth in any one of SEQ ID Nos: 2-13 and preferably, the sequence set forth in SEQ ID NO: 12, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto) or a combination or mixture of said peptides or epitopes or fragments for a time and under conditions sufficient for an antigen-antibody complex to form and then detecting the formation of an antigen-antibody complex. The sample is an antibody-containing sample e.g., a sample that comprises blood or serum or plasma or an immunoglobulin fraction obtained from the subject. The sample may contain circulating antibodies in the form of complexes with TetR antigenic fragments. Generally, the antigen-antibody complex will be detected in such assay formats using antibodies capable of binding to the patient's immunoglobulin e.g., anti-human Ig antibodies.

It is within the scope of the present invention to include a multi-analyte test in this assay format, wherein multiple antigenic epitopes derived from proteins e.g., selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database

Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342) an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof, are used to confirm a diagnosis obtained using a TetR or peptide derived therefrom.

For example, the patient sample may be contacted with TetR or immunogenic TetR peptide or fragment or epitope and with a M. tuberculosis Bsx protein (e.g., SwissProt Database Accession No. 053759) or immunogenic peptide derived there from, e.g., a peptide derived from a Bsx protein, or comprising a sequence selected from the group consisting of: MRQLAERS GVSNPYL (SEQ ID NO: 14), ERGLRKPSADVLSQI (SEQ ID NO: 15), LRKPSAD VLSQIAKA (SEQ ID NO: 16), PSADVLSQIAKALRV (SEQ ID NO: 17), S QI AKALRVS AEVL Y (SEQ ID NO: 18), AKALRVSAEVLYVRA (SEQ ID NO: 19), VRAGILEPSETSQVR (SEQ ID No: 20), TAITERQKQILLDIY (SEQ ID NO; 21), SQIAKALRVSAEVLYVRAC (SEQ ID NO: 22), MSSEEKLCDPTPTDD (SEQ ID NO: 23) and VRAGILEPSETSQVRC (SEQ ID NO: 24). Immunogenic M. tuberculosis Bsx and peptide derivatives for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.

Alternatively, or in addition, the patient sample may be contacted with TetR or immunogenic TetR peptide or fragment or epitope and with a M. tuberculosis glutamine synthetase (GS) protein (e.g., SwissProt Database Accession No. 033342) or immunogenic peptide derived there from, e.g., a peptide derived from a surface- exposed region of a GS protein, or comprising the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 25) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 26). Immunogenic M. tuberculosis GS and peptide derivatives for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.

Assays for one or more secondary analytes e.g., antibodies that bind to Bsx and/or glutamine synthetase, are conveniently performed in the same manner as for detecting antibodies that bind to TetR in serum or plasma or other body fluid. The assays may be performed simultaneously or at different times, and using the same or different patient samples. The assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the different antibodies, e.g., anti-human Ig labelled using different reporter molecules such as different coloured dyes, fluorophores, radionucleotides or enzymes.

As used herein, the term "infection" shall be understood to mean invasion and/or colonisation by a microorganism and/or multiplication of a micro-organism, in particular, a bacterium or a virus, in the respiratory tract of a subject. Such an infection may be unapparent or result in local cellular injury. The infection may be localised, subclinical and temporary or alternatively may spread by extension to become an acute or chronic clinical infection. The infection may also be a past infection wherein residual TetR antigen, or alternatively, reactive host antibodies that bind to isolated TetR or peptides, remain in the host. The infection may also be a latent infection, in which the microorganism is present in a subject, however the subject does not exhibit symptoms of disease associated with the organism. Preferably, the infection is a pulmonary or extra-pulmonary infection by M. tuberculosis, and more preferably an extra-pulmonary infection. By "pulmonary" infection is meant an infection of the airway of the lung, such as, for example, an infection of the lung tissue, bronchi, bronchioles, respiratory bronchioles, alveolar ducts, alveolar sacs, or alveoli. By "extrapulmonary" is meant outside the lung, encompassing, for example, kidneys, lymph, urinary tract, bone, skin, spinal fluid, intestine, peritoneal, pleural and pericardial cavities. The antibodies of the present invention are also useful in the diagnosis of tuberculosis or infection by M. tuberculosis. For example, the present invention also provides a method of diagnosing tuberculosis or infection by M, tuberculosis in a subject comprising detecting in a biological sample from said subject an immunogenic TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof, wherein the presence of said protein or immunogenic fragment or epitope in the sample is indicative of disease, disease progression or infection. In a related embodiment, the presence of said protein or immunogenic fragment or epitope in the sample is indicative of infection.

For example, the method may be an immunoassay, e.g., comprising contacting a biological sample derived from the subject with an antibody that binds to the endogenous TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein (e.g., comprising an amino acid sequence set forth in any one of SEQ ID Nos: 2-13 and preferably, comprising SEQ ID NO: 12, or an immunologically cross-reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto) or a combination or mixture of said peptides or epitopes or fragments for a time and under conditions sufficient for an antigen-antibody complex to form and then detecting the formation of an antigen- antibody complex. Preferred samples according to this embodiment are those samples in which M. tuberculosis or peptide fragments from bacterial debris are likely to be found, or immunoglobulin-containing fraction, e.g., an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof; body fluid(s) such as sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or derivatives thereof e.g., sputum, serum, plasma, whole blood, saliva, urine, pleural fluid, etc. The sample may contain circulating antibodies complexed with TetR antigenic fragments.

It is within the scope of the present invention to include a multi-analyte test in this assay format, wherein multiple antibodies are used to confirm a diagnosis obtained using antibodies that bind to TetR or epitope. For example, the patient sample may be contacted with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis Bsx protein (e.g., SwissProt Database Accession No. 053759) or antibodies that bind to an immunogenic peptide derived there from, e.g., a peptide derived from a Bsx protein,^" or comprising a sequence selected from the group consisting of: MRQLAERSGVSNPYL (SEQ ID NO: 14), ERGLRKPSADVLSQI (SEQ ID NO: 15), LRKPSAD VLSQIAKA (SEQ ID NO: 16), PSADVLSQIAKALRV (SEQ ID NO: 17), SQIAKALRVSAEVLY (SEQ ID NO: 18), AKALRVSAEVLYVRA (SEQ ID NO: 19), VRAGILEPSETSQVR (SEQ ID No: 20), TAITERQKQILLDIY (SEQ ID NO; 21), SQIAKALRVSAEVLYVRAC (SEQ ID NO: 22), MSSEEKLCDPTPTDD (SEQ ID NO: 23) and VRAGILEPSETSQVRC (SEQ ID NO: 24). Antibodies that bind to an immunogenic M. tuberculosis Bsx protein or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.

Alternatively, or in addition, the patient sample may be contacted with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to an immunogenic M. tuberculosis glutamine synthetase (GS) protein (e.g., SwissProt Database Accession No. 033342) or antibodies that bind to an immunogenic peptide derived from GS, e.g., a peptide derived from a surface-exposed region of a GS protein, or comprising the sequence RGTDGS AVFADSNGPHGMS SMFRSF (SEQ ID NO: 25) or WASGYRGLTPASD YNID YAI (SEQ ID NO: 26). Antibodies that bind to an immunogenic M. tuberculosis GS or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.

Assays for one or more secondary analytes e.g., Bsx and/or glutamine synthetase, are conveniently performed in the same manner as for detecting TetR in the sample. The assays may be performed simultaneously or at different times, and using the same or different patient samples. The assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the bound antibodies, e.g., secondary antibodies that bind to the anti-TetR antibodies and antibodies that bind to the secondary analyte(s).

As with antibody-based assays, antigen-based assay systems can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more isolated ligands according to any embodiment described herein, especially any peptide ligand, antibody or an immune-reactive fragment thereof capable of binding to a TetR or an immunogenic fragment or epitope thereof, and detecting the formation of a complex e.g., an antigen-antibody complex. In a particularly preferred embodiment, the ligand is an antibody, preferably a polyclonal or monoclonal antibody or antibody fragment that binds specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. Whilst useful for subjects who are not immunocompromised, e.g., HIV-negative subjects, the assay is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is infected with human immunodeficiency virus (i.e., "HIV+"). The samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof. The present invention also provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is enhanced, or not decreased or decreasing, compared to the level of that protein or fragment or epitope detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection. For example, the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a TetR or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen- antibody complex, hi a particularly preferred embodiment, an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. Whilst useful for subjects who are not immunocompromised, e.g., HIV-negative subjects, the diagnostic assay of the present invention is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+. The samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.

The present invention also provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is lower than the level of the protein or fragment or epitope detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection. For example, the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a TetR or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex. In a particularly preferred embodiment, an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. Whilst useful for subjects who are not immunocompromised, e.g., HIV-negative subjects, the diagnostic assay of the present invention is also particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+. The samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.

The present invention also provides a method of monitoring disease progression, responsiveness to therapy or infection status by M. tuberculosis in a subject comprising determining the level of a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject at different times, wherein a change in the level of the putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope indicates a change in disease progression, responsiveness to therapy or infection status of the subject. In a preferred embodiment, the method further comprises administering a compound for the treatment of tuberculosis or infection by M. tuberculosis when the level of putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope increases over time. For example, the method can comprise an immunoassay e.g., contacting a biological sample derived from the subject with one or more antibodies capable of binding to a TetR or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen- antibody complex. In a particularly preferred embodiment, an antibody is an isolated or recombinant antibody or immune reactive fragment of an antibody that binds specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. Whilst useful for subjects who are not immunocompromised, e.g., HIV-negative subjects, the diagnostic assay of the present invention is particularly useful for detecting TB in a subject that is immune compromised or immune deficient, e.g., a subject that is HIV+. The samples used for conducting such assays include, for example, (i) an extract from a tissue selected from the group consisting of brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone and mixtures thereof; (ii) body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof; and (iii) samples derived from body fluid(s) selected from the group consisting of sputum, serum, plasma, whole blood, saliva, urine, pleural fluid and mixtures thereof.

In a particularly preferred embodiment, circulating immune complexes (CICs) are detected in an antigen-based assay platform or antibody-based assay platform. For antigen-based assay platforms, the detection of CICs may provide a signal amplification over the detection of isolated antigen in circulation, by virtue of detecting the immunoglobulin moiety of the CIC. In accordance with this embodiment, a capture reagent e.g., a capture antibody is used to capture TetR antigen (TetR polypeptide or an immune reactive fragment or epitope thereof) complexed with the subject's immunoglobulin, in addition to isolated antigen in the subject's circulation. Anti-Ig antibodies, optionally conjugated to a detectable label, are used to specifically bind the captured CIC thereby detecting CIC patient samples. Within the scope of this invention, the anti-Ig antibody binds preferentially to IgM, IgA or IgG in the sample. In a particularly preferred embodiment, the anti-Ig antibody binds to human Ig, e.g., human IgA, human IgG or human IgM. The anti-Ig antibody may be conjugated to any standard detectable label known in the art. This is particularly useful for detecting infection by a pathogenic agent, e.g., a bacterium or virus, or for the diagnosis of any disease or disorder associated with CICs. Accordingly, the diagnostic methods described according to any embodiment herein are amenable to a modification wherein the sample derived from the subject comprises one or more circulating immune complexes comprising immunoglobulin (Ig) bound to TetR of Mycobacterium tuberculosis or one or more immunogenic TetR peptides, fragments or epitopes thereof and wherein detecting the formation of an antigen-antibody complex comprises contacting an anti-Ig antibody with an immunoglobulin moiety of the circulating immune complex(es) for a time and under conditions sufficient for a complex to form than then detecting the bound anti-Ig antibody.

It is also within the scope of the present invention to include a multi-analyte test in one or more of the preceding antigen-based assay formats, wherein multiple antibodies of different specificities, e.g., selected from the group consisting of antibodies that bind to M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342) an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9 or an immunogenic protein derived from GS, or any combination of said antibodes, are used to confirm a diagnosis obtained using antibodies raised against TetR and/or antibodies raised against a TetR peptide, thereby enhancing specificity and/or selectivity.

For example, the patient sample may be contacted with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and antibodies that bind to M. tuberculosis Bsx and/or ribosomal protein S9 and/or glutamine synthetase (GS) proteins or immunogenic peptide derived there from, e.g., antibodies prepared against a peptide derived from a surface-exposed region of a Bsx or S9 or GS protein or comprising a sequence selected from the group consisting of SEQ ID Nos: 14-28 and mixtures thereof.

Antibodies that bind to immunogenic M tuberculosis Bsx peptides are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety; and antibodies that bind to M. tuberculosis GS peptides are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is also incorporated herein in its entirety.

The antigen-antibody complexes formed are then detected using antibodies capable of binding to each protein analyte, or in the case of CIC detections, antibodies capable of binding to human immunoglobulins. The assays may be performed simultaneously or at different times, and using the same or different patient samples. The assays may also be performed in the same reaction vessel, provided that different detection systems are used to detect the different antigens or CICs comprising the different antigens, e.g., anti-human Ig labelled using different reporter molecules such as different coloured dyes, fluorophores, radionucleotides, enzymes, or colloidal gold particles; or differentially-labelled anti-TetR antibodies, anti-Bsx antibodies, anti-S9 antibodies and anti-GS antibodies. As with other immunoassays described herein, the secondary antibody is optionally conjugated to a suitable detectable label e.g., horseradish peroxidase (HRP) or β-galactosidase or β-glucosidase, colloidal gold particles, amongst others. Standard methods for employing such labels in the detection of the complexes formed will be apparent to the skilled artisan.

The present invention also provides a method of treatment of tuberculosis or infection ^' by M. tuberculosis comprising:

(i) performing a diagnostic method according to any embodiment described herein thereby detecting the presence of M. tuberculosis infection in a biological sample from a subject; and

(ii) administering a therapeutically effective amount of a pharmaceutical composition to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject.

The present invention also provides a method of treatment of tuberculosis or infection by M. tuberculosis comprising: (i) performing a diagnostic method according to any embodiment described herein thereby detecting the presence of M. tuberculosis infection in a biological sample from a subject being treated with a first pharmaceutical composition; and

(ii) administering a therapeutically effective amount of a second pharmaceutical composition to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject.

The present invention also provides a method of treatment of tuberculosis in a subject comprising performing a diagnostic method or prognostic method as described herein. In one embodiment, the present invention provides a method of prophylaxis comprising: (i) detecting the presence of M. tuberculosis infection in a biological sample from a subject; and

(ii) administering a therapeutically effective amount of a pharmaceutical composition to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject. More particularly, an immunogenic TetR or one or more immunogenic TetR peptides, fragments or epitopes thereof induce(s) the specific production of a high titer antibody when administered to an animal subject.

Accordingly, the invention also provides a method of eliciting the production of antibody against M. tuberculosis comprising administering an immunogenic TetR or one or more immunogenic TetR peptides or immunogenic TetR fragments or epitopes thereof to said subject for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis.

The present invention clearly contemplates the use of an immunogenic TetR or one or more immunogenic TetR peptides or immunogenic TetR fragments or epitopes thereof in the preparation of a therapeutic or prophylactic subunit vaccine against M. tuberculosis infection in a human or other animal subject.

Accordingly, this invention also provides a vaccine comprising an immunogenic TetR or one or more immunogenic TetR peptides or immunogenic TetR fragments or epitopes thereof in combination with a pharmaceutically acceptable diluent. Preferably, the protein or peptide(s) or fragment(s) or epitope(s) thereof is(are) formulated with a suitable adjuvant.

Alternatively, the peptide or derivative or variant is formulated as a cellular vaccine via the administration of an autologous or allogeneic antigen presenting cell (APC) or a dendritic cell that has been treated in vitro so as to present the peptide on its surface.

Nucleic acid-based vaccines that comprise nucleic acid, such as, for example, DNA or RNA, encoding an immunogenic TetR or one or more immunogenic TetR peptides or immunogenic TetR fragments or epitopes thereof cloned into a suitable vector (eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector) are also contemplated. Preferably, DNA encoding an immunogenic TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof is formulated into a DNA vaccine, such as, for example, in combination with the existing Calmette-Guerin (BCG) or an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.

The present invention further provides for the use of an immunogenic TetR or one or more immunogenic TetR peptides or one or more immunogenic TetR fragments or one or more epitopes thereof in the preparation of a composition for the prophylactic or therapeutic treatment or diagnosis of tuberculosis or infection by M. tuberculosis in a subject, such as, for example, a subject infected with HIV-I and/or HIV-2, including the therapeutic treatment of a latent M. tuberculosis infection in a human subject.

In an alternative embodiment, the present invention provides for the use of an immunogenic TetR or one or more immunogenic TetR peptides or one or more immunogenic TetR fragments or one or more epitopes thereof in the preparation of a composition for the prophylactic or therapeutic treatment or diagnosis of tuberculosis or infection by M. tuberculosis in a subject wherein the subject has been subjected previously to antiviral therapy against HIV-I and/or HIV-2.

The present invention also provides a kit for detecting M. tuberculosis infection in a biological sample, said kit comprising:

(i) one or more isolated antibodies or immune reactive fragments thereof that bind specifically to the isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope; and (ii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use. The present invention also provides a kit for detecting M. tuberculosis infection in a biological sample, said kit comprising:

(i) isolated or recombinant immunogenic TetR of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments; and (ii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use.

The assays described herein are amenable to any assay format, and particularly to solid phase ELISA, flow through immunoassay formats, lateral flow formats, capillary formats, and for the purification or isolation of immunogenic proteins, peptides, fragments and epitopes and CICs.

Accordingly, the present invention also provides a solid matrix having adsorbed thereto an isolated or recombinant TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any one embodiment described herein or a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. For example, the solid matrix may comprise a membrane, e.g., nylon or nitrocellulose. Alternatively, the solid matrix may comprise a polystyrene or polycarbonate microwell plate or part thereof (e.g., one or more wells of a microtiter plate), a dipstick, a glass support, or a chromatography resin.

In an alternative embodiment, the invention also provides a solid matrix having adsorbed thereto an antibody that binds to an isolated or recombinant TetR or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any embodiment described herein or to a combination or mixture of said peptides or epitopes or fragments or to a fusion protein or protein aggregate comprising said immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide, fragment or epitope. For example, the solid matrix may comprise a membrane, e.g., nylon or nitrocellulose. Alternatively, the solid matrix may comprise a polystyrene or polycarbonate microwell plate or part thereof (e.g., one or more wells of a microtiter plate), a dipstick, a glass support, or a chromatography resin.

It is clearly within the scope of the present invention for such solid matrices to comprise additional antigens and/or antibodies as required to perform an assay described herein, especially for multianalyte tests employing multiple antigens or multiple antibodies.

3. Definitions

As used herein, the term "TetR" will be taken to mean M. tuberculosis protein composition comprising or having substantially the same sequence set forth in SEQ ID NO: 1 of the present application for the purposes of producing immunogenic peptides or preparing antibodies that cross react with Mycobacteria or clinical matrix from subjects infected with Mycobacteria and not requiring any other functionality e.g., transcriptional regulatory activity characteristic of a protein having sequence similarity to a protein of the tetracycline repressor family of proteins, e.g., putative transcriptional regulatory protein of M. tuberculosis. Until the present invention, the M. tuberculosis protein was not known to be expressed in vivo, or to be immunogenic or immunologically non-cross-reactive with other organisms, and information in relation to the TetR protein was derived from a bioinformatic analysis of open reading frame in the M. tuberculosis genome that encodes the polypeptide of SEQ ID NO: 1.

As used herein the term "derived from" shall be taken to indicate that a specified integer may be obtained from a particular source albeit not necessarily directly from that source.

Unless the context requires otherwise or specifically stated to the contrary, integers, steps, or elements of the invention recited herein as singular integers, steps or elements clearly encompass both singular and plural forms of the recited integers, steps or elements.

The embodiments of the invention described herein with respect to any single embodiment and, in particular, with respect to any protein or a use thereof in the diagnosis, prognosis or therapy of M. tuberculosis shall be taken to apply mutatis mutandis to any other embodiment of the invention described herein.

The diagnostic embodiments described here for individual subjects clearly apply mutatis mutandis to the epidemiology of a population, racial group or sub-group or to the diagnosis or prognosis of individuals having a particular MHC restriction. All such variations of the invention are readily derived by the skilled artisan based upon the subject matter described herein.

Throughout this specification, unless the context requires otherwise, the word "comprise", or variations such as "comprises" or "comprising", will be understood to imply the inclusion of a stated step or element or integer or group of steps or elements or integers but not the exclusion of any other step or element or integer or group of elements or integers.

Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations or any two or more of said steps or features.

The present invention is not to be limited in scope by the specific examples described herein. Functionally equivalent products, compositions and methods are clearly within the scope of the invention, as described herein. The present invention is performed without undue experimentation using, unless otherwise indicated, conventional techniques of molecular biology, microbiology, proteomics, virology, recombining DNA technology, peptide synthesis in solution, solid phase peptide synthesis, and immunology. Texts 1-17 infra teaching such conventional techniques are incorporated herein in their entirety by way of reference.

Brief description of the drawings

Figure 1 is a graphical representation showing the titration of polyclonal antibodies prepared in chickens against recombinant protein comprising SEQ ID NO:1. Recombinant TetR (SEQ ID NO: 1) was immobilized onto ELISA plate at a concentration of 5 μg/ml. Dilutions of- antisera designated "Pink 4" (■) and "Pink 5" (X) as indicated on the x-axis, and dilutions of pre-immune sera from the same animals (♦ for Pink 4; A for Pink 5) as indicated on the x-axis, were contacted with the immobilized TetR for a time and under conditions sufficient for an antigen: antibody complex to form. The ELISA plate was washed and complexes detected by binding sheep anti-chicken IgG horseradish peroxidase (HRP) conjugate diluted 1:5000 (v/v) using TMB to detect bound HRP activity. Optical density (OD) was determined for each sample (y-axis). Data indicate antibody titers of at least about 1 :64,000 (v/v) for Pink 4 and at least about 1:128,000 (v/v) for Pink 5 for both antibody preparations. The antibody "Pink 4" is also referred to herein as "Ch4"; and the antibody "Pink 5" is also referred to herein as "Ch5".

Figure 2 is graphical representation showing the detection limits of polyclonal antibodies prepared in rabbits against SEQ ID NO: 12. Streptavidin was immobilized onto an ELISA plate at a concentrate of 5 μg/ml. Biotin conjugated to a peptide consisting of the sequence set forth in SEQ ID NO: 12 at concentrations in the range 204.8 μg/ml to 100 pg/ml as shown on the x-axis was contacted with the plate for a time and under conditions sufficient to immobilize the peptide via a biotin-streptavidin interaction. Dilutions (1:500 (v/v) or 1:2,000 (v/v)) of rabbit antisera or pre-immune sera were added for a time and under conditions sufficient to form an antigen: antibody complexes, and bound antibodies were then detected as described in the legend of Figure I₅ except that the secondary antibody was a sheep anti-rabbit IgG HRP conjugate, Rabbit sera was designated RCP 18 (■ for preimmune sera at 1:500 (v/v) dilutions; ♦ for immune sera at 1:500 (v/v) dilutions; X for preimmune sera at 1:2,000 (v/v) dilutions ; and ▲ for immune sera at 1 :2,000 (v/v) dilutions). Optical density (OD) is indicated on the y-axis. Data indicate that the limits of detection of RPC 18 is about 0.1-0.5 ng/ml.

Figure 3 is a graphical representation of a standard sandwich ELISA using the polyclonal antisera RCP 18 (=Rbl8 in the figure) as a capture antibody and a pool of polyclonal antibodies designated "Ch.4/5" which comprises the polyclonal antibodies Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (=antibody "Pink 5" referred to herein) as detector antibody. This figure shows the effect of using these two antibody preparations in the sandwich ELISA. Wells of an ELISA plate were coated overnight with 50 μl of RCP18 (Rbl8) antibody at 5 μg/ml or 10 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 50 ng/ml starting concentration to 80 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plates (x-axis). Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., Ch4/5 for detecting TetR-RCP18 complexes was contacted with the bound antigen- body complexes at a concentration of 5 μg/ml or 10 μg/ml or 20 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1:5000 (v/v) dilution of secondary antibody (i.e., sheep anti-chicken IgG for detecting Ch4/5) conjugated to horseradish peroxidase (HRP)₃ washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background (y-axis). Without limiting the invention, data suggest that the combination of 5 μg/ml RCP 18 as capture antibody and 5 μg/ml Ch4/5 as detector antibody is preferred in this sandwich ELISA format and detects TetR to at least 5ng/ml of protein.

Figure 4 is a graphical representation of a standard sandwich ELISA using a pool of polyclonal antibodies designated "Ch4/5" which comprises the polyclonal antibodies

Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (^antibody "Pink 5" referred to herein) as capture antibody, and the polyclonal antisera RCP 18 (=Rbl8 in the figure) as a detector antibody. The figure shows the effect of using these two antibody preparations in the sandwich ELISA. Wells of an ELISA plate were coated overnight with 50 μl of Ch4/5 antibody at 5 μg/ml or 10 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 50 ng/ml starting concentration to 80 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plates (x-axis). Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., RCPl 8 for detecting TetR-Ch4/5 complexes was contacted with the bound antigen- body complexes at a concentration of 5 μg/ml or 10 μg/ml or 20 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1 :5000 (v/v) dilution of secondary antibody (i.e., sheep anti-rabbit IgG for detecting Ch4/5) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background (y-axis). Without limiting the invention, data suggest that the combination of 5 μg/ml Ch4/5 as capture antibody and 5 μg/ml RCP 18 as detector antibody is preferred in this sandwich ELISA format, and marginally improved compared to the reverse orientation of antibodies shown in Figure 3.

Figure 5 is a graphical representation of a standard sandwich ELISA using a pool of polyclonal antibodies designated "Ch4/5" which comprises the polyclonal antibodies Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (=antibody "Pink 5" referred to herein) as capture antibody, and one of two monoclonal antibody preparations designated 784F and 785E as detector antibody. The figure shows the effect of using these antibody preparations in the sandwich ELISA. Wells of an ELISA plate were coated overnight with 50 μl of Ch4/5 antibody at 500 ng/ml or 1 μg/ml or 2 μg/ml or 4 μg/ml or 8 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 5 ng/ml starting concentration to 2.29 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody- coated ELISA plates (x-axis). Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., M 784F or M 785E for detecting TetR- Ch.4/5 complexes was contacted with the bound antigen-body complexes at a concentration of 2 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1 :5000 (v/v) dilution of secondary antibody (i.e., sheep anti-mouse IgG for detecting the mouse monoclonal antibodies) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background (y-axis). Without limiting the invention, data suggest that the 785E monoclonal antibody provides the lowest background signal and, when combined with the Ch4/5 capture antibody, provides higher signals than the rabbit polyclonal RCPl 8. The combination of 500 ng/ml Ch4/5 as capture antibody and 2 μg/ml 785E as detector antibody provided the lowest background signal, however the combination of 2 μg/ml Ch4/5 as capture antibody and 2 μg/ml 785E as detector antibody provided the highest signal :noise ratio in this sandwich ELISA format.

