WO2014011645A1 - Protective vaccine based on staphylococcus aureus sa2493 protein - Google Patents

Abstract

The present invention relates to methods of inducing an immune response to Staphylococcus comprising administering a composition comprising an SA2493-related polypeptide from Staphylococcus aureus as well as derivatives or fragments thereof. The present invention also encompasses methods of treating and/or reducing the likelihood of a Staphylococcus infection by administering a composition comprising an SA2493-related polypeptide or an antibody that specifically binds to an SA2493 polypeptide, derivative or fragments thereof. Compositions administered in the methods of the invention can include one or more additional antigens including, but not limited to, IsdB. Compositions used to practice the methods of the invention are also encompassed.

Description

TITLE OF THE INVENTION

PROTECTIVE VACCINE BASED ON STAPHYLOCOCCUS AUREUS SA2493 PROTEIN

FIELD OF THE INVENTION

The present invention relates to methods of inducing an immune response to

Staphylococcus using an SA2493 protein from Staphylococcus aureus as well as derivatives or fragments thereof. The present invention also relates to a composition, particularly an 5^*. aureus vaccine, comprising an SA2493 polypeptide, derivative or fragment thereof, alone or in combination with one or more additional immunogens, capable of inducing a protective immune response.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S.S.N. 61/669,947, filed July 10, 2012, which is herein incorporated by reference in its entirety.

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The sequence listing of the present application is submitted electronically via EFS- Web as an ASCII formatted sequence listing with a file name "MRLIFD00050WOPCT- SEQLIST-26JUN2013.txt", creation date of June 26, 2013, and a size of 13.1 KB. This sequence listing submitted via EFS-Web is part of the specification and is herein incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

Staphylococcus aureus is a bacterial pathogen responsible for a wide range of diseases and conditions, ranging from minor skin infections to serious life-threatening wound infections, bacteraemia, endocarditis, pneumonia, osteomyelitis and toxic shock syndrome. While S. aureus commonly colonizes in the nose and skin of healthy humans, often causing only minor infections (e.g., pimples, boils), it can also cause systemic infections. Examples of diseases and conditions caused by S. aureus include bacteremia, infective endocarditis, folliculitis, furuncle, carbuncle, impetigo, bullous impetigo, cellulitis, botryomyosis, toxic shock syndrome, scalded skin syndrome, central nervous system infections, infective and inflammatory eye disease, osteomyelitis and other infections of joints and bones, and respiratory tract infections. (The Staphylococci in Human Disease, Crossley and Archer (eds.), Churchill Livingstone Inc. 1997; Archer, 1998, Clin. Infect. Dis. 26: 1 179-1181.)

Staphylococcus aureus is a nosocomial as well as a community-acquired pathogen which causes several diseases ranging from. See Lowy et ah, 1998, N. Engl. J. Med. 339:520-32. The worldwide growing incidence of staphylococcal infections is strongly related to the increased use of surgical devices and a growing number of immunocompromised patients. The situation has become more serious since the increased use of antibiotics led to the emergence of methicillin-resistant S. aureus strains (MRSA). See Selvey et al, 2000, Infect. Control. Hosp. Epidemiol. 21 :645-8; Peacock et al., 1980, Ann. Intern. Med. 93:526-32.

Additionally, S. aureus isolates with reduced susceptibility to vancomycin, the antibiotic of choice against MRSA strains, were described in the lab as well as the clinic. See Tenover et al., 2001, Emerg. Infect. Dis. 7:327-32; Tenover et al., 1998, J. Clin. Microbiol. 36: 1020-7; Palazzo et al., 2005, J. Clin. Microbiol. 43 : 179-85. The rising emergence of multidrug-resistant staphylococci has led to a growing interest in the development of alternative approaches to prevent and treat staphylococcal infections.

Information concerning S. aureus polypeptide sequences has been obtained from sequencing the S. aureus genome. See Kuroda et al, 2001, Lancet 357: 1225-1240; Baba et al., 2000, Lancet 359: 1819-1827; Gill et al., 2005, J. Bacteriol. 187:2426-2438, European Patent Publication EP 0 786 519, WO 02/094868, and WO 2010/1 19343. To some extent,

bioinformatics has been employed in efforts to characterize polypeptide sequences obtained from genome sequencing. See, e.g., European Patent Publication EP 0 786 519 and US Patent No. 6,593, 1 14.

Techniques such as those involving display technology and sera from infected patients have also been used in an effort to help identify genes coding for potential antigens. See, e.g., International Publication Nos. WO 01/98499 and WO 02/059148; and Etz et al., 2002, Proc. Natl. Acad. Sci. USA 99:6573-6578. Numerous staphylococcal surface proteins have been identified so far using recently adopted technologies, like proteomics (see Brady et al., 2006, Infect. Immun. 74:3415; Gatlin et al., 2006, Proteomics 6: 1530; Pieper et al., 2006, Proteomics 6:4246; Vytvytska et al., 2002, Proteomics 2:580; Nandakumar et al., 2005, J. Proteome Res. 4:250) or protein selection methods based on expression libraries (see Clarke et al., 2006, J. Infect. Dis. 193: 1098; Etz et al., 2002, Proc. Natl. Acad. Sci. USA 99:6573-8; Weichhart et al., 2003, Infect. Immun. 71 :4633; and Yang et al., 2006, Vaccine 24: 1 117).

Vaccines consisting of one or more particular antigenic determinants can provide protection against lethal challenge with S. aureus in mice. See Stranger-Jones et al., 2006, Proc. Natl. Acad. Sci. USA 103 : 16942-7 and Kuklin et al., 2006, Infect. Immun. 74:2215.

Recombinantly expressed polypeptides can readily be made, purified, and formulated as vaccines. Additionally, recombinant proteins can be combined with additional components to make multicomponent polypeptide vaccines that induce a spectrum of immune responses.

Despite this, there are no reported protein based vaccines for staphylococcal infections in humans or animals to date. Thus, there remains a need for immunogens that can provide protective immunity against Staphylococcal infections in human and/or animals. SUMMARY OF THE INVENTION

It is shown herein that SA2493 -related polypeptides can provide protective immunity against 5^*. aureus infection in a relevant animal model system. Accordingly, one aspect of the invention provides a composition comprising an immunologically effective amount of a polypeptide that is at least 95% identical to an SA2493 polypeptide (represented by SEQ ID NO:2) or a fragment of the polypeptide and a pharmaceutically acceptable carrier. In some embodiments of the invention, the polypeptide is not SEQ ID NO:2. In preferred embodiments, the polypeptide is at least 98% identical to SEQ ID NO:2.

Also provided by the invention are compositions as described above, which further comprise one or more additional 5^*. aureus antigens or one or more additional antigens from another Staph species, such a S. epidermidis. The compositions of the invention may further comprise an adjuvant.

The present invention is further related to a method of inducing a protective immune response in a patient against an 5^*. aureus infection comprising the steps of

administering to the patient an immunologically effective amount of any of the compositions or vaccines described herein. The compositions are administered to a patient in need thereof, wherein the patient is a human or a non-human mammal such as a cow. In some embodiments of the methods described herein, the compositions are given to a patient who suffers from weakened immunity, has received a foreign body implant or is on renal dialysis.

Also provided by the invention is the use of a polypeptide that is at least 95% identical to SEQ ID NO:2 or a fragment of the polypeptide in the manufacture of a medicament for inducing a protective immune response in a patient against 5^*. aureus infection or the use of the compositions herein for inducing protective immunity against 5^*. aureus.

Further provided by the invention is a method of conferring passive immunity to S. aureus infection in a patient comprising administering to the patient one or more antibodies that specifically bind to a polypeptide of SEQ ID NO:2.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGURE 1 shows the native nucleotide sequence (SEQ ID NO: l) of SA2493 (Fig. 1A) and the actual cloned nucleotide sequence (SEQ ID NO:3) from S. aureus strain COL (Fig. IB).

