KELLY SEAN (US)
CLAIMS What is claimed is: 1. A UPEC conjugate peptide comprising: (i) a self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn); and (ii) at least one UPEC epitope conjugated to a terminus of the self-assembling peptide, wherein the UPEC epitope is selected from pIroN (YLLYSKGNGCPKDITSGGCYLIGNKDLDPE, SEQ ID NO: 80), pIutA (VDDIDYTQQQKIAAGKAISADAIPGGSVD, SEQ ID NO: 81), or pIreA (GIAKAFRAPSIREVSPGFGTLTQGGASIMYGN, SEQ ID NO: 82), or a combination thereof. 2. The UPEC conjugate peptide of claim 1, wherein each self-assembling peptide forms a beta sheet and comprises a polypeptide having an amino acid sequence selected from QQKFQFQFEQQ (SEQ ID NO: 12), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn). 3. The UPEC conjugate peptide of claim 1, wherein each self-assembling peptide forms an alpha-helix and comprises a polypeptide having an amino acid sequence of bXXXb (SEQ ID NO: 1), wherein X is independently any amino acid and b is independently any positively charged amino acid. 4. The UPEC conjugate peptide according to claim 1 or 2, wherein the self-assembling peptide comprises the sequence QQKFQFQFEQQ (SEQ ID NO: 12) or Ac- QQKFQFQFEQQ-NH2 (SEQ ID NO: 13) or bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid). 5. The UPEC conjugate peptide of claim 1, 3, or 4, wherein b is independently selected from Arg and Lys. 6. The UPEC conjugate peptide of claim 1, 3, 4, or 5, wherein bXXXb (SEQ ID NO: 1) is RAYAR (SEQ ID NO: 2) or KAYAK (SEQ ID NO: 3). 7. The UPEC conjugate peptide of any one of claims 1 and 3-6, wherein the self- assembling peptide comprises an amino acid sequence of ZnbXXXbZm (SEQ ID NO: 5), wherein b is independently any positively charged amino acid, Z is independently any amino acid, X is independently any amino acid, n is an integer from 0 to 20, and m is an integer from 0 to 20. 8. The UPEC conjugate peptide of claim 7, wherein the self-assembling peptide comprises an amino acid sequence selected from QARILEADAEILRAYARILEAHAEILRAQ (Coil29, SEQ ID NO: 6), or QAKILEADAEILKAYAKILEAHAEILKAQ (SEQ ID NO: 7), or ADAEILRAYARILEAHAEILRAQ (SEQ ID NO: 8), or Ac- QARILEADAEILRAYARILEAHAEILRAQ-NH2 (SEQ ID NO: 9), or Ac- QAKILEADAEILKAYAKILEAHAEILKAQ-NH2 (SEQ ID NO: 10), or Ac- ADAEILRAYARILEAHAEILRAQ-NH2 (SEQ ID NO: 11). 9. The UPEC conjugate peptide of any one of claims 1-8, wherein the at least one UPEC epitope is attached to the C-terminus or the N-terminus of the self-assembling peptide. 10. The UPEC conjugate peptide of any one of claims 1-9, wherein 1 to 10 UPEC epitopes are attached to the C-terminus or the N-terminus of the self-assembling peptide. 11. The UPEC conjugate peptide of any one of claims 1-10, further comprising: (iii) a PEG molecule or a PAS peptide conjugated to the self-assembling peptide. 12. The UPEC conjugate peptide of claim 11, wherein the PAS peptide comprises a sequence of Pro-Ala-Ser or comprises the sequence of ASPAAPAPASPAAPAPSAPA (SEQ ID NO: 97), or a peptide having at least 80%, 85%, 90%, or 95% identity thereto. 13. The UPEC conjugate peptide of claim 11, wherein the PEG molecule comprises PEG-2000. 14. The UPEC conjugate of any one of claims 11-13, wherein the PEG molecule or the PAS peptide is conjugated to the self-assembling peptide at the same or the opposite terminus from wherein the UPEC epitope is attached. 15. The UPEC conjugate peptide of any one of claims 1-14, further comprising: (iv) at least one linker. 16. The UPEC conjugate peptide of claim 15, wherein the at least one linker comprises a first linker between the at least one UPEC epitope and the self-assembling peptide, and a second linker between the PEG molecule or the PAS peptide and the self-assembling peptide. 17. The UPEC conjugate peptide of claim 15 or 16, wherein the at least one linker comprises an amino acid sequence independently selected from SEQ ID NO: 83 (SGSG), SEQ ID NO: 84 ((Ser-Gly)2), SEQ ID NO: 85 (CCCCSGSG), SEQ ID NO: 86 (Gn wherein n is an integer from 1 to 10), SEQ ID NO: 87 (GSGS), SEQ ID NO: 88 (SSSS), SEQ ID NO: 89 (GGGS), SEQ ID NO: 90 (GGC), SEQ ID NO: 91 ((GGC)8), SEQ ID NO: 92 ((G4S)3), SEQ ID NO: 93 (KSGSG), SEQ ID NO: 94 (KKSGSG), SEQ ID NO: 95 (EAAAK)2, and SEQ ID NO: 96 (GGAAY). 18. The UPEC conjugate peptide of any one of claims 1-17, wherein the UPEC conjugate peptide comprises a sequence selected from PEG-Q11-pIroN, PEG-Q11-pIutA, or PEG-Q11-pIreA, or a combination thereof. 19. A nanofiber comprising a plurality of the UPEC conjugate peptide of any one of claims 1-18, wherein the conjugate peptide self-assembles into the nanofiber. 20. A nanofiber comprising: (i) at least one UPEC conjugate peptide of any one of claims 1-19; and (ii) at least one T-cell epitope-conjugate peptide comprising: a self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn); and at least one T-cell epitope conjugated to a terminus of the self-assembling peptide, wherein the at least one T-cell epitope is selected from PADRE and VAC, and wherein PADRE comprises a polypeptide having the amino acid sequence of aKXVAAWTLKAa (SEQ ID NO: 99, wherein “X” comprises cyclohexylalanine and “a” comprises D-alanine), and wherein VAC comprises a polypeptide having the amino acid sequence of QLVFNSISARALKAY (SEQ ID NO: 100). 