WO2011112983A2 - Psrp is a protective antigen against pneumococcal infection - Google Patents

Abstract

Disclosed are method of inhibiting or preventing bacterial aggregation or biofilm formation that involve use of (a) an antibody or fragment thereof that binds to an epitope within an amino acid sequence selected from the group consisting of (i) an amino acid sequence that has at least 90% identity to SEQ ID NO: 1 (BR domain of PsrP), (ii) an amino acid sequence that has at least 90% identity to SEQ ID NO:2 (NR domain of SraP), and (iii) an amino acid sequence that has at least 90% identity to SEQ ID NO:3. These methods find particular application in the treatment or prevention of bacterial disease associated with bacterial aggregation, such as empyema and pneumococcal disease. Related kits, vaccines, and compositions are disclosed.

Description

DESCRIPTION

PsrP IS A PROTECTIVE ANTIGEN AGAINST PNEUMOCOCCAL INFECTION

The present application claims benefit of priority to U.S. Provisional application Serial No. 61/313,506 filed March 12, 2010, the entire contents of which are hereby incorporated by reference.

BACKGROUND OF THE INVENTION

This invention was made with government support under grant no. AI078972 awarded by the National Institutes of Health. The government has certain rights in the invention

Field of the Invention

The present invention relates generally to the fields of immunology, microbiology, and infectious diseases. More particularly, it concerns compositions and methods for treating infections associated with gram-positive biofilm formation.

Description of Related Art

Streptococcus pneumoniae is a leading cause of otitis media (OM), community- acquired pneumonia, sepsis and meningitis. Primarily a commensal, S. pneumoniae typically colonizes the nasopharynx asymptomatically, however in susceptible individuals such as infants, the elderly, persons who are immunocompromised, and those with sickle cell anemia, the pneumococcus is often able to cause opportunistic diseases (Pneumococcal Vaccines: WHO Position Paper, 1999; Lexau et al, 2005; Overturf and Powars, 1980; Wong et al, 1992). Worldwide, S. pneumoniae is responsible for up to 15 cases of invasive pneumococcal disease (IPD) per 100,000 persons per year and over 1.5 million deaths annually (Pneumococcal Vaccines: WHO Position Paper, 1999). In the elderly the mortality-rate associated with IPD can exceed 20% and for those in nursing homes may be as high as 40% (Torres et al, 1999). Thus, the pneumococcus has been and remains a major cause of morbidity and mortality worldwide.

psrP-secY2A2 is a S. pneumoniae pathogenicity island whose presence has been positively correlated with the ability to cause human disease (Embry et al, 2007; Obert et al, 2006). Analyses of the published S. pneumoniae genomes has demonstrated that psrP- secY2A2 is present and conserved in a number of globally distributed invasive clones, in particular those belonging to serotypes not covered by the current heptavalent conjugate vaccine (Lexau et al, 2005; Shivshanka et al., 2009; Beall et al., 2006). To date, numerous studies have shown that deletion of genes within psrP-secY2A2 attenuated the ability of S. pneumoniae to cause disease in mice. psrP-secY2A2 mutants were shown to be unable to attach to lung cells, establish lower respiratory tract infection, and were delayed in their ability to enter the bloodstream from the lungs. Importantly, the same studies found that psrP-secY2A2 did not play an important role during nasopharyngeal colonization or during sepsis following intraperitoneal challenge (Embry et al., 2007; Shivshankar et al., 2009; Hava and Camilli, 2002; Rose et al., 2008). Thus psrP-secY2A2 is currently understood to be a lung-specific virulence determinant.

In TIGR4, a virulent serotype 4 laboratory strain, psrP-sec Y2A2 is 37-kb in length and encodes 18 proteins. These include the Pneumococcal serine-rich repeat protein (PsrP), which is a lung cell adhesin, 9 putative glycosyltranferases, and 8 proteins homologous to components of an accessory Sec translocase (Tettelin et al., 2001). To date, the latter 17 genes remain uncharacterized; however, based on their homology to genes found within the Serine-rich repeat protein (SRRP) locus of Streptococcus gordonii, the encoded proteins are putatively responsible for the intracellular glycosylation of PsrP and for its transport to the bacterial surface (Obert et al, 2006; Takamatsu et al, 2005; Takamatsu et al, 2004a; Bensing et al, 2004; Takamatsu et al, 2004b). PsrP in TIGR4 is composed of 4,776 amino acids, has been confirmed to be glycosylated, and separates at a molecular weight of 2,300 kDa on an agarose gel (Shivshankar et al, 2009). It is the largest bacterial protein known. PsrP is organized into multiple domains including a cleavable N-terminal signal peptide, a small serine-rich repeat region (SRR1), a unique non-repeat region (NR), followed by a second extremely long serine-rich region (SRR2), and a C-terminal cell wall anchor domain containing an LPXTG motif (FIG. 1A). The SRRl and SRR2 domains of PsrP are composed of 8 and 539 serine-rich repeats (SRR) of the amino acid sequence SAS[A/E/V]SAS[T/I], respectively, and are the domains believed to be glycosylated (Obert et al, 2006; Shivshankar et al, 2009; Rose et al, 2008). The NR domain of PsrP has a predicted pi value of 9.9, for this reason it is called the Basic Region (BR) domain.

S. pneumoniae is surrounded by a polysaccharide capsule that protects the bacteria from phagocytosis but also inhibits adhesion to epithelial cells (Hammerschmidt et al, 2005). Based on the size and domain organization of PsrP, it was hypothesized that the extremely long SRR2 domain serves to extend the BR domain through the capsular polysaccharide to mediate lung cell adhesion (FIG. IB) (Shivshankar et al, 2009; Rose et al, 2008). Consistent with this model, it has been shown that PsrP is expressed on the bacterial surface, that the BR domain, in particular amino acids 273-341, was responsible for PsrP -mediated adhesion to Keratin 10 (K10) on lung cells, and that complementation of psrP deficient mutants with a truncated version of the protein (having only 33 SRRs in its SRR2 domain) restored the ability of uncapsulated but not capsulated PsrP mutants to adhere to A549 cells, a human type II pneumocyte cell line (Shivshankar et ah, 2009).

It is now recognized that biofilms play an important role during infectious diseases. Briefly, bacteria in biofilms are more resistant to host-defense mechanisms including phagocytosis and serve as a recalcitrant source of bacteria during antimicrobial therapy (Moscoso et ah, 2009; Hall-Stoodley and Stoodley, 2009). For S. pneumoniae, pneumococcal biofilms have been shown to occur in the middle ears of children with chronic otitis media and is thought to contribute to its refractory nature (Hall-Stoodley et ah, 2006). Likewise, biofilms have been detected in the nasopharynx of infected chinchillas (Reid et al., 2009). However, until now biofilm structures have not been described within the lungs during pneumococcal pneumonia. This is in contrast to other respiratory tract pathogens, such as Pseudomonas aeroginosa and Bordatella pertussis, for which in vivo biofilm production is now recognized to be an important pathogenic mechanism (Hall-Stoodley and Stoodley, 2009).

Given the role of biofilm production in infectious disease, there is the need to identify more effective treatment of infections associated with biofilm formation.

SUMMARY OF THE INVENTION

The present invention is in part based on the identification of particular domains of bacterial proteins that are responsible for bacterial aggregation and biofilm formation. For example, the inventor has identified the Basic Region (BR) domain of Pneumococcal serine- rich repeat protein (PsrP) to be responsible for bacterial aggregation in vivo and in vitro. This region mediates inter-bacterial adhesion during growth in vitro and in vivo. Targeting of these regions can be applied in the treatment and prevention of bacterial infection in subjects, particularly those infections associated with bacteria aggregation and biofilm formation, such as during parapneumonic empyema (PPE).

Certain aspects of the present invention generally concern methods of inhibiting or preventing bacterial aggregation or biofilm formation in a subject, involving administering to a subject that is known or suspected to have a bacterial infection a pharmaceutically effective amount of a composition that includes (a) a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO: l (the BR domain of PsrP), a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO:2 (the NR domain of SraP), and/or a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO:3 (the NR domain of GspB), and (b) a pharmaceutically acceptable carrier, wherein bacterial aggregation or biofilm formation is inhibited or prevented. The compound may be a small molecule, a peptide, a polypeptide, a protein, an antibody, an antibody fragment, a DNA, or an RNA.

More particular aspects of the present invention generally concern methods of inhibiting or preventing bacterial aggregation or biofilm formation in a subject, involving administering to a subject that is known or suspected to have a bacterial infection a pharmaceutically effective amount of a composition that includes: (a) an antibody or fragment thereof that binds to an epitope within an amino acid sequence selected from the group consisting of an amino acid sequence that has at least 90%> identity to SEQ ID NO: l, an amino acid sequence that has at least 90% identity to SEQ ID NO:2, and an amino acid sequence that has at least 90% identity to SEQ ID NO:3, and (b) a pharmaceutically acceptable carrier, wherein bacterial aggregation in the subject is inhibited or prevented. In some embodiments, the bacterial infection is a S. pneumoniae infection and the amino acid sequence has at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity or greater to the BR domain of PsrP. The BR domain of PsrP is SEQ ID NO: l, or amino acids 122-304 of full-length PsrP (full-length PsrP is SEQ ID NO:4). In a specific embodiment, the amino acid sequence comprises SEQ ID NO: l . In a more specific embodiment, the amino acid sequence consists of SEQ ID NO: l .

In further embodiments, the bacterial infection is a S. aureus infection and the amino acid sequence has at least 90%>, at least 91%>, at least 92%, at least 93%>, at least 94%>, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater identity to SEQ ID NO:2. In a specific embodiment, the amino acid sequence comprises SEQ ID NO:2. In a more specific embodiment, the amino acid sequence consists of SEQ ID NO:2.

