WO2026019703A1 - Therapeutic compositions and methods - Google Patents

Therapeutic compositions and methods

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Publication number
WO2026019703A1
WO2026019703A1 PCT/US2025/037527 US2025037527W WO2026019703A1 WO 2026019703 A1 WO2026019703 A1 WO 2026019703A1 US 2025037527 W US2025037527 W US 2025037527W WO 2026019703 A1 WO2026019703 A1 WO 2026019703A1
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WO
WIPO (PCT)
Prior art keywords
amino acid
vaccine
subject
antibiotic
seq
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/US2025/037527
Other languages
French (fr)
Inventor
Wendy Picking
William PICKING
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of Missouri Columbia
University of Missouri St Louis
Original Assignee
University of Missouri Columbia
University of Missouri St Louis
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Application filed by University of Missouri Columbia, University of Missouri St Louis filed Critical University of Missouri Columbia
Publication of WO2026019703A1 publication Critical patent/WO2026019703A1/en
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/407—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with other heterocyclic ring systems, e.g. ketorolac, physostigmine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
    • A61K31/425—Thiazoles
    • A61K31/427—Thiazoles not condensed and containing further heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7028—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages
    • A61K31/7034—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin
    • A61K31/7036—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin having at least one amino group directly attached to the carbocyclic ring, e.g. streptomycin, gentamycin, amikacin, validamycin, fortimicins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/025—Enterobacteriales, e.g. Enterobacter
    • A61K39/0258—Escherichia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/104—Pseudomonadales, e.g. Pseudomonas
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/21—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Pseudomonadaceae (F)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
    • C07K14/245—Escherichia (G)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/55—Fusion polypeptide containing a fusion with a toxin, e.g. diphteria toxin

Definitions

  • the presently disclosed subject matter relates to methods of treating existing infections, e.g., gram-negative bacterial infections, such as Pseudomonas aeruginosa (Pa) infections, in subjects with cystic fibrosis (CF) via administration of a therapeutic fusion polypeptide-based vaccine.
  • the presently disclosed subject matter further relates to combinations of fusion polypeptide-based vaccines and antibiotics for use in treating infections in subjects with CF.
  • Pa BACKGROUND Pseudomonas aeruginosa
  • CF cystic fibrosis
  • the subject with CF has a Pa infection.
  • the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide having an amino acid Attorney Docket No.3289.0008WO sequence of SEQ ID NO: 2 (PaF) or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 2.
  • the LTA1 is 5’ of the fusion of the needle tip protein or an antigenic fragment thereof and/or the translocator protein fusion or an antigenic fragment thereof, optionally wherein the LTA1 has an amino acid sequence of SEQ ID NO: 6, or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 6.
  • the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 (L-PaF), or an amino acid sequence having at least 90% homology to SEQ ID NO: 4.
  • the vaccine comprises an oil-in-water emulsion, optionally wherein said emulsion comprises squalene, further optionally wherein the vaccine comprises MedImmune Emulsion (ME).
  • the vaccine is administered to the subject at least two times.
  • the method comprises administering an antibiotic to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine.
  • the antibiotic is selected from the group comprising a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, colistimethate, and a combination thereof, optionally wherein the antibiotic comprises an aminoglycoside, further optionally wherein the antibiotic comprises tobramycin.
  • the route of administration for the antibiotic is selected from intravenous, oral or inhalation.
  • the infection in the subject is reduced by at least about 25%, at least about 50%, at least about 75%, at least about 90%, at least about 95%, or more. In some embodiments, the infection in the subject is reduced to below about 300 colony forming units per lung (CFU/lung), below about 200 CFU/lung, below about 100 CFU/lung, below about 50 CFU/lung or below about 10 CFU/lung. In some embodiments, the infection is substantially or entirely cleared from the CF subject.
  • CFU/lung colony forming units per lung
  • the presently disclosed subject matter provides a combination therapeutic treatment method for treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), the combination Attorney Docket No.3289.0008WO therapeutic treatment method comprising: administering to the subject with CF a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa), and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli, optionally wherein the vaccine further comprises a squalene-based oil-in-water emulsion; and administering to the subject with CF
  • T3SS
  • the antibiotic comprises tobramycin. In some embodiments, the antibiotic is administered substantially simultaneously with the vaccine. In some embodiments, the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4.
  • the presently disclosed subject matter provides a composition for use in treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), wherein the composition comprises: (a) a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa) and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli; and (b) a therapeutically effective amount of an antibiotic.
  • T3SS Type III secretion system
  • LTA1 labile toxin
  • the antibiotic comprises Tobramycin.
  • the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4. Accordingly, it is an object of the presently disclosed subject matter to provide a method of treating an infection, e.g., a Pa infection, in a subject with CF and to methods of treating infections in a subject with CF using a combination of a fusion protein-based therapeutic vaccine and an antibiotic.
  • Attorney Docket No.3289.0008WO This and other objects are achieved in whole or in part by the presently disclosed subject matter.
  • FIGURES is a graph showing the results of an in vivo efficacy study of tobramycin in cystic fibrous model (CF) rats.
  • CF rats were challenged with Pseudomonas aeruginosa (Pa; strain mPA0831, 3 x 10 6 colony forming units (CFUs)) and then treated with the antibiotic tobramycin (3 milligrams per kilogram per day (mg/kg/day) for 7 days).
  • Pa Pseudomonas aeruginosa
  • CFUs colony forming units
  • FIG. 1B is a graph showing the in vivo efficacy of antibiotic alone, of fusion protein vaccine alone, and of a combination of antibiotic and fusion protein vaccine in treating a bacterial infection in cystic fibrosis model (CF) rats.
  • Groups of CF rats were treated with tobramycin (Tob; 3 milligrams per kilogram per day (mg/kg/day) for 7 days) starting on day 14 after challenge with Pseudomonas aeruginosa (Pa, strain mPA0831, 3 x 10 6 colony forming units (CFUs)); vaccinated three times with a fusion protein oil-in-water emulsion of the presently disclosed subject matter (L-PaF/ME, Vaccine; 30 micrograms ( ⁇ g)) on days 28, 42, and 56 after Pa challenge; or treated with tobramycin (3 mg/kg/day for 7 days) starting on day 14 following Pa challenge and vaccinated with the vaccine on day 28, 42, and 56 following Pa challenge; Tob + Vax).
  • tobramycin tobramycin
  • Rats were rechallenged with Pa (strain mPA0831, 3 x 10 6 CFUs) on day 70 of the study.
  • Pa phosphate buffered saline
  • CFU burden per lung was determined on day 84 after the first Pa challenge.
  • Figure 2 is a graph showing the results of an in vivo efficacy study of Attorney Docket No.3289.0008WO single agent treatments or a combination treatment in cystic fibrosis model (CF) rats.
  • Groups of CF rats were treated with tobramycin (Tob; 3 milligrams per kilogram per day (mg/kg/day) for 7 days) starting on day 21 after challenge with Pseudomonas aeruginosa (Pa; starin mPA0831, 3 x 10 6 colony forming units (CFUs)); with two administrations of L-PaF/ME vaccine (Vaccine; 30 micrograms ( ⁇ g)) on days 28 and 42 after Pa challenge; or with tobramycin (3 mg/kg/day for 7 days) starting on day 21 following Pa challenge followed by two administrations of the vaccine (on day 28 and 42 following Pa challenge) (Tob + Vax).
  • CFU burden per lung was determined on day 56 of the study.
  • FIG. 3 is a graph showing the results of an in vivo efficacy study of a combination treatment in cystic fibrosis model (CF) rats.
  • Groups of CF rats were treated with tobramycin (3 milligrams per kilogram (mg/kg)) and L- PaF/ME vaccine (30 micrograms ( ⁇ g)) on day 21 after challenge with Pseudomonas aeruginosa (Pa; strain mPA0831, 3 x 10 6 colony forming units (CFUs)) and then with tobramycin (3 mg/kg) on each of days 22-27.
  • CFU burden per lung (CFU/lung) was determined on day 28 of the study.
  • the term “about,” when referring to a value or to an amount of a composition, dose, homology or sequence identity (e.g., when comparing two or more nucleotide or amino acid sequences), mass, weight, temperature, time, volume, concentration, percentage, etc., is meant to encompass variations of in some embodiments ⁇ 20%, in some embodiments ⁇ 10%, in some embodiments ⁇ 5%, in some embodiments ⁇ 1%, in some embodiments ⁇ 0.5%, and in some embodiments ⁇ 0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions.
  • the phrase “consisting essentially of” limits the scope of a claim to the specified materials or steps, plus those that do not materially affect the basic and novel characteristic(s) of the claimed subject matter. With respect to the terms “comprising”, “consisting of”, and “consisting essentially of”, where one of these three terms is used herein, the presently disclosed and claimed subject matter can include the use of either of the other two terms.
  • the term “and/or” when used in the context of a listing of entities refers to the entities being present singly or in combination.
  • the phrase “A, B, C, and/or D” includes A, B, C, and D individually, but also includes any and all combinations and subcombinations of A, B, C, and D.
  • An "increase" can refer to any change that results in a greater amount of a symptom, disease, composition, condition or activity.
  • An increase can be any individual, median, or average increase in a condition, symptom, activity, composition in a statistically significant amount.
  • the increase can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% increase so long as the increase is statistically significant.
  • a decrease can refer to any change that results in a smaller amount of a symptom, disease, composition, condition, or activity.
  • a substance is also understood to decrease the genetic output of a gene when the genetic output of the gene product with the substance is less relative to the output of the gene product without the substance.
  • a decrease can be a change in the symptoms of a disorder such that the symptoms are less than previously observed.
  • a decrease can be any individual, median, or average decrease in a condition, symptom, activity, composition in a statistically significant amount.
  • the decrease can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% decrease so long as the decrease is statistically significant.
  • inhibitor means to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This can also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level.
  • the reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels.
  • reduce or other forms of the word, such as “reducing” or “reduction,” in the context of a bacterial infection is meant lowering the number of bacteria or the number of viable bacteria (i.e., colony forming units (CFUs) Attorney Docket No.3289.0008WO of a bacteria). It can also refer to lowering a level of a biological marker of the infection (e.g., lowering white blood cell count in a subject with the infection, etc.).
  • prevent or other forms of the word, such as “preventing” or “prevention,” is meant to stop a particular event or characteristic, to stabilize or delay the development or progression of a particular event or characteristic, or to minimize the chances that a particular event or characteristic will occur. Prevent does not require comparison to a control as it is typically more absolute than, for example, reduce. As used herein, something could be reduced but not prevented, but something that is reduced could also be prevented. Likewise, something could be prevented but not reduced, but something that is prevented could also be reduced.
  • the term “subject” refers to any individual who is the target of administration or treatment.
  • the subject can be a vertebrate, for example, a mammal.
  • the subject can be human, non-human primate, bovine, equine, porcine, canine, or feline.
  • the subject can also be a guinea pig, rat, hamster, rabbit, mouse, or mole.
  • the subject can be a human or veterinary patient.
  • patient refers to a subject under the treatment of a clinician, e.g., physician.
  • the term “therapeutically effective” refers to the amount of the composition used is of sufficient quantity to ameliorate one or more causes or symptoms of a disease or disorder. Such amelioration only requires a reduction or alteration, not necessarily elimination.
  • treatment refers to the medical management of a patient with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This term includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological condition, or disorder, and also includes causal treatment, that is, treatment Attorney Docket No.3289.0008WO directed toward removal of the cause of the associated disease, pathological condition, or disorder.
  • this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological condition, or disorder.
  • Effective amount refers to a sufficient amount of an agent to provide a desired effect. The amount of agent that is “effective” will vary from subject to subject, depending on many factors such as the age and general condition of the subject, the particular agent or agents, and the like.
  • an “effective amount” of an agent can also refer to an amount covering both therapeutically effective amounts and prophylactically effective amounts.
  • An “effective amount” of an agent necessary to achieve a therapeutic effect can vary according to factors such as the age, sex, and weight of the subject. Dosage regimens can be adjusted to provide the optimum therapeutic response. For example, several divided doses can be administered daily, or the dose can be proportionally reduced as indicated by the exigencies of the therapeutic situation.
  • a “pharmaceutically acceptable” component can refer to a component that is not biologically or otherwise undesirable, i.e., the component can be incorporated into a pharmaceutical formulation provided by the disclosure and administered to a subject as described herein without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the formulation in which it is contained.
  • the term When used in reference to administration to a human, the term generally implies the component has met the required standards of toxicological and manufacturing Attorney Docket No.3289.0008WO testing or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration.
  • pharmaceutically acceptable carrier means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non- toxic and includes a carrier that is acceptable for veterinary and/or human pharmaceutical or therapeutic use.
  • carrier or “pharmaceutically acceptable carrier” can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents.
  • carrier encompasses, but is not limited to, any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in pharmaceutical formulations and as described further herein.
  • “Pharmacologically active” (or simply “active”), as in a “pharmacologically active” derivative or analog, can refer to a derivative or analog (e.g., a salt, ester, amide, conjugate, metabolite, isomer, fragment, etc.) having the same type of pharmacological activity as the parent compound and approximately equivalent in degree.
  • “Therapeutic agent” refers to any composition that has a beneficial biological effect.
  • Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition (e.g., a non-immunogenic cancer).
  • the terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like.
  • therapeutic agent when used, then, or when a particular agent is specifically identified, it is to be understood that the term includes the agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc.
  • “Therapeutically effective amount” or “therapeutically effective dose” of a composition refers to an amount Attorney Docket No.3289.0008WO that is effective to achieve a desired therapeutic result.
  • a desired therapeutic result is the control of an infection.
  • Therapeutically effective amounts of a given therapeutic agent will typically vary with respect to factors such as the type and severity of the disorder or disease being treated and the age, gender, and weight of the subject.
  • the term can also refer to an amount of a therapeutic agent, or a rate of delivery of a therapeutic agent (e.g., amount over time), effective to facilitate a desired therapeutic effect, such as pain relief.
  • the precise desired therapeutic effect will vary according to the condition to be treated, the tolerance of the subject, the agent and/or agent formulation to be administered (e.g., the potency of the therapeutic agent, the concentration of agent in the formulation, and the like), and a variety of other factors that are appreciated by those of ordinary skill in the art.
  • Vaccine as used herein is a preparation that stimulates an immune response that produces immunity against a particular antigen or antigens, e.g. a component of a gram-negative bacteria.
  • Vaccines can be administered prophylactically (for example, to prevent or inhibit the establishment of an infection) or therapeutically (e.g., to inhibit, reduce, or treat an established infection, or to ameliorate the effects or symptoms of an existing infection).
  • Vaccines can contain, but are not limited to, live, attenuated infectious material such as viruses or bacteria, and dead or inactivated organisms or purified products or fragments derived therefrom.
  • the vaccine of the presently disclosed subject matter comprises a “subunit vaccine”, i.e., a vaccine comprising purified fragments from a pathogen.
  • the vaccine comprises an antigenic fusion polypeptide.
  • a vaccine can be administered by injection (e.g., subcutaneous (sc), intramuscular (im), intraperitoneal (ip), intradermal (id) or intravenous (iv) injection), orally, or by inhalation.
  • the presently disclosed subject matter relates to vaccines that are used therapeutically.
  • fusion as used herein with reference to polypeptides and portions of polypeptides that are “fused” together means that the amino acid Attorney Docket No.3289.0008WO sequences are covalently joined to each other, e.g., by peptide bonds, directly or via a linking amino acid sequence.
  • fusion protein or “fusion polypeptide” refers to a non-naturally occurring protein or polypeptide, e.g., a protein or polypeptide having an amino acid sequence comprising at least two partial or complete sequences derived from, obtained from, or isolated from different polypeptides that are not naturally adjoined.
  • a fusion protein or fusion polypeptide can be the functional product of a fusion gene or fusion nucleic acid sequence.
  • a fusion gene can further be modified by mutation, deletion, insertion or substitution of heterologous sequences, or by any means available using recombinant DNA technology.
  • fragment refers to a peptide or polypeptide of formed by at least 6 amino acid residues which are linked to each other via peptide bonds, but which contains less amino acid residues (e.g., 5 less, 10 less, 20 less, 30 less, 40 less amino acid residues) than a recited “parent” polypeptide.
  • an “antigenic fragment” is a peptide or polypeptide capable of eliciting an immune response, including the production of antibodies directed to that immunogenic fragment or to the protein having the immunogenic fragment.
  • an antigenic fragment of the needle tip protein PcrV has the ability to elicit the production of antibodies against PcrV.
  • antibody and “immunoglobulin” refer to a protein produced by the B-cells of the immune system that can identify, bind and neutralize an antigen.
  • an antibody is produced by the immune system and binds a bacterial protein, e.g., such as PcrV or PopB.
  • the antibody can have neutralizing properties and be capable of suppressing or reducing the biological activity of the bacterial protein.
  • active immunization refers to immunization that stimulates the immune system to produce antibodies against an antigen (self or foreign).
  • Active immunization can be induced through vaccination. Active immunization is often long-lasting and can be reactivated by repeated injection of boosters. In contrast, passive Attorney Docket No.3289.0008WO immunization occurs when antibodies directed against specific antigen are administered to a subject.
  • adjuvant refers to a substance that increases the intensity of the immune response after co-administration with an immunogen. An adjuvant can act as an immunopotentiator, e.g., providing for more potent and/or persistent immune responses, while reducing the dose and number of boosters. Adjuvant can also increase the stability of the immunogenic composition or vaccine. II.
  • Pseudomonas aeruginosa referred to as “Pa”, “Pseudomonas” and/or “P. aeruginosa” infections
  • CF cystic fibrosis
  • the standard of treatment for CF patients with lung infections, including Pa infections is the aminoglycoside antibiotic tobramycin.
  • tobramycin does not clear Pa infections. Accordingly, the presently disclosed subject matter provides methods and therapeutic compositions for use in treating infections.
  • the methods and compositions can provide therapeutic efficacy in the treatment of existing bacterial infections, such as Pa infections, in subjects with CF.
  • the present disclosure is directed to the use of a subunit vaccine as a therapeutic vaccine, e.g., in subjects with CF and existing bacterial infections.
  • the vaccine comprises (1) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pa and (2) an adjuvant, such as the A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli.
  • T3SS Type III secretion system
  • the fusion peptide referred to herein as “Pa fusion” or PaF is a fusion of two essential surface localized T3SS proteins from Pa, i.e., the needle tip protein PcrV (which has the amino acid sequence of SEQ ID NO: 8) and the translocator protein PopB (which has the amino acid sequence of SEQ ID NO: 10).
  • T3SS scaffold proteins are highly conserved (>96- Attorney Docket No.3289.0008WO 99%) among PAO1/PA14-like strains of PA. Because they are involved in the early stages of pathogenesis for PAO1/PA14-like strains, vaccine escape is unlikely since mutation of these proteins impacts assembly of the T3SS apparatus, rendering the mutant non-pathogenic.
  • PaF refers to the polypeptide having the amino acid sequence of SEQ ID NO: 2 or the amino acid sequence encoded by the nucleic acid sequence of SEQ ID NO: 1.
  • the vaccine comprises a fusion comprising an amino acid sequence of PcrV (SEQ ID NO: 8) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to the amino acid sequence SEQ ID NO: 8.