Figure 6 is a graphical representation comparing an optimized amplified sandwich ELISA to standard sandwich ELISA for detecting recombinant M. tuberculosis TetR protein. An ELISA plate was coated overnight with capture antibody Ch4/5 at 2 μg/ml concentration. Following washing to remove unbound antibody, recombinant TetR protein was diluted from 100 ng/ml starting concentration to 490 fg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plates (x- axis). Following incubation for 1 hour, plates were washed to remove unbound antigen. Unlabelled monoclonal antibody 785E was contacted with the bound antigen- body complexes at 2.5 μg/ml concentration for standard sandwich ELISA. For amplified sandwich ELISA, monoclonal antibody 785E was biotinylated and the biotinylated antibody contacted with the bound antigen-body complexes at 2.5 μg/ml concentration. Following incubation at room temperature for 1 hour, plates were washed, and incubated with 50 μl of a 1:5,000 (v/v) dilution of a secondary antibody consisting of HRP-conjugated sheep anti-mouse IgG (standard sandwich ELISA) or 50 μl of a 1 :2,500 (v/v) dilution of HRP80-streptavidin. Plates were then incubated for a further one hour at room temperature, and washed as before. Finally, all samples were incubated with TMB for 30 mins (standard ELISA) or 10 mins (amplified ELISA). Absorbance was determined at 450-620 nm (y-axis). Data indicate significant enhancement of detection using the amplified sandwich ELISA under these conditions: The limit of detection of this optimized sandwich ELISA is about 18 pg/ml TetR protein, with half-maximum detection of about 1 ng/ml TetR protein. This compares favourably to the observed limit of detection of the standard sandwich ELISA of about 176 pg/ml TetR protein.

Figure 7 is a graphical representation of sandwich ELISA results showing detection of M. tuberculosis TetR protein in whole cell extracts of the clinical M. tuberculosis isolates CSU93 and HN878, and in the laboratory strain H37Rv. Amplified sandwich ELISA conditions were essentially as described in the legend to Figure 6, except for the following: (i) cellular extracts were assayed as indicated on the x-axis; (ii) the whole cell extracts were spiked with recombinant TetR protein to a final concentration of 50, 16.7, 5.6 and 1.8 μg/ml; and (iii) the concentration of endogenous TetR protein was determined by interpolation from a standard curve of TetR concentration against signal strength, and corrected for the level of recombinant TetR protein spike in the samples. Data are presented as picograms endogenous TetR protein per microgram of total protein in the cellular extract (y-axis) for two separate experiments. Average protein levels are also indicated.

Figure 8 is a graphical representation of sandwich ELISA results showing lack of significant cross-reactivity of antibodies against M. tuberculosis TetR protein with whole cell lysates from yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa. Assay conditions were essentially as described in the legend to Figure 7 except that HRP40-streptavidin as opposed to HRP80-streptavidin was used at 1 :2500 (v/v) dilution, TMB was developed for 15 min for signal detection, and 450 fg/ml to 1 ng/ml purified recombinant TetR protein or a serial dilution [1:3 (v/v)] of cellular extract i.e., 11.1 μg/ml or 33.3 μg/ml or 100 μg/ml was assayed as indicated on the x- axis. Buffer without protein or cellular extract served as a negative control. Data show no cross-reactivity between M. tuberculosis and whole cell lysates from yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa. Figure 9 is a graphical representation showing a comparison of the concentration of recombinant BSX detected using a chicken anti-BSX polyclonal antibody preincubated with recombinant BSX (solid diamonds); a chicken anti-BSX antibody without preincubation (grey squares); a rabbit anti-BSX polyclonal antibody (solid triangles) and a mouse anti-BSX monoclonal antibody (solid squares). The concentration of the recombinant protein is indicated on the X-axis and the optical density indicated on the Y-axis.

Figure 10 is a graphical representation showing the detection of recombinant BSX using a sandwich ELISA in which monoclonal antibody 403B was used as a capture reagent and polyclonal antibody C44 was used as a detection reagent. Titrating amounts of recombinant BSX from 50ng/ml down to 0.39ng/ml were screened. Concentrations of detection and capture reagents are indicated. The concentration of BSX is shown on the X-axis and the mean OD is shown on the Y-axis.

Figure 11 is a graphical representation showing the detection of BSX in sputa of TB and control subjects using a Sandwich ELISA. The optical density is indicated on the Y-axis and the sample type and number is indicated on the X-axis.

Figure 12 is a graphical representation showing the detection of recombinant BSX using an amplified sandwich ELISA in which monoclonal antibody 403 B was used as a capture reagent detection reagent (as indicated) and polyclonal antibody C44 was used as a detection reagent or capture reagent (as indicated). Titrating amounts of recombinant BSX from 50ng/ml down to 0.39ng/ml were screened. Concentrations of detection and capture reagents are indicated. The concentration of BSX is shown on the X-axis and the mean OD is shown on the Y-axis.

Figure 13 is a graphcal representation showing the detection of recombinant BSX using an amplified ELISA in which C44 is used as a capture reagent. Purified chicken anti- BSX pAb C44 was immobilised onto an ELISA plate as a Capture antibody at a concentration of 20 μg/ml using 50 μl per well. Titrating amounts of recombinant BSX from 10 ng/ml down to 0.078 ng/ml were then screened by sequential addition of purified Rabbit anti-BSX (Peptide 28) pAb at a concentration of 5 μg/ml, and then a Goat anti-Rabbit IgG at a dilution of either 1:30,000 (v/v) or 1:60,000 (v/v), as a second Detector. Donkey anti-Goat IgG HRP at a dilution of 1:5,000 (v/v) and TMB were used for signal detection.

Figure 14 is a graphical representation showing the measurement of detection limits of standard sandwich ELISA versus biotin based Amplification System. Purified Rabbit anti-BSX pAb Rl 6 was immobilised onto an ELISA plate at a concentration of 20 μg/ml. Titrating amounts of recombinant BSX were added at a concentration of 50 ng/ml down to 0.39 ng/ml for 1 hr unless specified otherwise (i.e 2 hr). Antigen detection was performed using either a standard sandwich system where Chicken anti- BSX p Ab C44 was added at a concentration of 5 μg/ml followed by Sheep anti- Chicken IgG HRP conjugate at a dilution of 1:5000 (v/v), or an amplifying system where Chicken anti-BSX was first added at 5 μg/ml followed by Donkey anti-Chicken IgG biotin conjugate at various dilutions as specified above, and finally streptavidin- HRP at a 1:5000 (v/v) dilution. Background (i.e. signal without BSX present) has been subtracted from the above curves.

Figure 15 is a graphical representation showing detection of titrating amounts of recombinant BSX using a Biotin -based amplified ELISA. Purified Rabbit anti-BSX (anti-Peptide 28) pAb Rl 6 was immobilised onto an ELISA plate as a capture antibody at a concentration of either 20 or 40 μg/ml. Titrating amounts of recombinant BSX from 10 ng/ml down to 4.9 pg/ml were then screened by sequential addition of purified chicken anti-BSX pAb C44 at a concentration of 5 μg/ml, and then a Donkey anti- Chicken IgG biotin conjugate at a dilution of 1:20,000 (v/v) as a second detector. Streptavidin HRP conjugate at a dilution of 1 :5000 (v/v) and TMB were used for signal detection. Background OD intensity was obtained for both of the Rabbit anti-BSX capture concentrations where the recombinant BSX was not added. Figure 16 is a graphical representation showing screening of sputum for endogenous BSX using sandwich ELISA with a Biotin Amplification System. Sputum samples (50 μl + 50 μl blocking buffer) from South African TB patients and control patients with non-TB respiratory disease from South Africa (prefix 'M') and Australia (prefix 'CGS') respectively were screened by sandwich ELISA for the presence of BSX antigen. Purified Rabbit anti-BSX (peptide 28) pAb was immobilised onto the ELISA plate as a Capture antibody at a concentration of 20 μg/ml. Purified Chicken anti-BSX pAb, C44, at a concentration of 5 μg/ml, was used as the Detector antibody. Biotinylated Donkey anti-Chicken IgG at a dilution of 1:20000 (v/v) was used as a second detector. Streptavidin HRP at a dilution of 1 :5000 (v/v) and TMB were used for signal detection. Sputum from control patient CGS25 was spiked with 5 ng/ml and 1 ng/ml recombinant BSX as a positive control.

Figure 17 is a graphical representation showing the Effect of Multiple Sample Loads on Detection of BSX by Amplified Sandwich ELISA. Rabbit anti-BSX pAb Rl 6 was immobilised onto an ELISA plate as the capture antibody at a concentration of 20 μg/ml using 50 μl per well. Sputum samples from TB patients and non-TB respiratory disease control patients were diluted at a 1:1 (v/v) ratio with blocker solution. The positive control is recombinant BSX at 1 ng/ml spiked in CGS23 sputum sample. Sputum samples were either (i) incubated for 1 hr as per a standard ELISA; (ii) incubated for 2 hr; or (iii) incubated for 2 hr, removed and fresh sputum added for an additional 1 hr of incubation. Endogenous BSX was detected using purified Chicken anti-BSX pAb C44 at 5 μg/ml, followed by Donkey anti-Chicken IgG biotin conjugate at a dilution of 1:20,000 (v/v) and finally with stretpavidin HRP conjugate at 1:5000 (v/v) dilution.

Detailed description of the preferred embodiments

Isolated or recombinant TetR and immunogenic fragments and epitopes thereof One aspect of the present invention provides an isolated or recombinant TetR or an immunogenic fragment or epitope thereof. This aspect of the invention encompasses any synthetic or recombinant peptides derived from a TetR referred to herein, including the full-length putative transcriptional regulatory protein TetR, or TetR-derived peptide, and/or a derivative or analogue of a TetR or an immunogenic fragment or epitope thereof.

As used herein, the term "TetR " shall be taken to mean any peptide, polypeptide, or protein having at least about 80% amino acid sequence identity to the amino acid sequence set forth in SEQ ID NO: 1. Preferably, the percentage identity of a TetR to SEQ ID NO: 1 is at least about 85%, more preferably at least about 90%, even more preferably at least about 95% and still more preferably at least about 99%. The present invention is not to be restricted to the use of the exemplified M. tuberculosis TetR because, as will be known to those skilled in the art, it is possible to define a fragment of a protein having sequence identity and immunological equivalence to a region of the exemplified M. tuberculosis TetR without undue experimentation. For example, the M. bovis TetR is identical to M. tuberculosis TetR .

In determining whether or not two amino acid sequences fall within the defined percentage identity limits supra, those skilled in the art will be aware that it is possible to conduct a side-by-side comparison of the amino acid sequences. In such comparisons or alignments, differences will arise in the positioning of non-identical residues depending upon the algorithm used to perform the alignment. In the present context, references to percentage identities and similarities between two or more amino acid sequences shall be taken to refer to the number of identical and similar residues respectively, between said sequences as determined using any standard algorithm known to those skilled in the art. In particular, amino acid identities and similarities are calculated using software of the Computer Genetics Group, Inc., University Research Park, Maddison, Wisconsin, United States of America, eg., using the GAP program of Devereaux et at, Nucl. Acids Res. 12, 387-395, 1984, which utilizes the algorithm of Needleman and Wunsch, J. MoI. Biol. 48, 443-453, 1970. Alternatively, the CLUSTAL W algorithm of Thompson et al, Nucl. Acids Res. 22, 4673-4680, 1994, is used to obtain an alignment of multiple sequences, wherein it is necessary or desirable to maximise the number of identical/similar residues and to minimise the number and/or length of sequence gaps in the alignment. Amino acid sequence alignments can also be performed using a variety of other commercially available sequence analysis programs, such as, for example, the BLAST program available at NCBI.

Particularly preferred fragments include those that include an epitope, in particular a B cell epitope or T cell epitope.

A B-cell epitope is conveniently derived from the amino acid sequence of an immunogenic putative transcriptional regulatory protein TetR, or TetR-derived peptide.

Idiotypic and anti-idiotypic B cell epitopes against which an immune response is desired are specifically encompassed by the invention, as are lipid-modified B cell epitopes or a Group B protein. A preferred B-cell epitope will be capable of eliciting the production of antibodies when administered to a mammal, preferably neutralizing antibody against M. tuberculosis, and more preferably, a high titer neutralizing antibody. Shorter B cell epitopes are preferred, to facilitate peptide synthesis.

Preferably, the length of the B cell epitope will not exceed about 30 amino acids in length. More preferably, the B cell epitope sequence consists of about 25 amino acid residues or less, and more preferably less than 20 amino acid residues, and even more preferably about 5-20 amino acid residues in length derived from the sequence of the full-length protein.

A CTL epitope is also conveniently derived from the full length amino acid sequence of a TetR and will generally consist of at least about 9 contiguous amino acids of said TetR and have an amino acid sequence that interacts at a significant level with a MHC Class I allele as determined using a predictive algorithm for determining MHC Class I- binding epitopes, such as, for example, the SYFPEITHI algorithm of the University of Tuebingen, Germany, or the algorithm of the HLA Peptide Binding Predictions program of the Biolnformatics and Molecular Analysis Section (BIMAS) of the National Institutes of Health of the Government of the United States of America. More preferably, the CTL epitope will have an amino acid sequence that binds to and/or stabilizes a MHC Class I molecule on the surface of an antigen presenting cell (APC). Even more preferably, the CTL epitope will, have a sequence that induces a memory CTL response or elicits IFN-γ expression by a T cell, such as, for example, CD8⁺ T cell, cytotoxic T cell (CTL). Still even more preferably, the CTL will have a sequence that stimulates CTL activity in a standard cytotoxicity assay. Particularly preferred CTL epitopes of a TetR are capable of eliciting a cellular immune response against M. tuberculosis in human cells or tissues, such as, for example, by recognizing and lysing human cells infected with M. tuberculosis, thereby providing or enhancing cellular immunity against M. tuberculosis.

Suitable fragments will be at least about 5, e.g., 10, 12, 15 or 20 amino acids in length. They may also be less than 200, 100 or 50 amino acids in length.

Preferably, an immunogenic fragment or epitope of TetR comprises an amino acid sequence set forth in any one of SEQ ID NOs: 2-13, and preferably an immunogenic fragment or epitope thereof comprising the amino acid sequence set forth in SEQ ID .NO: 12.

The amino acid sequence of a TetR or immunogenic .fragment or epitope thereof may be modified for particular purposes according to methods well known to those of skill in the art without adversely affecting its immune function. For example, particular peptide residues may be derivatized or chemically modified in order to enhance the immune response or to permit coupling of the peptide to other agents, particularly lipids. It also is possible to change particular amino acids within the peptides without disturbing the overall structure or antigenicity of the peptide. Such changes are therefore termed "conservative" changes and tend to rely on the hydrophilicity or polarity of the residue. The size and/or charge of the side chains also are relevant factors in determining which substitutions are conservative.

The present invention clearly encompasses a covalent fusion between one or more immunogenic TetR peptides, including a homo-dimer, homo-trimer, homo-tetranier or higher order homo-multimer of a peptide, or a hetero-dimer, hetero-trimer, hetero- tetramer or higher order hetero-multimer comprising two or more different immunogenic peptides.

The present invention also encompasses a non-covalent aggregate between one or more immunogenic TetR peptides, e.g., held together by ionic, hydrostatic or other interaction known in the art or described herein.

It is well understood by the skilled artisan that, inherent in the definition of a biologically functional equivalent protein is the concept that there is a limit to the number of changes that may be made within a defined portion of the molecule and still result in a molecule with an acceptable level of equivalent biological activity.

Biologically functional equivalent proteins are thus defined herein as those proteins in which specific amino acids are substituted. Particular embodiments encompass variants that have one, two, three, four, five or more variations in the amino acid sequence of the peptide. Of course, a plurality of distinct proteins/peptides with different substitutions may easily be made and used in accordance with the invention.

Those skilled in the art are well aware that the following substitutions are permissible conservative substitutions (i) substitutions involving arginine, lysine and histidine; (ii) substitutions involving alanine, glycine and serine; and (iii) substitutions involving phenylalanine, tryptophan and tyrosine. Derivatives incorporating such conservative substitutions are defined herein as biologically or immunologically functional equivalents.

The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte & Doolittle, J. MoI. Biol. 157, 105-132, 1982). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. The hydropathic index of amino acids also may be considered in determining a conservative substitution that produces a functionally equivalent molecule. Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics, as follows: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (- 3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5). In making changes based upon the hydropathic index, the substitution of amino acids whose hydropathic indices are within .+/- 0.2 is preferred. More preferably, the substitution will involve amino acids having hydropathic indices within .+/- 0.1, and more preferably within about +/- 0.05.

It is also understood in the art that the substitution of like amino acids is made effectively on the basis of hydrophilicity, particularly where the biological functional equivalent protein or peptide thereby created is intended for use in immunological embodiments, as in the present case (e.g. US Patent No. 4,554,101), In fact, the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with its immunogenicity and antigenicity. As detailed in US Patent No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 +/- 0.1); glutamate (+3.0 +/- 0.1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 +/- 0.1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (- 2.5); tryptophan (-3.4). In making changes based upon similar hydrophilicity values, it ^• is preferred to substitute amino acids having hydrophilicity values within about +/- 0.2 of each other, more preferably within about +/- 0.1, and even more preferably within about +/- 0.05

The TetR polypeptide or peptide fragment thereof comprising an epitope is readily synthesized using standard techniques, such as the Merrifield method of synthesis (Merrifield, J Am Chem Soc, 85, :2149-2154, 1963) and the myriad of available improvements on that technology (see e.g., Synthetic Peptides: A User's Guide, Grant, ed. (1992) W.H. Freeman & Co., New York, pp. 382; Jones (1994) The Chemical Synthesis of Peptides, Clarendon Press, Oxford, pp. 230.); Barany, G. and Merrifield, R.B. (1979) in The Peptides (Gross, E. and Meienhofer, J. eds,), vol. 2, pp. 1-284, Academic Press, New York; Wtinsch, E., ed. (1974) Synthese von Peptiden in Houben- Weyls Metoden der Organischen Chemie (Mϋler, E., ed.), vol. 15, 4th edn., Parts 1 and 2, Thieme, Stuttgart; Bodanszky, M. (1984) Principles of Peptide Synthesis, Springer- Verlag, Heidelberg; Bodanszky, M. & Bodanszky, A. (1984) The Practice of Peptide Synthesis, Springer-Verlag, Heidelberg; Bodanszky, M. (1985) Int. J. Peptide Protein Res. 25, 449-474.d/

As is known in the art, synthetic peptides can be produced with additional hydrophilic N-terminal and/or C-terminal amino acids added to the sequence of a fragment or B- cell epitope derived from the full-length putative transcriptional regulatory protein TetR, or TetR-derived peptide, such as, for example, to facilitate synthesis or improve peptide solubility. Glycine and/or serine residues are particularly preferred for this purpose. Each of the peptides set forth in SEQ ID NO 2-13 may be modified to include additional spacer sequences flanking TetR fragments, said spacers comprising hetero- polymers (trimers or tetramers) comprising glycine and serine.

The peptides of the invention are readily modified for diagnostic purposes, for example, by addition of a natural or synthetic hapten, an antibiotic, hormone, steroid, nucleoside, nucleotide, nucleic acid, an enzyme, enzyme substrate, an enzyme inhibitor, biotin, avidin, streptavidin, polyhistidine tag, glutathione, GST, polyethylene glycol, a peptidic polypeptide moiety (e.g. tuftsin, poly-lysine), a fluorescence marker (e.g. FITC, RITC, dansyl, luminol or coumarin), a bioluminescence marker, a spin label, an alkaloid, biogenic amine, vitamin, toxin (e.g. digoxin, phalloidin, amanitin, tetrodotoxin), or a complex-forming agent. Biotinylated peptides are especially preferred.

In another embodiment, a TetR is produced as a recombinant protein. For expressing protein by recombinant means, a protein-encoding nucleotide sequence is placed in operable connection with a promoter or other regulatory sequence capable of regulating expression in a cell-free system or cellular system. In one embodiment of the invention, nucleic acid comprising a sequence that encodes a TetR or an epitope thereof in operable connection with a suitable promoter sequence, is expressed in a suitable cell for a time and under conditions sufficient for expression to occur. Nucleic acid encoding TetR is readily derived from the publicly available amino acid sequence e.g., the sequence of the M. tuberculosis Rv3160c gene.

In another embodiment, a TetR is produced as a recombinant fusion protein, such as for example, to aid in extraction and purification. To produce a fusion polypeptide, the open reading frames are covalently linked in the same reading frame, such as, for example, using standard cloning procedures as described by Ausubel et al. (Current Protocols in Molecular Biology, Wiley Interscience, ISBN 047150338, 1992), and expressed under control of a promoter. Examples of fusion protein partners include glutathione-S-transferase (GST), FLAG (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys), hexa- histidine, GAL4 (DNA binding and/or transcriptional activation domains) and β- galactosidase. It may also be convenient to include a proteolytic cleavage site between the fusion protein partner and the protein sequence of interest to allow removal of fusion protein sequences. Preferably the fusion protein will not hinder the immune function of the putative transcriptional regulatory protein TetR, or TetR-derived peptide.

Reference herein to a "promoter" is to be taken in its broadest context and includes the transcriptional regulatory sequences of a classical genomic gene, including the TATA box which is required for accurate transcription initiation, with or without a CCAAT box sequence and additional regulatory elements (i.e., upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli, or in a tissue-specific manner. In the present context, the term "promoter" is also used to describe a recombinant, synthetic or fusion molecule, or derivative which confers, activates or enhances the expression of a nucleic acid molecule to which it is operably connected, and which encodes the polypeptide or peptide fragment. Preferred promoters can contain additional copies of one or more specific regulatory elements to further enhance expression and/or to alter the spatial expression and/or temporal expression of the said nucleic acid molecule.

Placing a nucleic acid molecule under the regulatory control of, i.e., "in operable connection with", a promoter sequence means positioning said molecule such that expression is controlled by the promoter sequence. Promoters are generally positioned 5' (upstream) to the coding sequence that they control.

The prerequisite for producing intact polypeptides and peptides in bacteria such as E. coli is the use of a strong promoter with an effective ribosome binding site. Typical promoters suitable for expression in bacterial cells such as E. coli include, but are not limited to, the lacz promoter, temperature-sensitive λi, or λ_R promoters, T7 promoter or the IPTG-inducible tac promoter. A number of other vector systems for expressing the nucleic acid molecule of the invention in E. coli are well-known in the art and are described, for example, in Ausubel et al (In: Current Protocols in Molecular Biology. Wiley Interscience, ISBN 047150338, 1987) or Sambrook et al (In: Molecular cloning, A laboratory manual, second edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989). Numerous plasmids with suitable promoter sequences for expression in bacteria and efficient ribosome binding sites have been described, such as for example, ρKC30 (λ_L: Shimatake and Rosenberg, Nature 292, 128, 1981); pKK173- 3 (tac: Aniann and Brosius, Gene 40, 183, 1985), pET-3 (T7: Studier and Moffat, J. MoI. Biol. 189, 113, 1986); the pBAD/TOPO or pBAD/Thio-TOPO series of vectors containing an arabinose-inducible promoter (Invitrogen, Carlsbad, CA), the latter of which is designed to also produce fusion proteins with thioredoxin to enhance solubility of the expressed protein; the pFLEX series of expression vectors (Pfizer Inc., CT, USA); or the pQE series of expression vectors (Qiagen, CA), amongst others.

Typical promoters suitable for expression in viruses of eukaryotic cells and eukaryotic cells include the SV40 late promoter, SV40 early promoter and cytomegalovirus (CMV) promoter, CMV IE (cytomegalovirus immediate early) promoter amongst others. Preferred vectors for expression in mammalian cells (eg. 293, COS, CHO, 1OT cells, 293T cells) include, but are not limited to, the pcDNA vector suite supplied by Invitrogen, in particular pcDNA 3.1 myc-His-tag comprising the CMV promoter and encoding a C-terminal 6xHis and MYC tag; and the retrovirus vector pSRαtkneo (Muller et al., MoI. Cell. Biol, 11, 1785, 1991). The vector pcDNA 3.1 myc-His (Invitrogen) is particularly preferred for expressing a secreted form of a TetR or a derivative thereof in 293T cells, wherein the expressed peptide or protein can be purified free of conspecific proteins, using standard affinity techniques that employ a Nickel column to bind the protein via the His tag.

A wide range of additional host/vector systems suitable for expressing the diagnostic protein of the present invention or an immunological derivative (eg., an epitope or other fragment) thereof are available publicly, and described, for example, in Sambrook et al (Jn: Molecular cloning, A laboratory manual, second edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N. Y., 1989).

Means for introducing the isolated nucleic acid molecule or a gene construct comprising same into a cell for expression are well-known to those skilled in the art. The technique used for a given organism depends on the known successful techniques. Means for introducing recombinant DNA into animal cells include microinjection, transfection mediated by DEAE-dextran, transfection mediated by liposomes such as by using lipofectamine (Gibco, MD, USA) and/or cellfectin (Gibco, MD, USA), PEG- mediated DNA uptake, electroporation and microparticle bombardment such as by using DNA-coated tungsten or gold particles (Agracetus Inc., WI, USA) amongst others.

Proteins of the invention can be produced in an isolated form, preferably substantially free of conspecific protein. Antibodies and other affinity ligands are particularly preferred for producing isolated protein. Preferably, the protein will be in a preparation wherein more than about 90% (e.g. 95%, 98% or 99%) of the protein in the preparation is a TetR or an epitope thereof.

Isolated or recombinant secondary analyte protein, peptides and epitopes thereof It is to be understood that methods described herein above for the production of isolated and recombinant TetR or immunogenic fragments thereof apply mutatis mutandis to the production of secondary analyte proteins, peptides and fragments that are to be used in an immunoassay format e.g., for the purposes of diagnosis or prognosis of tuberculosis or infection by M. tuberculosis, antibody production, analyte purification, vaccine formulation, etc. As will be understood by the skilled artisan, such extrapolation is dependent on substituting TetR immunogen for the secondary analyte in question e.g., M. tuberculosis Bsx protein or GS protein or immunogenic fragment thereof according to any embodiment described herein or a combination or mixture of said peptides or epitopes or fragments. Such substitution is readily performed without undue experimentation from the disclosure herein.