In other embodiments, the bacterial infection is a S. gordonii infection and the amino acid sequence has at least 90%>, at least 91%>, at least 92%, at least 93%>, at least 94%>, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater identity to SEQ ID NO:3. In a specific embodiment, the amino acid sequence comprises SEQ ID NO:3. In a more specific embodiment, the amino acid sequence consists of SEQ ID NO:3. Other aspects of the present invention generally concern methods of inhibiting or preventing bacterial aggregation or biofilm formation on a surface, involving contacting the surface with a composition comprising (a) a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO: l, a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO:2, or a compound that binds to an amino acid sequence that has at least 90% identity to SEQ ID NO:3, and (b) a carrier, wherein bacterial aggregation or biofilm formation on the surface is inhibited or prevented. In particular aspects, the compound impairs function of the BR domain of PsrP, thus resulting in impaired aggregation and biofilm formation of gram positive bacteria such as Strep. pneumoniae.

The surface may be an organic surface (such as a body surface of a subject) or a nonorganic surface. Non-limiting examples of nonorganic surfaces include surfaces of medical devices and other medical equipment, floors, hospital equipment, catheters, stents, tubes, prosthetic valves, and the like.

As to administration to a subject, the subject may be known to have a bacterial infection, suspected to have a bacterial infection, or at risk of developing a bacterial infection. The bacterial infection may be a gram positive bacterial infection. In particular embodiments, the subject is known or suspected to have an empyema or a pleural effusion. In more particular embodiments, the subject is known or suspected to have a parapneumonic empyema. The subject may also be a subject that is known or suspected to have otitis media or infective endocarditis. The subject may also be a subject that is known or suspected to have pneumonia, such as pneumococcal pneumonia.

The subject may be any subject, such as a mammal or avian species. Non-limiting examples of mammals include mice, rats, rabbits, dogs, cats, pigs, cows, horses, goats, primates, and humans. In a specific embodiment, the subject is a human.

The composition may be administered using any method known to those of ordinary skill in the art. For example, the composition may be administered aerosol, by spray, intravenously, intradermally, intraarterially, intramuscularly, intrathecally, intratracheally, intrathoracically, intrapleurally, subcutaneously, orally, topically, or intraperitoneally.

In a specific embodiment, the subject is a human that is known or suspected to have parapneumonic empyema, and the subject is administered an antibody or antibody fragment that binds to the BR domain of PsrP. In a more particular embodiment, the human is age 16 or less, and has parapneumonic empyema. The present invention also contemplates methods of inhibiting or preventing contact between a first bacterium and a second bacterium, comprising contacting a first bacterium and/or a second bacterium with an effective amount of a composition that includes an antibody or fragment thereof that binds to an epitope within an amino acid sequence selected from the group consisting of: (i) an amino acid sequence that has at least 90% identity to SEQ ID NO: l; (ii) an amino acid sequence that has at least 90% identity to SEQ ID NO:2; and (iii) an amino acid sequence that has at least 90% identity to SEQ ID NO:3, wherein contact between the first bacterium and the second bacterium is inhibited or prevented following said contact. The bacterium may be Strep, pneumonia, Staph, aureus, or Step. gordonii.

In certain embodiments, the antibody or fragment thereof binds to an epitope that is an amino acid sequence that has at least 95%, 96%, 97%, 98%, or 99% or greater identity to SEQ ID NO: 1. In more particular embodiments, the antibody or fragment thereof binds to an epitope that is an amino acid sequence comprising SEQ ID NO: l or consisting of SEQ ID NO: l .

The present invention also concerns kits for treating or preventing empyema, pneumonia, otitis media, or infective endocarditis n a subject or any other condition associated with biofilm formation due to gram positive bacteria. The kit include, in one or more sealed vials a pharmaceutical composition that includes (a) an antibody or fragment thereof that binds an epitope within an amino acid sequence selected from the group consisting of (i) an amino acid sequence that has at least 90% identity to SEQ ID NO: l; (ii) an amino acid sequence that has at least 90% identity to SEQ ID NO:2; and (iii) an amino acid sequence that has at least 90% identity to SEQ ID NO:3, and (b) instructions for administering to a subject that is known or suspected to have an empyema (such as parapneumonic empyema), otitis media, or infective endocarditis the pharmaceutical composition. In a particular embodiment, the kit includes an antibody or fragment thereof binds to an epitope that has at least 95% identity to SEQ ID NO: l . In a more particular embodiment, the kit includes an antibody or fragment thereof binds to an epitope that has at least 99% identity to SEQ ID NO: l . The kit may optionally include one or more additional components, such as a syringe, thoracentesis syringe, vial, tube, or needle. In some embodiments, the composition further includes one or more therapeutic agents for the treatment or prevention of empyema, otitis media, or infective endocarditis in a subject. In specific embodiments, the instructions for use are in a computer-readable form. It is specifically contemplated that any limitation discussed with respect to one embodiment of the invention may apply to any other embodiment of the invention. Furthermore, any composition of the invention may be used in any method of the invention, and any method of the invention may be used to produce or to utilize any composition of the invention.

The use of the term "or" in the claims is used to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternative are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and "and/or."

Throughout this application, the term "about" is used to indicate that a value includes the standard deviation of error for the device and/or method being employed to determine the value.

As used herein the specification, "a" or "an" may mean one or more, unless clearly indicated otherwise. As used herein in the claim(s), when used in conjunction with the word "comprising," the words "a" or "an" may mean one or more than one. As used herein "another" may mean at least a second or more.

Other objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE FIGURES

The following figures form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1A, IB. Hypothetical model of PsrP on the surface of S. pneumoniae. A) Domain structure of PsrP: N-terminal signal peptide (S); serine-rich repeat motif 1 (SAS[A/E/V]SAST X 11) (SRR1); basic region (BR); serine-rich repeat motif 2 (SRR2); and the cell wall anchoring domain (CWAD) at the C-terminus. B) Illustration of PsrP on the bacterial surface. Based on the structural organization of PsrP and studies demonstrating that the BR domain binds to K10 on lung cells (Shivshankar et al., 2009), the CWAD attaches the protein to the cell wall, while the long glycosylated SRR2 domain serves to extend BR through the capsular polysaccharide to mediate interactions.

FIG. 2A, 2B, 2C. PsrP promotes the formation of large bacterial aggregates in vivo.

A) Micrographs of TIGR4 (WT) and T4 ApsrP (ApsrP) Gram-stained bacteria from either BAL or nasal lavage (IN) elutes. Images were taken at 400^x magnification. Images are not representative of the total bacteria population, but instead are shown to demonstrate the typical pneumococcal aggregate containing at least 10 or more individual diplococci (10+).

B) Actual percentages of pneumococcal aggregate based on size in the nasopharynx and C) lungs following counting of > 100 randomly selected CFUs per biological replicate. Note that TIGR4 had significantly greater levels of 2-9 and 10+ aggregates compared to T4 ApsrP. Furthermore, while 10+ aggregates were observed in mice infected with T4 ApsrP, albeit infrequently, the largest of these aggregates were not comparable in size to those formed by TIGR4. Statistical analyses were performed using a Student's t-test.

FIG. 3A, 3B, 3C. Deletion of psrP alters bacterial interactions in mature biofilms but not during early bio film attachment. A) Attachment of TIGR4 (WT) and T4 ApsrP (ApsrP) to the bottom of 96-well polystyrene microtiter plate wells over a 24 hour period. Early biofilms were produced by inoculation of THB in the wells with mid-logarithmic phase bacteria and incubation of the plates at 37° C in 5% C0₂. Biomass of early biofilms was measured by staining with crystal violet (CV), washing the bacteria with water, solubilization of CV with ethanol, and measurement of the supernatant optical density (CV₅₄₀). Assays were performed in triplicate with group averages with standard deviation shown. B) Micrographs of mature TIGR4 and T4 ApsrP biofilms. Bacteria were grown in THB at 37° C in 5% C0₂ on glass slides within a flow cell under once-through flow conditions for 3 days. For visualization, bacteria were stained with Live/Dead BacLight stain. Biofilms were viewed at 400^x magnification using an inverted confocal laser scanning microscope. C) Quantitative analysis of biofilms was performed using COMSTAT image analysis software. Flow cell experiments were performed in triplicate. Statistical analyses were performed using a two-tailed Student's t-test. For panel C error bars denote standard error.

FIG. 4A, 4B, 4C, 4D. PsrP promotes bacterial aggregation in a line biofilm model. Mid- logarithmic growth phase TIGR4 (WT) and T4 ApsrP (ApsrP) were used to inoculate 1 meter of a 0.8 mm diameter silicone-lined plastic tubing. Biofilms were grown in THB at 37°C in 5% C0₂ under once-through conditions. After 3 days biofilms within the lines were extruded, suspended in a total volume of 1 ml PBS, and visual and quantitative analyses performed. A) Representative photograph of the exudate suspension immediately following its collection. B) Optical density (OD₅₄₀) of bacterial exudates. C). Microscopic images of CV stained bacteria extracted from the lines. Note the formation of aggregates by TIGR4 but not T4 ApsrP. D) Levels of protein in bacteria line exudates as determined by bicinchoninic acid assay (BCA) following detergent lysis of the bacteria. Images are representative of at least 3 experiments. Statistical analyses were performed using a two-tailed Student's t-test. Error bars denote standard error.

FIG. 5A, 5B, 5C, 5D. The BR domain of PsrP mediates inter-bacterial interactions. Encapsulated and unencapsulated mutants of TIGR4, lacking PsrP (T4 QpsrP, T4R QpsrP, respectively), were complemented with plasmids expressing: a truncated version of PsrP having only 33 SRR2 repeats (PsrP (33)), the truncated version of PsrP missing the BR domain (PsrP(33)__BR), or with the empty expression vector (pNEl). These bacteria were used to inoculate silicone coated tubing and form biofilms in lines under previously described conditions. After 3 days biofilms were extruded and analyzed. A) Microscopic images of CV stained bacteria from each of the biofilm lines. B) Optical density (OD₅₄₀) of biofilm line exudates. C) Biomass of the biofilms as determined by protein levels using the BCA assay. For panels B and C images are representative of at least 3 independent experiments. Statistical analyses were performed using 1-Way ANOVA analysis. Error bars denote standard error. Asterisks denote statistical significance versus WT. Number sign denotes statistical significance versus the empty vector control. D) Far Western analyses of recombinant BR interactions with truncated versions of PsrP expressed in S. pneumoniae. Whole cell lysates from S. pneumoniae strains expressing PsrP or truncated versions of PsrP were blotted onto nitrocellulose and blocked. Membranes were incubated with GST tagged- BR (lug/mL) overnight at 4°C. The next day, following washing of the membrane, protein interactions were detected by immunoblotting with monoclonal antibodies specific for the GST tag HRP conjugated goat anti-mouse antibody.