21. The nanofiber of claim 20, wherein the T-cell epitope-conjugate peptide further comprises a linker between the T-cell epitope and the self-assembling peptide. 22. The nanofiber of claim 21, wherein the linker comprises an amino acid sequence selected from SEQ ID NO: 83 (SGSG), SEQ ID NO: 84 ((Ser-Gly)2), SEQ ID NO: 85 (CCCCSGSG), SEQ ID NO: 86 (Gn wherein n is an integer from 1 to 10), SEQ ID NO: 87 (GSGS), SEQ ID NO: 88 (SSSS), SEQ ID NO: 89 (GGGS), SEQ ID NO: 90 (GGC), SEQ ID NO: 91 ((GGC)8), SEQ ID NO: 92 ((G4S)3), SEQ ID NO: 93 (KSGSG), SEQ ID NO: 94 (KKSGSG), SEQ ID NO: 95 (EAAAK)2, and SEQ ID NO: 96 (GGAAY). 23. The nanofiber of any one of claims 20-22, wherein the cyclohexylalanine comprises D-alanine. 24. The nanofiber of any one of claims 20-23, further comprising: (iii) a plain self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn). 25. The nanofiber of any one of claims 20-24, wherein the nanofiber comprises a combination of 10 to 10,000, or 100 to 10,000 peptides comprising UPEC conjugate peptides and T-cell epitope-conjugate peptides. 26. The nanofiber of any one of claims 20-24, wherein the nanofiber comprises a combination of 10 to 10,000, or 100 to 10,000 peptides comprising UPEC conjugate peptides, T-cell epitope-conjugate peptides, and plain self-assembling peptides. 27. The nanofiber of any one of claims 20-26, wherein at least about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 97.5% of the peptides in the nanofiber are UPEC conjugate peptides. 28. The nanofiber of any one of claims 20-27, wherein at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or 15% of the peptides in the nanofiber are T-cell epitope-conjugate peptides. 29. The nanofiber of any one of claims 20-28, wherein the UPEC peptide conjugate and the T-cell epitope-peptide conjugate are present in the nanofiber at a ratio of about 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 12:1, 14:1, 16:1, 18:1, 20:1, 22:1, 24:1, 26:1, 28:1, 30:1, 32:1, 34:1, 36:1, 38:1, or 40:1. 30. The nanofiber of any one of claims 20-29, wherein the self-assembling peptide forms a fibril including beta-sheet structures or a fibril having a coiled coil structure. 31. The nanofiber of any one of claims 20-29, wherein the self-assembling peptide forms a fibril having a structure of a helical filament formed around a central axis. 32. The nanofiber of claim 31, wherein the N-terminus of each self-assembling peptide is positioned at the exterior of the helical filament. 33. The nanofiber of any one of claims 20-32, wherein the UPEC molecules are exposed on the exterior surface of the nanofiber. 34. The nanofiber of any one of claims 20-33, wherein the nanofiber is about 5-30 nm in width. 35. The nanofiber of any one of claims 20-34, wherein the nanofiber is about 100 nm to 1 μm, 100 nm to 2 μm, 100 nm to 3 μm, 100 nm to 4 μm, or 100 nm to 5 μm in length. 36. A pharmaceutical composition comprising: (a) the UPEC conjugate peptide of any one of claims 1-19 or the nanofiber of any one of claims 20-35; and (b) a pharmaceutically acceptable carrier, diluent, and/or excipient. 37. The pharmaceutical composition of claim 36, further comprising: (c) an adjuvant selected from cyclic-di-AMP, CpG, cyclic GMP-AMP (cGAMP), cholera toxin B subunit (CTB), retinoic acid, or heat labile toxin B subunit, or a combination thereof. 38. The pharmaceutical composition of claim 36 or 37, formulated into a tablet. 39. The pharmaceutical composition of claim 38, wherein the tablet is a dissolving tablet. 40. A method of treating a urinary tract infection (UTI), the method comprising administering to a subject a therapeutically effective amount of the UPEC conjugate peptide of any one of claims 1-19, or the nanofiber of any one of claims 20-35, or the pharmaceutical composition of any one of claims 36-39. 41. A method of treating a bacterial infection, the method comprising administering to a subject a therapeutically effective amount of the UPEC conjugate peptide of any one of claims 1-19, or the nanofiber of any one of claims 20-35, or the pharmaceutical composition of any one of claims 36-39. 42. The method of claim 40 or 41 , wherein the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition is administered sublingually. 43. The method of any one of claims 40-42, wherein pathogenic bacteria are reduced. 44. The method of claim 43, wherein pathogenic bacteria comprise uropathogenic Escherichia coli. 45. The method of claim 43 or 44, wherein pathogenic bacteria comprise CFT073. 46. The method of any one of claims 40-45, wherein non-pathogenic bacteria are not reduced. 47. The method of any one of claims 40-46, wherein the microbiome in the colon is maintained. 48. The method of any one of claims 40-47, wherein the microbiome in the colon statistically maintains a Shannon Diversity Index. |
[000106] In some embodiments, the compositions described herein are formulated for sublingual administration. The compositions may be formulated into a tablet. For example, the compositions may be formulation into a dissolving tablet. The dissolving tablet may be placed under the tongue. The compositions may be formulated into a table by a variety of suitable means, for example, the compositions may be freeze dried and pressed into a tablet form.