For convenience, preferred secondary analytes e.g., for use in multi-analyte antigen- based tests, will comprise an amino acid sequence selected from the group set forth in SEQ ID NOS: 14-26.

For example, the M. tuberculosis Bsx protein can be expressed and fragments obtained therefrom by standard means, or alternatively, synthetic peptides can be synthesized based on the sequence of the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 053759). Exemplary immunogenic peptides from the full-length Bsx protein will comprise a sequence selected from the group consisting of: MRQLAERSGVSNPYL (SEQ ID NO: 14), ERGLRKPSADVLSQI (SEQ ID NO: 15), LRKPSADVLSQIAKA (SEQ ID NO: 16), PSADVLSQIAKALRV (SEQ ID NO: 17), SQIAKALRVSAEVLY (SEQ ID NO: 18), AKALRVSAEVLYVRA (SEQ ID NO: 19), VRAGILEPSETSQVR (SEQ ID NO: 20), TAITERQKQILLDIY (SEQ ID NO: 21), SQIAKALRVSAEVLYVRAC (SEQ ID NO: 22), MSSEEKLCDPTPTDD (SEQ ID NO: 23) and VRAGILEPSETSQVRC (SEQ ID NO: 24). Methods for producing such fragments are described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.

Alternatively, or in addition, M. tuberculosis glutamine synthetase (GS) protein can be expressed and fragments obtained therefrom by standard means, or alternatively, synthetic peptides can be synthesized based on the sequence of the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 033342). Exemplary immunogen fragments of the GS protein are derived from a surface-exposed region of a GS protein, or comprise the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 25) or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 26). Methods for producing such fragments are described in detail in the instant in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.

Antibodies that bind to a TetR or an epitope thereof

A second aspect of the present invention provides an antibody that binds specifically to a TetR or an immunogenic fragment or epitope thereof, such as, for example, a monoclonal or polyclonal antibody preparation suitable for use in the assays described herein.

Reference herein to antibody or antibodies includes whole polyclonal and monoclonal antibodies, and parts thereof, either alone or conjugated with other moieties. Antibody parts include Fab and F(ab)₂ fragments and single chain antibodies. The antibodies may be made in vivo in suitable laboratory animals, or, in the case of engineered antibodies (Single Chain Antibodies or SCABS, etc) using recombinant DNA techniques in vitro.

In accordance with this aspect of the invention, the antibodies may be produced for the purposes of immunizing the subject, in which case high titer or neutralizing antibodies that bind to a B cell epitope will be especially preferred. Suitable subjects for immunization will, of course, depend upon the immunizing antigen or antigenic B cell epitope. It is contemplated that the present invention will be broadly applicable to the immunization of a wide range of animals, such as, for example, farm animals (e.g. horses, cattle, sheep, pigs, goats, chickens, ducks, turkeys, and the like), laboratory animals (e.g. rats, mice, guinea pigs, rabbits), domestic animals (cats, dogs, birds and the like), feral or wild exotic animals (e.g. possums, cats, pigs, buffalo, wild dogs and the like) and humans.

Alternatively, the antibodies may be for commercial or diagnostic purposes, in which case the subject to whom TetR or immunogenic fragment or epitope thereof is administered will most likely be a laboratory or farm animal. A wide range of animal species are used for the production of antisera. Typically the animal used for production of antisera is a rabbit, mouse, rabbit, rat, hamster, guinea pig, goat, sheep, pig, dog, horse, or chicken. Because of the relatively large blood volumes of rabbits and sheep, these are preferred choice for production of polyclonal antibodies. However, as will be known to those skilled in the art, larger amounts of immunogen are required to obtain high antibodies from large animals as opposed to smaller animals such as mice. In such cases, it will be desirable to isolate the antibody from the immunized animal.

Preferably, the antibody is a high titer antibody. By "high titer" means a sufficiently high titer to be suitable for use in diagnostic or therapeutic applications. As will be known in the art, there is some variation in what might be considered "high titer". For most applications a titer of at least about 10³-10⁴ is preferred. More preferably, the antibody titer will be in the range from about 10⁴ to about 10^s , even more preferably in the range from about 10⁵ to about 10⁶.

More preferably, in the case of B cell epitopes from pathogens, viruses or bacteria, the antibody is a neutralizing antibody (i.e. it is capable of neutralizing the infectivity of the organism from which the B cell epitope is derived). To generate antibodies, TetR or immunogenic fragment or epitope thereof, optionally formulated with any suitable or desired carrier, adjuvant, BRM, or pharmaceutically acceptable excipient, is conveniently administered in the form of an injectable composition. Injection may be intranasal, intramuscular, sub-cutaneous, intravenous, intradermal, intraperitoneal, or by other known route. For intravenous injection, it is desirable to include one or more fluid and nutrient replenishers. Means for preparing and characterizing antibodies are well known in the art. (See, e.g., ANTIBODIES: A

LABORATORY MANUAL, Cold Spring Harbor Laboratory, 1988, incorporated herein by reference) .

Preferred immunogenic peptides for generating polyclonal or monoclonal antibodies are selected from the group set forth in the Sequence Listing. In one embodiment, an immunogenic peptide such as, for example, an immunogenic peptide comprising the amino acid sequence set forth in any one of SEQ ID NOS: 2-13 or an immunogenic fragment thereof, is covalently coupled to an immunogenic carrier protein, such as Diphtheria toxoid (DT), Keyhole Limpet Hemocyanin (KLH), tetanus toxoid (TT) or the nuclear protein of influenza virus (NP), using one of several conjugation chemistries known in the art. This enhances the immunogenicity of peptides that are otherwise not highly immunogenic in animals e.g., mice, rats, chickens etc.

Methods of preparing carrier proteins for such coupling are well known in the art. For instance, DT is preferably produced by purification of the toxin from a culture of Cotγnebacterium diphtheriae followed by chemical detoxification, but is alternatively made by purification of a recombinant, or genetically detoxified analogue of the toxin (for example, CRM197, or other mutants as described in U.S. Pat. Nos. 4,709,017, 5,843,711, 5,601,827, and 5,917,017). Preferably, the toxoid is derivatized using as a spacer a bridge of up to 6 carbons, such as provided by use of the adipic acid hydrazide derivative of diphtheria toxoid (D-AH). For coupling, peptides derived from the full-length TetR can be synthesized chemically or produced by recombinant expression means, treated with hydroxylamine to form free sulfhydryl groups, and cross-linked via the free sulfhydryl groups to a maleimide- modified diphtheria toxoid, tetanus toxoid or influenza NP protein or other carrier molecule. One of the most specific and reliable conjugation chemistries uses a cysteine residue in the peptide and a maleimide group added to the carrier protein, to form a stable thioether bond (Lee, A.C., et al, MoI Immunol. 17, 749-756 1980). For example, if no sulfhydryl groups are present in the peptide, TetR -derived peptides can be prior modified by the addition of a C-terminal cysteine residue to facilitate this procedure. The immunogenic TetR peptides are preferably produced under non- denaturing conditions, treated with hydroxylamine, thiol reducing agents or by acid or base hydrolysis to generate free sulfhydryl groups and the free sulfhydryl-containing peptide is conjugated to a carrier by chemical bonding via the free sulfhydryl groups. Such conjugation may be by use of a suitable bis-maleimide compound. Alternatively, the conjugation of the HA protein may be to a maleimide-modified carrier protein, such as diphtheria toxoid, tetanus toxoid or influenza (NP) protein or to a carbohydrate, such as alginic acid, dextran or polyethylene glycol. Such maleimide-modified carrier molecules may be formed by reaction of the carrier molecule with a hetero-bifunctional cross-linker of the maleimide-N-hydroxysuccinimide ester type. Examples of such bifunctional esters include maleimido-caproic-N-hydroxysuccinimide ester (MCS), maleimido-benzoyl-N-hydroxysuccinimide ester (MBS), maleimido-benzoylsul- fosuccinimide ester (sulfo-MBS), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1- carboxylate (SMCC), succinimidyl-4-(p-maleimido-phenyl)butyrate (SMPP), sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane- 1 -carboxylate (sulfo-SMCC) and sulfosuccinimidyl-4-(p-maleimidophenyl) butyrate (sulfo-SMPP). The N-hydroxy- succinimide ester moiety reacts with the amine groups of the carrier protein leaving the maleimide moiety free to react with the sulfhydryl groups on the antigen to form the cross-linked material. The conjugate molecules so produced may be purified and employed in immunogenic compositions to elicit, upon administration to a host, an immune response to TetR peptide which is potentiated in comparison to TetR peptide alone.

Diphtheria toxoid is obtained commercially or prepared from Corynebacterium diphtheriae grown in submerged culture by standard methods. The production of Diphtheria Toxoid is divided into five stages, namely maintenance of the working seed, growth of Corynebacterium diphtheriae, harvest of Diphtheria Toxin, detoxification of Diphtheria Toxin and concentration of Diphtheria Toxoid. The purified diphtheria toxoid (DT) used as carrier in the preparation is preferably a commercial toxoid modified (derivatized) by the attachment of a spacer molecule, such as adipic acid dihydrazide (ADH), using the water-soluble carbodiimide condensation method. The modified toxoid, typically the adipic hydrazide derivative D-AH, is then freed from unreacted ADH.

The efficacy of TetR or immunogenic fragment or epitope thereof in producing an antibody is established by injecting an animal, for example, a mouse, chicken, rat, rabbit, guinea pig, dog, horse, cow, goat or pig, with a formulation comprising TetR or immunogenic fragment or epitope thereof, and then monitoring the immune response to the B cell epitope, as described in the Examples. Both primary and secondary immune responses are monitored. The antibody titer is determined using any conventional immunoassay, such as, for example, ELISA, or radio immunoassay.

The production of polyclonal antibodies may be monitored by sampling blood of the immunized animal at various points following immunization. A second, booster injection, may be given, if required to achieve a desired antibody titer. The process of boosting and titering is repeated until a suitable titer is achieved. When a desired level of immunogenicity is obtained, the immunized animal is bled and the serum isolated and stored, and/or the animal is used to generate monoclonal antibodies (Mabs). Monoclonal antibodies are particularly preferred. For the production of monoclonal antibodies (Mabs) any one of a number of well-known techniques may be used, such as, for example, the procedure exemplified in US Patent No. 4,196,265, incorporated herein by reference.

For example, a suitable animal will be immunized with an effective amount of TetR or immunogenic fragment or epitope thereof under conditions sufficient to stimulate antibody producing cells. Rodents such as rabbits, mice and rats are preferred animals, however, the use of sheep or frog cells is also possible. The use of rats may provide certain advantages, but mice or rabbits are preferred, with the BALB/c mouse being most preferred as the most routinely used animal and one that generally gives a higher percentage of stable fusions. Rabbits are known to provide high affinity monoclonal antibodies.

Following immunization, somatic cells with the potential for producing antibodies, specifically B lymphocytes (B cells), are selected for use in the MAb generating protocol. These cells may be obtained from biopsies of spleens, tonsils or lymph nodes, or from a peripheral blood sample. Spleen cells and peripheral blood cells are preferred, the former because they are a rich source of antibody-producing cells that are in the dividing plasmablast stage, and the latter because peripheral blood is easily accessible. r

Often, a panel of animals will have been immunized and the spleen of animal with the highest antibody titer removed. Spleen lymphocytes are obtained by homogenizing the spleen with a syringe. Typically, a spleen from an immunized mouse contains approximately 5 x 10⁷ to 2 x 10⁸ lymphocytes.

The B cells from the immunized animal are then fused with cells of an immortal myeloma cell, generally derived from the same species as the animal that was immunized with TetR or immunogenic fragment or epitope thereof. Myeloma cell lines suited for use in hybridoma-producing fusion procedures preferably are non- antibody-producing, have high fusion efficiency and enzyme deficiencies that render them incapable of growing in certain selective media which support the growth of only the desired fused cells, or hybridomas. Any one of a number of myeloma cells may be used and these are known to those of skill in the art (e.g. murine P3-X63/Ag8, X63- Ag8.653, NS 1/1. Ag 4 1, Sp210-Agl4, FO, NSO/U, MPC-I l, MPC11-X45-GTG 1.7 and S194/5XX0; or rat R210.RCY3, Y3-Ag 1.2.3, IR983F and 4B210; and U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6). A preferred murine myeloma cell is the NS-I myeloma cell line (also termed P3-NS-l-Ag4-l), which is readily available from the NIGMS Human Genetic Mutant Cell Repository under Accession No. GM3573. Alternatively, a murine myeloma SP2/0 non-producer cell line that is 8- azaguanine-resistant is used.

To generate hybrids of antibody-producing spleen or lymph node cells and myeloma cells, somatic cells are mixed with myeloma cells in a proportion between about 20:1 to about 1:1 (v/v), respectively, in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes. Fusion methods using Sendai virus have been described by Kohler and Milstein, Nature 256, 495-497, 1975; and Kohler and Milstein, Eur. J. Immunol. 6, 511-519, 1976. Methods using polyethylene glycol (PEG), such as 37% (v/v) PEG, are described in detail by Gefter et al, Somatic Cell Genet. 3, 231-236, 1977. The use of electrically induced fusion methods is also appropriate.

Hybrids are amplified by culture in a selective medium comprising an agent that blocks the de novo synthesis of nucleotides in the tissue culture media. Exemplary and preferred agents are aminopterin, methotrexate and azaserine. Aminopterin and methotrexate block de novo synthesis of both purines and pyrimidines, whereas azaserine blocks only purine synthesis. Where aminopterin or methotrexate is used, the media is supplemented with hypoxanthine and thymidine as a source of nucleotides (HAT medium). Where azaserine is used, the media is supplemented with hypoxanthine.

The preferred selection medium is HAT, because only those hybridomas capable of operating nucleotide salvage pathways are able to survive in HAT medium, whereas myeloma cells are defective in key enzymes of the salvage pathway, (e.g., hypoxanthine phosphoribosyl transferase or HPRT)₅ and they cannot survive. B cells can operate this salvage pathway, but they have a limited life span in culture and generally die within about two weeks. Accordingly, the only cells that can survive in the selective media are those hybrids formed from myeloma and B cells.

The amplified hybridomas are subjected to a functional selection for antibody specificity and/or titer, such as, for example, by immunoassay (e.g. radioimmunoassay, enzyme immunoassay, cytotoxicity assay, plaque assay, dot immunoassay, and the like).

The selected hybridomas are serially diluted and cloned into individual antibody- producing cell lines, which clones can then be propagated indefinitely to provide MAbs. The cell lines may be exploited for MAb production in two basic ways. A sample of the hybridoma is injected, usually in the peritoneal cavity, into a histocompatible animal of the type that was used to provide the somatic and myeloma cells for the original fusion. The injected animal develops tumors secreting the specific monoclonal antibody produced by the fused cell hybrid. The body fluids of the animal, such as serum or ascites fluid, can then be tapped to provide MAbs in high concentration. The individual cell lines could also be cultured in vitro, where the MAbs are naturally secreted into the culture medium from which they are readily obtained in high concentrations. MAbs produced by either means may be further purified, if desired, using filtration, centrifugation and various chromatographic methods such as HPLC or affinity chromatography.

Alternatively, ABL-MYC technology (NeoClone, Madison WI 53713, USA) is used to produce cell lines secreting monoclonal antibodies (mAbs) against immunogenic TetR peptide antigens. In this process, BALB/cByJ female mice are immunized with an amount of the peptide antigen over a period of about 2 to about 3 months. During this time, test bleeds are taken from the immunized mice at regular intervals to assess antibody responses in a standard ELISA. The spleens of mice having antibody titers of at least about 1,000 are used for subsequent ABL-MYC infection employing replication-incompetent retrovirus comprising the oncogenes v-abl and c-myc. Splenocytes are transplanted into naive mice which then develop ascites fluid containing cell lines producing monoclonal antibodies (mAbs) against TetR peptide antigen. The mAbs are purified from ascites using protein G or protein A, e.g., bound to a solid matrix, depending on the isotype of the mAb. Because there is no hybridoma fusion, an advantage of the ABL-MYC process is that it is faster, more cost effective, and higher yielding than conventional mAb production methods. In addition, the diploid plasmacytomas produced by this method are intrinsically more stable than polyploid hybridomas, because the ABL-MYC retrovirus infects only cells in the spleen that have been stimulated by the immunizing antigen. ABL-MYC then transforms those activated B-cells into immortal, mAb-producing plasma cells called plasmacytomas. A "plasmacytoma" is an immortalized plasma cell that is capable of uncontrolled cell division. Since a plasmacytoma begins with just one cell, all of the plasmacytomas produced from it are therefore identical, and moreover, produce the same desired "monoclonal" antibody. As a result, no sorting of undesirable cell lines is required. The ABL-MYC technology is described generically in detail in the following disclosures which are incorporated by reference herein: 1. Largaespada et α/., Curr. Top. Microbiol. Immunol, 166, 91-96. 1990; 2. Weissinger et al.Proc. Natl. Acad. Sci. USA, 88, 8735-8739, 1991;

3. Largaespada et al, Oncogene, 7, 811 -819, 1992;

4. Weissinger et al, J. Immunol Methods 168, 123-130, 1994;

5. Largaespada et al, J. Immunol. Methods. 197(1-2), 85-95, 1996; and

6. Kumar et al, Immuno. Letters 65, 153-159, 1999.

Monoclonal antibodies of the present invention also include anti-idiotypic antibodies produced by methods well-known in the art. Monoclonal antibodies according to the present invention also may be monoclonal heteroconjugates, (i.e., hybrids of two or more antibody molecules). In another embodiment, monoclonal antibodies according to the invention are chimeric monoclonal antibodies. In one approach, the chimeric monoclonal antibody is engineered by cloning recombinant DNA containing the promoter, leader, and variable-region sequences from a mouse anti-PSA producing cell and the constant-region exons from a human antibody gene. The antibody encoded by such a recombinant gene is a mouse-human chimera. Its antibody specificity is determined by the variable region derived from mouse sequences. Its isotype, which is determined by the constant region, is derived from human DNA.

In another embodiment, the monoclonal antibody according to the present invention is a "humanized" monoclonal antibody, produced by any one of a number of techniques well-known in the art. That is, mouse complementary determining regions ("CDRs") are transferred from heavy and light V-chains of the mouse Ig into a human V-domain, followed by the replacement of some human residues in the framework regions of their murine counterparts. "Humanized" monoclonal antibodies in accordance with this invention are especially suitable for use in vivo in diagnostic and therapeutic methods.

As stated above, the monoclonal antibodies and fragments thereof according to this invention are multiplied according to in vitro and in vivo methods well-known in the art. Multiplication in vitro is carried out in suitable culture media such as Dulbecco's modified Eagle medium or RPMI 1640 medium, optionally replenished by a mammalian serum such as fetal calf serum or trace elements and growth-sustaining supplements, e.g., feeder cells, such as normal mouse peritoneal exudate cells, spleen cells, bone marrow macrophages or the like. In vitro production provides relatively pure antibody preparations and allows scale-up to give large amounts of the desired antibodies. Techniques for large scale hybridoma cultivation under tissue culture conditions are known in the art and include homogenous suspension culture, (e.g., in an airlift reactor or in a continuous stirrer reactor or immobilized or entrapped cell culture).

Large amounts of the monoclonal antibody of the present invention also may be obtained by multiplying hybridoma cells in vivo. Cell clones are injected into mammals which are histocompatible with the parent cells, (e.g., syngeneic mice, to cause growth of antibody-producing tumors. Optionally, the animals are primed with a hydrocarbon, especially oils such as Pristane (tetramethylpentadecane) prior to injection.

In accordance with the present invention, fragments of the monoclonal antibody of the invention are obtained from monoclonal antibodies produced as described above, by methods which include digestion with enzymes such as pepsin or papain and/or cleavage of disulfide bonds by chemical reduction. Alternatively, monoclonal antibody fragments encompassed by the present invention are synthesized using an automated peptide synthesizer, or they may be produced manually using techniques well known in the art.

The monoclonal conjugates of the present invention are prepared by methods known in the art, e.g., by reacting a monoclonal antibody prepared as described above with, for instance, an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate. Conjugates with fluorescein markers are prepared in the presence of these coupling agents, or by reaction with an isothiocyanate. Conjugates with metal chelates are similarly produced. Other moieties to which antibodies may be conjugated include radionuclides such as, for example, ³H, ¹²⁵1, ³²P, ³⁵S, ¹⁴C, ⁵¹Cr, ³⁶Cl, ⁵⁷Co, ⁵⁸Co, ⁵⁹Fe₅ ⁷⁵Se, and ¹⁵²Eu.

The present invention clearly includes antibodies when coupled to any detectable ligand or reagent, including, for example, an enzyme such as horseradish peroxidase or alkaline phosphatase, or a fluorophore, radionuclide, coloured dye, gold particle, colloidal gold, etc.

Radioactively labelled monoclonal antibodies of the present invention are produced according to well-known methods in the art. For instance, monoclonal antibodies are iodinated by contact with sodium or potassium iodide and a chemical oxidizing agent such as sodium hypochlorite, or an enzymatic oxidizing agent, such as lactoperoxidase. Monoclonal antibodies according to the invention may be labelled with technetium" by ligand exchange process, for example, by reducing pertechnate with stannous solution, chelating the reduced technetium onto a Sephadex column and applying the antibody to this column or by direct labelling techniques, (e.g., by incubating pertechnate, a reducing agent such as SNCl₂, a buffer solution such as sodium-potassium phthalate solution, and the antibody).

A variety of techniques for the recombinant antibody production and manipulation are well known in the art or available from commercial sources.

To produce recombinant antibodies, genetic material encoding antibodies is isolated from a hybridoma cell line produced as described herein, or alternatively, amplified by polymerase chain reaction amplification using degenerate primers to prime antibody- producing cells obtained from an immunized animal, inserted into a vector and expressed in a suitable host e.g., a bacterium such as E. coli. Recombinant antibodies are then selected by any one of a number of techniques, of which the most commonly- used are phage display, ribosome display and yeast display. In phage display, host cells are infected with phagemid vectors bearing antibody gene fragments fused to a phage coat protein gene, and host cells carrying the phagemid are selected for expression of an antibiotic resistance marker. The cloned antibody genes are expressed as a fusion protein consisting of a bacterial 'leader sequence,' the antibody gene fragment, and the phage coat protein. The leader sequence directs the proteins to the periplasmic space, where the fused antibody fragment is incorporated into viable phage particles via the coat protein. Phage are secreted through the host cell's outer membrane and display one copy of the encoded antibody fragment. Phage displaying the desired antibodies are selected by 'phage panning,' which is somewhat similar to solid-phase immunoassay. In this process, the antigen of interest is immobilized on microplate wells, on magnetic beads, or on a column. The phage are then added. After extensive washing to remove all non-specific material, the bound phage are eluted and amplified by replication in new host cells. The selection procedure is repeated several times, resulting in a population that consists almost entirely of phage that express the desired antibodies (i.e. those that bind the antigen of interest). After this selection step, the antibody genes are isolated and inserted into an expression vector. To produce soluble antibody fragments, the antibody genes cloned into the phagemid must be expressed without the phage coat protein. Cloned Fab fragments are obtained by isolating the Fab genes for light and heavy chains using restriction enzymes or PCR amplification and religating them into a new vector that does not contain the phage protein gene. Following introduction into new host cells, the transformed cells are isolated as single colonies, each producing a defined, and therefore monoclonal, antibody. Antibodies are obtained from cell lysates. Soluble antibody fragments (e.g. Fab or scFv) produced by bacterial colonies, are typically purified by one-step affinity chromatography using peptide tags that have been fused to the C-terminus of the antibody fragment. A commonly used peptide tag for this step is the hexahistidine tag complexed by metal chelates such as Ni-NTA. To mimic the affinity and avidity of IgG, recombinant antibody fragments can be dimerized or further multimerized by engineering.

Phage display technology is described in detail e.g., in U.S. Pat. Nos. 5,565,332; 5,580,717; 5,733,743 and 6,265,150; and by Winter et al, Annu. Rev. Immunol. 12, 433-455 (1994), each of which is incorporated herein by way of reference.

McCafferty et al, Nature 348, 552-553 (1990) describes the use of phage display technology to produce human antibodies and antibody fragments in vitro from immunoglobulin variable (VH and/or V_L) domain gene repertoires of non-immunized donors. According to this technique, antibody V domain genes are cloned in-frame into either a major or minor coat protein gene of a filamentous bacteriophage, such as M 13 or fd, and displayed as functional antibody fragments on the surface of the phage particle. Because the filamentous particle contains a single-stranded DNA copy of the phage genome, selections based on the functional properties of the antibody also result in selection of the gene encoding the antibody exhibiting those properties. Thus, the phage mimics some of the properties of the B cell. Phage display is amenable to a variety of formats e.g., as described by Johnson et al, Curr. Opinion Structural Biol. 3, 564-571 (1993).

Several sources of V-gene segments can be used for phage display. For example, Clackson et al, Nature 352, 624-628 (1991) isolated a diverse array of anti-oxazolone antibodies from a small random combinatorial library of V genes derived from the spleens of immunized mice. A repertoire of V genes from unimmunized human donors can be constructed and antibodies to a diverse array of antigens (including self- antigens) can be isolated essentially following the techniques described by Mark et al, J. MoI Biol 222, 581-597 (1991), or Griffith et al, EMBO J. 12, 725-734 (1993).

The affinity of a primaryr recombinant antibody can also be enhanced by sequentially replacing the heavy and light chain V region genes with repertoires of naturally occurring variants (repertoires) of V domain genes obtained from unimmunized donors. This technique allows the production of antibodies and antibody fragments with affinities in the pM-nM range. A strategy for making very large phage antibody repertoires has been described by Waterhouse et al, Nucl Acids Res. 21, 2265-2266 (1993). Gene shuffling can also be used to derive human antibodies from rodent antibodies, where the human antibody has similar affinities and specificities to the starting rodent antibody. According to this method, which is also referred to as "epitope imprinting", the heavy or light chain V domain gene of rodent antibodies obtained by phage display technique is replaced with a repertoire of human V domain genes, creating rodent-human chimeras. Selection on antigen results in isolation of human variable regions capable of restoring a functional antigen-binding site, i.e., the epitope governs (imprints) the choice of partner. When the process is repeated in order to replace the remaining rodent V domain, a human antibody is obtained (WO 93/06213, published Apr. 1, 1993). Unlike traditional humanization of rodent antibodies by CDR grafting, this technique provides completely human antibodies, which have no framework or CDR residues of rodent origin. Chimeric or hybrid antibodies also may be prepared in vitro using known methods of synthetic protein chemistry, including those involving cross-linking agents. For example, immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate.

