Identification of microbial polynucleotides expressed during infection of a host

Abstract

The invention provides methods useful for identifying polynucleotides expressed in vivo by a microbe during infection of a host. Antibodies against antigens that are expressed by the microbe in vivo and in vitro are adsorbed with cells or cellular extracts of the microbe that have been grown in vitro. Unadsorbed antibodies are isolated and are probed against a phage display library of the microbe's DNA or RNA. A polynucleotide of the microbe that is expressed in vivo is isolated and identified.

Description

TECHNICAL AREA OF THE INVENTION

[0002] This invention provides methods and compositions for identifying and obtaining microbial polynucleotides expressed during infection of a host and the use of these polynucleotides and translated peptides in the diagnosis, treatment, and prevention of microbial infections.

BACKGROUND OF THE INVENTION

[0003] Microbial infections are complex, dynamic processes that evolve constantly within the host. In many instances, virulence gene expression is modulated in response to the changing environment encountered at the site of infection. Mekalanos, J. Bacteriol. 174:1-7 (1992); Mahan et al. Science 259:686-688 (1993). It is unlikely that all regulated virulence determinants of a pathogen can be identified in vitro because it is technically impossible to determine and mimic all of the complex and changing environmental stimuli that occur at the site of an infection. Pioneering technologies such as in vivo expression technology (IVET), signature-tagged mutagenesis (STM) and differential fluorescence induction (DFI) were designed to identify genes specifically expressed in vivo and to fill the gaps in our understanding of microbial pathogenesis. Handfield & Levesque, FEMS Microbiol. Rev. 23:69-91 (1999); Heithoff et al., Trends Microbiol. 5:509-513 (1997); Chiang et al., Ann. Rev. Microbiol. 53:129-154 (1999); Hautefort & Hinton, Phil. Trans. R. Soc. London Ser. B, 255:601-611 (2000). All of these methods depend on a reasonable assumption: namely, that genes which are specifically induced during in vivo growth are likely to be important to the pathogenic process.

[0004] Although remarkably powerful, all of these technologies have certain limitations. Their major drawback is that they depend on the use of animal models of infection; animal models are not available for many pathogens and, in those cases where an animal model is available, it might not closely approximate the human condition. Consequently, a number of examples exist in the literature of erroneous conclusions being drawn by extrapolation of results from animal models to human infections. Smith, Trends Microbiol. 6:239-243 (1998). Further, many of these schemes are not readily applicable to genetically “undomesticated” microbes, that is microbes for which there is no well established or reliable means for genetic manipulation. Additionally, IVET, STM, and related technologies are technically difficult, and therefore restrict analysis to a single representative strain of the microbe and to only one or several time points in the infection process.

[0005] An example of a microbe that is not easily characterized by IVET, STM, and related technologies is Actinobacillus actinomycetemcomitans (Aa), an etiologic agent of periodontal diseases. Aa has emerged as one of the best examples of a bacterium demonstrating a direct correlation with disease manifestation in the oral cavity. Aa is known to be the etiologic agent for localized juvenile periodontitis (LJP). See, Slots & Ting, Periodontol. 2000, 20:82-121 (1999). Despite the fact that some Aa virulence factors have been identified, other important contributors to the infectious process have yet to be identified.

SUMMARY OF THE INVENTION

[0006] It is an object of the invention to provide methods for identifying polynucleotides useful for vaccine design, diagnostics, and antibiotherapy. It is a further object of the invention to provide methods and compositions useful in vaccine design, diagnosis, and therapy of A. actinomycetemcomitans infection. This and other objects of the invention are provided by one or more of the embodiments described below.

[0007] The invention provides methods useful for identifying polynucleotides expressed by a microbe during infection of a host. One embodiment provides a method of identifying a polynucleotide of a microbe that is expressed specifically in vivo. The method comprises absorbing antibodies against antigens that are expressed by the microbe both in vivo and in vitro with cells or cellular extracts of the microbe that have been grown in vitro; isolating unadsorbed antibodies; and probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies. The step of probing a display library comprises: immobilizing the unadsorbed antibodies on a solid support; adding the display library of the microbe's DNA or RNA to the solid support; washing unbound display library members from the solid support; and recovering display library members that are bound to the solid support. A polynucleotide of the microbe that is expressed in vivo is isolated and identified.

[0008] The solid support can be blocked with a blocking agent before the library is added. The solid support can be nitrocellulose, nylon, polystyrene, polyvinylchloride, latex, fiberglass, glass, microsphere, liposome, sepharose, sephadex, or a magnetic particle. The polynucleotide can encode an antigen or epitope. The antigen or epitope can be capable of eliciting an immune response in an animal, such as humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, and shellfish. The antibodies can comprise sera from one or more hosts infected with, or previously infected with the microbe. The microbe can be bacterium, a virus, a parasite, a prion, or a fungus, including for example, Candida, Aspergillus, Sporothrix, Blastomyces, Histoplasma, Cryptococcus, Pneumocystis, Coccidioides, Tinea, Toxoplasma, Plasmodium, Pseudomonas, Actinobacillus, Staphylococcus, Bacillus, Clostridium, Listeria, Corynebacterium, Actinomyces, Mycoplasma, Nocardia, Bordetella, Brucella, Francisella, Legionella, Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, Shigella, Streptococcus, Yersinia, Vibrio, Campylobacter, Helicobacter, Bacteroides, Chlamydia, Borrelia, Treponema, Leptospira, Aeromonas, Rickettsia, Ascaris, Cryptosporidium, Cyclospora, Entamoeba, Giardia, Shistosoma, Trypanosoma, herpes virus, cytomegalovirus, Epstein-Barr virus, hepatitis virus, adenovirus, papillomavirus, polyomavirus, enterovirus, rotavirus, influenza virus, paramyxovirus, rubeola virus, rhabdovirus, human immunodeficiency virus, arenavirus, rhinovirus, or reovirus. The host can be an animal including, for example, humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, or shellfish. The method can further comprise the step of determining the nucleic acid sequence of the polynucleotide. The display library can be a phage display library.

[0009] Another embodiment of the invention can comprise a method of comparing polynucleotides of a microbe that are expressed in vivo at different stages of infection of the microbe. The method can comprise adsorbing a first sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host is in about the same stage of the infection; adsorbing a second sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host is in about the same stage of the infection, wherein the stage of the infection is different from the first stage of infection; isolating unadsorbed antibodies from the first serum sample and from the second serum sample; probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing a display library with the unadsorbed antibodies from the second serum sample. The steps of probing display libraries comprise: immobilizing the unadsorbed antibodies on a solid support; adding the display library of the microbe's DNA or RNA to the solid support; washing unbound display library members from the solid support; and recovering display library members that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample. The polynucleotides of the microbe that are expressed in vivo at different stages of infection of the microbe are compared.

[0010] The display library probed with the unadsorbed antibodies from the first serum sample and the display library probed with the unadsorbed antibodies from the second serum sample can be the same display library or different display libraries. The display library can be a phage display library.

[0011] Still another embodiment of the invention provides a method of comparing polynucleotides of a microbe that are expressed in vivo, wherein the microbe has infected its host by different routes of infection. The method comprises absorbing a first sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host has been infected by about the same route of infection; absorbing a second sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host has been infected by about the same route of infection, wherein the route of infection is different from the first route of infection; isolating unadsorbed antibodies from the first serum sample and from the second serum sample; probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing a display library with the unadsorbed antibodies from the second serum sample. The steps of probing display libraries comprise: immobilizing the unadsorbed antibodies on a solid support; adding the display library of the microbe's DNA or RNA to the solid support; washing unbound display library members from the solid support; and recovering display library members that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample. The polynucleotides of the microbe that are expressed in vivo by different routes of infection of the microbe are compared.

[0012] The display library probed with the unadsorbed antibodies from the first serum sample and the display library probed with the unadsorbed antibodies from the second serum sample can be the same display library or different display libraries. The display library can be a phage display library.

[0013] Yet another embodiment of the invention provides a method of confirming an animal model of microbial infection as a valid model. The method comprises the steps of: adsorbing a first sera sample from one or more animal model hosts infected with or previously infected with a microbe, with cells or cellular extracts of the microbe that have been grown in vitro; adsorbing a second sera sample from one or more second hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro; wherein the second host is a different species of animal than the animal model host; isolating unadsorbed antibodies from the first serum sample and from the second serum sample; probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing a display library with the unadsorbed antibodies from the second serum sample. The probing of display library steps comprise: immobilizing the unadsorbed antibodies on a solid support; adding the display library of the microbe's DNA or RNA to the solid support; washing unbound members of the display library from the solid support; and recovering display library members that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample. The polynucleotides of the microbe that are expressed in vivo in the animal model host and the second host are compared wherein if the polynucleotides expressed in vivo in the animal model and in the second host are the same or similar, then the animal model is confirmed as a valid model.

[0014] The display library probed with the unadsorbed antibodies from the first serum sample and the display library probed with the unadsorbed antibodies from the second serum sample can be the same display library or different phage display libraries The display library can be a phage display library. The animal model host and the second host can comprise humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, or shellfish.

[0015] The invention thus provides methods for identifying antigens expressed during an actual microbial infection that do not rely on animal models. The methods can be used with microbes for which there is no well established or reliable means for genetic manipulation and allow for the analysis of a pool of strains of a microbe that represent all of the various clinically important clonotypes. The methods of the invention further provide a technique of defining a timeline for antigen production by the microbe throughout the course of a natural infection process. The staging of individual in vivo induced antigens provides relevant information on the pathogenesis of the microorganism and on the host response to the infection. This in turn provides valuable insights for rationale vaccine design, diagnostics, and antibiotherapy.

[0016] The combination of screening, confirmation, and staging methods of the invention to identify and test in vivo induced antigens is far superior to existing in vivo expression technologies by virtue of its efficiency and direct assessment in natural human and animal infections. The methods are rapid and simple, which renders the screening of a whole genome possible in a timely fashion.

[0017] The invention further provides for the first time methods for a comprehensive analysis of the expression of infection-related antigens at the genomic level of different clinical strains of a microbe and of different stages of infection in the host.

[0018] Additionally, polynucleotides isolated by the methods of the invention can advantageously be studied by conventional techniques, including mutant analysis in animal models, with the confidence that the polynucleotide is actually expressed in infections, which is not the case with other available technologies.

