# Patent

## Title
Antibodies to S. aureus surface determinants

## Abstract

Antibodies and antigen binding fragments thereof directed against Staphylococcus aureus (S. aureus) surface determinant antigens and secreted toxins are disclosed. Methods of detecting, diagnosing and treating S. aureus using the antibodies and antigen binding fragments thereof are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a U.S. National Stage application of International Application No. PCT/US2013/068624, filed on Nov. 6, 2013, said International Application No. PCT/US2013/068624 claims benefit under 35 U.S.C. §119(e) of U.S. Provisional Application Nos. 61/723,137, filed Nov. 6, 2012, and 61/782,405, filed Mar. 14, 2013. Each of the above listed applications is incorporated by reference herein in its entirety for all purposes.


REFERENCE TO THE SEQUENCE LISTING
This application incorporates by reference a Sequence Listing submitted with this application as text file entitled ATOX-150US1_SL, created on May 5, 2015, and having a size of 6.16 MB.
The present disclosure relates generally to antibodies that bind to Staphylococcus aureus (S. aureus) surface determinants and antibodies that bind to S. aureus secreted toxins. The present disclosure also relates to combinations of antibodies that bind to S. aureus surface determinants together with antibodies that bind to S. aureus secreted toxins, compositions comprising such combinations of antibodies, and methods of preventing S. aureus-associated diseases comprising administering such combinations of antibodies.
Staphylococcus aureus is a Gram-positive, aerobic, clump-forming cocci bacteria that commonly colonizes the nose and skin of healthy humans. Approximately 20-30% of the population is colonized with S. aureus at any given time. Staphylococcus aureus bacteria, sometimes also referred to as “staph”, “Staph. aureus”, or “S. aureus”, are considered opportunistic pathogens that cause minor infections (e.g., pimples, boils and other soft tissue infections) and systemic infections (e.g., pneumonia, septicemia, osteomyelitis, and endocarditis).
Mucosal and epidermal barriers (skin) normally protect against S. aureus infections. Interruption of these natural barriers as a result of injuries (e.g., burns, trauma, and surgical procedures) dramatically increases the risk of infection. Diseases that compromise the immune system (e.g., diabetes, end-stage renal disease, and cancer) also increase the risk of infection. Opportunistic S. aureus infections can become serious, causing a variety of diseases or conditions, non-limiting examples of which include bacteremia, cellulitis, eyelid infections, food poisoning, joint infections, skin infections, scalded skin syndrome, toxic shock syndrome, pneumonia, osteomyelitis, endocarditis, meningitis and abscess formation.
S. aureus expresses a number of surface determinant antigens, including the serine-aspartic acid repeat proteins SdrC, SdrD, and SdrE, the clumping factor proteins ClfA and ClfB, the iron-regulated surface determinant proteins IsdA, IsdB, IsdC, IsdE and IsdH, S. aureus protein A (SpA) and polysaccharide poly-N-aceytlglucosamine (PNAG). These surface antigens play a role in colonization of host tissue, evasion of the host immune response, and bacterial fitness. Mutations to ClfA, SpA, IsdA, IsdB, and IsdH have been shown to reduce S. aureus virulence.
Proteins such as IsdH play a role in the ability of S. aureus to evade certain host immune responses, such as neutrophil-mediated phagocytosis, a process that is critical for S. aureus to cause infection. IsdH is part of a complex that is activated under iron-restricted conditions, serving to bind hemoglobin and the haptoglobin-hemoglobin complex, and then extracting and transporting heme into the cytoplasm. Three N-terminal NEAr Transporter (NEAT) motifs are present within IsdH, the determined structure of NEAT1 indicating that certain residues within this motif are involved in ligand binding. IsdH-defective mutants of S. aureus have been shown to have reduced virulence compared with wild-type, and are engulfed more rapidly by human neutrophils in the presence of serum opsonins. The protective mechanism of IsdH appears to stem from an accelerated degradation of the serum opsonin C3b. IsdH thus plays a role in the anti-phagocytic properties of the S. aureus organism.
ClfA is a virulence factor that binds fibrinogen. This function of ClfA appears to further contribute to the anti-phagocytic properties of S. aureus. In addition, ClfA also promotes S. aureus agglutination in blood and biofilm formation to biomaterial surfaces.
S. aureus also expresses several additional virulence factors, including capsular polysaccharides and protein toxins. One virulence factor often associated with S. aureus infection is alpha toxin (also known as alpha-hemolysin or Hla), a pore-forming and hemolytic exoprotein produced by most pathogenic strains of S. aureus. The toxin forms heptameric pores in membranes of susceptible cells such as white blood cells, platelets, erythrocytes, peripheral blood monocytes, macrophages, keratinocytes, fibroblasts and endothelial cells. Alpha toxin pore formation often leads to cell dysfunction or lysis. It can also lead to a disruption of epithelial and endothelial tight junctions and immune dysregulation.
Currently, S. aureus is the leading cause of infection-related mortality in the US, and is the leading cause of hospital-acquired infection. Further, growing antibiotic resistance to S. aureus has compounded the problem. Therefore, it would be desirable to develop effective alternative methods of diagnosing and treating S. aureus infections, including combination antibody therapies.
As disclosed previously in U.S. Prov. Appl. No. 61/440,581 and in Intl. Appl. No. PCT/US2012/024201 (published as WO2012/109205), the contents of each which are herein incorporated by reference, antibodies that bind to S. aureus alpha-toxin have been shown to reduce CA-MRSA disease severity in a murine dermonecrosis model and promote bacterial clearance in a mouse model of staphycoccal pneumonia. Thus, such antibodies can be utilized for the treatment of various S. aureus-associated diseases.
In addition to antibodies that bind to S. aureus alpha-toxin, the present disclosure provides for antibodies directed against S. aureus surface determinant antigens, as well as combinations thereof. The present invention provides for compositions comprising such antibodies, or combinations of such antibodies, as well as methods of prevention and/or treatment of S. aureus-associated diseases using such antibodies, or combinations of such antibodies. Methods of prevention and/or treatment of S. aureus-associated diseases using antibodies that bind to S. aureus alpha-toxin are described in U.S. Prov. Appl. No. 61/440,581 and in Intl. Appl. No. PCT/US2012/024201 (published as WO2012/109205), the contents of which are herein incorporated by reference, as well as in the U.S. Provisional Application filed concomitantly with the current application, to Sellman et al., entitled “Methods of Treating S. Aureus Associated Diseases,” the contents of which are herein incorporated by reference.
The present invention also provides for certain combinations of antibodies, such as an antibody that binds to an S. aureus surface determinant in combination with an antibody that binds to S. aureus alpha toxin, where such combinations work synergistically together. The present invention also provides for combining an antibody that targets an S. aureus surface determinant antigen involved in evading opsonophagocytic functions of the host together with an antibody that targets an S. aureus secreted toxin involved in directly damaging host cells.



DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the percentage of opsonophagocytic killing (OPK) induced by anti-IsdH antibodies B11, 2F4, and A7, as compared to percent OPK induced by control antibody R347, when tested with S. aureus strains Newman and USA300.
FIG. 2 shows binding of anti-IsdH antibodies B11, 2F4, A7, and 1C1, as compared to control antibody R347, with S. aureus strains ARC2081 and USA300.
FIG. 3A is a plot of competitive binding between antibody 1C1 and haptoglobin (Hp) for binding to subunit Neat-1 on IsdH, as compared to competitive binding between control antibody R347 and Hp. FIG. 3B is a plot of competitive binding between antibody 2F4 and Hp for binding to subunit Neat-2 on IsdH, as compared to competitive binding between control antibody R347 and Hp.
FIG. 4A shows the concentration of S. aureus colony forming units (CFU) measured in a mouse bacteremia model in the presence of antibody 1C1. CFU concentration is reported as log10[CFU/ml]. FIG. 4B shows the concentration of S. aureus CFU measured in a mouse bacteremia model in the presence of antibody A7. CFU concentration is reported as log10[CFU/ml]. FIG. 4C shows the concentration of S. aureus CFU measured in a mouse bacteremia model in the presence of antibody IsdH0016. CFU concentration is reported as log10[CFU/ml]. FIG. 4D shows the concentration of S. aureus CFU measured in a mouse bacteremia model in the presence of antibody IsdH003. CFU concentration is reported as log [CFU/ml].
FIG. 5A and FIG. 5B show results from two exemplary assessments of antibody efficacy utilizing a mouse bacteremia model. FIG. 5A shows the concentration of S. aureus colony forming units (CFU) measured in a mouse bacteremia model in the presence of antibody 2F4 with the results having a p value of 0.02, whereas FIG. 5B shows the concentration of S. aureus colony forming units (CFU) measured in a mouse bacteremia model in the presence of antibody 2F4 with the results having a p value of 0.005. CFU concentration is reported as log10[CFU/ml].
FIG. 6 illustrates 2F4 binding, measured as a percentage of maximum binding, as compared to control antibody R347, at time T0, T1hr, and T4hr in S. aureus strains ARC2379 (USA100), ARC2081 (USA200) and BAA-1556 (USA 300).
FIG. 7A shows the percentage OPK induced by antibody 2F4, as compared to percent OPK induced by control antibody R347, when tested with S. aureus strain Newman. FIG. 7B shows the percentage OPK induced by antibody 2F4, as compared to percent OPK induced by control antibody R347, when tested with S. aureus strain ARC634. FIG. 7C shows the percentage OPK induced by antibody 2F4, as compared to percent OPK induced by control antibody R347, when tested with S. aureus strain ARC2081 (USA200). FIG. 7D shows the percentage OPK induced by antibody 2F4, as compared to percent OPK induced by control antibody R347, when tested with S. aureus strain BAA-1556 (USA300).
FIG. 8 shows evaluation of 2F4 for affinity to IsdH and to the Neat-2 subunit in a hulgGFc capture assay.
FIG. 9A shows the kidney CFU concentration of S. aureus strain USA300 (administered at an initial concentration of 2.05e8) measured in an organ burden model after treatment with 2F4 alone, 2A3 alone, or a combination of 2F4 and 2A3. CFU concentration is reported as log10[CFU/organ]. FIG. 9B shows the kidney CFU concentration of S. aureus strain USA300 (administered at an initial concentration of 2.05e8) measured in an organ burden model after treatment with 2F4 alone, 2A3 alone, or a combination of 2F4 and 2A3. CFU concentration is reported as log10[CFU/organ].
FIG. 10 shows that anti-ClfA antibodies inhibit ClfA binding to immobilized fibrinogen. Anti-ClfA antibodies 23D6, 27H4, 11H10 shown increased inhibition of binding to fibrinogen as compared to the control R347.
FIG. 11 shows that anti-ClfA antibodies inhibit S. aureus agglutination in human plasma. The ability of anti-ClfA antibodies 23D6, 27H4, 11H10 to inhibit agglutination of three different strains of S. aureus (NR S112, BAA 1556 and UAMS-1) as compared to control R347, no mAb and ClfA protein was tested. The anti-ClfA antibody 11H10 exhibited the largest strain coverage in this assay.
FIG. 12 shows that the anti-ClfA antibody 11H10 binds to a different epitope on ClfA as compared to the anti-ClfA antibodies 23D6 and 27H4.
FIG. 13 demonstrates that the anti-ClfA antibody 11H10 and anti-AT antibody LC10 reduce bacteria load in the heart.
FIG. 14 shows the effect of the anti-ClfA antibody 11H10 in a murine sepsis model.
FIG. 15 shows the effect of the anti-ClfA antibody 11H10, the anti-AT antibody LC10 and the combination of anti-ClfA antibody 11H10 with the anti-AT antibody LC10 in a murine sepsis model (IV lethal challenge) with CA-MRSA USA300 challenge.
FIG. 16 shows the effect of the combination of anti-ClfA antibody 11H10 with the anti-At antibody LC10 in a murine sepsis model (IV lethal challenge) with HA-MRSA USA100 challenge.
FIG. 17 shows the effect of the combination of anti-ClfA antibody 11H10 with the anti-AT antibody LC10 in a murine sepsis model (IV lethal challenge) with HA-MRSA USA200 challenge.
FIG. 18 shows the effect of the combination of anti-C1fA antibody 11H10 with the anti-AT antibody LC10 in a murine sepsis model (IV lethal challenge) with HA-MSSA USA200 challenge.



DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
Reference will now be made in detail to certain exemplary embodiments according to the present disclosure, certain examples of which are illustrated in the accompanying drawings.
Disclosed herein are antibodies, including human, humanized and/or chimeric forms, as well as fragments, derivatives/conjugates and compositions thereof, that bind to S. aureus surface determinant antigens and antibodies that bind to S. aureus secreted toxins. Such antibodies can be useful for detecting and/or visualizing S. aureus and therefore may be useful in diagnostic methods and assays. Antibodies described herein also interfere with S. aureus surface determinants, thereby interfering with colonization and immune evasion, making the antibodies useful for therapeutic and prophylactic methods. Likewise, antibodies described herein can bind S. aureus secreted toxins, thereby reducing the virulence of S. aureus infection. Combining antibodies that target both S. aureus surface determinants and secreted toxins can increase the therapeutic or prophylactic effect achieved by either antibody when administered individually.
S. aureus expresses a number of surface determinant antigens that are important for S. aureus colonization, immune evasion, and fitness. Such surface determinants include SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, SpA, FnbA and PNAG. Antibodies disclosed herein can target the surface determinant antigens.
S. aureus also produces a large number of secreted and cell-associated proteins, many of which are involved in pathogenesis, such as alpha-toxin (AT), beta-toxin, gamma-toxin, delta-toxin, leukocidin, toxic shock syndrome toxin (TSST), enterotoxins, coagulase, protein A, fibrinogen, and the like. Alpha toxin is one of the virulence factors of Staphylococcus aureus and is produced by the majority of pathogenic S. aureus strains.
A. Antibodies Directed Against S. aureus Surface Determinants and Secreted Toxins
As used herein, the terms “antibody,” “antibodies” (also known as immunoglobulins) and “antigen-binding fragments,” encompass monoclonal antibodies (including full-length monoclonal antibodies), polyclonal antibodies, multispecific antibodies formed from at least two different epitope binding fragments (e.g., bispecific antibodies), human antibodies, humanized antibodies, camelid antibodies, chimeric antibodies, single-chain Fvs (scFv), single-chain antibodies, single domain antibodies, domain antibodies, Fab fragments, F(ab′)2 fragments, antibody fragments that exhibit the desired biological activity (e.g., the antigen binding portion), disulfide-linked Fvs (dsFv), and anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies herein provided), intrabodies, and epitope-binding fragments of any of the above. In particular, antibodies include immunoglobulin molecules and immunologically active fragments of immunoglobulin molecules, i.e., molecules that contain at least one antigen-binding site. Immunoglobulin molecules can be of any isotype (e.g., IgG, IgE, IgM, IgD, IgA and IgY), subisotype (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or allotype (e.g., Gm, e.g., G1m(f, z, a or x), G2m(n), G3m(g, b, or c), Am, Em, and Km(1, 2 or 3)). Antibodies may be derived from any mammal, including, but not limited to, humans, monkeys, pigs, horses, rabbits, dogs, cats, mice, and the like, or other animals such as birds (e.g., chickens).
In certain embodiments, an antibody, or immunospecific fragment thereof of the invention includes an antigen binding domain. An antigen binding domain is formed by antibody variable regions that vary from one antibody to another. Naturally occurring antibodies comprise at least two antigen binding domains, i.e., they are at least bivalent. As used herein, the term “antigen binding domain” includes a site that specifically binds an epitope on an antigen (e.g., a cell surface or soluble antigen). The antigen binding domain of an antibody typically includes at least a portion of an immunoglobulin heavy chain variable region and at least a portion of an immunoglobulin light chain variable region. The binding site formed by these variable regions determines the specificity of the antibody.
As used herein, unless otherwise specifically indicated, a “mutation” encompasses an addition, deletion, substitution (including conservative substitution) or other alteration of at least one amino acid or nucleic acid. A “conservative substitution,” unless otherwise specifically indicated, refers to the replacement of a first amino acid by a second amino acid that does not substantially alter the chemical, physical and/or functional properties of the antibody or antigen binding fragment thereof (e.g., the antibody or antigen binding fragment thereof retains the same charge, structure, polarity, hydrophobicity/hydrophilicity, and/or preserves functions such as the ability to bind alpha toxin and thereby reduce S. aureus virulence). A conservative substitution also refers to the replacement of a first nucleic acid by a second nucleic acid encoding for the conservative amino acid substitution described previously.
Antibodies provided herein include full length or intact antibodies, antibody fragments, native sequence antibodies or amino acid variants of native antibodies, human, humanized, post-translationally modified, chimeric or fusion antibodies, immunoconjugates, and functional fragments thereof. The antibodies can be modified in the Fc region, and certain modifications can provide desired effector functions or altered serum half-life.
The numbering of amino acids in the variable domain, complementarity determining region (CDRs) and framework regions (FR), of an antibody follow, unless otherwise indicated, the Kabat definition as set forth in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or CDR of the variable domain. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a “standard” Kabat numbered sequence. Maximal alignment of framework residues frequently requires the insertion of “spacer” residues in the numbering system, to be used for the Fv region. In addition, the identity of certain individual residues at any given Kabat site number may vary from antibody chain to antibody chain due to interspecies or allelic divergence.
In certain embodiments, isolated antibodies are provided. The term “isolated antibody,” as used herein, refers to an antibody which is substantially free of other antibodies and molecules normally present in the native cellular environment. Thus, in some embodiments, antibodies provided are isolated antibodies where they have been separated from antibodies with a different antigen specificity. An isolated antibody may be a monoclonal antibody or a polyclonal antibody. An isolated antibody that specifically binds to an epitope, isoform or variant of S. aureus surface antigen or secreted toxin may, however, have cross-reactivity to other related antigens, e.g., from other species (e.g., Staphylococcus species homologs). An isolated antibody as provided may be substantially free of one or more other cellular materials. In some embodiments, a combination of “isolated” monoclonal antibodies is provided, and pertains to antibodies having different specificities and combined in a defined composition.
Also disclosed are isolated nucleic acid sequences that encode for the amino acid sequences of the disclosed antibodies and antigen binding fragments thereof of antibodies. Due to the degeneracy of the nucleotide code, more than one nucleotide may be present at any nucleic acid position while still encoding for the same amino acid. In some embodiments, nucleic acid sequences are provided that encode for amino acid sequences that are 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% identical (or any percentage in between) to the amino acid sequence of a disclosed antibody or antigen binding fragment thereof that binds an S. aureus surface antigen or secreted toxin. In further embodiments, the nucleic acid sequences encode for amino acid sequences that retain the functional abilities of the disclosed antibodies and antigen binding fragments thereof, e.g. to bind an S. aureus surface antigen or secreted toxin and thereby reduce S. aureus colony growth, evasion of opsonophagocytosis, or toxicity of a secreted toxin.
In various embodiments, the antibodies or fragments disclosed herein can specifically bind to an S. aureus surface antigen or secreted toxin polypeptide or antigenic fragment thereof. In certain embodiments, the surface antigen is SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, SpA, FnbA or PNAG. In further embodiments, the surface antigen is IsdH. In other embodiments, the surface antigen is ClfA. In some embodiments, the secreted toxin is alpha toxin or a phenol-soluble modulin. In further embodiments, the secreted toxin is alpha toxin. Certain amino acid and nucleic acid sequences for alpha toxin antibodies useful in the present disclosure are disclosed in U.S. Prov. Appl. No. 61/440,581 and in Intl. Appl. No. PCT/US2012/024201 (published as WO2012/109205), the contents of each which are hereby incorporated in their entireties.
Antibodies provided herein can specifically bind to one or more epitopes specific to an S. aureus surface determinant antigen or secreted toxin protein, and generally do not specifically bind to other polypeptides. The term “epitope” as used herein refers to a peptide, subunit, fragment, portion, oligomer or any combination thereof capable of being bound by an antibody.
In certain embodiments, an S. aureus surface determinant antigen or secreted toxin antibody or antigen binding fragment thereof may bind an epitope conserved across species. In some embodiments, an antibody or antigen binding fragment thereof binds an S. aureus surface determinant antigen or secreted toxin or a homolog or ortholog from another bacterial species, as well as antigenic fragments thereof. In some embodiments the antibody or antigen binding fragment thereof may bind to one or more isoforms of a surface determinant antigen or secreted toxin.
In various embodiments, an epitope is comprised of at least a portion of an S. aureus surface determinant antigen. These surface determinant antigens can include SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, SpA, FnbA or PNAG. In some embodiments, the antigen is IsdH. In other embodiments, the antigen is ClfA. In other embodiments, an epitope is comprised of at least a portion of an S. aureus secreted toxin. In some embodiments, the secreted toxin is alpha toxin, which is involved in formation of an alpha toxin heptamer complex.
A specified epitope can comprise any amino acid sequence comprising at least 3 contiguous amino acid residues from the amino acid sequence of the target antigen. The epitope may comprise longer amino acid sequences, up to and including the entire amino acid sequence of the target antigen. In some embodiments, the epitope comprises at least 4 amino acid residues, at least 5 amino acid residues, at least 6 amino acid residues, at least 7 amino acid residues, at least 8 amino acid residues, at least 9 amino acid residues, at least 10 amino acid residues, at least 11 amino acid residues, at least 12 amino acid residues, at least 13 amino acid residues, at least 14 amino acid residues, or at least 15 amino acid residues from the amino acid sequence of the target antigen. In certain other embodiments, the epitope comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 contiguous or non-contiguous amino acid residues from the amino acid sequence of the target antigen.
In certain embodiments, a combination is provided, comprising an isolated antibody or antigen binding fragment thereof that specifically binds to an S. aureus secreted toxin and an isolated antibody that specifically binds to an S. aureus surface determinant antigen. In further embodiments, the antibody that binds an S. aureus surface determinant antigen binds an antigen selected from SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, SpA, FnbA or PNAG. In still further embodiments, the surface determinant antigen is IsdH. In certain embodiments, the antibody that binds an S. aureus secreted toxin binds a toxin selected from alpha toxin and a phenol-soluble modulin. In further embodiments, the secreted toxin is alpha toxin.
In certain embodiments, the antibody or combination of antibodies is present in an aqueous solution. In other embodiments, the antibody or combination of antibodies is present in a powdered or lyophilized form. In certain embodiments, the antibody or combination of antibodies is at a concentration sufficient for therapeutic or diagnostic uses. In some embodiments, the antibody or combination of antibodies is present in a sterile vessel or container.
In certain embodiments, an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin is prepared from a parent antibody. As used herein, the term “parent antibody” refers to an antibody that is encoded by an amino acid sequence used for the preparation of a variant or derivative antibody, as defined herein. A parent polypeptide may comprise a native antibody sequence (i.e., a naturally occurring antibody polypeptide, including a naturally occurring allelic variant) or an antibody sequence with pre-existing amino acid sequence modifications (such as insertions, deletions and/or substitutions) of a naturally occurring sequence. A parent antibody may be a humanized antibody or a human antibody. In specific embodiments, the S. aureus surface antigen or secreted toxin antibodies and antigen binding fragments thereof are variants of the parent antibody. As used herein, the term “variant” refers to antibody or antigen binding fragment thereof that differs in its amino acid sequence from a “parent” antibody or antigen binding fragment thereof amino acid sequence by virtue of addition, deletion and/or substitution of one or more amino acid residue(s) from the parent antibody sequence.
The present S. aureus surface antigen or secreted toxin antibodies and antigen binding fragments thereof comprise at least one antigen binding domain. The antigen-binding portion of an antibody comprises one or more fragments of an antibody that retain the ability to specifically bind to an antigen. These retained portions may comprise the heavy and/or light chain variable region from a parent antibody or a variant of a parent antibody.
B. Anti-IsdH Antibodies
As used herein, the terms “percent (%) sequence identity” or “homology” are defined as the percentage of amino acid residues or nucleotides in a candidate sequence that are identical with the amino acid residues or nucleotides in the reference sequences after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and excluding conservative substitutions. Optimal alignment of the sequences for comparison may be produced, besides manually, by means of local homology algorithms known in the art or by means of computer programs which use these algorithms (e.g., GAP, BESTFIT, FASTA, BLAST P, BLAST N and TFASTA).
In some embodiments, an isolated antibody or antigen binding fragment thereof that specifically binds to the surface antigen IsdH comprises a heavy chain variable region (VH) having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88. In certain embodiments, an antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a light chain variable region (VL) having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89. In particular embodiments, an antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a VH having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88 and a VL comprising the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.
In particular embodiments, an antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a VH and a VL, wherein the VH and VL are selected from the group consisting of SEQ ID NOs: 80 and 81; SEQ ID NOs: 82 and 83; SEQ ID NOs: 84 and 85; SEQ ID NOs: 86 and 87; and SEQ ID NOs: 88 and 89. In certain embodiments an antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a VH and a VL, wherein the VH and VL correspond to SEQ ID NOs: 80 and 81. Example 7, Table 12 provides for representative VH and VL sequences as presented herein which can be present in any combination to form an anti-surface antigen antibody or antigen binding fragment thereof.
In further embodiments the antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a VH amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88. In various embodiments the antibody or antigen binding fragment thereof that specifically binds to IsdH comprises a VL amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.
In certain embodiments, the antibody or antigen binding fragment that specifically binds to the surface antigen IsdH has one or more of the following characteristics:
(a) disassociation constant (KD) for an S. aureus surface antigen of about 100 nM or less, about 90 nM or less, about 80 nM or less, about 70 nM or less, about 60 nM or less, about 50 nM or less, about 40 nM or less, about 20 nm or less, about 10 nm or less, about 9, 8, 7, 6, 5, 4, 3, 2, or 1 nm. (or any value in between);
(b) reduces the ability of S. aureus to evade opsonophagocytosis by immune cells by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as measured by an opsonophagocytic killing assay;
(c) reduces the concentration of S. aureus colony forming units (CFUs) by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as measured by a bacteremia model; or
(d) reduces immune cell infiltration, bacterial burden, and pro-inflammatory cytokine release.
The present antibodies and antigen binding fragments thereof that specifically bind S. aureus surface antigens or secreted toxins comprise at least one antigen binding domain that includes at least one complementarity determining region (e.g., at least one of CDR1, CDR2 or CDR3). In some embodiments, an antibody or antigen binding fragment thereof comprises a VH that includes at least one VH CDR (e.g., VH CDR1, VH CDR2 or VH CDR3). In certain embodiments, an antibody or antigen binding fragment thereof comprises a VL that includes at least one VL CDR (e.g., VL CDR1, VL CDR2 or VL CDR3). In some embodiments, an antibody or antigen binding fragment thereof comprises a VH that includes at least one VH CDR and at least one VL CDR.
The CDR regions disclosed herein can be combined in a variety of combinations, as each CDR region can be independently selected and combined with any other CDR region for a given antibody. In certain embodiments VH and/or VL CDR sequences can be present in any combination to form an antibody or antigen binding fragment thereof directed against an S. aureus surface antigen or secreted toxin.
In some embodiments, an isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH and includes (a) a VH CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, SEQ ID NO: 90, 96, 102, 108, or 114; (b) a VH CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 91, 97, 103, 109, or 115; and/or (c) a VH CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 92, 98, 104, 110, or 116.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that that specifically binds to IsdH includes, (a) a VL CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 93, 99, 105, 111, or 117; (b) a VL CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 94, 100, 106, 112, or 118; and/or (c) a VL CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 95, 101, 107, 113, or 119.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to: (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 90, 96, 102, 108, or 114; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 91, 97, 103, 109, or 115; (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 92, 98, 104, 110, or 116; (d) a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 93, 99, 105, 111, or 117; (e) a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 94, 100, 106, 112, or 118; and (f) a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 95, 101, 107, 113, or 119.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 are selected from the group consisting of SEQ ID NOs: 90, 91, 92, 93, 94 and 95; SEQ ID NOs: 96, 97, 98, 99, 100, and 101; SEQ ID NOs: 102, 103, 104, 105, 106, and 107; SEQ ID NOs: 108, 109, 110, 111, 112, and 113; SEQ ID NOs: 114, 115, 116, 117, 118 and 119. In a further embodiment, the isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 corresponds to SEQ ID NOs: 90, 91, 92, 93, 94 and 95.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH corresponds to any one of the isolated antibody or antigen-binding fragments as described above, and has one or more of the following characteristics:
(a) disassociation constant (KD) for an S. aureus surface antigen of about 100 nM or less, about 90 nM or less, about 80 nM or less, about 70 nM or less, about 60 nM or less, about 50 nM or less, or about 40 nM or less, about 20 nm or less, about 10 nm or less, about 9, 8, 7, 6, 5, 4, 3, 2, or 1 nm. (or any value in between);
(b) reduces the ability of S. aureus to evade opsonophagocytosis by immune cells by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as measured by an opsonophagocytic killing assay;
(c) reduces the number of S. aureus colony forming units (CFUs) by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as measured by a bacteremia model; or
(d) reduces immune cell infiltration, bacterial burden, and pro-inflammatory cytokine release.
In further embodiments, the invention provides an isolated antibody or antigen-binding fragment thereof which specifically binds to the same IsdH epitope as any one of the anti-ClfA antibodies or antigen binding fragments described above.
C. Anti-ClfA Antibodies
In some embodiments, an isolated antibody or antigen binding fragment thereof that specifically binds to the surface antigen ClfA comprises a heavy chain variable region (VH) having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to the amino acid sequence of SEQ ID NO: 132 or 140. In certain embodiments, an antibody or antigen binding fragment thereof that specifically binds to ClfA comprises a light chain variable region (VL) having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to amino acid sequence of SEQ ID NO: 136 or 144. In particular embodiments, an antibody or antigen binding fragment thereof that specifically binds to ClfA comprises a VH having 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identity to the amino acid sequence of SEQ ID NO: 132 or 136 and a VL comprising the amino acid sequence of SEQ ID NO: 140 or 144. In particular embodiments, an antibody or antigen binding fragment thereof that specifically binds to ClfA comprises a VH and a VL, wherein the VH and VL are selected from the group consisting of SEQ ID NOs: 132 and 140; and SEQ ID NOs: 136 and 144. Example 7, Table 14 provides for representative VH and VL sequences as presented herein which can be present in any combination to form an anti-surface antigen antibody or antigen binding fragment thereof.
In further embodiments the isolated antibody or antigen binding fragment thereof that specifically binds to ClfA comprises a VH amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 132 or 140. In various embodiments the antibody or antigen binding fragment thereof that specifically binds to ClfA comprises a VL amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 136 or 144.
In some embodiments, an isolated antibody or antigen-binding fragment thereof that specifically binds to ClfA and includes (a) a VH CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, SEQ ID NO: 133 or 141; (b) a VH CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 134 or 142; and/or (c) a VH CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 135 or 143.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that that specifically binds to ClfA includes, (a) a VL CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 137 or 145; (b) a VL CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 138 or 146; and/or (c) a VL CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 139 or 147.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to ClfA comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to: (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 133 or 141; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 134 or 142; (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 135 or 143; (d) a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 137 or 145; (e) a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 138 or 146; and (f) a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 139 or 147.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to IsdH comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 are selected from the group consisting of SEQ ID NOs: 133, 134, 135, 137, 138 and 139; and SEQ ID NOs: 141, 142, 143, 144, 145, 146 and 147.
In further embodiments, the invention provides an isolated antibody or antigen-binding fragment thereof which specifically binds to the same ClfA epitope as any one of the anti-ClfA antibodies or antigen binding fragments described above.
D. Anti-Alpha Toxin (AT) Antibodies
In some embodiments, an antibody or antigen binding fragment thereof directed against a secreted toxin comprises a VH comprising the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In certain embodiments, an anti-secreted toxin antibody or antigen binding fragment thereof comprises a VL comprising the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In yet another embodiment, an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VH comprising the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and a VL comprising the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. See Example 7, Table 7 for a representation of VH and VL sequences as presented herein which can be present in any combination to form an anti-alpha toxin antibody or antigen binding fragment thereof, or present in a combination to form a mAb of the invention. In some embodiments, the VH is SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In various embodiments, the VL is SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.
Certain VH and VL nucleotide sequences encoding the VH and VL amino acid sequences discussed herein are presented in Example 7, Table 8.
In some embodiments, the isolated antibodies or antigen-binding fragments disclosed herein comprise a VH and a VL, where the VH and VL have amino acid sequences represented by SEQ ID NOs: 20 and 19; SEQ ID NOs; 22 and 21; SEQ ID NOs: 24 and 23; SEQ ID NOs: 26 and 25; SEQ ID NOs: 28 and 27; SEQ ID NOs: 41 and 42; SEQ ID NOs: 43 and 44; SEQ ID NOs: 45 and 46; SEQ ID NOs: 47 and 48; SEQ ID NOs: 47 and 48; SEQ ID NOs: 49 and 50; SEQ ID NOs: 51 and 52; SEQ ID NOs: 51 and 52; SEQ ID NOs: 53 and 54; SEQ ID NOs: 55 and 56; SEQ ID NOs: 57 and 58; SEQ ID NOs: 59 and 60; SEQ ID NOs: 61 and 58; SEQ ID NOs: 62 and 58; SEQ ID NOs: 62 and 63; SEQ ID NOs: 79 and 63.
In certain embodiments, antibodies or fragments directed against S. aureus surface antigens or secreted toxins comprise a VH and/or VL that has a given percent identify to at least one of the VH and/or VL sequences disclosed in Table 7.
In some embodiments, an anti-secreted toxin antibody or antigen binding fragment thereof comprises a VH amino acid sequence comprising at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% (or any percentage in between) identity to the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In certain embodiments the antibody or antigen binding fragment thereof comprises a VH amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. As used herein, a “conservative substitution” refers to the replacement of a first amino acid by a second amino acid that does not substantially alter the chemical, physical and/or functional properties of the antibody or antigen binding fragment thereof (e.g., the antibody or antigen binding fragment thereof retains the same charge, structure, polarity, hydrophobicity/hydrophilicity, and/or preserves functions such as the ability to bind alpha toxin and thereby reduce S. aureus virulence). In certain embodiments, the antibody or antigen binding fragment thereof comprises a VH amino acid sequence with a given percent identify to SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and has one or more of the following characteristics:
(a) disassociation constant (KD) for S. aureus alpha toxin of about 13 nM or less;
(b) inhibits the formation of alpha toxin oligomers by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between);
(c) reduces alpha toxin cytolytic activity by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between) (e.g., as determined by cell lysis and hemolysis assays); or
(d) reduces immune cell infiltration, bacterial burden, and pro-inflammatory cytokine release (e.g., in an animal pneumonia model).
In certain embodiments, an anti-secreted toxin antibody or antigen binding fragment thereof comprises a VL amino acid sequence comprising at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% (or any percentage in between) identity to the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In various embodiments the antibody or antigen binding fragment thereof comprises a VL amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In certain embodiments, the antibody or antigen binding fragment thereof comprises a VL amino acid sequence with a given percent identify to SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63 and has one or more of the following characteristics:
(a) disassociation constant (KD) for S. aureus alpha toxin of about 13 nM or less;
(b) inhibits the binding of alpha toxin to the cell surface thereby disrupting formation of alpha toxin oligomers by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between);
(c) reduces alpha toxin cytolytic activity by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between) (e.g., as determined by cell lysis and hemolysis assays); or
(d) reduces immune cell infiltration, bacterial burden, and pro-inflammatory cytokine release (e.g., in an animal pneumonia model).
In some embodiments, the isolated antibody or antigen-binding fragment specifically binds to a Staphylococcus aureus alpha toxin polypeptide and includes (a) a VH CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 8, 11, 14, 17, 70 or 75; and/or (c) a VH CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78.