Single chain Fv fragments may also be produced, such as described by Iliades et al, FEBS Letters, 409, 437-441 (1997). Coupling of such single chain fragments using various linkers is described in Kortt et al, Protein Engineering, 10, 423-433 (1997).

Any immunoassay may be used to monitor antibody production by TetR or immunogenic fragment or epitope thereof . Immunoassays, in their most simple and direct sense, are binding assays. Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs) and radioimmunoassays (RIA) known in the art. Immunohistochemical detection using tissue sections is also particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and Western blotting, dot blotting, FACS analyses, and the like may also be used.

Most preferably, the assay will be capable of generating quantitative results.

For example, antibodies are tested in simple competition assays. A known antibody preparation that binds to the B cell epitope and the test antibody are incubated with an antigen composition comprising the B cell epitope, preferably in the context of the native antigen. "Antigen composition" as used herein means any composition that contains some version of the B cell epitope in an accessible form. Antigen-coated wells of an ELISA plate are particularly preferred. In one embodiment, one would pre-mix the known antibodies with varying amounts of the test antibodies (e.g., 1:1 (v/v), 1:10 (v/v) and 1:100 (v/v)) for a period of time prior to applying to the antigen composition. If one of the known antibodies is labelled, direct detection of the label bound to the antigen is possible; comparison to an unmixed sample assay will determine competition by the test antibody and, hence, cross-reactivity. Alternatively, using secondary antibodies specific for either the known or test antibody, one will be able to determine competition.

An antibody that binds to the antigen composition will be able to effectively compete for binding of the known antibody and thus will significantly reduce binding of the latter. The reactivity of the known antibodies in the absence of any test antibody is the control. A significant reduction in reactivity in the presence of a test antibody is indicative of a test antibody that binds to the B cell epitope (i.e., it cross-reacts with the known antibody).

In one exemplary ELISA, the antibodies that bind to TetR or immunogenic fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a composition containing a peptide comprising the B cell epitope is added to the wells. After binding and washing to remove non-specifically bound immune complexes, the bound epitope may be detected. Detection is generally achieved by the addition of a second antibody that is known to bind to the B cell epitope and is linked to a detectable label. This type of ELISA is a simple "sandwich ELISA". Detection may also be achieved by the addition of said second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.

In an alternative embodiment (i.e., amplified ELISA), antibodies that bind to TetR or immunogenic fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate. Then, a composition containing a peptide comprising the B cell epitope is added to the wells. After binding and washing to remove non-specifically bound immune complexes, antibodies that bind to the B cell epitope are contacted with the bound peptide for a time and under conditions sufficient for a complex to form. The signal is then amplified using secondary and preferably tertiary, antibodies that bind to the antibodies recognising the B cell epitope. Detection is then achieved by the addition of a further antibody that is known to bind to the secondary or tertiary antibodies, linked to a detectable label.

In another exemplary immunoassay format applicable to both flow through and solid phase ELISA, antibodies that bind to the immunogenic TetR or immunogenic TetR peptide or immunogenic TetR fragment or B cell epitope are immobilized onto a selected surface exhibiting protein affinity, such as a well in a polystyrene microtiter plate or a column. A sample comprising the immunogenic TetR or immunogenic peptide or immunogenic fragment comprising the B cell epitope to which the antibody binds is added for a time and under conditions sufficient for an antigen-antibody complex to form. In this case, the added putative transcriptional regulatory protein TetR, or TetR-derived peptide or fragment is complexed with human Ig. In the case of patient sera, for example, the peptide is preferably complexed with human Ig by virtue of an immune response of the patient to the M. tuberculosis putative transcriptional regulatory protein TetR, or TetR-derived peptide. After binding and washing to remove non-specifically bound immune complexes, the bound epitope is detected by the addition of a second antibody that is known to bind to human Ig in the immune complex and is linked to a detectable label. This is a modified "sandwich ELISA". Detection may also be achieved by the addition of said second antibody, followed by the addition of a third antibody that has binding affinity for the second antibody, with the third antibody being linked to a detectable label.

Antibodies of the invention may be bound to a solid support and/or packaged into kits in a suitable container along with suitable reagents, controls, instructions and the like.

Antibodies that bind to a secondary analyte

It is to be understood that methods described herein above for the production of antibodies against TetR or an immunogenic fragment thereof apply mutatis mutandis to the production of antibodies against a secondary analyte that is to be used in an immunoassay format e.g., for the purposes of diagnosis or prognosis of tuberculosis or infection by M. tuberculosis. As will be understood by the skilled artisan, such extrapolation is dependent on substituting TetR immunogen for the secondary analyte in question e.g., M. tuberculosis Bsx protein or GS protein or S9 protein or immunogenic fragment thereof according to any embodiment described herein. Such substitution is readily performed without undue experimentation from the disclosure herein.

For convenience, preferred immunizing peptides for the production of antibodies against secondary analytes e.g., for use in multi-analyte antigen-based tests, will comprise an amino acid sequence selected from the group set forth in SEQ ID NOs: 14- 26 and combinations/mixtures thereof.

For example, antibodies that bind to M. tuberculosis Bsx protein can be prepared from the full-length protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 053759) or from a peptide fragment thereof e.g., comprising a sequence selected from the group consisting of: MRQLAERS GVSNPYL (SEQ ID NO: 14), ERGLRKPSADVLSQI (SEQ ID NO: 15), LRKPSAD VLSQIAKA (SEQ ID NO: 16), PSADVLSQIAKALRV (SEQ ID NO: 17), SQIAKALRVSAEVLY (SEQ ID NO: 18), AKALRVSAEVLYVRA (SEQ ID NO: 19), VRAGILEPSETSQVR (SEQ ID NO: 20), TAITERQKQILLDIY (SEQ ID NO: 21), S QI AKALRVS AEVL Y VRAC (SEQ ID NO: 22), MSSEEKLCDPTPTDD (SEQ ID NO: 23) and VRAGILEPSETSQVRC (SEQ ID NO: 24) and combinations/mixtures thereof. Antibodies that bind to an immunogenic M. tuberculosis Bsx protein or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co- pending International Patent Application No. PCT/AU2005/001254 filed August 19, 2005 (WO 2006/01792) the disclosure of which is incorporated herein in its entirety.

Alternatively, or in addition, antibodies that bind to M. tuberculosis glutamine synthetase (GS) protein (e.g., comprising the sequence set forth in SwissProt Database Accession No. 033342) or from an immunogenic peptide derived thereof, e.g., comprising a surface-exposed region of a GS protein, or comprising the sequence RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 25) and/or WASGYRGLTPASDYNIDYAI (SEQ ID NO: 26). Antibodies that bind to an immunogenic M. tuberculosis GS or peptide for detecting tuberculosis or infection by M. tuberculosis are also described in detail in the instant applicant's co-pending International Patent Application No. PCT/AU2005/000930 filed June 24 2005 (WO 2006/000045) the disclosure of which is incorporated herein in its entirety.

The present invention clearly contemplates antibodies against secondary analytes other than Bsx or GS or S9 or immunogenic fragments thereof, the description of which is provided for the purposes of exemplification.

Diagnostic/prognostic methods for detecting tuberculosis or M. tuberculosis infection

1. Antigen-based assays

This invention provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject a TetR or an immunogenic fragment or epitope thereof, wherein the presence of said protein or immunogenic fragment or epitope in the sample is indicative of infection.

One advantage of detecting M. tuberculosis antigen, as opposed to an antibody-based assay is that severely immunocompromised patients may not produce antibody at detectable levels, and the level of the antibody in any patient does not reflect bacilli burden. On the other hand antigen levels should reflect bacilli burden and, being a product of the bacilli, are a direct method of detecting its presence.

In one embodiment of the diagnostic assays of the invention, there is provided a method for detecting M. tuberculosis infection in a subject, the method comprising contacting a biological sample derived from the subject with an antibody capable of binding to a TetR or an immunogenic fragment or epitope thereof, and detecting the formation of an antigen-antibody complex.

In another embodiment, the diagnostic assays of the invention are useful for determining the progression of tuberculosis or an infection by M. tuberculosis in a subject. In accordance with these prognostic applications of the invention, the level of TetR or an immunogenic fragment or epitope thereof in a biological sample is positively correlated with the infectious state. For example, a level of TetR or an immunogenic fragment thereof that is less than the level of TetR or fragment detectable in a subject suffering from the symptoms of tuberculosis or an infection indicates that the subject is recovering from the infection. Similarly, a higher level of the protein or fragment in a sample from the subject compared to a healthy individual indicates that the subject has not been rendered free of the disease or infection.

Accordingly, a further embodiment of the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is enhanced compared to the level of that protein or fragment or epitope detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection.

In an alternative embodiment, the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is lower than the level of the protein or fragment or epitope detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection. Clearly, if the level of TetR or fragment or epitope thereof is not detectable in the subject, the subject has responded to treatment.

In a further embodiment, the amount of a TetR in a biological sample derived from a patient is compared to the amount of the same protein detected in a biological sample previously derived from the same patient. As will be apparent to a person skilled in the art, this method may be used to continually monitor a patient with a latent infection or a patient that has developed tuberculosis. In this way a patient may be monitored for the onset or progression of an infection or disease, with the goal of commencing treatment before an infection is established, particularly in an HIV+ individual.

Alternatively, or in addition, the amount of a protein detected in a biological sample derived from a subject with tuberculosis may be compared to a reference sample, wherein the reference sample is derived from one or more tuberculosis patients that do not suffer from an infection or disease or alternatively, one or more tuberculosis patients that have recently received successful treatment for infection and/or one or more subjects that do not have tuberculosis and that do not suffer from an infection or disease.

In one embodiment, a TetR or immunogenic fragment thereof is not detected in a reference sample, however, said TetR or immunogenic fragment thereof is detected in the patient sample, indicating that the patient from whom the sample was derived is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection.

Alternatively, the amount of TetR or immunogenic fragment thereof may be enhanced in the patient sample compared to the level detected in a reference sample. Again, this indicates that the patient from whom the biological sample was isolated is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection.

In one embodiment of the diagnostic/prognostic methods described herein, the biological sample is obtained previously from the subject. In accordance with such an embodiment, the prognostic or diagnostic method is performed ex vivo. In yet another embodiment, the subject diagnostic/prognostic methods further comprise processing the sample from the subject to produce a derivative or extract that comprises the analyte (eg., pleural fluid or sputum or serum).

Suitable samples include extracts from tissues such as brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle and bone tissues, or body fluids such as sputum, serum, plasma, whole blood, sera or pleural fluid.

Preferably, the biological sample is a bodily fluid or tissue sample selected from the group consisting of: saliva, plasma, blood, serum, sputum, urine, and lung. Other samples are not excluded.

It will be apparent from the description herein that preferred samples may comprise circulating immune complexes comprising TetR or fragments thereof complexed with human immunoglobulin. The detection of such immune complexes is clearly within the scope of the present invention. In accordance with this embodiment, a capture reagent e.g., a capture antibody is used to capture TetR antigen (TetR polypeptide or an immunoactive fragment or epitope thereof) complexed with the subject's immunoglobulin, in addition to isolated antigen in the subject's circulation. Anti-Ig antibodies, optionally conjugated to a detectable label, are used to specifically bind the captured CIC thereby detecting CIC patient samples. Within the scope of this invention, the anti-Ig antibody binds preferentially to IgM, IgA or IgG in the sample. In a particularly preferred embodiment, the anti-Ig antibody binds to human Ig, e.g., human IgA, human IgG or human IgM. The anti-Ig antibody may be conjugated to any standard detectable label known in the art. This is particularly useful for detecting infection by a pathogenic agent, e.g., a bacterium or virus, or for the diagnosis of any disease or disorder associated with CICs. Accordingly, the diagnostic methods described according to any embodiment herein are amenable to a modification wherein the sample derived from the subject comprises one or more circulating immune complexes comprising immunoglobulin (Ig) bound to TetR of Mycobacterium tuberculosis or one or more immunogenic TetR peptides, fragments or epitopes thereof and wherein detecting the formation of an antigen-antibody complex comprises contacting an anti-Ig antibody with an immunoglobulin moiety of the circulating immune complex(es) for a time and under conditions sufficient for a complex to form than then detecting the bound anti-Ig antibody.

The present invention clearly encompasses multianalyte tests for diagnosing infection by M. tuberculosis. For example, assays for detecting antibodies that bind to M. tuberculosis TetR can be combined with assays for detecting M. tuberculosis Bsx or glutamine synthetase (GS) protein. In this respect, the present inventors have also produced plasmacytomas producing monoclonal antibodies that bind to an immunogenic fragment or peptide or epitope of Bsx or GS or S9.

2. Antibody-based assays

The present invention provides a method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject antibodies that bind to a TetR or an immunogenic fragment or epitope thereof, wherein the presence of said antibodies in the sample is indicative of infection. The infection may be a past or present infection, or a latent infection.

Antibody-based assays are primarily used for detecting active infections by M. tuberculosis. Preferably, the clinical history of the subject is considered due to residual antibody levels that may persist in recent past infections or chronic infections by M. tuberculosis.

The format is inexpensive and highly sensitive, however not as useful as an antigen- based assay format for detecting infection in immunocompromised individuals. However, antibody-based assays are clearly useful for detecting M. tuberculosis infections in HIV^" or HIV⁺ individuals who are not immunocompromised.

In one alternative embodiment, the present invention provides a method for detecting M. tuberculosis infection in a subject, the method comprising contacting a biological sample derived from the subject with a TetR or an immunogenic fragment or epitope thereof and detecting the formation of an antigen-antibody complex.

In the antibody based assays described herein, it is preferred that TetR or immunogenic fragment or epitope thereof used to detect the antibodies is not highly cross-reactive with anti-sera from non-infected subjects. Accordingly, recombinant TetR or SEQ ID NO: 12 is preferred for use in the antibody-based assay platforms described herein.

In another embodiment, the diagnostic assays of the invention are useful for determining the progression of tuberculosis or an infection by M. tuberculosis in a subject. In accordance with these prognostic applications of the invention, the amount of antibodies that bind to a TetR or fragment or epitope in blood or serum, plasma, or an immunoglobulin fraction from the subject is positively correlated with the infectious state. For example, a level of the anti-TetR antibodies thereto that is less than the level of the anti-TetR antibodies detectable in a subject suffering from the symptoms of tuberculosis or an infection indicates that the subject is recovering from the infection. Similarly, a higher level of the antibodies in a sample from the subject compared to a healthy individual indicates that the subject has not been rendered free of the disease or infection.

In a further embodiment of the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting antibodies that bind to a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the antibodies that is enhanced compared to the level of the antibodies detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection. Again, SEQ ID NO: 12 is preferred. In an alternative embodiment, the present invention provides a method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting antibodies that bind to a TetR or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the antibodies that is lower than the level of the antibodies detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection.

The amount of an antibody against TetR or fragment that is detected in a biological sample from a subject with tuberculosis may be compared to a reference sample, wherein the reference sample is derived from one or more healthy subjects who have not been previously infected with M. tuberculosis or not recently-infected with M. tuberculosis. Such negative control subjects will have a low circulating antibody titer making them suitable standards in antibody-based assay formats. For example, antibodies that bind to a TetR or immunogenic fragment thereof are not detected in the reference sample and only in a patient sample, indicating that the patient from whom the sample was derived is suffering from tuberculosis or infection by M. tuberculosis or will develop an acute infection. A peptide comprising SEQ ID NO: 12 is preferred for use in such embodiments.

In one embodiment of the diagnostic/prognostic methods described herein, the biological sample is obtained previously from the subject. In accordance with such an embodiment, the prognostic or diagnostic method is performed ex vivo.

In yet another embodiment, the subject diagnostic/prognostic methods further comprise processing the sample from the subject to produce a derivative or extract that comprises the analyte (e.g., blood, serum, plasma, or any immunoglobulin-containing sample).

Suitable samples include, for example, extracts from tissues comprising an immunoglobulin such as blood, bone, or body fluids such as serum, plasma, whole blood, an immunoglobulin-containing fraction of serum, an immunoglobulin- containing fraction of plasma, an immunoglobulin-containing fraction of blood.

3. Detection systems Preferred detection systems contemplated herein include any known assay for detecting proteins or antibodies in a biological sample isolated from a human subject, such as, for example, SDS/PAGE, isoelectric focusing, 2-dimensional gel electrophoresis comprising SDS/PAGE and isoelectric focusing, an immunoassay, a detection based system using an antibody or non-antibody ligand of the protein, such as, for example, a small molecule (e.g. a chemical compound, agonist, antagonist, allosteric modulator, competitive inhibitor, or non-competitive inhibitor, of the protein). In accordance with these embodiments, the antibody or small molecule may be used in any standard solid phase or solution phase assay format amenable to the detection of proteins. Optical or fluorescent detection, such as, for example, using mass spectrometry, MALDI-TOF, biosensor technology, evanescent fiber optics, or fluorescence resonance energy transfer, is clearly encompassed by the present invention. Assay systems suitable for use in high throughput screening of mass samples, particularly a high throughput spectroscopy resonance method (e.g. MALDI-TOF, electrospray MS or nano- ^~ electrospray MS), are particularly contemplated.

Immunoassay formats are particularly preferred, e.g., selected from the group consisting of, an immunoblot, a Western blot, a dot blot, an enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), enzyme immunoassay. Modified immunoassays utilizing fluorescence resonance energy transfer (FRET), isotope-coded affinity tags (ICAT), mass spectrometry, e.g., matrix-assisted laser desorption/ionization time of flight (MALDI-TOF), electrospray ionization (ESI), biosensor technology, evanescent fiber-optics technology or protein chip technology are also useful.

Preferably, the assay is a semi-quantitative assay or quantitative assay. Standard solid phase ELISA formats are particularly useful in determining the concentration of a protein or antibody from a variety of patient samples.

In one form such as an assay involves immobilising a biological sample comprising anti-TetR antibodies, or alternatively TetR or an immunogenic fragment thereof, onto a solid matrix, such as, for example a polystyrene or polycarbonate microwell or dipstick, a membrane, or a glass support (e.g. a glass slide).

In the case of an antigen-based assay, an immobilised antibody that specifically binds a TetR is brought into direct contact with the biological sample, and forms a direct bond with any of its target protein present in said sample. For an antibody-based assay, an immobilised isolated or recombinant TetR or an immunogenic fragment or epitope thereof will be contacted with the biological sample. The added antibody or protein in solution is generally labelled with a detectable reporter molecule, such as for example, colloidal gold, a fluorescent label (e.g. FITC or Texas Red) or an enzyme (e.g. horseradish peroxidase (HRP)), alkaline phosphatase (AP) or β-galactosidase.

Alternatively, or in addition, a second labelled antibody can be used that binds to the first antibody or to the isolated/recombinant TetR antigen. Following washing to remove any unbound antibody or TetR antigen, the label may be detected either directly, in the case of a fluorescent label, or through the addition of a substrate, such as for example hydrogen peroxide, TMB, or toluidine, or 5-bromo-4-chloro-3-indol-beta-

D-galaotopyranoside (x-gal).

Such ELISA based systems are particularly suitable for quantification of the amount of a protein or antibody in a sample, such as, for example, by calibrating the detection system against known amounts of a standard.

In another form, an ELISA consists of immobilizing an antibody that specifically binds a TetR on a solid matrix, such as, for example, a membrane, a polystyrene or polycarbonate microwell, a polystyrene or polycarbonate dipstick or a glass support. A patient sample is then brought into physical relation with said antibody, and the antigen in the sample is bound or 'captured'. The bound protein can then be detected using a labelled antibody. For example if the protein is captured from a human sample, an anti- human antibody is used to detect the captured protein.

One example of this embodiment of the invention comprises:

(i) immobilizing an antibody that specifically binds an immunogenic TetR peptide (e.g., a peptide comprising a sequence set forth in any one or more of SEQ ID NOs: 2-13 or a mixture thereof) to a solid matrix or support;

(ii) contacting the bound antibody with a sample obtained from a subject, preferably an antibody-containing sample such as blood, serum, or Ig-containing fraction thereof for a time and under conditions sufficient for the immobilized antibody to bind to an TetR or fragment thereof in the sample thereby forming an antigen- antibody complex; and

(iii) detecting the antigen-antibody complex formed in a process comprising contacting said complex with an antibody that recognizes human Ig, wherein the presence of said human Ig indicates the presence of M. tuberculosis in the patient sample.

In accordance with this embodiment, specificity of the immobilized antibody ensures that isolated or immunocomplexed TetR or fragments comprising the epitope that the antibody recognizes actually bind, whilst specificity of anti-human Ig ensures that only immunocomplexed TetR or fragment is detected. In this context, the term

"immunocomplexed" shall be taken to mean that TetR or fragments thereof in the patient sample are complexed with human Ig such as human IgA or human IgM or human IgG, etc. Accordingly, this embodiment is particularly useful for detecting the presence of M. tuberculosis or an infection by M. tuberculosis that has produced an immune response in a subject. By appropriately selecting the detection antibody, e.g., anti-human IgA or anti-human IgG or anti-human IgM, it is further possible to isotype the immune response of the subject. Such detection antibodies that bind to human IgA, IgM and IgG are publicly available to the art. Alternatively or in addition to the preceding embodiments, a third labelled antibody can be used that binds the second (detecting) antibody.

It will be apparent to the skilled person that the assay formats described herein are amenable to high throughput formats, such as, for example automation of screening processes, or a microarray format as described in Mendoza et al, Biotechniques 27(4): 778-788, 1999. Furthermore, variations of the above described assay will be apparent to those skilled in the art, such as, for example, a competitive ELISA.

Alternatively, the presence of anti-TetR antibodies, or alternatively a TetR or an immunogenic fragment thereof, is detected using a radioimmunoassay (RIA). The basic principle of the assay is the use of a radiolabeled antibody or antigen to detect antibody antigen interactions. For example, an antibody that specifically binds to a TetR can be bound to a solid support and a biological sample brought into direct contact with said antibody. To detect the bound antigen, an isolated and/or recombinant form of the antigen is radiolabeled is brought into contact with the same antibody. Following washing the amount of bound radioactivity is detected. As any antigen in the biological sample inhibits binding of the radiolabeled antigen the amount of radioactivity detected is inversely proportional to the amount of antigen in the sample. Such an assay may be quantitated by using a standard curve using increasing known concentrations of the isolated antigen.

As will be apparent to the skilled artisan, such an assay may be modified to use any reporter molecule, such as, for example, an enzyme or a fluorescent molecule, in place of a radioactive label.

Western blotting is also useful for detecting a TetR or an immunogenic fragment thereof. In such an assay, protein from a biological sample is separated using sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis (SDS-PAGE) using techniques well known in the art and described in, for example, Scopes (In± Protein Purification: Principles and Practice, Third Edition, Springer Verlag, 1994). Separated proteins are then transferred to a solid support, such as, for example, a membrane or more specifically, nitrocellulose membrane, nylon membrane or PVDF membrane, using methods well known in the art, for example, electrotransfer. This membrane may then be blocked and probed with a labelled antibody or ligand that specifically binds a putative transcriptional regulatory protein TetR, or TetR-derived peptide. Alternatively, a labelled secondary, or even tertiary, antibody or ligand can be used to detect the binding of a specific primary antibody.

High-throughput methods for detecting the presence or absence of anti-TetR antibodies, or alternatively TetR or an immunogenic fragment thereof are particularly preferred.

In one embodiment, mass spectrometry, e.g., MALDI-TOF is used for the rapid identification of a protein that has been separated by either one- or two-dimensional gel electrophoresis. Accordingly, there is no need to detect the proteins of interest using an antibody or ligand that specifically binds to the protein of interest. Rather, proteins from a biological sample are separated using gel electrophoresis using methods well known in the art and those proteins at approximately the correct molecular weight and/or isoelectric point are analysed using MALDI-TOF to determine the presence or absence of a protein of interest.

Alternatively, mass spectrometry, e.g., MALDI or ESI, or a combination of approaches is used to determine the concentration of a particular protein in a biological sample, such as, for example sputum. Such proteins are preferably well characterised previously with regard to parameters such as molecular weight and isoelectric point.

Biosensor devices generally employ an electrode surface in combination with current or impedance measuring elements to be integrated into a device in combination with the assay substrate (such as that described in U.S. Patent No. 5,567,301). An antibody or ligand that specifically binds to a protein of interest is preferably incorporated onto the surface of a biosensor device and a biological sample isolated from a patient (for example sputum that has been solubilised using the methods described herein) contacted to said device. A change in the detected current or impedance by the biosensor device indicates protein binding to said antibody or ligand. Some forms of biosensors known in the art also rely on surface plasmon resonance to detect protein interactions, whereby a change in the surface plasmon resonance surface of reflection is indicative of a protein binding to a ligand or antibody (U.S. Patent No. 5,485,277 and 5,492,840).

Biosensors are of particular use in high throughput analysis due to the ease of adapting such systems to micro- or nano-scales. Furthermore, such systems are conveniently adapted to incorporate several detection reagents, allowing for multiplexing of diagnostic reagents in a single biosensor unit. This permits the simultaneous detection of several epitopes in a small amount of body fluids.

Evanescent biosensors are also preferred as they do not require the pretreatment of a biological sample prior to detection of a protein of interest. An evanescent biosensor generally relies upon light of a predetermined wavelength interacting with a fluorescent molecule, such as for example, a fluorescent antibody attached near the probe's surface, to emit fluorescence at a different wavelength upon binding of the diagnostic protein to the antibody or ligand.

To produce protein chips, the proteins, peptides, polypeptides, antibodies or ligands that are able to bind specific antibodies or proteins of interest are bound to a solid support such as for example glass, polycarbonate, polytetrafluoroethylene, polystyrene, silicon oxide, metal or silicon nitride. This immobilization is either direct (e.g. by covalent linkage, such as, for example, Schiff s base formation, disulfide linkage, or amide or urea bond formation) or indirect. Methods of generating a protein chip are known in the art and are described in for example U.S. Patent Application No. 20020136821, 20020192654, 20020102617 and U.S. Patent No. 6,391,625. In order to bind a protein to a solid support it is often necessary to treat the solid support so as to create chemically reactive groups on the surface, such as, for example, with an aldehyde-containing silane reagent. Alternatively, an antibody or ligand may be captured on a microfabricated polyacrylamide gel pad and accelerated into the gel using microelectrophoresis as described in, Arenkov et al. Anal. Biochem. 278:123- 131, 2000.