FIGURE 2 shows the native amino acid sequence of SA2493 (SEQ ID NO:2, Fig. 2A). Also shown is the translated sequence of the actual cloned sequence of SA2493 with a carboxy-terminal 8 His-tag (SEQ ID NO:4, Fig. 2B), which was added to facilitate purification of the antigen.

FIGURE 3 shows the results from two independent murine lethal challenge experiments (MSE#100 and MSE#120), as described in Example 3. Balb/c mice were immunized with either His-tagged SACOL2493 or negative control antigen (either BSA or non- protective S. aureus antigen SACOL1490) formulated on Merck aluminum adjuvant (MAA) (see EXAMPLE 2) and were challenged with 5^*. aureus Becker.

FIGURE 4 shows the results of two non-human primate immunogenicity studies in which rhesus macaques were immunized intramuscularly with His-tagged SACOL2493 formulated on MAA (see Example 4). Animals were bled post vaccination to characterize the humoral (Staph #8, Staph #9) and cellular (Staph #9) immune response to the test antigen. In Staph #8 (panel A) rhesus macaques were vaccinated 3 times i.m. with either His-tagged SACOL2493, or negative control antigen, formulated on Merck alum adjuvant. Shown is the geometric mean titer (n=3) as a function of time post immunization (weeks). In Staph #9, rhesus macaques (n=3; 01D351, 05D104, and 05D039) were vaccinated a single time i.m. with test antigen SACOL2493 formulated on MAA, at time 0. At eight weeks post vaccination, animals were challenged with a sub-lethal dose of S. aureus Becker, to stimulate a memory response in the animals (indicated with an arrow, panels B and C). The B-cell response (IgG titer, RLU), measured with a Mesoscale assay, for each of the three animals (panel B), as well as the T-cell response (ELISpot assay of IL17 in SFC/million cells, panel C) is provided. Also shown (table in panel C) are the Thl7 and Thl (IFNy) responses (ELISpot assay) for each of the three animals.

DETAILED DESCRIPTION OF THE INVENTION

As stated above, there is a need for the identification of S. aureus immunogens that can provide protective immunity against Staphylococcal infections. To that end, the present invention provides vaccines and methods of use thereof based on SACOL2493 from S. aureus (Gill et ah, 2005, J. Bacterioh 187:2426-2438); which is known as tandem lipoprotein.

SACOL2493 (also referred to herein as SA2493) was originally identified for use as a potential immunogen in a Staph-based vaccine using a transcriptomics approach, as described in Example 1. Experiments described herein have shown that SA2493 is useful as an immunogen to provide protective efficacy against 5^*. aureus infection and/or the effects thereof.

The inventors have shown herein that SA2493 containing a His-tag (SEQ ID NO:4) is able to provide protective immunity from challenge with 5^*. aureus strain Becker in a murine model system; e.g. Balb/c mice. It is further shown herein that SA2493 -related sequences (e.g. SEQ ID NO:4) can induce an immune response in rhesus monkeys. The vaccines of the present invention can provide protection against infection with 5^*. aureus strains, e.g. strain Becker or strain COL.

A S. aureus SA2493 gene sequence was cloned from S. aureus strain COL and expressed recombinantly in E. coli. The recombinant protein is immunogenic in rodents and protects the animals from 5^*. aureus infection. As used herein, the term "SA2493" refers to a polypeptide of SEQ ID NO:2 or a naturally occurring allelic variant or a homolog from another S. aureus strain. Examples of other strains of S. aureus include Becker, MW2, N315 (see Kuroda et ah, 2001, Lancet 357: 1225), Newman, USA300 (see Diep et ah, 2006, Lancet 367:731), MSA817, and Mu3. In one embodiment, SA2493 is SEQ ID NO:2, which is from S. aureus strain COL. SA2493 may also be from another 5^*. aureus strain. "SA2493-related sequences" refer to sequences that are highly identical to the SA2493 provided in SEQ ID NO:2, or derivatives or fragments thereof. Embodiments of the invention provide pharmaceutical compositions that comprise an immunologically effective amount of a SA2493 immunogen and a pharmaceutically acceptable carrier, wherein the SA2493 immunogen is not SEQ ID NO:2 and wherein the SA2493 immunogen is a polypeptide that is at least 95% identical to SEQ ID NO:2. SA2493 immunogens useful in the present invention are further defined, infra.

In one embodiment, SA2493 polypeptides, derivatives or fragments thereof are used as a vaccine for the treatment of staphylococcal infections and/or reducing the likelihood of staphylococcal infections or clinical manifestations of such infections. Methods of the invention encompass administering a composition comprising a vaccine of the invention to a non-human animal or human patient in need thereof to induce an immune response. In a specific embodiment of the invention, one or more additional antigens are provided in the composition comprising an isolated SA2493 polypeptide, derivative or fragment thereof. In one embodiment, the additional antigen is IsdB (also known as ORF0657) or a derivative or fragment thereof.

As used herein, the phrase "induce an immune response" refers to the ability of a polypeptide, derivative, or fragment thereof to produce an immune response in a patient, preferably a mammal, to which it is administered, wherein the response includes, but is not limited to, the production of elements, such as antibodies, which specifically bind S. aureus or said polypeptide, derivative or fragment thereof. The immune response provides a protective effect against S. aureus infection, ameliorates at least one pathology associated with S. aureus infection and/or reduces the likelihood that a patient will contract an 5^*. aureus infection. In a specific embodiment, the immune response induces opsonophagocytic activity of human neutrophils for S. aureus.

As used herein, the phrase "an immunologically effective amount" refers to the amount of an immunogen that can induce a protective immune response against 5^*. aureus when administered to a patient. The amount should be sufficient to significantly reduce the likelihood or severity of an 5^*. aureus infection and/or the clinical manifestations thereof. Animal models such as those described in the Examples, infra, and those known in the art can be used to assess the protective effect of administration of immunogen. For example, a murine, lethal-challenge model (see, e.g., Thakker et al, 1998, Inflmmun 66:5183-5189; Fattom et al, 1996, Inflmmun 64: 1659-1665) and a rat, indwelling-catheter, sub-lethal challenge model (see, e.g., Ulphani et al, 1999, Lab Animal Sc. 49:283-287; Baddour et al, 1992, JInfDis 165:749-53; Ebert et al, Human Vaccines 7(6): 1-9 (201 1)) can be used.

In another embodiment, SA2493 polypeptides, derivatives or fragments thereof are used as a target for generating antibodies. These antibodies can be administered to a patient for the treatment and/or reduction of the likelihood of staphylococcal infections due to passive immunity.

As used herein, the phrase "passive immunity" refers to the transfer of active humoral immunity in the form of antibodies. Passive immunity provides immediate protective effect to the patient from the pathogen recognized by the administered antibodies and/or ameliorates at least one pathology associated with pathogen infection. However, the patient does not develop an immunological memory to the pathogen and therefore must continue to receive the administered antibodies for protection from the pathogen to persist.

Embodiments of the invention also include one or more of the polypeptide immunogens or compositions thereof, described herein, or a vaccine comprising or consisting of said immunogens or compositions (i) for use in, (ii) for use as a medicament for, or (iii) for use in the preparation of a medicament for: (a) therapy (e.g., of the human body); (b) medicine; (c) inhibition of S. aureus replication; (d) treatment or prophylaxis of infection by S. aureus; or, (e) treatment, prophylaxis of, or delay in the onset or progression of S. awrews-associated disease(s), including, but not limited to: skin infections, wound infections, bacteremia, endocarditis, pneumonia, osteomyelitis, toxic shock syndrome, infective endocarditis, folliculitis, furuncle, carbuncle, impetigo, bullous impetigo, cellulitis, botryomyosis, scalded skin syndrome, central nervous system infections, infective and inflammatory eye disease, osteomyelitis and other infections of joints and bones, and respiratory tract infections. The polypeptide immunogens of the invention are also useful for treatment, prophylaxis of, or delay in the onset or progression of S. awm/s-associated disease common to animals including: bovine mastitis, respiratory disease in swine, skeletal problems, and skin infections in companion animals such as horses, dogs and cats. In these uses, the polypeptide immunogens, compositions thereof, and/or vaccines comprising or consisting of said immunogens or compositions can optionally be employed in combination with one or more anti-bacterial agents (e.g., anti-bacterial compounds; combination vaccines, described infra).