  • the fusion comprises an amino acid sequence of PopB (SEQ ID NO: 10) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to the amino acid sequence of SEQ ID NO: 10.
  • the fusion comprises an amino acid sequence of PaF (SEQ ID NO: 2) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 2.
  • the LTA1 subunit from the labile toxin (LT) of Enterotoxigenic E. coli serves as the adjuvant of the presently disclosed vaccine.
  • LTA1 retains the toxin's ADP-ribosylation (ADPr) activity and the ability to promote dendritic cell (DC) maturation but does not possess detectable toxicity.
  • ADPr ADP-ribosylation
  • DC dendritic cell
  • LTA1 stimulates a balanced Th1/Th2 response along with a mucosal response characterized by production of mucosal IgA, as well as IL-17. Recently, it was shown that the addition of LTA1 to Fluzone increased IgA, while decreasing levels of IL-6 post-H1N1 challenge.
  • compositions and methods using compositions comprising an adjuvant (e.g., LTA1 or a peptide having at least about 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98% or 99% homology to LTA1 (SEQ ID NO: 6)) and a fusion of a needle tip protein or fragment thereof and a translocator protein or fragment there as separate components or as a fusion Attorney Docket No.3289.0008WO polypeptide (e.g., PaF (SEQ ID NO: 2 or a sequence having about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.5% homology thereto)).
  • an adjuvant e.g., LTA1 or a peptide having at least about 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98% or 99% homology to LTA1 (SEQ ID NO: 6)
  • LTA1 is fused to the N-terminus of the PaF polypeptide to provide the fusion polypeptide LTA1-PaF (also referred to herein as “L-PaF”, and which has the amino acid sequence of SEQ ID NO: 4), thus providing simultaneous uptake of the adjuvant-antigen by antigen presenting cells to enhance cellular immunity.
  • L-PaF also referred to herein as “L-PaF”, and which has the amino acid sequence of SEQ ID NO: 4
  • the L-PaF vaccine was used as a preventative vaccine that acted as a precautionary measure to bolster a subject’s immune system to an associated illness. The goal was to prevent the infection or disease from occurring.
  • the studies disclosed herein demonstrate for the first time that L-PaF, alone or in conjunction with an antibiotic, can be used as a surprisingly effective therapeutic treatment for infections in subjects, including those suffering from CF.
  • provided herein are methods for using a therapeutically effective amount of any of the vaccines or fusion polypeptides disclosed herein and/or in PCT/US2022/030565, alone or in combination with an antibiotic composition, e.g. tobramycin, to treat an infection in subjects with an infection.
  • the subject is a human or other mammalian subject.
  • the subject with an infection is also suffering from CF. More particularly, the presently disclosed subject matter provides for therapeutically treating subjects suffering from CF by administering a composition comprising a vaccine comprising a fusion polypeptide comprising i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) LTA1 from enterotoxigenic Escherichia coli, alone or in combination with an antibiotic composition, e.g. tobramycin.
  • an antibiotic composition e.g. tobramycin.
  • disclosed herein are methods of treating, decreasing, reducing, and/or ameliorating an infection in a subject with CF, or other condition related to or Attorney Docket No.3289.0008WO susceptible to a bacterial infection whether a Pa infection or other bacterial, comprising administering to the subject a therapeutically effective amount of any of the vaccines or fusion polypeptides disclosed herein, e.g. L-PaF/ME, optionally administered in combination with an appropriate antibiotic composition.
  • a composition comprising a fusion polypeptide comprising i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) the LTA1 from enterotoxigenic Escherichia coli, alone or in combination with tobramycin or any other appropriate antibiotic.
  • the infection is a Pa infection, although the same therapeutic can be used to treat other types of infections in CF patients or non-CF patients, e.g.
  • the fusion polypeptide comprises an amino acid sequence of PcrV (SEQ ID NO: 8) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 8.
  • the fusion polypeptide comprises an amino acid sequence of PopB (SEQ ID NO: 10) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 10.
  • the fusion polypeptide comprises an amino acid sequence of PaF (SEQ ID NO: 2) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 2.
  • the fusion polypeptide comprises an amino acid sequence of LTA1 (SEQ ID NO: 6) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% homology to SEQ ID NO: 6.
  • the fusion polypeptide comprises an amino acid sequence of L-PaF (SEQ ID NO: 4) or a sequence having at least 50%, at least 60%, at least 70%, at least Attorney Docket No.3289.0008WO 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 4.
  • the presently disclosed subject matter provides a method for treating an infection in a subject with cystic fibrosis (CF) comprising administering to the subject a therapeutically effective amount of: (a) a vaccine comprising a fusion polypeptide wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) LTA1 from enterotoxigenic Escherichia coli; and (b) optionally, an antibiotic.
  • the subject is a human.
  • the subject with CF has a Pa infection.
  • the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide comprising an amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, or 99.5%) homology thereto.
  • the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide comprising an amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, or 99.5%) homology thereto.
  • the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide having an amino acid sequence of SEQ ID NO: 2 (PaF) or an amino acid sequence having at least 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5%) homology to the amino acid sequence of SEQ ID NO: 2.
  • the LTA1 is 5’ of the fusion of the needle tip protein or an antigenic fragment thereof and/or the translocator protein fusion or an antigenic fragment thereof.
  • the LTA1 has an amino acid sequence of SEQ ID NO: 6, or an amino acid sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) Attorney Docket No.3289.0008WO homology to the amino acid sequence of SEQ ID NO: 6.
  • the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 (L-PaF), or an amino acid sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5%) homology to SEQ ID NO: 4.
  • the vaccine comprises (e.g., the fusion polypeptide is formulated as) an emulsion, e.g., a microemulsion (e.g., containing dispersed droplets having a diameter of about 5 micrometers ( ⁇ m) to about 50 ⁇ m) or nanoemulsion (e.g., containing dispersed droplets having a diameter of about 20 nanometers (nm) to about 100 nm).
  • the emulsion is an oil-in-water emulsion.
  • the emulsion comprises squalene.
  • the vaccine comprises MedImmune Emulsion (ME), i.e., an emulsion comprising about 20 millimolar (mM) Histidine, about 10% sucrose, about 4% squalene, and about 1% polysorbate-80, having a pH of about 6, and a droplet size of about 100 nm.
  • ME MedImmune Emulsion
  • the vaccine can be referred to as “the L-PaF/ME vaccine.”
  • the vaccine can be administered via any convenient route, e.g., orally, by injection or intravenously, or intranasally. In some embodiments, the vaccine is administered via injection. In some embodiments, the vaccine is administered intranasally.
  • the vaccine (e.g., the L-PaF or L-PaF/ME vaccine) can be administered a single time or multiple times. In some embodiments, the vaccine is administered multiple times to the same subject.
  • “prime- boost” regimens can be used according to the presently disclosed subject matter
  • the first administration of the vaccine can be referred to as a “prime” or “priming” dose, while subsequent administrations can be referred to as “boosts”.
  • Separate administrations of the vaccine are typically separated by an intervening period of at least about one week or more (e.g., about two weeks, about three weeks, about four weeks, about five weeks, about six weeks, etc.).
  • separate administrations can be separated by an intervening period of one or more months (e.g., about 1 month to about 12 months) or one or more years (e.g., about 2 years to about Attorney Docket No.3289.0008WO 10 years).
  • a typical regimen can comprise an immunization followed by booster administration (e.g. by injection) at regular time intervals, such as 2-, 3-, 4-, or 6-week intervals.
  • booster administration e.g. by injection
  • booster injections can be on an irregular basis as indicated by monitoring of immune response (e.g. when the level of the antibodies is below a threshold determined by a doctor or a person skilled in the art).
  • the vaccine (e.g., the L-PaF or L-PaF/ME vaccine) is administered one time. In some embodiments, the vaccine (e.g., the L-PaF or L-PaF/ME vaccine) is administered to the subject at least two times. In some embodiments, the vaccine is administered to the subject two times. In some embodiments, the vaccine is administered to the subject three times. In some embodiments, the vaccine doses are administered about two weeks apart. In some embodiments, the method comprises administering an antibiotic to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine. Thus, in some embodiments, the method comprises administering an antibiotic to the subject prior to administration (e.g., initial administration) of the vaccine.
  • the method comprises administering an antibiotic to the subject prior to administration (e.g., initial administration) of the vaccine.
  • the antibiotic is administered to the subject one or more days (e.g., about 1, 2, 3, 4, 5, 6, or 7 days) prior to administration of the vaccine. In some embodiments, the antibiotic is administered to the subject one or more weeks (e.g., about 1, 2, 3, 4, 5, or 6 weeks) prior to administration of the vaccine. In some embodiments, the antibiotic is administered to the subject a few hours (e.g., about 4 to about 12 hours) prior to administration of the vaccine.
  • the vaccine is administered to the subject simultaneously with the vaccine or substantially simultaneously with administration (e.g., initial administration) of the vaccine (e.g., within about 5 minutes, about 10 minutes, about 15 minutes, about 30 minutes, about 45 minutes, about 60 minutes, about 90 minutes, or about 120 minutes) of administration of the vaccine).
  • the antibiotic is administered to the subject after administration (e.g., initial administration) of the vaccine.
  • the antibiotic is administered a few hours (e.g., about 4-12 hours) after administration of the vaccine, one or more days (e.g., about 1, 2, 3, 4, 5, 6, or 7 days) after administration of the vaccine, or one or more weeks (e.g., about 1, 2, 3, 4, 5, or about 6 weeks) after administration of the vaccine.
  • the antibiotic composition can be any suitable antibiotic.
  • the antibiotic composition can comprise more than one particular antibiotic or antibiotics of more than one chemical class.
  • the antibiotic can be a penicillin (e.g.
  • piperacillin and tazobactam a cephalosporin (e.g., ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam), an aminoglycoside (e.g., tobramycin, amikacin, gentamicin), a macrolide (e.g., azithromycin), a quinolone (e.g., ciprofloxacin, levofloxacin), a carbapenem (e.g., meropenem, meropenem-vaborbactam, imipenem/cilastatin, doripenem), aztreonam, colistimethate, or combination thereof.
  • a cephalosporin e.g., ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam
  • the antibiotic is one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate.
  • the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate.
  • the antibiotic comprises or consists of an aminoglycoside. In some embodiments, the antibiotic comprises or consists of tobramycin.
  • the antibiotic can be administered to a subject or patient to be treated via any suitable route of administration.
  • the route of administration for the antibiotic can be intravenous, oral or inhalation.
  • the antibiotic can be administered in multiple times (e.g., over the course of one or more days, weeks, or months).
  • the antibiotic is administered to the subject at least two times.
  • the antibiotic is administered to the subject at Attorney Docket No.3289.0008WO least three times, at least four times, at least five times, at least six times, at least seven times, at least 10 times, at least 12 times, or at least 14 times.
  • the antibiotic doses are administered one or more hours, days or weeks apart.
  • the antibiotic is administered daily for two or more days (e.g., 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, or more). In some embodiments, the antibiotic is administered daily for 7 days.
  • the vaccine e.g., the L-PaF or L-PAF/ME vaccine
  • the vaccine can be administered with an antibiotic as discussed herein and/or with any other suitable therapeutic component, including but not limited to a biologic (e.g. antibody, peptide, blood, blood components, allergenics, somatic cells, gene therapy, tissues, and recombinant therapeutic proteins), or small molecule drugs or low molecular weight compounds.
  • the infection to be treated in the subject can be reduced (e.g., the number of colony forming units (CFUs) per organ (e.g., lung) or tissue can be reduced) by at least about 25% or more.
  • the infection can be reduced by at least about 50% or more (e.g., by at least about 75%, at least about 90%, or by at least about 95% or more).
  • the infection in the subject can be reduced to below about 300 CFU/lung, below about 200 CFU/lung, below about 100 CFU/lung, below about 50 CFU/lung, below about 25 CFU/lung or below about 10 CFU/lung.
  • the infection can be substantially or entirely cleared from the CF subject.
  • substantially cleared refers to reducing the infection to about 10 CFU/lung or less.
  • the presently disclosed subject matter provides a combination therapeutic treatment method for treating a Pa infection in a subject with CF, the combination therapeutic treatment method comprising: administering to the subject with CF a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic Attorney Docket No.3289.0008WO fragment thereof from a T3SS of Pa and ii) an LTA1 from enterotoxigenic Escherichia coli, optionally wherein the vaccine further comprises a squalene- based oil-in-water emulsion (e.g., an ME e
  • a squalene- based oil-in-water emulsion e.g., an
  • the antibiotic can comprise any suitable antibiotic such as described above.
  • the antibiotic can comprise one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate.
  • the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate.
  • the antibiotic comprises or consists of an aminoclycoside.
  • the antibiotic comprises tobramycin.
  • the antibiotic can be administered to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine.
  • the antibiotic e.g., at least one dose of the antibiotic
  • the fusion polypeptide comprises the amino acid sequence of LTA1 (SEQ ID NO: 6) or an amino acid sequence having at least about 90% homology thereto.
  • the fusion polypeptide comprises the amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% homology thereto.
  • the fusion polypeptide comprises the amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PaF (SEQ ID NO: 2) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the Attorney Docket No.3289.0008WO fusion polypeptide comprises L-PaF (i.e., SEQ ID NO: 4) or an amino acid having at least 90% homology to SEQ ID NO: 4.
  • the fusion polypeptide comprises an amino acid sequence having at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% homology to SEQ ID NO: 4.
  • the vaccine comprises L-PaF/ME.
  • the presently disclosed subject matter provides a composition for use in treating a Pa infection (i.e., an existing Pa infection) in a subject with CF, wherein the composition comprises: (a) a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa)and ii) an LTA1 from enterotoxigenic Escherichia coli; and (b) a therapeutically effective amount of an antibiotic.
  • the antibiotic can comprise any suitable antibiotic such as described above.
  • the antibiotic can comprise one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate.
  • the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate.
  • the antibiotic comprises or consists of an aminoglycoside.
  • the antibiotic comprises tobramycin.
  • the fusion polypeptide comprises the amino acid sequence of LTA1 (SEQ ID NO: 6) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises Attorney Docket No.3289.0008WO the amino acid sequence of PaF (SEQ ID NO: 2) or an amino acid sequence having at least about 90% homology thereto.
  • the fusion polypeptide comprises L-PaF (i.e., SEQ ID NO: 4) or an amino acid having at least 90% homology to SEQ ID NO: 4. In some embodiments, the fusion polypeptide comprises an amino acid sequence having at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% homology to SEQ ID NO: 4.
  • the vaccine comprises an oil-in-water emulsion (e.g., a squalene-based oil-in-water emulsion). In some embodiments, the vaccine comprises L-PaF/ME. III.
  • the presently disclosed subject matter relates to methods comprising the administration of polypeptides.
  • the polypeptides can be prepared via chemical synthesis, according to methods known in the field.
  • the polypeptides are recombinant polypeptides.
  • the presently disclosed subject matter relates to recombinant polypeptides and the nucleic acids encoding the polypeptides.
  • the polynucleotides disclosed herein can be introduced into an expression vector, such that the expression vector comprises a promoter and the polynucleotides encoding the peptides or polypeptides described herein.
  • the expression vector can provide for expression of the peptides or polypeptides in a suitable expression system using techniques well known in the art, followed by isolation or purification of the expressed peptide or polypeptide of interest.
  • a suitable expression system using techniques well known in the art, followed by isolation or purification of the expressed peptide or polypeptide of interest.
  • a variety of bacterial, yeast, plant, mammalian, and insect expression systems are available in the art and any such expression system can be used.
  • a polynucleotide encoding a peptide of use herein can be translated in a cell-free translation system.
  • nucleic acid sequence (SEQ ID NO: 1): Attorney Docket No.3289.0008WO CATATGGAAGTCAGAAACCTTAATGCCGCTCGCGAGCTGT TCCTGGACGAGCTCCTGGCCGCGTCGGCGGCGCCTGCC AGTGCCGAGCAGGAGGAACTGCTGGCCCTGTTGCGCAGC GAGCGGATCGTGCTGGCCCACGCCGGCCAGCCGCTGAG CGAGGCGCAAGTGCTCAAGGCGCTCGCCTGGTTGCTCGC GGCCAATCCGTCCGCGCCTCCGGGGCAGGGCCTCGAGG TACTCCGCGAAGTCCTGCAGGCACGTCGGCAGCCCGGTG CGCAGTGGGATCTGCGTGAGTTCCTGGTGTCGGCCTATTT CAGCCTGCACGGGCGTCTCGACGAGGATGTCATCGGTGT CTACAAGGATGTCCTGCAGACCCAGGACGGCAAGCGCAA GGCGCTGCTCGACGAGCTCAAGCGCAA GGCGCTGCTCGACGAGCTCAAGCGCAA GGCG
  • Homology between two amino acid sequences indicates the percentage of Attorney Docket No.3289.0008WO amino acids that are identical between the sequences. Said percentage is purely statistical, and the differences between the two sequences can be but are not necessarily randomly distributed over the entire length of the sequences to be compared. Comparisons of two sequences are usually carried out by comparing said sequences, after optimal alignment, with respect to a segment or “window of comparison”, in order to identify local regions of corresponding sequences. The optimal alignment for a comparison can be carried out manually or with the aid of the local homology algorithm by Smith and Waterman, 1981, Ads App. Math. 2, 482, with the aid of the local homology algorithm by Needleman and Wunsch, 1970, J. Mol.
  • the homology is given for a region which is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90% or about 100% of the entire length of the reference sequence.
  • the homology is given for at least about 100, at least about 120, at least about 140, at least about 160, at least about 180, or about 200 nucleotides, in some embodiments in continuous nucleotides.
  • the homology is given for the entire length of the reference sequence.
  • Nucleic acid sequences or amino acid sequences having a homology to a given nucleic acid sequence or amino acid sequence, respectively, can have at least one functional property of said given sequence, e.g., and in some instances, are functionally equivalent to said given sequence.
  • a nucleic acid sequence or amino acid sequence having a Attorney Docket No.3289.0008WO particular homology to a given nucleic acid sequence or amino acid sequence is functionally equivalent to said given sequence.
  • variants of polypeptides herein disclosed typically have at least about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence.
  • sequences would be said to have the stated identity.
  • a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above.
  • Proteins and Protein Variants As discussed herein there are numerous variants of the needle tip protein, translocator protein, the fusion polypeptides thereof (such as, for example, PcrV, PopB, PaF and L-PaF) that are herein contemplated.
  • the known functional strain variants there are derivatives of the needle tip protein and translocator protein which also function in the disclosed methods and compositions. Protein variants and derivatives are well understood to those of skill in the art and can involve amino acid sequence Attorney Docket No.3289.0008WO modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants.
  • Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues.
  • Immunogenic fusion protein derivatives such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. In some embodiments, no more than from about 2 to about 6 residues are deleted at any one site within the protein molecule.
  • variants ordinarily can be prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture.
  • Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example M13 primer mutagenesis and PCR mutagenesis.
  • Amino acid substitutions are typically of single residues but can occur at a number of different locations at once; insertions usually will be on the order of from about 1 to about 10 amino acid residues; and deletions will range from about 1 to about 30 residues.
  • Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues.
  • substitutions, deletions, insertions or any combination thereof can be combined to arrive at a final construct.