FIG. 6A, 6B. Recombinant BR interacts only with pneumococci that carry amino acids 122-304 of PsrP. A) The designated recombinant PsrP constructs were expressed and purified from E. coli as described in Example 1. B) Micrographs of FITC-labeled bacteria following their incubation with CY3 -labeled recombinant BR or the designated truncated versions. Note that only CY3 -labeled BR and BR. A bound to TIGR4. Moreover, neither bound to T4 ApsrP. This suggests that recombinant BR binds to PsrP on the bacteria surface. FIG. 7 A, 7B, 7C. Amino acids 122-304 of the BR domain mediate aggregation. A) Separation of recombinant BR under 12% SDS-PAGE and non-denaturing 10% glycine gel conditions. Detection of proteins was done by Coomassie Brilliant Blue staining. B) Far Western analyses using GST-tagged recombinant BR. Truncated versions of His-tagged rBR expressed and purified from E. coli were spotted on nitrocellulose membranes and probed with recombinant Gst-tagged rBR. C) Co-immunoprecipitation of Gst-tagged rBR (65 kDa) from spiked bacterial cell lysates of E.coli expressing His-tagged rBR constructs using beads conjugated to monoclonal antibodies specific for the His tag.

FIG. 8 A, 8B, 8C. Antibodies to the BR domain but not the serine-rich motif block inter-bacterial interactions. THB was supplemented with either a 1 : 1000 dilution of naive rabbit serum (control), rabbit antiserum from rabbits immunized with a SASASASTSASASAST peptide (SEQ ID NO:7) designed after the SRR motif, or rabbit antiserum to recombinant BR. TIGR4 biofilms were grown with these media in the line model at 37°C in 5% C0₂, under once through conditions for 3 days. Following incubation, bacteria within the lines were extruded and analyzed. A) Micrographs of CV stained bacteria extruded from the biofilm lines. B) Optical density (OD₅₄₀) of bacterial exudates. C) Levels of protein in bacterial line exudates as determined by BCA analysis. Images are representative of at least 3 independent experiments. Statistical analyses were performed using a two-tailed Student's t-test. Number sign denotes statistical significance versus whole serum. Asterisks denote statistical significance versus anti-SRR serum. Error bars denote standard error.

FIG. 9A, 9B, 9C, 9D. The SRRPs of S. gordonii and S. aureus promote bacterial aggregation. Light microscopic images of CV stained A) S. gordonii M99 and B) S. aureus ISP479C and their respective isogenic SRRP mutants following 24 hours of growth in a 96- well polystyrene microtiter biofilm model. Early biofilms were produced by inoculation media with mid logarithmic phase bacteria and incubation at 37°C in 5% C0₂. B) Average biomass of early biofilms in the microtiter wells as determined by CV₅₄₀ analyses. Error bars denote standard deviation. C) Microscopic images of bacteria extruded from the biofilm lines after 3 days for S. gordonii and 1 day for S. aureus. Bacteria were stained with CV for visualization. D) Measurement of optical density (OD₆₂o) of bacterial exudates collected from the biofilm lines. Error bars denote standard deviation. E) Far-western analysis using GST- tagged recombinant proteins corresponding to the NR domains of S. gordonii and S. aureus. Whole cell lysates from S. gordonii, S. aureus, and their respective isogenic SRRP mutants were spotted onto nitrocellulose membranes and probed with recombinant GST-tagged proteins. Images are representative of three individual experiments. For panels B) and D) statistical analyses were performed using a Student's t-test.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

The present invention is based on the finding of particular bacterial protein domains that function to mediate inter-bacterial (species-specific) adhesion during growth in vitro and in vivo. For example, the inventors have found that the Basic Region (BR) domain of Pneumococcal serine-rich repeat protein (PsrP) mediates interbacterial adhesion during growth in vitro and in vivo. The presence of PsrP was also positively correlated with clinical isolates that caused bio film-related manifestations, including pediatric parapneumonic empyema (PPE), a disease characterized by pus and bacterial aggregates in the pleural cavity. It was found that antibodies against PsrP block bacterial aggregation and can protect against infection with S. pneumoniae. Biofilm-related diseases are on the rise due to mutations of bacteria, such as mutations of the pneumococcal strains that the available pneumococcal vaccine targets. Targeting of these proteins, such as with antibodies, can be applied in treating and preventing infections, particularly those where biofilm formation is involved in the pathogenesis.

A. PsrP, GspB, and SraP

1. PsrP Polypeptides

The full-length amino acid sequence of PsrP is designated SEQ ID NO:4. The full- length amino acid sequence of SraP is SEQ ID NO:5. The full-length amino acid sequence of GspB is SEQ ID NO:6.

Some embodiments of the compositions and methods set forth herein concern polypeptides that are equivalent of the foregoing full-length polypeptides set forth above. It is well understood by the skilled artisan that there is a limit to the number of changes that may be made within a defined portion of the molecule and still result in a molecule with an acceptable level of equivalent biological activity. "Polypeptide equivalent" is thus defined herein as any polypeptide in which some, or most, of the amino acids may be substituted so long as the polypeptide retains substantially similar activity in the context of the uses set forth herein. In some embodiments, the polypeptide may include an amino acid segment that has a certain percent identity to a consecutive series of polypeptides of SEQ ID NO:4, 5, or 6. Identical" or "identity" as used herein in the context of two or more nucleic acids or polypeptide sequences, may mean that the sequences have a specified percentage of residues that are the same over a specified region. The percentage may be calculated by optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity. In cases where the two sequences are of different lengths or the alignment produces one or more staggered ends and the specified region of comparison includes only a single sequence, the residues of single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and R A, thymine (T) and uracil (U) may be considered equivalent. Identity may be performed manually or by using a computer sequence algorithm such as BLAST or BLAST 2.0.

For example, the amino acid segment may have at least 50% sequence identity, at least 55% sequence identity, at least 60%> sequence identity, at least 65 % sequence identity, at least 70%) sequence identity, and least 75% sequence identity, at lest 80%> sequence identity, at least 85% sequence identity, at least 90%> sequence identity, at least 95% sequence identity, at least 96% sequence identity, at least 97% sequence identity, at least 98% sequence identity, or at least 99% sequence identity to an amino acid sequence.

Of course, a plurality of distinct proteins/polypeptides/peptides with different substitutions may easily be made and used in accordance with the invention. Additionally, in the context of the invention, an equivalent can be a homolog or ortholog polypeptide from any species or organism, including, but not limited to, a human polypeptide. One of ordinary skill in the art will understand that many equivalents would likely exist and can be identified using commonly available techniques.

The present invention may utilize polypeptides purified from a natural source or from recombinantly-produced material. Those of ordinary skill in the art would know how to produce these polypeptides from recombinantly-produced material. This material may use the 20 common amino acids in naturally synthesized proteins, or one or more modified or unusual amino acids. Generally, "purified" will refer to a composition that has been subjected to fractionation to remove various other proteins, polypeptides, or peptides, and which composition substantially retains its activity. Purification may be substantial, in which the polypeptide is the predominant species, or to homogeneity, which purification level would permit accurate degradative sequencing.

Amino acid sequence mutants also are encompassed by the present invention, and are included within the definition of "polypeptide equivalent." Amino acid sequence mutants of the polypeptide can be substitutional mutants or insertional mutants. Insertional mutants typically involve the addition of material at a non-terminal point in the peptide. This may include the insertion of a few residues; an immunoreactive epitope; or simply a single residue. The added material may be modified, such as by methylation, acetylation, and the like. Alternatively, additional residues may be added to the N-terminal or C-terminal ends of the peptide.

Amino acid substitutions are generally based on the relative similarity of the amino acid side-chain substituents, or example, their hydrophobicity, hydrophilicity, charge, size, and the like. An analysis of the size, shape and type of the amino acid side-chain substituents reveals that arginine, lysine and histidine are all positively charged residues; that alanine, glycine and serine are all a similar size; and that phenylalanine, tryptophan and tyrosine all have a generally similar shape. Therefore, based upon these considerations, arginine, lysine and histidine; alanine, glycine and serine; and phenylalanine, tryptophan and tyrosine; are defined herein as biologically functional equivalents.

Amino acid substitutions are generally based on the relative similarity of the amino acid side-chain substituents, or example, their hydrophobicity, hydrophilicity, charge, size, and the like. An analysis of the size, shape and type of the amino acid side-chain substituents reveals that arginine, lysine and histidine are all positively charged residues; that alanine, glycine and serine are all a similar size; and that phenylalanine, tryptophan and tyrosine all have a generally similar shape. Therefore, based upon these considerations, arginine, lysine and histidine; alanine, glycine and serine; and phenylalanine, tryptophan and tyrosine; are defined herein as biologically functional equivalents.

In making changes, the hydropathic index of amino acids may be considered. Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics, these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (- 0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5). The importance of the hydropathic amino acid index in conferring interactive biological function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporated by reference herein). It is known that certain amino acids may be substituted for other amino acids having a similar hydropathic index or score and still retain a similar biological activity. In making changes based upon the hydropathic index, the substitution of amino acids whose hydropathic indices are within + 2 is preferred, those which are within +1 are particularly preferred, and those within + 0.5 are even more particularly preferred.

It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent protein. As detailed in U.S. Patent 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 1); glutamate (+3.0 + 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 + 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); tryptophan (-3.4).

In making changes based upon similar hydrophilicity values, the substitution of amino acids whose hydrophilicity values are within + 2 is preferred, those which are within + 1 are particularly preferred, and those within + 0.5 are even more particularly preferred.

B. Antigens and Vaccines

Certain embodiments of the present invention involves the use of polypeptides disclosed herein to "immunize" subjects or as "vaccines". As used herein, "immunization" or "vaccination" means increasing or activating an immune response against an antigen. It does not require elimination or eradication of a condition but rather contemplates the clinically favorable enhancement of an immune response toward an antigen. The vaccine may be a prophylactic vaccine or a therapeutic vaccine. A prophylactic vaccine comprises one or more epitopes associated with a disorder for which the individual may be at risk. The epitope may be an epitope within SEQ ID NO: l, SEQ ID NO:2, or SEQ ID NO:3. Therapeutic vaccines comprise one or more epitopes associated with a particular disorder affecting the individual, such as tumor associated antigens in cancer patients.