In particular embodiments, the isolated antibody or antigen-binding fragment that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2 and VH CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 7, 8 and 9; SEQ ID NOs: 10, 11 and 12; SEQ ID NOs: 13, 14 and 15; SEQ ID NOs: 7, 17 and 18; SEQ ID NOs: 7, 8 and 16; SEQ ID NOs: 7, 8 and 65; SEQ ID NOs: 7, 8 and 66; SEQ ID NOs 7, 8, and 67; SEQ ID NOs: 7, 8 and 78; SEQ ID NOs: 69, 70 and 71; SEQ ID NOs: 7, 8 and 72; SEQ ID NOs: 69, 75 and 71; SEQ ID NOs: 69, 75 and 76; or SEQ ID NOs: 69, 70 and 71.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide includes (a) a VL CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 1 or 4; (b) a VL CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 2, 5, 73 or 77; and/or (c) a VL CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 3, 6, 64, 68 or 74.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 1, 2 and 3; SEQ ID NOs: 4, 5 and 6; SEQ ID NOs: 1, 2 and 64; SEQ ID NOs: 1, 2 and 68; SEQ ID NOs: 1, 73 and 74; or SEQ ID NOs: 1, 77 and 74.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to: (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 8, 11, 14, 17, 70 or 75; (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78; (d) a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 1 or 4; (e) a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 2, 5, 73, or 77; or (f) a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 3, 6, 64, 68 or 74.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2, and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 7, 8, 9, 1, 2 and 3; SEQ ID NOs: 10, 11, 12, 1, 2 and 3; SEQ ID NOs: 13, 14, 15, 4, 5 and 6; SEQ ID NOs: 7, 17, 18, 1, 2 and 3; SEQ ID NOs: 7, 8, 16, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 64; SEQ ID NOs; 7, 8, 66, 1, 2 and 64; SEQ ID NOs: 7, 8, 67, 1, 2 and 68; SEQ ID NOs: 7, 8, 67, 1, 2 and 64; SEQ ID NOs: 7, 8, 78, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 68; SEQ ID NOs: 69, 70, 71, 1, 2 and 68; SEQ ID NOs: 7, 8, 72, 1, 73 and 74; SEQ ID NOs: 69, 75, 71, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 77 and 74; or SEQ ID NOs: 69, 70, 71, 1, 77 and 74.
In some embodiments, provided is a composition that comprises an isolated antibody or antigen-binding fragment thereof that (i) includes a VH chain domain comprising three CDRs and a VL chain domain comprising three CDRs; and (ii) specifically binds to a Staphylococcus aureus alpha toxin polypeptide, where the three CDRs of the VH chain domain include (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 8, 11, 14, 17, 70 or 75; and (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78. In particular embodiments, the VH CDR1, VH CDR2 and VH CDR3 correspond to SEQ ID NOs: 7, 8 and 9; SEQ ID NOs: 10, 11 and 12; SEQ ID NOs: 13, 14 and 15; SEQ ID NOs: 7, 17 and 18; SEQ ID NOs: 7, 8 and 16; SEQ ID NOs: 7, 8 and 65; SEQ ID NOs: 7, 8 and 66; SEQ ID NOs 7, 8, and 67; SEQ ID NOs: 7, 8 and 78; SEQ ID NOs: 69, 70 and 71; SEQ ID NOs: 7, 8 and 72; SEQ ID NOs: 69, 75 and 71; SEQ ID NOs: 69, 75 and 76; or SEQ ID NOs: 69, 70 and 71.
In certain embodiments, an antibody or antigen binding fragment thereof specifically binds an S. aureus secreted toxin and comprises (a) a VH CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 8, 11, 14, 17, 70 or 75; and (c) a VH CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78; (d) a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 1 or 4; (e) a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 2, 5, 73, or 77; and (f) a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 3, 6, 64, 68 or 74 and has one or more of the following characteristics:
(a) dissociation constant (KD) for alpha toxin of about 13 nM or less;
(b) binds to alpha toxin monomers;
(c) inhibits the formation of alpha toxin oligomers by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between);
(d) reduces alpha toxin cytolytic activity by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between) (e.g., as determined by cell lysis and hemolysis assays); or
(e) reduces immune cell infiltration, bacterial burden and pro-inflammatory cytokine release (e.g., in animal pneumonia model).
In certain embodiments, an antibody or antibody fragment specifically binds to an S. aureus surface antigen or secreted toxin and comprises a heavy chain variable domain comprising at least 90% identity to the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, 62, 80, 82, 84, 86, or 88 and comprises a light chain variable domain comprising at least 90% identity to the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 63, 81, 83, 85, 87, or 89. In further embodiments, the antibody or antigen binding fragment thereof reduces the ability of S. aureus to evade opsonophagocytosis by at least 50%. In further embodiments, the antibody or antigen binding fragment thereof reduces the concentration of S. aureus CFUs by at least 50%. In other embodiments, the antibody or antigen binding fragment thereof inhibits the binding of one or more alpha toxin monomers to each other (e.g., inhibits oligomerization) and/or reduces S. aureus virulence.
In some embodiments, the isolated antibody or antigen-binding fragment specifically binds to a Staphylococcus aureus alpha toxin polypeptide and includes (a) a VH CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 8, 11, 14, 17, 70 or 75; and/or (c) a VH CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78.
In particular embodiments, the isolated antibody or antigen-binding fragment that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2 and VH CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 7, 8 and 9; SEQ ID NOs: 10, 11 and 12; SEQ ID NOs: 13, 14 and 15; SEQ ID NOs: 7, 17 and 18; SEQ ID NOs: 7, 8 and 16; SEQ ID NOs: 7, 8 and 65; SEQ ID NOs: 7, 8 and 66; SEQ ID NOs 7, 8, and 67; SEQ ID NOs: 7, 8 and 78; SEQ ID NOs: 69, 70 and 71; SEQ ID NOs: 7, 8 and 72; SEQ ID NOs: 69, 75 and 71; SEQ ID NOs: 69, 75 and 76; or SEQ ID NOs: 69, 70 and 71.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide includes (a) a VL CDR1 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 1 or 4; (b) a VL CDR2 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 2, 5, 73 or 77; and/or (c) a VL CDR3 comprising an amino acid sequence identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO: 3, 6, 64, 68 or 74.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 1, 2 and 3; SEQ ID NOs: 4, 5 and 6; SEQ ID NOs: 1, 2 and 64; SEQ ID NOs: 1, 2 and 68; SEQ ID NOs: 1, 73 and 74; or SEQ ID NOs: 1, 77 and 74.
In some embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to: (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 8, 11, 14, 17, 70 or 75; (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78; (d) a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 1 or 4; (e) a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 2, 5, 73, or 77; or (f) a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 3, 6, 64, 68 or 74.
In particular embodiments, the isolated antibody or antigen-binding fragment thereof that specifically binds to a Staphylococcus aureus alpha toxin polypeptide comprises a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2, and VL CDR3 comprising amino acid sequences identical to, or comprising 1, 2, or 3 amino acid residue mutations in each CDR relative to SEQ ID NOs: 7, 8, 9, 1, 2 and 3; SEQ ID NOs: 10, 11, 12, 1, 2 and 3; SEQ ID NOs: 13, 14, 15, 4, 5 and 6; SEQ ID NOs: 7, 17, 18, 1, 2 and 3; SEQ ID NOs: 7, 8, 16, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 64; SEQ ID NOs; 7, 8, 66, 1, 2 and 64; SEQ ID NOs: 7, 8, 67, 1, 2 and 68; SEQ ID NOs: 7, 8, 67, 1, 2 and 64; SEQ ID NOs: 7, 8, 78, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 68; SEQ ID NOs: 69, 70, 71, 1, 2 and 68; SEQ ID NOs: 7, 8, 72, 1, 73 and 74; SEQ ID NOs: 69, 75, 71, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 77 and 74; or SEQ ID NOs: 69, 70, 71, 1, 77 and 74.
In some embodiments, provided is a composition that comprises an isolated antibody or antigen-binding fragment thereof that (i) includes a VH chain domain comprising three CDRs and a VL chain domain comprising three CDRs; and (ii) specifically binds to a Staphylococcus aureus alpha toxin polypeptide, where the three CDRs of the VH chain domain include (a) a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 7, 10, 13 or 69; (b) a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 8, 11, 14, 17, 70 or 75; and (c) a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78. In particular embodiments, the VH CDR1, VH CDR2 and VH CDR3 correspond to SEQ ID NOs: 7, 8 and 9; SEQ ID NOs: 10, 11 and 12; SEQ ID NOs: 13, 14 and 15; SEQ ID NOs: 7, 17 and 18; SEQ ID NOs: 7, 8 and 16; SEQ ID NOs: 7, 8 and 65; SEQ ID NOs: 7, 8 and 66; SEQ ID NOs 7, 8, and 67; SEQ ID NOs: 7, 8 and 78; SEQ ID NOs: 69, 70 and 71; SEQ ID NOs: 7, 8 and 72; SEQ ID NOs: 69, 75 and 71; SEQ ID NOs: 69, 75 and 76; or SEQ ID NOs: 69, 70 and 71.
In certain embodiments, the combination of CDR sequences present to form an anti-secreted toxin antibody include a VH CDR1 comprising SEQ ID NO: 7, 10, 13 or 69, a VH CDR2 comprising SEQ ID NO: 8, 11, 14, 17, 70 or 75 and a VH CDR3 comprising SEQ ID NO: SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78, as depicted in Table 9. In some embodiments, the VL CDR1 comprises SEQ ID NO: 1 or 4, the VL CDR2 comprises SEQ ID NO: 2, 5, 73, or 77 and the VL CDR3 comprises SEQ ID NO: 3, 6, 64, 68 or 74, as depicted in Table 9.
Antibodies and antigen binding fragments thereof, as disclosed herein, can comprise one or more amino acid sequences substantially the same as an amino acid sequences described herein. Amino acid sequences that are substantially the same include sequences comprising conservative amino acid substitutions, as well as amino acid deletions and/or insertions.
E. Framework Regions
Variable domains of the heavy and light chains each comprise at least one framework regions (FR1, FR2, FR3, FR4 or alternatively FW1, FW2, FW3, FW4). The framework regions of the heavy chain are here designated VH FR, while the framework regions of the light chain are here designated VL FR. In certain embodiments the framework regions can contain substitutions, insertions, or other alterations. In certain embodiments, these alterations result in an improvement or optimization in the binding affinity of the antibody. Non-limiting examples of framework region residues that can be modified include those that non-covalently bind antigen directly, interact with/effect the conformation of a CDR, and/or participate in the VL-VH interface.
In certain embodiments a framework region may comprise one or more amino acid changes for the purposes of “germlining.” For example, the amino acid sequences of selected antibody heavy and light chains can be compared to germline heavy and light chain amino acid sequences and where certain framework residues of the selected VL and/or VH chains differ from the germline configuration (e.g., as a result of somatic mutation of the immunoglobulin genes used to prepare the phage library), it may be desirable to “back mutate” the altered framework residues of the selected antibodies to the germline configuration (i.e., change the framework amino acid sequences of the selected antibodies so that they are the same as the germline framework amino acid sequences). Such “back mutation” (or “germlining”) of framework residues can be accomplished by standard molecular biology methods for introducing specific mutations (e.g., site-directed mutagenesis or PCR-mediated mutagenesis). In some embodiments, variable light and/or heavy chain framework residues are back mutated. In certain embodiments, a variable heavy chain of an isolated antibody or antigen-binding fragment disclosed presently is back mutated. In certain embodiments, a variable heavy chain of an isolated antibody or antigen-binding fragment comprises at least one, at least two, at least three, at least four or more back mutations.
In certain embodiments, the VH of an anti-alpha toxin antibody or antigen binding fragment thereof may comprise an FR1, FR2, FR3 and/or FR4 having amino acid sequences that are about 65% to about 100% identical to the corresponding VH framework regions within SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In some embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR regions of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In certain embodiments an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62.
In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof may comprise a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62. In particular FR1, FR2, FR3 or FR4 of the VH may each have an amino acid sequence identical to or comprising 1, 2 or 3 amino acid mutations relative to the corresponding FR1, FR2, FR3 or FR4 of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62.
In certain embodiments, the VL of an anti-alpha toxin antibody or antigen binding fragment thereof herein provided may comprise an FR1, FR2, FR3 and/or FR4 having amino acid sequences that are about 65% to about 100% identical to the corresponding framework regions within the FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In some embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In certain embodiments an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.
In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof comprises a VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63. In particular FR1, FR2, FR3 or FR4 of the VL may each have an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR1, FR2, FR3 or FR4 of VH SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds an S. aureus secreted toxin comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising amino acid sequences identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and/or VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.
In certain embodiments, an isolated antibody or antigen-binding fragment thereof specifically binds an S. aureus secreted toxin and comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and/or VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63, and where the antibody has one or more of the following characteristics:
(a) affinity constant (KD) for alpha toxin of about 13 nM or less;
(b) binds to alpha toxin monomers;
(c) inhibits the formation of alpha toxin oligomers by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between);
(d) reduces alpha toxin cytolytic activity by at least 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between) (e.g., as determined by cell lysis and hemolysis assays); or
(e) reduces immune cell infiltration, bacterial burden and pro-inflammatory cytokine release (e.g., in animal pneumonia model).
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds the S. aureus IsdH surface antigen is provided, comprising VH FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VH framework regions within SEQ ID NOs: 80, 82, 84, 86, or 88. In some embodiments, the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding amino acid sequences of the four FR regions of VH SEQ ID NOs: 80, 82, 84, 86, or 88. In certain embodiments the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VH SEQ ID NOs: 80, 82, 84, 86, or 88.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds IsdH is provided, comprising VL FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VL framework regions within SEQ ID NOs: 81, 83, 85, 87, or 89. In some embodiments, the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 81, 83, 85, 87, or 89. In certain embodiments the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 81, 83, 85, 87, or 89.
In certain embodiments, an isolated antibody or antigen-binding fragment specifically binds IsdH and comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 80, 82, 84, 86, or 88 and/or comprises a VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 81, 83, 85, 87, or 89.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds IsdH is provided, comprising VH FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VH framework regions within SEQ ID NOs: 80, 82, 84, 86, or 88. In some embodiments, the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding amino acid sequences of the four FR regions of VH SEQ ID NOs: 80, 82, 84, 86, or 88. In certain embodiments the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VH SEQ ID NOs: 80, 82, 84, 86, or 88.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds IsdH is provided, comprising VL FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VL framework regions within SEQ ID NOs: 81, 83, 85, 87, or 89. In some embodiments, the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 81, 83, 85, 87, or 89. In certain embodiments the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 81, 83, 85, 87, or 89.
In certain embodiments, an isolated antibody or antigen-binding fragment specifically binds IsdH and comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 80, 82, 84, 86, or 88 and/or comprises a VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 81, 83, 85, 87, or 89.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds the S. aureus ClfA surface antigen is provided, comprising VH FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VH framework regions within SEQ ID NOs: 132 or 140. In some embodiments, the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding amino acid sequences of the four FR regions of VH SEQ ID NOs: 132 or 140. In certain embodiments the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VH SEQ ID NOs: 132 or 140.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds ClfA is provided, comprising VL FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VL framework regions within SEQ ID NOs: 136 or 144. In some embodiments, the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 136 or 144. In certain embodiments the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 136 or 144.
In certain embodiments, an isolated antibody or antigen-binding fragment specifically binds ClfA and comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 132 or 136 and/or comprises a VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 136 or 144.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds ClfA is provided, comprising VH FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VH framework regions within SEQ ID NOs: 132 or 140. In some embodiments, the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding amino acid sequences of the four FR regions of VH SEQ ID NOs: 132 or 140. In certain embodiments the antibody or antigen binding fragment thereof comprises a VH FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VH SEQ ID NOs: 132 or 140.
In certain embodiments, an isolated antibody or antigen-binding fragment that specifically binds IsdH is provided, comprising VL FR1, FR2, FR3 and/or FR4 regions having amino acid sequences that are about 65% to about 100% identical to the corresponding amino acid sequences of the four VL framework regions within SEQ ID NOs: 136 or 144. In some embodiments, the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 136 or 144. In certain embodiments the antibody or antigen binding fragment thereof comprises a VL FR amino acid sequence (FR1, FR2, FR3 and/or FR4) at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical (or any percentage in between) to the corresponding FR regions of VL SEQ ID NOs: 136 or 144.
In certain embodiments, an isolated antibody or antigen-binding fragment specifically binds ClfA and comprises a VH FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VH SEQ ID NO: 132 or 140 and/or comprises a VL FR (FR1, FR2, FR3 and/or FR4) comprising an amino acid sequence identical to, or comprising 1, 2 or 3 amino acid mutations relative to, the corresponding FR of VL SEQ ID NO: 136 or 144.
F. Nucleotide Sequences Encoding Anti-Alpha Toxin Antibodies and Antigen Binding Fragments Thereof
In addition to the amino acid sequences described above, further provided are nucleotide sequences corresponding to the amino acid sequences disclosed herein. In some embodiments, a nucleotide sequence encodes an antibody or antigen binding fragment thereof directed against an S. aureus surface antigen or secreted toxin. The nucleotide sequences are provided in Example 7, Table 8. Thus, also provided are polynucleotide sequences encoding VH and VL regions, including FR regions and CDRs, for the antibodies or fragments described herein, as well as expression vectors for their efficient expression in cells (e.g., mammalian cells).
Also disclosed herein are polynucleotides substantially identical to those coding for the amino acid sequences disclosed herein. Substantially identical sequences may be polymorphic sequences, i.e., alternative sequences or alleles in a population. Substantially identical sequences may also comprise mutagenized sequences, including sequences comprising silent mutations. A mutation may comprise one or more residue changes, a deletion of one or more residues, or an insertion of one or more additional residues. Substantially identical sequences may also comprise various nucleotide sequences that encode for the same amino acid at any given amino acid position in an amino acid sequence disclosed herein, due to the degeneracy of the nucleic acid code.
Also disclosed herein are polynucleotides that hybridize under highly stringent or lower stringency hybridization conditions to polynucleotides that encode an antibody or antigen binding fragment thereof directed against an S. aureus surface antigen or secreted toxin. The term “stringency” as used herein refers to experimental conditions (e.g., temperature and salt concentration) of a hybridization experiment to denote the degree of homology between two nucleic acids; the higher the stringency, the higher percent homology between the two nucleic acids. As used herein, the phrase “hybridizing” or grammatical variations thereof, refers to binding of a first nucleic acid molecule to a second nucleic acid molecule under low, medium or high stringency conditions, or under nucleic acid synthesis conditions. Hybridizing can include instances where a first nucleic acid molecule binds to a second nucleic acid molecule, where the first and second nucleic acid molecules are complementary.
Stringent hybridization conditions include, but are not limited to, hybridization to filter-bound DNA in 6× sodium chloride/sodium citrate (SSC) at about 45 degrees Celsius, followed by one or more washes in 0.2×SSC/0.1% SDS at about 50-65 degrees Celsius. Other stringent conditions include hybridization to filter-bound DNA in 6×SSC at about 45 degrees Celsius followed by one or more washes in 0.1×SSC/0.2% SDS at about 65 degrees Celsius. Other hybridization conditions of known stringency are familiar to one of skill and are included herein.
In certain embodiments, a nucleic acid disclosed herein may encode the amino acid sequence of an antibody or antigen binding fragment thereof directed against an S. aureus surface antigen or secreted toxin, or the nucleic acid may hybridize under stringent conditions to a nucleic acid including a nucleotide sequence that encodes the amino acid sequence of the antibody or antigen binding fragment thereof.
In certain embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence of an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin and which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the VH amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, 62, 80, 82, 84, 86, or 88. In certain embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, 62, 80, 82, 84, 86, or 88. In some embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence of an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin and which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to a VH nucleotide sequence of SEQ ID NO: 30, 32, 34, 36, 38, 120, 122, 124, 126, or 128.
In certain embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence of an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin and which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to the VL amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 63, 81, 83, 85, 87, or 89. In certain embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence having 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mutations (including additions, deletions, and substitutions, such as conservative substitutions) in the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 63, 81, 83, 85, 87, or 89. In some embodiments, the polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence of an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin and which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to a VL nucleotide sequence of SEQ ID NO: 29, 31, 33, 35, 37, 121, 123, 125, 127, or 129.
In particular embodiments, a polynucleotide sequence may comprise a nucleotide sequence encoding an amino acid sequence of an antibody or antigen binding fragment thereof capable of binding an S. aureus surface antigen or secreted toxin and which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to a VH amino acid sequence and at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical (or any percentage in between) to a VL amino acid sequence, where the VH and VL sequences are represented by SEQ ID NOs: 20 and 19; SEQ ID NOs; 22 and 21; SEQ ID NOs: 24 and 23; SEQ ID NOs: 26 and 25; SEQ ID NOs: 28 and 27; SEQ ID NOs: 41 and 42; SEQ ID NOs: 43 and 44; SEQ ID NOs: 45 and 46; SEQ ID NOs: 47 and 48; SEQ ID NOs: 47 and 48; SEQ ID NOs: 49 and 50; SEQ ID NOs: 51 and 52; SEQ ID NOs: 51 and 52; SEQ ID NOs: 53 and 54; SEQ ID NOs: 55 and 56; SEQ ID NOs: 57 and 58; SEQ ID NOs: 59 and 60; SEQ ID NOs: 61 and 58; SEQ ID NOs: 62 and 58; SEQ ID NOs: 62 and 63; SEQ ID NOs: 79 and 63; SEQ ID NOs: 80 and 81; SEQ ID NOs: 82 and 83; SEQ ID NOs: 84 and 85; SEQ ID NOs: 86 and 87; SEQ ID NOs: 88 and 89.
The disclosed polynucleotides may be obtained, and the nucleotide sequence of the polynucleotides determined, by any method known in the art. For example, if the nucleotide sequence of an antibody is known, a polynucleotide encoding the antibody may be assembled from chemically synthesized oligonucleotides. This would involve, for example, the synthesis of overlapping oligonucleotides containing portions of the sequence encoding the antibody, annealing and ligating of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR. The disclosed polynucleotides can also be generated from any suitable source of nucleic acids, such as an antibody cDNA library, or a cDNA library isolated from any tissue or cells expressing the antibody (e.g., from hybridoma cells selected to express an antibody).
G. Functional Characteristics of Antibodies or Fragments Directed Against S. aureus Surface Antigens or Secreted Toxins
In certain embodiments, an antibody or antigen binding fragment thereof directed against an S. aureus surface antigen alters the biological properties of S. aureus cells that express the surface antigen. In various embodiments, the antibody binds an S. aureus surface antigen, thereby enhancing opsonophagocytosis by host cells. In further embodiments, opsonophagocytosis is increased by 50%, 60%, 70%, 80%, 90%, or 95% (or any percentage in between), as measured by an opsonophagocytic killing assay. In some embodiments, binding of the antibody to the surface determinant antigen prevents interaction between the surface antigen and a surface adhesin, thereby reducing the concentration of colony forming units (CFUs) present in a host tissue, as measured in a mouse bacteremia model. In further embodiments, the CFU concentration is reduced by 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as compared to the CFU concentration in the presence of a negative control antibody or in the absence of the antibody or antigen binding fragment thereof. For example, an anti-IsdH antibody may reduce CFU concentration by 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between). In some embodiments, an anti-surface antigen antibody can compete with haptoglobin and/or hemoglobin for binding to S. aureus, thereby inhibiting the ability of S. aureus to access and utilize the iron within hemoglobin. In certain embodiments, antibodies or fragments directed against a surface antigen reduce the ability of S. aureus to bind haptoglobin and/or hemoglobin by 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between), as compared to S. aureus binding in the absence of antibody. For example, an anti-IsdH antibody can reduce the ability of S. aureus to bind haptoglobin and/or hemoglobin by 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% (or any percentage in between).
As used herein, an “opsonophagocytic killing assay” (OPK) refers to any assay used to measure the percentage of phagocytic killing induced in a host tissue in vitro following addition of an antibody to a sample of tissue containing S. aureus of known concentration. This reduction in CFU is normalized against a control level of OPK observed in the presence of a control antibody. The assay measures the ability of a target antibody to induce complement activation and subsequent phagocytosis. For example, the OPK can comprise combining 10 μl of antibody and 10 μl of S. aureus (106 cells/ml), followed by adding 10 μl of human promyelocytic leukemia (HL-60) cells (107 cells/ml) and 10 μl of human sera pre-absorbed against S. aureus. 10 μl of the mixture can then be plated (at time T0), followed by cell lysis using 1% saponin (at time T60) and determination of S. aureus CFU concentration. Percentage killing can be calculated as follows: 100×(1−(T60/T0)), where T60 refers to the CFU concentration at the end of the assay (i.e., at 60 minutes) and T0 refers to the CFU concentration at the beginning of the assay.
As used herein, a “bacteremia model” refers to any in vivo model of S. aureus infection used to evaluate the impact of an antibody on S. aureus bacterial burden, expressed as a percent reduction in CFUs. For example, the bacteremia model can comprise injecting an antibody into a mouse, subsequently injecting 108 CFU of S. aureus intraperitoneally, and later collecting blood and measuring the CFU concentration, as compared to the CFU concentration after injecting a control antibody.
In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof alters the biological properties of alpha toxin and/or alpha toxin expressing cells. In some embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof neutralizes the biological activity of alpha toxin by binding to the polypeptide and inhibiting membrane binding and the assembly of alpha toxin monomers into a transmembrane pore (e.g., alpha toxin heptamer). Neutralization assays can be performed using methods known in the art using, in some circumstances, commercially available reagents. Neutralization of alpha toxin often is measured with an IC50 of 1×10−6 M or less, 1×10−7 M or less, 1×10−8 M or less, 1×10−9 M or less, 1×10−10 M or less and 1×10−11 M or less. The term “inhibitory concentration 50%” (abbreviated as “IC50”) represents the concentration of an inhibitor (e.g., an anti-alpha toxin antibody or antigen binding fragment thereof provided herein) that is required for 50% inhibition of a given activity of the molecule the inhibitor targets (e.g., alpha toxin oligomerization to form a transmembrane pore heptamer complex). A lower IC50 value generally corresponds to a more potent inhibitor.