BRIEF DESCRIPTION OF THE DRAWINGS

[0019] FIG. 1 shows an in vivo induced antigen technology (IVIAT) scheme. IVIAT can begin with serum from one or more patients who have or recently had the disease or infection of interest. Such sera are individually tested to verify that they exhibit measurable antibody titers versus the microbial pathogen. One or more such reactive serum samples are adsorbed with cultured cells and lysates of the pathogen to remove antibodies reactive with antigens made during in vitro growth. The resulting adsorbed serum still contains antibodies reactive with immunogenic proteins produced by the pathogen only during in vivo growth. It is used to probe an expression library of the pathogen's DNA or RNA cloned in a convenient host. Reactive clones are isolated, and the cloned insert is sequenced. If more than one open reading frame is present on an insert, each can be individually subdloned and retested with the adsorbed serum to identify which one encodes the reactive antigen. For independent verification, the polynucleotide is overexpressed, and the resulting recombinant protein is purified and used to raise monospecific antibodies. The antibodies are used to probe biological samples taken from patients infected with the pathogen. Reactivity with cells of the pathogen in clinical samples, but not with cells of the pathogen grown in vitro, provides direct confirmation that the antigen is expressed only during in vivo growth.

[0020] FIG. 2 shows sequential adsorption of pooled serum to eliminate antibodies reactive with in vitro expressed antigens. The pooled sera were subjected to five successive adsorptions with whole cells, two adsorptions with French press extracts, and two adsorptions with heat denatured French press extracts.

[0021] FIG. 3 shows the probing of a partial genomic library. Plates containing appropriate numbers of colonies were replicated onto medium with IPTG to induce expression of the cloned fragments. The colonies were lifted onto duplicate membranes, which were then reacted with either the pooled unadsorbed (panel A) or pooled adsorbed (panel B) sera. Reactive clones were visualized by probing with peroxidase-conjugated goat anti-human immunoglobulin as a secondary reagent followed by development with a chemiluminescent substrate and autoradiography.

[0022] FIG. 4 shows specific in vivo induction of Aa2008. Plaque samples were thawed on ice, homogenized by brief vortexing at 4° C., and immediately heat-fixed on microscope slides. Plaque samples and matched in vitro grown A. actinomycetemcomitans isolates taken from selective medium (Slots, Clin. Microbiol. 15:606 (1982)) were probed in parallel with fluorescein isothiocyanate (FITC)-labeled monospecific antibody directed against antigen Aa2008 and the TR-labeled A. actinomycetemcomitans-specific monoclonal antibody. Samples were examined by fluorescence microscopy (excitation wavelength 488 nm). Double color analysis, using matched differential emission filters, was performed to identify individual cells that were simultaneously labeled with FITC and Texas red (TR). Bacterial cells in plaque that reacted with TR-labeled anti-A. actinomycetemcomitans monoclonal antibody (panel A) also reacted with FITC-labeled anti-Aa2008 antibody (panel B) and these signals were found to colocalize (panel C). In contrast, matched in vitro grown A. actinomycetemcomitans reacted with the TR-labeled anti-A. actinomycetemcomitans monoclonal antibody panel D) but not with FITC-labeled anti-Aa2008 antibody (panel E) and therefore no colocalization was observed (panel F).

[0023] FIG. 5 shows western blot analysis indicating immunoreactivity of patient and control subjects' sera to Aa2008. Western blots of the inclusion body preparation of Aa2008 were probed using individual, unadsorbed sera from 20 periodontitis patients and 9 control subjects.

[0024] FIG. 6 shows Table 2 and demonstrates confirmation and characterization of IVIAT subclones. In the table, the references are as follows: 14. Chanyangam et al., Infect. Immun. 59:600 (1991); 15. Yoshida et al., Infect. Immun. 66:107 (1998); 16. Li et al., J. Bacteriol. 176:6015 (1994); 17. Fleischmann et al., Science 269:496 (1995).

DETAILED DESCRIPTION OF THE INVENTION

[0025] The present invention provides methods and compositions for identifying, isolating and validating polynucleotides that are expressed only during in vivo growth of a microbe or pathogen. Briefly, the methods, termed in vivo induced antigen technologies (IVIAT), comprise obtaining a sample of antibodies against antigens that are expressed by the microbe in vivo and in vitro and adsorbing these antibodies with cells or cellular extracts of the microbe that have been grown in vitro. An example of a sample of antibodies that can be used in the invention is sera from patients who have been or are infected with the microbe. See, e.g. FIG. 1. The unadsorbed antibodies are isolated and are used to probe an expression or display library of the microbe's DNA or RNA. Reactive clones can be isolated and the cloned fragments sequenced.

[0026] IVIAT Methodology

[0027] A sample of antibodies against antigens that are expressed by a microbe in vivo is collected. The sample can comprise the serum of a host or hosts currently infected with or previously infected with the microbe. Because a host from which serum is collected has undergone or is actively engaged in an actual infection by the microbe of interest, the host's serum contains antibodies produced against microbial antigens expressed during the in vivo infectious process. Serum from an individual host may be used or pooled sera from two or more bosts can be used. For example, sera from about 2, 5, 25, 100, 500, or 1,000 hosts may be pooled for use in the instant invention.

[0028] The optimum number of serum samples to use depends on the type of information that is being sought. If the main interest is in targets for vaccines and diagnostics, one or several sera samples should suffice to identify those proteins that are immunogenic in most individuals. On the other hand, if the main interest is a more detailed analysis of the potential molecular mechanisms used by the pathogen, the use of a larger pool of sera would reduce the possibility of missing genes or polynucleotides of interest due to variability in the human immune response. In cases where the pathogen causes protracted disease, pooled serum from patients in early, middle and late stages of infection or sequential samples taken from patients during acute and convalescent phases of infection would offer the best chance of identifying transiently expressed in vivo induced proteins. Also, certain pathogens can infect humans by more than one route (e.g., via a wound, gastrointestinal tract, respiratory tract, or skin); in such cases, selective pooling of serum from patients infected by various routes can enable the identification of route-specific in vivo induced proteins. In cases where different clonal variants or strains of the microbe cause disease, selective pooling of serum from patients infected by various clonal variants or strains can enable the study of the pathogenesis of each variant or strain.

[0029] A host may be any kind of animal. For example, hosts can comprise humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, and shellfish.

[0030] The microbe or pathogen can be any kind of a bacterium, a virus, a parasite, a prion, or a fungus. For example, the microbe can be Candida, Aspergillus, Sporothrix, Blastomyces, Histoplasma, Cryptococcus, Pneumocystis, Coccidioides, Tinea, Toxoplasma, Plasmodium, Pseudomonas, Actinobacillus, Staphylococcus, Bacillus, Clostridium, Listeria, Corynebacterium, Actinomyces, Mycoplasma, Nocardia, Bordetella, Brucella, Francisella, Legionella, Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, Shigella, Streptococcus, Yersinia, Vibrio, Campylobacter, Helicobacter, Bacteroides, Chlamydia, Borrelia, Treponema, Leptospira, Aeromonas, Rickettsia, Ascaris, Cryptosporidium, Cyclospora, Entamoeba, Giardia, Shistosoma, Trypanosoma, herpes virus, cytomegalovirus, Epstein-Barr virus, hepatitis virus, adenovirus, papillomavirus, polyomavirus, enterovirus, rotavirus, influenza virus, paramyxovirns, rubeola virus, rhabdovirus, human immunodeficiency virus, arenavirus, rhinovirus, and reovirus. The microbe or pathogen can also be any kind of veterinary microbe or pathogen. See e.g., Veterinary Microbiology, Hirsh & Zee, Eds., Blackwell Science, Inc., Malden, Mass., 1999; Clinical Veterinary Microbiology, Quinn, Ed., Wolfe Publishing, London, (1994).

[0031] Antibodies that bind to antigens that are produced during in vitro propagation of the microbe of interest are eliminated from the sample of antibodies against antigens that are expressed by the microbe in vivo. The antibodies that are reactive with antigens produced in vitro can be removed from the sample by, for example, adsorbtion. Preferably, a sample containing antibodies against antigens that are expressed by the microbe in vivo and in vitro, such as a serum sample of an infected host, are contacted with in vitro grown whole cells, cell extracts or both of the microbe, or whole cells, extracts of whole cells, or both of cells that are infected with the microbe of interest, e.g. a prokaryotic or eukaryotic cell infected with a virus or parasite.

[0032] All or substantially all of the antibodies in the antibody sample whose corresponding antigens are derived from in vitro grown microbes will bind to these antigens to form immune complexes. However, antibodies directed against antigens that are specifically expressed during the in vivo infectious process will remain uncomplexed since their corresponding antigens are not present in the in vivo grown cells and/or cell extracts. The adsorbtion step can be performed by, for example, contacting the antibody sample with whole cells and/or cell extracts that are immobilized on a solid support, such as a nitrocellulose membrane. See, Brady & Daphtary, J. Infect. Dis. 158:965-972 (1988). Optionally, the whole cell and/or cell extract sample can be denatured before use to expose additional immunoreactive epitopes. Several successive adsorbtions can be performed using the same or different adsorbtion methodologies.

[0033] After the adsorbtion step or steps, unbound antibodies are separated from the antibody-antigen complexes. After elimination of antibodies reactive with microbial antigens expressed in vitro, the sample will comprise antibodies produced in response to antigens specifically expressed in vivo. This sample can then be used to screen one or more, same or different, genomic expression libraries, for example, plasmid or bacteriophage genomic expression libraries, of the microbe of interest. Methods of constructing genomic expression libraries are well known in the art. See, e.g., Ausubel (ed.), Current Protocols in Molecular Biology, John Wiley and Sons, Inc. (1994); T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor laboratory, Cold Spring Harbor, N.Y. (1989). Optionally, DNA or RNA from more than one strain or clonal variant of the microbe of interest can be pooled for expression library construction. Methods for screening these libraries with one or more labeled or unlabeled antibody-containing samples and for identifying and isolating clones from the library that encode the reactive antigens or epitopes of interest are also well known in the art, e.g., colony blotting methods See, e.g., Ausubel (1994); Maniatis (1989).