[000107] The compositions described herein may be formulated into a pharmaceutical composition as neutral or salt forms. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the peptide) and those that are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.
[000108] Typically, compositions are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective and immunogenic. The quantity to be administered depends on the subject to be treated, including the capacity of the individual’s immune system to synthesize antibodies and the degree of protection desired. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner. However, suitable dosage ranges are of the order of several hundred micrograms active ingredient per vaccination. Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed by subsequent inoculations or other administrations.
[000109] The manner of application may be varied widely. Any of the conventional methods for administration of a vaccine are applicable. These are believed to include oral application on a solid physiologically acceptable base or in a physiologically acceptable dispersion, parenterally, by injection and the like. The dosage of the vaccine will depend on the route of administration and will vary according to the size and health of the subject.
[000110] The compositions and related methods, particularly administration of a peptide conjugate or nanofiber, may also be used in combination with the administration of traditional therapies. These include, but are not limited to, the administration of antibiotics such as streptomycin, ciprofloxacin, doxycycline, gentamycin, chloramphenicol, trimethoprim, sulfamethoxazole, ampicillin, tetracycline or various combinations of antibiotics.
[000111] In one aspect, it is contemplated that a peptide conjugate or nanofiber or pharmaceutical composition is used in conjunction with an additional treatment described herein. Alternatively, the therapy may precede or follow the other agent treatment by intervals ranging from minutes to weeks. In embodiments where the other agents and/or a proteins is administered separately, one may generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent and antigenic composition would still be able to exert an advantageously combined effect on the subject. In such instances, it is contemplated that one may administer both modalities within about 12-24 h of each other and, more preferably, within about 6-12 h of each other . In some situations, it may be desirable to extend the time period for administration significantly, however, where several days (2, 3, 4, 5, 6, or 7) to several weeks (1 , 2, 3, 4, 5, 6, 7, or 8) lapse between the respective administrations.
[000112] Various combinations may be employed, for example antibiotic therapy is “A” and the immunogenic composition is “B”:
A/B/A B/A/B B/B/A A/A/B A/B/B B/A/A A/B/B/B B/A/B/B
B/B/B/A B/B/A/B A/A/B/B A/B/A/B A/B/B/A B/B/A/A
B/A/B/A B/A/A/B A/A/A/B B/A/A/A A/B/A/A A/A/B/A
[000113] Administration of the pharmaceutical compositions to a patient/subject will follow general protocols for the administration of such compounds, taking into account the toxicity, if any. It is expected that the treatment cycles would be repeated as necessary. It also is contemplated that various standard therapies, such as hydration, may be applied in combination with the described therapy.
[000114] In some embodiments, pharmaceutical compositions are administered to a subject. Different aspects involve administering an effective amount of a composition to a subject. In some embodiments, immunogenic compositions may be administered to the patient to protect against infection by one or more microbial pathogens. Additionally, such compounds can be administered in combination with an antibiotic or other known antimicrobial therapy. Such compositions will generally be dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredients, its use in immunogenic and therapeutic compositions is contemplated. Supplementary active ingredients, such as other anti-cancer agents, can also be incorporated into the compositions.
[000115] In addition to the compounds formulated for parenteral administration, such as those for intravenous or intramuscular injection, other pharmaceutically acceptable forms include, e.g., tablets or other solids for oral administration; time release capsules; and any other form currently used, including creams, lotions, mouthwashes, inhalants and the like.
[000116] The active compounds can be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, or even intraperitoneal routes. Typically, such compositions can be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for use to prepare solutions or suspensions upon the addition of a liquid prior to injection can also be prepared; and, the preparations can also be emulsified.
[000117] Solutions of the active compounds as free base or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
[000118] The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil, or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that it may be easily injected. It also should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
[000119] The proteinaceous compositions may be formulated into a neutral or salt form.
Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. [000120] The carrier also can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin. [000121] Administration of the compositions will typically be via any common route. This includes, but is not limited to oral, nasal, or buccal administration. Alternatively, administration may be by orthotopic, intradermal, subcutaneous, intramuscular, intraperitoneal, intranasal, or intravenous injection. In certain embodiments, a vaccine composition may be inhaled (e.g., U.S. Patent No.6,651,655, which is specifically incorporated by reference). Such compositions would normally be administered as pharmaceutically acceptable compositions that include physiologically acceptable carriers, buffers or other excipients. In some embodiments, the composition is administered to the subject intravenously, intraarterially, intraperitoneally, subcutaneously, intranasally, intramuscularly, or intratumorally. In some embodiments, the immunogenic composition is administered orally. In some embodiments, the immunogenic composition is administered sublingually. [000122] For parenteral administration in an aqueous solution, for example, the solution may be suitably buffered, if necessary, and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in isotonic NaCl solution and either added to hypodermoclysis fluid or injected at t he proposed site of infusion, (see for example, Remington’s Pharmaceutical Sciences, 1990). Some variation in dosage will necessarily occur depending on the condition of the subject. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. [000123] An effective amount of therapeutic or prophylactic composition is determined based on the intended goal. The term “unit dose” or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the composition calculated to produce the desired responses discussed above in association with its administration, i.e., the appropriate route and regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the protection desired. [000124] Precise amounts of the composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the subject, route of administration, intended goal of treatment (alleviation of symptoms versus cure), and potency, stability, and toxicity of the particular composition. [000125] Upon formulation, solutions may be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective. The formulations may be easily administered in a variety of dosage forms, such as the type of injectable solutions described above. [000126] In some embodiments, the pharmaceutical compositions comprising the UPEC peptide conjugate or nanofibers detailed herein further include at least one additional therapeutic agent. The at least one additional therapeutic agent may comprise antibiotics, NSAIDS, anti-inflammatory compounds, hemoperfusion devices, quorum sensing inhibitors, lytic bacteriophage, polyclonal or monoclonal antibodies, non-immune tolerizing approaches, liposome-based cytotoxin inhibitors, or combinations thereof. The at least one additional therapeutic agent may comprise an adjuvant. In some embodiments, the adjuvant comprises CpG, cholera toxin B subunit (CTB), STING agonists like cyclic dinucleotides such as cyclic-di-AMP and/or cyclic GMP-AMP (cGAMP), retinoic acid, or heat labile toxin B subunit, or a combination thereof. 8. Methods a. Methods of Treating a Urinary Tract Infection (UTI) [000127] Further provided herein are methods of treating a urinary tract infection (UTI). Further provided herein are methods of treating or reducing a bacterial infection. Further provided herein are methods of treating or reducing a uropathogenic Escherichia coli infection. The methods may include administering to the subject a UPEC conjugate peptide, or nanofiber, or pharmaceutical composition as detailed herein. The UPEC conjugate peptide, or nanofiber, or pharmaceutical composition may be administered intraperitoneally, orally, sublingually, intravenously, nasally, buccally, transdermally, intranasally, or intramuscularly. In some embodiments, the UPEC conjugate peptide, or nanofiber, or pharmaceutical composition is administered sublingually. [000128] In some embodiments, method further comprises administering at least one additional therapeutic agent. The at least one additional therapeutic agent may be administered prior to the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition, or concurrently with the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition, or after the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition. The at least one additional therapeutic agent may comprise antibiotics, NSAIDS, anti-inflammatory compounds, hemoperfusion devices, quorum sensing inhibitors, lytic bacteriophage, polyclonal or monoclonal antibodies, non-immune tolerizing approaches, liposome-based cytotoxin inhibitors, or combinations thereof. The at least one additional therapeutic agent may comprise an adjuvant. In some embodiments, the adjuvant comprises CpG, cholera toxin B subunit (CTB), STING agonists like cyclic dinucleotides such as cyclic-di-AMP and/or cyclic GMP-AMP (cGAMP), retinoic acid, or heat labile toxin B subunit, or a combination thereof. [000129] Upon or after administration, a bacterial infection, such as in the urinary tract, may be treated or reduced. The bacteria may be reduced by at least about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold, relative to a control. The bacteria may be reduced by less than about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, or 10-fold, relative to a control. The bacteria be reduced by about 5-95%, 10-90%, 15-85%, 20-80%, or 1.5-fold to 10-fold, relative to a control. The bacterial infection may be caused by uropathogenic bacteria. The uropathogenic bacteria may comprise uropathogenic E. coli. Upon or after administration, pathogenic bacteria, for example, in the urinary tract, may be reduced. The pathogenic bacteria may comprise CFT073. Upon or after administration, non-pathogenic bacteria may not be reduced. Upon or after administration, the microbiome in the gastrointestinal tract may not be reduced. Bacterial diversity in the colon may not be reduced. Bacteria in the gut may include, for example, bacteria from the genus Corynebacterium, Bifodobacterium, Atopobium, Faecalibacterium, Clostridium, Roseburia, Ruminococcus, Dialister, Lactobaccillus, Enterococcus, Staphylococcus, Sphingobacterium, Bacteroides, Tannerella, Parabacteroides, Alistipes, Prevotella, Escherichia, Shigella, Desulfovibrio, Bilophila, Helicobacter, Fusobacterium, and Akkermansia, or a combination thereof. Bacteria in the gut may include, for example, bacteria from the species Bifodobacterium longum, Bifodobacterium bifidum, Faecalibacterium prausnitzii, Clostridium spp., Roseburia intestinalis, Ruminococcus faecis, Dialister invisus, Lactobaccillus reuteri, Enterococcus faecium, Staphylococcus leei, Bacteroides fragilis, Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Alistipes finegoldii, Prevotella spp., Escherichia coli, Shigella flexneri, Desulfovibrio intestinalis, Bilophila wadsworthia, Helicobacter pylori, Fusobacterium nucleatum, and Akkermansia muciniphila, or a combination thereof. The microbiome in the colon may be maintained. In some embodiments, the microbiome in the colon statistically maintains a Shannon Diversity Index. b. Methods of Inducing an Immune Response [000130] Further provided herein are methods of inducing an