Polypeptides

The amino acid sequence of a wild type full length SA2493 from S. aureus subsp. aureus COL is SEQ ID NO:2. SEQ ID NO:2 as well as derivatives and fragments thereof can be used in the methods of the invention. Collectively, derivatives and fragments of SEQ ID NO:2 are termed "altered polypeptides" or "SA2493-related sequences". SEQ ID NO:4 is a His- tagged derivative of SEQ ID NO:2 which was shown herein to provide protective immunity against 5^*. aureus infections in animal model systems.

As used herein, the term "isolated" indicates a different form than found in nature.

The different form of the polypeptide can be, for example, a different purity than found in nature.

In one embodiment, the term refers to polypeptides that are substantially or essentially free from components that normally accompany it in its native state. As used herein, the terms "purified" with regard to, for example, a polypeptide immunogen indicates the presence of such polypeptide in an environment lacking one or more other polypeptides with which it is naturally associated and/or is represented by at least about 10% of the total protein present. In different embodiments, the purified polypeptide represents at least about 50%, at least about 75%, at least about 95%, or at least about 99% of the total protein in a sample or preparation.

As used herein, the term "fragment" refers to a continuous segment of an SA2493 polypeptide (i.e., SEQ ID NO:2) or derivatives thereof having at least 5 amino acid residues, at least 10 amino acid residues, at least 15 amino acid residues, or at least 20 amino acid residues and which is shorter than the full length SA2493 polypeptide. Preferably, fragments will comprise at least one antigenic determinant or epitopic region. In some embodiments, a fragment of the invention will comprise a domain of the SA2493 polypeptide including, but not limited to, the extracellular domain or T cell epitopes (either from the intracellular or extracellular portion of SA2493). One or more fragments comprising at least one antigenic determinant or epitopic region may be fused together.

As used herein, the terms "epitope" or "antigenic determinant" refer to a site on an antigen to which an antibody and/or T cell receptor binds. Epitopes can be formed both from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Epitopes formed from contiguous amino acids are typically retained on exposure to denaturing solvents whereas epitopes formed by tertiary folding are typically lost on treatment with denaturing solvents. An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation. Methods of determining spatial conformation of epitopes include, for example, x-ray crystallography and 2-dimensional nuclear magnetic resonance.

As used herein, the term "derivative" refers to a polypeptide having one or more alterations, which can be changes in the amino acid sequence (including additions and deletions of amino acid residues) and/or chemical modifications. In preferred embodiments, the derivative is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identical to the original sequence prior to alteration. In some preferred embodiments, the polypeptide is not SEQ ID NO:2. In general, derivatives retain the activity of inducing a protective immune response. In some embodiments, SA2493 or a fragment thereof has been altered to a derivative of the invention such that one or more epitopes have been enhanced.

Epitope enhancement improves the efficacy of a polypeptide to induce a protective immune response. Epitope enhancement can be performed using different techniques such as those involving alteration of anchor residues to improve peptide affinity for MHC molecules and those that increase the affinity of the peptide-MHC complex for a T-cell receptor (Berzofsky et ah, 2001, Nature Review 1 :209-219). In one embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by one or more amino acid substitutions. Amino acid substitutions may be regarded as "conservative" where an amino is replaced with a different amino acid with broadly similar properties. "Non-conservative" substitutions are where amino acids are replaced with amino acids of a different type. Broadly speaking, fewer non-conservative substitutions will be possible without altering the biological activity of the polypeptide. In some embodiments, no more than 12 amino acid residues, 11 amino acid residues, 10 amino acid residues, 9 amino acid residues, 8 amino acid residues, 7 amino acid residues, 6 amino acid residues, 5 amino acid residues, 4 amino acid residues, 3 amino acid residues, 2 amino acid residues, or 1 amino acid residue is/are substituted.

In another embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by having one or more amino acid deletions and/or additions in any combination. Deleted or added amino acids can be either contiguous or individual residues. In some embodiments, no more than 25 amino acid residues, no more than 20 amino acid residues, no more than 15 amino acid residues, no more than 12 amino acid residues, no more than 10 amino acid residues, no more than 8 amino acid residues, no more than 7 amino acid residues, no more than 6 amino acid residues, no more than 5 amino acid residues, no more than 4 amino acid residues, no more than 3 amino acid residues, no more than 2 amino acid residues, or no more than 1 amino acid residue is/are deleted or added. Addition of amino acids may include fusion (either directly or via a linker) to at least one functional protein domain including, but not limited to, marker polypeptides, carrier

polypeptides (including, but not limited to, OMPC, BSA, OVA, THY, KLH, tetanus toxoid, HbSAg, HBcAg, rotavirus capsid proteins, LI protein of the human papilloma virus, diptheria toxoid CRM 197 protein, flagellin and HPV VLP), polypeptides holding adjuvant properties or polypeptides that assist in purification. Additionally, it will be appreciated that the additional amino acid residues can be derived from S. aureus or an unrelated source and may produce an immune response effective against S. aureus or another pathogen.

In another embodiment, a derivative is a polypeptide that has an amino acid sequence which differs from the base sequence from which it is derived by having one or more chemical modifications of the protein. Chemical modifications include, but are not limited to, modification of functional groups (such as alkylation, hydroxylation, phosphatation, thiolation, carboxilation and the like), incorporation of unnatural amino acids and/or their derivatives during protein synthesis and the use of crosslinkers and other methods which impose conformational constraints on the polypeptides.

Any method known in the art can be used to determine the degree of difference between SA2493 (e.g., SEQ ID NO:2) and a derivative. In one embodiment, sequence identity is used to determine relatedness. Derivatives of the invention will be at least 85% identical, at least 90% identical, at least 95% identical, at least 97% identical, at least 99% identical to the base sequence (e.g., SEQ ID NO:2). The percent identity is defined as the number of identical residues divided by the total number of residues and multiplied by 100. If sequences in the alignment are of different lengths (due to gaps or extensions), the length of the longest sequence will be used in the calculation, representing the value for total length.

In another embodiment, hybridization is used to determine relatedness. Nucleic acids encoding derivatives of the invention will hybridize to nucleic acids encoding SA2493 (e.g., SEQ ID NO: 1) under highly stringent conditions. Stringency of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. Generally, stringent conditions are selected to be about 5°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium. Since target sequences are generally present at excess, at Tm, 50% of the probes are occupied at equilibrium. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3; and the temperature is at least about 30°C for short probes, primers or oligonucleotides (e.g., 10 to 50 nucleotides) and at least about 60°C for longer probes, primers and oligonucleotides. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide. For additional details and explanation of stringency of hybridization reactions, see Ausubel et ah, Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).

As used here, the phrase "high stringency" refers to conditions that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium

chloride/0.0015 M sodium citrate, 0.1% SDS at 50°C; (2) employ a denaturing agent, such as formamide, during hybridization for example, 50% (v/v) formamide with 0.1% BSA, 0.1% Ficoll, 0.1% polyvinylpyrrolidone, 50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride/50 mM sodium citrate at 42°C; or (3) employ 50% formamide, 5xSSC, 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5xDenhardt's solution, sonicated salmon sperm DNA (50 μ§/πι1), 0.1% SDS, and 10% dextran sulfate at 42°C, with washes at 42°C in 0.2.x SSC and at 55°C in 50% formamide, followed by a high-stringency wash consisting of O. lxSSC containing EDTA at 55°C. Polypeptide Production

The polypeptides, derivatives or fragments thereof for use in the methods of the invention can be produced recombinantly and, if needed, chemically modified. Recombinant expression of a polypeptide requires construction of an expression vector containing a polynucleotide that encodes the polypeptide of interest (i.e., an SA2493 polypeptide, derivative or fragment thereof). Once a polynucleotide encoding the polypeptide of interest has been obtained, the vector for the production of the polypeptide of interest may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing a polypeptide of interest by expressing a polynucleotide encoding said polypeptide are described herein.