[0034] In another embodiment of the invention, a display library of the microbe's DNA can be constructed. A display library is produced by a system where the product of a cloned polynucleotide is displayed on the surface of a display library member. A display library member is one host vector of the display library, e.g., a eukaryotic cell, a prokaryotic cell, a phage particle, or virus particle. For example, a vector such as bacteriophage T7 select 10-3 (Novagen, Madison, Wis.) can be used to construct a phage display library. An example of a bacterial display library is the PurePro Caulobacter Expression System (Invitrogen, Carlsbad, Calif.). Unadsorbed antibodies are immobilized on a solid support. A solid support can be any solid material to which an antibody can be attached, for example, a microtiter plate, nitrocellulose, nylon, a plastic material, for example, polystyrene or polyvinylchloride, latex, fiberglass, glass, microsphere, liposome, sepharose, and sephadex. A solid support can also be a magnetic particle or an optical biosensor. Antibodies can be immobilized onto the solid support using any means known in the art, including, for example, physical adsorbtion (i.e., without the use of chemical linkers) or chemical binding (i.e., with the use of chemical linkers). Chemical binding can generate strong attachment of antibodies on a solid support and provide defined orientation and conformation of the surface-bound molecules.

[0035] The solid support can optionally be subjected to a blocking step to reduce non-specific attachment of members of the display library to the solid support. A blocking solution can comprise, for example, 5% non-fat dry milk, 0.25% Tween-20™, and a lysate of wild-type T7, initially containing greater than 1010 pfu/ml that has been UV irradiated so that viable pfu/ml is less than 104 (i.e., 6 logs of killing). The display library is added to the solid support. In one embodiment of the invention, a phage display library, (typically 106 to 109 plaque forming units, pfu) is added to the solid support and incubated to allow attachment of antibody to the microbe's proteins that are displayed on the phage capsid protein. Unbound phage are washed away from the solid support and bound phage are recovered. This ‘biopanning” procedure can be repeated one, two, three, or more additional times to increase the proportion of recovered display library members that express microbial antigens induced under a first environmental condition or under infectious conditions. Polynucleotides encoding an antigen or epitope of interest can be isolated from the display library members.

[0036] A display library screening approach allows for a dramatic increase in speed and ease of screening. An entire microbe's chromosome or chromosomes can be screened at five times coverage (i.e., about 99.9% confidence level) in a matter of days as compared to more conventional means of screening, such as colony or plaque lift and screening procedures. Another advantage of a display library screening method is that the cloned insert does not have to be extensively analyzed, as in the case where vectors like pET vectors are used (i.e., genomic expression library screening), to determine which of the open reading frames is responsible for expression of the reactive peptide/protein. In the case of phage display, the open reading frame encoding the reactive peptide/protein is fused in frame to the bacteriophage T7 capsid gene.

[0037] The lysates of interesting clones (i.e., clones that are isolated by biopanning and verified by a secondary confirmation step, e.g., a dot blot method) can be used for immunizing animals. For example, a phage can be purified and concentrated using PEG8000 and injected, with or without adjuvant, into mice, rats, rabbits or other suitable animal. Sera is recovered from the animal and tested for reactivity with the displayed protein by, for example, enzyme-linked immunosorbant assay (ELISA) after adsorbing out antibodies reactive with wild-type T7 or by western blot using the purified phage as a target. Two bands should be identified in the western blot using an anti-T7 capsid antibody. The smaller molecular weight band represents the wild-type T7 capsid protein (about 40,000 Daltons). The larger molecular weight band represents the capsid protein with fused peptide from the cloned open reading frame. This methodology can simplify the steps required to identify an antibody reactive with the cloned protein.

[0038] Another step can be added to the methodology to take into account the possibility that titers of antibodies specific for certain proteins of interest may be lower than titers of antibodies specific for other proteins. This could bias the results of the biopanning step. To prevent this result the IgG fraction of the pooled sera can be purified using, for example, a HPLC/protein A column. The purified IgG is adsorbed with whole cells of the in vitro grown pathogen, native and denatured extracts of in vitro grown pathogens, and with UV killed T7 lysates. The IgG is adsorbed with the pathogen's genomic library displayed on T7 under conditions where IgG is saturating. For example, the IgG can be added to the genomic library, which can be covalently attached to, for example, microspheres. Material not bound to the microspheres is washed away and the bound antibodies are eluted from the microspheres. This “normalized” IgG is then used for biopanning and secondary screening. This method also has the benefit of increasing sensitivity of the biopanning by eliminating IgG molecules that are not specific for the pathogen.

[0039] Reactive clones identified by screening expression libraries of the microbe of interest can be characterized by conventional analysis. For example, the clone can be sequenced and the presence of open reading frames can be predicted, for example, using Fickett's, start/stop codon or other methods. See, e.g., Fickett, Nucleic Acids Res. 10:5303-5318 (1982); Solovyev, Nucleic Acids Res. 22:5156-5163 (1994); Saqi, Protein Eng. 8:1069-1073 (1995), Ladunga and Smith, Protein Eng. 20:101-110 (1997); Birney, Nucleic Acids Res. 24:2730-2739 (1996).

[0040] Identification of signal sequences, particularly likely ribosome binding sites and transcription termination sequences, can also be made since the information provided by these analysis can be helpful in prioritizing the subdloning of open reading frames if more than one is present on the cloned insert. Moreover, the obtained sequence information can be used to identify sequence similarities to known polynucleotides, e.g., by BLAST analysis, and possible relationships to proven or putative virulence factors can be evaluated. In instances where more than one open reading frame is present on a cloned insert, all of them may be analyzed for their ability to express in vivo induced antigens. For example, each open reading frame can be independently subdloned and tested with the adsorbed serum to identify in vivo induced antigens.

[0041] In vivo induced antigens identified by WIAT can be directly verified as actually expressed by the microbe at the site of infection in the host by directly probing biological samples taken from disease sites of infected patients by any method known in the art. For example, a polypeptide which is expressed from a clone suspected of expressing an in vivo induced antigen or epitope can be used to raise polyclonal antibodies in mice. Optionally, the polynucleotide encoding the suspected antigen or epitope can be overexpressed and the resulting polypeptide purified and used to raise polyclonal antibodies. The antibodies can be labeled with, for example, fluorescein isothiocyanate (FITC). A biological sample from a disease site of a host infected with the microbe of interest is obtained. The biological sample and a matched in vitro grown sample of the microbe are assayed by, for example, immunofluorescence microscopy. The labeled antibodies will react with the microbe found in the biological sample, but will not react with in vitro grown cells. These results can provide direct evidence that the microbe expresses the IVIAT antigen exclusively during in vivo growth.

[0042] Once an antigen has been identified and confirmed as an in vivo induced antigen, the purified antigen can be used to screen the sera of individual patients for reactive antibodies. For example, a serum sample can be obtained from a patient suspected of having a particular microbial infection. The sample can be probed for reactive antibodies with a labeled, purified antigen.

[0043] For those microbes that actually have a validated animal model, the polynucleotides identified by IVIAT can also be studied by conventional techniques, including mutant analysis, with the a priori confidence that the polynucleotide is actually expressed and relevant in host infections. IVIAT can also be used to validate in vitro and animal models by identifying those that reproduce the same or similar expression pattern seen with IVIAT in humans or other animal hosts. These confirmed models can then be used for further conventional analysis of the pathogen.

[0044] Polypeptides

[0045] Polypeptides of the invention can either be full-length polypeptides or fragments of polypeptides. For example, fragments of polypeptides of the invention can comprise about 5, 10, 25, 50, 100, 200, 250, 500, 750, or 1,000 amino acids of polypeptides of the invention. Examples of polypeptides of the invention include Actinobacillus actinomycetemcomitans (Aa) SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, and SEQ ID NO:20. Homologous amino acid sequences which are at least about 75, preferably about 90, 96, 98, or 99% identical to the nucleotide sequences shown in SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, and SEQ ID NO:20 are also Aa polypeptides.

[0046] Percent sequence identity has an art recognized meaning and there are a number of methods to measure identity between two polypeptide or polynucleotide sequences. See, e.g., Lesk, Ed., Computational Molecular Biology, Oxford University Press, New York, (1988); Smith, Ed., Biocomputing: Informatics And Genome Projects, Academic Press, New York, (1993); Griffin & Griffin, Eds., Computer Analysis Of Sequence Data, Part I, Humana Press, New Jersey, (1994); von Heinje, Sequence Analysis In Molecular Biology, Academic Press, (1987); and Gribskov & Devereux, Eds., Sequence Analysis Primer, M Stockton Press, New York, (1991). Methods for aligning polynucleotides or polypeptides are codified in computer programs, including the GCG program package (Devereux et al., Nuc. Acids Res. 12:387 (1984)), BLASTP, BLASTN, FASTA (Atschul et al., J. Molec. Biol. 215:403 (1990)), and Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711) which uses the local homology algorithm of Smith and Waterman (Adv. App. Math., 2:482-489 (1981)). For example, the computer program ALIGN which employs the FASTA algorithm can be used, with an affine gap search with a gap open penalty of −12 and a gap extension penalty of −2.

[0047] When using any of the sequence alignment programs to determine whether a particular sequence is, for instance, about 95% identical to a reference sequence, the parameters are set such that the percentage of identity is calculated over the full length of the reference polynucleotide and that gaps in identity of up to 5% of the total number of nucleotides in the reference polynucleotide are allowed.

[0048] Polypeptides of the invention further comprise biologically functional equivalents of at least about 5, 10, 25, 50, 100, 200, 250, or 500 amino acids of the polypeptides shown in SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, and SEQ ID NO:20. A polypeptide is a biological equivalent if it reacts about the same to a polypeptide of the invention in an assay such as an immunohistochemical assay, an ELISA, an RIA, or a western blot assay. Preferably, the assay is a competition assay wherein the biologically equivalent polypeptide is capable of reducing binding of the polypeptide of the to a corresponding reactive antigen or antibody by about 80, 95, 99, or 100%.

[0049] Polypeptides of the invention preferably comprise an antigen that is recognized by an antibody reactive against the microbe of interest. The antigen preferably comprises one or more epitopes (or antigenic determinants). An epitope can be a linear, sequential epitope or a conformational epitope. Epitopes within a polypeptide of the invention can be identified by several methods. See, e.g., U.S. Pat. No. 4,554,101; Jameson & Wolf, CABIOS 4:181-186 (1988). For example, a polypeptide of the invention can be isolated and screened. A series of short peptides, which together span the entire polypeptide sequence, can be prepared by proteolytic cleavage. By starting with, for example, 100-mer polypeptide fragments, each fragment can be tested for the presence of epitopes recognized in an enzyme-linked immunosorbent assay (ELISA). For example, in an ELISA assay a microbial polypeptide, such as a 100-mer polypeptide fragment, is attached to a solid support, such as the wells of a plastic multi-well plate. A population of antibodies are labeled, added to the solid support and allowed to bind to the unlabeled antigen, under conditions where non-specific adsorption is blocked, and any unbound antibody and other proteins are washed away. Antibody binding is detected by, for example, a reaction that converts a colorless substrate into a colored reaction product. Progressively smaller and overlapping fragments can then be tested from an identified 100-mer to map the epitope of interest.