immune response in a subject. The methods may include administering to the subject a UPEC conjugate peptide, or nanofiber, or pharmaceutical composition as detailed herein. In some embodiments, the B1a cells in the subject express antibodies upon or subsequent to administration. The antibodies may be selected from IgM, IgG, and IgA, or a combination thereof. Further provided herein is an antibody produced in the immune response. In some embodiments, the UPEC peptide conjugate or the nanofiber is administered to the subject intraperitoneally, orally, sublingually, intravenously, nasally, buccally, transdermally, intranasally, or intramuscularly. In some embodiments, the UPEC conjugate peptide, or nanofiber, or pharmaceutical composition is administered sublingually. In some embodiments, method further comprises administering at least one additional therapeutic agent. The at least one additional therapeutic agent may be administered prior to the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition, or concurrently with the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition, or after the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition. The at least one additional therapeutic agent may comprise an adjuvant. In some embodiments, the adjuvant comprises CpG, cholera toxin B subunit (CTB), STING agonists like cyclic dinucleotides such as cyclic-di-AMP and/or cyclic GMP-AMP (cGAMP), retinoic acid, or heat labile toxin B subunit, or a combination thereof. 9. Examples [000131] The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. One skilled in the art will appreciate readily that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those objects, ends and advantages inherent herein. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art. Example 1 Materials and Methods [000132] Peptide-Polymer Synthesis and Nanofiber Preparation. Peptides were synthesized using standard Fmoc solid-phase synthesis on Rink amide resins. PEG- peptides were synthesized by on-resin conjugation of 2000 MW mPEG-NHS (Creative PEGWorks PLS-214) to the N-terminus. Peptides were cleaved for 2 h at room temperature in a 95/2.5/2.5 TFA/triisopropylsilane/water cocktail, followed by washing with cold diethyl ether. Peptides were purified by reverse-phase HPLC using a C4 column (PEG-peptides) or C18 column (non-PEGylated peptides) and lyophilized. Peptide identity was confirmed using matrix-assisted laser desorption/ionization mass spectrometry (MALDI) on a Bruker Autoflex Speed LRF MALDI-TOF spectrometer using α-cyano-4-hydroxycinnamic acid (Sigma Aldrich, 70990) as the matrix. [000133] To prepare nanofiber solutions, lyophilized peptides were dissolved at 8 mM in sterile water and incubated at 4°C overnight. The solutions were then brought to the final concentrations in 1X PBS by addition of sterile water and sterile 10X PBS and incubated at room temperature for 3 h to before use to allow for fibrillization. Co-assembled nanofibers were prepared by vortexing lyophilized B-cell epitope peptides (PEG-Q11pIreA, PEG- Q11pIutA, PEG-Q11pIroN) for 20 minutes and dissolving in a VACQ11 or Q11 solution at 8 mM total peptide. For multiple nanofiber formulations for immunization, each nanofiber was separately assembled and combined just prior to immunization. [000134] For adjuvanted solutions, nucleotide adjuvants (cyclic-di-AMP, CpG) were added just prior to fibrillization; all other adjuvants were added after fibrillization. Adjuvants were included in formulations at the following dosages per mouse: 10 μg cholera toxin B subunit (List Labs, 104), 10 μg cyclic-di-AMP (Invivogen, vac-nacda), 25 μg CpG (Invivogen, tlrl- 1826), 20 μg CRX-527 (Invivogen, tlrl-crx527), 15 μg compound 48/80 (Millipore Sigma, C2313). [000135] Nanofiber Characterization by Electron Microscopy. To visualize nanofiber morphology by transmission electron microscopy, nanofiber solutions were diluted to 0.2 mM in 1X PBS and deposited onto Formvar/carbon-coated 400 mesh copper grids (Electron Microscopy Sciences, EMS400-Cu) for 1 min, rinsed with ultrapure water, and negatively stained for 1 min with 1% w/v uranyl acetate (EMS, 22400-1) prior to wicking away with filter paper. Samples were imaged on an FEI Tecnai G 2 Twin electron microscope at 120 kV. [000136] Tablet Production Process. Reverse tablet molds were designed in FreeCAD and 3D-printed with a MakerBot Ultimaker 3. PDMS molds were prepared using SYLGARD 184 kits (Sigma, 761028). Fibrillized nanofiber solutions were mixed with adjuvants and sugars to a final concentration of 7.8 wt% each of trehalose (Santa Cruz Biotechnology, 394303), dextran (Alfa Aesar, J61216), and mannitol (Millipore Sigma, M4125). Final solutions were pipetted into the PDMS tray (30 µL per tablet), frozen at -80°C, and lyophilized (Kelly, et al. Advanced Healthcare Materials 2021, 10, 2001614, incorporated herein by reference). [000137] Estimation of Clinical Tablet Dissolution Time. Five immunization-formulation tablets containing PEG-Q11(PIreA/PIutA/PIroN/VAC) were individually tested. For each tablet, 1.0 mL of pooled human saliva (Innovative Research, IRHUSL) was warmed to 37°C and dispersed on a petri dish. A tablet was dropped atop the saliva and the dissolution time was measured, using USP guidelines to determine the point of disintegration (https://www.usp.org/sites/default/files/usp/document/harmon ization/gen-chapter/april-2019- m99460.pdf). A previous study showed 1.0 mL to be the approximate volume of saliva in a human mouth prior to swallowing. [000138] Animals and Immunizations. Animal experiments were approved by the Institutional Care and Use Committee of Duke University under protocol #A264-18-11. Murine immunizations were initiated with female C57BL/6 mice (Envigo) aged 9-12 weeks. For sublingual immunizations, mice were deeply anesthetized by a cocktail delivering 100 mg/kg ketamine and 10 mg/kg xylazine. For droplet immunizations, a micropipette with a 20 µL tip was used to apply 8 µL of the immunizing solution below the tongue. For tablet immunizations, the tablet was placed below the tongue of anesthetized mice using tweezers. For droplet and tablet immunizations, the mouse’s heads were placed in anteflexion for 20 min following administration to prevent swallowing of the material. [000139] Rabbit immunizations were conducted with 8 month old female New