In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof inhibits one or more biological activities of alpha toxin. The term “inhibition” as used herein, refers to any statistically significant decrease in biological activity, including full blocking of the activity. For example, “inhibition” can refer to a decrease of about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% in biological activity, or any percentage in between. In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof inhibits one or more biological activities of alpha toxin by at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%, or any percentage in between.
In some embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof may deplete alpha toxin secreted by pathogenic S. aureus. In some embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof may achieve at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or about 100% depletion of alpha toxin secreted by S. aureus, or any percentage in between. In particular embodiments, virtually all detectable secreted alpha toxin is depleted from cells infected with S. aureus. 
In certain embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof may inhibit the expression of one or more inducible genes that respond directly or indirectly to the environment created by an S. aureus infection and/or alpha toxin expression and function. In specific embodiments, an anti-alpha toxin antibody or antigen binding fragment thereof inhibits the expression of one or more inducible genes that responds directly or indirectly to the environment created by S. aureus alpha toxin expression and function by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, or by at least 90%, or any percentage in between.
H. Methods of Making Antibodies Against S. aureus Surface Antigens and Secreted Toxins
The following describes exemplary techniques for the production of the antibodies disclosed herein. In some embodiments, recombinant or hybridoma methods can be used to generate antibodies or fragments disclosed herein. In other embodiments, antibodies or antibody fragments can be isolated from antibody phage libraries generated using techniques known in the art. Other techniques for preparing antibodies, known in the art, can also be used to prepare antibodies against S. aureus surface antigens and secreted toxins.
In some embodiments, anti-IsdH antibodies can be generated using native S. aureus IsdH, mutant IsdH, a variant, or an antigenic fragment of IsdH. S. aureus cells expressing IsdH can also be used to generate antibodies. IsdH, for use in producing anti-IsdH antibodies, can also be produced recombinantly in an isolated form from bacterial or eukaryotic cells using standard recombinant DNA methodology.
Polyclonal antibodies to a secreted toxin or surface antigen, such as IsdH, can be produced by various procedures known in the art. For example, an IsdH polypeptide or immunogenic fragment thereof can be administered to various host animals via subcutaneous or intraperitoneal injections of the relevant antigen to induce the production of sera containing polyclonal antibodies specific for the antigen. Host animals include, but are not limited to, rabbits, mice, and rats. In some embodiments, various adjuvants can be used to increase the immunological response, depending on the host species, and include but are not limited to, Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. Other adjuvants known in the art may also be used.
Monoclonal antibodies to a secreted toxin or surface antigen, such as IsdH, can be prepared using a wide variety of techniques known in the art, including the use of hybridoma, recombinant, and phage display technologies, or a combination thereof. The term “monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous or isolated antibodies, e.g., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. The modifier “monoclonal” is not to be construed as requiring production of the antibody by any particular method. Monoclonal antibodies include monoclonal mammalian, chimeric, humanized, human, domain, diabodies, vaccibodies, linear and multispecific antibodies.
Once an antibody disclosed herein has been produced, it may be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, and sizing column chromatography), centrifugation, differential solubility, or by any other technique for the purification of proteins. Further, the antibodies of the present technology or fragments thereof may be fused to heterologous polypeptide sequences (including epitope “tags” and other fusion proteins such as GST fusions) to facilitate antibody purification and use in subsequent assays.
In certain embodiments, the antibodies disclosed herein are chimeric antibodies. Chimeric antibodies are antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while another portion of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity. Chimeric antibodies disclosed herein include “primatized” antibodies comprising variable domain antigen-binding sequences derived from a nonhuman primate (e.g., Old World Monkey, such as baboon, rhesus or cynomolgus monkey) and human constant region sequences. Chimeric antibodies disclosed herein also include humanized antibodies, which are generated using methods known in the art.
In other embodiments, the antibodies disclosed herein are human antibodies and are generated using methods known in the art. For example, fully human antibodies can be generated through the introduction of nucleic acids encoding functional human antibody loci into a rodent or other animal so that the rodent or other animal produces fully human antibodies. In another example, human antibodies can be derived by in vitro methods. Suitable examples include but are not limited to phage display, ribosome display, yeast display, and other methods known in the art. Additional examples of methods for making human antibodies or fragments directed against S. aureus surface antigens or secreted toxins include the VelocImmune® mouse technology (Regeneron Pharmaceuticals). See, e.g., U.S. Pat. No. 6,596,541 (incorporated by reference in its entirety).
In certain embodiments, it may be desirable to revert a framework sequence of an antibody disclosed herein to the germline sequence, revert a CDR to germline, and/or remove a structural liability. Thus, in some embodiments, where a particular antibody disclosed herein differs from its respective germline sequence at the amino acid level, the antibody sequence can be mutated back to the germline sequence. Such corrective mutations can occur at one, two, three or more positions, or a combination of any of the mutated positions, using standard molecular biological techniques.
In certain embodiments, the present disclosure encompasses antibody fragments or antibodies comprising these fragments. The antibody fragment comprises a portion of the full length antibody, which generally is the antigen binding or variable region thereof. Examples of such antibody fragments include Fab, Fab′, F(ab′)2, Fd and Fv fragments; diabodies; linear antibodies, single-chain antibody molecules; and multispecific antibodies are antibodies formed from these antibody fragments.
In addition to the above described human, humanized and/or chimeric antibodies, the antibodies disclosed herein can also be further modified to comprise one or more of the following: at least one amino acid residue and/or polypeptide substitution, addition and/or deletion in the VL domain and/or VH domain and/or Fc region, and post translational modifications. Any combination of deletion, insertion, and substitution can be made to arrive at a final construct, provided that the final construct possesses desired characteristics.
Included in these modifications are antibody conjugates where an antibody has been covalently attached to a moiety. Moieties suitable for attachment to the antibodies include but are not limited to, proteins, peptides, drugs, labels, and cytotoxins. These changes to the antibodies may be made to alter or optimize antibody characteristics (e.g., biochemical, binding and/or functional) as is appropriate for detection, diagnosis, and/or treatment of S. aureus infection and related diseases or disorders. Methods for forming conjugates, making amino acid and/or polypeptide changes, and post-translational modifications are known in the art. Also included in these modifications are fusion proteins, i.e., the antibody, or a fragment thereof, fused to a heterologous protein, polypeptide, or peptide.
In certain embodiments, antibodies or fragments directed against S. aureus surface antigens or secreted toxins are produced to comprise an altered Fc region (also referred to herein as “variant Fc region”) in which one or more alterations have been made in the Fc region in order to change functional and/or pharmacokinetic properties of the antibodies. Such alterations may result in altered effector function, reduced immunogenicity, and/or an increased serum half life. In certain embodiments, effector function of an antibody can be modified through changes in the Fc region, including but not limited to, amino acid substitutions, amino acid additions, amino acid deletions and changes in post translational modifications to Fc amino acids (e.g., glycosylation).
In some embodiments an Fc variant antibody is prepared that has altered binding properties for an Fc ligand (e.g., an Fc receptor such as C1q) relative to a native Fc antibody. Examples of binding properties include but are not limited to, binding specificity, equilibrium dissociation constant (Ka), dissociation and association rates (koff and kon respectively), binding affinity and/or avidity.
In certain embodiments, the antibodies disclosed herein are glycosylated in order to alter effector function of antibodies or to alter the affinity of the antibody for a target antigen. In some embodiments, the glycosylation pattern in the variable region of the present antibodies is modified. For example, an aglycosylated antibody can be made (i.e., the antibody lacks glycosylation). Glycosylation can be altered to, for example, increase the affinity of the antibody for a target antigen. Such carbohydrate modifications can be accomplished by, for example, altering one or more sites of glycosylation within the antibody sequence. For example, one or more amino acid mutations can be made that result in elimination of one or more variable region framework glycosylation sites to thereby eliminate glycosylation at that site.
In certain embodiments, the antibodies disclosed herein are conjugated or covalently attached to another substance using methods known in the art. In some embodiments, the attached substance is a detectable label (also referred to herein as a reporter molecule) or a solid support. Suitable substances for attachment to antibodies include, but are not limited to, an amino acid, a peptide, a protein, a polysaccharide, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten, a drug, a hormone, a lipid, a lipid assembly, a synthetic polymer, a polymeric microparticle, a biological cell, a virus, a fluorophore, a chromophore, a dye, a toxin, a hapten, an enzyme, an antibody, an antibody fragment, a radioisotope, solid matrixes, semi-solid matrixes and combinations thereof. Methods for conjugation or covalently attaching another substance to an antibody are known in the art.
I. Methods of Treatment Using S. aureus Surface Antigen or Secreted Toxin Antibodies or Fragments
The antibodies or fragments disclosed herein can be administered individually, in combination with each other, or in combination with additional pharmaceutical agents such as antibiotics, for the prevention of S. aureus infections and related symptoms and conditions (e.g., to treat the hyperinflammation induced by alpha toxin). The antibodies and combinations of antibodies or fragments can be used to treat or prevent a wide range of conditions/diseases, including both chronic and acute conditions, such as, but not limited to, bacteremia, burns, cellulitis, dermonecrosis, eyelid infections, food poisoning, joint infections, neonatal conjunctivitis, osteomyelitis, pneumonia, skin infections, surgical wound infection, scalded skin syndrome, endocarditis, meningitis, abscess formation and toxic shock syndrome. Further detail regarding potential diseases/conditions suitable for S. aureus therapy are provided below.
In certain embodiments, at least one antibody disclosed herein can be administered in combination with at least one additional therapeutic agent (e.g., an antibiotic). Examples of antibiotics that can be administered in the combination include: penicillin, oxacillin, flucloxacillin, vancomycin and gentamicin. In certain embodiments, combination therapy using an antibiotic and at least one antibody or antigen binding fragment thereof disclosed herein enhances treatment efficacy by, for example, reducing S. aureus CFU concentration in a host tissue, reducing the ability of S. aureus to evade opsonophagocytosis, and/or reducing S. aureus virulence, as compared to antibody therapy alone.
Combinations therapy (e.g., treatment or prevention with more than one antibody) can provide benefit over individual therapy by providing multiple non-overlapping S. aureus therapeutic targets. For example, an antibody targeting a secreted toxin can neutralize the harmful effects of the toxin, such as the hyperinflammation induced by alpha toxin. At the same time, a co-administered antibody targeting a surface antigen (e.g., IsdH) can inhibit S. aureus colony growth and opsonophagocytic evasion, which are not altered by the antibody targeting the secreted toxin. Combination therapy can also ensure that therapy will be effective against a broader range of S. aureus strains or mutants, some of which may lack an antigenic target for a particular antibody.
In particular combination therapy can comprise one or more antibodies or antigen binding fragments thereof that specifically bind to a surface determinant, such as SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, or PNAG and one or more antibodies or antigen binding fragments thereof that bind to a secreted toxin, such as alpha toxin (AT). In particular embodiments, combination therapy can comprise an antibody or antigen binding fragment thereof that specifically binds to IsdH and an antibody or antigen binding fragment thereof that specifically binds to AT; an antibody or antigen binding fragment thereof that specifically binds to ClfA and an antibody or antigen binding fragment thereof that specifically binds to AT; an antibody or antigen binding fragment thereof that specifically binds to IsdH and an antibody or antigen binding fragment thereof that specifically binds to AT; an antibody or antigen binding fragment thereof that specifically binds to ClfA and an antibody or antigen binding fragment thereof that specifically binds to IsdH; or an antibody or antigen binding fragment thereof that specifically binds to IsdH, an antibody or antigen binding fragment thereof that specifically binds to ClfA and an antibody or antigen binding fragment thereof that specifically binds to AT. In particular embodiments, the combination therapy can comprise an antibody or antigen binding fragment thereof that specifically binds to IsdH and an antibody or antigen binding fragment thereof that specifically binds to AT, where the anti-IsdH antibody or fragment thereof comprises the VH and/or VL, or a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VLCDR3 of mAb 2F4, and where the anti-AT antibody or fragment thereof comprises the VH and/or VL, or a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VLCDR3 of mAb LC10 or comprises SEQ ID NO: 130 and SEQ ID NO: 131.
In particular embodiments, the anti-AT antibodies or antigen binding fragments thereof can comprise a VH and/or VL, or a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VLCDR3 of any of the antibodies listed in Table 7 or 10, the anti-IsdH or antigen binding fragments thereof can comprise a VH and/or VL, or a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VLCDR3 of any of the antibodies listed in Table 12 and the anti-ClfA antibodies or antigen binding fragments thereof can comprise a VH and/or VL, or a VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VLCDR3 of any of the antibodies listed in Table 14.
In various embodiments, the disclosed antibodies, combinations of antibodies, and/or combinations of antibodies and antibiotics can be administered therapeutically to treat an S. aureus infection or as prophylaxis to prevent infection. For example, combination therapy can be administered prior to surgery to prevent S. aureus complication, or after surgery to treat an S. aureus infection acquired during surgery.
Pharmaceutical compositions for use in treating S. aureus infections or as prophylaxis are also provided herein. In several embodiments, a pharmaceutical composition comprises at least one antibody disclosed herein and a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” means one or more non-toxic materials that do not interfere with the effectiveness or biological activity of the active ingredients. Such preparations may contain salts, buffering agents, preservatives, compatible carriers, and optionally other therapeutic agents. Such pharmaceutically acceptable preparations may also contain compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human. The term “carrier” denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate pharmaceutical administration.
Therapeutic compositions of the present technology may be formulated for a particular dosage. Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic response). For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. In some embodiments, the selected dosage is suitable for intravenous, intramuscular, intranasal, oral, topical or subcutaneous delivery. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the subject being treated, and the particular mode of administration.
Also disclosed herein is a pharmaceutical kit for therapeutic use in treating an S. aureus infection or as prophylaxis against such an infection. In some embodiments, the kit comprises one or more containers filled with a sterile therapeutic liquid formulation or lyophilized formulation comprising at least one antibody or antigen binding fragment thereof disclosed herein and a pharmaceutically-acceptable carrier. In some embodiments, the container filled with the liquid formulation is a pre-filled syringe. In other embodiments, the container filled with sterile lyophilized powder formulation is suitable for reconstitution and subsequent administration. In certain embodiments, the formulations comprise antibodies and antigen binding fragments thereof recombinantly fused or chemically conjugated to at least one other moiety, including but not limited to, a heterologous protein, a heterologous polypeptide, a heterologous peptide, a large molecule, a small molecule, a marker sequence, a diagnostic or detectable agent, a therapeutic moiety, a drug moiety, a radioactive metal ion, a second antibody, and a solid support. In certain embodiments, the formulations are formulated in single dose vials as sterile liquids. In some embodiments, the formulation is supplied in a pre-filled syringe.
J. Diseases Associated with S. aureus Infection
Antibodies and antigen binding fragments thereof, as disclosed herein, can be used for detecting, diagnosing, preventing and/or treating a disease associated with an S. aureus infection. The antibodies can also be used to alleviate and/or prevent one or more symptoms of a disease associated with an S. aureus infection.
Provided also herein is a method for preventing, treating or managing pneumonia in a subject, including: administering a composition that includes an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, to a subject in need thereof in an amount effective for preventing, treating or managing the pneumonia.
As used herein, the terms “treat,” “treating” or “treatment” refer to therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) an undesired physiological change or disorder, such as the progression of the disease. Beneficial or desired clinical results include, but are not limited to, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state. “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. Those in need of treatment include those already with the condition or disorder as well as those prone to have the condition or disorder or those in which the condition or disorder is to be prevented.
Provided in some embodiments is a method for preventing, treating or managing a skin infection condition in a subject that includes: administering a composition that includes an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof according to the present invention to a subject in need thereof in an amount effective for preventing, treating or managing the skin infection condition. In certain embodiments, the skin infection condition is dermonecrosis. In some embodiments, the skin infection condition includes a S. aureus infection of the skin. In certain embodiments, the method prevents the skin infection condition.
In some embodiments, provided is a method for preventing, treating or managing a S. aureus infection associated with dialysis treatment, high-risk surgery, pneumonia, ventilator-associated pneumonia (VAP), or reinfection after prior release from a hospital for previous treatment or surgery that includes administering a composition that includes an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, to a subject in need thereof.
Also provided in some embodiments is a method for preventing, treating or managing a condition associated with S. aureus infection that includes administering a composition that includes an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant to a subject in need thereof, in an amount effective to reduce cell lysis. In certain embodiments, the method prevents a condition associated with S. aureus infection. In some embodiments, the cell is an erythrocyte from the blood or the lung.
Provided herein are methods for preventing or reducing the severity of S. aureus-associated sepsis in a mammalian subject comprising administering to the subject an effective amount of an isolated an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof. Also provided are methods of reducing S. aureus bacterial load in the bloodstream or heart of a mammalian subject comprising administering to the subject an effective amount of an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof. Methods of reducing S. aureus bacterial agglutination and/or thromboembolic lesion formation in a mammalian subject comprising administering to the subject an effective amount of an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, are also provided.
Methods of preventing S. aureus-associated sepsis in a mammalian subject suitably comprise administering an effective amount of an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, to the subject prior to an infection event. As used herein, “infection event” refers to an event during which the subject is, or could be, exposed to S. aureus infection. Exemplary infection events include, but are not limited to, surgery on any part of the body, including head, mouth, hands, arms, legs, trunk, internal organs (e.g., heart, brain, bowels, kidneys, stomach, lungs, liver, spleen, pancreas, etc.), bones, skin. Surgery provides conditions, such as open surgical wounds and organs, which can readily be infected with S. aureus. Additional infection events include trauma to any part of the body that provides open wounds or otherwise access to the bloodstream via which S. aureus infection could enter the body. Additional infection events include blood transfusions, injections of medications or illegal or legal drugs, needle pricks, tattoo needles, insertion and maintenance of intravenous (IV) lines, insertion and maintenance of surgical drains, and sites of skin breakdown e.g., bedsores (decubitus ulcers).
In embodiments where the methods provide prevention of S. aureus-associated sepsis, the isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, is suitably administered at least 1 hour prior to an infection event. For example, at least 1 hour prior to surgery (the infection event). Suitably, the isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, is administered at least 6 hours, at least 12 hours, at least 18 hours, at least 24 hours, at least 30 hours, at least 36 hours, at least 42 hours, at least 48 hours, or longer, prior to the infection event. In embodiments, the isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, is suitably administered about 6 hours to about 36 hours, about 6 hours to about 36 hours, about 12 hours to about 36 hours, about 12 hours to about 24 hours, about 24 hours to about 36 hours, about 20 hours to about 30 hours, about 20 hours to about 28 hours, about 22 hours to about 26 hours, or about 12 hours, about 13 hours, about 14 hours, about 15 hours, about 16 hours, about 17 hours, about 18 hours, about 19 hours, about 20 hours, about 21 hours, about 22 hours, about 23 hours, about 24 hours, about 25 hours, about 26 hours, about 27 hours, about 28 hours, about 29 hours, or about 30 hours, or about 31 hours, or about 32 hours, or about 33 hours, or about 34 hours, or about 35 hours, or about 36 hours, prior to the infection event.
As used herein “prevention” of S. aureus-associated sepsis refers to reducing the risk of a subject acquiring S. aureus-associated sepsis at the time of the infection event. Suitably, the risk of a subject acquiring S. aureus-associated sepsis is reduced by at least 30% as compared to a subject that has not been administered an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, prior to the infection event. More suitably the risk is reduced by at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or the risk is completely eliminated as compared to a subject that has not been administered an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, prior to the infection event.
In methods for reducing the severity of S. aureus-associated sepsis in a mammalian subject, such methods suitably comprise administering an effective amount of an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof, thereof to a subject that is exhibiting symptoms of S. aureus-associated sepsis. Such symptoms can include, for example, chills, confusion or delirium, fever or low body temperature (hypothermia), light-headedness due to low blood pressure, rapid heartbeat, shaking, skin rash and warm skin.
As used herein “reducing the severity” as it is used with reference to sepsis refers to reducing the symptoms that a subject that has acquired S. aureus-associated sepsis is exhibiting. Suitably, the symptoms are reduced by at least 30% as compared to the symptoms that a subject that also has acquired S. aureus-associated sepsis is exhibiting, but the subject has not been administered an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof. More suitably the symptoms are is reduced by at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or the symptoms are completely eliminated (i.e., the subject is cured of the infection and the sepsis) as compared to a subject that has not been administered an isolated antibody or antigen-binding fragment thereof that immunospecifically binds to a S. aureus toxin or surface determinant, or a combination thereof prior to the infection event.
Non-limiting examples of some common conditions caused by S. aureus infection include burns, cellulitis, dermonecrosis, eyelid infections, food poisoning, joint infections, pneumonia, skin infections, surgical wound infection, scalded skin syndrome and toxic shock syndrome. In addition, it is a frequent pathogen in foreign body infections, such as intravascular lines, pacemakers, artificial heart valves and joint implants. Some of the conditions or diseases caused by S. aureus are described further below. Some or all of the conditions and diseases described below may involve the direct action of secreted toxins as a component of infection or mediator of the condition or disease state, while some or all of the conditions may involve the indirect or secondary action of secreted toxins (e.g., as primary virulence factors that cause the main symptom or majority of symptoms associated with the condition, or as agents that act to further advance the disease through disruption of cellular function or cell lysis).
a) Burns
Burn wounds are often sterile initially. However, moderate and severe burns generally compromise physical and immune barriers to infection (e.g., blistering, cracking or peeling of the skin), causing a loss of fluid and electrolytes and result in local or general physiological dysfunction. Contact of the compromised skin with viable bacteria can result in mixed colonization at the injury site. Infection may be restricted to the non-viable debris on the burn surface (“eschar”), or the colonization may progress into full skin infection and invade viable tissue below the eschar. More severe infections may reach below the skin, enter into the lymphatic system and/or blood circulation, and develop into septicemia. S. aureus typically is found among the pathogens that colonize burn wound infections. S. aureus can destroy granulation tissue and produce severe septicemia.
b) Cellulitis
Cellulitis is an acute infection of the skin that often begins as a superficial infection that can spread below the cutaneous layer. Cellulitis is most commonly caused by a mixed infection of S. aureus in conjunction with S. pyogenes. Cellulitis can lead to systemic infection.
c) Dermonecrosis
Dermonecrosis is an infection of the skin and subcutaneous tissues, easily spreading across the fascial plane within the subcutaneous tissue. The condition causes the upper and/or lower layers of skin to become necrotic, and can spread to underlying and surrounding tissues.
d) Necrotizing Fasciitis
Necrotizing fasciitis is referred to as “flesh-eating disease” or “flesh eating bacteria syndrome.” Necrotizing fasciitis can be caused by a polymicrobial infection (e.g., type I, caused by a mixed bacterial infection), or by a monomicrobial infection (e.g., type II, caused by a single pathogenic strain of bacteria). Many types of bacteria can cause necrotizing fasciitis, non-limiting examples of which include; Group A streptococcus (e.g., Streptococcus pyrogenes), Staphylococcus aureus, Vibrio vulnificus, Clostridium perfringens, and Bacteroides fragilis. Individuals with depressed or compromised immune systems are more likely to suffer from dermonecrosis (e.g., necrotizing fasciitis).