[0050] Preferably, a polypeptide of the invention is produced recombinantly. A polynucleotide encoding a polypeptide of the invention can be introduced into a recombinant expression vector, which can be expressed in a suitable expression host cell system using techniques well known in the art. A variety of bacterial, yeast, plant, mammalian, and insect expression systems are available in the art and any such expression system can be used. Optionally, a polynucleotide encoding a polypeptide can be translated in a cell-free translation system.

[0051] If desired, a polypeptide can be produced as a fusion protein, which can also contain other amino acid sequences, such as amino acid linkers or signal sequences, as well as ligands useful in protein purification, such as glutathione-S-transferase, histidine tag, and staphylococcal protein A. More than one polypeptide of the invention can be present in a fusion protein.

[0052] Polynucleotides

[0053] Polynucleotides of the invention contain less than an entire microbial genome and can be RNA or single- or double-stranded DNA. Preferably, the polynucleotides are purified free of other components, such as proteins and lipids. The polynucleotides of the invention encode the polypeptides described above. Polynucleotides of the invention can also comprise other nucleotide sequences, such as sequences coding for linkers, signal sequences, heterologous signal sequences, TMR stop transfer sequences, transmembrane domains, or ligands useful in protein purification such as glutathione-S-transferase, histidine tag, and staphylococcal protein A.

[0054] Degenerate nucleotide sequences encoding the polypeptides of the invention, as well as homologous nucleotide sequences which are at least about 75, preferably about 90, 96, 98, or 99% identical to the nucleotide sequences shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, and SEQ ID NO:19 and the complements thereof are also polynucleotides of the invention. Percent sequence identity can be calculated as described in the “Polypeptides” section. Complementary DNA (cDNA) molecules, species homologs, and variants of Aa polynucleotides which encode biologically active Aa polypeptides also are Aa polynucleotides. Preferably, a polynucleotide of the invention comprises about 5, 10, 15, 50, 100, 500, or 1,000 nucleotides of a nucleic acid sequences shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 11, SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, and SEQ ID NO:19.

[0055] Polynucleotides of the invention can be isolated from nucleic acid sequences present in, for example, a biological sample, such as plaque, saliva, sputum, blood, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudate, or tissue, from an infected individual. Polynucleotides can also be synthesized in the laboratory, for example, using an automatic synthesizer. An amplification method such as PCR can be used to amplify polynucleotides from either genomic DNA or cDNA encoding the polypeptides.

[0056] Polynucleotides of the invention can comprise coding sequences for naturally occurring polypeptides or can encode altered sequences which do not occur in nature. If desired, polynucleotides can be cloned into an expression vector comprising, for example, promoters, enhancers, or other regulatory elements that drive expression of the polynucleotides of the invention in host cells. An expression vector can be, for example, a plasmid, such as pBR322, pUC, or Co1E1, or an adenovirus vector, such as an adenovirus Type 2 vector or Type 5 vector. Optionally, other vectors can be used, including but not limited to Sindbis virus, simian virus 40, alphavirus vectors, poxvirus vectors, and cytomegalovirus and retroviral vectors, such as murine sarcoma virus, mouse mammary tumor virus, Moloney murine leukemia virus, and Rous sarcoma virus. Minichromosomes such as MC and MC1, bacteriophages, phagemids, yeast artificial chromosomes, bacterial artificial chromosomes, virus particles, virus-like particles, cosmids (plasmids into which phage lambda cos sites have been inserted) and replicons (genetic elements that are capable of replication under their own control in a cell) can also be used.

[0057] A vector comprising a polynucleotide of the invention can be transformed into, for example, bacterial, yeast, insect, or mammalian cells so that the polypeptides of the invention can be expressed in and isolated from cell culture. Any of those techniques which are available in the art can be used to introduce polynucleotides into the host cells. These include, but are not limited to, transfection with naked or encapsulated nucleic acids, cellular fusion, protoplast fusion, viral infection, and electroporation.

[0058] Polynucleotides of the invention can be used, for example, as probes or primers to detect the presence of microbial polynucleotides in a sample, such as abiological sample. The ability of such probes to specifically hybridize to microbial polynucleotide sequences will enable them to be of use in detecting the presence of complementary sequences in a given sample. Polynucleotide probes of the invention can hybridize to complementary sequences in a sample such as a biological sample, including plaque, saliva, sputum, blood, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudate, or tissue. Polynucleotides from the sample can be, for example, subjected to gel electrophoresis or other size separation techniques or can be dot blotted without size separation. The polynucleotide probes are preferably labeled. Suitable labels, and methods for labeling probes are known in the art, and include, for example, radioactive labels incorporated by nick translation or by kinase, biotin, fluorescent probes, and chemiluminescent probes. The polynucleotides from the sample are then treated with the probe under hybridization conditions of suitable stringencies.

[0059] Depending on the application, varying conditions of hybridization can be used to achieve varying degrees of selectivity of the probe towards the target sequence. For applications requiring high selectivity, relatively stringent conditions can be used, such as low salt and/or high temperature conditions, such as provided by a salt concentration of from about 0.02 M to about 0.15 M salt at temperatures of from about 50° C. to about 70° C. For applications requiring less selectivity, less stringent hybridization conditions can be used. For example, salt conditions from about 0.14M to about 0.9M salt, at temperatures ranging form about 20° C. to about 55° C. The presence of a hybridized complex comprising the probe and a complementary polynucleotide from the sample indicates the presence of the microbe or polynucleotide sequence in the sample.

[0060] Methods of Eliciting an Immune Response

[0061] Polypeptides or polynucleotides of the invention can be used to elicit an immune response in a host. Elicitation of an immune response can be used, inter alia, to provide model systems to optimize immune responses to microbes and to provide prophylactic or therapeutic treatment against microbial infection. Elicitation of an immune response can also be used to treat, prevent, or ameliorate a disease or infection caused by a microbe or pathogen. An immune response includes humoral immune responses and cell mediated immune responses, or a combination thereof. Preferably, an immune response is a humoral immune response.

[0062] The generation of an antibody titer by an animal against a microbe can be important in protection from infection and clearance of infection. Detection and/or quantification of antibody titers after delivery of a polypeptide or polynucleotide can be used to identify epitopes that are particularly effective at eliciting antibody titers. Epitopes responsible for a strong antibody response to a microbe can be identified by eliciting antibodies directed against microbial polypeptides of different lengths. Antibodies elicited by a particular polypeptide epitope can then be tested using an ELISA assay to determine which polypeptides contain epitopes that are most effective at generating a strong response. Polypeptides or fusion proteins which contain these epitopes or polynucleotides encoding the epitopes can then be constructed and used to elicit a strong antibody response.

[0063] A polypeptide or a polynucleotide of the invention can be administered to an animal, such as a mouse, rabbit, guinea pig, macaque, baboon, chimpanzee, human, cow, sheep, pig, horse, dog, cat, chicken, and duck, to elicit antibodies in vivo. Injection of a polynucleotide has the practical advantages of simplicity of construction and modification. Further, injection of a polynucleotide results in the synthesis of a polypeptide in the host. Thus, the polypeptide is presented to the host immune system with native post-translational modifications, structure, and conformation. A polynucleotide is preferably delivered as “naked DNA.”

[0064] Administration of a polynucleotide or a polypeptide can be by any means known in the art, including intramuscular, intradermal, intraperitoneal, or subcutaneous injection, intranasal, mucosal, topical, and oral, including injection using a biological ballistic gun (“gene gun”). Preferably, a polynucleotide or polypeptide is accompanied by a protein carrier for oral administration. A combination of administration methods may also be used to elicit an immune response.

[0065] Administration of polypeptides or polynucleotides can elicit an immune response in the animal that lasts for at least 1 week, 1 month, 3 months, 6 months, 1 year, or longer. Optionally, an immune response can be maintained in an animal by providing one or more booster injections of the polypeptide or polynucleotide at 1 month, 3 months, 6 months, 1 year, or more after the primary injection.

[0066] A composition of the invention comprising a polypeptide, polynucleotide, or a combination thereof is administered in a manner compatible with the particular composition used and in an amount which is effective to elicit an immune response as detected by, for example, an ELISA, as described above. A polynucleotide is preferably injected intramuscularly to a large mammal, such as a baboon, chimpanzee, or human, at a dose of 1 ng/kg, 10 ng/kg, 100 ng/kg, 1000 ng/kg, 0.001 mg/kg, 0.1 mg/kg, or 0.5 mg/kg. A polypeptide is preferably injected intramuscularly to a large mammal, such as a human, at a dose of 0.01, 0.05, 0.5, 0.75, 1.0, 1.5, 2.0, 2.5, 5 or 10 mg/kg. Polypeptides and/or polynucleotides can be administered either to an animal that is not infected with a microbe of interest or can be administered to a microbe-infected animal. The particular dosages polynucleotides or polypeptides in a composition will depend on many factors including, but not limited to the species, age, and general condition of the mammal to which the composition is administered, and the mode of administration of the composition. An effective amount of the composition of the invention can be readily determined using only routine experimentation. In vitro and in vivo models described herein can be employed to identify appropriate doses. If desired, co-stimulatory molecules or adjuvants can also be provided before, after, or together with the compositions.