  • the mutations should not place the sequence out of reading frame and preferably should not create complementary regions that could produce secondary mRNA structure.
  • substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Table 2 and are referred to as conservative substitutions. Table 1, below, lists the amino acid residues and their abbreviations. Attorney Docket No.3289.0008WO Table 1. Amino Acids, Three Letter and One Letter Abbreviations. Amino Acid Abbreviations Alanine Ala A abe .
  • seryl or threonyl is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine, in this case, or (e) by increasing the number of sites for sulfation and/or glycosylation.
  • a hydrophobic residue e.g. leucyl, isoleu
  • substitutional or deletional mutagenesis can be employed to insert sites for N-glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr).
  • Deletions of cysteine or other labile residues also can be desirable.
  • Deletions or substitutions of potential proteolysis sites e.g. Arg
  • Arg is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues.
  • Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues Attorney Docket No.3289.0008WO are deamidated under mildly acidic conditions.
  • SEQ ID NO: 2 sets forth a particular sequence of Pa needle tip protein-translocator protein fusion (PaF) and SEQ ID NO: 4 sets forth a particular sequence of a LTA1-PaF fusion protein.
  • PaF Pa needle tip protein-translocator protein fusion
  • SEQ ID NO: 4 sets forth a particular sequence of a LTA1-PaF fusion protein.
  • variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the stated sequence.
  • the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
  • homology can be performed by published algorithms.
  • Optimal alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman Adv. App.
  • nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences are not necessarily written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequences.
  • SEQ ID NO: 1 one of the many nucleic acid sequences that can encode the protein sequence set forth in SEQ ID NO: 2 is set forth in SEQ ID NO: 1. It is understood that for this mutation all of the nucleic acid sequences that encode this particular derivative of the PaF are also disclosed.
  • amino acids can readily be incorporated into polypeptide chains by charging tRNA molecules with the amino acid of choice and engineering genetic constructs that utilize, for example, amber codons, to insert the analog amino acid into a peptide chain in a site-specific way.
  • Attorney Docket No.3289.0008WO Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage.
  • linkages for amino acids or amino acid analogs can include —CH2NH—, —CH2S—, —CH2—CH2—, — CH ⁇ CH-(cis and trans), —COCH2—, —CH(OH)CH2—, and —CHH2SO—
  • Spatola A. F. in Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F., Vega Data (March 1983), Vol. 1, Issue 3, Peptide Backbone Modifications (general review); Morley, Trends Pharm.
  • EP 45665 CA (1982): 97:39405 (1982) (—CH(OH)CH2—); Holladay et al. Tetrahedron. Lett 24:4401-4404 (1983) (—C(OH)CH2—); and Hruby Life Sci 31:189-199 (1982) (—CH2—S—); each of which is incorporated herein by reference.
  • a particularly preferred non-peptide linkage is —CH2NH—. It is understood that peptide analogs can have more than one atom between the bond atoms, such as ⁇ -alanine, ⁇ -aminobutyric acid, and the like.
  • Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others.
  • D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such.
  • Systematic substitution of one or more amino acids of a consensus sequence with a D- amino acid of the same type e.g., D-lysine in place of L-lysine
  • D-lysine in place of L-lysine
  • Cysteine residues can be used to cyclize or attach two or more peptides together. This can be beneficial to constrain peptides into particular conformations.
  • Attorney Docket No.3289.0008WO the polypeptides administered according to the methods described herein can include antigenic fragments of one or more of subunit (e.g. PcrV or PopB). Fragments of the sequences of PcrV or PopB can be assessed, for example, by determining the ability of the fragments to bind to antibodies that have specific binding to PcrV, PopB, or Pa and/or to elicit antibodies that cross react with full length PcrV, PopB, or Pa.
  • subunit e.g. PcrV or PopB
  • the antigenic fragment should retain at least about 50%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% of the antibody binding activity of parent polypeptide.
  • III.C. Nucleic Acids There are a variety of molecules disclosed herein that are nucleic acid based, including for example the nucleic acids that encode, for example PcrV, PopB, PaF, LTA1 or antigenic fragments thereof, as well as various functional nucleic acids.
  • the disclosed nucleic acids are made up of, for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein.
  • a nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage.
  • the base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T).
  • the sugar moiety of a nucleotide is a ribose or a deoxyribose.
  • the phosphate moiety of a nucleotide is pentavalent phosphate.
  • a non-limiting example of a nucleotide would be 3′- AMP (3′-adenosine monophosphate) or 5′-GMP (5′-guanosine monophosphate).
  • a nucleotide analog is a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties.
  • nucleotides Modifications to nucleotides are well known in the art and would include for example, 5- methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, and 2-aminoadenine, as well as modifications at the sugar or phosphate Attorney Docket No.3289.0008WO moieties. There are many varieties of these types of molecules available in the art and available herein. Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA).
  • PNA peptide nucleic acid
  • Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid. There are many varieties of these types of molecules available in the art and available herein. It is also possible to link other types of molecules (conjugates) to nucleotides or nucleotide analogs to enhance for example, cellular uptake. Conjugates can be chemically linked to the nucleotide or nucleotide analogs.
  • the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, N1, and C6 positions of a purine-based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine- based nucleotide, nucleotide analog, or nucleotide substitute.
  • a Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA.
  • the Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.
  • nucleic Acid Delivery There are a number of compositions and methods which can be used to deliver nucleic acids to cells, either in vitro or in vivo. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems.
  • the nucleic acids can be delivered through a number of direct delivery systems Attorney Docket No.3289.0008WO such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al.
  • plasmid or viral vectors are agents that transport the disclosed nucleic acids into the cell without degradation and include a promoter yielding expression of the gene in the cells into which it is delivered.
  • Viral vectors are, for example, Adenovirus, Adeno-associated virus, Herpes virus, Vaccinia virus, Polio virus, AIDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors.
  • Retroviruses include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector.
  • a retrovirus is essentially a package which has packed into it nucleic acid cargo.
  • the Attorney Docket No.3289.0008WO nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat.
  • a packaging signal In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus.
  • a retroviral genome contains the gag, pol, and env genes which are involved in the making of the protein coat. It is the gag, pol, and env genes which are typically replaced by the foreign DNA that it is to be transferred to the target cell.
  • Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5′ to the 3′ LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the LTRs that enable the insertion of the DNA state of the retrovirus to insert into the host genome.
  • a packaging signal for incorporation into the package coat a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5′ to the 3′ LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the
  • gag, pol, and env genes allow for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert. Since the replication machinery and packaging proteins in most retroviral vectors have been removed (gag, pol, and env), the vectors are typically generated by placing them into a packaging cell line.
  • a packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery but lacks any packaging signal.
  • AAV type vectors can transport about 4 to 5 kb and wild type AAV is known to stably insert into chromosome 19. Vectors which contain this site specific integration property are preferred.
  • An especially preferred embodiment of this type of vector is the P4.1 C vector produced by Avigen, San Francisco, CA, which can contain the herpes simplex virus thymidine kinase gene, HSV-tk, and/or a marker gene, such as the gene encoding the green fluorescent protein, GFP.
  • the AAV contains a pair of inverted terminal repeats (ITRs) which flank at least one cassette containing a promoter which directs cell-specific expression operably linked to a heterologous gene.
  • ITRs inverted terminal repeats
  • compositions can comprise, in addition to the disclosed needle tip protein-translocator protein fusion (such as, for example, PaF) or vectors for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, DC-cholesterol) or anionic liposomes.
  • liposomes can further comprise proteins to facilitate targeting a particular cell, if desired.
  • Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract.
  • liposomes see, e.g., Brigham et al. Am. J. Resp. Cell. Mol.
  • the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage.
  • Attorney Docket No.3289.0008WO In the methods described above which include the administration and uptake of exogenous DNA into the cells of a subject (i.e., gene transduction or transfection), delivery of the compositions to cells can be via a variety of mechanisms.
  • viral integration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid-based Attorney Docket No.3289.0008WO system of delivery, such as a liposome, so that the nucleic acid contained in the delivery system can become integrated into the host genome.
  • Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome.
  • the transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.
  • III.E. Expression Systems The nucleic acids that are delivered to cells typically contain expression controlling systems.
  • the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product.
  • a promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site.
  • a promoter contains core elements required for Attorney Docket No.3289.0008WO basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements.
  • Preferred promoters controlling transcription from vectors in mammalian host cells can be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter.
  • the early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al., Nature, 273: 113 (1978)).
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment (Greenway, P. J.
  • Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression.
  • Preferred examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the promotor and/or enhancer can be specifically activated either by light or specific chemical events which trigger their function.
  • Systems can be Attorney Docket No.3289.0008WO regulated by reagents such as tetracycline and dexamethasone.
  • reagents such as tetracycline and dexamethasone.
  • the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed.
  • the promoter and/or enhancer region be active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time.
  • a preferred promoter of this type is the CMV promoter (650 bases).
  • Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR. It has been shown that all specific regulatory elements can be cloned and used to construct expression vectors that are selectively expressed in specific cell types such as melanoma cells.
  • the glial fibrillary acetic protein (GFAP) promoter has been used to selectively express genes in cells of glial origin.
  • Expression vectors used in eukaryotic host cells can also contain sequences for the termination of transcription which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3′ untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contains a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA.
  • polyadenylation signals in expression constructs are well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs.
  • the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases. It is also preferred that the transcribed units contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct.
  • Attorney Docket No.3289.0008WO The viral vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed.
  • Preferred marker genes are the E.
  • Coli lacZ gene which encodes B-galactosidase, and green fluorescent protein.
  • the marker can be a selectable marker.
  • suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media.
  • CHO DHFR-cells and mouse LTK-cells. These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media.
  • An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non- supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line.
  • compositions employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or Attorney Docket No.3289.0008WO neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puromycin. IV.
  • Pharmaceutical Compositions The active ingredients (e.g., the fusion polypeptide vaccine and/or antibiotic) of the presently disclosed subject matter can be provided in pharmaceutical compositions comprising additional components, e.g., a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable is meant a material that is not biologically or otherwise undesirable, i.e., the material can be administered to a subject 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.
  • the carrier would naturally be selected to minimize any degradation of the active ingredient(s) (e.g., the vaccine and/or antibiotic) and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
  • compositions can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including intranasally (e.g., via topical intranasal administration or administration by inhalant).
  • topical intranasal administration means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the active ingredients.
  • Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism.
  • compositions can also be directly to any area of the respiratory system (e.g., lungs) via intubation.
  • the exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the infection being treated, the particular active ingredient(s) used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein. Attorney Docket No.3289.0008WO Parenteral administration of the composition, if used, is generally characterized by injection.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
  • a more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No.3,610,795, which is incorporated by reference herein.
  • the active ingredients can be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells) or emulsion (e.g., an oil- in-water emulsion). In some embodiments, these be targeted to a particular cell type via antibodies, receptors, or receptor ligands.
  • Suitable pharmaceutical carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, PA 1995.
  • an appropriate amount of a pharmaceutically acceptable salt is used in the formulation to render the formulation isotonic.
  • the pharmaceutically acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution.
  • the pH of the solution is preferably from about 5 to about 8, more preferably from about 7 to about 7.6, and most preferably about 7.5.
  • Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing an active ingredient, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers can be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.
  • Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH.
  • the compositions can be administered intramuscularly or subcutaneously. Other compounds can be administered according to standard procedures used by those skilled in the art.
  • compositions can include carriers, thickeners, diluents, Attorney Docket No.3289.0008WO buffers, preservatives, surface active agents and the like in addition to the molecule of choice.
  • Pharmaceutical compositions can also include one or more additional active ingredients such as antimicrobial agents, anti- inflammatory agents, anesthetics, and the like.
  • the pharmaceutical composition can be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration can be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection.
  • the disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.
  • Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions.
  • non- aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives can also be present such as, for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like.
  • Formulations for topical administration can include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like can be desirable.
  • Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets.
  • compositions can potentially be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, tri-alkyl and aryl amines and substituted ethanolamines.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid
  • organic acids such as formic acid, acetic acid, propi
  • Effective dosages and schedules for administering the compositions can be determined empirically, and making such determinations is within the skill in the art.
  • the dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms of the infection are affected.
  • the dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like.
  • the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art.
  • the dosage can be adjusted by the individual physician in the event of any counterindications. Dosage can vary, and can be administered in one or more dose administrations daily, weekly, or monthly.
  • the amount of polypeptide that is administered per dose of vaccine is in the range of from about 0.0001 to about 1000 ⁇ g/kg. In some embodiments, the amount is in the range of from about 0.001 to about 1000 ⁇ g/kg of body weight of the recipient. In some embodiments, the amount is in the range of from about 0.01 to about 1000 ⁇ g/kg of body weight of the recipient. In some embodiments, the amount is in the range of from about 0.01 to about 100 ⁇ g/kg of body weight of the recipient.
  • EXAMPLES provide illustrative embodiments. In light of the present disclosure and the general level of skill in the art, those of skill will appreciate that the following EXAMPLES are intended to be exemplary only that that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently disclosed subject matter.
  • L-PaF can be prepared as described in U.S. Patent No. 11,439,700 and PCT International Patent Application Publication No. WO2022/246327, the disclosures of which are incorporated herein by reference in their entireties.
  • the PaF sequence had a 3’ stop codon prior to the XhoI restriction site.
  • the plasmid pACYC-His-PcrH-LTA1-PaF was transformed into Tuner cells.
  • E. coli Tuner cells expressing L-PaF/His-Tag PcrH were grown in TB media supplemented with chloramphenicol (34 ⁇ g/ml) with a fed-batch mode in a 10 L bioreactor (Labfors 5, Infors USA Inc., MD).
  • An overnight starter was Attorney Docket No.3289.0008WO expanded to 1 L and approximately 800 mL was transferred to the bioreactor containing 9 L of TB media supplemented with chloramphenicol (34 ⁇ g/ml).
  • the culture temperature was maintained at 30°C and protein expression was induced adding IPTG to 1 mM when the culture reached an A600 of about 25. After 3 h, the bacteria were collected and processed for purification.
  • the L- PaF/His-Tag PcrH was captured on an IMAC column followed by Q anion exchange chromatography. Lauryldimethylamine oxide (LDAO) was added to a final concentration of 0.1% to release the HT-PcrH.
  • LDAO Lauryldimethylamine oxide
  • the protein solution was passed over a final IMAC column with the L-PaF passing through the column. L-PaF was dialyzed into PBS with 0.05% LDAO and stored at ⁇ 80°C.
  • PA Infection Unless described otherwise, Pa infection/challenge and rechallenge of CF rats was performed by intratracheal administration of 3 x 10 6 CFUs of PA strain mPA0831. Tobramycin Unless described otherwise, tobramycin administration to CF rats was performed by intranasal administration of 3 mg/kg body weight tobramycin (Sigma) per day for 7 days. EXAMPLE 1 Two groups of six CF rats were infected with PA.

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Abstract

Methods of treating existing infections by administration of a composition comprising a fusion protein-based vaccine, alone or in combination with an antibiotic agent, are described. The methods can involve treating existing Pseudomonas aeruginosa infections and/or treating infections in a subject with cystic fibrosis. Compositions comprising combinations of fusion protein-based vaccines and antibiotics for use in treating infections are also described.