Historically, Group A streptococcus was diagnosed as the cause of the majority of cases of Type II dermonecrotic infections. However, since 2001, methicillin-resistant Staphylococcus aureus (MRSA) has been observed with increasing frequency as the cause of monomicrobial necrotizing fasciitis. The infection begins locally, sometimes at a site of trauma, which may be severe (such as the result of surgery), minor, or even non-apparent. Patients usually complain of intense pain that may seem in excess given the external appearance of the skin. With progression of the disease, tissue becomes swollen, often within hours. Diarrhea and vomiting are also common symptoms.
Sign of inflammation may not be apparent in the early stages of infection, if the bacteria are deep within the tissue. If the bacteria are not deep, signs of inflammation, such as redness and swollen or hot skin, show quickly. Skin color may progress to violet, and blisters may form, with subsequent necrosis (e.g., death) of the subcutaneous tissues. Patients with necrotizing fasciitis typically have a fever and appear very ill. Mortality rates have been noted as high as 73 percent if left untreated.
e) Pneumonia
S. aureus has also been identified as a cause of Staphylococcal pneumonia. Staphylococcal pneumonia causes inflammation and swelling of the lung, which in turn causes fluid to collect in the lung. Fluid collecting in the lung can prevent oxygen from entering the bloodstream. Those with influenza are at risk for developing bacterial pneumonia. Staphylococcus aureus is the most common cause of bacterial pneumonia in those already suffering from influenza. Common symptoms of staphylococcal pneumonia include coughing, difficulty breathing, and fever. Additional symptoms include fatigue, yellow or bloody mucus, and chest pain that worsens with breathing. Methicillin resistant S. aureus (MRSA) is increasingly being diagnosed as the strain identified in staphylococcal pneumonia.
f) Surgical Wound Infections
Surgical wounds often penetrate far into the body. Infection of such wounds thus pose a grave risk to a patient, if the wound becomes infected. S. aureus is frequently a causative agent of infections in surgical wounds. S. aureus is unusually adept at invading surgical wounds, sutured wounds can be infected by far fewer S. aureus cells then are necessary to cause infection in normal skin. Invasion of surgical wounds can lead to severe S. aureus septicemia. Invasion of the blood stream by S. aureus can lead to seeding and infection of internal organs, particularly heart valves and bone, causing systemic diseases, such as endocarditis and osteomyelitis.
g) Scalded Skin Syndrome
S. aureus is likely a major causative agent of “scalded skin syndrome,” also referred to as “staphylococcal scalded skin syndrome,” “toxic epidermal necrosis,” “localized bullous impetigo,” “Ritter's disease” and “Lyell's disease.” Scalded skin syndrome frequently occurs in older children, typically in outbreaks caused by flowering of S. aureus strains that produce epidermolytic exotoxins (e.g., exfoliatin A and B, sometimes referred to as scalded skin syndrome toxin), which cause detachment within the epidermal layer. One of the exotoxins is encoded by the bacterial chromosome and the other is encoded by a plasmid. The exotoxins are proteases that cleave desmoglein-1, which normally holds the granulosum and spinosum layers of the skin together.
The bacteria may initially infect only a minor lesion, however, the toxin destroys intercellular connections, spreads epidermal layers and allows the infection to penetrate the outer layer of the skin, producing the desquamation that typifies the disease. Shedding of the outer layer of skin generally reveals normal skin below, but fluid lost in the process can produce severe injury in young children if it is not treated properly.
h) Toxic Shock Syndrome
Toxic shock syndrome (TSS) is caused by strains of S. aureus that produce the so-called “toxic shock syndrome toxin.” The disease can be caused by S. aureus infection at any site, but is often erroneously viewed exclusively as a disease solely of women who use tampons. The disease involves toxemia and septicemia, and can be fatal.
Symptoms of toxic shock syndrome vary depending on the underlying cause. TSS resulting from infection with the bacteria Staphylococcus aureus typically manifests in otherwise healthy individuals with high fever, accompanied by low blood pressure, malaise and confusion, which can rapidly progress to stupor, coma, and multi-organ failure. The characteristic rash, often seen early in the course of illness, resembles a sunburn, and can involve any region of the body, including the lips, mouth, eyes, palms and soles. In patients who survive the initial onslaught of the infection, the rash desquamates, or peels off, after 10-14 days.
As noted above, due to the increase of multi-drug resistant strains of S. aureus, an increasing number of antibiotics commonly used to treat S. aureus infections, no longer control or eliminate infections of methicillin- and multidrug-resistant Staphylococcus aureus. Antibodies against S. aureus surface determinants and secreted toxins, as described herein, can help reduce the severity of infection and also may aid in clearing, preventing (prophylactically) or reducing pathogenic S. aureus from an infected host. The antibodies can also be used to detect S. aureus and, when in a patient sample, diagnose S. aureus infections.
K. Methods of Detecting S. aureus Using Antibodies or Fragments Directed Against S. aureus Surface Antigens or Secreted Toxins
In various embodiments, the antibodies disclosed herein can be used individually or in combination to detect the presence of S. aureus in a sample.
In certain embodiments, the method comprises contacting a test sample with one of the isolated antibodies or fragments disclosed herein. The antibody or antigen binding fragment thereof then bind to an S. aureus surface antigen or secreted toxin to form an antigen-antibody complex. In further embodiments, the method comprises contacting the antigen-antibody complex with a detectable label, wherein the signal produced by the detectable label is directly correlated with the presence of S. aureus in the sample. For example, the detectable label can comprise one or more fluorescent markers that bind the antibody or antigen in the antibody-antigen complex, such that an increase in fluorescence correlates with an increased concentration of S. aureus or secreted toxin in a sample.
In other embodiments, the detectable label competes with the S. aureus surface antigen or secreted toxin for binding to the antibody or antigen binding fragment thereof, wherein the signal produced by the detectable label is indirectly correlated with the concentration of S. aureus or secreted toxin in the sample. For example, the detectable label can comprise one or more fluorescent markers that compete with the surface antigen or secreted toxin for antibody binding, such that a decrease in fluorescence correlates with an increased concentration of S. aureus or secreted toxin in a sample
In certain embodiments, the detectable signal produced by the detectable label in the test sample is compared to the signal from at least one control sample having a known concentration of antigen and antibody. In embodiments using control samples, antibody-antigen complex is detected in the control and test samples using the detectable label, and any statistically significant difference in the detectable signal between the samples is indicative of the concentration, presence, or absence of S. aureus and/or secreted toxin in the test sample.
In other embodiments, a combination of antibodies is used to detect S. aureus in a sample. In various embodiments, the method comprises contacting a test sample with an isolated antibody or antigen binding fragment thereof directed against an S. aureus surface antigen and an isolated antibody or antigen binding fragment thereof directed against an S. aureus secreted toxin. The combination of antibodies or fragments then bind to an S. aureus surface antigen and a secreted toxin to form two antigen-antibody complexes. In further embodiments, the method comprises contacting the test sample containing the antigen-antibody complexes with at least one detectable label, wherein the signal produced by the detectable label(s) is directly correlated with the presence of S. aureus in the sample. For example, the detectable label(s) can comprise one or more fluorescent markers that bind the antibody or antigen in at least one of the antibody-antigen complexes, such that an increase in fluorescence correlates with an increased concentration of S. aureus and/or secreted toxin in a sample.
In other embodiments, the at least one detectable label competes with the S. aureus surface antigen and/or secreted toxin for binding to the combination of antibodies or fragments. The signal produced by the detectable label(s) is thus indirectly correlated with the concentration of S. aureus in the sample. For example, the detectable label(s) can comprise one or more fluorescent markers that compete with the surface antigen and/or secreted toxin for antibody binding, such that a decrease in fluorescence correlates with an increased concentration of S. aureus and/or secreted toxin in a sample.
In certain embodiments, the detectable signals produced by the detectable labels in the test sample are compared to the signal from at least one control sample having known concentrations of antigens and antibodies. In embodiments using control samples, antibody-antigen complexes are detected in the control and test samples using the detectable labels, and any statistically significant difference in the detectable signals between the samples is indicative of the concentration, presence, or absence of S. aureus and/or secreted toxin in the test sample.
In certain embodiments, the method of detection is used to detect the presence of S. aureus in a patient sample, and the method further comprises diagnosing a patient with an S. aureus infection. In some embodiments, the method is adapted for use in an automated or semi-automated system.
In certain embodiments, kits comprising at least one antibody or antigen binding fragment thereof disclosed herein are also provided that are useful for various research and diagnostic purposes. For example, the kits can be used to detect S. aureus in a sample, or to immunoprecipitate an S. aureus secreted toxin. For isolation and purification purposes, the kit may contain an antibody or antigen binding fragment thereof coupled to a bead (e.g., sepharose beads).
In this application, the use of the singular includes the plural unless specifically stated otherwise. Also in this application, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including,” as well as other forms, such as “includes” and “included,” are not limiting. Any range described herein will be understood to include the endpoints and all values between the endpoints.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including but not limited to patents, patent applications, articles, books, and treatises, are hereby expressly incorporated by reference in their entirety for any purpose. To the extent publications and patents or patent applications incorporated by reference contradict the invention contained in the specification, the specification will supersede any contradictory material.
EXAMPLES
The following examples serve to illustrate, and in no way limit, the present disclosure.
Example 1—Materials and Methods
Materials and methods utilized for Example 2 to Example 9 are provided hereafter
Neutralization of Hemolytic Activity
Fifty microliters of each B cell hybridoma culture supernatant was mixed with recombinant alpha toxin-His (rAT-his, 0.1 μg/ml final concentration) in 96 well plates, followed by the addition of 50 μl of 5% rabbit red blood cells (RBC) in PBS. Control wells contained RBC and culture media alone with or without AT. Plates were incubated for 1 h at 37° C., and the intact cells pelleted by centrifugation. 50 μl of the supernatants were transferred to a new 96 well plate and the A490 measured in a spectrophotometer. Neutralizing activity was calculated relative to lysis with RBC and rAT-his alone and calculated: % inhibition=100×[100−(A490 nAT+Ab)/(A490 nAT no Ab)].
Inhibition with the purified mAbs also was tested. Anti-AT mAbs were added to a 96-well plate at about 80 μg/mL in PBS and the samples serially diluted (twofold) in PBS to a final volume of 50 μL. A nonspecific IgG1 (R347) was included as an isotype control. Twenty five microliters of mAb dilutions were mixed with 25 μL of nAT (native alpha toxin) at about 0.1 μg/mL in 96 well round bottom plates, followed by the addition of 50 μL 5% RBC. Inhibition of hemolytic activity was calculated as above.
Neutralization of A549 Lysis
A549 cells were maintained in a 5% CO2 37° C. incubator in RMPI supplemented with non essential amino acid, glutamine and 10% fetal bovine serum. Cells were washed once with Hank's balanced media, and plated at 104/well under 50 μl in RPMI, 5% FBS, and incubated at 37° C. with 5% CO2 for 20 hr. Anti-AT mAbs were added to a 96-well plate at 80 μg/mL in RPMI and the samples serially diluted (two-fold) in RPMI. An irrelevant IgG1 (R347) was included as an isotype control. In a separate 96-well plate, 30 μl of the diluted antibodies were mixed with 30 μl of nAT (final concentration, 5 μg/ml). Fifty microliters from each well was transferred to the plate containing adherent A549 cells. Control wells of A549 cells with or without nAT were included. Plates were incubated 37° C. with 5% CO2 for 3 h, centrifuged and 50 μl supernatant transferred to a new 96-well plate. Cell lysis was measured as the release of lactate dehydrogenase (LDH) using a Cytotox 96 non radioactive assay kit (Promega) following the manufacturer's protocol. Background LDH was subtracted from each well and the inhibition of LDH release calculated: % inhibition=100×[100−(A590 nAT+Ab)/(A590 nAT no Ab)].
Neutralization of THP-1 Lysis
THP-1 cells were maintained in a 5% CO2 37° C. incubator in RPMI medium (Invitrogen) supplemented with non essential amino acids (Invitrogen), 2 mM glutamine (Invitrogen) and 10% fetal bovine serum (Invitrogen). Anti-AT mAbs were added to a 96-well plate at 80 μg/ml in RPMI and the samples serially diluted (two-fold) in RPMI to a final volume of 50 μL. An irrelevant IgG1 (R347) was included as an isotype control. Twenty five microliters of the mAb dilutions were mixed with 25 μl native alpha toxin (nAT) at 1.5 μg/ml final, followed by the addition of 50 μl of RMPI washed THP-1 cells (106 cells/ml in RPMI with 10% FBS) in a 96-well plate. Control wells consisted in THP-1 cells with alone or with nAT. Plates were incubated in a 5% CO2 37° C. incubator for 3 h, centrifuged and 50 μl of the supernatant transferred to a new 96 well plate. Cell lysis was measured as the release of lactate dehydrogenase (LDH) using the Cytotox 96 non radioactive assay kit (Promega) following the manufacturer's instructions. Inhibition of LDH release was calculated as described above.
Murine Pneumonia Model
Twenty-four hours prior to infection groups of ten 7-9 wk-old C57BL/6J mice (Harlan) received 0.5 ml of mAb at the concentrations indicated via i.p injection. The animals were then anesthetized with isofluorane, held vertically and 0.05 ml of S. aureus bacterial suspension (1×108 CFU to 3×108 CFU) in sterile PBS were inoculated into the left and right nostrils. Animals were placed into a cage in a supine position for recovery and were observed twice daily for the time course of study. Animal survival was monitored for a maximum of 6 days.
Alternatively, animals were euthanized by CO2 inhalation 48 h after bacterial infection. A lung and kidney were removed into sterile PBS, homogenized, diluted and plated for bacterial enumeration. Statistical significance of mortality studies was determined using log-rank test. The significance of bacterial recovery from organs was calculated using analysis of variance and Dunnett's post-test.
Murine Model of Dermonecrosis
Groups of five 6-8 weeks old female BALB/c mice (Harlan) were shaved on their back and administered by intraperitoneal injection of 0.5 ml IgG at the concentration indicated on the graph. Twenty-four hours later, the mice were infected by subcutaneous injection of 50 μL of a bacterial suspension (1×108 S. aureus). The animals were monitored twice daily for signs of infection and the size of the abscess measured at the same time daily. The area of the lesions was calculated using the formula A=L×W. Statistical significance was determined using analysis of variance and Dunnett's post-test.
Murine Model of Sepsis
Preparation of Bacteria Challenge Dose: S. aureus SF8300 (USA300) was provided by Binh Diep (University California San Francisco). Bacteria were cultured overnight at 37° C. in 50 mL of tryptic soy broth (TSB) shaking at 250 rpm. Ten mL from the overnight culture were added to 1 L of fresh TSB and the bacteria grown at 37° C. with shaking to an optical density at 600 nm (OD600) of 0.8. Bacteria were recovered by centrifugation at 8000 rpm for 15 min at 4° C. and washed in phosphate buffer saline (PBS). The bacteria was collected by centrifugation and resuspended in PBS with 10% glycerol to a final bacterial stock concentration of  ̃2×1010 cfu/mL.
Mouse Challenge and Survival: Groups of ten 8-9 week old female BALB/c mice were injected intra-peritoneally (IP) with LC10 at indicated concentrations or R347 (45 mg/kg) mAbs in 500 μL PBS. Animals were then challenged intravenously (IV) in the tail vein 24 h later with 200 μL of a bacterial suspension (5×107 cfu diluted in PBS, pH 7.2, from frozen stock). Mice were monitored for survival for 14 days post challenge. Statistical analysis was assessed with a logrank test: R347 (control) versus LC10 (anti-AT Ab) immunized animals.
Bacterial Load in Heart: Infected mice were euthanized with CO2 14 h post infection. The heart was removed, homogenized in lysing matrix A tubes in 1 mL cold PBS, and plated on TSA plates for bacterial enumeration. The bacterial load in heart tissue was analyzed in pairwise comparison between R347 and LC10 mAbs with an unpaired two-tailed Student's t-test. Data were considered significant if p<0.05.\
Bacteria Load in Blood: Animals were euthanized with CO2 at 8, 24, 48, 72, and 144 h post infection. Blood was collected by cardiac puncture, and 100 μL was plated immediately on a TSB plate for cfu enumeration. Data were analyzed with an unpaired student t test. Values were considered statistically different between LC10 and R347 mAbs if p<0.05.
Receptor Binding Assay
Red blood cell ghosts were prepared by incubating 5 mL of washed and packed rabbit red blood cells (RBC) in 500 mL of lysis buffer (5 mM phosphate, 1 mM EDTA, pH 7.4) o/n at 4° C. with constant stirring. Tim ghosts were then removed by centrifugation at 15,000×g and washed 3× with lysis buffer. They were then washed in PBS and resuspended in a final volume of 3 mL.
To assess binding of nAT to cell membranes RBC ghosts were diluted to OD600 approximately 0.2 in PBS and 50 μL were coated onto 1⁄2-well 96 well plates (Costar) and incubated overnight at 4° C. Theliquid was then removed from the plates and the wells were blocked with 100 μL of 1% BSA in PBS, pH7.4 for 2 hr at 4° C. and washed 3× with PBS. A 20 molar excess of IgG was mixed with nAT at 3 μg/mL and 50 μL was added to the blocked plates. The plates were incubated at 4° C. for 2 hr and washed 3× with PBS. Biotin labeled rabbit anti-AT IgG was added to the wells at 1 mg/mL and incubated at 4° C. for 1 hr, washed 3× and incubated with streptavidin peroxidase conjugate (1:30,000, Jackson Immunoresearch). The wells were washed 3× and developed with Sure Blue Reserve (KPL, Inc.). The A450 was read using a plate reader (Molecular Devices) and the % AT bound calculated. % AT bound=100×(A450−AT+IgG/A450−AT alone).
Measurement of Kinetic Rate and Binding Constants (KD)
Kinetic rate constants (kon, koff) for the binding of the anti-AT IgG antibodies to purified nAT were measured employing an IgG-capture assay format on a BIAcore 3000 instrument (BIAcore, Inc). Briefly, a rat anti-mouse-IgG was immobilized on a CM5 sensor chip according to manufacturer's instructions. The final surface density of the capture reagent on the sensor chip was approximately 2500 response units (RUs), as described herein. A reference flow cell surface was also prepared on this sensor chip using the identical immobilization protocol, and omitting nAT. Anti-AT IgG antibodies were prepared at 20 nM in instrument buffer (HBS-EP buffer containing 0.01 M HEPES, pH 7.4, 0.15 M NaCl, 3 mM EDTA and 0.005% P-20) along with two-fold serial dilutions of the nAT. nAT serial dilutions were made in the range of about 0.78 nM to about 50 nM, in instrument buffer.
A sequential approach was utilized for kinetic measurements. Each anti-AT IgG was first injected over the capture and reference surfaces at a flow rate of 50 μL/min. Once the binding of the captured IgG had stabilized, a single concentration of the nAT protein was injected over both surfaces, at a flow rate of 50 μL/min. The resultant binding response curves was used to determine the association phase data. Following the injection of the nAT, the flow was then switched back to instrument buffer for 10 minutes to permit the collection of dissociation phase data followed by a 1 minute pulse of 10 mM glycine, pH 1.5 to regenerate the IgG capture surface on the chip. Binding responses from duplicate injections of each concentration of nAT were recorded against all anti-AT IgGs.
Additionally, several buffer injections were interspersed throughout the injection series. Select buffer injections were used along with the reference cell responses to correct the raw data sets for injection artifacts and/or non-specific binding interactions commonly referred to as “double-referencing” (D. G. Myszka, Improving biosensor analysis. J. Mol. Recognit. 12 (1999), pp. 279-284). Fully corrected binding data was then globally fit to a 1:1 binding model (BIAevaluation 4.1 software, BIAcore, Inc, Uppsala, Sweden) that included a term to correct for mass transport-limited binding, should it be detected. These analyses determined the kinetic rate (on, off) constants, from which the apparent KD was then calculated as koff/kon.
Measurement of Cytokine Levels in S. aureus Infected Lungs
Seven to nine wk-old C57BL/6J mice were treated with 2A3.1 hu (fully human 2A3.1) or R347 (45 mg/kg) by intraperitoneal injection 24 h before intranasal infection with 1.5×108 cfu USA300 (BAA-1556, ATCC). Four and twenty-four hours post infection the mice were euthanized and the lungs were flushed 3× with 1 ml of PBS. The bronchoalveolar lavage fluid (BAL) was stored at −70° C. Proinflammatory cytokines were quantified using the 7 pro-inflammatory II mouse cytokine kit (Mesoscale, Gaithersburg, Md.) according to manufacturer's instructions. Cytokine levels were expressed as pg/ml.
Dot Blot Assays
Overlapping peptides spanning amino acid 40 to 293 were chemically synthesized (New England Peptide). Synthesis of AT1-50 was attempted but not successful. Alpha toxin (AT), AT peptides and AT fragments (1 μg) were spotted on nitrocellulose and blocked 10 min with Blocker Casein in PBS. The blots were then probed with 2 μg/mL of the individual IgG for 3 hr at room temperature. The blots were washed and incubated with an alkaline phosphatase conjugated goat anti-mouse or goat anti rabbit IgG (1:1000, Caltag Laboratories) for 1 hr and developed using BCIP/NBT membrane phosphatase substrate system (KPL, Inc).
Example 2—Target Selection and Validation
Thirteen surface antigens and four secreted toxins were selected for validation as antibody targets, based on their conservation across clinical isolates and/or published vaccine potential. Included in this group were alpha toxin and three soluble modulins (PSMs). Also included were 8 staphylococcal cell wall-anchored antigens/adhesins. Five of the selected targets have homologues in S. aureus and S. epidermidis. These targets are involved in nutrient acquisition, biofilm formation, and cell division. Antibodies against alpha toxin were targeted as a hypothesized method to reduce or neutralize toxin activities such as tissue damage and immune dysregulation. Also targeted were S. aureus surface determinants (IsdH, SdrC, ClfB, ClfA and IsdB), which are important for S. aureus colonization, immune evasion, and fitness. A potential approach considered for enhancing antibody therapy involved combining opsonic and toxin-neutralizing monoclonal antibodies.
Antibodies raised against the identified targets were assessed in both in vitro and in vivo assays for reduced virulence and/or reduced colonization and immune evasion. Target fitness was also validated via active/passive immunization in murine infection models.
Example 3—Identification of Anti-IsdH Antibodies
A primary target identified was the S. aureus Iron regulated surface determinant H (IsdH). IsdH contains a 7 amino acid loop between the B1b and B2β-sheets, and this 7 amino acid loop is conserved across several members of the iron regulated surface determinants family, including in IsdA and IsdB. Mutations in this 7 amino acid loop reduce the ability of S. aureus to bind haemoglobin by greater than 100 fold and also impair the ability of S. aureus to evade phagocytic killing. Visai et al., J. Microbiology, 155(3): 667-679 (2008).
Anti-IsdH monoclonal antibodies (mAB) were identified using VelocImmune Mice® (Regeneron Pharmaceuticals) and phage panning (Dyax or CAT libraries). 59 IgG antibodies were purified (29 from the Dyax libraries, 16 from the CAT libraries, and 14 from the VelocImmune mice).
Example 4—Anti-IsdH mAB Screening Cascade
Identified anti-IsdH mABs were evaluated by ELISA for whole cell S. aureus binding in vitro. Antibodies were also screened by ELISA for inhibition of S. aureus haptoglobin binding. Antibodies were then evaluated in an opsonophagocytic killing assay (OPK) (described below). Eleven anti-IsdH IgG antibodies were identified that were opsonic for 4 S. aureus isolates. Five anti-IsdH antibodies effectively bound S. aureus following in vivo passage in a mouse infection model (described below). These top five anti-IsdH mABs (3 from the Dyax libraries and 2 from the CAT libraries) were selected for scale-up of antibody production, affinity testing, and subsequent in vivo testing. In vivo testing included studies in a bacteremia model (described below). Antibody 2F4 significantly reduced CFUs in the bacteremia model. The five antibodes were then characterized and evaluated for use in combination therapy.
The opsonophagocytic killing (OPK) assay involved combining 10 μl of S. aureus (106 cells/ml), 10 μl of monoclonal antibody, and 60 μl of DMEM plus 0.1% gelatin. The solution was incubated for 30 minutes at 4° C. After 30 minutes, 10 μl of human promyelocytic leukemia (HL-60) cells at 107 cells/ml were added, along with 10 μl of human sera pre-absorbed against S. aureus. At time T0, 10 μl of solution was plated and then incubated at 37° C. with 1500 rpm of shaking for 60 minutes. At time T60) the HL-60 cells were lysed with 1% saponin, replated, and CFU concentration determined. The percentage OPK was calculated as calculated as follows: 100×(1−(T60/T0)), where T60 refers to the CFU concentration at the end of the assay (i.e., at 60 minutes) and T0 refers to the CFU concentration at the beginning of the assay.
11 monoclonal anti-IsdH antibodies were identified that were sufficiently opsonic against 4 S. aureus isolates to merit further investigation. FIG. 1 illustrates that antibodies B11, 2F4, and A7 had an increased percentage OPK, as compared to control antibody R347, when tested in S. aureus strains Newman and USA300.
To determine whether the antigens targeted by the antibodies were expressed by S. aureus in vivo, antibody binding was assessed following in vivo passage in mouse. Mice were challenged intraperitoneally with approximately 5×108 CFU of S. aureus. After 1 to 6 hours, mice were ex-sanguinated and blood was pooled into ice cold citrate. Eukaryotic cells were lysed with 1% NP-40. Lysed cells were washed three times with phosphate buffered saline (PBS) and sonicated, followed by resuspension of S. aureus bacteria in buffer (approximately 0.5-10×106 CFU were recovered after lysis and resuspension). Anti-IsdH antibodies were administered to cell lysates, and antibody binding was evaluated by staining and FACs sorting.
Five of the eleven anti-IsdH mABs (designated 1C1, 2F4, A7, IsdH003, and IsdH0016) bound S. aureus following in vivo passage. FIG. 2 illustrates binding of antibodies B11, 2F4, A7, and 1C1, as compared to control antibody R347, in S. aureus strains ARC2081 and USA300. The figure shows that antibodies 2F4, A7, and 1C1 bind S. aureus ex vivo.
Two of the five anti-IsdH mABs (1C1 and 2F4) also competed with haptoglobin (Hp) for binding to IsdH, while the other three did not. FIG. 3 shows that antibody 1C1 competes with Hp for binding to subunit Neat-1 on IsdH. Increasing concentrations of 1C1 (in μg/ml) correlate with a reduction in Hp binding to IsdH, as compared to Hp binding in the presence of control antibody R347. Likewise, FIG. 3 shows that antibody 2F4 competes with Hp for binding to subunit Neat-2 on IsdH. Increasing concentrations of 2F4 (in μg/ml) correlate with a reduction in Hp binding to IsdH, as compared to Hp binding in the presence of control antibody R347.
To assess whether antibodies 1C1, 2F4, A7, IsdH003, and IsdH0016 were effective when administered in vivo, a mouse bacteremia model was employed. Mice were injected intra-peritoneally with a monoclonal antibody at 45, 15 or 5 mg/kg, then allowed to recover overnight. The following day, mice were infected intraperitoneally with approximately 108 CFU of S. aureus (Newman strain). Approximately 4 hours later, blood was collected and evaluated for CFU concentration, measured as log [CFU/ml]. FIG. 4 shows that antibodies 1C1, A7, IsdH003, and IsdH0016 did not reduce the CFU concentration in the bacteremia model. However, FIG. 5 shows that antibody 2F4 does reduce the CFU concentration in the murine bacteremia model.
Antibody 2F4 was further evaluated for ex vivo binding to various strains of S. aureus. The antibody bound to 23 of 25 isolates of S. aureus following in vivo passage and extraction in mouse. FIG. 6 illustrates 2F4 binding in strains ARC2379 (USA100), ARC2081 (USA200) and BAA-1556 (USA 300). The table below illustrates the results of binding experiments following in vivo passage of 25 S. aureus strains in mouse.
Binding of Antibody 2F4 Following In Vivo Passage of S. aureus Strains





