[0067] Antibodies and Their Use

[0068] Antibodies of the invention are antibody molecules that specifically and stably bind to a microbial polypeptide of the invention or fragment thereof. An antibody of the invention can be a polyclonal antibody, a monoclonal antibody, a single chain antibody (scFv), or a part of an antibody. Parts of antibodies include Fab and F(ab)2 fragments. Antibodies can be made in vivo in suitable laboratory animals or in vitro using recombinant DNA techniques. Means for preparing and characterizing antibodies are well know in the art. See, e.g., Dean, Methods Mol. Biol. 80:23-37 (1998); Dean, Methods Mol. Biol. 32:361-79 (1994); Baileg, Methods Mol. Biol. 32:381-88 (1994); Gullick, Methods Mol. Biol. 32:389-99 (1994); Drenckhahn et al. Methods Cell. Biol. 37:7-56 (1993); Morrison, Ann. Rev. Immunol. 10:239-65 (1992); Wright et al. Crit. Rev. Immunol. 12:125-68(1992). For example, polyclonal antibodies can be produced by administering a polypeptide of the invention to an animal, such as a mouse, a rabbit, a goat, or a horse. Serum from the immunized animal is collected and the antibodies are purified from the plasma by, for example, precipitation with ammonium sulfate, followed by chromatography, preferably affinity chromatography. Techniques for producing and processing polyclonal antibodies are known in the art.

[0069] Additionally, monoclonal antibodies directed against epitopes present on a polypeptide of the invention can also be readily produced. For example, normal B cells from a mammal, such as a mouse, immunized with a polypeptide of the invention can be fused with, for example, HAT-sensitive mouse myeloma cells to produce hybridomas. Hybridomas producing microbe-specific antibodies can be identified using RIA or ELISA and isolated by cloning in semi-solid agar or by limiting dilution. Clones producing microbe-specific antibodies are isolated by another round of screening. Techniques for producing and processing monoclonal antibodies are known in the art. Antibodies, either monoclonal and polyclonal, which are directed against microbial antigens, are particularly useful for detecting the presence of microbes or microbial antigens in a sample, such as a serum sample from a microbe-infected human. An immunoassay for a microbial antigen may utilize one antibody or several antibodies. An immunoassay for a microbial antigen may use, for example, a monoclonal antibody directed towards a microbial epitope, a combination of monoclonal antibodies directed towards epitopes of one microbial polypeptide, monoclonal antibodies directed towards epitopes of different microbial polypeptides, polyclonal antibodies directed towards the same microbial antigen, polyclonal antibodies directed towards different microbial antigens, or a combination of monoclonal and polyclonal antibodies. Immunoassay protocols may be based, for example, upon competition, direct reaction, or sandwich type assays using, for example, labeled antibody. The labels may be, for example, fluorescent, chemiluminescent, or radioactive.

[0070] The polyclonal or monoclonal antibodies may further be used to isolate microbes or microbial antigens by immunoaffinity columns. The antibodies can be affixed to a solid support by, for example, adsorption or by covalent linkage so that the antibodies retain their immunoselective activity. Optionally, spacer groups may be included so that the antigen binding site of the antibody remains accessible. The immobilized antibodies can then be used to bind microbes or microbial antigens from a sample, such as a biological sample including saliva, plaque, sputum, blood, urine, feces, cerebrospinal fluid, amniotic fluid, wound exudate, or tissue. The bound microbes or microbial antigens are recovered from the column matrix by, for example, a change in pH.

[0071] Antibodies of the invention can also be used in immunolocalization studies to analyze the presence and distribution of a polypeptide of the invention during various cellular events or physiological conditions. Antibodies can also be used to identify molecules involved in passive immunization and to identify molecules involved in the biosynthesis of non-protein antigens. Identification of such molecules can be useful in vaccine development.

[0072] Antibodies can be detected and/or quantified using for example, direct binding assays such as radioimmunoassay (RIA) or ELISA assays. Antibodies of the invention can also be used to treat, prevent, or ameliorate a microbial infection, to diagnose or detect the presence or absence of a microbe, and to purify an antigen or antigens that the antibody specifically binds.

[0073] Compositions Comprising Polypeptides or Polynucleotides

[0074] The invention also provides compositions comprising polypeptides or polynucleotides. Compositions of the invention preferably comprise a pharmaceutically acceptable carrier. The carrier should not itself induce the production of antibodies harmful to the host. Pharmaceutically acceptable carriers are well known to those in the art. Such carriers include, but are not limited to, large, slowly metabolized, macromolecules, such as proteins, polysaccharides such as latex functionalized sepharose, agarose, cellulose, cellulose beads and the like, polylactic acids, polyglycolic acids, polymeric amino acids such as polyglutamic acid, polylysine, and the like, amino acid copolymers, peptoids, lipitoids, and inactive, avirulent virus particles or bacterial cells.

[0075] Pharmaceutically acceptable salts can also be used in compositions of the invention, for example, mineral salts such as hydrochlorides, hydrobromides, phosphates, or sulfates, as well as salts of organic acids such as acetates, proprionates, malonates, or benzoates. Especially useful protein substrates are serum albumins, keyhole limpet hemocyanin, immunoglobulin molecules, thyroglobulin, ovalbumin, tetanus toxoid, and other proteins well known to those of skill in the art. Compositions of the invention can also contain liquids or excipients, such as water, saline, glycerol, dextrose, malodextrin, ethanol, or the like, singly or in combination, as well as substances such as wetting agents, emulsifying agents, or pH buffering agents. Liposomes can also be used as a carrier for a composition of the invention.

[0076] If desired, co-stimulatory molecules, which improve immunogen presentation to lymphocytes, such as B7-1 or B7-2, or cytokines such as MIP1α, GM-CSF, IL-2, and IL-12, can be included in a composition of the invention. Optionally, adjuvants can also be included in a composition. Adjuvants which can be used include, but are not limited to MF59-0, aluminum hydroxide, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-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-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), 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.

[0077] The compositions of the invention can be formulated into ingestable tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, injectable formulations, mouthwashes, dentifrices, and the like. The percentage of one or more polypeptides or polynucleotides of the invention in such compositions and preparations can vary from 0.1% to 60% of the weight of the unit.

[0078] The following are provided for exemplification purposes only and are not intended to limit the scope of the invention described in broad terms above. All references cited in this disclosure are incorporated herein by reference.

EXAMPLE 1

[0079] Identification Of In Vivo Induced Microbial Polypeptides From Actinobacillus actinomycetemcomitans (Aa)-Infected Patients: Adsorption of LJP Serum

[0080] To demonstrate the effectiveness of IVIAT, it was used to study in vivo gene induction of an oral pathogen, Actinobacillus actinomycetemcomitans (Aa) the putative etiologic agent of certain periodontal diseases, and, in particular, localized juvenile periodontitis (LJP) (Slots & Ting, Periodontol. 2000, 20:82-121 (1999)). Aa is well suited for this purpose since it typically evokes a strong humoral immune response in periodontitis patients (Kinane et al. Periodontol. 2000, 20:289 (2000)) and there is currently no reliable animal model with which to study this disease.

[0081] Serum samples were obtained from 20 periodontitis patients identified by family history and clinical and radiographic examinations. Microbiological and immunological analyses indicated a role for Aa as the etiologic agent in each of these cases. See, e.g., Ebersole et al. J. Clin. Immunol. 3:321 (1983); Tsai et al., J. Clin. Periodontol. 8:338 (1981). These sera were tested individually by a modified ELISA procedure (Ebersole, J. Peridont. Res. 15:621 (1980)) using French-press disrupted cell extracts of Aa strain HK1651 (ATCC Accession No. 700685) to verify that they retained their reactivity to Aa. HK1651 is a member of the clonotype distinguished by a 530 bp deletion in the promoter region of the leukotoxin gene, and which has been characterized as being particularly virulent and contagious. Haubek et al. J. Clin. Microbiol. 34:1576 (1996). Equal amounts (0.05 ml) of each patient's serum were then pooled. Pooled sera from patients were utilized in this instance to maximize the spectrum of antibodies reactive with Aa epitopes, including immunodominant ones.

[0082] Antibodies in the pooled serum that were reactive with proteins made by Aa HK1651 during in vitro cultivation were eliminated by repeated adsorptions using the methods of Brady et al. J. Infect. Dis. 158:965-972 (1988). Adsorptions were performed using both whole cells and cell extracts immobilized on nitrocellulose. Briefly, 500 μl of the pooled sera were subjected to five successive adsorptions against in vitro grown whole cells of Aa strain HK1651. The cells were grown in BHI broth at 37° C. in ambient atmosphere enriched with 5% CO2. Each adsorption consisted of an overnight incubation of the pooled sera with approximately 1011 bacteria in 100 μl phosphate buffered saline (PBS, pH 7.2) containing 0.02% sodium azide with mild agitation at 4° C. The serum was further adsorbed by incubation overnight at 4° C. with a nitrocellulose membrane (10 cm diameter) saturated with HK1651 extracts prepared by French-press treatment of 1011 in vitro grown, a cells. A final adsorption step was carried out using the same extract which was heat denatured in a boiling water bath (10 min.) before immobilization on nitrocellulose in order to expose additional immunoreactive epitopes.

[0083] To evaluate the efficiency of the adsorption steps, French-press cell extracts of HK1651 were immobilized in microtiter wells and, following a modified ELISA procedure (Ebersole, 1980), were reacted with serial dilutions of serum samples taken at different points in the adsorption process. Peroxidase-conjugated goat anti-human affinity-purified immunoglobulin (ICN Cappel; Aurora Ohio), reactive with all classes of human immunoglobulins, was used to determine the reactive antibody titers. As shown in FIG. 2, the successive adsorbtions essentially removed all of the antibodies reactive with in vitro grown HK1651. In preliminary studies it was determined that it was unnecessary to adsorb the serum with the Escherichia coli host strain since it produced a relatively low background signal.

EXAMPLE 2

[0084] Expression Library Construction And Screening With LJP Serum

[0085] Genomic expression libraries of HK1651 in PET30abc were prepared in E. coli strain BL21(DE3) (Novagen, Madison, Wis.). Briefly, genomic DNA purified from a strain HK1651 was partially digested with Sau3A to optimize the production of 0.5 to 1.5 kb fragments which were purified by agarose gel electrophoresis. The fragments were ligated into the multiple cloning site of pET30a inducible expression system (Novagen; Madison, Wis.) that had been digested with BamHI, dephosphorylated with calf intestinal phosphatase (New England Biolabs, Beverly, Mass.), and then transformed into Escherichia coli strain BL21 (DE3) (Novagen). Similar libraries were also constructed with pET30 b and c.