Methods which are well known to those skilled in the art can be used to construct expression vectors containing the coding sequences of the polypeptide of interest and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. The invention, thus, provides replicable vectors comprising a nucleotide sequence encoding a polypeptide of interest operably linked to a promoter.

The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce the polypeptide of interest. Thus, the invention includes host cells containing a polynucleotide encoding a polypeptide of interest operably linked to a heterologous promoter.

A variety of host-expression vector systems may be utilized to express the polypeptides of interest. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, express the polypeptide of interest in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, members of the Staphylococcus genus, such as S. aureus and S.

epidermidis; members of the Lactobacillus genus, such as L. plantarum; members of the Lactococcus genus, such as L. lactis; members of the Bacillus genus, such as B. subtilis;

members of the Corynebacterium genus such as C. glutamicum; and members of the

Pseudomonas genus such as Ps. fluorescens.) transformed with recombinant bacteriophage

DNA, plasmid DNA or cosmid DNA expression vectors containing coding sequences of interest; yeast (e.g., Saccharomyces genus such as S. cerevisiae or 5^*. pichia, members of the Pichia genus such as P. pastoris, members of the Hansenula genus such as H. polymorpha, members of the Kluyveromyces genus such as K. lactis or K. fragilis , and members of the Schizosaccharomyces genus such as S. pombe) transformed with recombinant yeast expression vectors containing coding sequences of interest; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing coding sequences of interest; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing coding sequences of interest; or mammalian cell systems (e.g., COS, CHO, BHK, 293, NSO, and 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter) and coding sequences of interest.

In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Eukaryotic modifications may include glycosylation and processing (e.g., cleavage) of protein products. Different host cells have characteristic and specific mechanisms for the post- translational processing and modification of proteins and gene products. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. As used herein, the terms "polypeptide" or "an amino acid sequence of a polypeptide" includes polypeptides containing one or more amino acids having a structure of a post- translational modification from a host cell, such as a yeast host.

Once a polypeptide of interest has been produced by recombinant expression, it may be purified by different methods, for example, by chromatography (e.g., ion exchange, affinity, sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, the polypeptides of interest may be fused or attached to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification. Examples of such protein tags include, but are not limited to, chitin binding protein (CBP), maltose binding protein (MBP), glutathione-S-transferase (GST), poly-histidine, hemagglutinin (HA) and polyanionic amino acids.

If desired, expression in a particular host can be enhanced through codon optimization. Codon optimization includes use of more preferred codons. Techniques for codon optimization in different hosts are well known in the art. Determination of Immunoreactive Derivatives and Fragments

The invention also extends to a method of identifying an immunoreactive derivative or fragments (collectively "altered polypeptides") of an SA2493 polypeptide. This method essentially comprises generating a derivative or fragment of the polypeptide, administering the altered polypeptide to a mammal; and detecting an immune response in the mammal. Such response will include production of elements which specifically bind S. aureus and/or said polypeptide, derivative or fragment and/or have a protective effect against S. aureus infection. Antibody titers and immunoreactivity against the native or parent polypeptide may then be determined by, for example, radioimmunoassay, ELISA, western blot or ELISPOT. Adjuvants

Adjuvants are substances that can assist an immunogen (e.g., a polypeptide, pharmaceutical composition containing a polypeptide) in producing an immune response.

Adjuvants can function by different mechanisms such as one or more of the following:

increasing the antigen biologic or immunologic half-life; improving antigen delivery to antigen- presenting cells; improving antigen processing and presentation by antigen-presenting cells; and, inducing production of immunomodulatory cytokines (Vogel, Clinical Infectious Diseases 30(suppl. 3):S266-270, 2000). In one embodiment of the present invention, an adjuvant is used.

A variety of different types of adjuvants can be employed to assist in the production of an immune response. Examples of particular adjuvants include aluminum hydroxide; aluminum phosphate, aluminum hydroxyphosphate, amorphous aluminum hydroxyphosphate sulfate adjuvant (AAHSA) or other salts of aluminum; calcium phosphate; DNA CpG motifs; monophosphoryl lipid A; cholera toxin; E. coli heat-labile toxin; pertussis toxin; muramyl dipeptide; Freund's incomplete adjuvant; MF59; SAF; immunostimulatory complexes; liposomes; biodegradable microspheres; saponins; nonionic block copolymers; muramyl peptide analogues; polyphosphazene; synthetic polynucleotides; IFN-γ; IL-2; IL-12; and ISCOMS. (Vogel, Clinical Infectious Diseases 30(suppl 3):S266-270, 2000; Klein et ah, 2000, Journal of Pharmaceutical Sciences 89:31 1-321; Rimmelzwaan et al, 2001, Vaccine 19: 1 180-1 187; Kersten, 2003, Vaccine 21 :915-920; O'Hagen, 2001, Curr. Drug Target Infect. Disord. 1 :273-286.)

Combination Vaccines

An SA2493 polypeptide, derivative or fragment thereof can be used alone, or in combination with other immunogens, to induce an immune response. Additional immunogens that may be present include one or more additional 5^*. aureus immunogens, one or more immunogens targeting one or more other Staphylococcus organisms such as S. epidermidis, S. haemolyticus, S. warneri, S. pyogenes, or 5^*. lugunensi, and/or one or more immunogens targeting other infectious organisms including, but not limited to, the pathogenic bacteria H. influenzae, M. catarrhalis, N. gonorrhoeae, E. coli, S. pneumoniae, C. difficile, C. perfringens, C. tetani, bacteria of the genuses Klebsiella, Serratia, Enterobacter, Proteus, Pseudomonas,

Legionella, and Citrobacter.

In one embodiment, the additional immunogen is IsdB (also known as ORF0657) or related polypeptides. Reference to an IsdB immunogen refers to an immunogen that produces a protective immune response that recognizes the IsdB protein in 5^*. aureus. In different embodiments, the IsdB immunogen produces an immune response that recognizes IsdB present on one or more of the following strains: COL, Becker, MW2, N315, Newman, USA300,

MSA817, and Mu3. The ability of an IsdB immunogen to provide protective immunity is illustrated in, for example, US Publication No. 2006/0177462 (which is incorporated by reference herein in its entirety).

In additional embodiments, the IsdB immunogen comprises a polypeptide region, said region (a) is at least 90%, at least 94%, at least 95% or at least 99% identical to SEQ ID NO:7 or a fragment thereof (including, but not limited to, amino acids 42-486, 42-522 and 42- 608 of SEQ ID NO:7); (b) differs from SEQ ID NO:7 or a fragment thereof (including, but not limited to, amino acids 42-486, 42-522 and 42-608 of SEQ ID NO:7) by 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 alterations, or up to 50 alterations; or (c) consists essentially or consists of SEQ ID NO:7 or a fragment thereof (including, but not limited to, amino acids 42-486, 42-522 and 42-608 of SEQ ID NO:7). Examples of alterations include amino acid substitutions, deletions, and insertions.

Reference to "consists essentially" of indicated amino acids indicates that the referred to amino acids are present and additional amino acids may be present. The additional amino acids can be at the carboxyl or amino terminus. In different embodiments 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, or 20 additional amino acids are present. In preferred embodiments methionine is present at the amino terminus; or methionine-glycine is present at the amino terminus.