A protein chip is preferably generated such that several proteins, ligands or antibodies are arrayed on said chip. This format permits the simultaneous screening for the presence of several proteins in a sample.

Alternatively, a protein chip may comprise only one protein, ligand or antibody, and be used to screen one or more patient samples for the presence of one polypeptide of interest. Such a chip may also be used to simultaneously screen an array of patient samples for a polypeptide of interest.

Preferably, a sample to be analysed using a protein chip is attached to a reporter molecule, such as, for example, a fluorescent molecule, a radioactive molecule, an enzyme, or an antibody that is detectable using methods well known in the art. Accordingly, by contacting a protein chip with a labelled sample and subsequent washing to remove any unbound proteins the presence of a bound protein is detected using methods well known in the art, such as, for example using a DNA microarray reader.

Alternatively, biomolecular interaction analysis-mass spectrometry (BIA-MS) is used to rapidly detect and characterise a protein present in complex biological samples at the low- to sub-femptamole (fmol) level (Nelson et al. Electrophoresis 21: 1155-1163, 2000). One technique useful in the analysis of a protein chip is surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) technology to characterise a protein bound to the protein chip. Alternatively, the protein chip is analysed using ESI as described in U.S. Patent Application 20020139751. As will be apparent to the skilled artisan, protein chips are particularly amenable to multiplexing of detection reagents. Accordingly, several antibodies or ligands each able to specifically bind a different peptide or protein may be bound to different regions of said protein chip. Analysis of a biological sample using said chip then permits the detecting of multiple proteins of interest, or multiple B cell epitopes of the putative transcriptional regulatory protein TetR, or TetR-derived peptide. Multiplexing of diagnostic and prognostic markers is particularly contemplated in the present invention.

In a further embodiment, the samples are analysed using ICAT or ITRAC, essentially as described in US Patent Application No. 20020076739. This system relies upon the labelling of a protein sample from one source (i.e. a healthy individual) with a reagent and the labelling of a protein sample from another source (i.e. a tuberculosis patient) with a second reagent that is chemically identical to the first reagent, but differs in mass due to isotope composition. It is preferable that the first and second reagents also comprise a biotin molecule. Equal concentrations of the two samples are then mixed, and peptides recovered by avidin affinity chromatography. Samples are then analysed using mass spectrometry. Any difference in peak heights between the heavy and light peptide ions directly correlates with a difference in protein abundance in a biological sample. The identity of such proteins may then be determined using a method well known in the art, such as, for example MALDI-TOF, or ESI.

In a particularly preferred embodiment, a biological sample comprising anti-TetR antibodies, or alternatively TetR or an immunogenic fragment thereof, is subjected to 2-dimensional gel electrophoresis. In accordance with this embodiment, it is preferable to remove certain particulate matter from the sample prior to electrophoresis, such as, for example, by centrifugation, filtering, or a combination of centrifugation and filtering. Proteins in the biological sample are then separated. For example, the proteins may be separated according to their charge using isoelectric focussing and/or according to their molecular weight. Two-dimensional separations allow various isoforms of proteins to be identified, as proteins with similar molecular weight are also separated by their charge. Using mass spectrometry, it is possible to determine whether or not a protein of interest is present in a patient sample.

As will be apparent to those skilled in the art a diagnostic or prognostic assay described herein may be a multiplexed assay. As used herein the term "multiplex", shall be understood not only to mean the detection of two or more diagnostic or prognostic markers in a single sample simultaneously, but also to encompass consecutive detection of two or more diagnostic or prognostic markers in a single sample, simultaneous detection of two or more diagnostic or prognostic markers in distinct but matched samples, and consecutive detection of two or more diagnostic or prognostic markers in distinct but matched samples. As used herein the term "matched samples" shall be understood to mean two or more samples derived from the same initial biological sample, or two or more biological samples isolated at the same point in time.

Accordingly, a multiplexed assay may comprise an assay that detects several anti-TetR antibodies and/or TetR epitopes in the same reaction and simultaneously, or alternatively, it may detect other one or more antigens/antibodies in addition to one or more anti-TetR antibodies and/or TetR epitopes.

The present invention clearly contemplates multiplexed assays for detecting TetR antibodies and epitopes in addition to detecting CD4+ T-helper cells via one or more receptors on the cell surface and/or one or more HIV-I and/or HIV-2 antigens. Such assays are particularly useful for simultaneously obtaining information on co-infection with M. tuberculosis and HIV-I and/or HIV-2, and/or for determining whether or not a subject with M. tuberculosis is immune-compromised. Clearly, such multiplexed assay formats are useful for monitoring the health of an HIV+/TB+ individual.

As will be apparent to the skilled artisan, if such an assay is antibody or ligand based, both of these antibodies must function under the same conditions. 4. Biological samples and reference samples

Preferably, the biological sample in which a TetR or anti-TetR antibody is detected is a sample selected from the group consisting of lung, lymphoid tissue associated with the lung, paranasal sinuses, bronchi, a bronchiole, alveolus, ciliated mucosal epithelia of the respiratory tract, mucosal epithelia of the respiratory tract, broncheoalveolar lavage fluid (BAL), alveolar lining fluid, sputum, mucus, saliva, blood, serum, plasma, urine, peritoneal fluid, pericardial fluid, pleural fluid, squamous epithelial cells of the respiratory tract, a mast cell, a goblet cell, a pneumocyte (type 1 or type 2), an intra epithelial dendritic cell, a PBMC, a neutrophil, a monocyte, or any immunoglobulin- containing fraction of any one or more of said tissues, fluids or cells.

In one embodiment a biological sample is obtained previously from a patient.

In one embodiment a biological sample is obtained from a subject by a method selected from the group consisting of surgery or other excision method, aspiration of a body fluid such as hypertonic saline or propylene glycol, broncheoalveolar lavage, bronchoscopy, saliva collection with a glass tube, salivette (Sarstedt AG, Sevelen,

Switzerland), Ora-sure (Epitope Technologies Pty Ltd, Melbourne, Victoria, Australia), omni-sal (Saliva Diagnostic Systems, Brooklyn, NY, USA) and blood collection using any method well known in the art, such as, for example using a syringe.

It is particularly preferred that a biological sample is sputum, isolated from lung of a patient using, for example the method described in Gershman, N.H. et al, J Allergy Clin Immunol, 10(4): 322-328, 1999. Preferably, the sputim is expectorated i.e., coughed naturally.

In another preferred embodiment a biological sample is plasma that has been isolated from blood collected from a patient using a method well known in the art. In one embodiment, a biological sample is treated to lyse a cell in said sample. Such methods include the use of detergents, enzymes, repeatedly freezing and thawing said cells, sonication or vortexing said cells in the presence of glass beads, amongst others.

In another embodiment, a biological sample is treated to denature a protein present in said sample. Methods of denaturing a protein include heating a sample, treating a sample with 2-mercaρtoethanol, dithiotreitol (DTT), N-acetylcysteine, detergent or other compound such as, for example, guanidinium or urea. For example, the use of DTT is preferred for liquefying sputum.

In yet another embodiment, a biological sample is treated to concentrate a protein is said sample. Methods of concentrating proteins include precipitation, freeze drying, use of funnel tube gels (TerBush and Novick, Journal of Biomolecular Techniques, 10(3); 1999), ultrafiltration or dialysis.

As will be apparent, the diagnostic and prognostic methods provided by the present invention require a degree of quantification to determine either, the amount of a protein that is diagnostic or prognostic of an infection or disease. Such quantification can be determined by the inclusion of appropriate reference samples in the assays described herein, wherein said reference samples are derived from healthy or normal individuals.

In one embodiment, the reference sample comprises for example cells, fluids or tissues from a healthy subject who has not been previously or recently infected and is not suffering from an infection or disease. Conveniently, such reference samples are from fluids or tissues that do not require surgical resection or intervention to obtain them. Accordingly, bodily fluids and derivatives thereof are preferred. Highly preferred reference samples comprise sputum, mucus, saliva, blood, serum, plasma, urine, BAL fluid, peritoneal fluid, pericardial fluid, pleural fluid, a PBMC, a neutrophil, a monocyte, or any immunoglobulin-containing fraction of any one or more of said tissues, fluids or cells. A reference sample and a test (or patient) sample are processed, analysed or assayed and data obtained for a reference sample and a test sample are compared. In one embodiment, a reference sample and a test sample are processed, analysed or assayed at the same time. In another embodiment, a reference sample and a test sample are processed, analysed or assayed at a different time.

In an alternate embodiment, a reference sample is not included in an assay. Instead, a reference sample may be derived from an established data set that has been previously generated. Accordingly, in one embodiment, a reference sample comprises data from a sample population study of healthy individuals, such as, for example, statistically significant data for the healthy range of the integer being tested. Data derived from processing, analysing or assaying a test sample is then compared to data obtained for the sample population.

Data obtained from a sufficiently large number of reference samples so as to be representative of a population allows the generation of a data set for determining the average level of a particular parameter. Accordingly, the amount of a protein that is diagnostic or prognostic of an infection or disease can be determined for any population of individuals, and for any sample derived from said individual, for subsequent comparison to levels of the expression product determined for a sample being assayed. Where such normalized data sets are relied upon, internal controls are preferably included in each assay conducted to control for variation.

Diagnostic assay kits The present invention provides a kit for detecting M. tuberculosis infection in a biological sample. In one embodiment, the kit comprises:

(i) one or more isolated antibodies that bind to a TetR or an immunogenic fragment or epitope thereof; and

(ii) means for detecting the formation of an antigen-antibody complex.

In an alternative embodiment, the kit comprises: (i) an isolated or recombinant TetR or an immunogenic fragment or epitope thereof; and (ii) means for detecting the formation of an antigen-antibody complex.

The antibodies, immunogenic TetR peptide, and detection means of the subject kit are preferably selected from the antibodies and immunogenic TetR peptides described herein above and those embodiments shall be taken to be incorporated by reference herein from the description. The selection of compatible kit components for any assay format will be readily apparent to the skilled artisan from the description.

In a particularly preferred embodiment, -the subject kit comprises: (i) an antibody that binds to an isolated or recombinant or synthetic peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 and 13 and mixtures thereof; and (ii) anti-human Ig.

Preferably, the kit further comprises an amount of one or more peptides each comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-13 and mixtures thereof, or a fusion between any two or more of said peptides.

Optionally, the kit further comprises means for the detection of the binding of an antibody, fragment thereof or a ligand to a putative transcriptional regulatory protein TetR, or TetR-derived peptide. Such means include a reporter molecule such as, for example, an enzyme (such as horseradish peroxidase or alkaline phosphatase), a substrate, a cofactor, an inhibitor, a dye, a radionucleotide, a luminescent group, a fluorescent group, biotin or a colloidal particle, such as colloidal gold or selenium. Preferably such a reporter molecule is directly linked to the antibody or ligand.

In yet another embodiment, a kit may additionally comprise a reference sample. Such a reference sample may for example, be a protein sample derived from a biological sample isolated from one or more tuberculosis subjects. Alternatively, a reference sample may comprise a biological sample isolated from one or more normal healthy individuals. Such a reference sample is optionally included in a kit for a diagnostic or prognostic assay.

In another embodiment, a reference sample comprises a peptide that is detected by an antibody or a ligand. Preferably, the peptide is of known concentration. Such a peptide is of particular use as a standard. Accordingly various known concentrations of such a peptide may be detected using a prognostic or diagnostic assay described herein.

In yet another embodiment, a kit optionally comprises means for sample preparations, such as, for example, a means for cell lysis. Preferably such means are means of solubilizing sputum, such as, for example, a detergent (e.g., tributyl phosphine, C7BZO, dextran sulfate, DTT, N-acetylcysteine, or polyoxyethylenesorbitan monolaurate).

In yet another embodiment, a kit comprises means for protein isolation (Scopes (In: Protein Purification: Principles and Practice, Third Edition, Springer Verlag, 1994).

Prophylactic and therapeutic method The TetR or immunogenic fragment or epitope thereof can induce the specific production of a high titer antibody when administered to an animal subject.

Accordingly, the invention provides a method of eliciting the production of antibody against M. tuberculosis comprising administering an isolated TetR or an immunogenic fragment or epitope thereof to said subject for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis.

It is within the scope of the present invention to further administer one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to elicit the production of antibodies, such as, for example, neutralizing antibodies that bind to M. tuberculosis. Such administration may be at the same time as administering TetR or fragment (i.e., co-administration) or alternatively, before or after TetR or fragment is administered to a subject-

Preferably, the neutralizing antibodies according got any of the preceding embodiments are high titer neutralizing antibodies.

The effective amount of TetR or other protein or epitope thereof to produce antibodies varies upon the nature of the immunogenic B cell epitope, the route of administration, the animal used for immunization, and the nature of the antibody sought. All such variables are empirically determined by art-recognized means.

In a preferred embodiment, the invention provides a method of inducing immunity against M. tuberculosis in a subject comprising administering to said subject an isolated or recombinant TetR or immunogenic fragment or epitope thereof forfa time and under conditions sufficient to elicit a humoral immune response against said an isolated or recombinant TetR or immunogenic fragment or epitope.

It is also within the scope of the present invention to further administer one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof for a > time and under conditions sufficient to elicit a humoral immune response against that antigen. Such administration may be _. at the same time as administering TetR or fragment (i.e., co-administration) or alternatively, before or after TetR or fragment is administered to a subject. ^' '

The immunizing antigen may be administered in the form of any convenient formulation as described herein.

By "humoral immune response" means that a secondary immune response is generated against the immunizing antigen sufficient to prevent infection by M. tuberculosis. Preferably, the humoral immunity generated includes eliciting in the subject a sustained level of antibodies that bind to a B cell epitope in the immunizing antigen. By a "sustained level of antibodies" is meant a sufficient level of circulating antibodies that bind to the B cell epitope to prevent infection by M. tuberculosis.

Preferably, antibodies levels are sustained for at least about six months or 9 months or 12 months or 2 years.

In an alternative embodiment, the present invention provides a method of enhancing the immune system of a subject comprising administering an immunologically active TetR or an epitope thereof or a vaccine composition comprising said TetR or epitope for a time and under conditions sufficient to confer or enhance resistance against M. tuberculosis in said subject.

It is also within the scope of the present invention to further administer one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to confer or enhance resistance against M. tuberculosis in said subject. Such administration may be at the same time as administering TetR or fragment (i.e., co-administration) or alternatively, before or after TetR or fragment is administered to a subject.

By "confer or enhance resistance" is meant that a M. tuberculosis-specific immune response occurs in said subject, said response being selected from the group consisting of: (i) an antibody against a TetR of M. tuberculosis or an epitope of said protein is produced in said subject;

(ii) neutralizing antibodies that bind to M. tuberculosis are produced in said subject; (iii) a cytotoxic T lymphocyte (CTL) and/or a CTL precursor that is specific for a

TetR of M. tuberculosis is activated in the subject; and (iv) the subject has enhanced immunity to a subsequent M. tuberculosis infection or reactivation of a latent M. tuberculosis infection. The invention will be understood to encompass a method of providing or enhancing immunity against M. tuberculosis in an uninfected human subject comprising administering to said subject an immunologically active TetR or an epitope thereof or a vaccine composition comprising said TetR or epitope for a time and under conditions sufficient to provide immunological memory against a future infection by M. tuberculosis.

It is also within the scope of the present invention to further administer one or more second antigens e.g., M. tuberculosis Bsx or GS or immunogenic fragment thereof for a time and under conditions sufficient to provide immunological memory against a future infection by M. tuberculosis. Such administration may be at the same time as administering TetR or fragment (i.e., co-administration) or alternatively, before or after TetR or fragment is administered to a subject.

The present invention provides a method of treatment of tuberculosis in a subject comprising performing a diagnostic method or prognostic method as described herein.

In one embodiment, the present invention provides a method of prophylaxis comprising:

(i) detecting the presence of M. tuberculosis infection in a biological sample from a subject; and

(ii) administering a therapeutically effective amount of a pharmaceutical composition described herein to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject.

As will be apparent from the disclosure herein, suitable compositions according to this embodiment comprise TetR or immunogenic fragment thereof optionally with on or more other immunogen M. tuberculosis proteins or peptide fragments, in combination with a pharmaceutically acceptable carrier or excipient. It is clearly within the scope of the present invention for such compositions to include TetR or fragment thereof according to any embodiment described herein e.g., any one of SEQ ID NOs: 1-13 or a combination thereof, and one or more second antigens e.g., M. tuberculosis Bsx and/or GS or immunogenic fragments thereof e.g., as set forth in any one of SEQ ID NOs: 14- 26 or a combination thereof.

Preferably, the composition is administered to a subject harboring a latent or active M. tuberculosis infection.

Without being bound by any theory or mode of action, the therapeutic method enhances the ability of a T cell to recognize and lyse a cell harboring M. tuberculosis, or that the ability of a T cell to recognize a T cell epitope of an antigen of M. tuberculosis is enhanced, either transiently or in a sustained manner. Similarly, reactivation of a T cell population may occur following activation of a latent M. tuberculosis infection, or following re-infection with M. tuberculosis, or following immunization of a previously- infected subject with a TetR or epitope or vaccine composition of the invention. Standard methods can be used to determine whether or not CTL activation has occurred in the subject, such as, for example, using cytotoxicity assays, ELISPOT, or determining IFN-γ production in PBMC of the subject.

Preferably, the peptide or derivative or variant or vaccine composition is administered for a time and under conditions sufficient to elicit or enhance the expansion of CD8⁺ T cells. Still more preferably, the peptide or derivative or variant or vaccine composition is administered for a time and under conditions sufficient for M. tuberculosis -specific cell mediated immunity (CMI) to be enhanced in the subject.

By "M tuberculosis -specific CMI" is meant that the activated and clonally expanded CTLs are MHC-restricted and specific for a CTL epitope of the invention. CTLs are classified based on antigen specificity and MHC restriction, (i.e., non-specific CTLs and antigen-specific, MHC-restricted CTLs). Non-specific CTLs are composed of various cell types, including NK cells and antibody-dependent cytotoxicity, and can function very early in the immune response to decrease pathogen load, while antigen- specific responses are still being established. In contrast, MHC-restricted CTLs achieve optimal activity later than non-specific CTL, generally before antibody production. Antigen-specific CTLs inhibit or reduce the spread of M. tuberculosis and preferably terminate infection.

CTL activation, clonal expansion, or CMI can be induced systemically or compartmentally localized. In the case of compartmentally localized effects, it is preferred to utilize a vaccine composition suitably formulated for administration to that compartment. On the other hand, there are no such stringent requirements for inducing CTL activation, expansion or CMI systemically in the subject.

The effective amount of TetR or epitope thereof, optionally in combination with one or more other proteins or epitopes e.g., derived from Bsx or GS proteins of M. tuberculosis, to be administered solus or in a vaccine composition to elicit CTL activation, clonal expansion or CMI, varies upon the nature of the immunogenic epitope, the route of administration, the weight, age, sex, or general health of the subject immunized, and the nature of the CTL response sought. AU such variables are empirically determined by art-recognized means.

The TetR or epitope thereof, optionally in combination with one or more other proteins or epitopes e.g., derived from Bsx or GS proteins of M. tuberculosis, and optionally formulated with any suitable or desired carrier, adjuvant, BRM, or pharmaceutically acceptable excipient, is conveniently administered in the form of an injectable composition. Injection may be intranasal, intramuscular, sub-cutaneous, intravenous, intradermal, intraperitoneal, or by other known route. For intravenous injection, it is desirable to include one or more fluid and nutrient replenishers.

The optimum dose to be administered and the preferred route for administration are established using animal models, such as, for example, by injecting a mouse, rat, rabbit, guinea pig, dog, horse, cow, goat or pig, with a formulation comprising the peptide, and then monitoring the CTL immune response to the epitope using any conventional assay. Adoptive transfer techniques may also be used to confer or enhance resistance against M. tuberculosis infection or to prevent or reduce the severity of a reactivated latent infection. Accordingly, in a related embodiment, there is provided a method of enhancing or conferring immunity against M. tuberculosis in an uninfected human subject comprising contacting ex vivo a T cell obtained from a human subject with an immunologically active TetR or an epitope thereof or a vaccine composition comprising said protein or epitope for a time and under conditions sufficient to confer M. tuberculosis activity on said T cells.

In a preferred embodiment, the invention provides a method of enhancing the M. tuberculosis -specific cell mediated immunity of a human subject, said method comprising:

(i) contacting ex vivo a T cell obtained from a human subject with an immunologically active TetR or a CTL epitope thereof or a vaccine composition comprising said protein or epitope for a time and under conditions sufficient to confer M. tuberculosis activity on said T cells; and

(ii) introducing the activated T cells autologously to the subject or allogeneically to another human subject.

As with other embodiments described herein, the present invention encompasses the administration of additional immunogenic proteins or epitopes e.g., derived from Bsx or GS proteins of M. tuberculosis.

The T cell may be a CTL or CTL precursor cell.

The human subject from whom the T cell is obtained may be the same subject or a different subject to the subject being treated. The subject being treated can be any human subject carrying a latent or active M. tuberculosis infection or at risk of M. tuberculosis infection or reactivation of M. tuberculosis infection or a person who is otherwise in need of obtaining vaccination against M, tuberculosis or desirous of obtaining vaccination against M. tuberculosis.

Such adoptive transfer is preferably carried out and M. tuberculosis reactivity assayed essentially as described by Einsele et al, Blood 99, 3916-3922, 2002, which procedures are incorporated herein by reference.

By "M. tuberculosis activity" is meant that the T cell is rendered capable of being activated as defined herein above (i.e. the T cell will recognize and lyse a cell harboring M. tuberculosis or able to recognize a T cell epitope of an antigen of M tuberculosis, either transiently or in a sustained manner). Accordingly, it is particularly preferred for the T cell to be a CTL precursor which by the process of the invention is rendered able to recognize and lyse a cell harboring M. tuberculosis or able to recognize a T cell epitope of an antigen of M. tuberculosis, either transiently or in a sustained manner.

For such an ex vivo application, the T cell is preferably contained in a biological sample obtained from a human subject, such as, for example, a biopsy specimen comprising a primary or central lymphoid organ (eg. bone marrow or thymus) or a secondary or peripheral lymphoid organ (eg. blood, PBMC or a buffy coat fraction derived there from).

Preferably, the T cell or specimen comprising the T cell was obtained previously from a human subject, such as, for example, by a consulting physician who has referred the specimen to a pathology laboratory for analysis.

Preferably, the subject method further comprises obtaining a sample comprising the T cell of the subject, and more preferably, obtaining said sample from said subject. Formulations

The present invention clearly contemplates the use of TetR or an immunogenic fragment or epitope thereof in the preparation of a therapeutic or prophylactic subunit vaccine against M. tuberculosis infection in a human or other animal subject.

Accordingly, the invention provides a pharmaceutical composition or vaccine comprising a TetR or an immunogenic fragment or epitope thereof in combination with a pharmaceutically acceptable diluent.

In a preferred embodiment, the composition according to this embodiment comprises TetR or immunogenic fragment thereof optionally with on or more other immunogenic M. tuberculosis proteins or peptide fragments, in combination with a pharmaceutically acceptable carrier or excipient. It is clearly within the scope of the present invention for such compositions to include TetR or fragment thereof according to any embodiment described herein e.g., any one of SEQ ID NOs: 1-13 or a mixture thereof, and one or more second antigens e.g., M. tuberculosis Bsx and/or GS or immunogenic fragments thereof e.g., as set forth in any one of SEQ ID NOs: 14-26 or a combination thereof.

The putative transcriptional regulatory protein TetR, or TetR-derived peptide, and optional other protein, or immunogenic fragment or epitope thereof is conveniently formulated in a pharmaceutically acceptable excipient or diluent, such as, for example, an aqueous solvent, non-aqueous solvent, non-toxic excipient, such as a salt, preservative, buffer and the like. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate. Aqueous solvents include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc. Preservatives include antimicrobial, anti-oxidants, chelating agents and inert gases. The pH and exact concentration of the various components the pharmaceutical composition are adjusted according to routine skills in the art. In certain situations, it may also be desirable to formulate TetR and optional other protein or an immunogenic fragment or epitope thereof, with an adjuvant to enhance the immune response to the B cell epitope. Again, this is strictly not essential. Such adjuvants include all acceptable immunostimulatory compounds such as, for example, a cytokine, toxin, or synthetic composition. Exemplary adjuvants include IL-I, IL-2, BCG, aluminium hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thur- MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(r-2'-dipalmitoyl- sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP) 1983 A, referred to as MTP- PE), lipid A, MPL and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion.

Particularly preferred adjuvants for use in a vaccine against M. tuberculosis are described for example by Elhay and Andersen Immunol. Cell Biol. 75, 595-603, 1997; or Lindblad et al., Infect. Immun. 65, 1997.

It may be desirable to co-administer biologic response modifiers (BRM) with TetR or immunogenic fragment or epitope thereof, to down regulate suppressor T cell activity. Exemplary BRM's include, but are not limited to, Cimetidine (CIM; 1200 mg/d) (Smith/Kline, PA, USA); Indomethacin (IND; 150 mg/d) (Lederle, NJ, USA); or low- dose Cyclophosphamide (CYP; 75, 150 or 300 mg/m.sup.2) (Johnson/Mead, NJ, USA).

Preferred vehicles for administration of TetR and optional other protein, or immunogenic fragment or epitope thereof, include liposomes. Liposomes are microscopic vesicles that consist of one or more lipid bilayers surrounding aqueous compartments. (Bakker-Woudenberg et ah, Eur. J. Clin. Microbiol. Infect. Dis.

12(Suppl. 1), S61 (1993); and Kim, Drugs 46, 618 (1993)). Liposomes are similar in composition to cellular membranes and as a result, liposomes generally are administered safely and are biodegradable. Techniques for preparation of liposomes and the formulation (e.g., encapsulation) of various molecules, including peptides and oligonucleotides, with liposomes are well known to the skilled artisan.

Depending on the method of preparation, liposomes may be unilamellar or multilamellar, and can vary in size with diameters ranging from 0.02 μm to greater than 10 μm. A variety of agents are encapsulated in liposomes. Hydrophobic agents partition in the bilayers and hydrophilic agents partition within the inner aqueous space(s) (Machy et al, LIPOSOMES IN CELL BIOLOGY AND PHARMACOLOGY (John Libbey 1987), and Ostro et al, American J. Hosp. Pharm. 46, 1576 (1989)).