[0086] The resulting HK1651 genomic expression library was serially diluted and plated on brain-heart infusion (BHI) medium containing kanamycin (50 μg/ml) to generate plates containing approximately 500 colonies per plate. These colonies were replicated using sterile velvet onto duplicate BHI plates containing kanamycin and IPTG (1 mM) and incubated for 5 hours at 37° C. to induce expression of the cloned polynucleotides. To lyse the bacteria the colonies were exposed to chloroform vapors for 15 min. and overlaid with nitrocellulose membranes for 15 min. at room temperature. The membranes were carefully removed and blocked with 5% non-fat skim-milk solution in PBS at pH 7.2 containing 0.5% Tween-20 (PBS-Tween™). The colonies were first probed with a 1:10,000 dilution of adsorbed serum (based on the results shown in FIG. 2) overnight at 4° C. and then with a 1:10,000 dilution of goat anti-human peroxidase conjugated antiserum under the same conditions. Reactive colonies were detected using the ECL kit and Hyperfilm™ ECL (Amersham Pharmacia Biotech, Piscataway N.J.). X ray film exposure times were adjusted to optimize signal to noise.

[0087] FIG. 3 demonstrates the reactivity observed when replica colony blots were probed in parallel with either unadsorbed or adsorbed pooled serum. Plates containing appropriate numbers of colonies were replicated onto medium with IPTG to induce expression of the cloned fragments. The colonies were lifted onto duplicate membranes, which were then reacted with either the pooled unadsorbed (panel A) or pooled adsorbed (panel B) sera. Reactive clones were visualized by probing with peroxidase-conjugated goat anti-human immunoglobulin as a secondary reagent followed by development with a chemiluminescent substrate and autoradiography.

[0088] The majority of clones reacted with the pooled unadsorbed serum, indicating that periodontitis patients had produced antibodies that recognized a broad array of A. actinomycetemcomitans proteins. Only a small subset of colonies tested (13 out of 20,000 screened) reacted with the pooled adsorbed serum. These IVIAT clones were isolated.

[0089] Potential bias created by using a single restriction enzyme is eliminated by using a second restriction enzyme (e.g., MboI), DNA sheared by a HydroShear™ apparatus (GeneMachines, San Carlos Calif.), or sonically sheared DNA to create a second, independent expression library in, for example, pET30abc. In the latter case, purified HK1651 DNA at a concentration of approximately 1 μg/μl is treated on ice with 3 second resonance frequency bursts of sonication using a Microson Ultrasonic Cell Distruptor (Heat Systems-Ultrasonics, Inc.). Samples taken at each time point are analyzed by agarose gel electrophoresis to determine the conditions required to optimize production of 0.75 to 1.5 Kb fragments. These conditions are employed in a large scale experiment to generate sufficient starting material for library construction. Terminal overhangs are removed with Klenow and dNTPs and the resulting blunt end products are ligated into the dephosphorylated EcoRV restriction site in the pET30abc multiple cloning site. The vector library is then be transformed into E. coli host strain, BL2 1 (DE3), with clones selected on BHI/kanamycin medium as previously described. Plates containing appropriate numbers of colonies are probed with the adsorbed serum and reactive colonies are detected using peroxidase-labeled goat anti-human immunoglobulin. Reactive colonies are isolated and their vector DNA purified.

EXAMPLE 3

[0090] Characterization Of polynucleotide Clones Reactive With Adsorbed LJP Serum

[0091] Sequencing of the cloned inserts in both directions indicated that the 13 recovered clones consisted of 8 unique clones. See SEQ ID NOs: 1-8. MacVector v.6.0.1 was used to identify open reading frames using both Fickett's and start/stop codon methods. In every instance, potential open reading frames were present on the cloned inserts oriented in both the same and opposite direction relative to the pET promoter (Table 1).

TABLE 1
Characterization of the IVIAT open reading frames. (* Putative ribosome
binding site.)
IVIAT		IPTG
clone	Schematic representation of ORFs	inducibility
17	1	+
26	2	+
30	3	+
37	4	+
39.1	5	+
46-2	6	+
47-4	7	−
58-3	8	−

[0092] In order to determine which of these was most likely to be the one encoding the antigen reactive with the adsorbed serum, a colony lift method was first used to determine if the level of expression of the antigen was regulated by IPTG. Briefly, Each IVIAT clone was grown overnight at 37° C. in BHI broth containing kanamycin, the cells were concentrated 200-fold, and 1 μl of each culture was spotted on BHI agar plates containing kanamycin with or without IPTG. Following incubation of the plates at 37° C. for five hours, the colonies were partially lysed with chloroform vapors, lifted onto nitrocellulose membranes, and reacted with the adsorbed serum. Two negative controls were included in this IPTG induction assay, namely pET30 a/BL21 (DE3) with no cloned insert and a randomly selected clone (WIAT-47) which contained a cloned DNA insert, but was non-reactive with the adsorbed serum.

[0093] This assay demonstrated that 6 of the 8 IVIAT clones expressed immunoreactive proteins that were induced by IPTG. See Table 1 and SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, and SEQ ID NO: 19). Therefore, their open reading frames of interest were likely cloned in the same orientation as the endogenous pET30 promoter. Their translation may either be initiated at the pET30 ribosome binding site or at their own ribosome binding site. We further examined 6 of the 11 possible open reading frames found in the IPTG inducible clones (Table 2 shown in FIG. 6). Each of these open reading frames was individually amplified by PCR and subcloned so that it was in-frame and under control of the pET30EkLIC (Novagen, Madison, Wis.) IPTG regulated promoter. See SEQ ID NO: 10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, and SEQ ID NO:20. Reactivity with the adsorbed serum and IPTG inducibility of these subdlones was confirmed using the colony lift method used previously (Table 2 shown in FIG. 6).

[0094] Four polynucleotides with demonstrable homology were found, including one (Aa2004) that is related to a known virulence factor (hlpA) in the closely related organism, Haemophilus influenza. There are three examples of polynucleotides with homology to genes encoding proteins with known function but with previously undemonstrated relevance to pathogenesis (Aa2005; Aa2009; Aa20011). Two polynucleotides were found with no homologues identified to date (Aa2008; Aa20010). These types of in vivo induced polynucleotides may well represent entirely novel virulence factors of Aa. Interestingly, none of the open reading frames thus far identified on the clones isolated by this invention show homology to genes with known housekeeping functions. The reason for this difference is uncertain, but this represents an important additional advantage of the method described herein.

EXAMPLE 4

[0095] Verification of Specific In Vivo Expression

[0096] It is possible to directly verify that in vivo induced antigens identified by IVIAT are actually expressed by the pathogen when it is growing at the site of infection in the human host. To accomplish this, a method to directly probe biological specimens taken from disease sites of infected patients was developed. The first step in this process involved optimization of recombinant protein production by the subdlones obtained in the previous step. Clone Aa2008 contains a 495 bp open reading frame (SEQ ID NO: 13) for a hypothetical protein subdloned into pET3OEkLIC (Table 2 shown in FIG. 6). Including the 5′ and 3′ sequences added by the vector, the molecular weight of the translated product should be approximately 28 Kda. Aa2008 was incubated in BHI broth containing kanamycin and IPTG (5 mM). Samples of the culture were removed at hourly intervals and analyzed by SDS-PAGE to determine the incubation time required for maximum production of the cloned protein. A major band (not seen in pET30EkLIC/BL21 (DE3) control samples) was found that had the expected molecular weight. Based on the results obtained, inclusion body preparations (Harlow & Lowes Eds., Antibodies, a Laboratory Manual, (CSHL Press, Plainview, N.Y., 1988)) were made from 10 ml batch cultures of Aa2008 incubated for 3 hours with IPTG. SDS-PAGE and western blot analysis was performed to confirm that the overexpressed protein was reactive with the adsorbed serum used in the original screening. The reactive band was excised from the Coomassie stained gel and used to raise polyclonal antibodies in mice.

[0097] Three female Balb/C mice are used per antigen. The 6-8 week old mice were injected subcutaneously (sc) with the purified polypeptide, using a concentration of 20, 50, or 100 μg/mouse. RIBI MPL+TDM emulsion was used an adjuvant. Two weeks later, the immunization protocol was repeated. Approximately 10 days after the second immunization, a small amount of blood was taken from the tail vein of each mouse, and assayed by ELISA to evaluate the response to the immunogen. Where the mice were responding well (i.e., detection at serum dilution greater than 1:500), one more sc injection was given 3-4 weeks after the second immunization, and four days before the scheduled hybridoma fusion. A mouse myloma cell line (Sp2/0) was cultured for several days prior to the scheduled fusion. Log phase cells were counted and washed.

[0098] The mouse exhibiting the best serum titer was anesthetized and bled out. The spleen was removed. The blood was clotted and spun down and the serum saved to be used as a positive control in the subsequent assays. The spleen cells were flushed out of the spleen capsule and separated into single cells, washed, and counted. Spleen cells were combined with Sp2/0 cells at a 7:1 ratio. Cells were pelleted by centrifugation. PEG 1500 at a concentration of 50% was slowly added to the cell pellet and then diluted. Cells were spun down and the pellet resuspended in HAT selective medium containing 20% horse serum and 25% conditioned media. Cells were plated into 96 well plates at a concentration of 2.5×105 cells/well. Cells were grown in a 37° C. incubator with 7% atmospheric CO2. After several days, colonies of hybridoma cells were visible. Feeding (removing and replacing approximately 50% of the total volume of growth medium) was performed at day seven and again at day nine or ten. When the hybridoma cells were nearly confluent in each well, a portion of the supernatant was removed and assayed by ELSIA to detect the presence of the desired antibody. The cells in the wells that tested positive on the primary screen were transferred to a 24 well plate, and the supernatant tested again by ELISA. The antibody activity and preliminary heavy chain isotype of each mass culture was determined and the wells that scored positive during this secondary round of screening were transferred to 6 well plates. At this point the cells were designated as mass cultures. Each mass culture chosen was cultured briefly in 6 well plate wells in order to freeze two vials of cells. Supernatant was saved for future expanded screening. The best mass cultures were selected for ascites production. Ascites were induced by intraperitoneal injection into one female Balb/C mouse, which was monitored daily for 7 days. The ascitic fluids were collected every day for 3 days (for a final volume of ca. 10 ml).

[0099] Ascites fluid were filtered and circulated over a protein A affinity column to affinity purify IgG. The polyclonal antibodies were washed and eluted with 0.1 M glycine, pH 3.0, followed by neutralization with Tris, pH 9-10. The recovered antibodies were concentrated, and the buffer exchanged to 1× PBS with 0.02% azide. The yield and quality of the antibodies were evaluated spectrophotometrically (280 nm) and by SDS-PAGE, respectively.