Zealand White rabbits (Envigo). Rabbits were anesthetized with 20 mg/kg ketamine and 3 mg/kg xylazine. Tablets were placed under the rabbits’ tongue using tweezers, rabbits’ head were placed in anteflexion for 20 minutes, and recovery was initiated by atipamezole (xylazine reversal agent). [000140] The total peptide concentration was 5 mM for all immunizations. For single epitope immunizations with PADRE, the B-cell epitope was 4.75 mM and PADRE was 0.25 mM, unless indicated otherwise. For single-epitope immunizations with VAC, the B-cell epitope was 4.4 mM and VAC was 0.6 mM. For co-assembled multi-B cell epitope nanofibers (including tablets in both mice and rabbits), each B-cell epitope was 1.4 mM and VAC was 0.6 mM. For mixed nanofiber formulations, each B-cell epitope was at 3x the final concentration, to keep total epitope dose consistent with single nanofiber formulations after mixing. For no VAC tablets, VACQ11 was replaced with the same concentration of unmodified Q11 to keep the total peptide concentration constant. [000141] Measurement of Antibody Responses. Serum was collected via the submandibular vein. For analysis of epitope-specific IgG by ELISA, plates were coated with 20 μg/mL of streptavidin (Millipore Sigma, 189730) overnight at 4°C. Plates were washed with 0.5 g/L Tween-20 in PBS (1X PBST), coated for 1 hour with 20 μg/mL biotinylated pIreA, pIuta, or pIroN, and blocked with Super Block Blocking Buffer (Thermo Scientific, 37515). When indicated in figure legends, plates were coated with a 1:1:1 mixture of biotinylated pIreA, pIutA, and pIroN, at a total concentration of 20 μg/mL. Sera diluted in PBST-BSA or undiluted urine were added to the plate, and antigen-specific IgG was detected by horseradish peroxidase (HRP) conjugated Fcγ fragment specific goat anti- mouse IgG (Jackson Immuno Research, 15- 035-071). Results are reported as antibody titers calculated with an absorbance cutoff of 0.2 OD, or as background-subtracted A 450 values. For measuring antibody subclasses, HRP conjugated goat anti-mouse detection antibodies were purchased from Southern Biotech (IgG1: 1071-05, IgG2b: 1091-05, IgG2c: 1078-05). For whole-cell ELISAs, bacteria were cultured as indicated in the following section and plates were coated with an OD 600 = 1.0 solution in 1X PBS overnight and blocked for 2 h with 10% heat-inactivated fetal bovine serum in 1X PBS prior to addition of sera. Total (non antigen-specific) IgA was determined using a mouse IgA ELISA kit (Thermo Scientific, 88- 50450). [000142] Bacterial Culture and Challenge Model. The uropathogenic E. coli strain CFT073 was purchased from ATCC (700928); this strain was originally isolated from a pyelonephritis patient. CFT073 was cultured at 37°C with aeration in Luria broth (10 g/L tryptone, 5 g/L yeast extract, 10 g/L sodium chloride) at a 1:100 dilution from a starter culture. For iron-limited culture conditions, the chelator 2,2’-bipyridyl (Millipore Sigma, D216305) was present at 400 µM in Luria broth. The non-uropathogenic E. coli strain BL21 was purchased from New England BioLabs (C2530H) and cultured was performed as with CFT073, but with the use of terrific broth (Fisher Scientific, BP2468). [000143] For the bacteremia model, immunized or naive mice were challenged with intraperitoneal injection of 1x10 8 or 2x10 8 CFU of CFT073 in 1X PBS, as specified in figure captions. Temperature and body weight of mice were recorded at regular intervals for 72 h. Humane endpoints were set as a temperature below 32°C, loss of 25% of body weight, or exhibition of significant clinical symptoms, as prescribed by IACUC guidelines. [000144] For the transurethral infection model, water supply was removed from cages for one hour prior to infection to allow for voiding of bladder. Mice were sedated with an i.p. injection of a ketamine/xylazine cocktail and a sterilized plastic needle dabbed in surgical lubricant was used to deliver 5x10 7 CFU of CFT073 into the urethra. Mice were monitored as for the bacteremia model, but with sacrifice at 48 h. [000145] Microbiome Analysis. Fecal pellets were collected from mice and immediately frozen on dry ice prior to storage at -80 ºC. Samples were submitted to the Duke Center for Genomic and Computational Biology Microbiome Shared Resource core for microbiome analyses. In brief, the Duke Microbiome Core Facility (MCF) extracted DNA using the Qiagen PowerSoilPro DNA Kit (Qiagen, 47014). Bacterial community composition in isolated DNA samples was characterized by amplification of the V4 variable region of the 16S rRNA gene by polymerase chain reaction using the forward primer 515 and reverse primer 806 following the Earth Microbiome Project protocol (http://www.earthmicrobiome.org/). These primers (515F and 806R) carry unique barcodes that allow for multiplexed sequencing. Concentration of the PCR products were accessed using a Qubit dsDNA HS assay kit (ThermoFisher, Q32854) and a Promega GloMax plate reader. Equimolar 16S rRNA PCR products from all samples were pooled prior to sequencing, which was performed by the Duke Sequencing and Genomic Technologies (SGT) shared resource on an Illumina MiSeq instrument configured for 250 base-pair paired- end sequencing runs. [000146] Sequences were analyzed using QIIME2 software. Demultiplexed forward reads were assigned a cut off between 10-230 bp and reverse reads were assigned a cut off between 10-160 bp. Samples were trimmed to a depth of 94132 to retain 6,212,712 (73.67%) features in 66 (94.29%) samples. This sampling depth was used to rarefy the feature table to calculate alpha and beta diversity via a phylogenic rooted tree. Alpha rarefaction was plotted to confirm the richness of the samples had been fully observed. Sequences were then classified against the Greengenes 13_899% OTUs full-length sequences training set for taxonomic analysis. Example 2 Selection of B-cell epitopes from uropathogenic E. coli [000147] Human UTIs can be caused by several genera of bacteria, but over 80% are the result of infection by a diverse set of uropathogenic E. coli strains, collectively referred to as UPEC. While a vaccine against UPEC would not be universally effective in the human population, it would represent a dramatic step towards changing how UTIs are prevented and treated. UPEC themselves are a heterogeneous set of strains with variable