In other embodiments, the one or more additional immunogens include, but are not limited to, ORF0657/ORF0190 hybrid polypeptides (International Publication No. WO 05/009378 and US Publication No. 2006/0188515); ORF0688-related polypeptides; ORF0452- related polypeptides (US Publication 2008/131447); 5". epidermidis ORF 1319E-related polypeptides (WO 08/140632); 5". epidermidis ORF2695E-related polypeptides (WO

08/1 15415); ORF0912-related polypeptides; ORF 1902-related polypeptides; sai-l-related polypeptides (International Publication No. WO 05/79315); ORF0594-related polypeptides (International Publication No. WO 05/086663); ORF0826-related polypeptides (International Publication No. WO 05/1 15113); PBP4-related polypeptides (International Publication No. WO 06/033918); AhpC-related polypeptides and AhpC-AhpF compositions (International Publication No. WO 06/078680); PBP4-related polypeptides (WO06/033918); SACOL1902-related polypeptides (WO 10/062814); SACOL0912-related polypeptides (WO 10/062815); SA0024- related polypeptides (WO 07/001361); SACOL 2451-related polypeptides; SACOL2412 -related polypeptides (PCT/US1 1/43499), SACOL 1789-related polypeptides (PCT/US1 1/43274), SA2074-related polypeptides; S. aureus type 5 and type 8 capsular polysaccharides (Shinefield et ah, 2002, N. Eng. J. Med. 346:491-496); collagen adhesin, fibrinogen binding proteins, and clumping factor (Mamo et ah, 1994, FEMS Immunol. Med. Microbiol. 10:47-54; Nilsson et ah, 1998, J. Clin. Invest. 101 :2640-2649; Josefsson et ah, 2001, J. of Infect. Dis. 184: 1572-1580); and polysaccharide intercellular adhesin and fragments thereof (Joyce et ah, 2003, Carbohydrate Research 338:903-922). Nucleic Acid Vaccine

The nucleic acid sequence of wild type full length SA2493 from S. aureus subsp. aureus COL is SEQ ID NO: 1 (Figure 1C). SEQ ID NO: 1 or other nucleic acids that encode an SA2493 polypeptide of SEQ ID NO:2, derivative or fragment thereof can be introduced into a patient using vectors suitable for therapeutic administration. Suitable vectors can deliver the nucleic acid into a target cell without causing an unacceptable side effect. Examples of vectors that can be employed include plasmid vectors and viral based vectors. (Barouch, 2006, J.

Pathol. 208:283-289; Emini et al, International Publication No. WO 03/031588.)

Cellular expression is achieved using a gene expression cassette encoding the desired polypeptide. The gene expression cassette contains regulatory elements for producing and processing a sufficient amount of nucleic acid inside a target cell to achieve a beneficial effect.

Examples of viral vectors include first and second generation adenovectors, helper dependent adenovectors, adeno-associated viral vectors, retroviral vectors, alphavirus vectors (e.g., Venezuelan Equine Encephalitis virus vectors), and plasmid vectors. (Hitt et al, 1997, Advances in Pharmacology 40: 137-206; Johnston et al., U.S. Patent No. 6, 156,588; Johnston et al., International PCT Publication no. WO 95/32733; Barouch, 2006, J. Pathol. 208:283-289; Emini et al, International PCT Publication no. WO 03/031588.)

Adenovectors can be based on different adenovirus serotypes such as those found in humans or animals. Examples of animal adenoviruses include bovine, porcine, chimpanzee, murine, canine, and avian (CELO). (Emini et al., International PCT Publication no. WO 03/031588; Colloca et al, International PCT Publication no. WO 05/071093.) Human adenovirus include Group B, C, D, or E serotypes such as type 2 ("Ad2"), 4 ("Ad4"), 5 ("Ad5"), 6 ("Ad6"), 24 ("Ad24"), 26 ("Ad26"), 34 ("Ad34") and 35 ("Ad35").

Nucleic acid vaccines can be administered using different techniques and dosing regimes (see, e.g., International Publication No. WO 03/031588 and US Patent No. 7,008,791). For example, the vaccine can be administered intramuscular by injection with or without one or more electric pulses. Electric mediated transfer can assist genetic immunization by stimulating both humoral and cellular immune responses. Examples of dosing regimes include prime-boost and heterologous prime-boost approaches.

SA2493 Antibodies

An SA2493 polypeptide, derivative or fragment thereof can be used to generate antibodies and antibody fragments that bind to SA2493 or to S. aureus. Such antibodies and antibody fragments can be used in polypeptide purification, S. aureus identification, and/ or in therapeutic treatment of S. aureus infection. In preferred embodiments, antibodies and/or antibody fragments thereof are administered to a patient in need thereof to provide passive immunity to S. aureus. As used herein, the term "antibody" as used includes monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g. bispecific antibodies), single-chain Fvs (scFv) (including bi-specific scFvs), single chain antibodies, Fab fragments, F(ab') fragments, disulfide-linked Fvs (sdFv), and epitope-binding fragments of any of the above, so long as they exhibit the desired biological activity. In preferred embodiments, antibodies of the invention are monoclonal. In a more preferred embodiment, the monoclonal antibodies used in the methods of the invention are humanized or human antibodies.

As used herein, the term "monoclonal antibody" refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler and Milstein, Nature 256, 495 (1975), or may be made by recombinant methods, e.g., as described in U.S. Pat. No. 4,816,567. The monoclonal antibodies for use with the present invention may also be isolated from phage antibody libraries using the techniques described in Clackson et al. Nature 352: 624-628 (1991), as well as in Marks et al, J. Mol. Biol 222: 581-597 (1991).

"Humanized" forms of non-human (e.g., murine) antibodies are immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab¾ or other antigen- binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins

(recipient antibody) in which residues from a complementarity-determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity, and capacity. Thus, a humanized antibody is a recombinant protein in which the CDRs from an antibody from one species; e.g., a rodent antibody, is transferred from the heavy and light variable chains of the rodent antibody into human heavy and light variable domains. The constant domains of the antibody molecule are derived from those of a human antibody. In some instances, Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and optimize antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (see, e.g., Yamashita et ah, 2007, Cytotech. 55:55; Kipriyanov and Le Gall, 2004, Mol. Biotechnol. 26:39 and Gonzales et ah, 2005, Tumour Biol. 26:31).

Completely human antibodies may be desirable for therapeutic treatment of human patients. Human antibodies can be made by a variety of methods known in the art including phage display methods described above using antibody libraries derived from human immunoglobulin sequences. See U.S. Pat. Nos. 4,444,887 and 4,716,1 1 1; and PCT publications WO 98/46645; WO 98/50433; WO 98/24893 and WO 98/16654, each of which is incorporated herein by reference in its entirety. Human antibodies can also be produced using transgenic mice which are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes., see, e.g., PCT publications WO 98/24893; European Patent No. 0 598 877; U.S. Pat. Nos. 5,916,771; and 5,939,598, which are incorporated by reference herein in their entireties.

In some embodiments, Fc engineered variants antibodies of the invention are also encompassed by the present invention. Such variants include antibodies or antigen binding fragments thereof which have been engineered so as to introduce mutations or substitutions in the Fc region of the antibody molecule so as to improve or modulate the effector functions of the underlying antibody molecule relative to the unmodified antibody. In general, improved effector functions refer to such activities as CDC, ADCC and antibody half life (see, e.g., US Patent Nos. 7,371,826; 7,217,797; 7,083,784; 7,317,091; and 5,624,821, each of which is incorporated herein in its entirety).

There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM. The

IgG and IgA classes are further divided into subclasses on the basis of relatively minor differences in the constant heavy region sequence and function, e.g., humans express the following subclasses: IgGl, IgG2, IgG3, IgG4, IgAl, and IgA2. In preferred embodiments, the antibodies of the invention are IgGl .

Proper glycosylation can be important for antibody function (Yoo et ah, 2002, J.

Immunol. Methods 261 : 1-20; Li et ah, 2006, Nature Biotechnol. 24:210-215). Naturally occurring antibodies contain at least one N-linked carbohydrate attached to a heavy chain (Yoo et al, supra). Additional N-linked carbohydrates and O-linked carbohydrates may be present and may be important for antibody function Id.

Different types of host cells can be used to provide for efficient post-translational modifications including mammalian host cells and non-mammalian cells. Examples of mammalian host cells include Chinese hamster ovary (Cho), HeLa, C6, PC12, and myeloma cells (Yoo et al, supra; Persic et ah, 1997, Gene 187:9-18). Non-mammalian cells can be modified to replicate human glycosylation (Li et ah, 2006, Nature Biotechnol. 24:210-215). Glycoengineered Pichia pastoris is an example of such a modified non-mammalian cell (Li et ah, supra).