Liposomes can also adsorb to virtually any type of cell and then release the encapsulated agent. Alternatively, the liposome fuses with the target cell, whereby the contents of the liposome empty into the target cell. Alternatively, an absorbed liposome may be endocytosed by cells that are phagocytic. Endocytosis is followed by intralysosomal degradation of liposomal lipids and release of the encapsulated agents (Scherphof et al, Ann. N. Y. Acad Sci. 446, 368 (1985)). In the present context, TetR or immunogenic fragment or epitope thereof may be localized on the surface of the liposome, to facilitate antigen presentation without disruption of the liposome or endocytosis. Irrespective of the mechanism or delivery, however, the result is the intracellular disposition of the associated TetR or immunogenic fragment or epitope thereof.

Liposomal vectors may be anionic or cationic. Anionic liposomal vectors include pH sensitive liposomes which disrupt or fuse with the endosomal membrane following endocytosis and endosome acidification. Cationic liposomes are preferred for mediating mammalian cell transfection in vitro, or general delivery of nucleic acids, but are used for delivery of other therapeutics, such as peptides or lipopeptides.

Cationic liposome preparations are made by conventional methodologies (Feigner et al, Proc. Nat'l Acad. Sci USA 84, 7413 (1987); Schreier, Liposome Res. 2, 145 (1992)). Commercial preparations, such as Lipofectin (Life Technologies, Inc., Gaithersburg, Md. USA), are readily available. The amount of liposomes to be administered are optimized based on a dose response curve. Feigner et al., supra.

Other suitable liposomes that are used in the methods of the invention include multilamellar vesicles (MLV), oligolamellar vesicles (OLV), unilamellar vesicles (UV), small unilamellar vesicles (SUV), medium-sized unilamellar vesicles (MUV), large unilamellar vesicles (LUV), giant unilamellar vesicles (GUV), multivesicular vesicles (MVV), single or oligolamellar vesicles made by reverse-phase evaporation method (REV), multilamellar vesicles made by the reverse-phase evaporation method (MLV-REV), stable plurilamellar vesicles (SPLV), frozen and thawed MLV (FATMLV), vesicles prepared by extrusion methods (VET), vesicles prepared by French press (FPV), vesicles prepared by fusion (FUV), dehydration-rehydration vesicles (DRV), and bubblesomes (BSV). The skilled artisan will recognize that the techniques for preparing these liposomes are well known in the art. (See COLLOIDAL DRUG DELIVERY SYSTEMS, vol. 66, J. Kreuter, ed., Marcel Dekker, Inc. 1994).

Other forms of delivery particle, for example, microspheres and the like, also are contemplated for delivery of TetR and optional other protein, or immunogenic fragment or epitope thereof.

Guidance in preparing suitable formulations and pharmaceutically effective vehicles, are found, for example, in REMINGTON'S PHARMACEUTICAL SCIENCES, chapters 83-92, pages 1519-1714 (Mack Publishing Company 1990) (Remington's), which are hereby incorporated by reference.

Alternatively, the peptide or derivative or variant is formulated as a cellular vaccine via the administration of an autologous or allogeneic antigen presenting cell (APC) or a dendritic cell that has been treated in vitro so as to present the peptide on its surface. Nucleic acid-based vaccines that comprise nucleic acid, such as, for example, DNA or RNA, encoding the immunologically active TetR and optional other protein, or epitope(s) thereof, and cloned into a suitable vector (eg. vaccinia, canary pox, adenovirus, or other eukaryotic virus vector) are also contemplated. Preferably, DNA encoding a TetR and optional other protein, is formulated into a DNA vaccine, such as, for example, in combination with the existing Calmette-Guerin (BCG) or an immune adjuvant such as vaccinia virus, Freund's adjuvant or another immune stimulant.

The present invention is further described with reference to the following non-limiting examples.

EXAMPLE 1 Preparation of sputum, serum or plasma

Patient sputum, serum or plasma is applied to a column of protein G-sepharose (Amersham Biosciences), previously equilibrated with 2OmM phosphate buffer pH7 and incubated on ice with occasional inversion. The mixture is centrifuged at 600Og for 10 minutes at 4⁰C and the supernatant decanted. The sepharose pellet is washed with 2OmM phosphate buffer. The IgG bound to the sepharose is eluted by addition of 5OmM glycine pH2.7 for 20 minutes. After centrifugation as above, the supernatant is discarded and the glycine step repeated. The supernant is then precipitated with cold acetone at -2O⁰C for 48 hr then centrifuged at 5000g for 20 mins at 4°C. The precipitate is resolubilised in l-2mls of sample buffer containing 7M urea, 2M thiourea, 2% CHAPS, 4OmM Tris, then simultaneously reduced and alkylated with 5mM tributyl phosphine (TBP) and 1OmM acrylamide for Ih. Denatured IgG-containing samples are pre-fractionated using a multicompartment electrolyzer (MCE) to produce an acidic fraction (pi = 3.6-5.0) and an alkaline fraction (pi = 6.5-11.0). EXAMPLE 2 Analytical methods

The protein content of the samples is estimated using a Bradford assay. Samples were diluted with sample buffer as above replacing 4OmM Tris with 5mM Tris.

Prior to rehydration of IPG strips, samples are centrifuged at 21000 x g for 10 minutes. The supernatant is collected and 10 μl of 1% Orange G (Sigma) per ml added as an indicator dye.

Two-dimensional gel electrophoresis First Dimension

Dry 11 cm IPG strips (Amersham-Biosciences) are rehydrated for 16-24 hours with 180 μl of protein sample. Rehydrated strips are focussed on a Protean IEF Cell (Bio- Rad, Hercules, CA) or Proteome System's IsoElectrIQ electrophoresis equipment for approx 140 kVhr at a maximum of 10 kV. Focussed strips are then equilibrated in urea/SDS/Tris-HCl/bromophenol blue buffer.

Second Dimension

Equilibrated strips are inserted into loading wells of 6-15% (w/v) tris-acetate SDS- PAGE pre-cast 10cm x 15cm GelChips (Proteome Systems, Sydney Australia). Electrophoresis is performed at 50mA per gel for 1.5 hours, or until the tracking dye reached the bottom of the gel. Proteins are stained using SyproRuby (Molecular Probes). Gel images are scanned after destaining using an Alphalmager System (Alpha Innotech Corp.). Gels are then stained with Coomassie G-250 to assist visualisation of protein spots in subsequent analyses.

Mass Spectrometry: Prior to mass spectrometry protein samples are prepared by in-gel tryptic digestion. Protein gel pieces are excised, destained, digested and desalted using an Xcise™, an excision/liquid handling robot (Proteome Systems, Sydney, Australia and Shimadzu- Biotech, Kyoto, Japan) in association with the Montage In-GeI Digestion Kit (developed by Proteome Systems and distributed by Millipore, Billerica, Ma, 01821, USA). Prior to spot cutting, the 2-D gel is incubated in water to maintain a constant size and prevent drying. Subsequently, the 2-D gel is placed on the Xcise, a digital image was captured and the spots to be cut are selected. After automated spot excision, gel pieces are subjected to automated liquid handling and in-gel digestion. Briefly, each spot is destained with 100 μl of 50% (v/v) acetonitrile in 100 mM ammonium bicarbonate. The gel pieces are dried by adding 100% acetonitrile, the acetonitrile is removed after 5 seconds and the gels dried completely by evaporating the residual acetonitrile at 37⁰C. Proteolytic digestion is performed by rehydrating the dried gel pieces with 30 μl of 50 mM ammonium bicarbonate (pH 7.8) containing 5 μg/mL modified porcine trypsin and incubated at 37°C overnight.

Ten microliters (10 μl) of the tryptic peptide mixture is removed to a clean microtitre plate in the event that additional analysis by Liquid Chromatography (LC) - Electrospray Ionisation (ESI) MS was required.

Automated desalting and concentration of tryptic peptides prior to MALDI MS is performed using R2-based chromatography. Adsorbed peptides are eluted from the tips onto a 384-position MALDI MS sample target plate (Kratos, Manchester, UK or Bruker Daltronics, Germany) using 2 μl of 2 mg/ml α-cyano-4-hydroxycinnamic acid in 90% (v/v) acetonitrile and 0.085% (v/v) TFA.

Digests are analysed using an Axima-CFR MALDI-TOF mass spectrometer (Kratos, Manchester, UK) in positive ion reflectron mode. A nitrogen laser with a wavelength of 337 nm is used to irradiate the sample. The spectra are acquired in automatic mode in the mass range 600 Da to 4000 Da applying a 64-point raster to each sample spot. Only spectra passing certain criteria are saved. AU spectra undergo an internal two point calibration using an autodigested trypsin peak mass, m/z 842.51 Da and spiked adenocorticotropic hormone (ACTH) peptide, m/z 2465.117 Da. Software designed by Proteome Systems, as contained in the web-based proteomic data management system BioinformatlQ™ (Proteome Systems), is used to extract isotonic peaks from MS spectra.

Protein identification is performed by matching the monoisotopic masses of the tryptic peptides (i.e. the peptide mass fingerprint) with the theoretical masses from protein databases using IonlQ or MASCOT database search software (Proteome System Limited, North Ryde, Sydney, Australia). Querying is done against the non-redundant SwissProt (Release 40) and TrEMBL (Release 20) databases (June 2002 version), and protein identities are ranked through a modification of the MOWSE scoring system. Propionamide-cysteine (cys-PAM) or carboxyamidomethyl-cysteine (cys-CAM) and oxidized methionine modifications are taken into account and a mass tolerance of 100 ppm is allowed.

Miscleavage sites are only considered after an initial search without miscleavages had been performed. The following criteria are used to evaluate the search results: the MOWSE score, the number and intensity of peptides matching the candidate protein, the coverage of the candidate protein's sequence by the matching peptides and the gel location.

In addition, or alternatively, proteins are analysed using LC-ESI-MS. Tryptic digest solutions of proteins (10 μl) are analysed by nanoflow LC/MS using an LCQ Deca Ion Trap mass spectrometer (ThermoFinnigan, San Jose, CA) equipped with a Surveyor LC system composed of an autosampler and pump. Peptides are separated using a PepFinder kit (Thermo-Finnigan) coupled to a Cl 8 PicoFrit column (New Objective). Gradient elution from water containing 0.1% (v/v) formic acid (mobile phase A) to 90% (v/v) acetonitrile containing 0.1% (v/v) formic acid (mobile phase B) is performed over a 30-60-minute period. The mass spectrometer is set up to acquire three scan events - one full scan (range from 400 to 2000 amu) followed by two data dependant MS/MS scans. Bioinformatic Analysis:

Following automated collection of mass spectra peaks, data are processed as follows. AU spectra are firstly checked for correct calibration of peptide masses. Spectra are then processed to remove background noise including masses corresponding to trypsin peaks and matrix. The data are then searched against publicly-available SwissProt and TrEMBL databases using Proteome Systems search engine IonlQ v69 and/or MASCOT. PSD data is searched against the same databases using the in-house search engine FragmentastIQ. LC MS-MS data is also searched against the databases using the SEQUEST search engine software.

EXAMPLE 3 Identification of TetR as a diagnostic marker of M. tuberculosis infection

Protein fragments were recognized in the immunoglobulin fraction of plasma and sputum from TB⁺ samples. The sequences of six peptides from MALDI MS data of plasma samples (SEQ ID Nos: 2-13 inclusive) and the sequences of a further four peptides from MALDI MS data of sputum (SEQ ID NOs: 8-11) matched a protein having SwissProt Accession No. 053310 (SEQ ID NO: 1). The percent coverage of

053310 by the 6 plasma-derived peptides (SEQ ID NOs: 2-13) was about 22%, and the percentage coverage of 053310 by the 4 sputum-derived peptides (SEQ ID NOs: 8-11) was 33% suggesting that the peptide fragments in both cases were derived from this same protein marker.

The identified protein having the amino acid sequence set forth in SEQ ID NO: 1 was designated as "TetR " or simply "TetR". The estimated molecular weight of TetR is about 23.1 kDa, and the estimated isoelectric point is about 4.9. EXAMPLE 4

Antibodies that bind to TetR of M. tuberculosis or TetR-derived peptides Synthesis of TetR Peptides Synthetic peptides comprising amino acid residues 147-174 (SEQ ID NO: 12) or residues 113-127 (SEQ ID NO: 13) of full length TetR were synthesized according to standard procedures. These peptides can be coupled separately to keyhole limpet Hemocyanin (KHL) via a maleimidocaproyl-N-hydroxysuccinimide linker.

To facilitate detection of antibodies raised against an epitope of SEQ ID NO: I₅ the peptides can also be synthesized separately, each with a GSGS spacer and attached to biotin.

Polyclonal antibody production 1. Immunization of rabbits and chickens

Chickens and rabbits were immunized respectively with recombinant protein comprising the sequence set forth in SEQ ID NO: I₅ and with a synthetic peptide comprising the amino acid sequence set forth in SEQ ID NO: 12 according to standard procedures. Animal bleeds were obtained. All blood were was collected in sterile containers and serum collected after clot removal.

2. Polyclonal antibody titration

To titrate antisera against recombinant protein (SEQ ID NO: 1) produced in chickens, the recombinant protein immunogen was immobilized at a concentration of 5 μg/ml onto Nunc immunoplates. The solution was removed and wells blocked using blocking buffer (1% (w/v) casein, 0.1% (v/v) Tween 2O₅ 0.1% (w/v) sodium azide in PBS). Blocking buffer was removed and serum diluted in the range 1 :500 (v/v) to 1 : 1,024,000 (v/v) in PBS added and incubated for a sufficient time for antibodies to complex with bound putative transcriptional regulatory protein TetR, or TetR-derived peptide, generally for about 1 hour at room temperature. Plates were washed and binding of the antibody to TetR was detected using HRP-conjugated sheep anti-chicken IgG diluted 1:5000 (v/v) in conjugate diluent buffer. Fifty millilitres (50 ml) of TMB (3,3',5',5- Tetramethylbenzidine; Sigma) were added to each well and the plate incubated in the dark for 30 minutes. Development was stopped by addition of 50 μL per well of 0.5M sulphuric acid. The optical density of each well was read with a microtitre plate reader (PowerWaveχ 340 plate reader, Bio-Tek Instruments Inc., Winooski, VT) using a wavelength of 450nm and an extinction at 620nm. The titration results are shown in Figure 1.

For testing rabbit antisera against a synthetic peptide comprising SEQ ID NO: 12, streptavidin (Sigma Aldrich) was diluted to 5 μg/ml in double-distilled water (ddH₂O) and incubated in a Nunc plate overnight at 4⁰C. The solution was then flicked out of the plate and 250 μL of blocking buffer (1% (w/v) casein, 0.1% (v/v) Tween 20, 0.1% (w/v) sodium azide in PBS) added to each well and incubated at room temperature for 1 hour. The blocking buffer was flicked out and biotinylated peptide (SEQ ID NO: 12) diluted to a concentration range of 204.8 ng/ml to 100 pg/ml was added in blocking buffer at 3 μg/ml to 50 μl/well and incubated for one hour at room temperature on a shaker. The plate was washed in an Elx405 Auto Plate Washer (Bio-Tek Instruments Inc., Winooski, VT), with 0.5 x PBS / 0.05% (v/v) Tween 20 solution and excess solution tapped out of the plate onto a paper towel. Rabbit sera and preimmune sera were diluted in blocking buffer 1 :500 (v/v) or 1 :2000 (v/v) and incubated for 1 hour at 50 μl/well at room temperature on a shaker. Plates were washed with the plate washer using 0.5 x PBS/ 0.05% (v/v) Tween 20 solution, and the excess solution tapped out on a paper towel. Binding of the rabbit antibodies to SEQ ID NO: 12 was detected using HRP-conjugated Sheep anti-rabbit IgG (Chemicon) diluted 1:5000 (v/v) in conjugate diluent buffer. Fifty millilitres (50 ml) were added to each well and incubated for one hour at room temperature on a shaker. Plates were washed with the plate washer using 0.5 x PBS and excess solution tapped out on a paper towel. Fifty millilitres (50 ml) of TMB (3,3',5',5-Tetramethylbenzidine; Sigma) were added to each well and the plates incubated in the dark for 30 minutes. Development was stopped by addition of 50 μL per well of 0.5M sulphuric acid. The optical density of each well was read with a microtitre plate reader (PowerWaveχ 340 plate reader, Bio-Tek Instruments Inc., Winooski, VT) using a wavelength of 450nm and an extinction at 620nm. The data are shown in Figure 2.

Monoclonal antibody production 1. Antigen

The full length recombinant TetR protein (SEQ ID NO: 1) was used as an antigen for antibody production, according to standard procedures. Approximately 2 mg of protein was provided to NeoClone, Madison, Wisconsin, USA for generation of monoclonal antibodies according to their standard protocol. About 1 mg of the protein was provided as biotinylated peptide for quality control.

2. Antibody production

Immunization

Five BALB/cByJ female mice were immunized with protein according to Neoclone's standard immunization process.

Test Bleeds

Test bleeds of the immunized mice were performed at regular intervals for use in the quality control sera ELISAs using biotinylated peptide. Polyclonal sera having the highest titer were determined using ELISA. Mice having polyclonal antibody titers of at least 1,000 were used for the ABL-MYC infection process.

Infection

For each monoclonal antibody to be produced, the spleens of 3 mice having the highest titers of polyclonal antibodies cross-reactive with peptide antigen were used for the ABL-MYC infection, according to NeoClone's standard infection procedure.

Transplantation

For each monoclonal antibody to be produced, the splenocytes of the ABL-MYC- infected mice were transplanted into approximately 20 naive mice. Ascites development

Ascites fluid developed in the transplanted mice were isolated and screened for cells producing monoclonal antibodies (mAbs) that bind to the target peptide antigen.

Six cell lines (i.e., plasmacytomas) producing distinct mAbs designated 784A, 784D₅ 784F, 785E₅ 785F and 785C were isolated. Binding affinities and isotype specificities of the mAbs were confirmed using ELISA. The mAbs were provided in 1 ml aliquots (approximately) in ascites, together with the associated cell line.

3. Deposit of biological material

For the purposes of nomenclature, the mouse plasmacytoma cell line designated Mo 785E or 785E was deposited under the provisions of the Budapest treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure with the American Type Culture Collection (ATCC). and assigned ATCC Accession No. .

EXAMPLE 5 Standard sandwich ELISA using antibodies prepared against

M. tuberculosis TetR or TetR-derived peptides

This example demonstrates effective detection of TetR protein by sandwich ELISA using the polyclonal and monoclonal antibodies described in Example 4, and optimization of standard ELISA using a pool of chicken polyclonal antibodies Ch4 (= Pink 4) and Ch5 (=Pink 5) i.e., Ch4/5 as a capture reagent and the monoclonal antibodies 784F and 785E as a detection reagent. The antibody pair Ch4/5 and 785E was eventually selected due to, for example, of their higher signal:noise ratio in sandwich ELISA than other antibody combinations described herein. Preferred antibody combination

In a first set of diagnostic tests, a standard sandwich ELISA was performed to determine optimum capture and detection antibodies, and appropriate antibody concentrations for use.

In one example, a standard sandwich ELISA was performed using the polyclonal antisera RCP 18 (=Rbl8) as a capture antibody and a pool of polyclonal antibodies designated "Ch4/5" which comprises the polyclonal antibodies Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (=antibody "Pink 5" referred to herein) as detector antibody. Briefly, the wells of an ELISA plate were coated overnight with 50 μl of RCP 18 (Rb 18) antibody at 5 μg/ml or 10 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 50 ng/ml starting concentration to 80 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plates. Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., Ch4/5 for detecting TetR-RCP18 complexes was contacted with the bound antigen-body complexes at a concentration of 5 μg/ml or 10 μg/ml or 20 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1:5000 (v/v) dilution of secondary antibody (i.e., sheep anti-chicken IgG for detecting Ch4/5) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background. Data presented in Figure 3 suggest that the combination of 5 μg/ml RCP 18 as capture antibody and 5 μg/ml Ch4/5 as detector antibody is preferred in this sandwich ELISA format.

In a second example, a standard sandwich ELISA was performed using a pool of polyclonal antibodies designated "Ch4/5" which comprises the polyclonal antibodies Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (=antibody "Pink 5" referred to herein) as capture antibody, and the polyclonal antisera RCP 18 (=Rbl8) as a detector antibody. Briefly, the wells of an ELISA plate were coated overnight with 50 μl of Ch4/5 antibody at 5 μg/ml or 10 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 50 ng/ml starting concentration to 80 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plate. Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., RCP 18 for detecting TetR-Ch4/5 complexes was contacted with the bound antigen-body complexes at a concentration of 5 μg/ml or 10 μg/ml or 20 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1 :5000 (v/v) dilution of secondary antibody (i.e., sheep anti-rabbit IgG for detecting Ch4/5) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background. Data presented in Figure 4 suggest that the combination of 5 μg/ml Ch4/5 as capture antibody and 5 μg/ml RCP 18 as detector antibody is preferred in this sandwich ELISA format, and marginally improved compared to the reverse orientation of antibodies shown in Figure 3.

In a further diagnostic test, a standard sandwich ELISA was performed using a pool of polyclonal antibodies designated "Ch4/5" which comprises the polyclonal antibodies Ch4 (=antibody "Pink 4" referred to herein) and Ch5 (=antibody "Pink 5" referred to herein) as capture antibody, and one of two monoclonal antibody preparations designated 784F and 785E as detector antibody. The wells of an ELISA plate were coated overnight with 50 μl of Ch4/5 antibody at 500 ng/ml or 1 μg/ml or 2 μg/ml or 4 μg/ml or 8 μg/ml concentration. Following blocking and washing to remove unbound antibody, recombinant TetR protein was diluted from 5 ng/ml starting concentration to 2.29 pg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody- coated ELISA plates. Following incubation for 1 hour and washing to remove unbound antigen, the detection antibody i.e., 784F or 785E for detecting TetR-Ch4/5 complexes was contacted with the bound antigen-body complexes at a concentration of 2 μg/ml. Following incubation at room temperature for 1 hour, plates were washed, incubated with 50 μl of a 1 :5000 (v/v) dilution of secondary antibody (i.e., sheep anti-mouse IgG for detecting the mouse monoclonal antibodies) conjugated to horseradish peroxidase (HRP), washed, incubated with TMB for 30 mins, and absorbance at 450-620 nm was determined after subtraction of background. Data presented in Figure 5 suggest that the 785E monoclonal antibody provides the lowest background signal and, when combined with the Ch4/5 capture antibody, provides higher signals than the rabbit polyclonal RCPl 8. The combination of 500 ng/ml Ch4/5 as capture antibody and 2 μg/ml 785E as detector antibody provided the lowest background signal, however the combination of 2 μg/ml Ch4/5 as capture antibody and 2 μg/ml 785E as detector antibody provided the highest signal:noise ratio in this sandwich ELISA format.

EXAMPLE 6 Amplified sandwich ELISA using polyclonal capture antibody Ch4/5 and rnAb 785E as detector antibody to detect M. tuberculosis TetR

1. Optimizing the limits of detection using amplified sandwich ELISA The inventors also investigated whether or not a biotinylated antibody and streptavidin poly-HRP conjugate could improve ELISA sensitivity compared to conventional biotin-streptavidin-HRP systems or HRP-conjugated secondary antibodies.

An ELISA plate was coated overnight with capture antibody Ch4/5 at 2 μg/ml concentration. Following washing to remove unbound antibody, recombinant TetR protein was diluted from 100 ng/ml starting concentration to 490 fg/ml, and 50 μl aliquots of each dilution were added the wells of the antibody-coated ELISA plates. Following incubation for 1 hour, plates were washed to remove unbound antigen. Unlabelled monoclonal antibody 785E was contacted with the bound antigen-body complexes at 2.5 μg/ml concentration for standard sandwich ELISA. For amplified sandwich ELISA, monoclonal antibody 785E was biotinylated and the biotinylated antibody contacted with the bound antigen-body complexes at 2.5 μg/ml concentration. Following incubation at room temperature for 1 hour, plates were washed, and incubated with 50 μl of a 1:5,000 (v/v) dilution of a secondary antibody consisting of HRP-conjugated sheep anti-mouse IgG (standard sandwich ELISA) or 50 μl of a 1 :2,500 (v/v) dilution of HRP80-streptavidin. Plates were then incubated for a further one hour at room temperature, and washed as before. Finally, all samples were incubated with TMB for 30 mins (standard ELISA) or 10 mins (amplified ELISA). Absorbance was determined at 450-620 nm.

As shown in Figure 6, there was significant enhancement of detection using the amplified sandwich ELISA under these conditions: The limit of detection of this optimized sandwich ELISA is about 18 pg/ml TetR protein, with half-maximum detection of about 1 ng/ml TetR protein. This compares favourably to the observed limit of detection of the standard sandwich ELISA of about 176 pg/ml TetR protein.

The further additional optimization is also able to be performed to increase signal:

a. Replacement amplification

To further enhance sandwich ELISA sensitivity, the inventors will further modify the basic assay by employing iterative antigen binding following coating of the ELISA plate with capture antibody. Essentially, this results in an increased amount of antigen being bound to the capture antibody notwithstanding the 50 μl volume limitations of a 96-well ELISA plate. Briefly, this iterative antigen loading involves repeating the antigen binding step in the sandwich ELISA several times, e.g., 2 or 3 or 4 or 5 times, etc. before washing and adding detection antibody. Naturally, each aliquot of antigen sample is removed following a standard incubation period before the next aliquot is added. The number of iterations can be modified to optimize the assay (e.g., parameters such as signal: noise ratio, detection limit and amount of antigen detected at half-maximum signal), depending upon the nature of the sample being tested (e.g., sample type), without undue experimentation.