NRS 22
NRS 123
NRS 383
NRS 384
NRS 484
ARC 797
ARC 1206
ARC2558



USA 600
USA 400
USA 200
USA 300
USA 1100
USA 500
USA 700
USA 400





T0
neg.
neg.
neg.
neg.
neg.
+/−
+/−
+/−


1 hr
+
+
+
+
+
+/−
+
+


4 hr
+
+
+
+
+
+/−
+
+






UAMS-1

BAA1556
NRS 261
NRS 382
ARC2379
ARC 517
NRS385



USA 200
NEWMAN
USA 300
MSSA
USA 100
USA 100
USA 600
USA500





T0
neg.
neg.
neg.
neg.
+/−
+/−
neg.
+/−


1 hr
neg.
+
+
+
+
+
+
neg.


4 hr
neg.
+
+
+
neg.
+
+
+




















NR5655
1056
ARC2464
ARC 516
NRS 234
NRS 249
ARC633
ARC634
ARC635



USA300
USA300
USA300
USA 800
MSSA
MRSA
MSSA
MRSA
MRSA





T0
+/−
+/−
neg.
+
neg.
neg.
neg.
+
neg.


1 hr
+
+/−
+
+
+/−
+
+
+
+


4 hr
+
+
+
+
+
+
N/A
+
N/A









Antibody 2F4 was also evaluated in OPK assays involving the S. aureus clinical isolates—Newman, ARC634 (USA100), ARC2081 (USA200), and BAA-1556 (USA300). FIG. 7 shows that 2F4 was opsonic for the major S. aureus clinical isolates.
2F4 was subsequently evaluated for affinity to IsdH and to the Neat-2 subunit in a hu_IgGFc capture assay. The mean affinity, averaged across three experiments, revealed a KD for IsdH of 3.66 nM and a KD for Neat-2 of 2.57 nM. FIG. 8.
Example 5—Anti-IsdH & Anti-AT Antibody Combination Therapy
Alpha toxin and IsdH play different roles during pathogenesis following S. aureus infection. The former is a secreted toxin, while the latter is a surface protein important for colonization, immune evasion, and bacterial fitness. The two may be differentially expressed by S. aureus during infection. Combining monoclonal antibodies with different methods of action could potentially produce additive or synergistic effects, while reducing the risk that a strain will evade therapy.
2A3, an anti-alpha toxin antibody was evaluated for use in combination with 2F4, an anti-IsdH antibody. When administered in combination, antibodies 2A3 and 2F4 exhibited synergistic effects in the organ burden model. FIG. 9 shows that the kidney distribution of S. aureus strain USA300 was reduced in the presence of both antibodies, as compared to either antibody alone or to control antibody R347.
The results of these combination therapy experiments suggest that a combination approach to prophylaxis or treatment of S. aureus may be effective.
Example 6—Anti-ClfA mAbs Inhibit ClfA Binding
Anti-ClfA mAbs inhibit ClfA binding to immobilized fibrinogen in vitro. ClfA as a virulence factor has been reported to promote S. aureus binding to fibrinogen present in plasma. This results in bacteria agglutination in blood.
The ability of three anti-ClfA mAbs generated through B cell hybridoma technology to inhibit ClfA binding to immobilized fibrinogen was evaluated. The antibody R347 was used as a negative control. Each anti-ClfA mAb activity in this assay was calculated at an IC50, the concentration required to promote 50% binding inhibition. As shown in FIG. 10, together with the IC50 of each antibody, the anti-ClfA antibodies inhibit ClfA binding to immobilized fibrinogen.
Example 7—Anti-ClfA mAb11H10 Inhibits S. Aureus Agglutination in Human Plasma with Three Different Clinical Isolates
To assess S. aureus agglutination in human plasma, bacteria was incubated with each anti-ClfA mAb, and bacteria clumping was examined visually after 3 min incubation at 37° C. For a more accurate comparison, mAb activities in this assay were compared at the minimum concentration required to inhibit agglutination. 11H10 was more efficient than 27H4 or 23D6 (FIG. 11). In addition, agglutination experiments were conducted with three different clinical isolates, and 11H10 exhibited inhibition against these three isolates as compared to the two other anti-ClfA mAbs covering one or two strains.
Example 8—Epitope Binding for 11H10
Given the differing characteristics of 11H10 as compared to 23D6 and 27H4 as discussed above, its binding characteristics were further explored. Epitope competition binding was run by Octet to assess if 11H10 bind a different epitope than 23D6 and 27H4. As seen in FIG. 12, 23D6 and 27H4 competed for binding to ClfA suggesting they may share a common region on ClfA for binding. However, there was no competition between 11H10 and 23D6 or 11H10 and 27H4 demonstrating that 11H10 epitope on ClfA is different than for 23D6 and 27H4.
Example 9—Passive Immunization with Anti-ClfA mAb 11H10 Demonstrates Efficacy in a Lethal IV Challenge Model
Bacteria Load in Heart
To test whether staphylococcal agglutination occurred in vivo, mice were first challenged in tail vein with a USA300 isolate, and bacteria number were enumerated in the heart after 14 h infection. As shown in FIG. 13, prophylactic administration of the anti-ClfA mAb 11H10 intra-peritoneally (IP) at 45 mg/kg resulted in significant decrease of bacteria cfu in heart (p=0.031). This was dose dependent since 11H10 at 15 mg/kg only slightly reduced the bacteria load in the heart as compared to the negative control R347.
Survival
The USA300 challenge dose for IV challenge was determined to induce 20% survival after 2 weeks. The capacity of anti-ClfA mAb 11H10 to increase animal survival was investigated in this model. FIG. 14 shows that 11H10 injection resulted in significant increase of survival (p=0.0114 at 45 mg/kg, and p=0.0239 at 15 mg/kg) over 2 weeks post infection.
Example 10—Efficacy of Anti-ClfA mAB 11H10 and Anti-AT Ab LC10 Combination in a Lethal IV Challenge Model
Six week old BALB/c mice female were passively immunized intraperitoneally (IP) with mAbs at indicated concentrations (diluted in 500 μl PBS), and intravenously (IV) challenged with an LD20 dose of bacteria in the tail vein (in 200 ul PBS) 24 h later. Survival was monitored until 14 days post infection.
Data were analyzed with a Log Rank (mantel-cox) test, and p value considered statistically significant if ≦0.05. To test whether staphylococcal agglutination occurred in vivo, mice were first challenged in the tail vein with a CA-MRSA USA300, HA-MRSA-100 or HA-MSSA USA200 isolate, and bacteria number were enumerated in the heart and kidney after 14 h infection.
The efficacy of the combination of anti-ClfA mAB 11H10 and anti-AT Ab LC10 combination in a lethal IV challenge model was tested. As shown in FIG. 15, prophylactic administration of the anti-ClfA mAb 11H10, the anti-AT LC10 mAb, and the combination of both anti-ClfA mAb and anti-AT LC10 mAb resulted in a significant decrease of bacteria cfu in the heart (FIG. 15b) and the kidney (15c).
FIG. 15 also demonstrates the capacity of anti-ClfA mAb 11H10, anti-AT mAb LC10 and the combination of anti-ClfA mAb 11H10 and anti-At mAb LC10 to increase animal survival as investigated in the IV challenge model using a USA300 challenge dose. FIG. 15a shows that the combination of both resulted in significant increase in response with respect to survival over 2 weeks post infection as compared to control and as compared to either anti-ClfA mAb and anti-AT mAb alone.
FIGS. 16 and 17 further demonstrate the capacity of the combination of anti-ClfA mAb 11H10 and anti-At mAb LC10 to increase animal survival as investigated in the IV challenge model using an HA-MRSA USA100 challenge dose (FIG. 16) and an HA-MSSA USA200 challenge dose (FIG. 17).
Example 11—Efficacy of Anti-IsdH mAb 2F4 and Anti-AT Ab LC10 Combination in a Lethal IV Challenge Model
Experiments were performed as described above in Example 10.
The efficacy of the combination of anti-IsdH mAb 2F4 and anti-AT Ab LC10 combination in a lethal IV challenge model was tested. As shown in FIG. 18, the combination of anti-IsdH mAb 2F4 and anti-At mAb LC10 increased animal survival as investigated in the IV challenge model using a HA-MRSA USA100 challenge dose. FIG. 18 shows that the combination resulted in significant increase in response with respect to survival over 6 days post infection as compared to the R347 control.
Tables of Sequences







TABLE 1







VL CDR sequences for mAbs 2A3.1, 10A7.5, 12B8.19


and 25E9.1









SEQ ID NO:
Description
Sequence





SEQ ID NO: 1
VL CDR1
RASQSISSWLA


 


SEQ ID NO: 2
VL CDR2
KASSLES


 


SEQ ID NO: 3
VL CDR3
QQYNSYWT
















TABLE 2







VL CDR sequences for mAB 28F6.1











SEQ ID NO:
Description
Sequence







SEQ ID NO: 4
mAb 28F6.1 VL CDR1
RASQGIRNDLG



 



SEQ ID NO: 5
mAb 28F6.1 VL CDR2
DASSLQS



 



SEQ ID NO: 6
mAb 28F6.1 VL CDR3
LQDYNYPWT

















TABLE 3







VH CDR sequences for mAb 2A3.1









SEQ ID NO:
Description
Sequence





SEQ ID NO: 7
VH CDR1
SYDMH


 


SEQ ID NO: 8
VH CDR2
GIGTAGDTYYPGSVKG


 


SEQ ID NO: 9
VH CDR3
DNYSSTGGYYGMDV
















TABLE 4







VH CDR sequences for mAbs 10A7.5 and 12B8.19









SEQ ID NO:
Description
Sequence





SEQ ID NO: 10
VH CDR1
RYDMH


 


SEQ ID NO: 11
VH CDR2
VIGTDGDTYYPGSVKG


 


SEQ ID NO: 12
VH CDR3
DRYSSSNHYNGMDV
















TABLE 5







VH CDR sequences for mAb 28F6.1









SEQ ID NO:
Description
Sequence





SEQ ID NO: 13
mAb 28F6.1 VH CDR1
SYAMT


 


SEQ ID NO: 14
mAb 28F6.1 VH CDR2
VISGSGGSTYYADSVKG


 


SEQ ID NO: 15
mAb 28F6.1 VH CDR3
DGRQVEDYYYYYGMDV
















TABLE 6







VH CDR sequences for mAb 25E9.1









SEQ ID NO:
Description
Sequence





SEQ ID NO: 7
mAb 25E9.1 VH CDR1
SYDMH


 


SEQ ID NO: 17
mAb 25E9.1 VH CDR2
VIDTAGDTYYPGSVKG


 


SEQ ID NO: 18
mAb 25E9.1 VH CDR3
DRYSGNFHYNGMDV
















TABLE 7







VL and VH amino acid sequences for anti-alpha toxin mAbs












VH or VL sequence (with





Description
CDRs in bold)
CDR1
CDR2
CDR3





mAb 2A3.1
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYNSYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T (SEQ ID



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
NO: 3)



SGSGTEFTLTISSLQPDDFATY
NO: 1)





YCQQYNSYWTFGQGTKVEIK






(SEQ ID NO: 19)





 


mAb 2A3.1
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DNYSSTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
GYYGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQLNS

NO: 8)
NO: 9)



LRAGDTAVYFCARDNYSSTGG






YYGMDVWGQGTTVTVSS






(SEQ ID NO: 20)





 


mAb 10A7.5
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYNSYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 3)



YCQQYNSYWTFGQGTKVEIK






(SEQ ID NO: 21)





 


mAb 10A7.5
EVQLVESGGGLVQPGGSLRLS
RYDMH
VIGTDGDT
DRYSSSNH


VH
CAASGFTFSRYDMHWVRQAT
(SEQ ID
YYPGSVKG
YNGMDV



GKGLEWVSVIGTDGDTYYPGS
NO: 10)
(SEQ ID
(SEQ ID



VKGRFIISRENAKNSLYLEMNS

NO: 11)
NO: 12)



LRAGDTAVYYCARDRYSSSNH






YNGMDVWGQGTTVTVSS






(SEQ ID NO: 22)





 


mAb
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYNSYW


12B8.19 VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKVLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 3)



YCQQYNSYWTFGQGTKVEIK






(SEQ ID NO: 23)





 


mAb
EVQLVESGGGLVQPGGSLRLS
RYDMH
VIGTDGDT
DRYSSSNH


12B8.19 VH
CAASGFTFSRYDMHWVRQAT
(SEQ ID
YYPGSVKG
YNGMDV



GKGLEWVSVIGTDGDTYYPGS
NO: 10)
(SEQ ID
(SEQ ID



VKGRFIISRENAKNSLYLEMNS

NO: 11)
NO: 12)



LRAGDTAVYYCARDRYSSSNH






YNGMDVWGQGTTVTVSS






(SEQ ID NO: 24)





 


mAb 28F6.1
AIQMTQSPSSLSASVGDRVTIT
RASQGIRN
DASSLQS
LQDYNYP


VL
CRASQGIRNDLGWYQQKPGK
DLG (SEQ
(SEQ ID
WT



APKLLIYDASSLQSGVPSRFSG
ID NO: 4)
NO: 5)
(SEQ ID



SGSGTDFTLTISSLQPEDFATY


NO: 6)



YCLQDYNYPWTFGQGTKVEIK






(SEQ ID NO: 25)





 


mAb 28F6.1
EVQLLESGGGLVQPGGSLRLS
SYAMT
VISGSGGS
DGRQVED


VH
CAASGFTFSSYAMTWVRQAP
(SEQ ID
TYYADSVK
YYYYYGM



GKGLEWVSVISGSGGSTYYAD
NO: 13)
G
DV



SVKGRFTVSRDNSKNTLYLQM

(SEQ ID
(SEQ ID



NSLRAEDTAVYYCAKDGRQVE

NO: 14)
NO: 15)



DYYYYYGMDVWGQGTTVTVS






S






(SEQ ID NO: 26)





 


mAb 25E9.1
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYNSYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 3)



YCQQYNSYWTFGQGTKVEIK






(SEQ ID NO: 27)





 


mAb 25E9.1
EVQLVESGGGLVQPGGSLRLS
SYDMH
SVIDTAGD
DRYSGNF


VH
CTASGFTFSSYDMHWVRQAT
(SEQ ID
TYYPGSVK
HYNGMDV



GKGLEWVSVIDTAGDTYYPGS
NO: 7)
G
(SEQ ID



VKGRFTISRENAKNSLYLQMN

(SEQ ID
NO: 18)



SLRAGDTAVYYCVRDRYSGNF

NO: 17)




HYNGMDVWGQGTTVTVSS






(SEQ ID NO: 28)





 


mAb QD20
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DRYSPTGH


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
YMGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 16)



SLRAGDTAVYYCARDRYSPTG






HYMGMDVWGQGTTVTVSS






(SEQ ID NO: 41)





 


mAb QD20
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYDTYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 64)



YCQQYDTYWTFGQGTKVEIK






(SEQ ID NO: 42)





 


mAb QD33
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DRYSRTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
HYMGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 65)



SLRAGDTAVYYCARDRYSRTG






HYMGMDVWGQGTTVTVSS






(SEQ ID NO: 43)





 


mAb QD33
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYDTYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 64)



YCQQYDTYWTFGQGTKVEIK






(SEQ ID NO: 44)





 


mAb QD37
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DRYSRTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
HYMGMSL



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 66)



SLRAGDTAVYYCARDRYSRTG






HYMGMSLWGQGTTVTVSS






(SEQ ID NO: 45)





 


mAb QD37
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYDTYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 64)



YCQQYDTYWTFGQGTKVEIK






(SEQ ID NO: 46)





 


mAb QD3
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DNYSRTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
HYMGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 67)



SLRAGDTAVYYCARDNYSRTG






HYMGMDVWGQGTTVTVSS






(SEQ ID NO: 47)





 


mAb QD3 VL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
KQYADYW



CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 68)



YCKQYADYWTFGQGTKVEIK






(SEQ ID NO: 48)





 


mAb QD4
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DNYSRTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
HYMGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 67)



SLRAGDTAVYYCARDNYSRTG






HYMGMDVWGQGTTVTVSS






(SEQ ID NO: 49)





 


mAb QD4 VL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYDTYW



CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 64)



YCQQYDTYWTFGQGTKVEIK






(SEQ ID NO: 50)





 


mAb QD23
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DRYSPTGH


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
YMGMSL



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 78)



SLRAGDTAVYYCARDRYSPTG






HYMGMSLWGQGTTVTVSS






(SEQ ID NO: 51)





 


mAb QD23
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYDTYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 64)



YCQQYDTYWTFGQGTKVEIK






(SEQ ID NO: 52)





 


mAb QD32
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DRYSRTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
HYMGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
NO: 65)



VKGRFTISRENAKNSLYLQMN

NO: 8)




SLRAGDTAVYYCARDRYSRTG






HYMGMDVWGQGTTVTVSS






(SEQ ID NO: 53)





 


mAb QD32
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
KQYADYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 68)



YCKQYADYWTFGQGTKVEIK






(SEQ ID NO: 54)





 


mAb 2A3GL
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DNYSSTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
GYYGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 9)



SLRAGDTAVYYCARDNYSSTG






GYYGMDVWGQGTTVTVSS






(SEQ ID NO: 55)





 


mAb 2A3GL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
QQYNSYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 3)



YCQQYNSYWTFGQGTKVEIK






(SEQ ID NO: 56)





 


mAb LC10
EVQLVESGGGLVQPGGSLRLS
SHDMH
GIGTAGDT
DRYSPTGH


VH
CAASGFTFSSHDMHWVRQAT
(SEQ ID
YYPDSVKG
YYGMDV



GKGLEWVSGIGTAGDTYYPDS
NO: 69)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 70)
NO: 71)



SLRAGDTAVYYCARDRYSPTG






HYYGMDVWGQGTTVTVSS






(SEQ ID NO: 57)





 


mAb LC10
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
KQYADYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 68)



YCKQYADYWTFGQGTKVEIK






(SEQ ID NO: 58)





 


mAb TVES
EVQLVESGGGLVQPGGSLRLS
SYDMH
GIGTAGDT
DNYSPTG


VH
CAASGFTFSSYDMHWVRQAT
(SEQ ID
YYPGSVKG
GYYGMDV



GKGLEWVSGIGTAGDTYYPGS
NO: 7)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 8)
NO: 72)



SLRAGDTAVYYCARDNYSPTG






GYYGMDVWGQGTTVTVSS






(SEQ ID NO: 59)





 


mAb TVES
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLKS
QQYESYW


VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLKSGVPSRFSG
(SEQ ID
NO: 73)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 74)



YCQQYESYWTFGQGTKVEIK






(SEQ ID NO: 60)





 


mAb
EVQLVESGGGLVQPGGSLRLS
SHDMH
GIGTRGDT
DRYSPTGH


3H7KAD VH
CAASGFTFSSHDMHWVRQAT
(SEQ ID
YYPDSVKG
YYGMDV



GKGLEWVSGIGTRGDTYYPDS
NO: 69)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 75)
NO: 71)



SLRAGDTAVYYCARDRYSPTG






HYYGMDVWGQGTTVTVSS






(SEQ ID NO: 61)





 


mAb
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
KQYADYW


3H7KAD VL
CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 68)



YCKQYADYWTFGQGTKVEIK






(SEQ ID NO: 58)





 


mAb LC9 VH
EVQLVESGGGLVQPGGSLRLS
SHDMH
GIGTRGDT
DKYSPTGH



CAASGFTFSSHDMHWVRQAT
(SEQ ID
YYPDSVKG
YYGMDV



GKGLEWVSGIGTRGDTYYPDS
NO: 69)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 75)
NO: 76)



SLRAGDTAVYYCARDKYSPTG






HYYGMDVWGQGTTVTVSS






(SEQ ID NO: 62)





 


mAb LC9 VL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLES
KQYADYW



CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLESGVPSRFSG
(SEQ ID
NO: 2)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 68)



YCKQYADYWTFGQGTKVEIK






(SEQ ID NO: 58)





 


mAb LC4 VH
EVQLVESGGGLVQPGGSLRLS
SHDMH
GIGTRGDT
DKYSPTGH



CAASGFTFSSHDMHWVRQAT
(SEQ ID
YYPDSVKG
YYGMDV



GKGLEWVSGIGTRGDTYYPDS
NO: 69)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 75)
NO: 76)



SLRAGDTAVYYCARDKYSPTG






HYYGMDVWGQGTTVTVSS






(SEQ ID NO: 62)





 


mAb LC4 VL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLVK
QQYESYW



CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLVKGVPSRFSG
(SEQ ID
NO: 77)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 74)



YCQQYESYWTFGQGTKVEIK






(SEQ ID NO: 63)





 


mAb LC5 VH
EVQLVESGGGLVQPGGSLRLS
SHDMH
GIGTAGDT
DRYSPTGH



CAASGFTFSSHDMHWVRQAT
(SEQ ID
YYPDSVKG
YYGMDV



GKGLEWVSGIGTAGDTYYPDS
NO: 69)
(SEQ ID
(SEQ ID



VKGRFTISRENAKNSLYLQMN

NO: 70)
NO: 71)



SLRAGDTAVYYCARDRYSPTG






HYYGMDVWGQGTTVTVSS






(SEQ ID NO: 79)





 


mAb LC5 VL
DIQMTQSPSTLSASVGDRVTIT
RASQSISS
KASSLVK
QQYESYW



CRASQSISSWLAWYQQKPGK
WLA
(SEQ ID
T



APKLLIYKASSLVKGVPSRFSG
(SEQ ID
NO: 77)
(SEQ ID



SGSGTEFTLTISSLQPDDFATY
NO: 1)

NO: 74)



YCQQYESYWTFGQGTKVEIK






(SEQ ID NO: 63)
















TABLE 8







VL and VH nucleotide sequences for anti-alpha toxin mAbs









SEQ ID NO:
Description
Sequence





SEQ ID NO: 29
mAb 2A3.1 VL
GACATCCAGATGACCCAGTCTCCTTCCA



nucleotide sequence
CCCTGTCTGCATCTGTAGGAGACAGAGT




CACCATCACTTGCCGGGCCAGTCAGAGT




ATTAGTAGCTGGTTGGCCTGGTATCAGC




AGAAACCAGGGAAAGCCCCTAAACTCCT




GATCTATAAGGCGTCTAGTTTAGAAAGTG




GGGTCCCATCAAGGTTCAGCGGCAGTGG




ATCTGGGACAGAATTCACTCTCACCATCA




GCAGCCTGCAGCCTGATGATTTTGCAAC




TTATTACTGCCAACAGTATAATAGTTATTG




GACGTTCGGCCAAGGGACCAAGGTGGA




AATCAAA


 


SEQ ID NO: 30
mAb 2A3.1 VH
GAGGTGCAGCTGGTGGAGTCTGGGGGA



nucleotide sequence
GGCTTGGTACAGCCTGGGGGGTCCCTG




AGACTCTCCTGTGCAGCCTCTGGATTCA




CCTTCAGTAGCTACGACATGCACTGGGT




CCGCCAAGCTACAGGAAAAGGTCTGGAG




TGGGTCTCAGGTATTGGCACTGCTGGTG




ACACATATTATCCAGGCTCCGTGAAGGG




CCGATTCACCATCTCCAGAGAAAATGCC




AAGAACTCCTTGTATCTTCAATTGAACAG




CCTGAGAGCCGGGGACACGGCTGTGTA




CTTCTGTGCAAGAGACAATTATAGCAGCA




CCGGGGGGTACTACGGTATGGACGTCTG




GGGCCAAGGGACCACGGTCACCGTCTC




CTCA


 


SEQ ID NO: 31
mAb 10A7.5 VL
GACATCCAGATGACCCAGTCTCCTTCCA



nucleotide sequence
CCCTGTCTGCATCTGTAGGAGACAGAGT




CACCATCACTTGCCGGGCCAGTCAGAGT




ATTAGTAGCTGGTTGGCCTGGTATCAGC




AGAAACCAGGGAAAGCCCCTAAACTCCT




GATCTATAAGGCGTCTAGTTTAGAAAGTG




GGGTCCCATCAAGGTTCAGCGGCAGTGG




ATCTGGGACAGAATTCACTCTCACCATCA




GCAGCCTGCAGCCTGATGATTTTGCAAC




TTATTACTGCCAACAGTATAATAGTTATTG




GACGTTCGGCCAAGGGACCAAGGTGGA




AATCAAA


 


SEQ ID NO: 32
mAb 10A7.5 VH
GAGGTGCAGCTGGTGGAGTCTGGGGGA



nucleotide sequence
GGCTTGGTACAGCCTGGGGGGTCCCTG




AGACTCTCCTGTGCAGCCTCTGGATTCA




CCTTCAGTAGGTACGACATGCACTGGGT




CCGCCAAGCTACAGGAAAAGGTCTGGAG




TGGGTCTCAGTTATTGGTACTGATGGTGA




CACATACTATCCAGGCTCCGTGAAGGGC




CGATTCATCATCTCCAGAGAAAATGCCAA




GAACTCCTTGTATCTTGAAATGAACAGCC




TGAGAGCCGGGGACACGGCTGTGTATTA




CTGTGCAAGAGATCGGTATAGCAGCTCG




AACCACTACAACGGTATGGACGTCTGGG




GCCAAGGGACCACGGTCACCGTCTCCTC




A


 


SEQ ID NO: 33
mAb 12B8.19 VL
GACATCCAGATGACCCAGTCTCCTTCCA



nucleotide sequence
CCCTGTCTGCATCTGTAGGAGACAGAGT




CACCATCACTTGCCGGGCCAGTCAGAGT




ATTAGTAGCTGGTTGGCCTGGTATCAGC




AGAAACCAGGGAAAGCCCCTAAGGTCCT




GATCTATAAGGCGTCTAGTTTAGAAAGTG




GGGTCCCATCAAGGTTCAGCGGCAGTGG




ATCTGGGACAGAATTCACTCTCACCATCA




GCAGCCTGCAGCCTGATGATTTTGCAAC




TTATTACTGCCAACAGTATAATAGTTATTG




GACGTTCGGCCAAGGGACCAAGGTGGA




AATCAAA


 