As used herein, "vaccine" means an organism or material that contains an antigen in an innocuous form. The vaccine is designed to trigger an immunoprotective response. The vaccine may be recombinant or non-recombinant. When inoculated into a non-immune host, the vaccine will provoke active immunity to the organism or material, but will not cause disease. Vaccines may take the form, for example, of a toxoid, which is defined as a toxin that has been detoxified but that still retains its major immunogenic determinants; or a killed organism, such as typhoid, cholera and poliomyelitis; or attenuated organisms, that are the live, but non-virulent, forms of pathogens, or it may be antigen encoded by such organism, or it may be a live tumor cell or an antigen present on a tumor cell.

"Epitope" refers to an antigenic determinant of a peptide, polypeptide, or protein; an epitope comprises three or more amino acids in a spatial conformation unique to the epitope. Generally, an epitope consists of at least 5 such amino acids and more usually consists of at least 8 to 10 amino acids. Methods of determining spatial conformation of amino acids are known in the art and include, for example, x-ray crystallography and 2-dimensional nuclear magnetic resonance. Antibodies that recognize the same epitope can be identified in a simple immunoassay showing the ability of one antibody to block the binding of another antibody to a target antigen.

Certain embodiments of the present invention pertain to methods of inducing an immune response to an antigen in a subject. The term "antigen" means a substance that is recognized and bound specifically by an antibody or by a T cell antigen receptor. Antigens can include peptides, proteins, glycoproteins, polysaccharides, complex carbohydrates, sugars, gangliosides, lipids and phospholipids; portions thereof and combinations thereof. The antigens can be those found in nature or can be synthetic. Preferably, antigens elicit an antibody response specific for the antigen. Haptens are included within the scope of "antigen." A hapten is a low molecular weight compound that is not immunogenic by itself but is rendered immunogenic when conjugated with an immunogenic molecule containing antigenic determinants. Small molecules may need to be haptenized in order to be rendered antigenic. Preferably, antigens of the present invention include peptides and polypeptides. In this regard, the immunogenic polypeptides set forth herein include an antigen polypeptide.

An antigen polypeptide is an amino acid sequence that under appropriate conditions results in an immune response in a subject. The immune response may be a an antibody response. For example, the antibody response can be measured as an increase in antibody production, as measured by any number of techniques well-known to those of ordinary skill in the art (e.g., ELISA). The immune response may also be a T cell response, such as increased antigen presentation to T cells, or increased proliferation of T cells.

In some embodiments, the antigen polypeptide is administered with the intent of inducing an immune response. Depending on the intended mode of administration, the compounds of the present invention can be in various pharmaceutical compositions. The compositions will include a unit dose of the selected polypeptide in combination with a pharmaceutically acceptable carrier and, in addition, can include other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, and excipients. "Pharmaceutically acceptable" means a material that is not biologically or otherwise undesirable, i.e., the material can be administered to an individual along with the fusion protein or other composition without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.

Preparation of vaccines and immunizing agents is generally well understood in the art, as exemplified by U.S. Pat. Nos. 4,608,251; 4,601,903; 4,599,231; 4,599,230; 4,596,792; and 4,578,770, all incorporated herein by reference. Typically, such vaccines are prepared as injectables either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants which enhance the effectiveness of the vaccines.

Examples of physiologically acceptable carriers include saline solutions such as normal saline, Ringer's solution, PBS (phosphate-buffered saline), and generally mixtures of various salts including potassium and phosphate salts with or without sugar additives such as glucose. The active immunogenic ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like, and combinations thereof. Nontoxic auxiliary substances, such as wetting agents, buffers, or emulsifiers may also be added to the composition. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. In one embodiment of the invention, adjuvants are not required for immunization.

Parenteral administration, if used, is generally characterized by injection. Sterile injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions.

The vaccine compositions set forth herein may comprise an adjuvant and/or a carrier.

Adjuvants are any substance whose admixture into the vaccine composition increases or otherwise modifies the immune response to an antigen.

Adjuvants could for example be selected from the group consisting of: A1K(S0₄)2, AlNa(S0₄)₂, A1NH(S0₄)₄, silica, alum, AI(OH)₃, Ca (P0₄)₂, kaolin, carbon, aluminum hydroxide, muramyl dipeptides, N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-DMP), N-acetyl-nornuramyl-L-alanyl-D-isoglutamine (CGP 11687, also referred to as nor-MDP), N- acetylmuramyul-L-alanyl-D-isoglutaminyl-L-alanine-2-( 2^,-dipalmitoyl-s- n-glycero-3- hydroxphosphoryloxy)-ethylamine (CGP 19835 A, also referred to as MTP-PE), RIBI (MPL+TDM+CWS) in a 2% squalene/Tween-80.RTM. emulsion, lipopolysaccharides and its various derivatives, including lipid A, Freund's Complete Adjuvant (FCA), Freund's Incomplete Adjuvants, Merck Adjuvant 65, polynucleotides (for example, poly IC and poly AU acids), wax D from Mycobacterium, tuberculosis, substances found in Corynebacterium parvum, Bordetella pertussis, and members of the genus Brucella, liposomes or other lipid emulsions, Titermax, ISCOMS, Quil A, ALUN (see U.S. Pat. No 5,554,372), Lipid A derivatives, choleratoxin derivatives, HSP derivatives, LPS derivatives, synthetic peptide matrixes or GMDP, Interleukin 1, Interleukin 2, Montanide ISA-51 and QS-21.

Other agents which stimulate the immune response can also be administered to the subject. For example, other cytokines are also useful in vaccination protocols as a result of their lymphocyte regulatory properties. Many other cytokines useful for such purposes will be known to one of ordinary skill in the art, including interleukin-12 (IL-12) which has been shown to enhance the protective effects of vaccines, GM-CSF and IL-18. Thus cytokines can be administered in conjunction with antigens and adjuvants to increase the immune response to the antigens.

A vaccine composition according to the present invention may comprise more than one different adjuvant. Furthermore, the invention encompasses a therapeutic composition further comprising any adjuvant substance including any of the above or combinations thereof. It is also contemplated that ML-IAP, or one or more fragments thereof, and the adjuvant can be administered separately in any appropriate sequence.

In certain embodiments, the vaccine composition includes a carrier. The carrier may be any suitable carrier known to the person skilled in the art, for example a protein or an antigen presenting cell. Examples include serum proteins such as transferrin, bovine serum albumin, human serum albumin, thyroglobulin or ovalbumin, immunoglobulins, or hormones, such as insulin or palmitic acid. For immunization of humans, the carrier must be a physiologically acceptable carrier acceptable to humans and safe. However, tetanus toxoid and/or diptheria toxoid are suitable carriers in one embodiment of the invention. Alternatively, the carrier may be dextrans for example sepharose.

The timing of administration of the vaccine and the number of doses required for immunization can be determined from standard vaccine administration protocols. Typically a vaccine composition will be administered in two doses. The first dose will be administered at the elected date and a second dose will follow at one month from the first dose. A third dose may be administered if necessary, and desired time intervals for delivery of multiple doses of a particular antigen containing HCH2 polymer can be determined by one of ordinary skill in the art employing no more than routine experimentation. The antigen containing HCH2 polymer may be given as a single dose.

For each recipient, the total vaccine amount necessary can be deduced from protocols for immunization with other vaccines. The exact amount of antigen-HCH2 polymer required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the particular fusion protein used, its mode of administration, and the like. Generally, dosage will approximate that which is typical for the administration of other vaccines, and will preferably be in the range of about 10 ng/kg to 1 mg/kg.

Methods for the preparation of mixtures or emulsions of polypeptides disclosed herein and adjuvant are well known to those of skill in the art of vaccination (see, e.g. Plotkin and Orenstein, 2004).

Immunizations against toxins and viral infection can be tested using in vitro assays and standard animal models. For example a mouse can be immunized with a viral antigen polypeptide expressed as a fusion protein with HCH2 polymers and delivered by the methods detailed herein. After the appropriate period of time to allow immunity to develop against the antigen, for example two weeks, a blood sample is tested to determine the level of antibodies, termed the antibody titer, using ELISA. In some instances the mouse is immunized and, after the appropriate period of time, challenged with the virus to determine if protective immunity against the virus has been achieved. Using these techniques the proper combination of antigen, adjuvant, and other vaccine components can be optimized to boost the immune response. Testing in humans can be contemplated after efficacy is demonstrated in animal models. Methods for immunization, including formulation of a vaccine composition and selection of doses, route of administration and the schedule of administration (e.g. primary and one or more booster doses), are well known in the art (e.g. see Vaccines: From concept to clinic, 1999).

Generally accepted animal models can be used for testing of immunization against cancer using a tumor and cancer antigen polypeptides. For example, cancer cells (human or murine) can be introduced into a mouse to create a tumor, and one or more cancer associated antigens can be delivered by the methods described herein. The effect on the cancer cells (e.g., reduction of tumor size) can be assessed as a measure of the effectiveness of the immunization. Of course, immunization can include one or more adjuvants and/or cytokines to boost the immune response. The tests also can be performed in humans, where the end point is to test for the presence of enhanced levels of circulating cytotoxic T lymphocytes against cells bearing the antigen, to test for levels of circulating antibodies against the antigen, to test for the presence of cells expressing the antigen and so forth.

In some embodiments, the vaccine composition includes antigen presenting cells. The antigen presenting cell can be a dendritic cells (DC). DC may be cultivated ex vivo or derived in culture from peripheral blood progenitor cells (PBPC) and peripheral blood stem cells (PBSC). The dendritic cells may be prepared and used in therapeutic procedures according to any suitable protocol known to those of ordinary skill in the art. It will be appreciated by the person skilled in the art that the protocol may be adopted to use with patients with different HLA types and different diseases. Incubation of cultured dendritic cells with HCH2 polymers of the invention is envisaged as a means of loading dendritic cells with antigen for subsequent transfer into hosts.