expression of virulence factors, such that a vaccine would still likely need to target multiple antigens to be broadly effective against UPEC alone. For these reasons, we sought to design a multivalent vaccine that would broadly target UPEC strains to prevent a large majority of urinary tract infections. [000148] To prioritize safety and avoid adverse effects related to off-target immune responses against non-pathogenic E. coli or other commensals, we sought peptide epitopes that would be found near-exclusively on UPEC. A major set of UPEC virulence factors are iron receptor proteins, which allow UPEC to survive in the iron-poor urinary tract. These receptors are ideal antigenic targets because, in addition to being critical to the survival of UPEC, they are surface-expressed, allowing for possible antibody binding. We selected three peptide epitopes previously identified within UPEC receptor proteins, one each from the proteins IreA, IutA, and IroN. The genes encoding these proteins were found in 34%, 66%, and 74% of clinical UPEC isolates, respectively, suggesting that by targeting all three we could design a vaccine that would be broadly effective against human infection with UPEC (FIG.1D). Notably, the peptide epitopes from IutA and IroN have previously shown poor immunogenicity in mice after mucosal immunization, failing to raise systemic or urinary antibody responses even when given with high doses of the strong but non-translatable cholera toxin adjuvant. We viewed these poorly immunogenic peptide epitopes as an opportunity to utilize our sublingual peptide immunization technology. Example 3 Co-assembly of T-cell and B-cell epitopes in sublingual nanofiber vaccines elicits antibody responses against UPEC epitopes [000149] We sought to leverage our recently developed sublingual peptide vaccine platform to enhance the immunogenicity of these challenging peptide epitopes and develop a highly specific anti-UPEC vaccine. We designed self-assembling peptide-polymers with C- terminal peptide epitopes (referred to hereafter as pIreA, pIutA, and pIroN to distinguish them from their parent proteins), N-terminal PEG chains to promote sublingual mucus transport, and central Q11 peptide self-assembly domains to drive self-assembly into nanofibers (sequences are in TABLE 1). Each of the constructs – PEG-Q11pIreA, PEG- Q11pIutA, and PEG-Q11pIroN – assembled into supramolecular nanofibers, as evidenced by electron microscopy (FIGS.1A-1C). We co-assembled nanofibers containing both the UPEC B-cell epitopes and the universal helper T-cell epitope PADRE (Del Guercio, M.-F., et al. Vaccine 1997, 15, 441-448, incorporated herein by reference). Sublingual immunization with 8 µL droplets of solutions containing PEG-Q11(pIreA/PADRE) fibers and the adjuvant CTB (the non-toxic B subunit of cholera toxin) led to robust pIreA-specific serum antibody responses (FIG.1E). IL-4 + T-cell responses against the PADRE epitope were also observed (FIGS.2A-2C). Notably, the antibody responses were dependent on the ratio of B- to T-cell epitope within the nanofibers (FIG.1F). Co-assembly of PADRE did not promote antibody responses against either pIutA or pIroN, leading us to use an alternate universal T-helper epitope from vaccinia virus (Mora-Solano, C., et al. Biomaterials 2017, 149, 1-11, incorporated herein by reference) (referred to here as VAC). Sublingual immunization with PEG-Q11(pIutA/VAC) and PEG-Q11(pIroN/VAC) elicited epitope-specific antibody responses (FIG.1G). The efficacy of the selected VAC epitope over PADRE in this instance could be due to differences in affinity of binding between the epitopes and MHC-II molecules. The reported affinity of the VAC epitope for I-Ab (the haplotype of C57BL/6 mice) is 13.5 nM, compared with 94 nM for the PADRE epitope. These results highlighted the ability of our vaccine platform to raise antibody responses sublingually against poorly immunogenic peptide epitopes, and the modularity of the materials made it straightforward to assess different types and amounts of T-cell epitopes for advancement into the subsequent studies. Example 4 Multivalent nanofibers raise simultaneous responses against selected UPEC B-cell epitopes in serum and urine [000150] Having established that the selected B-cell epitopes were immunogenic in peptide nanofibers, we next sought to design a multi-epitope vaccine to elicit simultaneous antibody responses against all three epitopes, pIreA, pIutA, and pIroN. Again, we took advantage of the modularity of self-assembled peptide vaccines, which enabled a straightforward investigation of how the epitope arrangement within the nanofibers affected antibody responses in the context of different adjuvants. We immunized one set of mice with self-assemblies where all peptides were co-assembled into homogenous nanofibers bearing all three B-cell epitopes and one T-cell epitope, termed PEG-Q11(pIreA/pIutA/pIroN/VAC) (FIG.3A). For another set, we synthesized three types of nanofibers, each bearing only one of the B-cell epitopes along with T-cell epitopes, and we immunized mice with mixtures of these 3 nanofibers, termed (PEG-Q11(pIreA/PADRE) + PEG-Q11(pIutA/VAC) + PEG-Q11 (pIroN/VAC)). We further compared these two formulations when adjuvanted with either CTB adjuvant or the STING agonist cyclic-di-AMP. Each of the four formulations elicited epitope-specific antibody responses against each of the three UPEC B-cell epitopes (FIGS. 3B-3D). As a measure of the overall strength of the response, we calculated an arithmetic sum of the log 10 IgG endpoint titers against the three epitopes. By this combined measure, the single nanofiber bearing all three B-cell epitopes and adjuvanted with cyclic-di-AMP elicited the strongest responses (FIG.3E). The IgG subclasses of these responses were predominantly IgG2b and IgG2c, subclasses that are in many cases the most potent for anti- bacterial immunity (FIG.3F). The simplicity of the single nanofiber formulation and favorable translational profile of cyclic-di-AMP, along with its effectiveness at raising high-titer responses, led us to select this formulation for future studies. [000151] One advantage of using sublingual immunization as the route for a UTI vaccine is its demonstrated ability to raise immune responses in the urinary tract. To characterize the ability of our vaccines to raise