SEQ ID NO: 34
mAb 12B8.19 VH
GAGGTGCAGCTGGTGGAGTCTGGGGGA



nucleotide sequence
GGCTTGGTACAGCCTGGGGGGTCCCTG




AGACTCTCCTGTGCAGCCTCTGGATTCA




CCTTCAGTAGGTACGACATGCACTGGGT




CCGCCAAGCTACAGGAAAAGGTCTGGAG




TGGGTCTCAGTTATTGGTACTGATGGTGA




CACATACTATCCAGGCTCCGTGAAGGGC




CGATTCATCATCTCCAGAGAAAATGCCAA




GAACTCCTTGTATCTTGAAATGAACAGCC




TGAGAGCCGGGGACACGGCTGTGTATTA




CTGTGCAAGAGATCGGTATAGCAGCTCG




AACCACTACAACGGTATGGACGTCTGGG




GCCAAGGGACCACGGTCACCGTCTCCTC




A


 


SEQ ID NO: 35
mAb 28F6.1 VL
GCCATCCAGATGACCCAGTCTCCATCCT



nucleotide sequence
CCCTGTCTGCATCTGTAGGAGACAGAGT




CACCATCACTTGCCGGGCAAGTCAGGGC




ATTAGAAATGATTTAGGCTGGTATCAGCA




GAAACCAGGGAAAGCCCCTAAGCTCCTG




ATCTATGATGCATCCAGTTTACAAAGTGG




GGTCCCATCAAGGTTCAGCGGCAGTGGA




TCTGGCACAGATTTCACTCTCACCATCAG




CAGCCTGCAGCCTGAAGATTTTGCAACTT




ATTACTGTCTACAAGATTACAATTACCCG




TGGACGTTCGGCCAAGGGACCAAGGTG




GAAATCAAA


 


SEQ ID NO: 36
mAb 28F6.1 VH
GAGGTGCAGCTGTTGGAGTCTGGGGGA



nucleotide sequence
GGCTTGGTACAGCCTGGGGGGTCCCTG




AGACTCTCCTGTGCAGCCTCTGGATTCA




CCTTTAGCAGCTATGCCATGACCTGGGT




CCGCCAGGCTCCAGGGAAGGGGCTGGA




ATGGGTCTCAGTTATTAGTGGTAGTGGT




GGTAGCACATACTACGCAGACTCCGTGA




AGGGCCGGTTCACCGTCTCCAGAGACAA




TTCCAAGAACACGCTGTATCTGCAAATGA




ACAGCCTGAGAGCCGAGGACACGGCCG




TATATTACTGTGCGAAAGATGGGAGGCA




GGTCGAGGATTACTACTACTACTACGGTA




TGGACGTCTGGGGCCAAGGGACCACGG




TCACCGTCTCCTCA


 


SEQ ID NO: 37
mAb 25E9.1 VL
GACATCCAGATGACCCAGTCTCCTTCCA



nucleotide sequence
CCCTGTCTGCATCTGTAGGAGACAGAGT




CACCATCACTTGCCGGGCCAGTCAGAGT




ATTAGTAGCTGGTTGGCCTGGTATCAGC




AGAAACCAGGGAAAGCCCCTAAGCTCCT




GATCTATAAGGCGTCTAGTTTAGAAAGTG




GGGTCCCATCAAGGTTCAGCGGCAGTGG




ATCTGGGACAGAATTCACTCTCACCATCA




GCAGCCTGCAGCCTGATGATTTTGCAAC




TTATTACTGCCAACAGTATAATAGTTATTG




GACGTTCGGCCAAGGGACCAAGGTGGA




AATCAAA


 


SEQ ID NO: 38
mAb 25E9.1 VH
GAGGTGCAGCTGGTGGAGTCTGGGGGA



nucleotide sequence
GGCTTGGTACAGCCTGGGGGGTCCCTG




AGACTCTCCTGTACAGCCTCTGGATTCAC




CTTCAGTAGTTACGACATGCACTGGGTC




CGCCAAGCTACAGGAAAAGGTCTGGAGT




GGGTCTCAGTTATTGATACTGCTGGTGA




CACATACTATCCAGGCTCCGTGAAGGGC




CGATTCACCATCTCCAGAGAAAATGCCAA




GAACTCCTTGTATCTTCAAATGAACAGCC




TGAGAGCCGGGGACACGGCTGTGTATTA




CTGTGTAAGAGATAGGTATAGTGGGAAC




TTCCACTACAACGGTATGGACGTCTGGG




GCCAAGGGACCACGGTCACCGTCTCCTC




A
















TABLE 9







Alpha Toxin VL and VH CDR summary table










Description
SEQ ID NOs







VL CDR 1
1, 4



VL CDR 2
2, 5, 73, 77



VL CDR 3
3, 6, 64, 68, 74



VH CDR 1
7, 10, 13, 69



VH CDR 2
8, 11, 14, 17, 70, 75



VH CDR 3
9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76, 78

















TABLE 10







VL and VH amino acid sequences for anti-alpha toxin mAbs having Fc


variant region









SEQ ID NO:
Description
Sequence





SEQ ID NO: 130
LC 10-VH- IgG1-YTE:
EVQLVESGGGLVQPGGSLRLSCAASG




FTFSSHDMHWVRQATGKGLEWVSGIG




TAGDTYYPDSVKGRFTISRENAKNSLY




LQMNSLRAGDTAVYYCARDRYSPTGH




YYGMDVWGQGTTVTVSS-




ASTKGPSVFPLAPSSKSTSGGTAALGC




LVKDYFPEPVTVSWNSGALTSGVHTFP




AVLQSSGLYSLSSVVTVPSSSLGTQTYI




CNVNHKPSNTKVDKRVEPKSCDKTHT




CPPCPAPELLGGPSVFLFPPKPKDTLYI




TREPEVTCVVVDVSHEDPEVKFNWYV




DGVEVHNAKTKPREEQYNSTYRVVSVL




TVLHQDWLNGKEYKCKVSNKALPAPIE




KTISKAKGQPREPQVYTLPPSREEMTK




NQVSLTCLVKGFYPSDIAVEWESNGQP




ENNYKTTPPVLDSDGSFFLYSKLTVDK




SRWQQGNVFSCSVMHEALHNHYTQK




SLSLSPGK


 


SEQ ID NO: 131
LC10 VL-Kappa
DIQMTQSPSTLSASVGDRVTITCRASQ




SISSWLAWYQQKPGKAPKLLIYKASSLE




SGVPSRFSGSGSGTEFTLTISSLQPDD




FATYYCKQYADYWTFGQGTKVEIK-




RTVAAPSVFIFPPSDEQLKSGTASVVCL




LNNFYPREAKVQWKVDNALQSGNSQE




SVTEQDSKDSTYSLSSTLTLSKADYEK




HKVYACEVTHQGLSSPVTKSFNRGE
















TABLE 11





Alpha Toxin Amino Acid Sequences
















Staphylococcus
adsdiniktgttdigsnttvktgdlvtydkengmhkkvfysfiddknhnkkllvirtkgtiagqyrvyseega


aureus alpha toxin
nksglawpsafkvqlqlpdnevaqisdyyprnsidtkeymstltygfngnvtgddtgkiggliganvsigh



tlkyvqpdfktilesptdkkvgwkvifnnmvnqnwgpydrdswnpvygnqlfmktrngsmkaadnfld



pnkassllssgfspdfatvitmdrkaskqqtnidviyervrddyqlhwtstnwkgtntkdkwtdrsseryki



dwekeemtn (SEQ ID NO: 39)


 


S. aureus alpha
adsdiniktgttdigsnttvktgdlvtydkengmlkkvfysfiddknhnkkllvirtkgtiagqyrvyseegan


toxin H35L mutant
ksglawpsafkvqlqlpdnevaqisdyyprnsidtkeymstltygfngnvtgddtgkiggliganvsightl



kyvqpdfktilesptdkkvgwkvifnnmvnqnwgpydrdswnpvygnqlfmktrngsmkaadnfldp



nkassllssgfspdfatvitmdrkaskqqtnidviyervrddyqlhwtstnwkgtntkdkwtdrsserykid



wekeemtn (SEQ ID NO: 40)
















TABLE 12







Representative Amino Acid Sequences for Antibodies that


Specifically Bind to S. aureus surface antigen IsdH












VH or VL sequence (with





Description
CDRs in bold)
CDR1
CDR2
CDR3





mAb 2F4 VH
EVQLLESGGGLVQPGGSLRLS
PYMMQ(SEQ
SIWPSGGK
VRRGGAT



CAASGFTFSPYMMQWVRQAP
ID NO:
TYYADSVK
DY (SEQ ID



GKGLEWVSSIWPSGGKTYYA
90)
G (SEQ ID
NO: 92)



DSVKGRFTISRDNSKNTLY

NO: 91)




LQMNSLRAEDTAVYYCARVRR






GGATDYWGQGTLVTVSS






(SEQ ID NO: 80)





 


mAb 2F4 VL
DIQMTQSPATLSVSPGERATL
RASQSVSS
GASTRAT
QQYQNWP



SCRASQSVSSNLGWYQQKPG
NLG (SEQ
(SEQ ID
LLT (SEQ



QAPRLLIYGASTRATGIPTRFS
ID NO: 93)
NO: 94)
ID NO: 95)



GSGSGTEFTLTISSLQS






EDFATYYCQQYQNWPLLTFG






GGTKVEIK






(SEQ ID NO: 81)





 


mAb A7 VH
EVQLLESGGGLVQPGGSLRLS
NYYMW
VIGPSGGP
WGGRYSV



CAASGFTFSNYYMWWVRQAP
(SEQ ID
TQYADSVK
FET (SEQ



GKGLEWVSVIGPSGGPTQYA
NO: 96)
G (SEQ ID
ID NO: 98)



DSVKGRFTISRDNSKNTLY

NO: 97)




LQMNSLRAEDTAVYYCARWG






GRYSVFETWGQGTMVTVSS






(SEQ ID NO: 82)





 


mAb A7 VL
DIQMTQSPATLSVSPGGRATL
RASQSVR
GASTRAT
QQYSSWP



SCRASQSVRKNVAWYQQKPG
KNVA (SEQ
(SEQ ID
AF (SEQ ID



QPPRLLIYGASTRATGVPARF
ID NO: 99)
NO: 100)
NO: 101)



SGSGSGTEFTLTISRMQP






EDFVVYHCQQYSSWPAFGQG






TMVEIN






(SEQ ID NO: 83)





 


mAb 1C1 VH
EVQLLESGGGLVQPGGSLRLS
RYFMG
SIYSSGGY
RWRDGTF



CAASGFTFSRYFMGWVRQAP
(SEQ ID
TSYADSVK
DY (SEQ ID



GKGLEWVSSIYSSGGYTSYAD
NO: 102)
G (SEQ ID
NO: 104)



SVKGRFTISRDNSKNTLY

NO: 103)




LQMNSLRAEDTAVYYCARRW






RDGTFDYWGQGTLVTVSS






(SEQ ID NO: 84)





 


mAb 1C1 VL
DIQMTQSPSSLSASIGDRVTIS
RASQSVR
AASSLQS
QQSYSTRF



CRASQSVREYLNWYQQKPGK
EYLN (SEQ
(SEQ ID
T (SEQ ID



APKLLIFAASSLQSGVPSRFSG
ID NO: 105)
NO: 106)
NO: 107)



SGSGTDFTLTISSLQP






EDFATYYCQQSYSTRFTFGPG






TKVDIK






(SEQ ID NO: 85)





 


IsdH0003 VH
QVQLQQSGAEVKKPGSSVKV
SYPIS
KIIPIFGTTN
PNRPYNIG



SCKASGGTFSSYPISWVRQAP
(SEQ ID
YAQKFQG
WHYYFDY



GQGLEWMGKIIPIFGTTNYAQ
NO: 108)
(SEQ ID
(SEQ ID



KFQGRVTITADESTSTAY

NO: 109)
NO: 110)



MELSSLRSEDTAIYYCASPNRP






YNIGWHYYFDYWGKGTLVTVS






S






(SEQ ID NO: 86)





 


IsdH0003 VL
QSVLTQPASVSGSPGQSITISC
TGTSSDVG
EGSKRPS
SSYTTRST



TGTSSDVGGYNYVSWYQQHP
GYNYVS
(SEQ ID
RV



GKAPKLMIYEGSKRPSGVSNR
(SEQ ID
NO: 112)
(SEQ ID



FSGSRSGNTASLTISGL
NO: 111)

NO: 113)



QAEDEADYYCSSYTTRSTRVF






GGGTKLTVL






(SEQ ID NO: 87)





 


IsdH0016 VH
EVQLLESGGGLVQPGGSLRLS
SYAMS
AISGSGGS
DQDEGRA



CAASGFTFSSYAMSWVRQAP
(SEQ ID
TYYADSVK
NNWWIPP



GKGLEWVSAISGSGGSTYYAD
NO: 114)
G
GGR



SVKGRFTISRDNSKNTLY

(SEQ ID
(SEQ ID



LQMNSLRAEDTAVYYCARDQ

NO: 115)
NO: 116)



DEGRANNWWIPPGGRWGQG






TMVTVSS






(SEQ ID NO: 88)





 


IsdH0016 VL
SSELTQDPTLSVALGQTVRITC
QGDSLRR
GQNKRPA
NSRDARL



QGDSLRRSFASWYQKKPGQA
SFAS
(SEQ ID
NPYIL



PVLLIYGQNKRPAGIPDRFSGS
(SEQ ID
NO: 118)
(SEQ ID



RSGNSASLTITGAQ
NO: 117)

NO: 119)



AEDEADYYCNSRDARLNPYIL






FGGGTKLTVL






(SEQ ID NO: 89)
















TABLE 13







nucleotide sequences encoding VH and VL amino acid sequences for


mAbs directed against S. aureus surface antigen IsdH and ClfA









SEQ ID NO:
Description
Sequence





SEQ ID NO: 120
mAb 2F4 VH nucleotide
GAAGTTCAATTGTTAGAGTCTGGTGG



sequence
CGGTCTTGTTCAGCCTGGTGGTTCTT




TACGTCTTTCTTGCGCTGCTTCCGGA




TTCACTTTCTCTCCTTACATGATGCAG




TGGGTTCGCCAAGCTCCTGGTAAAGG




TTTGGAGTGGGTTTCTTCTATCTGGC




CTTCTGGTGGCAAGACTTATTATGCT




GACTCCGTTAAAGGTCGCTTCACTAT




CTCTAGAGACAACTCTAAGAATACTCT




CTACTTGCAGATGAACAGCTTAAGGG




CTGAGGACACGGCCGTGTATTACTGT




GCGAGAGTGCGGAGGGGGGGAGCT




ACTGACTACTGGGGCCAGGGAACCC




TGGTCACCGTCTCAAGC


 


SEQ ID NO: 121
mAb 2F4 VL nucleotide
GACATCCAGATGACCCAGTCTCCAGC



sequence
CACCCTGTCTGTGTCTCCAGGGGAAA




GAGCCACCCTCTCCTGCAGGGCCAG




TCAGAGTGTTAGCAGCAACTTAGGCT




GGTACCAGCAGAAACCTGGCCAGGC




TCCCAGGCTCCTCATCTATGGTGCAT




CCACCAGGGCCACTGGTATCCCAAC




CAGGTTCAGTGGCAGTGGGTCTGGG




ACAGAGTTCACTCTCACCATCAGCAG




CCTGCAGTCTGAAGATTTTGCAACTT




ATTACTGTCAGCAGTATCAGAACTGG




CCCTTGCTCACTTTCGGCGGAGGGA




CCAAGGTGGAAATCAAA


 


SEQ ID NO: 122
mAb A7 VH nucleotide
GAAGTTCAATTGTTAGAGTCTGGTGG



sequence
CGGTCTTGTTCAGCCTGGTGGTTCTT




TACGTCTTTCTTGCGCTGCTTCCGGA




TTCACTTTCTCTAATTACTATATGTGG




TGGGTTCGCCAAGCTCCTGGTAAAGG




TTTGGAGTGGGTTTCTGTTATCGGTC




CTTCTGGTGGCCCTACTCAGTATGCT




GACTCCGTTAAAGGTCGCTTCACTAT




CTCTAGAGACAACTCTAAGAATACTCT




CTACTTGCAGATGAACAGCTTAAGGG




CTGAGGACACGGCCGTGTATTACTGT




GCGAGATGGGGTGGGAGGTACTCTG




TATTTGAAACCTGGGGCCAAGGGACA




ATGGTCACCGTCTCAAGC


 


SEQ ID NO: 123
mAb A7 VL nucleotide
GACATCCAGATGACCCAGTCTCCAGC



sequence
CACTCTGTCTGTGTCTCCAGGGGGAA




GAGCCACCCTCTCCTGCAGGGCCAG




TCAGAGTGTTAGAAAAAACGTAGCCT




GGTATCAGCAGAAACCTGGCCAGCCT




CCCAGGCTCCTCATCTATGGTGCATC




CACCAGGGCCACTGGTGTCCCAGCC




AGGTTCAGTGGCAGTGGGTCTGGGA




CAGAGTTCACTCTCACCATCAGCAGG




ATGCAGCCTGAAGATTTTGTAGTTTAT




CACTGTCAGCAGTATAGTAGCTGGCC




GGCGTTCGGCCAGGGGACCATGGTG




GAAATCAAC


 


SEQ ID NO: 124
mAb 1C1 VH nucleotide
GAAGTTCAATTGTTAGAGTCTGGTGG



sequence
CGGTCTTGTTCAGCCTGGTGGTTCTT




TACGTCTTTCTTGCGCTGCTTCCGGA




TTCACTTTCTCTCGTTACTTTATGGGT




TGGGTTCGCCAAGCTCCTGGTAAAGG




TTTGGAGTGGGTTTCTTCTATCTATTC




TTCTGGTGGCTATACTTCTTATGCTGA




CTCCGTTAAAGGTCGCTTCACTATCT




CTAGAGACAACTCTAAGAATACTCTCT




ACTTGCAGATGAACAGCTTAAGGGCT




GAGGACACGGCCGTGTATTACTGTGC




GAGACGGTGGCGAGATGGCACCTTT




GACTACTGGGGCCAGGGAACCCTGG




TCACCGTCTCAAGC


 


SEQ ID NO: 125
mAb 1C1 VL nucleotide
GACATCCAGATGACCCAGTCTCCATC



sequence
CTCCCTGTCTGCATCTATTGGAGACA




GAGTCACCATCTCTTGCCGGGCAAGT




CAGAGCGTTAGAGAGTATCTAAATTG




GTATCAACAAAAACCAGGGAAAGCCC




CTAAACTCCTGATCTTTGCTGCATCCA




GTTTGCAGAGTGGGGTCCCATCAAGA




TTCAGTGGCAGTGGATCTGGGACAGA




TTTCACTCTCACCATCAGCAGTCTGC




AACCTGAAGATTTTGCAACTTATTACT




GTCAACAGAGTTACAGTACCCGATTC




ACTTTCGGCCCTGGGACCAAAGTGGA




CATCAAA


 


SEQ ID NO: 126
mAb IsdH0003 VH
CAGGTACAGCTGCAGCAGTCAGGGG



nucleotide sequence
CTGAGGTGAAGAAGCCTGGGTCCTC




GGTGAAGGTCTCCTGCAAGGCTTCTG




GAGG




CACCTTCAGCAGCTATCCTATCAGCT




GGGTGCGACAGGCCCCTGGACAAGG




GCTTGAGTGGATGGGAAAGATCATCC




CTA




TCTTTGGTACAACAAACTACGCGCAG




AAGTTCCAGGGCAGAGTCACGATTAC




CGCGGACGAATCCACGAGCACTGCC




TAC




ATGGAACTGAGCAGCCTGAGATCTGA




GGACACGGCCATATATTACTGTGCGA




GCCCCAATCGACCCTATAACATTGGC




TG




GCACTACTACTTTGACTACTGGGGCA




AAGGAACCCTGGTCACCGTCTCCTCA


 


SEQ ID NO: 127
mAb IsdH0003 VL
CAGTCTGTGCTGACTCAGCCTGCCTC



nucleotide sequence
CGTGTCTGGGTCTCCTGGACAGTCGA




TCACCATCTCCTGCACTGGAACCAGC




AGTGACGTTGGTGGTTATAACTATGT




CTCCTGGTACCAACAACACCCAGGCA




AAGCCCCCAAACTCATGATTTATGAG




GGCAGTAAGCGGCCCTCAGGGGTTT




CTAATCGCTTCTCTGGCTCCAGGTCT




GGCAACACGGCCTCCCTGACAATCTC




TGGGCTCCAGGCTGAGGACGAGGCT




GATTATTACTGCAGCTCATATACAACC




AGGAGCACTCGAGTCTTCGGCGGAG




GGACCAAGCTGACCGTCCTA


 


SEQ ID NO: 128
mAb IsdH0016 VH
GAGGTGCAGCTGTTGGAGTCTGGGG



nucleotide sequence
GAGGCTTGGTACAGCCTGGGGGGTC




CCTGAGACTCTCCTGTGCAGCCTCTG




GATTCACCTTTAGCAGCTATGCCATG




AGCTGGGTCCGCCAGGCTCCAGGGA




AGGGGCTGGAGTGGGTCTCAGCTAT




TAGTGGTAGTGGTGGTAGCACATACT




ACGCAGACTCCGTGAAGGGCCGGTT




CACCATCTCCAGAGACAATTCCAAGA




ACACGCTGTATCTGCAAATGAACAGC




CTGAGAGCCGAGGACACGGCCGTGT




ATTACTGTGCAAGAGATCAGGACGAA




GGTAGAGCGAACAACTGGTGGATCC




CCCCCGGGGGTCGCTGGGGCCAGG




GGACAATGGTCACCGTCTCGAGT


 


SEQ ID NO: 129
mAb IsdH0016 VL
TCTTCTGAGCTGACTCAGGACCCTAC



nucleotide sequence
TCTGTCTGTGGCCCTGGGACAGACA




GTCAGAATCACATGCCAAGGAGACAG




CCTCCGAAGATCTTTTGCAAGTTGGT




ACCAGAAGAAGCCAGGACAGGCCCC




TGTACTTCTCATCTATGGTCAAAATAA




GCGGCCCGCAGGGATCCCAGACCGA




TTCTCTGGCTCCAGGTCAGGAAACTC




AGCTTCGTTGACCATCACAGGGGCTC




AGGCGGAAGATGAGGCTGACTATTAC




TGTAATTCCCGCGACGCCAGACTTAA




CCCTTATATACTCTTCGGCGGTGGGA




CCAAGCTGACCGTCCTA
















TABLE 14







Representative Amino Acid Sequences for Antibodies that


Specifically Bind to S. aureus surface antigen ClfA












VH or VL sequence (with





Description
CDRs in bold)
CDR1
CDR2
CDR3





mAb 23D6
QVQLVESGGGVVQPGRSLRL
SYGMH
LIWFDGSN
RGGGYYY


VH
SCAASVFTFSSYGMHWVRQA
(SEQ ID
EYYADSVK
YGMDV



PGKGLEWVALIWFDGSNEYYA
NO: 133 )
G (SEQ ID
(SEQ ID



DSVKGRFTISRDNSKNTLY

NO: 134)
NO: 135)



LQMNSLRAEDTAVYYCARDR






GGGYYYYGMDVWGQGTTVTV






SS (SEQ ID NO: 132 )





 


mAb 23D6
DIQMTQSPSSLSASVGDRVTIT
RASQGIRN
AASSLQS
LQHNSYPY


VL
CRASQGIRNDLGWYQQKPGK
DLG (SEQ
(SEQ ID
T (SEQ ID



APKRLIYAASSLQSGVPSRFS
ID NO: 137)
NO: 138)
NO: 139)



GSGSGTEFTLTISSLQP






EDFATYYCLQHNSYPYTFGQG






TKLEIK (SEQ ID NO: 136)





 


mAb 27H4
QVQLVQSGAEVKKPGASVKVS
SYGIS
WISSYNGN
AARGYYY


VH
CKTSGYTFTSYGISWVRQAPG
(SEQ ID
TNYAQKL
GMD (SEQ



QGHEWMGWISSYNGNTNYAQ
NO: 141)
QG (SEQ ID
ID NO: 143)



KLQGRVTMTSDTSTSTAYMEL

NO: 142)




RSLRSDDTAVYYCARIAARGY






YYGMDVWGQGTTVTVSS






(SEQ ID NO: 140)





 


mAb 27H4
EIVLTQSPGTLSLSPGERATLS
RASQSISG
GASSRAT
QQYSSWP


VL
CRASQSISGSYLAWYQQKPG
SYLA (SEQ
(SEQ ID
AF(SEQ ID



QAPRLLIYGASSRATGIPDRFS
ID NO: 145)
NO: 146)
NO: 147)



GSGSGTDFTLTISRLE






PEDFAVYYCQQYGSSPWTFG






QGTKVEIK (SEQ ID NO: 144)









The preceding examples and Tables are intended to illustrate and in no way limit the present disclosure. Other embodiments of the disclosed devices and methods will be apparent to those skilled in the art from consideration of the specification and practice of the devices and methods disclosed herein.
The following are embodiments of the invention:
1. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) IsdH surface determinant antigen,
wherein the isolated antibody or antigen binding fragment thereof comprises a heavy chain variable region (VH) and a light chain variable region (VH), each of which comprises three complementarity determining regions (CDR1, CDR2, and CDR3)
and wherein:

    
    
        a. a VH CDR1 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 90, 96, 102, 108, or 114;
        b. a VH CDR2 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 91, 97, 103, 109, or 115; and
        c. a VH CDR3 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 92, 98, 104, 110, or 116;
        and/or
        d. a VL CDR1 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 93, 99, 105, 111, or 117;
        e. a VL CDR2 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 94, 100, 106, 112, or 118; and
        f. a VL CDR3 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 95, 101, 107, 113, or 119.