Description

Attorney Docket No.3289.0008WO THERAPEUTIC COMPOSITIONS AND METHODS CROSS-REFERENCE TO RELATED APPLICATION This application claims the benefit of U.S. Provisional Patent Application Serial No.63/671,854, filed July 16, 2024, the disclosure of which is incorporated herein by reference in its entirety. REFERENCE TO SEQUENCE LISITNG SUBMITTED ELECTRONICALLY The content of the electronically submitted sequence listing in XML format (Name: 3289_0008_WO.xml; Size: 24,108 bytes; and Date of Creation: June 9, 2025) filed with the application is incorporated herein by reference in its entirety. GOVERNMENT SUPPORT This invention was made with government support under AI169781 awarded by the National Institutes of Health. The Government has certain rights in the invention. TECHNICAL FIELD The presently disclosed subject matter relates to methods of treating existing infections, e.g., gram-negative bacterial infections, such as Pseudomonas aeruginosa (Pa) infections, in subjects with cystic fibrosis (CF) via administration of a therapeutic fusion polypeptide-based vaccine. The presently disclosed subject matter further relates to combinations of fusion polypeptide-based vaccines and antibiotics for use in treating infections in subjects with CF. BACKGROUND Pseudomonas aeruginosa (Pa) is an opportunistic human pathogen responsible for severe infections in patients with burns, severe wounds, pneumonia, and critically ill patients who are intubated (ventilator-associated Attorney Docket No.3289.0008WO pneumonia) or who have undergone catheterization (urinary tract infections). Clearing Pa has become increasingly difficult due to innate and acquired antibiotic resistant. Pa is also the major cause of pulmonary infection in cystic fibrosis (CF) patients. Currently, the standard of treatment for CF patients with lung infections is the administration of an antibiotic such as tobramycin. However, tobramycin does not clear bacterial infections, particularly Pa infections. Accordingly, there remains a need for effective methods and compositions for treating infections in CF patients. SUMMARY This Summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features. In some embodiments, the presently disclosed subject matter provides a method for treating an infection in a subject with cystic fibrosis (CF) comprising administering to the subject a therapeutically effective amount of: (a) a vaccine comprising a fusion polypeptide wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa) and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli; and (b) optionally, an antibiotic. In some embodiments, the subject with CF has a Pa infection. In some embodiments, the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide having an amino acid Attorney Docket No.3289.0008WO sequence of SEQ ID NO: 2 (PaF) or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 2. In some embodiments, the LTA1 is 5’ of the fusion of the needle tip protein or an antigenic fragment thereof and/or the translocator protein fusion or an antigenic fragment thereof, optionally wherein the LTA1 has an amino acid sequence of SEQ ID NO: 6, or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 6. In some embodiments, the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 (L-PaF), or an amino acid sequence having at least 90% homology to SEQ ID NO: 4. In some embodiments, the vaccine comprises an oil-in-water emulsion, optionally wherein said emulsion comprises squalene, further optionally wherein the vaccine comprises MedImmune Emulsion (ME). In some embodiments, the vaccine is administered to the subject at least two times. In some embodiments, the method comprises administering an antibiotic to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine. In some embodiments, the antibiotic is selected from the group comprising a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, colistimethate, and a combination thereof, optionally wherein the antibiotic comprises an aminoglycoside, further optionally wherein the antibiotic comprises tobramycin. In some embodiments, the route of administration for the antibiotic is selected from intravenous, oral or inhalation. In some embodiments, the infection in the subject is reduced by at least about 25%, at least about 50%, at least about 75%, at least about 90%, at least about 95%, or more. In some embodiments, the infection in the subject is reduced to below about 300 colony forming units per lung (CFU/lung), below about 200 CFU/lung, below about 100 CFU/lung, below about 50 CFU/lung or below about 10 CFU/lung. In some embodiments, the infection is substantially or entirely cleared from the CF subject. In some embodiments, the presently disclosed subject matter provides a combination therapeutic treatment method for treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), the combination Attorney Docket No.3289.0008WO therapeutic treatment method comprising: administering to the subject with CF a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa), and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli, optionally wherein the vaccine further comprises a squalene-based oil-in-water emulsion; and administering to the subject with CF a therapeutically effective amount of an antibiotic, wherein the Pa infection in the subject with CF is substantially reduced and/or cleared. In some embodiments, the antibiotic comprises tobramycin. In some embodiments, the antibiotic is administered substantially simultaneously with the vaccine. In some embodiments, the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4. In some embodiments, the presently disclosed subject matter provides a composition for use in treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), wherein the composition comprises: (a) a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa) and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli; and (b) a therapeutically effective amount of an antibiotic. In some embodiments, the antibiotic comprises Tobramycin. In some embodiments, the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4. Accordingly, it is an object of the presently disclosed subject matter to provide a method of treating an infection, e.g., a Pa infection, in a subject with CF and to methods of treating infections in a subject with CF using a combination of a fusion protein-based therapeutic vaccine and an antibiotic. Attorney Docket No.3289.0008WO This and other objects are achieved in whole or in part by the presently disclosed subject matter. Further, an object of the presently disclosed subject matter having been stated above, other objects and advantages of the presently disclosed subject matter will become apparent to those skilled in the art after a study of the following description, Figures, and Examples. BRIEF DESCRIPTIONS OF THE FIGURES Figure 1A is a graph showing the results of an in vivo efficacy study of tobramycin in cystic fibrous model (CF) rats. A group of CF rats were challenged with Pseudomonas aeruginosa (Pa; strain mPA0831, 3 x 106 colony forming units (CFUs)) and then treated with the antibiotic tobramycin (3 milligrams per kilogram per day (mg/kg/day) for 7 days). For comparison, a group of rats were challenged with Pa and not treated with antibiotic. CFU burden per lung (CFU/lung) was determined in these two groups (Tobramycin and Untreated, respectively) on day 28 post-Pa challenge. ****p<0.0001. Figure 1B is a graph showing the in vivo efficacy of antibiotic alone, of fusion protein vaccine alone, and of a combination of antibiotic and fusion protein vaccine in treating a bacterial infection in cystic fibrosis model (CF) rats. Groups of CF rats were treated with tobramycin (Tob; 3 milligrams per kilogram per day (mg/kg/day) for 7 days) starting on day 14 after challenge with Pseudomonas aeruginosa (Pa, strain mPA0831, 3 x 106 colony forming units (CFUs)); vaccinated three times with a fusion protein oil-in-water emulsion of the presently disclosed subject matter (L-PaF/ME, Vaccine; 30 micrograms (µg)) on days 28, 42, and 56 after Pa challenge; or treated with tobramycin (3 mg/kg/day for 7 days) starting on day 14 following Pa challenge and vaccinated with the vaccine on day 28, 42, and 56 following Pa challenge; Tob + Vax). Rats were rechallenged with Pa (strain mPA0831, 3 x 106 CFUs) on day 70 of the study. For comparison, data for rats that were challenged with Pa but administered phosphate buffered saline (PBS) in place of the tobramycin and vaccine is also shown. CFU burden per lung (CFU/lung) was determined on day 84 after the first Pa challenge. Figure 2 is a graph showing the results of an in vivo efficacy study of Attorney Docket No.3289.0008WO single agent treatments or a combination treatment in cystic fibrosis model (CF) rats. Groups of CF rats were treated with tobramycin (Tob; 3 milligrams per kilogram per day (mg/kg/day) for 7 days) starting on day 21 after challenge with Pseudomonas aeruginosa (Pa; starin mPA0831, 3 x 106 colony forming units (CFUs)); with two administrations of L-PaF/ME vaccine (Vaccine; 30 micrograms (µg)) on days 28 and 42 after Pa challenge; or with tobramycin (3 mg/kg/day for 7 days) starting on day 21 following Pa challenge followed by two administrations of the vaccine (on day 28 and 42 following Pa challenge) (Tob + Vax). CFU burden per lung (CFU/lung) was determined on day 56 of the study. * p<0.05. Figure 3 is a graph showing the results of an in vivo efficacy study of a combination treatment in cystic fibrosis model (CF) rats. Groups of CF rats were treated with tobramycin (3 milligrams per kilogram (mg/kg)) and L- PaF/ME vaccine (30 micrograms (µg)) on day 21 after challenge with Pseudomonas aeruginosa (Pa; strain mPA0831, 3 x 106 colony forming units (CFUs)) and then with tobramycin (3 mg/kg) on each of days 22-27. CFU burden per lung (CFU/lung) was determined on day 28 of the study. For comparison, data for Pa challenged CF rats treated only with the vaccine on day 21 is also shown. DETAILED DESCRIPTION The presently disclosed subject matter now will be described more fully hereinafter, in which some, but not all embodiments of the presently disclosed subject matter are described. Indeed, the presently disclosed subject matter can be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements. Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this pertains. The references disclosed are also individually and specifically incorporated by reference herein for the material contained in them that is discussed in the sentence in which the reference is relied upon. Attorney Docket No.3289.0008WO I. Definitions The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the presently disclosed subject matter. While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. All technical and scientific terms used herein, unless otherwise defined below, are intended to have the same meaning as commonly understood by one of ordinary skill in the art. References to techniques employed herein are intended to refer to the techniques as commonly understood in the art, including variations on those techniques or substitutions of equivalent techniques that would be apparent to one of skill in the art. While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. In describing the presently disclosed subject matter, it will be understood that a number of techniques and steps are disclosed. Each of these has individual benefit and each can also be used in conjunction with one or more, or in some cases all, of the other disclosed techniques. Accordingly, for the sake of clarity, this description will refrain from repeating every possible combination of the individual steps in an unnecessary fashion. Nevertheless, the specification and claims should be read with the understanding that such combinations are entirely within the scope of the invention and the claims. Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to "an antibiotic" includes a plurality of such antibiotics, and so forth. Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term Attorney Docket No.3289.0008WO “about”. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently disclosed subject matter. As used herein, the term “about,” when referring to a value or to an amount of a composition, dose, homology or sequence identity (e.g., when comparing two or more nucleotide or amino acid sequences), mass, weight, temperature, time, volume, concentration, percentage, etc., is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, and in some embodiments ±0.1% from the specified amount, as such variations are appropriate to perform the disclosed methods or employ the disclosed compositions. The term “comprising”, which is synonymous with “including” “containing” or “characterized by” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. “Comprising” is a term of art used in claim language which means that the named elements are essential, but other elements can be added and still form a construct within the scope of the claim. As used herein, the phrase “consisting of” excludes any element, step, or ingredient not specified in the claim. When the phrase “consists of” appears in a clause of the body of a claim, rather than immediately following the preamble, it limits only the element set forth in that clause; other elements are not excluded from the claim as a whole. As used herein, the phrase “consisting essentially of” limits the scope of a claim to the specified materials or steps, plus those that do not materially affect the basic and novel characteristic(s) of the claimed subject matter. With respect to the terms “comprising”, “consisting of”, and “consisting essentially of”, where one of these three terms is used herein, the presently disclosed and claimed subject matter can include the use of either of the other two terms. As used herein, the term “and/or” when used in the context of a listing of entities, refers to the entities being present singly or in combination. Thus, Attorney Docket No.3289.0008WO for example, the phrase “A, B, C, and/or D” includes A, B, C, and D individually, but also includes any and all combinations and subcombinations of A, B, C, and D. An "increase" can refer to any change that results in a greater amount of a symptom, disease, composition, condition or activity. An increase can be any individual, median, or average increase in a condition, symptom, activity, composition in a statistically significant amount. Thus, the increase can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% increase so long as the increase is statistically significant. As used herein, a "decrease" can refer to any change that results in a smaller amount of a symptom, disease, composition, condition, or activity. A substance is also understood to decrease the genetic output of a gene when the genetic output of the gene product with the substance is less relative to the output of the gene product without the substance. Also, for example, a decrease can be a change in the symptoms of a disorder such that the symptoms are less than previously observed. A decrease can be any individual, median, or average decrease in a condition, symptom, activity, composition in a statistically significant amount. Thus, the decrease can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% decrease so long as the decrease is statistically significant. As used herein, "inhibit," "inhibiting," and "inhibition" mean to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This can also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, the reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels. By “reduce” or other forms of the word, such as “reducing” or “reduction,” in the context of a bacterial infection is meant lowering the number of bacteria or the number of viable bacteria (i.e., colony forming units (CFUs) Attorney Docket No.3289.0008WO of a bacteria). It can also refer to lowering a level of a biological marker of the infection (e.g., lowering white blood cell count in a subject with the infection, etc.). It is understood that this is typically in relation to some standard or expected value, in other words it is relative (e.g., to the number or level prior to treatment), but that it is not always necessary for the standard or relative value to be referred to. By “prevent” or other forms of the word, such as “preventing” or “prevention,” is meant to stop a particular event or characteristic, to stabilize or delay the development or progression of a particular event or characteristic, or to minimize the chances that a particular event or characteristic will occur. Prevent does not require comparison to a control as it is typically more absolute than, for example, reduce. As used herein, something could be reduced but not prevented, but something that is reduced could also be prevented. Likewise, something could be prevented but not reduced, but something that is prevented could also be reduced. It is understood that where reduce or prevent are used, unless specifically indicated otherwise, the use of the other word is also expressly disclosed. As used herein, the term “subject” refers to any individual who is the target of administration or treatment. The subject can be a vertebrate, for example, a mammal. In one aspect, the subject can be human, non-human primate, bovine, equine, porcine, canine, or feline. The subject can also be a guinea pig, rat, hamster, rabbit, mouse, or mole. Thus, the subject can be a human or veterinary patient. The term “patient” refers to a subject under the treatment of a clinician, e.g., physician. The term “therapeutically effective” refers to the amount of the composition used is of sufficient quantity to ameliorate one or more causes or symptoms of a disease or disorder. Such amelioration only requires a reduction or alteration, not necessarily elimination. The term “treatment” refers to the medical management of a patient with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This term includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological condition, or disorder, and also includes causal treatment, that is, treatment Attorney Docket No.3289.0008WO directed toward removal of the cause of the associated disease, pathological condition, or disorder. In addition, this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological condition, or disorder. “Effective amount” of an agent refers to a sufficient amount of an agent to provide a desired effect. The amount of agent that is “effective” will vary from subject to subject, depending on many factors such as the age and general condition of the subject, the particular agent or agents, and the like. Thus, it is not always possible to specify a quantified “effective amount.” However, an appropriate “effective amount” in any subject case can be determined by one of ordinary skill in the art using routine experimentation. Also, as used herein, and unless specifically stated otherwise, an “effective amount” of an agent can also refer to an amount covering both therapeutically effective amounts and prophylactically effective amounts. An “effective amount” of an agent necessary to achieve a therapeutic effect can vary according to factors such as the age, sex, and weight of the subject. Dosage regimens can be adjusted to provide the optimum therapeutic response. For example, several divided doses can be administered daily, or the dose can be proportionally reduced as indicated by the exigencies of the therapeutic situation. A "pharmaceutically acceptable" component can refer to a component that is not biologically or otherwise undesirable, i.e., the component can be incorporated into a pharmaceutical formulation provided by the disclosure and administered to a subject as described herein without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the formulation in which it is contained. When used in reference to administration to a human, the term generally implies the component has met the required standards of toxicological and manufacturing Attorney Docket No.3289.0008WO testing or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration. As used herein, "pharmaceutically acceptable carrier" (sometimes referred to as a “carrier”) means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non- toxic and includes a carrier that is acceptable for veterinary and/or human pharmaceutical or therapeutic use. The terms "carrier" or "pharmaceutically acceptable carrier" can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil/water or water/oil emulsion) and/or various types of wetting agents. As used herein, the term "carrier" encompasses, but is not limited to, any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in pharmaceutical formulations and as described further herein. “Pharmacologically active” (or simply “active”), as in a “pharmacologically active” derivative or analog, can refer to a derivative or analog (e.g., a salt, ester, amide, conjugate, metabolite, isomer, fragment, etc.) having the same type of pharmacological activity as the parent compound and approximately equivalent in degree. “Therapeutic agent” refers to any composition that has a beneficial biological effect. Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition (e.g., a non-immunogenic cancer). The terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like. When the terms “therapeutic agent” is used, then, or when a particular agent is specifically identified, it is to be understood that the term includes the agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc. “Therapeutically effective amount” or “therapeutically effective dose” of a composition (e.g. a composition comprising an agent) refers to an amount Attorney Docket No.3289.0008WO that is effective to achieve a desired therapeutic result. In some embodiments, a desired therapeutic result is the control of an infection. Therapeutically effective amounts of a given therapeutic agent will typically vary with respect to factors such as the type and severity of the disorder or disease being treated and the age, gender, and weight of the subject. The term can also refer to an amount of a therapeutic agent, or a rate of delivery of a therapeutic agent (e.g., amount over time), effective to facilitate a desired therapeutic effect, such as pain relief. The precise desired therapeutic effect will vary according to the condition to be treated, the tolerance of the subject, the agent and/or agent formulation to be administered (e.g., the potency of the therapeutic agent, the concentration of agent in the formulation, and the like), and a variety of other factors that are appreciated by those of ordinary skill in the art. In some instances, a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years. “Vaccine” as used herein is a preparation that stimulates an immune response that produces immunity against a particular antigen or antigens, e.g. a component of a gram-negative bacteria. Vaccines can be administered prophylactically (for example, to prevent or inhibit the establishment of an infection) or therapeutically (e.g., to inhibit, reduce, or treat an established infection, or to ameliorate the effects or symptoms of an existing infection). Vaccines can contain, but are not limited to, live, attenuated infectious material such as viruses or bacteria, and dead or inactivated organisms or purified products or fragments derived therefrom. In some embodiments, the vaccine of the presently disclosed subject matter comprises a “subunit vaccine”, i.e., a vaccine comprising purified fragments from a pathogen. In some embodiments, the vaccine comprises an antigenic fusion polypeptide. A vaccine can be administered by injection (e.g., subcutaneous (sc), intramuscular (im), intraperitoneal (ip), intradermal (id) or intravenous (iv) injection), orally, or by inhalation. In some embodiments, the presently disclosed subject matter relates to vaccines that are used therapeutically. The term “fusion” as used herein with reference to polypeptides and portions of polypeptides that are “fused” together means that the amino acid Attorney Docket No.3289.0008WO sequences are covalently joined to each other, e.g., by peptide bonds, directly or via a linking amino acid sequence. As used throughout, the term “fusion protein” or “fusion polypeptide” refers to a non-naturally occurring protein or polypeptide, e.g., a protein or polypeptide having an amino acid sequence comprising at least two partial or complete sequences derived from, obtained from, or isolated from different polypeptides that are not naturally adjoined. A fusion protein or fusion polypeptide can be the functional product of a fusion gene or fusion nucleic acid sequence. A fusion gene can further be modified by mutation, deletion, insertion or substitution of heterologous sequences, or by any means available using recombinant DNA technology. As used throughout, the term “fragment” refers to a peptide or polypeptide of formed by at least 6 amino acid residues which are linked to each other via peptide bonds, but which contains less amino acid residues (e.g., 5 less, 10 less, 20 less, 30 less, 40 less amino acid residues) than a recited “parent” polypeptide. In the context of the presently disclosed subject matter, an “antigenic fragment” is a peptide or polypeptide capable of eliciting an immune response, including the production of antibodies directed to that immunogenic fragment or to the protein having the immunogenic fragment. For example, an antigenic fragment of the needle tip protein PcrV has the ability to elicit the production of antibodies against PcrV. As used throughout, the terms “antibody” and “immunoglobulin” refer to a protein produced by the B-cells of the immune system that can identify, bind and neutralize an antigen. In the context of the presently disclosed subject matter, an antibody is produced by the immune system and binds a bacterial protein, e.g., such as PcrV or PopB. The antibody can have neutralizing properties and be capable of suppressing or reducing the biological activity of the bacterial protein. As used throughout, the term “active immunization” refers to immunization that stimulates the immune system to produce antibodies against an antigen (self or foreign). Active immunization can be induced through vaccination. Active immunization is often long-lasting and can be reactivated by repeated injection of boosters. In contrast, passive Attorney Docket No.3289.0008WO immunization occurs when antibodies directed against specific antigen are administered to a subject. As used throughout, the term “adjuvant” refers to a substance that increases the intensity of the immune response after co-administration with an immunogen. An adjuvant can act as an immunopotentiator, e.g., providing for more potent and/or persistent immune responses, while reducing the dose and number of boosters. Adjuvant can also increase the stability of the immunogenic composition or vaccine. II. Methods of Treating Infections Opportunistic infections, including Pseudomonas aeruginosa (referred to as “Pa”, “Pseudomonas” and/or “P. aeruginosa”) infections, in cystic fibrosis (CF) patients are common and there is a need for an effective therapeutic to treat the life-threatening infection. Currently, the standard of treatment for CF patients with lung infections, including Pa infections, is the aminoglycoside antibiotic tobramycin. However, as shown in the Examples hereinbelow, tobramycin does not clear Pa infections. Accordingly, the presently disclosed subject matter provides methods and therapeutic compositions for use in treating infections. In particular, the methods and compositions can provide therapeutic efficacy in the treatment of existing bacterial infections, such as Pa infections, in subjects with CF. In some embodiments, the present disclosure is directed to the use of a subunit vaccine as a therapeutic vaccine, e.g., in subjects with CF and existing bacterial infections. In some embodiments, the vaccine comprises (1) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pa and (2) an adjuvant, such as the A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli. For example, the fusion peptide referred to herein as “Pa fusion” or PaF is a fusion of two essential surface localized T3SS proteins from Pa, i.e., the needle tip protein PcrV (which has the amino acid sequence of SEQ ID NO: 8) and the translocator protein PopB (which has the amino acid sequence of SEQ ID NO: 10). These T3SS scaffold proteins are highly conserved (>96- Attorney Docket No.3289.0008WO 99%) among PAO1/PA14-like strains of PA. Because they are involved in the early stages of pathogenesis for PAO1/PA14-like strains, vaccine escape is unlikely since mutation of these proteins impacts assembly of the T3SS apparatus, rendering the mutant non-pathogenic. In some embodiments, PaF refers to the polypeptide having the amino acid sequence of SEQ ID NO: 2 or the amino acid sequence encoded by the nucleic acid sequence of SEQ ID NO: 1. In some embodiments, the vaccine comprises a fusion comprising an amino acid sequence of PcrV (SEQ ID NO: 8) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to the amino acid sequence SEQ ID NO: 8. In some embodiments, the fusion comprises an amino acid sequence of PopB (SEQ ID NO: 10) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to the amino acid sequence of SEQ ID NO: 10. In some embodiments, the fusion comprises an amino acid sequence of PaF (SEQ ID NO: 2) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 2. In some embodiments, the LTA1 subunit from the labile toxin (LT) of Enterotoxigenic E. coli (which has the amino acid sequence of SEQ ID NO: 6) serves as the adjuvant of the presently disclosed vaccine. LTA1 retains the toxin's ADP-ribosylation (ADPr) activity and the ability to promote dendritic cell (DC) maturation but does not possess detectable toxicity. LTA1 stimulates a balanced Th1/Th2 response along with a mucosal response characterized by production of mucosal IgA, as well as IL-17. Recently, it was shown that the addition of LTA1 to Fluzone increased IgA, while decreasing levels of IL-6 post-H1N1 challenge. Disclosed herein are compositions and methods using compositions comprising an adjuvant (e.g., LTA1 or a peptide having at least about 50%, 60%, 70%, 80%, 85%, 90%, 95%, 98% or 99% homology to LTA1 (SEQ ID NO: 6)) and a fusion of a needle tip protein or fragment thereof and a translocator protein or fragment there as separate components or as a fusion Attorney Docket No.3289.0008WO polypeptide (e.g., PaF (SEQ ID NO: 2 or a sequence having about 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.5% homology thereto)). In some embodiments, LTA1 is fused to the N-terminus of the PaF polypeptide to provide the fusion polypeptide LTA1-PaF (also referred to herein as “L-PaF”, and which has the amino acid sequence of SEQ ID NO: 4), thus providing simultaneous uptake of the adjuvant-antigen by antigen presenting cells to enhance cellular immunity. The L-PaF vaccine was previously described for prophylactic use against a bacterial infection in PCT/US2022/030565, the disclosure of which is incorporated herein by reference in its entirety. That is, in PCT/US2022/030565, the L-PaF vaccine was used as a preventative vaccine that acted as a precautionary measure to bolster a subject’s immune system to an associated illness. The goal was to prevent the infection or disease from occurring. In contrast, the studies disclosed herein demonstrate for the first time that L-PaF, alone or in conjunction with an antibiotic, can be used as a surprisingly effective therapeutic treatment for infections in subjects, including those suffering from CF. In some embodiments, provided herein are methods for using a therapeutically effective amount of any of the vaccines or fusion polypeptides disclosed herein and/or in PCT/US2022/030565, alone or in combination with an antibiotic composition, e.g. tobramycin, to treat an infection in subjects with an infection. In some embodiments, the subject is a human or other mammalian subject. In some embodiments, the subject with an infection is also suffering from CF. More particularly, the presently disclosed subject matter provides for therapeutically treating subjects suffering from CF by administering a composition comprising a vaccine comprising a fusion polypeptide comprising i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) LTA1 from enterotoxigenic Escherichia coli, alone or in combination with an antibiotic composition, e.g. tobramycin. Thus, in some embodiments, disclosed herein are methods of treating, decreasing, reducing, and/or ameliorating an infection in a subject with CF, or other condition related to or Attorney Docket No.3289.0008WO susceptible to a bacterial infection whether a Pa infection or other bacterial, comprising administering to the subject a therapeutically effective amount of any of the vaccines or fusion polypeptides disclosed herein, e.g. L-PaF/ME, optionally administered in combination with an appropriate antibiotic composition. For example, disclosed herein are methods of treating, decreasing, reducing, and/or ameliorating an opportunistic infection in a subject with CF comprising administering to the subject a therapeutically effective amount of a composition comprising a fusion polypeptide comprising i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) the LTA1 from enterotoxigenic Escherichia coli, alone or in combination with tobramycin or any other appropriate antibiotic. In some embodiments, the infection is a Pa infection, although the same therapeutic can be used to treat other types of infections in CF patients or non-CF patients, e.g. Methicillin- resistant Staphylococcus aureus (MRSA). In some embodiments, the fusion polypeptide comprises an amino acid sequence of PcrV (SEQ ID NO: 8) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 8. In some embodiments, the fusion polypeptide comprises an amino acid sequence of PopB (SEQ ID NO: 10) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 10. In some embodiments, the fusion polypeptide comprises an amino acid sequence of PaF (SEQ ID NO: 2) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 2. In some embodiments, the fusion polypeptide comprises an amino acid sequence of LTA1 (SEQ ID NO: 6) or a sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% homology to SEQ ID NO: 6. In some embodiments, the fusion polypeptide comprises an amino acid sequence of L-PaF (SEQ ID NO: 4) or a sequence having at least 50%, at least 60%, at least 70%, at least Attorney Docket No.3289.0008WO 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or at least 99.5% homology to SEQ ID NO: 4. Accordingly, in some embodiments, the presently disclosed subject matter provides a method for treating an infection in a subject with cystic fibrosis (CF) comprising administering to the subject a therapeutically effective amount of: (a) a vaccine comprising a fusion polypeptide wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa and ii) LTA1 from enterotoxigenic Escherichia coli; and (b) optionally, an antibiotic. In some embodiments, the subject is a human. In some embodiments, the subject with CF has a Pa infection. In some embodiments, the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide comprising an amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, or 99.5%) homology thereto. In some embodiments, the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide comprising an amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, or 99.5%) homology thereto. In some embodiments, the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide having an amino acid sequence of SEQ ID NO: 2 (PaF) or an amino acid sequence having at least 90% (e.g., at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5%) homology to the amino acid sequence of SEQ ID NO: 2. In some embodiments, the LTA1 is 5’ of the fusion of the needle tip protein or an antigenic fragment thereof and/or the translocator protein fusion or an antigenic fragment thereof. In some embodiments, the LTA1 has an amino acid sequence of SEQ ID NO: 6, or an amino acid sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) Attorney Docket No.3289.0008WO homology to the amino acid sequence of SEQ ID NO: 6. In some embodiments, the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 (L-PaF), or an amino acid sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5%) homology to SEQ ID NO: 4. In some embodiments, the vaccine comprises (e.g., the fusion polypeptide is formulated as) an emulsion, e.g., a microemulsion (e.g., containing dispersed droplets having a diameter of about 5 micrometers (µm) to about 50 µm) or nanoemulsion (e.g., containing dispersed droplets having a diameter of about 20 nanometers (nm) to about 100 nm). In some embodiments, the emulsion is an oil-in-water emulsion. In some embodiments, the emulsion comprises squalene. In some embodiments, the vaccine comprises MedImmune Emulsion (ME), i.e., an emulsion comprising about 20 millimolar (mM) Histidine, about 10% sucrose, about 4% squalene, and about 1% polysorbate-80, having a pH of about 6, and a droplet size of about 100 nm. When the L-PaF vaccine comprises an ME emulsion, the vaccine can be referred to as “the L-PaF/ME vaccine.” The vaccine can be administered via any convenient route, e.g., orally, by injection or intravenously, or intranasally. In some embodiments, the vaccine is administered via injection. In some embodiments, the vaccine is administered intranasally. The vaccine (e.g., the L-PaF or L-PaF/ME vaccine) can be administered a single time or multiple times. In some embodiments, the vaccine is administered multiple times to the same subject. Thus, “prime- boost” regimens can be used according to the presently disclosed subject matter The first administration of the vaccine can be referred to as a “prime” or “priming” dose, while subsequent administrations can be referred to as “boosts”. Separate administrations of the vaccine are typically separated by an intervening period of at least about one week or more (e.g., about two weeks, about three weeks, about four weeks, about five weeks, about six weeks, etc.). In some embodiments, separate administrations can be separated by an intervening period of one or more months (e.g., about 1 month to about 12 months) or one or more years (e.g., about 2 years to about Attorney Docket No.3289.0008WO 10 years). A typical regimen can comprise an immunization followed by booster administration (e.g. by injection) at regular time intervals, such as 2-, 3-, 4-, or 6-week intervals. However, less regular booster administration, such as annual boosting can be performed for reasons of convenience and compliance. Alternatively, booster injections can be on an irregular basis as indicated by monitoring of immune response (e.g. when the level of the antibodies is below a threshold determined by a doctor or a person skilled in the art). In some embodiments, the vaccine (e.g., the L-PaF or L-PaF/ME vaccine) is administered one time. In some embodiments, the vaccine (e.g., the L-PaF or L-PaF/ME vaccine) is administered to the subject at least two times. In some embodiments, the vaccine is administered to the subject two times. In some embodiments, the vaccine is administered to the subject three times. In some embodiments, the vaccine doses are administered about two weeks apart. In some embodiments, the method comprises administering an antibiotic to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine. Thus, in some embodiments, the method comprises administering an antibiotic to the subject prior to administration (e.g., initial administration) of the vaccine. In some embodiments, the antibiotic is administered to the subject one or more days (e.g., about 1, 2, 3, 4, 5, 6, or 7 days) prior to administration of the vaccine. In some embodiments, the antibiotic is administered to the subject one or more weeks (e.g., about 1, 2, 3, 4, 5, or 6 weeks) prior to administration of the vaccine. In some embodiments, the antibiotic is administered to the subject a few hours (e.g., about 4 to about 12 hours) prior to administration of the vaccine. In some embodiments, the vaccine is administered to the subject simultaneously with the vaccine or substantially simultaneously with administration (e.g., initial administration) of the vaccine (e.g., within about 5 minutes, about 10 minutes, about 15 minutes, about 30 minutes, about 45 minutes, about 60 minutes, about 90 minutes, or about 120 minutes) of administration of the vaccine). In some embodiments, the antibiotic is administered to the subject after administration (e.g., initial administration) of the vaccine. In some Attorney Docket No.3289.0008WO embodiments, the antibiotic is administered a few hours (e.g., about 4-12 hours) after administration of the vaccine, one or more days (e.g., about 1, 2, 3, 4, 5, 6, or 7 days) after administration of the vaccine, or one or more weeks (e.g., about 1, 2, 3, 4, 5, or about 6 weeks) after administration of the vaccine. When administered as a combination therapy, i.e. the vaccine plus the antibiotic, the antibiotic composition can be any suitable antibiotic. In some embodiments, the antibiotic composition can comprise more than one particular antibiotic or antibiotics of more than one chemical class. By way of example and not limitation, when the CF patient is suffering from a Pa infection, the antibiotic can be a penicillin (e.g. piperacillin and tazobactam), a cephalosporin (e.g., ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam), an aminoglycoside (e.g., tobramycin, amikacin, gentamicin),a macrolide (e.g., azithromycin), a quinolone (e.g., ciprofloxacin, levofloxacin), a carbapenem (e.g., meropenem, meropenem-vaborbactam, imipenem/cilastatin, doripenem), aztreonam, colistimethate, or combination thereof. Thus, in some embodiments, the antibiotic is one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate. In some embodiments, the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate. In some embodiments, the antibiotic comprises or consists of an aminoglycoside. In some embodiments, the antibiotic comprises or consists of tobramycin. The antibiotic can be administered to a subject or patient to be treated via any suitable route of administration. By way of example and not limitation, the route of administration for the antibiotic can be intravenous, oral or inhalation. In some embodiments, the antibiotic can be administered in multiple times (e.g., over the course of one or more days, weeks, or months). In some embodiments, the antibiotic is administered to the subject at least two times. In some embodiments, the antibiotic is administered to the subject at Attorney Docket No.3289.0008WO least three times, at least four times, at least five times, at least six times, at least seven times, at least 10 times, at least 12 times, or at least 14 times. In some embodiments, the antibiotic doses are administered one or more hours, days or weeks apart. In some embodiments, the antibiotic is administered daily for two or more days (e.g., 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, or more). In some embodiments, the antibiotic is administered daily for 7 days. In some embodiments, the vaccine (e.g., the L-PaF or L-PAF/ME vaccine) can be administered with an antibiotic as discussed herein and/or with any other suitable therapeutic component, including but not limited to a biologic (e.g. antibody, peptide, blood, blood components, allergenics, somatic cells, gene therapy, tissues, and recombinant therapeutic proteins), or small molecule drugs or low molecular weight compounds. The infection to be treated in the subject, including a Pa infection in a subject suffering from CF, can be reduced (e.g., the number of colony forming units (CFUs) per organ (e.g., lung) or tissue can be reduced) by at least about 25% or more. In some embodiments, the infection can be reduced by at least about 50% or more (e.g., by at least about 75%, at least