Patient Population

A "patient" refers to a mammal capable of being infected with 5^*. aureus. In one preferred embodiment, the patient is a human. In alternative embodiments, the patient is a non- human mammal such as a dog or a cow. A patient can be treated prophylactically or therapeutically. Prophylactic treatment provides sufficient protective immunity to reduce the likelihood or severity of a 5^*. aureus infection. Therapeutic treatment can be performed to reduce the severity of a S. aureus infection.

Prophylactic treatment can be performed using a pharmaceutical composition containing a polypeptide, immunogen or antibody described herein. Pharmaceutical compositions can be administered to the general population or to those persons at an increased risk of S. aureus infection.

Those "in need of treatment" include those already with an infection, as well as those prone to have an infection or in which a reduction in the likelihood of infection is desired. Persons with an increased risk of S. aureus infection include health care workers; hospital patients; patients with weakened immunity; patients facing therapy leading to a weakened immunity (e.g., undergoing chemotherapy or radiation therapy for cancer or taking

immunosuppressive drugs); patients undergoing surgery; patients receiving foreign body implants (such a catheter or a vascular device); patients under diagnostic procedures involving foreign bodies; patients on renal dialysis and persons in professions having an increased risk of burn or wound injury. As used herein, "weakened immunity" refers to an immune system that is less capable of battling infections because of an immune response that is not properly functioning or is not functioning at the level of a normal healthy adult. Examples of patients with weakened immunity are patients that are infants, young children, elderly, pregnant or a patient with a disease that affects the function of the immune system such as HIV or AIDS.

Foreign bodies used in diagnostic or therapeutic procedures include indwelling catheters or implanted polymer device. Examples of foreign body-associated S. aureus infections include septicemia/endocarditis (e.g., intravascular catheters, vascular prostheses, pacemaker leads, defibrillator systems, prosthetic heart valves, and left ventricular assist devices); peritonitis (e.g., ventriculo-peritoneal cerebrospinal fluid (CSF) shunts and continuous ambulatory peritoneal dialysis catheter systems); ventriculitis (e.g., internal and external CSF shunts); and chronic polymer-associated syndromes (e.g., prosthetic joint/hip loosening, fibrous capsular contracture syndrome after mammary argumentation with silicone prosthesis and late- onset endophtalmisis after implantation of artificial intraocular lenses following cataract surgery). (See, Heilmann and Peters, Biology and Pathogenicity of Staphylococcus epidermidis, In: Gram Positive Pathogens, Eds. Fischetti et ah, American Society for Microbiology,

Washington D.C. 2000.)

Non-human patients that can be infected with S. aureus include cows, pigs, sheep, goats, rabbits, horses, dogs, cats, rats and mice. Treatment of non-human patients is useful in both protecting pets and livestock (e.g. against Staph-related disease common to animals such as bovine mastitis) and evaluating the efficacy of a particular treatment. In addition to the obvious benefits of preventing, or reducing the likelihood or severity of clinical manifestations of S. aureus infections clinical in vaccinated animals, additional benefits include the reduction of costs resulting from sick and underproductive livestock animals to a farmer; the reduction in the need for quarantine measures to a human or veterinary clinic by reducing the number of S. aureus infected patients, and reduced need for repeated rigorous decontamination of equipment and facilities; and a reduction of the number of S. aureus carriers in the human and animal populations, which reduces their potential contamination and spread to others. In an embodiment, a patient is treated prophylactically in conjunction with a therapeutic or medical procedure involving a foreign body. In additional embodiments, the patient is immunized at about 2 weeks, 1 month, about 2 months or about 2-6 months prior to the procedure. In another embodiment, the patient is immunized prophylactically not in conjunction with a particular contemplated procedure. For vaccinations, boosters are delivered as needed. Additionally, patients treated prophylactically may also receive passive immunotherapy by administration of an antibody protective against 5^*. aureus alone or in conjunction with vaccination.

Pharmaceutical Compositions

A further feature of the invention is the use of an SA2493 polypeptide, derivative or fragment thereof described herein ("immunogenic agent"), either alone or in combination with one or more additional antigens, in a composition, preferably an immunogenic composition or vaccine, for treating patients with an S. aureus infection, reducing the progression, onset or severity of pathological symptoms associated with S. aureus infection and/or reducing the likelihood of an 5^*. aureus infection. Suitably, the composition comprises a pharmaceutically acceptable carrier.

In some embodiment of the invention described above, the pharmaceutical compositions are used in human patients. In alternative embodiments, the pharmaceutical compositions are used in non-human patients.

A "pharmaceutically-acceptable carrier" is meant to mean a liquid filler, diluent or encapsulating substance that may be safely used in systemic administration. Depending upon the particular route of administration, a variety of pharmaceutically acceptable carriers, well known in the art may be used. These carriers may be selected from a group including sugars, starches, cellulose and its derivatives, malt, gelatine, talc, calcium sulfate, vegetable oils, synthetic oils, polyols, alginic acid, phosphate buffered solutions including phosphate buffered saline, emulsifiers, isotonic saline, and pyrogen-free water. In particular, pharmaceutically acceptable carriers may contain different components such as a buffer, sterile water for injection, normal saline or phosphate-buffered saline, sucrose, histidine, salts and polysorbate. Terms such as "physiologically acceptable", "diluent" or "excipient" can be used interchangeably.

The above compositions may be used as therapeutic or prophylactic vaccines. Accordingly, the invention extends to the production of vaccines containing as active ingredients one or more of the immunogenic agents of the invention. Any suitable procedure is

contemplated for producing such vaccines. Exemplary procedures include, for example, those described in New Generation Vaccines (1997, Levine et ah, Marcel Dekker, Inc. New York, Basel Hong Kong), which is incorporated herein by reference.

A polypeptide of the invention can be fused or attached to an immunogenic carrier. Useful carriers are well known in the art and include for example: thyroglobulin;

albumins such as human serum albumin; toxins, toxoids or any mutant crossreactive material

(CRM) of the toxin from tetanus, diptheria, pertussis, Pseudomonas, E. coli, Staphylococcus, and Streprococcus; polyamino acids such as poly(lysine:glutamic acid); influenza; Rotavirus VP6, Parvovirus VP1 and VP2; hepatitis B virus core protein; hepatitis B virus recombinant vaccine and the like. Alternatively, a fragment or epitope of a carrier protein or other immunogenic protein may be used. For example, a peptide of the invention can be coupled to a T cell epitope of a bacterial toxin, toxoid or CRM. In this regard, reference may be made to U.S. Patent No. 5,785,973, which is incorporated herein by reference.

Administration/Methods of Treatment

An SA2493 polypeptide, derivative or fragment thereof (alone or in combination with one or more immunogens) or an antibody described herein can be formulated and administered to a patient using the guidance provided herein along with techniques well known in the art. Guidelines for pharmaceutical administration in general are provided in, for example, Vaccines Eds. Plotkin and Orenstein, W.B. Sanders Company, 1999; Remington's

Pharmaceutical Sciences 20^th Edition, Ed. Gennaro, Mack Publishing, 2000; and Modern Pharmaceutics 2^nd Edition, Eds. Banker and Rhodes, Marcel Dekker, Inc., 1990.

Accordingly, the invention provides a method for inducing a protective immune response in a patient against an 5^*. aureus infection comprising the step of administering to the patient an immunologically effective amount of any of the vaccines or pharmaceutical compositions described herein. In one embodiment of this aspect of the invention, the patient is a human. In alternative embodiments, the patient is a non-human mammal.

Also provided by the invention is a method for treating 5^*. aureus infection, or for treating any pathological condition associated with 5^*. aureus infection, the method comprising the step of administering to the patient an immunologically effective amount of any of the vaccines or pharmaceutical compositions described herein. In one embodiment of this aspect of the invention, the patient is a human. In alternative embodiments, the patient is a non-human mammal.