For any of the ex vivo methods of the invention, peripheral blood progenitor cells

(PBPC) and peripheral blood stem cells (PBSC) are collected using apheresis procedures known in the art. Briefly, PBPC and PBSC are collected using conventional devices, for example, a Haemonetics.RTM. Model V50 apheresis device (Haemonetics, Braintree, Mass.). Four-hour collections are performed typically no more than five times weekly until, for example, approximately 6.5. times.10. sup.8 mononuclear cells (MNC)/kg patient are collected. The cells are suspended in standard media and then centrifuged to remove red blood cells and neutrophils. Cells located at the interface between the two phases (also known in the art as the buffy coat) are withdrawn and resuspended in HBSS. The suspended cells are predominantly mononuclear and a substantial portion of the cell mixture are early stem cells. The stem cells obtained in this manner can be frozen, then stored in the vapor phase of liquid nitrogen. Ten percent dimethylsulfoxide can be used as a cryoprotectant. After all collections from the donor have been made, the stem cells are thawed and pooled. Aliquots containing stem cells, growth medium, such as McCoy's 5A medium, 0.3% agar, and expansion factors (e.g. GM-CSF, IL-3, IL-4, flt3-ligand), are cultured and expanded at 37 degrees Celsius in 5% C0₂ in fully humidified air for 14 days.

C. Immunological Reagents

As used herein, the term "antibody" is intended to refer broadly to any immunologic binding agent such as IgG, IgM, IgA, IgD and IgE. Generally, IgG and/or IgM are preferred because they are the most common antibodies in the physiological situation and because they are most easily made in a laboratory setting.

The term "antibody fragment" is used to refer to any antibody-like molecule that does not fall within the definition of antibody but which includes an antigen-binding domain. Examples include Fab', Fab, F(ab')₂, single domain antibodies (DABs), Fv, scFv (single chain Fv), and the like. The techniques for preparing and using various antibody-based constructs and fragments are well known in the art. Means for preparing and characterizing antibodies are also well known in the art (See, e.g., Harlow and Lane, 1988; incorporated herein by reference).

Monoclonal antibodies (MAbs) are recognized to have certain advantages, e.g., reproducibility and large-scale production, and their use is generally preferred. The invention thus provides monoclonal antibodies of the human, murine, monkey, rat, hamster, rabbit and even chicken origin. Due to the ease of preparation and ready availability of reagents, murine monoclonal antibodies will often be preferred.

However, "humanized" antibodies are also contemplated, as are chimeric antibodies from mouse, rat, or other species, bearing human constant and/or variable region domains, bispecific antibodies, recombinant and engineered antibodies and fragments thereof. Methods for the development of antibodies that are "custom-tailored" to the patient's dental disease are likewise known and such custom-tailored antibodies are also contemplated.

MAbs may be readily prepared through use of well-known techniques, such as those exemplified in U.S. Patent 4,196,265, incorporated herein by reference. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified protein, polypeptide, peptide or domain, be it a wild-type or mutant composition. The immunizing composition is administered in a manner effective to stimulate antibody producing cells.

D. Pharmaceutical Preparations

Pharmaceutical preparations of antibodies and/or antibody fragments or polypeptides for administration to a subject are contemplated by the present invention.

1. Formulations Any type of pharmaceutical preparation is contemplated by the current invention.

One of skill in art would be familiar with the wide range of types of pharmaceutical preparations that are available, and would be familiar with skills needed to generate these pharmaceutical preparations.

In certain embodiments of the present invention, the pharmaceutical preparation will be an aqueous composition. Aqueous compositions of the present invention comprise an effective amount an antibody or fragment thereof, and the like, dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium. Aqueous compositions of gene therapy vectors expressing any of the foregoing are also contemplated. The phrases "pharmaceutical preparation suitable for delivery" or "pharmacologically effective" of "pharmaceutically acceptable" refer to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate.

As used herein, "pharmaceutical preparation" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions. For human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologies standards.

The biological material should be extensively dialyzed to remove undesired small molecular weight molecules and/or lyophilized for more ready formulation into a desired vehicle, where appropriate. The active compounds will then generally be formulated for administration by any known route, such as parenteral administration. The preparation of an aqueous composition containing an active agent of the invention disclosed herein as a component or active ingredient will be known to those of skill in the art in light of the present disclosure.

An agent or substance of the present invention can be formulated into a composition in a neutral or salt form. Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. A person of ordinary skill in the art would be familiar with techniques for generation of salt forms. The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.

The present invention contemplates therapeutic agents that will be in pharmaceutical preparations that are sterile solutions for intravascular injection or for application by any other route. A person of ordinary skill in the art would be familiar with techniques for generating sterile solutions for injection or application by any other route. Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients familiar to a person of skill in the art.

Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, but drug release capsules and the like can also be employed.

For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure.

The active agents disclosed herein may be formulated within a therapeutic mixture to comprise about 0.0001 to 1.0 milligrams, or about 0.001 to 0.1 milligrams, or about 0.1 to 1.0 or even about 10 milligrams per dose or so. Multiple doses can also be administered.

In addition to the compounds formulated for parenteral administration, such as intravenous or intramuscular injection, other pharmaceutically acceptable forms include, e.g., tablets or other solids for oral administration; liposomal formulations; time release capsules; and any other form currently used, including cremes. One may also use nasal solutions or sprays, aerosols or inhalants in the present invention.

Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders. A person of ordinary skill in the art would be familiar with well-known techniques for preparation of oral formulations. Such compositions and preparations should contain at least 0.1% of active compound. The percentage of the compositions and preparations may, of course, be varied and may conveniently be between about 2 to about 75% of the weight of the unit, or preferably between 25-60%. The amount of active compounds in such therapeutically useful compositions is such that a suitable dosage will be obtained.

The use of liposomes and/or nanoparticles is also contemplated for the introduction of the modulator of cell death or gene therapy vectors into host cells. The formation and use of liposomes is generally known to those of skill in the art.

Administration of the pharmaceutical compositions of the present invention may be by any method known to those of ordinary skill in the art. For example, administration may be topical, local, regional, systemic, by aerosol, by spray, intravenous, intradermal, intraarterial, intramuscular, intrathecal, intratracheal, subcutaneous, or intraperitoneal. Oral compositions are also contemplated by the present invention.

2. Dosage

An effective amount of the therapeutic or preventive agent is determined based on the intended goal, for example treatment or prevention of a bacterial infection in a subject. The quantity to be administered, both according to number of treatments and dose, depends on the subject to be treated, the state of the subject and the protection desired. Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual.

For example, a dose of the therapeutic agent may be about 0.0001 milligrams to about 1.0 milligrams, or about 0.001 milligrams to about 0.1 milligrams, or about 0.1 milligrams to about 1.0 milligrams, or even about 10 milligrams per dose or so. Multiple doses can also be administered. In some embodiments, a dose is at least about 0.0001 milligrams. In further embodiments, a dose is at least about 0.001 milligrams. In still further embodiments, a dose is at least 0.01 milligrams. In still further embodiments, a dose is at least about 0.1 milligrams. In more particular embodiments, a dose may be at least 1.0 milligrams. In even more particular embodiments, a dose may be at least 10 milligrams. In further embodiments, a dose is at least 100 milligrams or higher.

In other non-limiting examples, a dose may also comprise from about 1 microgram/kg/body weight, about 5 microgram/kg/body weight, about 10 microgram/kg/body weight, about 50 microgram/kg/body weight, about 100 microgram/kg/body weight, about 200 microgram/kg/body weight, about 350 microgram/kg/body weight, about 500 microgram/kg/body weight, about 1 milligram/kg/body weight, about 5 milligram/kg/body weight, about 10 milligram/kg/body weight, about 50 milligram/kg/body weight, about 100 milligram/kg/body weight, about 200 milligram/kg/body weight, about 350 milligram/kg/body weight, about 500 milligram/kg/body weight, to about 1000 mg/kg/body weight or more per administration, and any range derivable therein. In non-limiting examples of a derivable range from the numbers listed herein, a range of about 5 mg/kg/body weight to about 100 mg/kg/body weight, about 5 microgram/kg/body weight to about 500 milligram/kg/body weight, etc., can be administered, based on the numbers described above.

The dose can be repeated as needed as determined by those of ordinary skill in the art. Thus, in some embodiments of the methods set forth herein, a single dose is contemplated. In other embodiments, two or more doses are contemplated. Where more than one dose is administered to a subject, the time interval between doses can be any time interval as determined by those of ordinary skill in the art. For example, the time interval between doses may be about 1 hour to about 2 hours, about 2 hours to about 6 hours, about 6 hours to about 10 hours, about 10 hours to about 24 hours, about 1 day to about 2 days, about 1 week to about 2 weeks, or longer, or any time interval derivable within any of these recited ranges. 3. Secondary Treatment

Certain embodiments of the claimed invention provide for a method of treating or preventing an infection in a subject. Some of the methods set forth herein involve administering to the subject one or more secondary forms of therapy directed to the treatment or prevention of a bacterial infection. Examples of such therapies include other therapies directed to prevention or treatment of a bacterial infection such as Streptococcus pneumoniae, such as with antibiotics. Any such therapy known to those of ordinary skill in the art is contemplated as a secondary form of therapy.

E. Treatment and Prevention of Disease

"Treatment" and "treating" as used herein refer to administration or application of a therapeutic agent to a subject or performance of a procedure or modality on a subject for the purpose of obtaining a therapeutic benefit of a disease or health-related condition. For example, treatment of pneumonia may involve administration of a therapeutic agent for the reduction in symptoms of pneumonia, such as reduction in cough or improvement in respiratory function.

The term "therapeutic benefit" or "therapeutically effective" as used throughout this application refers to anything that promotes or enhances the well-being of the subject with respect to the medical treatment of this condition. This includes, but is not limited to, a reduction in the frequency or severity of the signs or symptoms of a disease.

"Prevention" and "preventing" are used according to their ordinary and plain meaning to mean "acting before" or such an act. In the context of a particular disease or health-related condition, those terms refer to administration or application of an agent, drug, or remedy to a subject or performance of a procedure or modality on a subject for the purpose of blocking the onset of a disease or health-related condition.