[0100] The purified IgG was shown to react in western blots with a protein of the appropriate size in extracts and inclusion body preparations made from clone Aa2008. The antibodies were labeled directly with fluorescein isothiocyanate (FITC) (Molecular Probes, Eugene, Oreg., USA). A murine monoclonal antibody specific for Aa, Mab 13(10B2), was labeled with Texas-red (TR).

[0101] Subgingival plaque from patients with LJP was sampled at the time of their diagnosis. Sterile paper points were inserted into mesial, buccal and distal sites of all four first molars that had significant (greater than or equal to 5 mm) bone loss. The points were immediately immersed in ice-cold BHI broth containing 50% glycerol, and after removing a small sample for microbiological identification of Aa, they were quick frozen in a dry ice/ethanol bath and stored at −80° C. Samples which were confirmed to contain Aa by growth on selective medium were used to directly demonstrate the presence of Aa2008.

[0102] Plaque samples and matched in vitro grown cells were assayed by immunofluorescence microscopy (FIG. 4). Briefly, plaque samples were thawed on ice, homogenized by brief vortexing at 4° C., and immediately heat-fixed on microscope slides. Plaque samples and matched in vitro grown Aa isolates taken from the selective medium were probed in parallel with FITC-labeled monospecific antibody directed against antigen Aa2008 and the TR-labeled Aa-specific monoclonal antibody. Samples were examined by fluorescence microscopy (excitation wavelength 488 nm). Double color analysis, using matched differential emission filters, was performed to identify individual cells that were simultaneously labeled with FITC and TR. Bacterial cells in plaque that reacted with TR-labeled anti-Aa monoclonal antibody (FIG. 4A) also reacted with FITC-labeled anti-Aa2008 antibody (FIG. 4B) and these signals were found to colocalize (FIG. 4C). In contrast, matched in vitro grown Aa reacted with the TR-labeled anti-Aa monoclonal antibody (FIG. 4D), but not with FITC-labeled anti-Aa2008 antibody (FIG. 4E) and therefore no colocalization was observed (FIG. 4F). These results provide direct evidence that Aa expresses antigen Aa2008 exclusively during in vivo growth.

[0103] Each anti-IVIAT antibody can be independently screened against all of the plaque samples collected (3 samples/tooth×maximum 4 teeth/patient×10 patients≦120 samples) in order to optimize the identification of Aa growing under environmental conditions appropriate for expression of the in vivo induced antigen. Aa-deficient samples are included to serve as an additional negative control for the species specific antibody and to identify possible cross-reacting antigens presented by other species that may be present in plaque. Based on our previous studies, we expect that approximately 75% of samples will contain measurable numbers of Aa. Of the three most likely outcomes, there will be instances where cells react with Texas red-labeled anti-Aa antibody and one or all of these cells also react with a FITC-labeled anti-IVIAT antibody. This indicates that this particular antigen is produced by Aa during growth in a site of infection. There is no requirement for all of the a cells in a sample to react with the anti-IVIAT antibody since there are likely to be numerous microenvironments present at each sampling site. As a second possible outcome, there may be instances where none of the cells which react with the Texas red-labeled anti-Aa antibody also react with a particular FITC-labeled anti-IVIAT antibody. This indicates that none of the plaque samples were taken from sites presenting the necessary environmental stimulus. Clearly, by using a large number of plaque samples taken from patients in different stages of infection, we hope to reduce the occurrence of this possibility. This result may also indicate that the in vivo induced antigen was expressed but not surface localized. Thus, in situations where a particular anti-IVIAT antibody does not react with Aa cells in any of the plaque samples, one may examine intra- and extra-cellular compartments for the antigen. This is done simply by examining plaque sample homogenates using a capture ELISA method: microtiter wells are coated with unlabeled anti-IVIAT antibody, reacted with homogenate, and then probed with FITC-labeled anti-IVIAT antibody according to Current Protocols in Immunology, John Wiley & Sons, NY (1998). The presence of reactivity, as measured by fluorescent light emission, is then correlated to the presence of Aa as determined by prior microbiological, ribotyping and immunological analyses of the plaque samples. As another possible outcome of interest, plaque samples may contain cells that react with a particular FITC-labeled anti-IVIAT antibody but which do not react with Texas red-labeled anti-Aa antibody. These are likely to represent instances where plaque samples contain other bacterial species which produce a cross-reacting antigen. However, it is also possible that these cells belong to a strain or variant of Aa which does not react with the species anti-Aa antibody. In these instances, previous culturing data along with ribotyping verification will help us to distinguish between these possibilities.

[0104] As an alternative approach to the microscopy methods described above, one may use FITC-labeled anti-WIAT antibodies and a fluorescence-activated cell sorting system (e.g., FACSort, Becton Dickinson; Franklin Lanes, N.J.). Recent reports have demonstrated the technical feasibility of using automated cell sorters for separating bacteria (Valdivia & Falkow, Science, 277:2007 (1997); Handfield & Levesque, FEMS Microbiol. Rev. 23:69-91 (1999). In addition, FACS can be used to effectively separate Aa from a mixed bacterial population using the green fluorescence protein (GFP) as a gene marker. In this study, a strain of Aa (SUNY 465) expressing the GFP under the leukotoxin 1tx promoter was separated from Aa strain Y4 with the FACSort.

EXAMPLE 5

[0105] Screening Patients for Reactive Antibodies

[0106] Once IVIAT has identified and confirmed an in vivo induced antigen, the purified antigen can be used to screen the sera of individual patients for reactive antibodies. Western blots of the inclusion body preparation of Aa2008 were probed using individual, unadsorbed sera from 20 periodontitis patients and 9 control subjects (FIG. 5). Densitometric analysis of Western blots showed that the patient group demonstrated significantly (p<0.05, independent student's T-test) higher reactivity with the recombinant Aa2008 protein (3.75±1.12, mean i standard deviation) than a control group that did not have periodontitis (2.79±0.98). These data suggest that Aa2008 is immunogenic in periodontitis patients, and confirms the conclusion drawn from fluorescence microscopy of plaque samples that this represents an in vivo expressed polynucleotide.

EXAMPLE 6

[0107] Method of Screening Using Phage Display Library

[0108] Instead of genomic expression library based screening, e.g., pET based screening, a display library based screening method can be used. Display library based methods provide marked advantages over genomic expression library based screening. For example, a display library screening approach allows for a dramatic increase in speed and ease of screening. An example of a display library based screening is provided below.

[0109] Serum Preparation

[0110] Serum is adsorbed to remove antibodies reactive with antigens expressed by the pathogen grown in vitro, thereby isolating antibodies that are reactive with antigens expressed by the pathogen only when it is growing in vivo. Sera is pooled from 10 patents and purified using a FPLC protein A column. The IgG is neutralized and washed into PBS/1%BSA/0.05% sodium azide (pH 7.2), aliquoted, and frozen at −80° C.

[0111] Samples of the IgG are is adsorbed with whole cells, with cell extracts, with heat treated extracts, and with T7. The IgG is purified using FPLC and a protein A column. The IgG is neutralized and washed into PBS/azide.

[0112] Preparation of DNA for Library

[0113] A SmaI (New England Biolabs (NEB)) digest of 10 μg (20 μl) of T7 select DNA is performed in buffer #4 (NEB) for 2 hours at room temp using 200 units of enzyme in a final volume of 200 μl. The DNA is then digested with 200 units of EcoRV (NEB) for 2 hr at 37° C. with NEB #3 (NEB) and 1× BSA present in a final volume of 1000 μl. 20 units of calf intestinal alkaline phosphatase (CIP) (NEB) is added and incubated for 1 hour at 37° C. The solution is heat treated at 80° C. for 20 min. The DNA is purified and desalted with 2 GeneClean® Turbo cartridges (Carlsbad, Calif.) and then concentrated to 0.5 μg/μl using Microcon™ 30 spin tubes (Millipore Corp., Bedford, Mass.). 5 μg of the microbe's DNA is sheared and 0.2-0.7 Kb fragments are gel purified. Freeze-squeeze columns are used to recover fragments and 4 GeneClean® Turbo cartridges are used to purify the DNA. The DNA is eluted from the cartridges. Epicenter Technologies (Madison, Wis.) fill-in (End-It™ DNA end-repair) kit is used according to their directions in a 50 μl final volume reaction. The DNA is heat treated at 80° C. for 10 minutes. Ligations are performed in a final volume of 5 μl. 0.5 μl of T7 is used per reaction and varying amounts of insert are used. The vector and insert DNA are heat treated at 60° C. for 5 min before adding ligase buffer and 0.1 μl of T4 ligase (NEB concentrated). The reaction tubes are incubated overnight at 16° C. and then at room temperature for 20 minutes before packaging.

[0114] Packaging DNA

[0115] Ligation reactions can be added directly to T7 Packaging Extracts (Novagen) for in vitro packaging. The best T7 packaging results are obtained when the extent of dilution of the extract is minimized. The extracts are supplied in 25 μl single reaction volumes, and the volume of the ligation reaction added to the packaging extract should not exceed 5 μl. The T7Select Packaging Extract Novagen, Madison, Wis.) is allowed to thaw on ice. The volume of the extract is 25 μl and will package up to 1 μg of vector DNA without a loss in efficiency. 5 μl ligation reaction per 25 μl extract is added and incubated. The reaction is stopped after two hours and the product can be stored or used immediately.

[0116] Plaque Assay to Determine the Number of Recombinants Generated

[0117] The phage titer, described in plaque forming units (pfu) per unit volume is the number of plaques on the assay plate times the dilution times 10 (to account for the 0.1 ml of dilution plated). If a sufficient library is obtained (≧105 independent pfu), the library is amplified.

[0118] Protein A Biopanning

[0119] 5 to 10 μl of the absorbed IgG to be used is added to 100 μl of UV irradiated T7 Select 10-3 lysate (approximately 1010 pfu/ml before irradiation) and incubated 8 hours at 4° C. 5-10 μl of the T7 library (1010 pfu/ml) are added and incubated 8 hours at 4° C. The adsorbed IgG is brought to room temperature, and 125 μl of Pierce (Rockford, Ill.) binding buffer is added. The solution is agitated by inversion. 50 μl of the Pierce Protein A sludge (kept at 4C in PBS+0.02% azide) is washed 2× with 1 ml volume of binding buffer in an eppendorf tube. The washed beads are resuspended in 750 μl binding buffer and are added to the equilibrated IgG and incubated 8 hours at 4° C. The beads are washed 10× with 1 ml of Binding Buffer at room temperature. The panned antibodies are eluted by adding 200 μl of Pierce Elution Buffer. The beads are vortexed for 30 sec. and removed by centrifuigation at 14K rpm for 2 min. The supernatant that contains the eluted antibodies and bound phage is removed and neutralized by adding 200 μl of Binding Buffer. The eluate is concentrated and resuspended in 100 μl of LB, and samples are amplified or individual plaques obtained using E. coli strain BLT 5615 as the host.