Vaccines and/or antibodies can be administered by different routes such as subcutaneous, intramuscular, intravenous, mucosal, parenteral or transdermal. Subcutaneous and intramuscular administration can be performed using, for example, needles or jet- injectors.

In some embodiments, the vaccines and/or antibodies of the invention can be formulated in or on virus-like particles (see, e.g., International Publication Nos. WO94/20137,; W096/11272; US Patent Nos. 5,985,610; 6,599,508; 6,361,778), liposomes (see, e.g., US Patent No. 5,709,879), bacterial or yeast ghosts (empty cells with intact envelopes; see, e.g.,

International Publication WO 92/01791, US Publication No. 2009/0239264 and 2008/0003239, US Patent No. 6,951,756), and outer membrane vesicles or blebs (de Moraes et ah, 1992, Lancet 340: 1074 and Bjune et ah, 1991, Lancet 338: 1093).

The compositions described herein may be administered in a manner compatible with the dosage formulation, and in such amount as is immunogenically-effective to treat and/or reduce the likelihood of S. aureus infection. The dose administered to a patient, in the context of the present invention, should be sufficient to effect a beneficial response in a patient over time such as a reduction in the level of S. aureus, or to reduce the likelihood of infection by S. aureus. The quantity of the immunogenic agent(s) to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof. In this regard, precise amounts of the immunogenic agent(s) required to be administered will depend on the judgment of the practitioner. In determining the effective amount of the immunogenic agent to be administered in the treatment or prophylaxis against 5^*. aureus, the physician may evaluate circulating plasma levels, progression of disease, and the production of anti- S. aureus antibodies. In any event, suitable dosages of the immunogenic agents of the invention may be readily determined by those of skill in the art. Such dosages may be in the order of nanograms to milligrams of the immunogenic agents of the invention.

Suitable dosing regimens are preferably determined taking into account factors well known in the art including age, weight, sex and medical condition of the patient; the route of administration; the desired effect; and the particular compound employed. The vaccine and/or antibody composition can be used in multi-dose formats. It is expected that a dose for a vaccine composition would consist of the range of 1.0 μg to 1.0 mg total polypeptide. In different embodiments of the present invention, the dosage range is from 5.0 μg to 500 μg, 0.01 mg to 1.0 mg, or 0.1 mg to 1.0 mg. When more than one polypeptide is to be administered (i.e., in combination vaccines), the amount of each polypeptide is within the described ranges.

It is expected that a dose for a passive immunity composition of the invention would consist of the range of 1 μg/kg to 100 mg/kg of antibody. In different embodiments, of the present invention, the dosage range is from 1 μg/kg to 15 mg/kg, 0.05 mg/kg to about 10 mg/kg, 0.5 mg/kg to 2.0 mg/kg, or lOmg/kg to 50mg/kg.

The timing of doses depends upon factors well known in the art. After the initial administration one or more additional doses may be administered to maintain and/or boost antibody titers.

For combination vaccinations, each of the polypeptides can be administered together in one composition or separately in different compositions. An SA2493 polypeptide described herein is administered concurrently with one or more desired immunogens. The term "concurrently" is not limited to the administration of the therapeutic agents at exactly the same time, but rather it is meant that the SA2493 polypeptides described herein and the other desired immunogen(s) are administered to a subject in a sequence and within a time interval such that the they can act together to provide an increased benefit than if they were administered otherwise. For example, each therapeutic agent may be administered at the same time or sequentially in any order at different points in time; however, if not administered at the same time, they should be administered sufficiently close in time so as to provide the desired therapeutic effect. Each therapeutic agent can be administered separately, in any appropriate form and by any suitable route.

All publications mentioned herein are incorporated by reference for the purpose of describing and disclosing methodologies and materials that might be used in connection with the present invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

Having described preferred embodiments of the invention with reference to the accompanying drawings, it is to be understood that the invention is not limited to those precise embodiments, and that various changes and modifications may be effected therein by one skilled in the art without departing from the scope or spirit of the invention as defined in the appended claims.

The following examples illustrate, but do not limit the invention.

EXAMPLE 1

Identification, Cloning and Expression of Antigen

SA2493 was originally identified for use as a potential immunogen in a Staph- based vaccine using a transcriptomics approach. Briefly, S. aureus MCL8538 bacteria was used to produce biofilm in rats. RNA was extracted from harvested biofilms, as well as from bacteria under in vivo planktonic growth conditions and hybridized to a microarray of S. aureus genes. A comparison was performed between the two growth conditions to identify genes upregulated during early biofilm formation. The results were further evaluated to identify antigens with potential as vaccine candidates due to a high likelihood of being surface expressed, using criteria such as the presence of a signal sequence and/or a substrate binding domain. Using this procedure, SA2493 was identified as a potential surface-expressed S. aureus protein.

Once identified from the screen above, SA2493 was cloned as described below. Genomic DNA was purified from S. aureus COL strain MB5393 and used as a template for PCR. The SA2493 gene (SEQ ID NO: 1) was amplified by PCR in a 50 volume reaction prepared in duplicate. Each reaction mixture contained 200 ng genomic DNA, 20 μΜ each forward (CACCATGATTCATTCAAAGAAATTAACGCTCGGTATATGCTTGGT; SEQ ID NO: 5) and reverse (TCAGTGGTGGTGGTGGTGGTGGTGGTGGTTTGACTCATACCTTGT; SEQ ID NO: 6) primer, 45 μΐ_^ AccuPrimPfx™ SuperMix (Invitrogen, Carlsbad, CA). The thermal cycling conditions were as follows: one cycle of 95°C for 5 minutes; 35 cycles of 95°C for 15 seconds, 55° C for 30 seconds, 68°C for one minute; one cycle of 68°C for 10 minutes. The amplified DNA (795 bp) was ligated into a cloning vector pENTR/SD/D and an expression vector pDEST42 via Gateway Cloning System (Invitrogen), respectively.

DNA sequencing of SA2493 was confirmed by Genewiz (South Plainfield, NJ). To test for expression of SA2493, an isolated colony was inoculated into 5 mL of liquid LB containing 100 μg/ml Ampicillin and incubated at 37°C and 250 rpm until the OD₆5₀ was between 0.5 and 1.0. A 1.0 ml culture volume of cells was subjected to centrifugation and resuspended in lysis buffer. The mixtures were held on ice for 5 minutes and subsequently sonicated three times for ten seconds, each with cooling in between. To obtain "soluble" and "insoluble" fractions the mixture was centrifuged at 13,000 rpm for 15 minutes at 4°C. The supernatant was designated "soluble" and the pellet was resuspended in lysis buffer and designated "insoluble."

Expression of SA2493 was analyzed by Coomassie staining of SDS-PAGE gels run under reducing and denaturing conditions. The gels were stained with Bio-Safe Coomassie, a Coomassie G250 stain (BIO-RAD) according to the manufacturer's protocol. Western blot was performed and the signal was detected by anti-His mAb (EMD Sciences). A 32 kDa protein was specifically detected by both Coomassie staining and Western blot in lysates.