The disease to be treated or prevented may be any bacterial infection. For example, the bacterial infection may be a Staphylococcus species, an E. coli, a streptococcus species, a chlamydia, salmonella, vibrio cholerae, Treponema pallidum, Neisseria gonorrhoeae, a borrelia species, a Mycobacterium species, a Yersinia species, or a bacillus species. In particular embodiments, the bacterial is a streptococcus. Non-limiting examples of streptococcus species include S. parasanguinis, S. peroris, S. pneumoniae, S. pyogenes, S. ratti, S. salivarius, S. salivarius ssp. Thermophilus, S. sanguinis, or S. viridans. In specific embodiments, the strep, species is S. pneumoniae.

Non-limiting examples of diseases contemplated for treatment include, but are not limited to, diseases of the respiratory tract, diseases of the gastronintestinal tract, diseases of the skin, disease of the central nervous system, diseases of the heart. Non-limiting more particular examples include pneumonia, bronchitis, endocarditis, sepsis, abscesses, meningitis, toxic shock syndrome, erysipelas, scarlet fever, rheumatic fever, Streptococcal pharyngitis, infective endocarditis enterocolitis, gastritis, necrotizing enteritis, and so forth. In a particular embodiment, the disease is pneumonia due to S. pneumoniae.

F. Kits

The technology herein includes kits. For example, a kit may include, for example, one or more components such as a sealed containing including an antibody or fragment thereof as discussed above. The kits may optionally include a reagent, an instruction sheet, and other elements useful to practice the technology described herein. These physical elements can be arranged in any way suitable for carrying out the invention.

Kits can include further buffers, enzymes, labeling compounds, and the like. Any of the compositions described herein may be comprised in a kit.

The kit may include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there is more than one component in the kit, the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a single vial. The kits of the present invention also will typically include a means for containing the nucleic acids or polypeptides set forth herein, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.

When the components of the kit are provided in one and/or more liquid solutions, the liquid solution is an aqueous solution, such as a sterile aqueous solution.

However, the components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means.

The container means will generally include at least one vial, test tube, flask, bottle, syringe and/or other container means, into which the nucleic acid formulations are placed, preferably, suitably allocated. The kits may also comprise a second container means for containing a sterile, pharmaceutically acceptable buffer and/or other diluent.

The kits of the present invention will also typically include a means for containing the vials in close confinement for commercial sale.

G. Examples

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention. EXAMPLE 1

The Pneumococcal Serine-Rich Repeat Protein is an Inter-Bacterial Adhesin that

Promotes Bacterial Aggregation In Vivo and in Biofilms

Methods Bacterial strains and media. Wild type strains used in this study included S. pneumoniae strain TIGR4 and T4R, the latter an unencapsulated derivative of TIGR4 9 Tettelin et al, 2001), and the previously described clinical isolates IPD-5, TNE-6012, and TBE-6050 (Obert et al, 2006; Rose et al, 2008). S. aureus ISP479C and S.gordonii M99 and their corresponding isogenic mutants ISP479C AsraP, and M99 AgspB have also been previously described (Bensing et al, 2004; Siboo et al, 2005). All of the S. pneumoniae mutants used in this study including T4 ApsrP, T4 psrP-secY2A2 , T4 QpsrP, and T4R QpsrP have been shown not to have polar effects on upstream and downstream gene transcription (Shivshankar et al, 2009; Rose et al, 2008). S. pneumoniae and S. gordonii were grown in Todd-Hewitt broth (THB) or on blood agar plates at 37° C in 5% C0₂. S. aureus were grown in Tryptic-Soy Broth (TSB) or on blood agar plates at 37°C. PsrP mutant strain stocks were grown in media supplemented with 1 μg/mL of erythromycin, those complemented with the expression vector pNEl were grown on media supplemented with 250 μg/mL of spectinomycin. SraP and GspB mutant stocks were grown in media supplemented with either 15 μg/mL of erythromycin or 5 μg/mL chloramphenicol respectively. E. coli strain DH5a (Invitrogen, Carlsbad CA) expressing recombinant PsrP constructs were grown with 50 μg/mL of kanamycin. Recombinant proteins were purified as previously described (Shivshankar et al, 2009; Takamatsu et al, 2005). To not affect the aggregative phenotype, no antibiotics were added to the media in any of the experiments described.

Mice experiments. Female BALB/cJ mice, 5-6 weeks old, were obtained from The

Jackson Laboratory (Bar Harbor, ME). Mice were anesthetized with 2.5% vaporized isoflurane prior to challenge. Exponential phase cultures of S. pneumoniae were centrifuged, washed, and suspended in sterile phosphate buffered saline (PBS). Cohorts of 6 mice were instilled with either 10⁷ cfu of TIGR4 or T4 ApsrP in 20

of PBS into the left nostril. Two days post-challenge, mice were anesthetized, and nasal lavage was collected by instillation and retraction of 20 μΐ PBS. Next, the mice were asphyxiated with compressed C0₂, and BAL fluid collected by flushing the lungs twice with 0.5 ml of PBS using a sterile catheter. All experiments were performed in compliance with an approved Institutional Animal Care and Use Committee protocol.

Visualization of mouse passaged bacterial aggregates. From each mouse BAL and 1 : 10 PBS diluted nasopharyngeal lavage elutes were smeared onto glass slides, heat fixed, and Gram-stained. Since the nasopharyngeal samples were mucoid, dilution of the samples was warranted. Bacteria were visualized using a CKX41 Olympus microscope at 200^x magnification. For each biological sample 100 CFU were randomly selected, taking note of the approximate number of diplococci composing each CFU, either 1, 2-10, or >10. Images of the bacteria were acquired at 400 x magnification to better show the multiple bacteria composing the aggregates.

Early biofilm formation using the 96-well microtiter plate assay. Early biofilm formation was examined by measuring the ability of cells to adhere and accumulate biomass on the bottom of a 96-well (flat-bottom) polystyrene plates (Costar, Corning Incorporated, Lowell MA) (Oggioni et ah, 2006). Briefly, microtiter wells with THB were inoculated with 10⁶ CFU of£ pneumoniae taken from cultures at mid-logarithmic phase growth (OD₆2o = 0.5) and incubated at 37° C in 5% C0₂. S. aureus and S. gordonii biofilm formation on microtiter plates was done in a similar manner, with the exception that TSB was used for S. aureus (Izano et ah, 2008; Loo et ah, 2000). Bacteria were grown for 2, 4, 6, 8, 18, and 24 h, after which the bio films were washed gently with PBS and stained with 100 of 0.1% CV. Biofilm biomass was subsequently quantified by image capture using an inverted microscope at 15 x and 100^x magnification and measuring the corresponding optical density (^540) of the supernatant following washing of the bacteria and solubilization of CV in 200 of 95% ethanol.

Mature biofilm formation using a continuous-flow tube reactor. Mature biofilms were grown under once through conditions in a glass slide chamber using a continuous-flow through reactor 9 Allegrucci et ah, 2006). Briefly, S. pneumoniae cells grown to mid- logarithmic phase served as the inoculum and were injected into a septum 4 cm upstream from the flow cell. Bacteria were allowed to attach to the glass substratum for 2 hours prior to initiating flow. The flow rate of the system was adjusted to 0.014 ml/min. Flow through the chamber was laminar, with a Reynolds number of <0.5, having a fluid residence time of 180 min. Biofilms were grown at 37°C in 5% C0₂ for 3 days under once through conditions. Biofilms were then visualized by confocal laser microscopy as described below. The flow cell was constructed of anodized aluminum containing a chamber (4.0 mm by 1.3 cm by 5.0 cm) having two glass surfaces, one being a microscope slide and the other being a glass coverslip serving as the substratum. Bio films were also grown on the interior surface of a 1- meter long, size 16 Masterflex silicone tubing (0.89mm Internal Diameter, Cole Parmer Inc.) using once-through continuous flow conditions. The line was inoculated with 5 mL of a mid- logarithmic culture of S. pneumoniae and the bacteria were allowed to attach for 2 hours. The flow rate of the system was adjusted to 0.035 ml/min and bacteria were grown for 3 days at 37°C in 5% C0₂. Bacterial cells were harvested from the interior surface by pinching the tube along its entire length, resulting in removal of the cell material from the lumen of the tubing. Removed exudates were gently suspended in 1 ml of PBS and the optical density (OD₆₂o) was measured. For light microscopy pictures, 50 μΐ of line exudate in saline was stained by the addition of 50 μΙ_, of 1% CV. A volume of 5 μΐ of stained line exudates were applied to glass slides, coverslipped, and images taken at 200X magnification using the microscope. Viable cell counts were determined by plating serial dilutions of exudates following the disruption of each sample by vortexing. Biofilm biomass was determined by measuring the total protein concentration of the exudates by BCA following the complete lysis of S. pneumoniae with saline containing 0.1% deoxycholate and 0.1% sodium-dodecyl sulfate, which activates the murein hydrolase autolysin, or use of French press for S. gordonii and S. aureus cultures.

Confocal scanning laser microscopy and image acquisition. Confocal scanning laser microscopy was performed with an LSM 510 Meta inverted microscope (Zeiss, Heidelberg, Germany). Images were obtained with an LD-Apochrome 40x/0.6 lens and the LSM 510 Meta image acquisition software (Zeiss). To visualize the biofilm architecture of 3 -day-old biofilms, biofilms were stained using the Live/Dead BacLight stain from Invitrogen (Carlsbad, CA). Quantitative analysis of epifluorescence microscopic images obtained from flow cell-grown biofilms at the 6-day time point was performed with COMSTAT image analysis software (Heydorn et ah, 2007).

Co-immunoprecipitation of rPsrP with BR. Immunoprecipitation of rBR and the truncated versions of rPsrP was carried out as previously described by Shivshankar et al. (2008). Protein G Sepharose beads (Amersham) were incubated overnight at 4°C with mouse monoclonal penta-His antibody (1 :50; Qiagen) in 500 ml of F12 media supplemented with 10% fetal bovine serum. Beads were incubated with 400 μΐ of whole bacterial lysates from E.coli expressing penta-His tagged recombinant versions of PsrP spiked with 200 μg of recombinant GST-BR full length and incubated overnight at 4° C with gentle agitation. Beads were washed with RIPA buffer, then boiled in sample buffer for 10 min (Ausubel et al, 2008). Samples were separated by a 12% gel Western blots and were carried out using mouse monoclonal GST Antibody (l :2000;ProtTech), which recognizes the GST tag on the recombinant protein as the primary antibody, and goat anti-mouse IgG antibody conjugated to HRP (1 :7500; Bio-Rad) as the secondary antibody.