For example, five iterations of sample loading (i.e., a 5x replacement amplification) may provide a low background signal, and reduce the detection limit for RV 1265 protein. EXAMPLE 7 Reactivity between antibodies against recombinant TetR protein and laboratory and clinical isolates of M. tuberculosis in amplified sandwich ELISA

To further assess the suitability of TetR as a diagnostic marker for the presence of M. tuberculosis in biological samples, the inventors compared antibody reactivities between cellular extracts of the clinical M. tuberculosis strains CSU93 and HN878, and the laboratory M. tuberculosis strain H37Rv by western blotting, immune precipitation, and amplified sandwich ELISA.

a) Western blotting

Briefly, Western blotting was performed on proteins separated by eletrophoresis on

10%(w/v) Bis-Tri Nu-PAGE (Invitrogen, Carlsbad CA, USA) and transferred to PVDF activated membrane (Immobilon-P, Millipore Inc, USA). Following transfer, membranes were incubated in 0.008% DB-71 (Sigma Chemical Co. USA) in 40% (v/v) ethanol/10% (v/v) acetic acid for 7 min, rinsed briefly in 40% (v/v) ethanol/10% (v/v) acetic acid, scanned to visually confirm protein transfer, and rinsed in Tris-buffered saline containing Triton-XIOO (TBS-T). Dried membranes were re-activated in methanol, and transferred to blocking buffer (TBS-T containing 1% (w/v) bovine serum albumin) overnight at 4⁰C. Primary antibody 785E was diluted to a concentration of 0.5 μg/ml in blocking buffer and incubated with the membranes for 90 min at room temperature, after which time the membranes were washed in TBS-T, incubated with HRP-conjugated secondary antibody i.e., a sheep anti-mouse IgG-HRP conjugate diluted 1:100,000 (v/v), for 60 min at room temperature, and washed as before. Binding of HRP-secondary antibody conjugate was detected by incubating membranes in SuperSignal™ West "Femto" Maximum Sensitivity Substrate (Pierce, Inc. USA), and visualizing chemiluminescence using the LAS-3000 multi-imager (FujiFilm Inc., Japan). Immunoreactive bands of about 24 kDa, consistent with the expected molecular masses of M. tuberculosis TetR protein, were detected in both clinical M. tuberculosis isolates CSU93 and HN878, and in the laboratory strain H37Rv (data not shown). In a control, recombinant TetR protein comprising a hexahistidine tag having an estimated molecular mass of about 25 kDa was also detected at the correct position (not shown). In a further experiment, the detection of these bands was prevented by pre-incubation of primary antibody in a 1000-fold molar excess of unlabelled recombinant TetR protein (data not shown).

b) Immune precipitation

Further validation of antibody specificity can be achieved by immunoprecipitation from whole cell extracts of strain H37RV using the Ch4/5 polyclonal antibody or 785E monoclonal antibody, and determining the amino acid sequence of the immunoprecipitated protein by LC-MS.

c) Amplified sandwich ELISA

The amplified ELISA described herein was also used to detect recombinant TetR protein in whole cell extracts of the laboratory strain H37RV and the clinical isolates CSU93 and HN878. Recombinant protein (1.8 μg/ml, 5.6 μg/ml, 16.7 μg/ml, and 50 μg/ml diluted in blocking buffer) was added to whole cell Iy sates, and the samples assayed in duplicate by amplified sandwich ELISA, performed essentially as described in Example 6. The concentration of endogenous TetR protein in the whole cell lysates was calculated by interpolation from the standard curve and subtraction of the signal corresponding to the recombinant TetR protein spike. Levels of endogenous M. tuberculosis TetR protein present in these strains, as determined from two independent experiments is indicated in Figure 7. Data indicate average TetR levels of about 3-5 pg/ μg cell extract for H37Rv and CSU93, and about 9 pg/μg in whole cell extracts of the clinical isolate HN878. In summary, the data obtained to date thus indicate that the amplified sandwich ELISA assay format is capable of detecting endogenous TetR protein in whole cell extracts of clinically-relevant and laboratory strains of M, tuberculosis.

EXAMPLE 8

Low cross-reactivity between antibodies against recombinant TetR protein and yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa in sandwich ELISA

To further assess the suitability of TetR as a diagnostic marker for the presence of M. tuberculosis in biological samples, the inventors compared antibody cross-reactivities in the optimized amplified sandwich ELISA performed essentially as described in Examples 6 and 7 between different concentrations of recombinant TetR protein and cellular extracts of yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa. Assay conditions were varied slightly, employing HRP40-streptavidin at 1:2500 (v/v) dilution as opposed to HRP80-streptavidin, and developing TMB for 15 min for signal detection. Buffer without protein or cellular extract served as a negative control. No replacement amplification or iterative sample loading was performed in this diagnostic test.

Data presented in Figure 8 show no detectable cross-reactivity of antibodies against M. tuberculosis TetR with yeast, Escherichia coli, Bacillus subtilis or Pseudomonas aeruginosa cellular extracts under the conditions tested. In particular there was little or no signal differential between the concentrations of cellular extracts tested, and the signal obtained were not significantly above background. In contrast, the assay detected as little as about 10 pg/ml recombinant TetR protein. EXAMPLE 9 Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis:

Western Blot analysis of BSX levels in sputum

Chicken polyclonal antibodies against full-length recombinant BSX protein or a peptide from BSX were produced using standard methods. The antibody against the full-length protein The antibody was purified by affinity chromatography using immobilised recombinant protein (without NUS).

Sputum (12 μl) from TB and non-TB patients was loaded onto 4-12% (w/v) ID gradient SDS polyacrylamide gels and separated using electrophoresis. Proteins were then electrotransferred onto PVDF membrane. All the membranes were blocked in solution containing 1% casein in IX PBS, 0.1% Tween-20 (PBST) at room temperature (RT) for 2 hours. Membranes were then incubated with 10 μg/ml purified chicken anti- BSX pAb solution at RT for 2 hr, following by 3 x lOmin washes with PBST. Membranes were then incubated with 1:25,000 (v/v) dilution of sheep anti-chicken IgG-HRP conjugated antibody solution at RT for 1 hr, followed by 5 x 10 min washes with PBST. Membranes were finally treated with 'Femto' chemiluminescence reagents (Pierce) for 5 min before exposure to x-ray films.

Screening for BSX in sputum detected positive signal in 15/19 South African TB patients (Sensitivity = 78.9%) and 4/18 Australian non-TB respiratory disease patients (Specificity = 77.8%) using a purified chicken antibody raised against a NUS- conjugated recombinant protein (Figures 3a and 3b).

By combining the results of the Western blot for BSX and those of the ELISA for TetR, the sensitivity of the multi-analyte assay is increased

It is important to appreciate that non-TB controls are those patients presenting with clinical symptoms of TB but have been diagnosed with other respiratory disease such as pneumonia or bronchitis based on negative results for smear and culture testing for TB. Given the poor sensitivity of current diagnostic tests, there is ~30% chance that some of these controls may indeed have undiagnosed TB. As a consequence, the specificity for the multi-analyte (or single analyte) assay may be higher than actually observed.

EXAMPLE 9 Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis:

An ELISA to detect M. tuberculosis BSX

An ELISA assay was performed using one of three different anti-BSX antibodies, namely rabbit polyclonal anti-BSX antibody (raised against a BSX peptide) designated Rl 6, a chicken anti-BSX polyclonal antibody designated C44 (raised against recombinant protein) and a mouse anti-BSX monoclonal antibody designated 403 B (raised against the C-terminus of BSX). Briefly, the ELISA was performed as follows:

The ELISA plate was coated with various anti-BSX proteins including Chicken (Ch) anti-BSX pAb C44, Rabbit (Ra) anti-BSX pAb Rl 6, and Mouse (Mo) anti-BSX mAb 403B all at 20 μg/ml using 50 μl per well. Titrating amounts of recombinant BSX were added at a concentration of 50 ng/ml down to 3 pg/ml. Antigen detection was performed using either Rabbit anti-BSX at 10 μg/ml (with and without pre-incubation with the recombinant BSX protein) followed by detection using Sheep anti-Rabbit Ig HRP conjugate at a 1:5000 (v/v) dilution (for Chicken Capture system), or Chicken anti-BSX pAb C44 at 20 μg/ml followed by Sheep anti-Chicken IgG HRP conjugate at 1:5000 (v/v) dilution (for Mouse and Rabbit Capture systems). Data are presented in Figure 9. EXAMPLE 10 Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis:

Detection of M. tuberculosis by sandwich ELISA

Determining the detection limit of the sandwich ELISA

Subsequent to determining detection limits of anti-BSX mAb 403B and pAb C44 for detection of purified recombinant BSX our initial studies addressed optimisation of a sandwich ELISA using mAb 403B as a capture antibody and pAb C44 as a detector antibody. Briefly, Anti-BSX mAb 403B was immobilised onto an ELISA plate as a capture antibody at concentrations ranging from 10-40 μg/ml as specified above. Titrating amounts of recombinant BSX from 50 ng/ml down to 0.39 ng/ml were then screened using a purified chicken anti-BSX pAb, C44, at concentrations of either 10 or 20 μg/ml as specified above as the detector antibody followed by incubations with a Sheep anti-Chicken IgG HRP at a dilution of 1:5000 (v/v) and TMB for signal detection. Data are presented in Figure 10.

Under these conditions, the limit of detection of recombinant BSX was ~ 2-3 ng/ml.

Detecting BSX in patient samples

Sputum samples (50 μl + 50 μl blocking buffer) from South African TB patients and control patients with non-TB respiratory disease from South Africa (prefix 'M') and Australia (prefix 'CGS'), respectively, were screened by sandwich ELISA for the presence of BSX antigen. Purified Rabbit anti-BSX (peptide 28) pAb, Rl 6, was immobilised onto the ELISA plate as a Capture antibody at a concentration of 20 μg/ml. Purified Chicken anti-BSX pAb, C44, at a concentration of 5 μg/ml, was used as the Detector antibody. Sheep anti-Chicken IgG HRP at a dilution of 1:5000 (v/v) and TMB were used for signal detection. Sputum from control patient CGS25 was spiked with 5 ng/ml recombinant BSX as a positive control (red). Results are shown in Figure 11. EXAMPLE I l

Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis: Detection of M. tuberculosis BSX in sputum by amplified sandwich ELISA

ELISA plates were coated with either purified anti-BSX mAb 403B at a concentration of 40 μg/ml or purified Chicken anti-BSX pAb C44 at a concentration of 5 μg/ml using 50 μl per well. Titrating amounts of purified recombinant BSX were added at a concentration of 50 ng/ml down to 0.39 ng/ml. Two amplification systems were performed using either Chicken anti-BSX at a concentration of 10 μg/ml followed by Donkey anti-Chicken IgG biotin conjugate at various dilutions and finally streptavidin- HRP at a 1:5000 (v/v) dilution, or anti-BSX mAb 403B at various concentrations followed by Goat anti-Mouse IgG at 1 :30000 (v/v) dilution and Donkey anti-Goat IgG HRP conjugate at a 1:5000 (v/v) dilution. The amplified systems were used to compare to a basic antigen detecting system where Chicken anti-BSX was used at a concentration of 10 μg/ml followed by Sheep anti-Chicken IgG HRP conjugate at a 1:5000 (v/v) dilution.

As shown in Figure 12, the amplified ELISA was approximately 10 fold more sensitive than the standard ELISA. Signal intensity is slightly higher when using the Rabbit pAb as a capture and the Chicken pAb as the first detector Ab in the amplified system (Figure 13).

We have also investigated an amplified ELISA system which, as shown in Figures 14 and 15, uses purified rabbit anti-BSX pAb Rl 6 as a capture antibody and purified chicken anti-BSX pAb C44 as a detector antibody followed by amplification with a biotinylated secondary detector Ab. This system provided a further 2-fold increase in sensitivity compared the amplification systems described earlier (Figure 14; Figure 15).

We have also performed studies using the amplified biotin based ELISA to screen clinical sputum samples from TB and non-TB respiratory disease control patients, always keeping in mind in the non-TB respiratory disease group there may be up to 30- 40% of the patients having TB co-infections due to the reduced sensitivity of smear microscopy and culture assays (Figure 16).

To investigate if antibody sites were being saturated with endogenous BSX we also compared the effect of (i) incubation time; and (ii) sequential incubations with a fresh aliquot of a sputum sample from the same respective patient. The increase from a 1 hr to a 2 hr incubation did not have any effect on signal intensity. In contrast, preliminary data indicates that sequential incubations with 2 different sample loads of sputum increased signal intensity (Figure 17). Whilst the increase is not large, these preliminary observations warrant further investigation. Interestingly, the increase in signal intensity was most marked for detection of a recombinant protein as a positive control.

EXAMPLE 12

Antibody-based diagnosis of tuberculosis or infection by M. tuberculosis: ELISA using M. tuberculosis Bsx protein fragments to diagnose the presence of antibodies against M. tuberculosis

1. Sera and peptides

A total of 30 TB-positive samples and 52 TB-negative samples were screened with the following peptides derived from the Bsx protein: MRQLAERSGVSNPYL (SEQ ID NO: 14), ERGLRKPSADVLSQI (SEQ ID NO: 15), LRKPS ADVLSQIAKA (SEQ ID NO: 16), PSADVLSQIAKALRV (SEQ ID NO: 17), SQIAKALRVSAEVLY (SEQ ID NO: 18), AKALRVSAEVLYVRA (SEQ ID NO: 19), VRAGILEPSETSQVR (SEQ ID NO: 20), TAITERQKQILLDIY (SEQ ID NO: 2I)₅ S QIAKALRVS AE VL YVRAC (SEQ ID NO: 22), MSSEEKLCDPTPTDD (SEQ ID NO: 23) and VRAGILEPSETSQVRC (SEQ ID NO: 24). In each case, the peptides were biotinylated to facilitate their detection. These samples included sera from South African (S.A.) Zulu TB-positive individuals, S. A. Zulu TB-negative individuals, S.A. Caucasian TB-negative individuals, World Health Organisation (WHO) TB-positive individuals of unknown race, WHO TB- negative individuals of unknown race, and Australian Caucasian TB-negative control individuals and plasma from Chinese TB-positive individuals and Chinese TB-negative individuals.

Samples were screened for the presence of antibodies using an ELISA system developed as described below.

2, ELISA Assay

Nunc-Immuno module maxisorp wells were coated overnight at room temperature or at 4⁰C over the weekend with lOOμl/well of 5μg/ml streptavidin diluted in milli-Q water. The streptavidin was flicked out of the wells and each well was blocked with 200 μl phosphate-buffered saline (PBS) containing 1.0% (w/v) casein, 0.1% (v/v) Tween 20 and 0.1% (w/v) Azide (blocker) per well. After 1 hour, the blocker was removed, and each well was coated with lOOμl of biotinylated peptide in blocker for 1 hour, with agitation of the plate. Subsequently, each well was washed 5 times with PBS/0.1% Tween 20, allowed to dry on absorbent paper, and either stored at 4⁰C with dessicant, or used immediately. This was followed by incubation for 1 hour with agitation in 50μl of patient serum or plasma, diluted 1:50 (v/v) in blocker. Following this incubation, all wells were washed 5 times, using PBS/0.1% Tween 20 in a laminar flow, and tapped dry. Then lOOμl Sheep anti-human IgG Horse Radish Peroxidase (HRP) conjugate was added to each well. The conjugate was diluted 1:10,000 (v/v) in PBS/0.1% (w/v) casein/0.1% (v/v) Tween 20/0.1% (w/v) thimerosal, and incubated for 1 hour with agitation. Each well was then washed 4 times using PBS/0.1% (v/v) Tween 20, and twice using PBS. Finally, lOOμl liquid TMB substrate based system (Sigma) was added to each well, and the wells incubated at room temperature in the dark for 20 mins. Reactions were stopped by addition of lOOμl 0.5M Sulfuric acid. Each peptide was assayed in duplicate and repeated if duplicates did not appear to be reproducible. Alongside the patient samples, four control samples were also tested, as follows:

1. Negative control: streptavidin/peptide 24/no serum or plasma/conjugate;

2. Peptide Control: streptavidin/no peptide/patient serum or plasma/conjugate; 3. Positive control: streptavidin/peptide 24/S.A. serum 7/conjugate; and 4. Serum background: no streptavidin/no peptide/patient serum or plasma/conjugate.

S.A. serum 7 was used for the positive control, due to its consistent reproducible positive results found in preliminary ELISA experimentation.

3. Data analysis

Immunogenic peptides represent outliers in the distribution of peptide absorbencies and are detected following log transformation normalisation by calculation of a normal score statistic, with a mean and standard deviation estimated by a robust M-Estimator.

4. Results

Mass screening of the TB-positive and TB-negative samples for the presence of antibodies to Bsx peptides demonstrate that about 47% of TB-positive samples contain anti-Bsx antibodies. A small number of TB-negative patients may test positive for any Bsx peptide. Differentiation of the total patient population to include HIV status will elucidate a TB/HIV correlation, where about 76% of the TB-positive samples that contain anti-Bsx antibodies are also HIV⁺. In the S.A. group, about 80% of the S.A. TB-positive/HIV⁺ samples should contain antibodies to Bsx.

Conversely, in Chinese populations that are HIV^" and categorised according to their pulmonary diagnosis, none of the extra-pulmonary or pulmonary TB-positive plasma should contain antibodies to Bsx, and only a small number of TB-negative plasma screened may contain anti-Bsx antibodies to one Bsx peptide. In summary, ELISA analysis of TB positive and TB negative serum or plasma reveals a number of immunogenic Bsx peptides containing B cell epitopes of the full-length Bsx protein of M. tuberculosis.

Several peptides are non-immunogenic in any control TB-negative serum or control plasma tested e.g., in sera from TB-negative S.A. Zulu subjects. These data reinforce the suitability of Bsx and/or any of its peptides as a diagnostic reagent, and as an immunogen for the preparation of monoclonal antibodies suitable for use in an antigen- based assay for M. tuberculosis infection.

Furthermore, the correlation between HIV status and TB status with respect to serological reactivity of a Bsx peptide has many therapeutic advantages, such as, for example, the ability to detect TB and HIV status and/or monitoring the TB status in HIV⁺ individuals. To further emphasise the correlation between TB and HIV, it is important to note that all of the Chinese samples investigated were HIV^" negative.

The absence of detectable antibodies that bind to Bsx in plasma from patients in a Chinese cohort may be associated with pulmonary TB being confined to the lung, whereas in the South African patients HIV positive status is often associated with extrapulmonary disease, which is more systemic. Alternatively, Bsx may not be as highly expressed in Chinese compared to South African TB patients.

EXAMPLE 13

Antibody-based diagnosis of tuberculosis or infection by M. tuberculosis: Screening of TB and non-TB sera against synthetic peptides derived from the Bsx protein 1. Synthetic peptides

Three peptides were synthesised from the amino acid sequence of the putative transcriptional regulator Bsx (SwissProt entry number 053759) and evaluated as capture agents for Human immunoglobulin G in TB-positive sera. One peptide, designated Bsx (23-24) peptide (SEQ ID NO: 22) comprises the sequence of a highly immunogenic Bsx peptide with additional N-terminal and C-terminal sequences flanking this sequence in the full-length protein and conjugated C-terminally to a cysteine residue. Another peptide, designated N-C terminal (SEQ ID NO: 23) comprised the N-terminal seven residues of Bsx protein fused to the C-terminal seven residues of Bsx by an intervening cysteine residue. A third peptide, designated peptide 28 (SEQ ID NO: 24) comprises another Bsx peptide conjugated C-terminally to a cysteine residue.

For ELISA formats, the peptides set forth in SEQ ID NOs: 22-24 additionally comprised an N-terminal linker (Ser-Gly-Ser-Gly) to the base peptide, to facilitate binding of the peptide to solid matrices.

The C-terminal and internal cysteine residues were included to facilitate cross-linking of the peptides for subsequent antibody production.

2. Sera/plasma

Sera and plasma were a panel obtained from 41- 44 TB-positive patients (i.e., TB- positive sera) in each experiment, and 51 healthy control subjects (i.e., non-TB sera).

3. ELISA Assay

Peptides comprising SEQ ID NOs: 22-24were coated on ELISA trays at 3 μg/mL on a streptavidin base of 5 μg/mL and then probed (after blocking) with Non-TB control sera and Known TB-positive sera and plasma. Sera and plasma were diluted 1 :50 (v/v) prior to use. Capture of human IgG was traced with enzyme-linked sheep anti- HuIgG/tetramethylbenzidine (TMB) substrate.

4. Statistical analyses

The sensitivity and specificity were analysed by taking the average substrate product

OD values (from the conjugated peroxidase/TMB reaction) and calculating the cut-off values for significance at two standard deviations above the average and three standard deviations above the mean (i.e., at the 95% and 99.7% significance levels, respectively). For the control sera, one sample produced an outlier OD value by Dixon's outlier test (N = 30). The analyses were compared including or excluding this outlier.

As used herein, term "sensitivity" in the context of a diagnostic/prognostic assay is understood to mean the proportion of TB-positive subjects that are diagnosed using a particular assay method (i.e., a "true" positive). Accordingly, an assay that has increased sensitivity is capable of detecting a greater proportion of TB -infected subjects than an assay with reduced or lower sensitivity.

As used herein, the term "specificity" in the context of a diagnostic/prognostic assay is understood to mean the proportion of non-TB subjects (i.e., non-infected subjects) that do not return a positive result using a particular assay method (i.e., "true" negatives). Accordingly, an assay that has increased or enhanced specificity returns fewer false positive results or is capable of distinguishing between infected and non-infected subjects to a greater degree than an assay with a reduced specificity.

5. Results a) Bsx (23-24) Peptide (SEQ ID NO: 22)

Bsx (23-24) peptide sequence showed a significant binding to confirmed TB-positive sera. Data indicate that a peptide comprising the sequence set forth in SEQ ID NO: 22 selectively identifies antibodies that bind to M. tuberculosis in patient sera. Data also show that the sensitivity and specificity with these revised criteria are relatively unchanged irrespective of whether or not the outliers is omitted, however there is a marginal increase in sensitivity at the 3 standard deviation level.

b) N-C terminal (SEQ ID NO: 23) and Peptide 28 (SEQ ID NO: 24)

These two peptides showed only weak interaction against a range of confirmed TB- positive sera. Assays using these peptides were not highly sensitive, albeit specific in so far as they omit false positive detection. The data indicate that Bsx (23-24) peptide (SEQ ID NO: 22) has utility in antibody- based assays to detected tuberculosis in patient samples, especially sera. The other two peptides tested in this example (SEQ ID NOs: 23 and/or 24) also have utility in eliminating false positive detection e.g., as part of a multi-analyte test.

EXAMPLE 14

Antibody-based diagnosis of tuberculosis or infection by M. tuberculosis: Screening of TB and non-TB sera against recombinant full-length Bsx protein

1. Sera/plasma

Sera and plasma were from 44 TB-positive (smear or culture) Chinese and South African patients (i.e., TB-positive sera), and 44 healthy control subjects (i.e., non-TB sera).

2. ELISA Assay

Recombinant Bsx protein was coated directly onto ELISA trays at 5 μg/mL and then probed (after blocking) with Non-TB control sera, and known TB-positive sera and plasmadiluted 1:100 (v/v) in buffer. Capture of human IgG was traced with enzyme- linked sheep anti-HuIgG/tetramethylbenzidine (TMB) substrate.

3. Statistical analyses

The sensitivity and specificity were analysed by taking the average substrate product OD values (from the conjugated peroxidase/TMB reaction) and calculating the cut-off values for significance at two standard deviations above the average and three standard deviations above the mean (i.e., at the 95% and 99.7% significance levels, respectively).

4. Results

Recombinant Bsx protein assayed under these conditions was highly specific in detecting TB-positive sera. Sensitivity of the assay over the populations tested was intermediate between SEQ ID NO: 22 and SEQ ID NOs: 23-24. On the other hand, the sensitivity of the assay in South African TB sera smears or culture positives is higher than the overall sensitivity (i.e., 35% compared to 25% at three standard deviations cut-off value). Using Chinese smear or culture TB sera, the sensitivity of the assay is lower than the overall sensitivity (i.e., 11% compared to 25% at three standard deviations cut-off value). In both Chinese and South African populations, the specificity of the assay is 100%, indicating robustness in this parameter.

EXAMPLE 15

Antibody-based diagnosis of tuberculosis or infection by M. tuberculosis: Screening of TB and non-TB sera according to HIV status

1. Sera/plasma Sera and plasma were obtained from the following subjects:

(i) Five (5) TB-positive and HIV-negative smear or culture South African patients

(i.e., TB⁺ HIV^" sera/plasma);

(ii) Twenty one (21) TB-positive and HIV-positive smear or culture South African patients (i.e., TB⁺ HIV⁺ sera/plasam); and (iii) Twenty (20) TB-negative and HIV-negative smear or culture subjects (i.e., healthy control sera/plasma).

2. ELISA Assay

Recombinant Bsx protein or Bsx (23-24) peptide (SEQ ID NO: 22) was coated directly onto ELISA trays at 5 μg/mL and then probed (after blocking) with Non-TB control sera and known TB-positive sera diluted 1:100 (v/v) in buffer. Alternatively, the Bsx(23-24) peptide was used as described in the preceding examples. Capture of human IgG was traced with enzyme-linked sheep anti-HuIgG/tetramethylbenzidine (TMB) substrate. 3. Statistical analyses

4. Results

Recombinant Bsx protein assayed under these conditions was highly specific in detecting TB-positive sera. Sensitivity of the assay over the populations tested was also quite high for HIV⁺ patients. Similar results were obtained using the Bsx(23-24) peptide. Thus, the full-length recombinant Bsx protein and Bsx(23-24) peptide separately detect about 40-45% of TB⁺ HIV⁺ subjects, and, in a multianalyte test format, detect about 65% to 70% of TB⁺HTV⁺ subjects, with only about 5% false- positive detection.

On the other hand, the sensitivity of the assay in South African TB sera and/or plasma smears or culture positives is higher than the overall sensitivity (i.e., 35% compared to 25% at three standard deviations cut-off value). Using Chinese smear or culture TB sera/plasma, the sensitivity of the assay is lower than the overall sensitivity (i.e., 11% compared to 25% at three standard deviations cut-off value). In both Chinese and South African populations, the specificity of the assay is absolute i.e., 100% indicating robustness in this parameter.

These data indicate that the full-length Bsx protein, e.g., expressed as a recombinant protein, can be used in combination with a synthetic peptide comprising the dominant B-cell epitope identified herein e.g., Bsx(23-24) peptide (SEQ ID NO: 22) , to diagnose the presence of an active infection or recent past infection by M. tuberculosis.

For example, recombinant full-length Bsx and Bsx(23-24) peptide are both biotinylated and immobilized onto a streptavidin base (5μg/ml) that has been preadsorbed onto wells of a microtitre plate. Standard ELISA reactions are carried out wherein (i) patient sera and control sera, each diluted 1:100 (v/v) in buffer, are added to separate wells, and (ii) capture of human IgG in the sera by the immobilized protein and peptide is traced using enzyme-linked sheep anti-HulgG detected using tetramethylbenzidine (TMB) substrate.

EXAMPLE 16

Isolation of monoclonal antibodies that bind to M. tuberculosis GS peptide 1. Antigen selection ELISA assays were performed to determine those GS peptide fragments against which an immune response was detected in sera from TB subjects and no immune response was detected in control subjects.