[0120] Perform Biopanning using ELISA Methodology

[0121] Antibodies are purified from adsorbed serum using a protein A column. Antibodies are applied to the wells of an ELISA plate and incubated. The wells are washed to remove unbound antibodies. Blocking reagent is added to the wells and incubated. The plate is washed. The phage lysate is diluted into TBST (TBS with 0.1% Tween-20™) to ca. 107-109 pfu/ml and 100 μl added to each well. The plate is incubated at 4° C. overnight and the plate is washed to remove unbound phage. 200 μl of E. coli BLT 5615 host cells in LB broth containing 1 mM of IPTG is added to each treated well and incubated for 10 minutes at room temperature. The cells are removed and the wells rinsed with an additional 4×200 μl of cells. The cells are pooled and samples can be plated for individual plaques or incubated with shaking to produce an amplified library. The biopanning is repeated 3 times using 100 μl of lysate in TBST, 100 μl final volume.

[0122] The bound phage can also be eluted and the biopanning repeated without amplification.

[0123] Analysis of Recovered Phage

[0124] A dilution of the lysate from the biopanning that yields approximately 1000 pfu/ml is prepared. 100 μl samples are diluted on 10 LB plates using 3 ml of molten top agar and incubated. Individual plaques are picked and amplified using E. coli BLT 5615 and a plate method. The phage lysates are blotted onto nitrocellulose membranes. The membranes are blocked and screened with adsorbed IgG/goat anti-human Ig-HRP (see below). Positive clones are determined by chemiluminescence imaging. Samples of positive clones are taken for PCR amplification of cloned inserts as described below.

[0125] Confirmation

[0126] Confirmation screening can also be accomplished by performing plaque lifts directly on plates that contain well isolated plaques. The nitrocellulose membranes are tested for reactivity with adsorbed serum and then positive plaques are picked. Nitrocellulose membranes can be used for plaque lifts and the membranes are allowed to air dry for 10-20 min. The membranes are soaked in 5% Blocking Reagent in 1× TBST. The membrane is treated with primary and secondary antibody, and developed. The imager result is aligned with the master plate and positive clones are picked using sterile Pasteur pipettes. The phage is eluted and stored.

[0127] Analysis of Cloned Inserts

[0128] The cloned inserts are PCR amplified and sequenced using Titanium Taq Plus (Clontech, Palo Alto, Calif.). The sequencing results can be subjected to Blast analysis and motif analysis to determine clones likely to express proteins that are surface localized. Recombinant T7 is amplified and purified using PEG8000 from interesting clones. The purified phage can be subjected to SDS-PAGE analysis and recombinant protein can be isolated and purified from the gel. The recombinant protein can also be isolated and purified using immunoaffinity techniques involving anti-capsid antibodies attached to a solid support. In this case, both wild-type and capsid proteins fused to the pathogen protein will be isolated. The PEG-purified phage can be used as an immunogen to raise antibodies in an animal. These antibodies can be used in Example 4.

Claims

1. A method of identifying a polynucleotide of a microbe that is expressed in vivo comprising the steps of: (a) adsorbing antibodies against antigens that are expressed by the microbe in vivo and in vitro with cells or cellular extracts of the microbe that have been grown in vitro; (b) isolating unadsorbed antibodies; and (c) probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies of step (b); wherein the step of probing a display library comprises: (i) immobilizing the unadsorbed antibodies on a solid support; (ii) adding the display library of the microbe's DNA or RNA to the solid support; (iii) washing unbound phage from the solid support; and (iv) recovering phage that are bound to the solid support; wherein a polynucleotide of the microbe that is expressed in vivo is isolated and identified.

2. The method of claim 1, wherein the solid support is blocked with a blocking agent before the library is added.

3. The method of claim 1, wherein the solid support is selected from the group consisting of nitrocellulose, nylon, polystyrene, polyvinylchloride, latex, fiberglass, glass, microsphere, liposome, sepharose, sephadex, and a magnetic particle.

4. The method of claim 1 wherein the polynucleotide encodes an antigen.

5. The method of claim 4 wherein the antigen is capable of eliciting an immune response in an animal.

6. The method of claim 5 wherein the animal is selected from the group consisting of humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, and shellfish.

7. The method of claim 1 further comprising the step of determining the nucleic acid sequence of the polynucleotide.

8. The method of claim 1 wherein the antibodies of step (a) comprise sera from one or more hosts infected with, or previously infected with the microbe.

9. The method of claim 1 wherein the microbe is selected from the group consisting of a bacterium, a virus, a parasite, a prion, and a fungus.

10. The method of claim 1 wherein the microbe is selected from the group consisting of Candida, Aspergillus, Sporothrix, Blastomyces, Histoplasma, Cryptococcus, Pneumocystis, Coccidioides, Tinea, Toxoplasma, Plasmodium, Pseudomonas, Actinobacillus, Staphylococcus, Bacillus, Clostridium, Listeria, Corynebacterium, Actinomyces, Mycoplasma, Nocardia, Bordetella, Brucella, Francisella, Legionella, Enterobacter, Escherichia, Klebsiella, Proteus, Salmonella, Shigella, Streptococcus, Yersinia, Vibrio, Campylobacter, Helicobacter, Bacteroides, Chlamydia, Borrelia, Treponema, Leptospira, Aeromonas, Rickettsia, Ascaris, Cryptosporidium, Cyclospora, Entamoeba, Giardia, Shistosoma, Trypanosoma, herpes virus, cytomegalovirus, Epstein-Barr virus, hepatitis virus, adenovirus, papillomavirus, polyomavirus, enterovirus, rotavirus, influenza virus, paramyxovirus, rubeola virus, rhabdovirus, human immunodeficiency virus, arenavirus, rhinovirus, and reovirus.

11. The method of claim 8 wherein the host is an animal selected from the group consisting of comprise humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, and shellfish.

12. The method of claim 1 wherein the display library is a phage display library.

13. A method of comparing polynucleotides of a microbe that are expressed in vivo at different stages of infection of the microbe comprising the steps of: (a) adsorbing a first sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host is in about the same stage of the infection; (b) adsorbing a second sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host is in about the same stage of the infection, wherein the stage of the infection is different from the stage of infection in step (a); (c) isolating unadsorbed antibodies from the first serum sample and from the second serum sample; (d) probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing the display library with the unadsorbed antibodies from the second serum sample, wherein the steps of probing display libraries comprise: (i) immobilizing the unadsorbed antibodies on a solid support; (ii) adding the display library of the microbe's DNA or RNA to the solid support; (iii) washing unbound display library members from the solid support; and (iv) recovering display library members that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample; and (e) comparing the polynucleotides of the microbe that are expressed in vivo at different stages of infection of the microbe.

14. The method of claim 13 wherein the display library used to probe the unadsorbed antibodies from the first serum sample and the display library used to probe the unadsorbed antibodies from the second serum sample are the same display library.

15. The method of claim 13 wherein the display library is a phage display library.

16. A method of comparing polynucleotides of a microbe that are expressed in vivo, wherein the microbe has infected its host by different routes of infection comprising the steps of: (a) adsorbing a first sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host has been infected by about the same route of infection; (b) adsorbing a second sera sample from one or more hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro, wherein each host has been infected by about the same route of infection, wherein the route of infection is different from the route of infection in step (a); (c) isolating unadsorbed antibodies from the first serum sample and from the second serum sample; (d) probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing a display library with the unadsorbed antibodies from the second serum sample, wherein the steps of probing the display library comprises: (i) immobilizing the unadsorbed antibodies on a solid support; (ii) adding the display library of the microbe's DNA or RNA to the solid support; (iii) washing unbound display library members from the solid support; (iv) recovering display library members that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample; and (e) comparing the polynucleotides of the microbe that are expressed in vivo by different routes of infection of the microbe.

17. The method of claim 16, wherein the display library used to probe the unadsorbed antibodies from the first serum sample and the display library used to probe the unadsorbed antibodies from the second serum sample are the same display library.

18. The method of claim 16, wherein the display library is phage display library.

19. A method of confirming an animal model of microbial infection as a valid model comprising the steps of: (a) adsorbing a first sera sample from one or more animal model hosts infected with or previously infected with a microbe, with cells or cellular extracts of the microbe that have been grown in vitro; (b) adsorbing a second sera sample from one or more second hosts infected with or previously infected with the microbe, with cells or cellular extracts of the microbe that have been grown in vitro; wherein the second host is a different species of animal than the animal model host; (c) isolating unadsorbed antibodies from the first serum sample and from the second serum sample; (d) probing a display library of the microbe's DNA or RNA with the unadsorbed antibodies from the first serum sample, and probing the display library with the unadsorbed antibodies from the second serum sample, wherein the probing of display library steps comprise: (i) immobilizing the unadsorbed antibodies on a solid support; (ii) adding the display library of the microbe's DNA or RNA to the solid support; (iii) washing unbound members of the display library from the solid support; and (iv) recovering members of the display library that are bound to the solid support; wherein polynucleotides of the microbe that are expressed in vivo are identified for the first and second serum sample; and (e) comparing the polynucleotides of the microbe that are expressed in vivo in the animal model host and the second host; wherein if the polynucleotides expressed in vivo in the animal model and in the second host are the same or similar, then the animal model is confirmed as a valid model.

20. The method of claim 19 wherein the display library used to probe the unadsorbed antibodies from the first serum sample and the display library used to probe the unadsorbed antibodies from the second serum sample are the same display library.

21. The method of claim 19 wherein the animal model host and the second host are selected from the group consisting of comprise humans, baboons, chimpanzees, macaques, cattle, sheep, pigs, horses, goats, dogs, cats, rabbits, guinea pigs, rats, mice, chickens, ducks, fish, and shellfish.

22. The method of claim 19, wherein the display library is a phage display library.