2. The isolated antibody or antigen binding fragment thereof of embodiment 1, wherein the isolated antibody or antigen binding fragment thereof comprises:

        a. a VH CDR1 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 90, 96, 102, 108, or 114;
        b. a VH CDR2 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 91, 97, 103, 109, or 115;
        c. a VH CDR3 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 92, 98, 104, 110, or 116;
        d. a VL CDR1 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 93, 99, 105, 111, or 117;
        e. a VL CDR2 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 94, 100, 106, 112, or 118; and
        f. a VL CDR3 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 95, 101, 107, 113, or 119.

3. The isolated antibody or antigen binding fragment thereof of embodiment 1 or 2, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 corresponds to the set of amino acid sequences selected from the group consisting of SEQ ID NOs: 90, 91, 92, 93, 94 and 95; SEQ ID NOs: 96, 97, 98, 99, 100 and 101; SEQ ID NOs: 102, 103, 104, 105, 106 and 107; SEQ ID NOs: 108, 109, 110, 111, 112 and 113; and SEQ ID NOs: 114, 115, 116, 117, 118 and 119.

4. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) IsdH surface determinant antigen, wherein the VH amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88.

5. The isolated antibody or antigen binding fragment thereof of embodiment 4, wherein the VH amino acid sequence is identical to, or comprises 1 to 10 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88.

6. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) IsdH surface determinant antigen, wherein the VL amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.

7. The isolated antibody or antigen binding fragment thereof of embodiment 6, wherein the VL amino acid sequence is identical to, or comprises 1 to 10 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.

8. An isolated antibody or antigen binding fragment thereof of any one of embodiments 1-7, wherein the VH amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88 and the VL amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.

9. The isolated antibody or antigen binding fragment thereof of embodiment 8, wherein the VH amino acid sequence corresponds to the amino acid sequence of SEQ ID NO: 80, 82, 84, 86, or 88 and the VL amino acid sequence corresponds to the amino acid sequence of SEQ ID NO: 81, 83, 85, 87, or 89.

10. The isolated antibody or antigen binding fragment thereof of any one of embodiments 1-8, wherein the VH and VL are selected from the group consisting of SEQ ID NOs: 80 and 81; SEQ ID NOs: 82 and 83; SEQ ID NOs: 84 and 85; SEQ ID NOs: 86 and 87; and SEQ ID NOs: 88 and 89.

11. The isolated antibody of fragment of any one of embodiments 1-3, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 corresponds to the set of amino acid sequences selected from the group consisting of SEQ ID NOs: 90, 91, 92, 93, 94 and 95.

12. The isolated antibody or antigen binding fragment thereof of embodiment 1 or 2, wherein the VH amino acid sequence comprises four VH framework regions (FR1, FR2, FR3, FR4), and wherein the four VH framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VH framework regions in SEQ ID NO: 80, 82, 84, 86, or 88.

13. The isolated antibody or antigen binding fragment thereof of embodiment 1 or 2, wherein the VL amino acid sequence comprises four VL framework regions (FR1, FR2, FR3, FR4), and wherein the four VL framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VL framework regions in SEQ ID NO: 81, 83, 85, 87, or 89.

14. The isolated antibody or antigen binding fragment thereof of embodiment 1 or 2, wherein the four VH framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VH framework regions in SEQ ID NO: 80, 82, 84, 86, or 88, and wherein the four VL framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VL framework regions in SEQ ID NO: 81, 83, 85, 87, or 89.

15. The isolated antibody or antigen binding fragment thereof of any of embodiments 1-14, wherein the VH and VL correspond to SEQ ID NOs 80 and 81.

16. The isolated antibody or antigen binding fragment thereof of any one of embodiments 1-15, wherein the antibody or antigen binding fragment thereof has at least one of:

        a. a disassociation constant (KD) for an S. aureus surface antigen of about 70 nM or less;
        b. an ability to reduce the capability of S. aureus to evade opsonophagocytosis by at least 50%, as measured by an opsonophagocytic killing assay; or
        c. an ability to reduce the number of S. aureus colony forming units (CFUs) by at least 50%, as measured by a bacteremia model.

17. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) IsdH surface determinant antigen, and wherein the antibody or antigen binding fragment thereof has at least one of:

        a. a disassociation constant (KD) for an S. aureus surface antigen of about 70 nM or less;
        b. an ability to reduce the capability of S. aureus to evade opsonophagocytosis by at least 50%, as measured by an opsonophagocytic killing assay;
        c. an ability to reduce the number of S. aureus colony forming units (CFUs) by at least 50%, as measured by a bacteremia model;
        d. an ability to reduce immune cell infiltration, bacterial burden, and pro-inflammatory cytokine release, as measured in an animal organ burden model.

18. An isolated antibody or antigen binding fragment thereof of embodiment 17, having the amino acid sequence of the antibody or antigen binding fragment thereof of any one of embodiments 1-16.

19. A composition comprising the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18, and a pharmaceutically acceptable excipient.

20. An isolated nucleic acid encoding the amino acid sequence of any one of embodiments 1-15.

21. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) ClfA surface determinant antigen,

        wherein the isolated antibody or antigen binding fragment thereof comprises a heavy chain variable region (VH) and a light chain variable region (VH), each of which comprises three complementarity determining regions (CDR1, CDR2, and CDR3) and wherein:
        a. a VH CDR1 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 133 or 141;
        b. a VH CDR2 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 134 or 142; and
        c. a VH CDR3 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 135 or 143;
        and/or
        d. a VL CDR1 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 137 or 145;
        e. a VL CDR2 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 138 or 146; and
        f. a VL CDR3 is identical to, or comprises 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 139 or 147.

22. The isolated antibody or antigen binding fragment thereof of embodiment 21, wherein the isolated antibody or antigen binding fragment thereof comprises:

        a. a VH CDR1 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 133 or 141
        b. a VH CDR2 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 134 or 142;
        c. a VH CDR3 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 135 or 143;
        d. a VL CDR1 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 137 or 145;
        e. a VL CDR2 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 138 or 146;

and

        f. a VL CDR3 identical to, or comprising 1, 2, or 3 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 139 or 147.

23. The isolated antibody or antigen binding fragment thereof of embodiment 21 or 22, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 corresponds to the set of amino acid sequences selected from the group consisting of SEQ ID NOs: 133, 134, 135, 137, 138 and 139; and SEQ ID NOs: 137, 138, 139, 145, 146 and 147.

24. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) ClfA surface determinant antigen, wherein the VH amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 132 or 140.

25. The isolated antibody or antigen binding fragment thereof of embodiment 24, wherein the VH amino acid sequence is identical to, or comprises 1 to 10 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 132 or 140.

26. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) ClfA surface determinant antigen, wherein the VL amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 136 or 144.

27. The isolated antibody or antigen binding fragment thereof of embodiment 26, wherein the VL amino acid sequence is identical to, or comprises 1 to 10 amino acid residue mutations relative to, the amino acid sequence of SEQ ID NO: 136 or 144.

28. An isolated antibody or antigen binding fragment thereof of any one of embodiments 21-27, wherein the VH amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 132 or 140 and the VL amino acid sequence is at least 80%, 85%. 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 136 or 144.

29. The isolated antibody or antigen binding fragment thereof of embodiment 28, wherein the VH amino acid sequence corresponds to the amino acid sequence of SEQ ID NO: 132 or 140; and the VL amino acid sequence corresponds to the amino acid sequence of SEQ ID NO: 136 or 144.

30. The isolated antibody or antigen binding fragment thereof of any one of embodiments 21-28, wherein the VH and VL are selected from the group consisting of SEQ ID NOs: 132 and 136; and SEQ ID NOs: 140 and 144.

31. The isolated antibody of fragment of any one of embodiments 21-23, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 corresponds to the set of amino acid sequences selected from the group consisting of SEQ ID NOs: 141, 142, 143, 144, 145, 146 and 147.

32. The isolated antibody or antigen binding fragment thereof of embodiment 21 or 22, wherein the VH amino acid sequence comprises four VH framework regions (FR1, FR2, FR3, FR4), and wherein the four VH framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VH framework regions in SEQ ID NO: 132 or 140.

33. The isolated antibody or antigen binding fragment thereof of embodiment 21 or 22, wherein the VL amino acid sequence comprises four VL framework regions (FR1, FR2, FR3, FR4), and wherein the four VL framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VL framework regions in SEQ ID NO: 136 or 144.

34. The isolated antibody or antigen binding fragment thereof of embodiment 21 or 22, wherein the four VH framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VH framework regions in SEQ ID NO: 132 or 144, and wherein the four VL framework regions have amino acid sequences that are at least about 80%, 85%. 90%, 95% or 100% identical to the corresponding amino acid sequences of the four VL framework regions in SEQ ID NO: 136 or 144.

35. The isolated antibody or antigen binding fragment thereof of any of embodiments 21-34, wherein the VH and VL correspond to SEQ ID NOs 140 and 144.

36. A composition comprising the isolated antibody or antigen binding fragment thereof of any one of embodiments 21-35, and a pharmaceutically acceptable excipient.

37. An isolated nucleic acid encoding the amino acid sequence of any one of embodiments 21-35.

38. A composition comprising an isolated antibody or antigen binding fragment thereof that specifically binds to an S. aureus alpha toxin (AT) and an isolated antibody or antigen binding fragment thereof that specifically binds to an S. aureus surface determinant antigen.

39. The composition of embodiment 38, wherein the S. aureus surface determinant antigen is selected from the group consisting of SdrC, SdrD, SdrE, ClfA, ClfB, IsdA, IsdB, IsdC, IsdE, IsdH, SpA, FnbA and PNAG.

40. The composition of embodiment 38 or 39, wherein the surface determinant antigen is IsdH.

41. The composition of embodiment 40, wherein the isolated antibody or antigen binding fragment thereof that specifically binds IsdH is an antibody or antigen binding fragment thereof according to any one of embodiments 1-18.

42. The composition of embodiment 38 or 39, wherein the surface determinant antigen is ClfA.

43. The composition of embodiment 42, wherein the isolated antibody or antigen binding fragment thereof that specifically binds ClfA is an antibody or antigen binding fragment thereof according to any one of embodiments 21-35.

44. The composition of any of embodiments 38-43, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises:

a. a VH CDR1 comprising an amino acid sequence identical to or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO 7, 10, 13, or 69;

b. a VH CDR2 comprising an amino acid sequence identical to or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO 8, 11, 14, 17, 70, or 75; and

c. a VH CDR3 comprising an amino acid sequence identical to or comprising 1, 2, or 3 amino acid residue mutations relative to SEQ ID NO 9, 12, 15, 16, 18, 65, 66, 67, 71, 72, 76, or 78;

and/or

d. a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 1 or 4;

e. a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 2, 5, 73 or 77;

and

f. a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 3, 6, 64, 68 or 74.

45. The composition of any of embodiments 38-43, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises:

a. a VH CDR1 comprising the amino acid sequence of SEQ ID NO: 7, 10, 13 or 69;

b. a VH CDR2 comprising the amino acid sequence of SEQ ID NO: 8, 11, 14, 17, 70 or 75;

c. a VH CDR3 comprising the amino acid sequence of SEQ ID NO: 9, 12, 15, 18, 16, 65, 66, 67, 71, 72, 76 or 78;

d. a VL CDR1 comprising the amino acid sequence of SEQ ID NO: 1 or 4;

e. a VL CDR2 comprising the amino acid sequence of SEQ ID NO: 2, 5, 73 or 77;

and

f. a VL CDR3 comprising the amino acid sequence of SEQ ID NO: 3, 6, 64, 68 or 74.

46. The composition of any one of embodiments 38-45, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 of the isolated antibody or antigen binding fragment thereof that specifically binds AT corresponds to the amino acid sequences of SEQ ID NOs: 7, 8, 9, 1, 2 and 3; SEQ ID NOs: 10, 11, 12, 1, 2 and 3; SEQ ID NOs: 13, 14, 15, 4, 5 and 6; SEQ ID NOs: 7, 17, 18, 1, 2 and 3; SEQ ID NOs: 7, 8, 16, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 64; SEQ ID NOs; 7, 8, 66, 1, 2 and 64; SEQ ID NOs: 7, 8, 67, 1, 2 and 68; SEQ ID NOs: 7, 8, 67, 1, 2 and 64; SEQ ID NOs: 7, 8, 78, 1, 2 and 64; SEQ ID NOs: 7, 8, 65, 1, 2 and 68; SEQ ID NOs: 69, 70, 71, 1, 2 and 68; SEQ ID NOs: 7, 8, 72, 1, 73 and 74; SEQ ID NOs: 69, 75, 71, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 2 and 68; SEQ ID NOs: 69, 75, 76, 1, 77 and 74; SEQ ID NOs: 69, 70, 71, 1, 77 and 74.

47. The composition of any one of embodiments 38-43, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises a heavy chain variable domain having at least 90% identity to the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and/or (iii) comprises a light chain variable domain having at least 90% identity to the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.

48. The composition of any one of embodiments 38-43, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises a heavy chain variable domain having the amino acid sequence of SEQ ID NO: 20, 22, 24, 26, 28, 41, 43, 45, 47, 49, 51, 53, 55, 57, 79, 59, 61, or 62 and (iii) comprises a light chain variable domain having the amino acid sequence of SEQ ID NO: 19, 21, 23, 25, 27, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60 or 63.

49. The composition of any one of embodiments 38-48, wherein the VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3 of the isolated antibody or antigen binding fragment thereof that specifically binds AT corresponds to the amino acid sequences of SEQ ID NOs: 69, 70, 71, 1, 2 and 68.

50. The composition of any one of embodiments 38-49, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises a heavy chain variable domain having the amino acid sequence of SEQ ID NO: 57 and comprises the light chain variable domain having the amino acid sequence of SEQ ID NO: 58.

51. The composition of any one of embodiment 38-50, wherein the isolated antibody or antigen binding fragment thereof hat specifically binds AT, further comprises an Fc variant region.

52. The composition of embodiment 51, wherein the isolated antibody or antigen binding fragment thereof that specifically binds AT comprises SEQ ID NO: 130 and SEQ ID NO: 131.

53. The composition of any of embodiments 30 or 40-41, further comprising an isolated antibody or antigen binding fragment thereof that specifically binds to ClfA.

54. The composition of embodiment 53, wherein the isolated antibody or antigen binding fragment thereof that specifically binds ClfA is an antibody or antigen binding fragment thereof according to any one of embodiments 21-35.

55. A method of determining the presence of S. aureus in a test sample, comprising contacting the test sample with the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-15 or 21-34 and a detectable label.

56. The method of embodiment 55, comprising:

a. contacting the test sample with the antibody or antigen binding fragment thereof, wherein the antibody or antigen binding fragment thereof binds to an S. aureus surface determinant antigen, so as to form a first complex;

b. contacting the complex with the detectable label, wherein the detectable label binds to the antibody or antigen binding fragment thereof, or to the antigen, so as to form a second complex; and

c. detecting the presence of S. aureus in the test sample based on the signal generated by the detectable label in the second complex, wherein the presence of S. aureus is directly correlated with the signal generated by the detectable label.

57. The method of embodiment 55, comprising:

a. contacting the test sample with the antibody or antigen binding fragment thereof, wherein the antibody or antigen binding fragment thereof binds to an S. aureus surface determinant antigen, so as to form a first complex;

b. contacting the complex with the detectable label, wherein the detectable label competes with the antigen for binding to the antibody or antigen binding fragment thereof so as to form a second complex; and

c. detecting the presence of S. aureus in the test sample based on the signal generated by the detectable label in the second complex, wherein the presence of S. aureus is indirectly correlated with the signal generated by the detectable label.

58. The method of any of embodiments 55-57, wherein the sample is a patient sample and the method further comprises diagnosing a patient with an S. aureus infection.

59. The method of any one of embodiments 55-58, wherein the method is adapted for use in an automated system or a semi-automated system.

60. A method of determining the presence of S. aureus in a test sample, comprising contacting the test sample with the composition of embodiment 19 or 36 and at least one detectable label.

61. The method of embodiment 60, comprising:

a. contacting the test sample with the composition of embodiment 13, wherein the composition binds to an S. aureus surface determinant antigen and an S. aureus secreted toxin polypeptide;

b. contacting the test sample with the at least one detectable label, wherein the at least one detectable label binds to the surface determinant antigen, the secreted toxin, or an antibody or antigen binding fragment thereof that is bound to the surface determinant antigen or the secreted toxin; and

c. detecting the presence of S. aureus in the test sample based on the signal generated by the at least one detectable label, wherein the presence of S. aureus is directly correlated with the signal generated by the at least one detectable label.

62. The method of embodiment 60, comprising:

a. contacting the test sample with the composition of embodiment 13, wherein the composition binds to an S. aureus surface determinant antigen and an S. aureus secreted toxin polypeptide;

b. contacting the test sample with the at least one detectable label, wherein the at least one detectable label competes with the surface determinant antigen or the secreted toxin for binding to an antibody in the composition of embodiment 13; and

c. detecting the presence of S. aureus in the test sample based on the signal generated by the at least one detectable label, wherein the presence of S. aureus is indirectly correlated with the signal generated by the at least one detectable label.

63. The method of any one of embodiments 60-62, wherein the sample is a patient sample and the method further comprises diagnosing a patient with an S. aureus infection.

64. The method of any one of embodiments 60-63, wherein the method is adapted for use in an automated system or a semi-automated system.

65. A method of treating an S. aureus infection in a patient, comprising administering the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18 or 21-35, or the composition of any one of embodiments 19, 36 or 38-54, to a patient.

66. A method for preventing or reducing the severity of S. aureus-associated sepsis in a patient, comprising administering the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18 or 21-35, or the composition of any one of embodiments 19, 36 or 38-54, to a patient.

67. A method of delaying the onset of sepsis associated with S. aureus infection in a patient, comprising administering the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18 or 21-35, or the composition of any one of embodiments 19, 36 or 38-54, to a patient.

68. A method of preventing the onset of sepsis associated with S. aureus infection in a patient, comprising administering the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18 or 21-35, or the composition of any one of embodiments 19, 36 or 38-54, to a patient.

69. A method of reducing S. aureus bacterial load in the bloodstream or heart in a patient comprising administering to said patient an effective amount of an isolated anti-the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18.

70. A method of reducing S. aureus bacterial agglutination and/or thromboembolic lesion formation in a patient comprising administering to said patient an effective amount of an isolated anti-the isolated antibody or antigen binding fragment thereof of any one of embodiments 1-18.

71. The method of any of embodiments 65-70, further comprising administering an antibiotic to the patient.

72. The method of embodiment 69, wherein the antibiotic is penicillin, oxacillin, flucloxacillin, or vancomycin.

## Claims

1. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) ClfA surface determinant antigen,
wherein the isolated antibody or antigen binding fragment thereof comprises a heavy chain variable region (VH) and a light chain variable region VL [(VH)], each of which comprises three complementarity determining regions (CDR1, CDR2, and CDR3)
and wherein:
a. a VH CDR1 is identical to the amino acid sequence of SEQ ID NO: 133;
b. a VH CDR2 is identical to the amino acid sequence of SEQ ID NO: 134; and
c. a VH CDR3 is identical to the amino acid sequence of SEQ ID NO: 135; and
d. a VL CDR1 is identical to the amino acid sequence of SEQ ID NO: 137;
e. a VL CDR2 is identical to the amino acid sequence of SEQ ID NO: 138; and
f. a VL CDR3 is identical to the amino acid sequence of SEQ ID NO: 139.

2. An isolated antibody or antigen binding fragment thereof of claim 1, wherein the VH amino acid sequence is 100% identical to the amino acid sequence of SEQ ID NO: 132 and the VL amino acid sequence is 100% identical to the amino acid sequence of SEQ ID NO: 136.

3. A composition comprising the isolated antibody or antigen binding fragment thereof of claim 1, and a pharmaceutically acceptable excipient.

4. An isolated antibody or antigen binding fragment thereof that specifically binds to the Staphylococcus aureus (S. aureus) ClfA surface determinant antigen,
wherein the isolated antibody or antigen binding fragment thereof comprises a heavy chain variable region (VH) and a light chain variable region VL [(VH)], each of which comprises three complementarity determining regions (CDR1, CDR2, and CDR3)
and wherein:
a. a VH CDR1 is identical to the amino acid sequence of SEQ ID NO: 141;
b. a VH CDR2 is identical to the amino acid sequence of SEQ ID NO: 142; and
c. a VH CDR3 is identical to the amino acid sequence of SEQ ID NO: 143; and
d. a VL CDR1 is identical to the amino acid sequence of SEQ ID NO: 145;
e. a VL CDR2 is identical to the amino acid sequence of SEQ ID NO: 146; and
f. a VL CDR3 is identical to the amino acid sequence of SEQ ID NO: 147.

5. An isolated antibody or antigen binding fragment thereof of claim 4, wherein the VH amino acid sequence is identical to the amino acid sequence of SEQ ID NO: 140 and the VL amino acid sequence is identical to the amino acid sequence of SEQ ID NO: 144.

6. A composition comprising the isolated antibody or antigen binding fragment thereof of claim 4, and a pharmaceutically acceptable excipient.