The amino acid sequence of the GS identified as being immunogenic in TB subjects (glutamine synthetase A4 or glnA4) was aligned with the amino acid sequence of other known TB glutamine synthetases (glnA, glnA2 and glnA3) and shown to have only 25% amino acid sequence identity with other known glutamine synthetase homologs. GS peptides were selected that are specifically immunoreactive with sera from TB⁺ subjects and not comprise sequences not conserved with other glutamine synthetases.

Finally, 3 -dimensional protein modelling was used to determine a region of the GS protein of the invention that was likely to be on the surface of the protein in vivo. Based on all of the studies described supra two peptides were selected that were immunogenic in TB sera and not control sera, corresponded to a non-conserved region of GS and are likely to be on the surface of the GS protein in vivo. These peptides comprise the following sequences:

(i) RGTDGSAVFADSNGPHGMSSMFRSF (SEQ ID NO: 25); and (ii) WASGYRGLTPASDYNIDYAI (SEQ ID NO: 26)

Antibodies that selectively bind to these peptides are unlikely to cross-react with another glutamine synthetase proteins. The two peptides were selected as antigens for antibody production, synthesized and attached to diphtheria toxoid.

2. Antibody production Antigen

Approximately 6 mgs of peptide antigen consisting of the sequence RGTDGSAVFADSNGPHGMSSMFRSF (set forth in SEQ ID NO: 25) conjugated to diphtheria toxoid was provided to NeoClone, Madison, Wisconsin, USA for generation of monoclonal antibodies according to their standard protocol. About 1 mg of the peptide was provided as biotinylated peptide for quality control.

Immunization

Five BALB/cByJ female mice were immunized with peptide conjugated to carrier according to Neoclone's standard immunization process.

Test Bleeds

Infection

The spleens of 3 mice having the highest titer of polyclonal antibodies cross-reactive with peptide antigen were used for the ABL-MYC infection, according to NeoClone's standard infection procedure.

Transplantation

The splenocytes of the ABL-MYC-infected mice were transplanted into approximately 20 naive mice. Ascites development

Ascites fluid developed in the transplanted mice were isolated and screened for cells producing monoclonal antibodies (mAbs) that bind to the target peptide antigen. A cell line (i.e., plasmacytoma) producing a rnAb designated 426C was isolated. Binding affinity and isotype specificity of the rnAb 426C was confirmed using ELISA.

The mAb designated 426C was provided in 1 ml aliquots (approximately) in ascites, together with the associated cell line.

The mAb designated 426C is purified from ascites using protein G or protein A columns.

3. Antibody titration

The monoclonal antibody designated 426C was coated on the bottom of an ELISA plate at 20 μg/ml and (i) an immunogenic glutamine synthetase (GS) peptide comprising SEQ ID NO: 25 and biotinylated at the N-terminus or (ii) a negative control peptide biotinylated at the N-terminus, were added at various concentrations to 10 pg/ml. The biotinylated GS peptide used had the sequence:

SGSGRGTDGSAVFADSNGPHGMSSMFRSFC. The peptide was detected by binding of streptavidin HRP conjugate under standard conditions. Absorbances were determined at 450nm and 620nm, and the difference in absorbance at 450nm and 620nm determined. Average data for duplicate samples were obtained. The data obtained show that the antibodies capture the immunogenic GS peptide antigen at concentrations of about lOpg/ml or greater, at a signaltnoise ratio of at least about 2.0. These data demonstrate efficacy of the antibodies as a capture reagent in immunoassays.

In a further assay to titre the monoclonal antibodies, the peptide was coated onto the bottom of the ELISA plate at a concentration of about 3 μg/ml. Duplicate aliquots of the monoclonal antibody-producing plasmacytoma designated 426C, and duplicate aliquots of a negative control monoclonal antibody were added at various final concentrations to lOpg/ml. Binding of the antibody was then detected using sheep anti- mouse HRP antibody conjugate under standard conditions. Absorbances were determined at 450nm and 620nm, and the difference in absorbance at 450nm and 620nm determined. Average data were obtained. The data show that the antibody successfully detects GS above assay background at concentrations of antibody as low as 10pg/ml, therefore demonstrating efficacy as a detection reagent in immunoassays.

EXAMPLE 17

Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis: Solid phase ELISA using mAb 426 to detect circulating immune complexes comprising M. tuberculosis glutamine synthetase (GS) polypeptide or GS fragments

This example describes an ELISA for the detection of circulating immune complexes (CIC) bound to M. tuberculosis glutamine synthetase (GS) in patient samples comprising circulating immune complexes or antibodies, such as a bodily fluid selected from the group consisting of blood, sera, sputa, plasma, pleural fluid, saliva, urine etc.

Whilst the assay is described herein for the detection of CIC comprising M. tuberculosis GS using mAb 426C, the skilled artisan will be aware that the assay is broadly applicable to the detection of any CIC comprising an antigen against which a capture antibody has been produced. In general, the assay uses antibodies that bind specific epitopes on a target antigen found, for example, in sputa and/or sera from a subject that is infected with a pathogen (i.e., the subject has an active infection). The antibodies are used in a capture ELISA to bind CIC comprising the target antigen and the bound CIC are detected by contacting a secondary antibody that recognizes human Ig, e.g. anti-human IgA or anti-human IgG antibody, for a time and under conditions sufficient for binding to occur and then detecting the bound secondary antibody. For example, the secondary antibody may be conjugated to a detectable label e.g., horseradish peroxidase (HRP). Additionally, whilst exemplified herein for TB, it is to be understood that the immunoassay format described herein is useful for detecting any disease or disorder which is associated with the presence of CIC, including any infection, Johne's disease, Bovine TB, or Crohne's disease.

Additionally, whilst the assay is described herein for ELISA, it is to be appreciated that the generic assay is readily applicable to any immunoassay format e.g., a rapid point- of-care diagnostic format, flow-through format, etc.

An advantage of this assay format is that it directly shows an active vs. latent infection. This immunoassay format is particularly useful for discriminating between active TB infection and other, non-TB infections, and for monitoring a response of a TB patient to treatment.

ELISA based assay

Monoclonal antibody 426C that binds to M. tuberculosis glutamine synthetase at a concentration of 20 μg/ml in water, was coated onto the bottom of one or more NUNC plates. Plates were left to dry at 37⁰C overnight. The plates were blocked for 1 to 3 hours at room temperature in blocking buffer [1% (w/v) casein/0.1% (v/v) Tween-20 in 0.5M phosphate buffered saline (PBS)]. The wells were flicked or tapped to remove blocking solution, and patient sera diluted 1:50 (v/v) in blocking buffer (50ul/well) added. The plates were then incubated for 1 hour at room temperature e.g., on a rotating shaker. The plates were washed about 3-5 times with 0.1% (v/v) Tween-20 in 0.5M phosphate buffered saline (PBS) such as, for example, using an automated plate washer. Sheep anti-human IgG antibody or anti-human IgA antibody, diluted 1:5000 (v/v) in blocking buffer was added to wells. The plates were then incubated for 1 hour at room temperature e.g., on a rotating shaker. The plates were washed as before, and TMB was added to the wells (50 μl /well). Plates were incubated for about 30 minutes, and the reactions were then stopped by addition of 0.5M H₂SO₄ (50 μl/well). Absorbances of each well was read at wavelengths of 450nm and 620nm, and the differences in these wavelengths is determined (Le₁A₄₅O-A₆₂₀). The incubation periods and volumes of reagents specified in the preceding paragraph can be changed without affecting the parameters of the test. Preferably, the concentrations of the patient sera, the capture antibody (e.g., rnAb 426C) and the detecting antibodies (i.e., anti-human IgG antibody or anti-human IgA antibody or anti- human IgM antibody).

Results

Sera/plasma from 45 South African subjects with confirmed TB were screened and compared with 19 (black) control sera/plasma and 14 (white) control sera/plasma. Three other South African sera/plasma were also included that had been diagnosed with diseases other than TB. A substantial number of the 45 TB sera tested detected levels of immune complexes comprising GS at greater than 3 standard deviations above control average. Furthermore, of the 36 non-TB sera/plasma, one was greater than 3 standard deviations above control average indicating that that the assay a high level of specificity.

When the limit was set at two standard deviations the true positive rate was substantially increased while the false positive rate did not change substantially.

Sera/plasma from 49 Chinese subjects with clinically-confirmed TB were also screened using the ELISA assay. Again this assay detected increased levels (greater than 2 or 3 times standard deviation of the control average) of CIC comprising GS in TB subjects. Furthermore, or the 41 of non-TB subjects only 5 returned readings greater than 2 or 3 standard deviations above control average indicating that that the assay a high level of specificity.

These results clearly indicate that the monoclonal antibody 426C is specific for GS of M. tuberculosis and does not cross react with human proteins to a significant degree. EXAMPLE 18

Antigen-based diagnosis of tuberculosis or infection by M. tuberculosis: Point-of-care test for diagnosing an active infection by M. tuberculosis using mAb 426

Monoclonal antibody 426C is striped onto a nitrocellulose membrane at a concentration of between about 0,5 and about 4 mg/ ml. The nitrocellulose membrane is allowed to dry at 4O⁰C for 20 minutes. The nitrocellulose sheet is then cut into a 1 cm x 1 cm squares and inserted into the base of the DiagnostIQ device (Proteome Systems Ltd) on top of a cellulose pad. The Pre-incubation frame is attached to the base and the test performed according to the procedure below.

1. About 100 μl to about 500 μl of patient or control sera/plasma are added to the pre-incubation well of the DiagnostIQ format with 150 μl of gold conjugated to an anti- human IgG and/or IgA antibody. 2. The sera/plasma are incubated with the nitrocellulose strip membrane for 30 seconds and the pre-incubation frame is pushed down onto the base of the test. 3. After about 1 minute, 2-4 drops of wash solution (0.5% (v/v) Tween 20 in 0.1 M phosphate buffer) is added to the pre-incubation well and allowed to flow through the device. 4. The pre-incubation frame is removed and the signal read by visually interpreted or read in a Readrite optical reader.

In a modification of this example, additional antibodies targeted against other specific epitopes on the same or different M. tuberculosis antigen are employed alongside mAb 426C. Additionally, the present invention clearly encompasses conjugation of the anti- IgG and/or anti-IgA antibody to the same gold particle to ensure the same amount of label is applied in each test. The gold particles may also be dried onto the preincubation pads, to thereby avoid the later addition of conjugate. Sensitivity of the assay may also be improved by increasing the amount of sera tested in each sample. EXAMPLE 19 Isolation of additional monoclonal antibodies that bind to M. tuberculosis GS or TetR 1. Antibody production Antigen

Approximately 6 mgs of peptide antigen consisting of TetR sequence set forth in SEQ ID NO: 12 or the GS sequence set forth in any one of SEQ ID NOs: 25-28 is conjugated to diphtheria toxoid and monoclonal antibodies prepared according to standard procedures e.g., according to a protocol of NeoClone, Madison, Wisconsin, USA. About 1 mg of the peptide is also produced as a biotinylated peptide for quality control.

Immunization

Five BALB/cByJ female mice are immunized with peptide conjugated to carrier according to Neoclone's standard immunization process.

Test Bleeds

Test bleeds of the immunized mice are performed at regular intervals for use in the quality control sera ELISAs using biotinylated peptide. Polyclonal sera having the highest titer are determined using ELISA. Mice having polyclonal antibody titers of at least 1,000 are used for the ABL-MYC infection process.

Infection

The spleens of 3 mice having the highest titer of polyclonal antibodies cross-reactive with peptide antigen are used for the ABL-MYC infection, according to NeoClone's standard infection procedure.

Transplantation

The splenocytes of the ABL-MYC-infected mice are transplanted into approximately 20 naive mice. Ascites development

Ascited fluid developed in the transplanted mice is isolated and screened for cells producing monoclonal antibodies (mAbs) that bind to the target peptide antigen. Cell lines (i.e., plasmacytoma) producing mAbs that bind to the peptide antigen are isolated. Binding affinity and isotype specificity of the mAbs is confirmed using ELISA.

A mAb that binds to the peptide antigen are is purified from ascites using protein G or protein A columns.

Antibody titration is performed essentially as described in the preceding examples.

Claims

WE CLAIM:

1. An isolated or recombinant immunogenic protein of Mycobacterium tuberculosis that is a putative transcriptional regulatory protein of the Tet repressor family (hereinafter "TetR") or an immunogenic peptide or immunogenic fragment or epitope thereof.

2. The isolated or recombinant immunogenic TetR protein according to claim 1 wherein said protein comprises the amino acid sequence set forth in SEQ ID NO: 1 or an amino acid sequence that is at least about 95% identical to SEQ ID NO: 1.

3. The immunogenic TetR peptide or immunogenic TetR fragment or epitope according to claim 1 wherein said peptide, fragment or epitope comprises at least about 5 consecutive amino acid residues of the sequence set forth in SEQ ID NO: 1.

4. The immunogenic TetR peptide or immunogenic TetR fragment or epitope according to claim 3 wherein said peptide, fragment or epitope comprises an amino acid sequence set forth in any one of SEQ ID Nos: 2-13 or an immunologically cross- reactive variant of any one of said sequences that comprises an amino acid sequence that is at least about 95% identical thereto.

5. The immunogenic TetR peptide or immunogenic TetR fragment or epitope according to claim 4 wherein said peptide, fragment or epitope comprises the amino acid sequence set forth in SEQ ID NO: 12.

6. The immunogenic TetR peptide or immunogenic TetR fragment or epitope according to any one of claims 1, 3, 4 or 5, wherein said peptide, fragment or epitope comprises one or more labels or detectable moieties.

7. A fusion protein comprising one or more immunogenic TetR peptides, fragments or epitopes according to any one of claims 1, 3, 4, 5 or 6 and a linker.

8. A fusion protein comprising a plurality of immunogenic TetR peptides, fragments or epitopes according to any one of claims 1, 3, 4, 5 or 6.

9. A fusion protein comprising the isolated or recombinant immunogenic TetR protein, immunogenic TetR peptide, immunogenic TetR fragment or epitope according to any one of claims 1 to 6 fused to a carrier protein, detectable label or reporter molecule.

10. Use of the isolated or recombinant immunogenic TetR protein of Mycobacterium tuberculosis or immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any one of claims 1 to 6 for detecting a past infection, active infection or latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of antibodies in a sample obtained from the subject to said isolated or recombinant immunogenic TetR protein or immunogenic TetR peptide or immunogenic TetR fragment or epitope.

11. An isolated or recombinant antibody that binds specifically to the isolated or recombinant immunogenic TetR protein, immunogenic TetR peptide, immunogenic TetR fragment or epitope according to any one of claims 1 to 6 or to a fusion protein or protein aggregate comprising said immunogenic TetR protein, peptide, fragment or epitope.

12. The isolated antibody according to claim 11 wherein said antibody is a polyclonal antibody.

13. The isolated antibody according to claim 11 wherein said antibody is a monoclonal antibody.

14. The recombinant antibody according to claim 11 wherein said antibody is a recombinant antibody.

15. The isolated or recombinant antibody according to any one of claims 11 to 14 wherein said antibody is labelled with a reporter molecule.

16. The isolated or recombinant antibody according to claim 15 wherein the reporter molecule is biotin.

17. An isolated antibody-producing cell or antibody-producing cell population that produces an antibody according to any one of claims 11 to 13.

18. Use of the isolated or recombinant antibody according to any one of claims 11 to 16 or an immune-reactive fragment thereof for detecting a past or present infection or a latent infection by M. tuberculosis in a subject, wherein said infection is determined by the binding of the antibody or fragment to M. tuberculosis TetR protein or an immunogenic fragment or epitope thereof present in a biological sample obtained from the subject.

19. Use of the isolated or recombinant antibody according to any one of claims 11 to 16 or an immune-reactive fragment thereof for identifying the bacterium M. tuberculosis or cells infected by M. tuberculosis or for sorting or counting of said bacterium or said cells.

20. Use of the isolated or recombinant antibody according to any one of claims 11 to 16 or an immune-reactive fragment thereof in medicine.

21. A composition comprising the isolated or recombinant antibody according to any one of claims 11 to 16 and a pharmaceutically acceptable carrier, diluent or excipient.

22. A method of diagnosing tuberculosis or an infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject antibodies against the immunogenic TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any one of claims 1 to 6, wherein the presence of said antibodies in the sample is indicative of infection.

23. The method of claim 22 comprising contacting a biological sample derived from the subject with the isolated or recombinant immunogenic TetR protein of

Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof for a time and under conditions sufficient for an antigen- antibody complex to form and then detecting the formation of an antigen-antibody complex.

24. The method of claim 23 wherein detecting the formation of an antigen-antibody complex comprises detecting human immunoglobulin in the antigen-antibody complex.

25. The method of claim 24 wherein detecting human immunoglobulin comprises contacting the antigen-antibody complex with a second antibody comprising anti- human immunoglobulin for a time and under conditions sufficient for said second antibody to bind to the human immunoglobulin in the complex and then detecting the bound anti-human immunoglobulin.

26. The method of claim 25 wherein the second antibody is labelled with a detectable marker or report molecule.

27. The method according to any one of claims 23 to 26 wherein the biological sample derived from the subject is contacted with the isolated or recombinant immunogenic TetR protein of Mycobacterium tuberculosis, said protein comprising an amino acid sequence set forth in SEQ ID NO: 1.

28. The method according to any one of claims 23 to 26 wherein the biological sample derived from the subject is contacted with an immunogenic TetR peptide comprising an amino acid sequence set forth in any one of SEQ ID NOs: 2-13.

29. The method according to any one of claims 23 to 27 further comprising contacting a biological sample derived from the subject with an immunogenic protein or peptide of Mycobacterium tuberculosis other than isolated or recombinant immunogenic TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof.

30. The method according to claim 29 wherein the immunogenic protein or peptide of Mycobacterium tuberculosis other than isolated or recombinant immunogenic TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof is selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342) an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

31. The method according to claim 29 wherein the immunogenic protein or peptide of Mycobacterium tuberculosis other than isolated or recombinant immunogenic TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof is selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

32. A method of diagnosing tuberculosis or infection by M. tuberculosis in a subject comprising detecting in a biological sample from said subject an immunogenic TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof using the isolated or recombinant antibody according to any one of claims 11 to 16, wherein the presence of said protein or immunogenic fragment or epitope in the sample is indicative of disease, disease progression or infection.

33. The method of claim 32 comprising contacting a biological sample derived from the subject with the isolated or recombinant antibody for a time and under conditions sufficient for an antigen-antibody complex to form and then detecting the formation of an antigen-antibody complex.

34. The method of claim 33 comprising performing an enzyme- linked immunosorbent assay (ELISA).

35. The method of claim 34 wherein the ELISA is a sandwich ELISA using a capture antibody and a detection antibody.

36. The method according to any one of claims 32 to 35 wherein the sample comprises an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof.

37. The method according to any one of claims 32 to 35 wherein the sample comprises a body fluid.

38. The method of claim 37 wherein the body fluid is sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or a derivative thereof.

39. The method according to any one of claims 32 to 38 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

40. The method according to any one of claims 32 to 39 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

41. The method according to any one of claims 32 to 40 wherein the subject is an immune-compromized or immune deficient subject.

42. The method of claim 41 wherein the immune-compromized or immune deficient subject is infected with human immunodeficiency virus (HIV).

43. A method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting M. tuberculosis TetR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject using the isolated or recombinant antibody according to any one of claims 11 to 16, wherein a level of the protein or fragment or epitope that is enhanced, or not decreased or decreasing, compared to the level of that protein or fragment or epitope detectable in a normal or healthy subject indicates that the subject is not responding to said treatment or has not been rendered free of disease or infection.

44. The method of claim 43 comprising contacting a biological sample derived from the subject with one or more of the isolated or recombinant antibodies and detecting the formation of an antigen-antibody complex.

45. The method of claim 44 comprising performing an enzyme- linked immunosorbent assay (ELISA).

46. The method of claim 45 wherein the ELISA is a sandwich ELISA using a capture antibody and a detection antibody.

47. The method according to any one of claims 43 to 46 wherein the sample comprises an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof.

48. The method according to any one of claims 43 to 46 wherein the sample comprises a body fluid.

49. The method of claim 48 wherein the body fluid is sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or a derivative thereof.

50. The method according to any one of claims 43 to 49 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

51. The method according to any one of claims 43 to 50 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

52. The method according to any one of claims 43 to 51 wherein the subject is an immune-compromized or immune deficient subject.

53. The method of claim 52 wherein the immune-compromized or immune deficient subject is infected with human immunodeficiency virus (HIV).

54 A method for determining the response of a subject having tuberculosis or an infection by M. tuberculosis to treatment with a therapeutic compound for said tuberculosis or infection, said method comprising detecting a TetR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject, wherein a level of the protein or fragment or epitope that is lower than the level of the protein or fragment or epitope detectable in a subject suffering from tuberculosis or infection by M. tuberculosis indicates that the subject is responding to said treatment or has been rendered free of disease or infection.

55. The method of claim 54 comprising contacting a biological sample derived from the subject with one or more of the isolated or recombinant antibodies and detecting the formation of an antigen-antibody complex.

56. The method of claim 55 comprising performing an enzyme- linked immunosorbent assay (ELISA).

57. The method of claim 56 wherein the ELISA is a sandwich ELISA using a capture antibody and a detection antibody.

58. The method according to any one of claims 54 to 57 wherein the sample comprises an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof.

59. The method according to any one of claims 54 to 57 wherein the sample comprises a body fluid.

60. The method of claim 59 wherein the body fluid is sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or a derivative thereof.

61. The method according to any one of claims 55 to 60 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

62. The method according to any one of claims 55 to 61 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

63. The method according to any one of claims 54 to 62 wherein the subject is an immune-compromized or immune deficient subject.

64. The method of claim 63 wherein the immune-compromized or immune deficient subject is infected with human immunodeficiency virus (HIV).

65. A method of monitoring disease progression, responsiveness to therapy or infection status by M. tuberculosis in a subject comprising determining the level of M tuberculosis TetR protein or an immunogenic fragment or epitope thereof in a biological sample from said subject at different times using the isolated or recombinant antibody according to any one of claims 11 to 16, wherein a change in the level of the TetR protein, fragment or epitope indicates a change in disease progression, responsiveness to therapy or infection status of the subject.

66. The method of claim 65 further comprising administering a compound for the treatment of tuberculosis or infection by M. tuberculosis when the level of TetR protein, fragment or epitope increases over time.

67. The method of claim 65 comprising contacting a biological sample derived from the subject with one or more of the isolated or recombinant antibodies and detecting the formation of an antigen-antibody complex.

68. The method of claim 67 comprising performing an enzyme- linked immunosorbent assay (ELISA).

69. The method of claim 68 wherein the ELISA is a sandwich ELISA using a capture antibody and a detection antibody.

70. The method according to any one of claims 65 to 69 wherein the sample comprises an extract from brain, breast, ovary, lung, colon, pancreas, testes, liver, muscle, bone or mixtures thereof.

71. The method according to any one of claims 65 to 69 wherein the sample comprises a body fluid.

72. The method of claim 71 wherein the body fluid is sputum, serum, plasma, whole blood, saliva, urine, pleural fluid or mixtures thereof or a derivative thereof.

73. The method according to any one of claims 66 to 72 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutaniine synthase (GS) protein (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

74. The method according to any one of claims 66 to 73 comprising contacting a sample with antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

75. The method according to any one of claims 65 to 74 wherein the subject is an immune-compromized or immune deficient subject.

76. The method of claim 75 wherein the immune-compromized or immune deficient subject is infected with human immunodeficiency virus (HIV).

77. A method of treatment of tuberculosis or infection by M. tuberculosis comprising:

(iii) performing a method according to any one of claims 22 to 76 thereby detecting the presence of M. tuberculosis infection in a biological sample from a subject; and

(iv) administering a therapeutically effective amount of a pharmaceutical composition to reduce the number of pathogenic bacilli in the lung, blood or lymph system of the subject.

78. A method of treatment of tuberculosis or infection by M. tuberculosis comprising: (i) performing a method according to any one of claims 65 to 76 thereby detecting the presence of M. tuberculosis infection in a biological sample from a subject being treated with a first pharmaceutical composition; and

79. A kit for detecting M. tuberculosis infection in a biological sample, said kit comprising: (i) one or more isolated or recombinant antibodies according to any one of claims 11-16 or an immune reactive fragment thereof that bind specifically to the isolated or recombinant immunogenic TetR protein of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof or to a fusion protein or protein aggregate comprising said immunogenic TetR protein, peptide, fragment or epitope; and

(ii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use.

80. The kit of claim 79 comprising a plurality of isolated or recombinant antibodies that bind specifically to the isolated or recombinant immunogenic TetR protein of

- Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof or to a fusion protein or protein aggregate comprising said immunogenic TetR protein, peptide, fragment or epitope.

81. The kit of claim 80 wherein at least one of the plurality of isolated or recombinant antibodies is immobilized onto a solid substrate.

82. A kit for detecting M. tuberculosis infection in a biological sample, said kit comprising: (i) the isolated or recombinant immunogenic TetR protein of Mycobacterium tuberculosis or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any one of claims 1-6; and

(iii) means for detecting the formation of an antigen-antibody complex, optionally packaged with instructions for use.

83. A solid matrix comprising an isolated or recombinant TetR protein or an immunogenic TetR peptide or immunogenic TetR fragment or epitope thereof according to any one of claims 1-6 or a fusion protein or protein aggregate comprising said immunogenic TetR protein, peptide, fragment or epitope adsorbed thereto.

84. A solid matrix comprising an isolated or recombinant antibody according to any one of claims 11-16 adsorbed thereto.

85. The solid matrix of claim 84 comprising antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), M. tuberculosis glutamine synthase (GS) protein (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, an immunogenic protein derived from GS, and combinations thereof.

86. The solid matrix of claim 84 or 85 comprising antibodies that bind to TetR or immunogenic TetR peptide or fragment or epitope and with antibodies that bind to M. tuberculosis protein selected from the group consisting of M. tuberculosis Bsx protein (SwissProt Database Accession No. 053759), M. tuberculosis ribosomal protein S9 (SwissProt Database Accession No. 033342), an immunogenic peptide derived from Bsx, an immunogenic peptide derived from S9, and combinations thereof.

87. The solid matrix according to any one of claims 83 to 86 comprising a membrane.

88. The solid matrix according to claim 87 wherein the membrane comprises nylon or nitrocellulose.

89. The solid matrix according to any one of claims 83 to 86 comprising a polystyrene or polycarbonate microwell plate.

90. The solid matrix according to any one of claims 83 to 86 comprising a dipstick.

91. The solid matrix according to any one of claims 83 to 86 comprising a glass support.

92. The solid matrix according to any one of claims 83 to 86 comprising a chromatography resin.