Direct scale-up of the above small scale procedure into stirred tank fermenters (50 liter scale) with a 50 liter working volume was achieved. An aliquot of the glycerol stock was plated on LB plates containing ampicillin. Isolated colonies were cultivated in a 250 ml flask containing 50mL of LB medium (plus ampicillin) for 6 hours. One ml of this seed was used to inoculate a 2L flask containing 500mL of LB medium (plus ampicillin) and allowed to grow overnight. This culture was used to inoculate 50L of LB medium (plus ampicillin). The culture was allowed to grow to an OD of 1.0 - 1.5 at 600nm at which time IPTG was added to a final concentration of ImM. The culture was allowed to incubate an additional 3 hours at

37°C. Cells were harvested via centrifugation at 8000G at 4°C for 20 minutes. Supernatants were decanted and the recombinant E. coli wet cell pellets were frozen until purification. Frozen recombinant E. coli cell paste (152 grams) was thawed and resuspended in 1520mL of IMAC Buffer A (50 mM NaCl, 5mM Imidazole, 20 mM Tris, 125 mM Brij-35, 10 mM TritonX-100, 5 mM Tween 20, pH 7.5; BSB-protease inhibitor cocktail). A lysate was prepared with a PANDA cell homogenizer (Niro Soavi). The lysate was clarified by

centrifugation at 10,000 x g for 60 minutes at 4°C using a Beckman JA-21 centrifuge with a JA- 18 rotor. The pellet was resuspended in 1520 ml of Refold Buffer A (20mM Tris-HCl, 8 M urea, pH 7.5). The suspension was subjected to end-over-end mixing overnight at room temperature and clarified at 10,000 x g, 1 hr. Ni Sepharose 6 Fast Flow resin (GE Healthcare) was poured into a Thomson column and the column was equilibrated with Refold Buffer A. Protein was loaded onto the column and the column was washed with IMAC Buffer A + 8M urea. Protein was eluted using a linear imidazole gradient of 0-100% Refold Buffer B (Refold Buffer A + 1 M Imidazole). Protein containing fractions were analyzed by SDS-PAGE followed by Coomassie staining and Western blotting (anti-His antibody). Prominent SA2493 containing fractions were pooled based on protein purity. The pool was dialyzed for 16 hours at room temperature against buffer containing 4M urea. In a dialysis scout, further reduction in the urea concentration led to heavy precipitation, so further dialysis was discontinued. Protein estimation was performed by the Bradford method using BSA as a standard The protein was thawed and adsorbed onto aluminum hydroxyphosphate adjuvant ("Merck Aluminum Adjuvant" or "MAA") at a final concentration of 0.2 mg/mL. This protein was used in immunogenicity and protection studies.

EXAMPLE 2

Immunogenicity Studies

In two independent experiments, MSE100 and MSE120, Balb/c mice (n=20) were vaccinated 3 times intramuscularly on days 0, 7 and 21, with 20 μg of antigen, either the test antigen (His-tagged SACOL 2493), or a negative control antigen (either non-protective S. aureus antigen SA1490 or BSA), formulated on Merck alum adjuvant. Mice were bled after dose 3, at day 21, to obtain sera for evaluating the antibody response to the test antigen. Immune sera from the mice were tested for reactivity to SACOL2493 by end point ELISA and found to contain antibody titers to the antigen (geo mean, from two experiments, n=10 total, 1 :2,787, range = 1 : 12,514 - 1 :621). Negative control antisera did not have antibody titers to SA2493 (data not shown). Results show the antigen was immunogenic in Balb/c mice.

EXAMPLE 3

Murine Lethal Challenge Model

In two independent experiments, Balb/c mice were immunized with either test antigen His-tagged SACOL2493, or a negative control antigen (either SA1490 or BSA) as described above and were challenged with 5^*. aureus Becker (5.25 x 10⁸ CFU/mouse, 100 μΐ challenge dose) injected via the tail vein on day 35 post immunization. Mice were monitored for survival for a period of 10 days post challenge. Results indicate that mice immunized with SACOL2493 had a higher survival rate than mice immunized with control antigens (SA1490, BSA) formulated with the same adjuvant (See Figure 3). At the end of the first experiment (#MSE100), 15 mice survived (75%) in the SACOL2493 polypeptide-immunized group, compared to 6 surviving in the negative control (SA1490) group (30%). Thus, the group of mice immunized with SA2493 had a significantly enhanced survival rate compared to the negative control mice immunized with SA1490 (p=0.0161). In the second experiment (#MSE120), 12 mice survived in the SACOL2493 polypeptide-immunized group (60%), compared to 5 surviving in the BSA control group (25%). Similar to the first experiment, mice immunized with SACOL2493 had a significantly enhanced survival rate compared to the negative control mice immunized with BSA (p=0.0221).

EXAMPLE 4

Rhesus macaque immunogenicity

Rhesus macaques (n=3, Staph#8) were immunized with 100 μg of His-tagged

SACOL2493 formulated on Merck alum adjuvant (MAA) intramuscularly, on day 0, week 4 and week 8. Animals were bled at designated time points and the immune response to the antigen measured using an ELISA type assay, with a Mesoscale instrument (as per the manufacturer's instructions). The titers were measured in RLU (relative luminescence units). The geo mean of the monkeys' titers was increased by 2 weeks post immunization and continued to rise until it reached a maximum at week 8 (see Figure 4A). A third dose of antigen did not lead to an increased titer after week 8. No titers to SACOL2493 were observed in animals (n=3) which were vaccinated with an alternative antigen (negative control titers).

In a second experiment (Staph#9), rhesus macaques (n=3) were vaccinated a single time at time 0, intramuscularly, with 50 μg test antigen His-tagged SACOL2493 formulated on MAA. At eight weeks post vaccination, the animals were challenged via the intravenous route with a sublethal dose of S. aureus Becker (2 x 10^Λ9 CFU). Sera and PBMC were obtained at designated times for testing of the immune response. Measurement of immune titers post challenge indicated that all three of the monkeys had increased Ab titers by week 4 post vaccination (see Figure 4B). After bacterial challenge, two of three animals had an increase in SACOL2493 Ab titers, indicating a memory response to the antigen on the bacteria.

Importantly, all three animals had a Thl7 response after vaccination with test antigen

SACOL2493 (see Figures 4C graph and table). This response was maintained for 16 weeks post vaccination, but did not increase after bacterial challenge. Only one of three animals had a modest Thl response (IFNy ELISpot response) to the antigen after vaccination (see 4C table).

Claims

WHAT IS CLAIMED IS:

1. A composition comprising an immunologically effective amount of a polypeptide that is at least 95% identical to SEQ ID NO:2 or a fragment of the polypeptide and a pharmaceutically acceptable carrier.

2. The composition of claim 1, wherein the polypeptide is not SEQ ID NO:2.

3. The composition of claim 1 wherein the polypeptide is at least 98% identical to SEQ ID NO:2.

4. A composition of any of claims 1-3 further comprising one or more additional S. aureus antigens.

5. The composition of any of claims 1-4 wherein the composition further comprises an adjuvant.

6. The composition of claim 5, wherein the adjuvant is an aluminum salt adjuvant.

7. A method of inducing a protective immune response in a patient against an 5^*. aureus infection comprising the steps of administering to the patient an immunologically effective amount of the composition of any of claims 1-6.

8. The method of claim 7 wherein the patient is human or a non-human mammal.

9. The method of claim 8 wherein the patient has weakened immunity, has received a foreign body implant or is on renal dialysis.

10. The method of claim 9 wherein the patient that weakened immunity has

HIV or AIDS.

11. The method of claim 9 wherein the foreign body implant is a catheter, a vascular device, pacemaker leads, defibrillator systems, or prosthetic heart valve.

12. Use of a polypeptide that is at least 95% identical to SEQ ID NO:2 or a fragment of the polypeptide in the manufacture of a medicament for inducing a protective immune response in a patient against 5^*. aureus infection.

13. The use of claim 12 wherein the polypeptide is SEQ ID NO:2.

14. The use of claim 12, wherein the patient is a human or a non-human mammal.

15. Use of S. aureus polypeptides or a fragment thereof in the manufacture of a medicament for inducing a protective immune response in a patient against 5^*. aureus infection, wherein one of the polypeptides is an SA2493 polypeptide that is at least 95% identical to SEQ ID NO:2.

16. The use of claim 15 wherein the medicament also comprises an additional

S. aureus immunogen.

17. The use of claim 15 or 16 wherein the SA2493 polypeptide is SEQ ID

NO:2.

18. A method of conferring passive immunity to S. aureus infection in a patient comprising administering to the patient one or more antibodies that specifically bind to a polypeptide of SEQ ID NO:2.

19. The method of claim 18 wherein the one or more antibodies are monoclonal antibodies.

20. The method of claim 18 wherein the one or more antibodies are selected from the group consisting of human antibodies and humanized antibodies.