Far Western analysis of BR interactions. Far Western analysis were carried out as described by Takamatsu et al. with minor modifications (Takamatsu et al., 2006). Nitrocellulose membranes were spotted with 1 μg of whole cell lysate of S. pneumoniae, S. gordonii, S. aureus or E. coli expressing various PsrP constructs. Membranes were incubated overnight in PBS with 4% bovine serum albumin and 0.1% Tween 20 (T-PBS) at room temperature. The next day, membranes were washed with T-PBS three times for 5 minutes, and incubated overnight at 4°C on an orbital platform rocker with T-PBS containing 1% bovine serum albumin (TB-PBS) with 1 μg/mL of recombinant GST-BR. Membranes were washed and incubated with monoclonal mouse anti-GST antibody (1 :5000 dilution) (Proto- Tech) overnight at 4°C in TB-PBS. Antibody binding was detected by incubating the membranes for l h with HRP-conjugated anti-mouse IgG (1 : 10 000 dilution) (Sigma), followed by development with the Super Signal chemiluminescent detection system (Thermo Scientific).

Visualization of recombinant BR bound to TIGR4. Recombinant full-length BR and truncated versions (BR.A, BR.B, BR.C) were expressed and purified from E. coli as previously described by Shivshankar et al. (2008). For labeling of bacteria, TIGR4 and T4 ApsrP were pelleted and suspended in 1 ml of carbonate buffer (pH 9.0) containing FITC (1 mg/ml) and incubated in the dark at room temperature with constant end-to-end tumbling. FITC-labeled bacteria were washed with PBS (pH 7.4) and centrifuged, until the supernatant became clear. rBR fragments were labeled using a FluorLink-Ab Cy3 labeling kit (Amersham) using the instructions provided by the manufacturer. Labeled bacteria were suspended in serum-free F12 media containing the labeled constructs for 1 hour and gently mixed. Subsequently, pneumococci were washed and suspended in F12 medium. Labeled bacteria and bound recombinant protein were visualized using an AX-70 fluorescent microscope and the images were captured at 0.1112-0.8886 ms exposure time for Cy2 and Cy3 filters. The magnification used for capture of digital images was lOOOx. Captured images were processed using Simple PCI software.

Western Blot and Native Gel Electrophoresis. Proteins and lysates (10 μg) were separated by SDS-PAGE and electrophoretically transferred to nitrocellulose membranes. Membranes were blocked with T-PBS containing 4% bovine serum for 30 min at room temperature. Membranes were then incubated overnight at 4°C with monoclonal antibody (mouse anti-His (1 :7500) or mouse anti-GST (1 :7500) (proto-tech)) in blocking buffer. Following incubation, membranes were washed with T-PBS three times for 5 minutes. HRP- conjugated goat anti-rabbit Immunoglobulin G (1 : 10 000) (Sigma) was used as the secondary antibody, followed by development with the Super Signal chemiluminescent detection system (Thermo Scientific). For native gel electrophoresis, proteins (2 μg) were separated under non- reducing conditions using a 10% Glycine gel at 80 V for 3 hours at room temperature. Following electrophoresis proteins were visualized by staining with Coomassie Brilliant Blue staining.

Statistical analysis. For pair-wise comparisons of groups statistical analyses were performed using a Student's t-test. For multivariant analyses a 1-Way AN OVA followed by a post-priori test using Sigma Stat software.

Results PsrP promotes pneumococcal aggregation in vivo. To test whether PsrP contributed to biofilm or microcolony formation in vivo, mice were infected with TIGR4 and its isogenic psrP deficient mutant, T4 ApsrP, and nasal lavage fluid and bronchoalveolar lavage (BAL) fluid were collected 2 days post-challenge. Aliquots from each biological sample were heat- fixed to glass slides, Gram-stained, and examined with a microscope. As would be expected for both the wild type and the mutant the majority of bacteria present in the lungs and nasopharynx were observed to be diplococci. However for TIGR4 the presence of bacterial aggregates was observed; some of which were composed of hundreds of individual bacteria (FIG. 2A). In all, the number of bacterial aggregates composed of 2-9, and >10 diplococci were significantly greater for mice infected with TIGR4 than T4 ApsrP in both the nasopharyngeal and BAL elute fluids (FIG. 2B, 2C). Moreover, the largest aggregates, those composed of > 100 bacteria, were only observed in mice infected with TIGR4. Thus, it was found that PsrP promoted the formation of large bacterial aggregates in vivo, including in the nasopharynx, a site previously shown not to require PsrP for bacterial colonization (Rose et al, 2008).

PsrP affects intimate bacteria to bacteria interactions. Given the previous results, moreover to develop an in vitro model that was amendable to manipulation, the ability of TIGR4 and T4 ApsrP to form biofilms was tested using the polystyrene microtiter plate model (Oggioni et al., 2006). As shown in FIG. 3 A, no differences were observed between wild type and the mutant suggesting that PsrP does not play a role in pneumococcal attachment to polystyrene or during the formation of early biofilm structures, in particular the bacteria lawn (Lizcano et al., 2010). The role of PsrP in 3-day old mature biofilms was examined using the once-through continuous flow cells previously described by Allegrucci et al. (2006). In this system, a stark difference in the architecture of TIGR4 and T4 ApsrP biofilms was observed (FIG. 3B). Wild type biofilms displayed a dense cloud-like morphology with extremely large aggregates that covered the glass surface. Closer inspection revealed that these aggregates were composed of tightly clustered pneumococci. In contrast, T4 ApsrP biofilms displayed a less intimate phenotype characterized by smaller aggregates, gaps, and the formation of columns, resulting in an overall patchier phenotype. Quantitative analysis of the biofilm structures using COMSTAT software confirmed that wild type biofilms had significantly greater total biomass and average thickness than those formed by the T4 ApsrP (FIG. 3C). No differences in either the maximum thickness of the biofilms or the roughness coefficient (a measure of biofilm heterogeneity) were observed (FIG. 3C; data not shown, respectively), indicating that T4 ApsrP could still form biofilms, although with distinct architecture. Importantly, T4 QpsrP-secY2A2, a mutant deficient in the entire psrP- secY2A2 pathogenicity island, behaved identical to T4 ApsrP, forming patchy biofilms with small aggregates and less intimate associated bacteria (FIG. 10). Of note, during planktonic growth TIGR4 and both T4 ApsrP and T4 QpsrP-secy2A2 were indistinguishable, growing either as short chains or diplococci, with a marked absence of aggregates.

To further investigate the role of PsrP, bacterial biofilms were grown under once through conditions in silicone tubing, after a designated time extruded from the line, and examined both visually and quantitatively. After 3 days of growth, differences between TIGR4 and T4 ApsrP in opacity of the exudates were visible to the eye (FIG. 4A) and could be confirmed using a spectrophotometer which showed a >3-fold difference in optical density (FIG. 4B). Microscopic visualization of the line exudates following crystal violet (CV) staining revealed that wild type bacteria were in large aggregates whereas T4 ApsrP exudates were primarily composed of small clusters or of individual diplococci (FIG. 4C). Increased biofilm biomass was supported by measurement of total protein concentrations, that showed that the wild type biofilm exudates had roughly 2-3 fold more protein than those corresponding to the mutant (FIG. 4D).

The BR domain mediates inter-bacterial interactions. To date a number of groups have shown that SRRPs mediate bacterial adhesion to host cells primarily through their NR domain (Shivshankar et al., 2009; Takamatsu et al, 2005; Siboo et al, 2005). For this reason tests were conducted to determine whether the BR domain of PsrP was also involved in biofilm/bacterial aggregation. The following were utilized: a pre-existing collection of encapsulated (T4 QpsrP) and unencapsulated (T4R QpsrP) S. pneumoniae mutants deficient in PsrP that either expressed a truncated version of PsrP with 33 SRRs in its SRR2 domain (PsrP_SRR2(33)), a similar truncated PsrP further lacking the BR domain (PsrP_SRR2(33)__BR), or carried the empty expression vector pNEl (Shivshankar et al, 2009). These strains were tested for their ability to form biofilms in silicone lines under once through conditions.

Complementation of T4 QpsrP with PsrP_SRR2(33), but not PsrP_SRR2(33)__BR or the empty pNEl vector, partially restored the ability of T4 QpsrP to form large aggregates in the lines when examined microscopically (FIG. 5A). However, measurement of other biofilm biomarkers such as optical density and total protein concentration showed no differences between any of the complemented mutants and the negative controls (FIG. 5B. 5C). Complementation of T4R QpsrP with PsrPs_RR2(33) also partially restored the ability of T4R QpsrP to form bacterial aggregates when examined microscopically (FIG. 5 A). However, in contrast to the encapsulated mutants, line exudates from T4R QpsrP with PsrPs_RR2(33) had significant more biofilm biomass than the negative controls. These findings suggested that the ability to form dense biofilms within the lines had been partially restored (FIG. 5B, 5C). Importantly, the truncated PsrP lacking the BR domain failed to complement T4R QpsrP suggesting that the BR domain was responsible for the inter-species aggregation observed. This was subsequently confirmed by Far-Western blot analyses that showed that recombinant BR (rBR) bound only to S. pneumoniae cell lysates that contained PsrP with the BR domain (FIG. 5D).

To further explore the role of the BR domain in the observed bacteria to bacteria interactions, the ability of a Cy3 labeled rBR constructs (FIG. 6A), purified from Escherichia coli, to interact with TIGR4 and T4 ApsrP was tested. Full length rBR interacted with TIGR4 but not with T4 ApsrP (FIG. 6B), confirming not only that BR bound to pneumococci, but also suggesting that its ligand was PsrP on the bacterial surface. Furthermore, only the rBR.A fragment retained the ability to attach to PsrP on the pneumococcus. Thus, it was determined that PsrP -mediated inter-species interactions occurred through amino acids located within 122-304 of PsrP.