about 90%, or by at least about 95% or more). Likewise, the infection in the subject can be reduced to below about 300 CFU/lung, below about 200 CFU/lung, below about 100 CFU/lung, below about 50 CFU/lung, below about 25 CFU/lung or below about 10 CFU/lung. In some instances, and as demonstrated in the experiments disclosed herein, the infection can be substantially or entirely cleared from the CF subject. In the context of the presently disclosed subject matter “substantially cleared” refers to reducing the infection to about 10 CFU/lung or less. In some embodiments, the presently disclosed subject matter provides a combination therapeutic treatment method for treating a Pa infection in a subject with CF, the combination therapeutic treatment method comprising: administering to the subject with CF a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic Attorney Docket No.3289.0008WO fragment thereof from a T3SS of Pa and ii) an LTA1 from enterotoxigenic Escherichia coli, optionally wherein the vaccine further comprises a squalene- based oil-in-water emulsion (e.g., an ME emulsion); and administering to the subject with CF a therapeutically effective amount of an antibiotic, wherein the Pa infection in the subject with CF is substantially reduced (e.g., reduced by at least about 90% or about 95%) and/or cleared. The antibiotic can comprise any suitable antibiotic such as described above. For example, the antibiotic can comprise one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate. In some embodiments, the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate. In some embodiments, the antibiotic comprises or consists of an aminoclycoside. In some embodiments, the antibiotic comprises tobramycin. The antibiotic can be administered to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine. In some embodiments, the antibiotic (e.g., at least one dose of the antibiotic) is administered substantially simultaneously (e.g., within about 5 minutes, within about 10 minutes, within about 15 minutes, within about 30 minutes) with administration of the vaccine. In some embodiments, the fusion polypeptide comprises the amino acid sequence of LTA1 (SEQ ID NO: 6) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PaF (SEQ ID NO: 2) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the Attorney Docket No.3289.0008WO fusion polypeptide comprises L-PaF (i.e., SEQ ID NO: 4) or an amino acid having at least 90% homology to SEQ ID NO: 4. In some embodiments, the fusion polypeptide comprises an amino acid sequence having at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% homology to SEQ ID NO: 4. In some embodiments, the vaccine comprises L-PaF/ME. In some embodiments, the presently disclosed subject matter provides a composition for use in treating a Pa infection (i.e., an existing Pa infection) in a subject with CF, wherein the composition comprises: (a) a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a T3SS of Pa)and ii) an LTA1 from enterotoxigenic Escherichia coli; and (b) a therapeutically effective amount of an antibiotic. The antibiotic can comprise any suitable antibiotic such as described above. For example, the antibiotic can comprise one or more antibiotics selected from the group including, but not limited to, a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, and colistimethate. In some embodiments, the antibiotic is selected from the group comprising piperacillin, tazobactam, ceftazidime, ceftazidime-avibactam, cefepime, ceftolozane-tazobactam, tobramycin, amikacin, gentamicin, azithromycin, ciprofloxacin, levofloxacin, meropenem- vaborbactam, imipenem/cilastatin, doripenem, aztreonam, and colistimethate. In some embodiments, the antibiotic comprises or consists of an aminoglycoside. In some embodiments, the antibiotic comprises tobramycin. In some embodiments, the fusion polypeptide comprises the amino acid sequence of LTA1 (SEQ ID NO: 6) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PcrV (SEQ ID NO: 8) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises the amino acid sequence of PopB (SEQ ID NO: 10) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises Attorney Docket No.3289.0008WO the amino acid sequence of PaF (SEQ ID NO: 2) or an amino acid sequence having at least about 90% homology thereto. In some embodiments, the fusion polypeptide comprises L-PaF (i.e., SEQ ID NO: 4) or an amino acid having at least 90% homology to SEQ ID NO: 4. In some embodiments, the fusion polypeptide comprises an amino acid sequence having at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% homology to SEQ ID NO: 4. In some embodiments, the vaccine comprises an oil-in-water emulsion (e.g., a squalene-based oil-in-water emulsion). In some embodiments, the vaccine comprises L-PaF/ME. III. Peptides and Nucleic Acids As will be understood by one of ordinary skill in the art, in some embodiments, the presently disclosed subject matter relates to methods comprising the administration of polypeptides. In some embodiments, the polypeptides can be prepared via chemical synthesis, according to methods known in the field. In some embodiments, the polypeptides are recombinant polypeptides. Thus, in some embodiments, the presently disclosed subject matter relates to recombinant polypeptides and the nucleic acids encoding the polypeptides. For example, in some embodiments, the polynucleotides disclosed herein can be introduced into an expression vector, such that the expression vector comprises a promoter and the polynucleotides encoding the peptides or polypeptides described herein. The expression vector can provide for expression of the peptides or polypeptides in a suitable expression system using techniques well known in the art, followed by isolation or purification of the expressed peptide or polypeptide of interest. A variety of bacterial, yeast, plant, mammalian, and insect expression systems are available in the art and any such expression system can be used. Alternatively, a polynucleotide encoding a peptide of use herein can be translated in a cell-free translation system. Exemplary nucleic acid and amino acid sequences described herein are as follows: PaF nucleic acid sequence (SEQ ID NO: 1): Attorney Docket No.3289.0008WO CATATGGAAGTCAGAAACCTTAATGCCGCTCGCGAGCTGT TCCTGGACGAGCTCCTGGCCGCGTCGGCGGCGCCTGCC AGTGCCGAGCAGGAGGAACTGCTGGCCCTGTTGCGCAGC GAGCGGATCGTGCTGGCCCACGCCGGCCAGCCGCTGAG CGAGGCGCAAGTGCTCAAGGCGCTCGCCTGGTTGCTCGC GGCCAATCCGTCCGCGCCTCCGGGGCAGGGCCTCGAGG TACTCCGCGAAGTCCTGCAGGCACGTCGGCAGCCCGGTG CGCAGTGGGATCTGCGTGAGTTCCTGGTGTCGGCCTATTT CAGCCTGCACGGGCGTCTCGACGAGGATGTCATCGGTGT CTACAAGGATGTCCTGCAGACCCAGGACGGCAAGCGCAA GGCGCTGCTCGACGAGCTCAAGGCGCTGACCGCGGAGTT GAAGGTCTACAGCGTGATCCAGTCGCAGATCAACGCCGC GCTGTCGGCCAGGCAGGGCATCAGGATCGACGCTGGCG GTATCGATCTGGTCGACCCCACGCTATATGGCTATGCCGT CGGCGATCCCAGGTGGAAGGACAGCCCCGAGTATGCGCT GCTGAGCAATCTGGATACCTTCAGCGGCAAGCTGTCGATC AAGGATTTTCTCAGCGGCTCGCCGAAGCAGAGCGGGGAA CTCAAGGGCCTCAGCGATGAGTACCCCTTCGAGAAGGAC AACAACCCGGTCGGCAATTTCGCCACCACGGTGAGCGAC CGCTCGCGTCCGCTGAACGACAAGGTCAACGAGAAGACC ACCCTGCTCAACGACACCAGCTCCCGCTACAACTCGGCG GTCGAGGCGCTCAACCGCTTCATCCAGAAATACGACAGC GTCCTGAGCGACATTCTCAGCGCGATCGGATCCATGAAC CCGATTACGCTGGAACGTGCTGGTCTGCCGTATGGTGTT GCCGATGCTGGTGACATCCCGGCTCTGGGTCGCCCGGTC GCACGTGATGTGGAAAGTCTGCGTGTTGAACGTCTGGCA GCACCGGCAGCTGCAAGCGCATCTGGCACCGGTGTCGCT CTGACGCCGCCGTCTGCAGCAAGTCAGCAACGTCTGGAA GTTGCTAACCGCGCGGAAATTGCCTCACTGGTCCAGGCA GTGGGTGAAGACGTGGGTCTGGCACGTCAAGTGGTTCTG GCAGGTGCATCGACCCTGCTGAGCGCAGGTCTGATGTCG CCGCAGGCGTTCGAAATTGAACTGGCCAAAATCACCGGC GAAGTTGAAAATCAGCAGAAAAAACTGAAACTGACGGAAA Attorney Docket No.3289.0008WO TCGAACAGGCCCGTAAACAGAACCTGCAAAAAATGGAAGA TAACCAGCAAAAAATCCGCGAATCGGAAGAAGCTGCGAAA GAAGCGCAGAAAAGCGGCCTGGCCGCAAAAATTTTTGGTT GGATTTCTGCTATCGCGAGTATTATCGTGGGTGCAATCAT GGTTGCAACCGGTGTCGGTGCTGCAGCAGGTGCACTGAT GATTGCTGGCGGTGTCATGGGTGTCGTGAGTCAGTCCGT GCAGCAAGCAGCTGCGGATGGTCTGATCTCAAAAGAAGT GATGGAAAAACTGGGCCCGGCCCTGATGGGTATTGAAAT GGCCGTGGCACTGCTGGCCGCAGTTGTCTCCTTTGGTGG TTCAGCAGTTGGTGGTCTGGCACGTCTGGGTGCAAAAATC GGCGGTAAAGCTGCGGAAATGACGGCATCCCTGGCTTCA AAAGTGGCAGACCTGGGCGGTAAATTCGGCTCTCTGGCG GGCCAGTCACTGTCGCATAGCCTGAAACTGGGTGTGCAA GTTTCTGATCTGACCCTGGACGTTGCAAACGGCGCCGCA CAGGCTACGCACAGTGGTTTTCAAGCGAAAGCTGCGAATC GTCAGGCCGATGTTCAAGAATCCCGTGCAGACCTGACCA CGCTGCAGGGTGTCATTGAACGTCTGAAAGAAGAACTGA GCCGCATGCTGGAAGCCTTTCAGGAAATTATGGAACGCAT CTTCGCAATGCTGCAAGCGAAAGGCGAAACCCTGCACAAT CTGTCTTCCCGTCCGGCGGCTATCTGAGGATCC PaF amino acid sequence (SEQ ID NO: 2): MEVRNLNAARELFLDELLAASAAPASAEQEELLALLRSERIVL AHAGQPLSEAQVLKALAWLLAANPSAPPGQGLEVLREVLQA RRQPGAQWDLREFLVSAYFSLHGRLDEDVIGVYKDVLQTQD GKRKALLDELKALTAELKVYSVIQSQINAALSARQGIRIDAGGI DLVDPTLYGYAVGDPRWKDSPEYALLSNLDTFSGKLSIKDFL SGSPKQSGELKGLSDEYPFEKDNNPVGNFATTVSDRSRPLN DKVNEKTTLLNDTSSRYNSAVEALNRFIQKYDSVLSDILSAIG SMNPITLERAGLPYGVADAGDIPALGRPVARDVESLRVERLA APAAASASGTGVALTPPSAASQQRLEVANRAEIASLVQAVGE DVGLARQVVLAGASTLLSAGLMSPQAFEIELAKITGEVENQQ KKLKLTEIEQARKQNLQKMEDNQQKIRESEEAAKEAQKSGLA Attorney Docket No.3289.0008WO AKIFGWISAIASIIVGAIMVATGVGAAAGALMIAGGVMGVVSQ SVQQAAADGLISKEVMEKLGPALMGIEMAVALLAAVVSFGGS AVGGLARLGAKIGGKAAEMTASLASKVADLGGKFGSLAGQS LSHSLKLGVQVSDLTLDVANGAAQATHSGFQAKAANRQADV QESRADLTTLQGVIERLKEELSRMLEAFQEIMERIFAMLQAK GETLHNLSSRPAAI LTA1-PaF (L-PaF) nucleic acid sequence (SEQ ID NO: 3): CATatggacaatggcgatcgtttataccgtgccgactcgcgtcccccag atgagattaaacgtagcggtgggttaatgccacgtgggcacaatgagta ttttgaccgtggaacacagatgaacattaacctttacgatcatgcccgtgg gacccagaccgggtttgtccgttatgatgacgggtatgttagtacgagtttg tccttacgctccgcacaccttgcgggacaaagtattttatcaggctacagc acatattacatttatgtgatcgccactgccccaaacatgttcaatgtgaacg atgtgttgggggtttacagcccccatccatatgaacaagaagtctcggcc cttggggggatcccatatagccagatttatggttggtaccgcgtaaattttg gtgtgattgatgaacgtttgcatcgtaaccgtgaataccgcgatcgctact accgtaacttgaacattgcacctgccgaggacggctatcgtttagcggga ttcccacccgatcatcaggcgtggcgtgaggaaccgtggatccatcacg cccctcaggggtgcgggaacagtagtcgcCATATGGAAGTCA GAAACCTTAATGCCGCTCGCGAGCTGTTCCTGGA CGAGCTCCTGGCCGCGTCGGCGGCGCCTGCCAG TGCCGAGCAGGAGGAACTGCTGGCCCTGTTGCG CAGCGAGCGGATCGTGCTGGCCCACGCCGGCCA GCCGCTGAGCGAGGCGCAAGTGCTCAAGGCGCT CGCCTGGTTGCTCGCGGCCAATCCGTCCGCGCC TCCGGGGCAGGGCCTCGAGGTACTCCGCGAAGT CCTGCAGGCACGTCGGCAGCCCGGTGCGCAGTG GGATCTGCGTGAGTTCCTGGTGTCGGCCTATTTC Attorney Docket No.3289.0008WO AGCCTGCACGGGCGTCTCGACGAGGATGTCATC GGTGTCTACAAGGATGTCCTGCAGACCCAGGAC GGCAAGCGCAAGGCGCTGCTCGACGAGCTCAAG GCGCTGACCGCGGAGTTGAAGGTCTACAGCGTG ATCCAGTCGCAGATCAACGCCGCGCTGTCGGCC AGGCAGGGCATCAGGATCGACGCTGGCGGTATC GATCTGGTCGACCCCACGCTATATGGCTATGCCG TCGGCGATCCCAGGTGGAAGGACAGCCCCGAGT ATGCGCTGCTGAGCAATCTGGATACCTTCAGCGG CAAGCTGTCGATCAAGGATTTTCTCAGCGGCTCG CCGAAGCAGAGCGGGGAACTCAAGGGCCTCAGC GATGAGTACCCCTTCGAGAAGGACAACAACCCGG TCGGCAATTTCGCCACCACGGTGAGCGACCGCT CGCGTCCGCTGAACGACAAGGTCAACGAGAAGA CCACCCTGCTCAACGACACCAGCTCCCGCTACAA CTCGGCGGTCGAGGCGCTCAACCGCTTCATCCA GAAATACGACAGCGTCCTGAGCGACATTCTCAGC GCGATCGGATCCATGAACCCGATTACGCTGGAAC GTGCTGGTCTGCCGTATGGTGTTGCCGATGCTGG TGACATCCCGGCTCTGGGTCGCCCGGTCGCACG TGATGTGGAAAGTCTGCGTGTTGAACGTCTGGCA GCACCGGCAGCTGCAAGCGCATCTGGCACCGGT GTCGCTCTGACGCCGCCGTCTGCAGCAAGTCAG CAACGTCTGGAAGTTGCTAACCGCGCGGAAATTG CCTCACTGGTCCAGGCAGTGGGTGAAGACGTGG GTCTGGCACGTCAAGTGGTTCTGGCAGGTGCATC GACCCTGCTGAGGGCAGGTCTGATGTCGCCGCA GGCGTTCGAAATTGAACTGGCCAAAATCACCGGC Attorney Docket No.3289.0008WO GAAGTTGAAAATCAGCAGAAAAAACTGAAACTGA CGGAAATCGAACAGGCCCGTAAACAGAACCTGCA AAAAATGGAAGATAACCAGCAAAAAATCCGCGAA TCGGAAGAAGCTGCGAAAGAAGCGCAGAAAAGC GGCCTGGCCGCAAAAATTTTTGGTTGGATTTCTG CTATCGCGAGTATTATCGTGGGTGCAATCATGGT TGCAACCGGTGTCGGTGCTGCAGCAGGTGCACT GATGATTGCTGGCGGTGTCATGGGTGTCGTGAGT CAGTCCGTGCAGCAAGCAGCTGCGGATGGTCTG ATCTCAAAAGAAGTGATGGAAAAACTGGGCCCGG CCCTGATGGGTATTGAAATGGCCGTGGCACTGCT GGCCGCAGTTGTCTCCTTTGGTGGTTCAGCAGTT GGTGGTCTGGCACGTCTGGGTGCAAAAATCGGC GGTAAAGCTGCGGAAATGACGGCATCCCTGGCTT CAAAAGTGGCAGACCTGGGCGGTAAATTCGGCTC TCTGGCGGGCCAGTCACTGTCGCATAGCCTGAAA CTGGGTGTGCAAGTTTCTGATCTGACCCTGGACG TTGCAAACGGCGCCGCACAGGCTACGCACAGTG GTTTTCAAGCGAAAGCTGCGAATCGTCAGGCCGA TGTTCAAGAATCCCGTGCAGACCTGACCACGCTG CAGGGTGTCATTGAACGTCTGAAAGAAGAACTGA GCCGCATGCTGGAAGCCTTTCAGGAAATTATGGA ACGCATCTTCGCAATGCTGCAAGCGAAAGGCGAA ACCCTGCACAATCTGTCTTCCCGTCCGGCGGCTA TCTGAGGATCC LTA1-PaF (L-PaF) amino acid sequence (SEQ ID NO: 4): MDNGDRLYRADSRPPDEIKRSGGLMPRGHNEYFDRGTQMN INLYDHARGTQTGFVRYDDGYVSTSLSLRSAHLAGQSILSGY Attorney Docket No.3289.0008WO STYYIYVIATAPNMENVNDVLGVYSPHPYEQEVSALGGIPYS QIYGWYRVNFGVIDERLHRNREYRDRYYRNLNIAPAEDGYR LAGFPPDHQAWREEPWIHHAPQGCGNSSRMEVRNLNAARE LFLDELLAASAAPASAEQEELLALLRSERIVLAHAGQPLSEAQ VLKALAWLLAANPSAPPGQGLEVLREVLQARRQPGAQWDL REFLVSAYFSLHGRLDEDVIGVYKDVLQTQDGKRKALLDELK ALTAELKVYSVIQSQINAALSARQGIRIDAGGIDLVDPTLYGYA VGDPRWKDSPEYALLSNLDTFSGKLSIKDFLSGSPKQSGELK GLSDEYPFEKDNNPVGNFATTVSDRSRPLNDKVNEKTTLLN DTSSRYNSAVEALNRFIQKYDSVLSDILSAIGSMNPITLERAG LPYGVADAGDIPALGRPVARDVESLRVERLAAPAAASASGT GVALTPPSAASQQRLEVANRAEIASLVQAVGEDVGLARQVV LAGASTLLSAGLMSPQAFEIELAKITGEVENQQKKLKLTEIEQ ARKQNLQKMEDNQQKIRESEEAAKEAQKSGLAAKIFGWISAI ASIIVGAIMVATGVGAAAGALMIAGGVMGVVSQSVQQAAAD GLISKEVMEKLGPALMGIEMAVALLAAVVSFGGSAVGGLARL GAKIGGKAAEMTASLASKVADLGGKFGSLAGQSLSHSLKLG VQVSDLTLDVANGAAQATHSGFQAKAANRQADVQESRADL TTLQGVIERLKEELSRMLEAFQEIMERIFAMLQAKGETLHNLS SRPAAI LTA1 nucleic acid sequence (SEQ ID NO: 5): CATAtggacaatggcgatcgtttataccgtgccgactcgcgtcccccagatgagatt aaacgtagcggtgggttaatgccacgtgggcacaatgagtattttgaccgtggaaca cagatgaacattaacctttacgatcatgcccgtgggacccagaccgggtttgtccgttat gatgacgggtatgttagtacgagtttgtccttacgctccgcacaccttgcgggacaaag tattttatcaggctacagcacatattacatttatgtgatcgccactgccccaaacatgttca atgtgaacgatgtgttgggggtttacagcccccatccatatgaacaagaagtctcggc ccttggggggatcccatatagccagatttatggttggtaccgcgtaaattttggtgtgatt gatgaacgtttgcatcgtaaccgtgaataccgcgatcgctactaccgtaacttgaacat tgcacctgccgaggacggctatcgtttagcgggattcccacccgatcatcaggcgtgg cgtgaggaaccgtggatccatcacgcccctcaggggtgcgggaacagtagtcgc Attorney Docket No.3289.0008WO LTA1 amino acid sequence (SEQ ID NO: 6): MDNGDRLYRADSRPPDEIKRSGGLMPRGHNEYFDRGTQMN INLYDHARGTQTGFVRYDDGYVSTSLSLRSAHLAGQSILSGY STYYIYVIATAPNMFNVNDVLGVYSPHPYEQEVSALGGIPYS QIYGWYRVNFGVIDERLHRNREYRDRYYRNLNIAPAEDGYR LAGFPPDHQAWREEPWIHHAPQGCGNSSR PcrV nucleic acid sequence (SEQ ID NO: 7): CATATGGAAGTCAGAAACCTTAATGCCGCTCGCGAGCTGT TCCTGGACGAGCTCCTGGCCGCGTCGGCGGCGCCTGCC AGTGCCGAGCAGGAGGAACTGCTGGCCCTGTTGCGCAGC GAGCGGATCGTGCTGGCCCACGCCGGCCAGCCGCTGAG CGAGGCGCAAGTGCTCAAGGCGCTCGCCTGGTTGCTCGC GGCCAATCCGTCCGCGCCTCCGGGGCAGGGCCTCGAGG TACTCCGCGAAGTCCTGCAGGCACGTCGGCAGCCCGGTG CGCAGTGGGATCTGCGTGAGTTCCTGGTGTCGGCCTATTT CAGCCTGCACGGGCGTCTCGACGAGGATGTCATCGGTGT CTACAAGGATGTCCTGCAGACCCAGGACGGCAAGCGCAA GGCGCTGCTCGACGAGCTCAAGGCGCTGACCGCGGAGTT GAAGGTCTACAGCGTGATCCAGTCGCAGATCAACGCCGC GCTGTCGGCCAGGCAGGGCATCAGGATCGACGCTGGCG GTATCGATCTGGTCGACCCCACGCTATATGGCTATGCCGT CGGCGATCCCAGGTGGAAGGACAGCCCCGAGTATGCGCT GCTGAGCAATCTGGATACCTTCAGCGGCAAGCTGTCGATC AAGGATTTTCTCAGCGGCTCGCCGAAGCAGAGCGGGGAA CTCAAGGGCCTCAGCGATGAGTACCCCTTCGAGAAGGAC AACAACCCGGTCGGCAATTTCGCCACCACGGTGAGCGAC CGCTCGCGTCCGCTGAACGACAAGGTCAACGAGAAGACC ACCCTGCTCAACGACACCAGCTCCCGCTACAACTCGGCG GTCGAGGCGCTCAACCGCTTCATCCAGAAATACGACAGC GTCCTGAGCGACATTCTCAGCGCGATC PcrV amino acid sequence (SEQ ID NO: 8): Attorney Docket No.3289.0008WO MEVRNLNAARELFLDELLAASAAPASAEQEELLALLRSERIVL AHAGQPLSEAQVLKALAWLLAANPSAPPGQGLEVLREVLQA RRQPGAQWDLREFLVSAYFSLHGRLDEDVIGVYKDVLQTQD GKRKALLDELKALTAELKVYSVIQSQINAALSARQGIRIDAGGI DLVDPTLYGYAVGDPRWKDSPEYALLSNLDTFSGKLSIKDFL SGSPKQSGELKGLSDEYPFEKDNNPVGNFATTVSDRSRPLN DKVNEKTTLLNDTSSRYNSAVEALNRFIQKYDSVLSDILSAI PopB nucleic acid sequence (SEQ ID NO: 9): ATGAACCCGATTACGCTGGAACGTGCTGGTCTGCCGTATG GTGTTGCCGATGCTGGTGACATCCCGGCTCTGGGTCGCC CGGTCGCACGTGATGTGGAAAGTCTGCGTGTTGAACGTC TGGCAGCACCGGCAGCTGCAAGCGCATCTGGCACCGGTG TCGCTCTGACGCCGCCGTCTGCAGCAAGTCAGCAACGTC TGGAAGTTGCTAACCGCGCGGAAATTGCCTCACTGGTCCA GGCAGTGGGTGAAGACGTGGGTCTGGCACGTCAAGTGGT TCTGGCAGGTGCATCGACCCTGCTGAGCGCAGGTCTGAT GTCGCCGCAGGCGTTCGAAATTGAACTGGCCAAAATCAC CGGCGAAGTTGAAAATCAGCAGAAAAAACTGAAACTGACG GAAATCGAACAGGCCCGTAAACAGAACCTGCAAAAAATGG AAGATAACCAGCAAAAAATCCGCGAATCGGAAGAAGCTGC GAAAGAAGCGCAGAAAAGCGGCCTGGCCGCAAAAATTTTT GGTTGGATTTCTGCTATCGCGAGTATTATCGTGGGTGCAA TCATGGTTGCAACCGGTGTCGGTGCTGCAGCAGGTGCAC TGATGATTGCTGGCGGTGTCATGGGTGTCGTGAGTCAGT CCGTGCAGCAAGCAGCTGCGGATGGTCTGATCTCAAAAG AAGTGATGGAAAAACTGGGCCCGGCCCTGATGGGTATTG AAATGGCCGTGGCACTGCTGGCCGCAGTTGTCTCCTTTG GTGGTTCAGCAGTTGGTGGTCTGGCACGTCTGGGTGCAA AAATCGGCGGTAAAGCTGCGGAAATGACGGCATCCCTGG CTTCAAAAGTGGCAGACCTGGGCGGTAAATTCGGCTCTCT GGCGGGCCAGTCACTGTCGCATAGCCTGAAACTGGGTGT GCAAGTTTCTGATCTGACCCTGGACGTTGCAAACGGCGC Attorney Docket No.3289.0008WO CGCACAGGCTACGCACAGTGGTTTTCAAGCGAAAGCTGC GAATCGTCAGGCCGATGTTCAAGAATCCCGTGCAGACCT GACCACGCTGCAGGGTGTCATTGAACGTCTGAAAGAAGA ACTGAGCCGCATGCTGGAAGCCTTTCAGGAAATTATGGAA CGCATCTTCGCAATGCTGCAAGCGAAAGGCGAAACCCTG CACAATCTGTCTTCCCGTCCGGCGGCTATCTGAGGATCC PopB amino acid sequence (SEQ ID NO: 10): MNPITLERAGLPYGVADAGDIPALGRPVARDVESLRVERLAA PAAASASGTGVALTPPSAASQQRLEVANRAEIASLVQAVGE DVGLARQVVLAGASTLLSAGLMSPQAFEIELAKITGEVENQQ KKLKLTEIEQARKQNLQKMEDNQQKIRESEEAAKEAQKSGLA AKIFGWISAIASIIVGAIMVATGVGAAAGALMIAGGVMGVVSQ SVQQAAADGLISKEVMEKLGPALMGIEMAVALLAAVVSFGGS AVGGLARLGAKIGGKAAEMTASLASKVADLGGKFGSLAGQS LSHSLKLGVQVSDLTLDVANGAAQATHSGFQAKAANRQADV QESRADLTTLQGVIERLKEELSRMLEAFQEIMERIFAMLQAK GETLHNLSSRPAAI III.A. Sequence Similarities It is understood that as discussed herein the terms “homology” and “% identity” mean the same thing as “similarity”. Thus, for example, if the use of the word homology is used between two amino acid or nucleic acid sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not. Homology between two nucleic acid sequences can indicate the percentage of nucleotides that are identical between the sequences. Homology between two amino acid sequences indicates the percentage of Attorney Docket No.3289.0008WO amino acids that are identical between the sequences. Said percentage is purely statistical, and the differences between the two sequences can be but are not necessarily randomly distributed over the entire length of the sequences to be compared. Comparisons of two sequences are usually carried out by comparing said sequences, after optimal alignment, with respect to a segment or “window of comparison”, in order to identify local regions of corresponding sequences. The optimal alignment for a comparison can be carried out manually or with the aid of the local homology algorithm by Smith and Waterman, 1981, Ads App. Math. 2, 482, with the aid of the local homology algorithm by Needleman and Wunsch, 1970, J. Mol. Biol.48, 443, with the aid of the similarity search algorithm by Pearson and Lipman, 1988, Proc. Natl Acad. Sci. USA 88, 2444, or with the aid of computer programs using said algorithms (GAP, BESTFIT, FASTA, BLAST P, BLAST N and TFASTA in Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Drive, Madison, Wis.), or by inspection. Homology is obtained by determining the number of identical positions at which the sequences to be compared correspond, dividing this number by the number of positions compared (e.g., the number of positions in the reference sequence) and multiplying this result by 100. In some embodiments, the homology is given for a region which is at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90% or about 100% of the entire length of the reference sequence. For example, if the reference nucleic acid sequence consists of 200 nucleotides, the homology is given for at least about 100, at least about 120, at least about 140, at least about 160, at least about 180, or about 200 nucleotides, in some embodiments in continuous nucleotides. In some embodiments, the homology is given for the entire length of the reference sequence. Nucleic acid sequences or amino acid sequences having a homology to a given nucleic acid sequence or amino acid sequence, respectively, can have at least one functional property of said given sequence, e.g., and in some instances, are functionally equivalent to said given sequence. In some embodiments, a nucleic acid sequence or amino acid sequence having a Attorney Docket No.3289.0008WO particular homology to a given nucleic acid sequence or amino acid sequence is functionally equivalent to said given sequence. In general, variants of polypeptides herein disclosed (such as, for example, PcrV, PopB, LTA1, or PaF,) typically have at least about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods can differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity. For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For instance, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method or any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages). III.B. Proteins and Protein Variants As discussed herein there are numerous variants of the needle tip protein, translocator protein, the fusion polypeptides thereof (such as, for example, PcrV, PopB, PaF and L-PaF) that are herein contemplated. In addition, to the known functional strain variants there are derivatives of the needle tip protein and translocator protein which also function in the disclosed methods and compositions. Protein variants and derivatives are well understood to those of skill in the art and can involve amino acid sequence Attorney Docket No.3289.0008WO modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Immunogenic fusion protein derivatives, such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. In some embodiments, no more than from about 2 to about 6 residues are deleted at any one site within the protein molecule. These variants ordinarily can be prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example M13 primer mutagenesis and PCR mutagenesis. Amino acid substitutions are typically of single residues but can occur at a number of different locations at once; insertions usually will be on the order of from about 1 to about 10 amino acid residues; and deletions will range from about 1 to about 30 residues. Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof can be combined to arrive at a final construct. The mutations should not place the sequence out of reading frame and preferably should not create complementary regions that could produce secondary mRNA structure. Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Table 2 and are referred to as conservative substitutions. Table 1, below, lists the amino acid residues and their abbreviations. Attorney Docket No.3289.0008WO Table 1. Amino Acids, Three Letter and One Letter Abbreviations. Amino Acid Abbreviations Alanine Ala A abe . xempary Conservave mno cd Subs uons Original Residue Substitution(s) Ala Ser Substantial changes in function or immunological identity can be made Attorney Docket No.3289.0008WO by selecting substitutions that are less conservative than those in Table 2, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine, in this case, or (e) by increasing the number of sites for sulfation and/or glycosylation. For example, the replacement of one amino acid residue with another that is biologically and/or chemically similar is known to those skilled in the art as a conservative substitution. For example, a conservative substitution would be replacing one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as, for example, Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gin; Ser, Thr; Lys, Arg; and Phe, Tyr. Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein. Substitutional or deletional mutagenesis can be employed to insert sites for N-glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr). Deletions of cysteine or other labile residues also can be desirable. Deletions or substitutions of potential proteolysis sites, e.g. Arg, is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues. Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues Attorney Docket No.3289.0008WO are deamidated under mildly acidic conditions. Other post-translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o-amino groups of lysine, arginine, and histidine side chains (T. E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco pp 79-86 [1983]), acetylation of the N-terminal amine and, in some instances, amidation of the C-terminal carboxyl. It is understood that one way to define the variants and derivatives of the disclosed proteins herein is through defining the variants and derivatives in terms of homology/identity to specific known sequences. For example, SEQ ID NO: 2 sets forth a particular sequence of Pa needle tip protein-translocator protein fusion (PaF) and SEQ ID NO: 4 sets forth a particular sequence of a LTA1-PaF fusion protein. Specifically disclosed are variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the stated sequence. Those of skill in the art readily understand how to determine the homology of two proteins. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level. As described above, homology can be performed by published algorithms. Optimal alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman Adv. App. Math.2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol.48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Nat. Acad. Sci. U.S.A.85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by inspection. The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol.183:281-306, 1989. It is understood that the description of conservative mutations and homology can be combined together in any combination, such as Attorney Docket No.3289.0008WO embodiments that have at least 70% homology to a particular sequence wherein the variants are conservative mutations. As the presently disclosed subject matter provides various proteins and protein sequences it is understood that the nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e. all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences. Thus, while each particular nucleic acid sequence is not necessarily written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequences. For example, one of the many nucleic acid sequences that can encode the protein sequence set forth in SEQ ID NO: 2 is set forth in SEQ ID NO: 1. It is understood that for this mutation all of the nucleic acid sequences that encode this particular derivative of the PaF are also disclosed. It is also understood that while no amino acid sequence indicates what particular DNA sequence encodes that protein within an organism, where particular variants of a disclosed protein are disclosed herein, the known nucleic acid sequence that encodes that protein in the particular needle tip protein-translocator protein fusion (such as, for example, PaF) from which that protein arises is also known and herein disclosed and described. It is understood that there are numerous amino acid and peptide analogs which can be incorporated into the disclosed compositions. For example, there are numerous D amino acids or amino acids which have a different functional substituent then the amino acids shown in Table 1 and Table 2. The opposite stereo isomers of naturally occurring peptides are disclosed, as well as the stereo isomers of peptide analogs. These amino acids can readily be incorporated into polypeptide chains by charging tRNA molecules with the amino acid of choice and engineering genetic constructs that utilize, for example, amber codons, to insert the analog amino acid into a peptide chain in a site-specific way. Attorney Docket No.3289.0008WO Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage. For example, linkages for amino acids or amino acid analogs can include —CH2NH—, —CH2S—, —CH2—CH2—, — CH═CH-(cis and trans), —COCH2—, —CH(OH)CH2—, and —CHH2SO— (These and others can be found in Spatola, A. F. in Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F., Vega Data (March 1983), Vol. 1, Issue 3, Peptide Backbone Modifications (general review); Morley, Trends Pharm. Sci (1980) pp.463-468; Hudson, D. et al., Int J Pept Prot Res 14:177-185 (1979) (—CH2NH—, —CH2CH2—); Spatola et al. life Sci 38:1243-1249 (1986) (—CH2—S); Hann J. Chem. Soc Perkin Trans. I 307- 314(1982) (—CH═CH—, cis and trans); Almquist et al. J. Med. Chem.23:1392-1398 (1980) (—COCH2—); Jennings-White et al. Tetrahedron Lett 23:2533 (1982) (—COCH2—); Szelke et al. European Appln, EP 45665 CA (1982): 97:39405 (1982) (—CH(OH)CH2—); Holladay et al. Tetrahedron. Lett 24:4401-4404 (1983) (—C(OH)CH2—); and Hruby Life Sci 31:189-199 (1982) (—CH2—S—); each of which is incorporated herein by reference. A particularly preferred non-peptide linkage is —CH2NH—. It is understood that peptide analogs can have more than one atom between the bond atoms, such as β-alanine, γ-aminobutyric acid, and the like. Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others. D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such. Systematic substitution of one or more amino acids of a consensus sequence with a D- amino acid of the same type (e.g., D-lysine in place of L-lysine) can be used to generate more stable peptides. Cysteine residues can be used to cyclize or attach two or more peptides together. This can be beneficial to constrain peptides into particular conformations. Attorney Docket No.3289.0008WO In some embodiments, the polypeptides administered according to the methods described herein can include antigenic fragments of one or more of subunit (e.g. PcrV or PopB). Fragments of the sequences of PcrV or PopB can be assessed, for example, by determining the ability of the fragments to bind to antibodies that have specific binding to PcrV, PopB, or Pa and/or to elicit antibodies that cross react with full length PcrV, PopB, or Pa. n some embodiments, the antigenic fragment should retain at least about 50%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% of the antibody binding activity of parent polypeptide. III.C. Nucleic Acids There are a variety of molecules disclosed herein that are nucleic acid based, including for example the nucleic acids that encode, for example PcrV, PopB, PaF, LTA1 or antigenic fragments thereof, as well as various functional nucleic acids. The disclosed nucleic acids are made up of, for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein. It is understood that for example, when a vector is expressed in a cell, that the expressed mRNA will typically be made up of A, C, G, and U. A nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an internucleoside linkage. The base moiety of a nucleotide can be adenin-9-yl (A), cytosin-1-yl (C), guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T). The sugar moiety of a nucleotide is a ribose or a deoxyribose. The phosphate moiety of a nucleotide is pentavalent phosphate. A non-limiting example of a nucleotide would be 3′- AMP (3′-adenosine monophosphate) or 5′-GMP (5′-guanosine monophosphate). There are many varieties of these types of molecules available in the art and available herein. A nucleotide analog is a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties. Modifications to nucleotides are well known in the art and would include for example, 5- methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, and 2-aminoadenine, as well as modifications at the sugar or phosphate Attorney Docket No.3289.0008WO moieties. There are many varieties of these types of molecules available in the art and available herein. Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid. There are many varieties of these types of molecules available in the art and available herein. It is also possible to link other types of molecules (conjugates) to nucleotides or nucleotide analogs to enhance for example, cellular uptake. Conjugates can be chemically linked to the nucleotide or nucleotide analogs. Such conjugates include but are not limited to lipid moieties such as a cholesterol moiety (see Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556). There are many varieties of these types of molecules available in the art and available herein. A Watson-Crick interaction is at least one interaction with the Watson- Crick face of a nucleotide, nucleotide analog, or nucleotide substitute. The Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, N1, and C6 positions of a purine-based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine- based nucleotide, nucleotide analog, or nucleotide substitute. A Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA. The Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides. III.D. Nucleic Acid Delivery There are a number of compositions and methods which can be used to deliver nucleic acids to cells, either in vitro or in vivo. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems. For example, the nucleic acids can be delivered through a number of direct delivery systems Attorney Docket No.3289.0008WO such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes. Appropriate means for transfection, including viral vectors, chemical transfectants, or physico-mechanical methods such as electroporation and direct diffusion of DNA, are described by, for example, Wolff, J. A., et al., Science, 247, 1465-1468, (1990); and Wolff, J. A. Nature, 352, 815-818, (1991). Such methods are well known in the art and readily adaptable for use with the compositions and methods described herein. Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)). As used herein, plasmid or viral vectors are agents that transport the disclosed nucleic acids into the cell without degradation and include a promoter yielding expression of the gene in the cells into which it is delivered. Viral vectors are, for example, Adenovirus, Adeno-associated virus, Herpes virus, Vaccinia virus, Polio virus, AIDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviruses include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector. Retroviral vectors are able to carry a larger genetic payload, i.e., a transgene or marker gene, than other viral vectors, and for this reason are a commonly used vector. However, they are not as useful in non-proliferating cells. Adenovirus vectors are relatively stable and easy to work with, have high titers, and can be delivered in aerosol formulation, and can transfect non- dividing cells. Pox viral vectors are large and have several sites for inserting genes, they are thermostable and can be stored at room temperature. A retrovirus is an animal virus belonging to the virus family of Retroviridae, including any types, subfamilies, genus, or tropisms. A retrovirus is essentially a package which has packed into it nucleic acid cargo. The Attorney Docket No.3289.0008WO nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat. In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus. Typically, a retroviral genome, contains the gag, pol, and env genes which are involved in the making of the protein coat. It is the gag, pol, and env genes which are typically replaced by the foreign DNA that it is to be transferred to the target cell. Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich sequence 5′ to the 3′ LTR that serve as the priming site for the synthesis of the second strand of DNA synthesis, and specific sequences near the ends of the LTRs that enable the insertion of the DNA state of the retrovirus to insert into the host genome. The removal of the gag, pol, and env genes allows for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert. Since the replication machinery and packaging proteins in most retroviral vectors have been removed (gag, pol, and env), the vectors are typically generated by placing them into a packaging cell line. A packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery but lacks any packaging signal. When the vector carrying the DNA of choice is transfected into these cell lines, the vector containing the gene of interest is replicated and packaged into new retroviral particles, by the machinery provided in cis by the helper cell. The genomes for the machinery are not packaged because they lack the necessary signals. Attorney Docket No.3289.0008WO The construction of replication-defective adenoviruses has been described (Berkner et al., J. Virology 61:1213-1220 (1987); Massie et al., Mol. Cell. Biol.6:2872-2883 (1986); Haj-Ahmad et al., J. Virology 57:267-274 (1986); Davidson et al., J. Virology 61:1226-1239 (1987); Zhang “Generation and identification of recombinant adenovirus by liposome-mediated transfection and PCR analysis” BioTechniques 15:868-872 (1993)). The benefit of the use of these viruses as vectors is that they are limited in the extent to which they can spread to other cell types, since they can replicate within an initial infected cell, but are unable to form new infectious viral particles. Recombinant adenoviruses have been shown to achieve high efficiency gene transfer after direct, in vivo delivery to airway epithelium, hepatocytes, vascular endothelium, CNS parenchyma and a number of other tissue sites (Morsy, J. Clin. Invest.92:1580-1586 (1993); Kirshenbaum, J. Olin. Invest.92:381-387 (1993); Roessler, J. Clin. Invest.92:1085-1092 (1993); Moullier, Nature Genetics 4:154-159 (1993); La Salle, Science 259:988-990 (1993); Gomez-Foix, J. Biol. Chem.267:25129-25134 (1992); Rich, Human Gene Therapy 4:461-476 (1993); Zabner, Nature Genetics 6:75-83 (1994); Guzman, Circulation Research 73:1201-1207 (1993); Bout, Human Gene Therapy 5:3-10 (1994); Zabner, Cell 75:207-216 (1993); Caillaud, Eur. J. Neuroscience 5:1287-1291(1993); and Ragot, J. Gen. Virology 74:501-507 (1993)). Recombinant adenoviruses achieve gene transduction by binding to specific cell surface receptors, after which the virus is internalized by receptor-mediated endocytosis, in the same manner as wild type or replication-defective adenovirus (Chardonnet and Dales, Virology 40:462-477 (1970); Brown and Burlingham, J. Virology 12:386-396 (1973); Svensson and Persson, J. Virology 55:442-449 (1985); Seth, et al., J. Virol.51:650-655 (1984); Seth, et al., Mol. Cell. Biol.4:1528-1533 (1984); Varga et al., J. Virology 65:6061-6070 (1991); Wickham et al., Cell 73:309-319 (1993)). A viral vector can be one based on an adenovirus which has had the E1 gene removed and these virons are generated in a cell line such as the human 293 cell line. In another preferred embodiment both the E1 and E3 genes are removed from the adenovirus genome. Attorney Docket No.3289.0008WO Another type of viral vector is based on an adeno-associated virus (AAV). This defective parvovirus is a preferred vector because it can infect many cell types and is nonpathogenic to humans. AAV type vectors can transport about 4 to 5 kb and wild type AAV is known to stably insert into chromosome 19. Vectors which contain this site specific integration property are preferred. An especially preferred embodiment of this type of vector is the P4.1 C vector produced by Avigen, San Francisco, CA, which can contain the herpes simplex virus thymidine kinase gene, HSV-tk, and/or a marker gene, such as the gene encoding the green fluorescent protein, GFP. In another type of AAV virus, the AAV contains a pair of inverted terminal repeats (ITRs) which flank at least one cassette containing a promoter which directs cell-specific expression operably linked to a heterologous gene. Heterologous in this context refers to any nucleotide sequence or gene which is not native to the AAV or B19 parvovirus. Typically, the AAV andB19 coding regions have been deleted, resulting in a safe, noncytotoxic vector. The AAV ITRs, or modifications thereof, confer infectivity and site-specific integration, but not cytotoxicity, and the promoter directs cell-specific expression. U.S. Pat. No.6,261,834 is herein incorporated by reference for material related to the AAV vector. The disclosed vectors thus provide DNA molecules which are capable of integration into a mammalian chromosome without substantial toxicity. The inserted genes in viral and retroviral usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements. Molecular genetic experiments with large human herpesviruses have provided a means whereby large heterologous DNA fragments can be cloned, propagated and established in cells permissive for infection with herpesviruses (Sun et al., Nature genetics 8: 33-41, 1994; Cotter and Robertson, Curr Opin Mol Ther 5: 633-644, 1999). These large DNA viruses Attorney Docket No.3289.0008WO (herpes simplex virus (HSV) and Epstein-Barr virus (EBV), have the potential to deliver fragments of human heterologous DNA>150 kb to specific cells. EBV recombinants can maintain large pieces of DNA in the infected B-cells as episomal DNA. Individual clones carried human genomic inserts up to 330 kb appeared genetically stable The maintenance of these episomes requires a specific EBV nuclear protein, EBNA1, constitutively expressed during infection with EBV. Additionally, these vectors can be used for transfection, where large amounts of protein can be generated transiently in vitro. Herpesvirus amplicon systems are also being used to package pieces of DNA>220 kb and to infect cells that can stably maintain DNA as episomes. Other useful systems include, for example, replicating and host- restricted non-replicating vaccinia virus vectors. The disclosed compositions can be also delivered to the target cells in a variety of ways. For example, the compositions can be delivered through electroporation, or through lipofection, or through calcium phosphate precipitation. The delivery mechanism chosen will depend in part on the type of cell targeted and whether the delivery is occurring for example in vivo or in vitro. Thus, the compositions can comprise, in addition to the disclosed needle tip protein-translocator protein fusion (such as, for example, PaF) or vectors for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, DC-cholesterol) or anionic liposomes. Liposomes can further comprise proteins to facilitate targeting a particular cell, if desired. Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract. Regarding liposomes, see, e.g., Brigham et al. Am. J. Resp. Cell. Mol. Biol.1:95-100 (1989); Feigner et al. Proc. Natl. Acad. Sci USA 84:7413-7417 (1987); U.S. Pat. No. 4,897,355. Furthermore, the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage. Attorney Docket No.3289.0008WO In the methods described above which include the administration and uptake of exogenous DNA into the cells of a subject (i.e., gene transduction or transfection), delivery of the compositions to cells can be via a variety of mechanisms. As one example, delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, MD), SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec, Inc., Madison, WI), as well as other liposomes developed according to procedures standard in the art. In addition, the disclosed nucleic acid or vector can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, CA) as well as by means of a SONOPORATION machine (ImaRx Pharmaceutical Corp., Tucson, AZ). The materials can be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These can be targeted to a particular cell type via antibodies, receptors, or receptor ligands. In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis have been reviewed (Brown and Greene, DNA and Cell Biology 10.6, 399-409 (1991)). Nucleic acids that are delivered to cells which are to be integrated into the host cell genome, typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used. These viral integration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid-based Attorney Docket No.3289.0008WO system of delivery, such as a liposome, so that the nucleic acid contained in the delivery system can become integrated into the host genome. Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome. These systems and the methods necessary to promote homologous recombination are known to those of skill in the art. As described above, the compositions can be administered in a pharmaceutically acceptable carrier and can be delivered to the subject's cells in vivo and/or ex vivo by a variety of mechanisms well known in the art (e.g., uptake of naked DNA, liposome fusion, intramuscular injection of DNA via a gene gun, endocytosis and the like). If ex vivo methods are employed, cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art. The compositions can be introduced into the cells via any gene transfer mechanism, such as, for example, calcium phosphate mediated gene delivery, electroporation, microinjection or proteoliposomes. The transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject. III.E. Expression Systems The nucleic acids that are delivered to cells typically contain expression controlling systems. For example, the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product. A promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site. A promoter contains core elements required for Attorney Docket No.3289.0008WO basic interaction of RNA polymerase and transcription factors and can contain upstream elements and response elements. Preferred promoters controlling transcription from vectors in mammalian host cells can be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis-B virus and most preferably cytomegalovirus, or from heterologous mammalian promoters, e.g. beta actin promoter. The early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al., Nature, 273: 113 (1978)). The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment (Greenway, P. J. et al., Gene 18: 355-360 (1982)). Of course, promoters from the host cell or related species also are useful herein. Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5′ (Laimins, L. et al., Proc. Natl. Acad. Sci.78: 993 (1981)) or 3′ (Lusky, M. L., et al., Mol. Cell Bio.3: 1108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J. L. et al., Cell 33: 729 (1983)) as well as within the coding sequence itself (Osborne, T. F., et al., Mol. Cell Bio.4: 1293 (1984)). They are usually between 10 and 300 bp in length, and they function in cis. Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Preferred examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The promotor and/or enhancer can be specifically activated either by light or specific chemical events which trigger their function. Systems can be Attorney Docket No.3289.0008WO regulated by reagents such as tetracycline and dexamethasone. There are also ways to enhance viral vector gene expression by exposure to irradiation, such as gamma irradiation, or alkylating chemotherapy drugs. In certain embodiments the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed. In certain constructs the promoter and/or enhancer region be active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time. A preferred promoter of this type is the CMV promoter (650 bases). Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR. It has been shown that all specific regulatory elements can be cloned and used to construct expression vectors that are selectively expressed in specific cell types such as melanoma cells. The glial fibrillary acetic protein (GFAP) promoter has been used to selectively express genes in cells of glial origin. Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant, animal, human or nucleated cells) can also contain sequences for the termination of transcription which can affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3′ untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contains a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA. The identification and use of polyadenylation signals in expression constructs is well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs. In certain transcription units, the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases. It is also preferred that the transcribed units contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct. Attorney Docket No.3289.0008WO The viral vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed. Preferred marker genes are the E. Coli lacZ gene, which encodes B-galactosidase, and green fluorescent protein. In some embodiments the marker can be a selectable marker. Examples of suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. There are two widely used distinct categories of selective regimes. The first category is based on a cell's metabolism and the use of a mutant cell line which lacks the ability to grow independent of a supplemented media. Two examples are: CHO DHFR-cells and mouse LTK-cells. These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media. An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non- supplemented media. The second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern P. and Berg, P., J. Molec. Appl. Genet.1: 327 (1982)), mycophenolic acid, (Mulligan, R. C. and Berg, P. Science 209: 1422 (1980)) or hygromycin, (Sugden, B. et al., Mol. Cell. Biol.5: 410-413 (1985)). The three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug G418 or Attorney Docket No.3289.0008WO neomycin (geneticin), xgpt (mycophenolic acid) or hygromycin, respectively. Others include the neomycin analog G418 and puromycin. IV. Pharmaceutical Compositions The active ingredients (e.g., the fusion polypeptide vaccine and/or antibiotic) of the presently disclosed subject matter can be provided in pharmaceutical compositions comprising additional components, e.g., a pharmaceutically acceptable carrier. By “pharmaceutically acceptable” is meant a material that is not biologically or otherwise undesirable, i.e., the material can be administered to a subject 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. The carrier would naturally be selected to minimize any degradation of the active ingredient(s) (e.g., the vaccine and/or antibiotic) and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art. The compositions can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including intranasally (e.g., via topical intranasal administration or administration by inhalant). As used herein, “topical intranasal administration” means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the active ingredients. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the infection being treated, the particular active ingredient(s) used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein. Attorney Docket No.3289.0008WO Parenteral administration of the composition, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No.3,610,795, which is incorporated by reference herein. The active ingredients can be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells) or emulsion (e.g., an oil- in-water emulsion). In some embodiments, these be targeted to a particular cell type via antibodies, receptors, or receptor ligands. Suitable pharmaceutical carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, PA 1995. In some embodiments, an appropriate amount of a pharmaceutically acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution. The pH of the solution is preferably from about 5 to about 8, more preferably from about 7 to about 7.6, and most preferably about 7.5. Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing an active ingredient, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers can be more preferable depending upon, for instance, the route of administration and concentration of composition being administered. Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously. Other compounds can be administered according to standard procedures used by those skilled in the art. Pharmaceutical compositions can include carriers, thickeners, diluents, Attorney Docket No.3289.0008WO buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions can also include one or more additional active ingredients such as antimicrobial agents, anti- inflammatory agents, anesthetics, and the like. The pharmaceutical composition can be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration can be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection. The disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally. Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non- aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives can also be present such as, for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like. Formulations for topical administration can include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like can be desirable. Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders can be desirable. Attorney Docket No.3289.0008WO Some of the compositions can potentially be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, tri-alkyl and aryl amines and substituted ethanolamines. Effective dosages and schedules for administering the compositions can be determined empirically, and making such determinations is within the skill in the art. The dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms of the infection are affected. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art. The dosage can be adjusted by the individual physician in the event of any counterindications. Dosage can vary, and can be administered in one or more dose administrations daily, weekly, or monthly. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products, e.g., antibiotics. In a preferred embodiment, the amount of polypeptide that is administered per dose of vaccine is in the range of from about 0.0001 to about 1000 μg/kg. In some embodiments, the amount is in the range of from about 0.001 to about 1000 μg/kg of body weight of the recipient. In some embodiments, the amount is in the range of from about 0.01 to about 1000 μg/kg of body weight of the recipient. In some embodiments, the amount is in the range of from about 0.01 to about 100 μg/kg of body weight of the recipient. Those of skill in the art will recognize that the precise dosage can vary from situation to situation and from patient to patient, depending on e.g. age, gender, overall health, various genetic factors, and other variables known to Attorney Docket No.3289.0008WO those of skill in the art. Dosages are typically determined e.g. in the course of animal and/or human clinical trials as conducted by skilled medical personnel, e.g. physicians or veterinarians. EXAMPLES The following EXAMPLES provide illustrative embodiments. In light of the present disclosure and the general level of skill in the art, those of skill will appreciate that the following EXAMPLES are intended to be exemplary only that that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently disclosed subject matter. Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative EXAMPLES, make and utilize the presently disclosed compositions and methods Materials and Methods L-PaF Preparation: L-PaF can be prepared as described in U.S. Patent No. 11,439,700 and PCT International Patent Application Publication No. WO2022/246327, the disclosures of which are incorporated herein by reference in their entireties. Briefly, using Novagen’s pACYCDuet-1 as the mother plasmid, the complex of LTA1-PaF/Histag-PcrHI was produced from the plasmid pACYC- His-PcrH-LTA1-PaF where the brcHI gene was inserted into the BamHI/HindIII sites providing for expression of His-tag PcrH (as set forth in SEQ ID NO: 12 and encoded by the nucleic acid sequence as set forth in SEQ ID NO 11) and LTA1-PaF (as set forth in SEQ ID NO: 4 and encoded by the nucleic acid sequences as set forth in SEQ ID NO: 3) which was inserted at the NdeI-XhoI site. The PaF sequence had a 3’ stop codon prior to the XhoI restriction site. The plasmid pACYC-His-PcrH-LTA1-PaF was transformed into Tuner cells. E. coli Tuner cells expressing L-PaF/His-Tag PcrH were grown in TB media supplemented with chloramphenicol (34 μg/ml) with a fed-batch mode in a 10 L bioreactor (Labfors 5, Infors USA Inc., MD). An overnight starter was Attorney Docket No.3289.0008WO expanded to 1 L and approximately 800 mL was transferred to the bioreactor containing 9 L of TB media supplemented with chloramphenicol (34 μg/ml). The culture temperature was maintained at 30°C and protein expression was induced adding IPTG to 1 mM when the culture reached an A600 of about 25. After 3 h, the bacteria were collected and processed for purification. The L- PaF/His-Tag PcrH was captured on an IMAC column followed by Q anion exchange chromatography. Lauryldimethylamine oxide (LDAO) was added to a final concentration of 0.1% to release the HT-PcrH. The protein solution was passed over a final IMAC column with the L-PaF passing through the column. L-PaF was dialyzed into PBS with 0.05% LDAO and stored at −80°C. LPS levels were determined using a NexGen PTS with EndoSafe cartridges (Charles River Laboratories, Wilmington, MA). All proteins had LPS levels<5 Endotoxin units/mg protein based on analysis using an Endosafe system (Charles River Labs). Preparation of L-PaF Formulation Squalene (8% by weight) and polysorbate 80 (2% by weight) were mixed to achieve a homogenous oil phase. Using a Silverson L5M-A standard high-speed mixer, 40 mM Histidine (pH 6) and 20% sucrose were added to the oil phase and mixed at 7500 RPM followed by six passes in a Microfluidics 110P microfluidizer at 20,000 psi to generate a milky emulsion of 4XME (MedImmune Emulsion). Polysorbate 80 acted as an emulsifying agent to stabilize the emulsion. The L-PaF protein was added to the ME with a final concentration of 0.67 mg/mI, vortexed and allowed to incubate overnight at 4°C. CF Rat Model Aberrant airway mucus is an important mediator of infection in CF. See Staudinger et al., Am. J. Respir. Crit. Care Med.2014; 189(7): 812-824. Rats develop extensive submucosal glands in the trachea, making them useful as a model for replicating the anatomy of the human airway. See Widdicomb et al., J. Anat. 2001; 198(Pt 2): 207-221. A CFTR-/- (KO) rat that replicates clinical CF pathology has been previously described (see Birket et al., JCI Insight.2018; 3(1) (doi: 10.1172/jci.insight.97199); Birket et al., Am. J. Respir. Crit. Care Med. 2020; 202(9): 1271-1282; and Green et al., Am. J. Physiol. Attorney Docket No.3289.0008WO Lung Cell Mol. Physiol. 2021 (doi 10.1152/ajplung.00082.2021)) and was used in the Examples below. PA Infection Unless described otherwise, Pa infection/challenge and rechallenge of CF rats was performed by intratracheal administration of 3 x 106 CFUs of PA strain mPA0831. Tobramycin Unless described otherwise, tobramycin administration to CF rats was performed by intranasal administration of 3 mg/kg body weight tobramycin (Sigma) per day for 7 days. EXAMPLE 1 Two groups of six CF rats were infected with PA. After 14 days, one group was treated with tobramycin (3 mg/kg/day for 7 days). On day 28 post PA infection, the rats from both groups were sacrificed and the CFU burden assessed by plating a portion of lung extract on Pseudomonas isolation agar (PIA). Results are shown in Figure 1A. Use of the antibiotic reduced the CFU burden, but did not clear the infection. In a further study, groups of CF rats were vaccinated (intranasally) three times with L-PaF/ME post-Pa infection and +/- tobramycin treatment as described in Table 3, below. The CF rats were then rechallenged with Pa on day 70. At the conclusion of the study (day 84), rats were sacrificed and CFU burden was assessed by plating a portion of lung extract on PIA. Table 3. Treatment Schedule CF Rats e Attorney Docket No.3289.0008WO (30 µg) (30 µg) Day 70 Pa challenge Pa challenge Pa challenge Pa challenge % of the CF rats of Pa. The addition of tobramycin did not significantly impact the resulting decrease in infection. EXAMPLE 2 CF rats were challenged with Pa. As shown in Table 4, below, one group of mice was treated with tobramycin and a second group was vaccinated two times with L-PaF/ME post Pa infection. A third group was vaccinated 2X post-Pa infection and post-tobramycin treatment. At the conclusion of the study, rats were sacrificed and CFU burden was assessed. Table 4. Treatment Schedule CF Rats Group 1 Group 2 Group 3 e Results are shown in Figure 2. Again, treatment with tobramycin alone did not clear the infection. In contrast, the vaccine alone reduced the Pa infection to ~100 CFU/lung while with tobramycin all CF rats were essentially cleared of the Pa infection. EXAMPLE 3 CF rats with Pa then either vaccinated with L-PaF/ME or vaccinated with L-PaF/ME with simultaneous administration of a first dose of tobramycin. See Table 5, below. Daily dosing with tobramycin continued until day 27. At Attorney Docket No.3289.0008WO the conclusion of the study, rats were sacrificed and CFU burden was assessed. Table 5. Treatment Schedule CF Rats Group 1 Group 2 . ccination post-Pa infection cleared Pa from 50% of the CF rats and reduced the other 50% to ~200 CFU/lung. However, simultaneous treatment with L-PaF/ME and tobramycin cleared Pa in five out of six CF rats. The last rat had a bacterial burden of 10 CFU/lung, which is below the level of detection. Whether administered alone, or in combination with tobramycin or any other suitable antibiotic, these data demonstrate that L-PaF/ME can be used as a therapeutic vaccine. Discussion of Examples 1-3 The presently disclosed studies confirm that tobramycin cannot clear a Pa infection completely. See Figure 1A. In contrast, administration of the L- PaF/ME vaccine resulted in significantly reduced bacterial burden in challenged CF rat lungs. Additionally, the combination of L-PaF/ME and tobramycin was surprisingly effective, providing complete clearance in the majority of cases. It will be understood that various details of the presently disclosed subject matter may be changed without departing from the scope of the presently disclosed subject matter. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation.

Claims

Attorney Docket No.3289.0008WO CLAIMS What is claimed is: 1. A method for treating an infection in a subject with cystic fibrosis (CF) comprising administering to the subject a therapeutically effective amount of: (a) a vaccine comprising a fusion polypeptide wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa) and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli; and (b) optionally, an antibiotic. 2. The method of claim 1, wherein the subject with CF has a Pa infection. 3. The method of claim 1 or claim 2, wherein the fusion of the needle tip protein or the antigenic fragment thereof and/or the translocator protein or the antigenic fragment thereof from the T3SS of Pa is a polypeptide having an amino acid sequence of SEQ ID NO: 2 (PaF) or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 2. 4. The method of any one of claims 1-3, wherein the LTA1 is 5’ of the fusion of the needle tip protein or an antigenic fragment thereof and/or the translocator protein fusion or an antigenic fragment thereof, optionally wherein the LTA1 has an amino acid sequence of SEQ ID NO: 6, or an amino acid sequence having at least 90% homology to the amino acid sequence of SEQ ID NO: 6. 5. The method of any one of claims 1-4, wherein the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 (L-PaF), or an amino acid sequence having at least 90% homology to SEQ ID NO: 4. Attorney Docket No.3289.0008WO 6. The method of any one of claims 1-5, wherein the vaccine comprises an oil-in-water emulsion, optionally wherein said emulsion comprises squalene, further optionally wherein the vaccine comprises MedImmune Emulsion (ME). 7. The method of any one of claims 1-6, wherein the vaccine is administered to the subject at least two times. 8. The method of any one of claims 1-7, wherein the method comprises administering an antibiotic to the subject prior to the vaccine, simultaneously with the vaccine, or after the vaccine. 9. The method of claim 8, wherein the antibiotic is selected from the group consisting of a penicillin, a cephalosporin, an aminoglycoside, a macrolide, a quinolone, a carbapenem, aztreonam, colistimethate, and a combination thereof, optionally wherein the antibiotic comprises an aminoglycoside, further optionally wherein the antibiotic comprises tobramycin. 10. The method of claim 8 or claim 9, wherein the route of administration for the antibiotic is selected from intravenous, oral or inhalation. 11. The method of any of claims 1-10, wherein the infection in the subject is reduced by at least about 25%, at least about 50%, at least about 75%, at least about 90%, at least about 95%, or more. 12. The method of any of claims 1-11, wherein the infection in the subject is reduced to below about 300 colony forming units per lung (CFU/lung), below about 200 CFU/lung, below about 100 CFU/lung, below about 50 CFU/lung or below about 10 CFU/lung. 13. The method of any of claims 1-12, wherein the infection is substantially or entirely cleared from the CF subject. Attorney Docket No.3289.0008WO 14. A combination therapeutic treatment method for treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), the combination therapeutic treatment method comprising: administering to the subject with CF a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa), and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli, optionally wherein the vaccine further comprises a squalene-based oil-in-water emulsion; and administering to the subject with CF a therapeutically effective amount of an antibiotic, wherein the Pa infection in the subject with CF is substantially reduced and/or cleared. 15. The combination therapeutic treatment method of claim 14, wherein the antibiotic comprises tobramycin. 16. The combination therapeutic treatment method of claims 14 or 15, wherein the antibiotic is administered substantially simultaneously with the vaccine. 17. The combination therapeutic treatment method of any one of claims 14- 67, wherein the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4. 18. A composition for use in treating a Pseudomonas aeruginosa (Pa) infection in a subject with cystic fibrosis (CF), wherein the composition comprises: (a) a therapeutically effective amount of a composition comprising a vaccine comprising a fusion polypeptide, wherein the fusion polypeptide comprises i) a fusion of a needle tip protein or an antigenic fragment thereof Attorney Docket No.3289.0008WO and/or a translocator protein or an antigenic fragment thereof from a Type III secretion system (T3SS) of Pseudomonas aeruginosa (Pa) and ii) an A1 subunit of the labile toxin (LTA1) from enterotoxigenic Escherichia coli; and (b) a therapeutically effective amount of an antibiotic. 19. The composition for use of claim 18, wherein the antibiotic comprises Tobramycin. 20. The composition for use of claim 18 or 19, wherein the fusion polypeptide has an amino acid sequence of SEQ ID NO: 4 or an amino acid having at least 90% homology to SEQ ID NO: 4.
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