Hereafter BR to BR interactions were confirmed using a number of techniques including native gel electrophoresis, Far Western and co-immunoprecipitation. Under reducing conditions of an SDS-PAGE gel, His-tagged rBR entered the gel and migrated at the predicted molecular weight of 37kDa (FIG. 7A). Contrary to this, under non-reducing conditions of a glycine native gel, rBR formed a large aggregate and failed to migrate into the gel (FIG. 7A). Far Western experiments using assorted E. coli cell lysates from bacteria expressing assorted PsrP constructs, confirmed that only lysates containing PsrP constructs with AA 122-304 bound successfully to GST-tagged rBR (FIG. 7B). This was also observed in co-immunoprecipitation experiments, whereby GST-rBR bound only to whole cell lysates from E.coli expressing versions of PsrP with amino acids 122-304 (FIG. 7C). Hence, using numerous assays it was determined that the BR domain had self-interacting properties that affected bacterial aggregation in biofilms and presumably in vivo. Importantly, because rBR constructs were purified form E. coli, and thus were not glycosylated, these findings also suggest that BR interactions were independent of glycoconjugates that are known to be present on PsrP.

Antibodies to the BR domain, but not to the SASASAST motif, block bacterial aggregation. Antibodies against the SRRl-BR domains of PsrP neutralized the ability of S. pneumoniae to attach to lung cells and that vaccination with rBR protected mice against pneumococcal challenge (Shivshankar et ah, 2009; Rose et ah, 2008). For this reason studies were conducted to test the ability of polyclonal antiserum against rBR and against a SRR motif peptide to block bacterial aggregation in the line model. Todd Hewitt Broth (THB) supplemented with a 1 : 1000 dilution of antiserum against the BR domain inhibited the formation of bacterial aggregates as observed by microscopic visualization of the bio film line exudates. In contrast, bacteria in media supplemented with antiserum to the SRR motif peptide or that from naive animals, formed aggregates similar to wild type bacteria grown under serum free conditions (FIG. 8A). Biofilm exudate optical density and protein concentrations supported these microscopic observations (FIG. 8B-C). To determine whether the effect of the BR antiserum on biofilm formation was specific for TIGR4, the ability of antibodies to the BR domain to block biofilm formation in unrelated clinical isolates was tested (FIG. 11). Antiserum against rBR from TIGR4 inhibited biofilm formation in two unrelated clinical isolates that carried PsrP. The same sera had no effect on biofilm formation by an invasive serotype 14 isolate that lacked PsrP. Therefore these studies confirmed previous observations that increased bacteria aggregation in biofilm models can occur independently of PsrP, but that if present, antiserum against BR can block the contribution of PsrP to these processes. SRRPs mediate inter-bacterial adhesion in pathogenic bacteria. To determine whether other SRRPs also mediated inter-species aggregation, studies were conducted to test the effect of GspB and SraP deletion on S. gordonii and S. aureus bio film architecture, respectively. In contrast to TIGR4, deletion of GspB and SraP negatively impacted biofilm formation in the microtiter biofilm model at 24 hours (FIG. 9A, 9B). Growth of wild type and mutant bacteria in the line models also demonstrated that both proteins contributed to the formation of large aggregates during surface attached growth; although this property was much more dramatic for S. gordonii than for S. aureus (FIG. 9C, 9D). Subsequent Far Western analysis using recombinant GST-tagged SRRl-NR from SraP and recombinant GST-tagged NR from GspB showed that these proteins bound only to cell lysates from wild type bacteria and not to cell lysates from their respective SRRP deficient mutant (FIG. 9E). Thus, like the BR domain of PsrP, the NR domains of GspB and SraP most likely mediated the observed bacterial aggregation. Finally, studies were conducted to test whether NR interactions were protein/species specific. Purified NR constructs from S. pneumoniae, S. aureus, and S. gordonii failed to bind NR constructs from the other SRRPs or cell lysates from other wild type bacteria. This indicates that SRRPs do not serve as a mechanism for intra-species bacterial aggregation.

All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. REFERENCES

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Claims

A method of inhibiting or preventing bacterial aggregation in a subject, comprising administering to a subject that is known or suspected to have a bacterial infection a pharmaceutically effective amount of a composition comprising: a. an antibody or fragment thereof that binds to an epitope within an amino acid sequence selected from the group consisting of:

i an amino acid sequence that has at least 90% identity to SEQ ID NO: l; ii an amino acid sequence that has at least 90% identity to SEQ ID NO:2; and iii an amino acid sequence that has at least 90% identity to SEQ ID NO:3, and b. a pharmaceutically acceptable carrier, wherein bacterial aggregation in the subject is inhibited or prevented.

Claim 2. The method of claim 1, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence has at least 90% identity to SEQ ID NO: l .

Claim 3. The method of claim 2, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence has at least 95% identity to SEQ ID NO: l .

Claim 4. The method of claim 3, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence has at least 98% identity to SEQ ID NO: l .

90395270.1 38 Claim 5. The method of claim 4, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence has at least 99% identity to SEQ ID NO: l . Claim 6. The method of claim 5, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence comprises SEQ ID NO: l .

Claim 7. The method of claim 6, wherein the bacterial infection is a S. pneumoniae infection and the amino acid sequence consists of SEQ ID NO: 1.

Claim 8. The method of claim 1, wherein the bacterial infection is a S. aureus infection and the amino acid sequence has at least 90% identity to SEQ ID NO:2.

Claim 9. The method of claim 8, wherein the bacterial infection is a S. aureus infection and the amino acid sequence has at least 95% identity to SEQ ID NO:2.

Claim 10. The method of claim 9, wherein the bacterial infection is a S. aureus infection and the amino acid sequence has at least 99% identity to SEQ ID NO:2. Claim 11. The method of claim 10, wherein the bacterial infection is a S. aureus infection and the amino acid sequence comprises SEQ ID NO:2.

Claim 12. The method of claim 11, wherein the bacterial infection is a S. aureus infection and the amino acid sequence consists of SEQ ID NO:2. Claim 13. The method of claim 1, wherein the bacterial infection is a S. gordonii infection and the amino acid sequence has at least 90% identity to SEQ ID NO:3.

Claim 14. The method of claim 13, wherein the bacterial infection is a S. gordonii infection and the amino acid sequence has at least 95% identity to SEQ ID NO:3.

90395270.1 39 Claim 15. The method of claim 14, wherein the bacterial infection is a S. gordonii infection and the amino acid sequence has at least 99% identity to SEQ ID NO:3.

Claim 16 The method of claim 15, wherein the bacterial infection is a S. gordonii infection and the amino acid sequence comprises SEQ ID NO:3.

Claim 17 The method of claim 16, wherein the bacterial infection is a S. gordonii infection and the amino acid sequence consists of SEQ ID NO:3.

Claim 18 The method of claim 1, wherein the subject is known or suspected to have an empyema or pleural effusion.

Claim 19 The method of claim 18, wherein the subject is known or suspected to have an empyema that is parapneumonic empyema.

Claim 20 The method of claim 1, wherein the subject is known or suspected to have otitis media or infective endocarditis.

Claim 21 The method of claim 1, wherein the subject is known or suspected to have pneumonia.

Claim 22 The method of claim 21, wherein the pneumonia is pneumococcal pneumonia. Claim 23 The method of claim 1, wherein the subject is a mammal.

Claim 24 The method of claim 23, wherein the mammal is a human.

90395270.1 40 The method of claim 1, wherein the composition is administered by aerosol, by spray, intravenously, intradermally, intraarterially, intramuscularly, intrathecally, intratracheally, intrathoracically, intrapleurally, subcutaneously, orally, topically, or intraperitoneally

The method of claim 1, wherein the subject is a human that is known or suspected to have parapneumonic empyema, and the amino acid sequence has at least 99% identity to SEQ ID NO: 1.

The method of claim 26, wherein the subject is a pediatric patient that is age 16 or less.

A method of inhibiting or preventing contact between a first bacterium and a second bacterium, comprising contacting a first bacterium and/or a second bacterium with an effective amount of a composition comprising an antibody or fragment thereof that binds to an epitope within an amino acid sequence selected from the group consisting of:

a. an amino acid sequence that has at least 90% identity to SEQ ID NO: 1 ; b. an amino acid sequence that has at least 90% identity to SEQ ID NO:2; and

c. an amino acid sequence that has at least 90% identity to SEQ ID NO:3, wherein contact between the first bacterium and the second bacterium is inhibited or prevented following said contact.

The method of claim 28, wherein the antibody or fragment thereof binds to an epitope that is an amino acid sequence that has at least 95% identity to SEQ ID NO: l . The method of claim 29, wherein the antibody or fragment thereof binds to an epitope that is an amino acid sequence that has at least 99% identity to SEQ ID NO: l .

The method of claim 30, wherein the antibody or fragment thereof binds to an epitope that is an amino acid sequence comprising SEQ ID NO: l .

A kit for treating or preventing empyema in a subject, comprising:

a. in one or more sealed vials a pharmaceutical composition comprising an antibody or fragment thereof that binds an epitope within an amino acid sequence selected from the group consisting of:

i an amino acid sequence that has at least 90% identity to SEQ ID NO: l; ii an amino acid sequence that has at least 90% identity to SEQ ID NO:2; and iii an amino acid sequence that has at least 90% identity to SEQ ID NO:3, and b. instructions for administering to a subject that is known or suspected to have an empyema the pharmaceutical composition.

The kit of claim 32, wherein the kit comprises an antibody or fragment thereof binds to an epitope that has at least 95% identity to SEQ ID NO: 1.

The kit of claim 33, wherein the kit comprises an antibody or fragment thereof binds to an epitope that has at least 99% identity to SEQ ID NO: 1.

The kit of claim 34, wherein the kit comprises an antibody or fragment thereof binds to an epitope that comprises SEQ ID NO: l . Claim 36. The kit of claim 32, further comprising a syringe.

Claim 37. The kit of claim 36, wherein the syringe is a thoracentesis syringe.

Claim 38. The kit of claim 32, wherein the composition further comprises one or more therapeutic agents for the treatment or prevention of empyema in a subject.

Claim 39. The kit of claim 32, wherein the instructions for use are in a computer- readable form.

90395270.1 43