antigen-specific IgG and IgA within the urinary tract, we assayed urine from immunized mice (FIG.3G). Individual groups were not statistically different from each other, though comparisons of IgA responses against different formulations approached significance, so to test the impact of adjuvant and nanofiber composition separately, we combined groups and ran t-tests on urinary antibody levels, using Holm-Šídák correction for multiple comparisons. Nanofiber composition was not significant for either IgG (p=0.95) or IgA (p=0.95) when CTB and cyclic-di-AMP adjuvanted groups were combined. I n contrast, we found that cyclic-di-AMP produced significantly higher epitope-specific IgA levels in the urine than CTB when one nanofiber and three nanofiber groups were combined (p=0.038), while IgG levels did not differ significantly (p=0.38). These results indicated that nanofiber sublingual vaccines could raise responses not only systemically, but also within the urinary tract. Example 5 Vaccine-induced antibody responses are specific for uropathogenic E.coli [000152] One motivation for utilizing peptide epitopes is that despite their generally poor immunogenicity, they are highly specific and in principle can be selected to target pathogenic bacterial strains while sparing non-pathogenic strains. To test the specificity of the antibody response raised by our vaccine, we compared their level of binding to both a uropathogenic strain of E. coli (CFT073) and a non-pathogenic lab strain of E. coli (BL21). Serum antibodies from all four immunization groups bound to CFT073 but had no detectable levels of anti-BL21 antibodies (FIG.3H). The CFT073 culture conditions used for this ELISA were expected to induce expression of pIutA, but not pIreA or pIroN. These results still highlighted that the induced antibodies do not bind non-pathogenic E. coli, and that antibodies raised by peptide nanofibers are able to bind to CFT073. Along with the demonstrated ability to raise multivalent responses and to elicit urinary antibodies, this specificity is a unique advantage. Example 6 STING and TLR9 agonists enhance urinary antibody levels after sublingual nanofiber immunization [000153] Based on our initial vaccine studies, we proceeded with a formulation of a single co-assembled nanofiber and cyclic-di-AMP adjuvant. To enhance the urinary antibody responses elicited by our initial formulations, we examined the effects of combining cyclic-di- AMP with additional adjuvants that act through different and potentially complementary pathways, such as those induced by toll-like receptors (TLRs). Combinatory adjuvant approaches are well-studied in the nanomaterials community and have recently been applied in the context of UPEC vaccines. We sublingually immunized mice with PEG- Q11(pIreA/pIutA/pIroN/VAC) nanofibers and cyclic-di-AMP, plus either CpG (a TLR9 agonist), CRX527 (a TLR4 agonist), or C48/80 (a mast cell stimulator). The addition of these adjuvants did not have a significant effect on serum antibody responses, as all groups raised multivalent responses against all three B-cell epitopes that were primarily of the IgG2b and IgG2c subclasses (FIGS.4A-4C). In contrast to the serum responses, however, the adjuvant combination strategy led to a significant increase in urinary antibodies. Specifically, the combination of cyclic-di-AMP and CpG led to significantly greater levels of epitope-specific IgA in the urine and urinary IgG levels that trended higher (FIG.4D). Example 7 Sublingual nanofiber vaccine raises no detectable gut IgA responses [000154] An advantage of UPEC-specific vaccine strategies is that they avoid potential immune responses against commensal E. coli or other commensals. A further safeguard against such effects is a vaccine that raises antibody responses in the desired systemic and urinary compartments, but not in the microbe-rich gut. Sublingual vaccines have been shown in some cases to raise immune responses in the gastrointestinal tract. Swallowing of vaccine material could contribute to gut responses; notably, we used a conservative volume of 8 μL for our sublingual immunizations, well below the amount at which inadvertent swallowing would be expected. We tested whether the sublingual nanofiber vaccines were eliciting gut antibodies along with those observed in the blood and urine. In contrast to the observable levels of IgA, we did not detect any epitope-specific IgA in fecal samples of immunized mice (FIG.4G). To confirm that our methods could detect fecal IgA, we examined the total fecal IgA and found it to be similar to published levels for C57BL/6 mice (Fransen, F., et al. Immunity 2015, 43, 527-540, incorporated herein by reference) (FIG.5). Example 8 Sublingual vaccine protects against UPEC-mediated sepsis with expression of a single antigen target [000155] To test the clinical relevance of the antibodies raised by our sublingual vaccine, we challenged mice with CFT073, a uropathogenic E. coli strain isolated from a pyelonephritis patient (Mobley, H., et al. Infection and immunity 1990, 58, 1281-1289, incorporated herein by reference). To directly assay the effectiveness of raised antibodies against the human pathogen, we performed intraperitoneal challenge of the previously immunized mice discussed above (FIG.4H). This challenge also provides a model of UPEC-mediated sepsis; notably, urosepsis accounts for a quarter of all sepsis cases. The motivation for a multivalent vaccine strategy was to generate an immune response that is protective against UPEC with varying virulence factor expression profiles. To test whether expression of a single antigenic target on the infecting pathogen was sufficient for the nanofiber vaccine to afford protection, we cultured CFT073 under conditions in which the IutA protein, but neither the IreA nor IroN proteins, is expressed (Hagen, Iron Acquisition by Uropathogenic Escherichia coli: ChuA and Hma Heme Receptors as Virulence Determinants and Vaccine Targets, 2009, incorporated herein by reference). [000156] After challenging mice with CFT073, we monitored body temperature and weight loss for 72 h to see if vaccinated groups would ameliorate these expected clinical symptoms of infection (Olfert et al. Ilar Journal 2000, 41, 99-104, incorporated herein by reference). Unimmunized control mice exhibited significant loss of body temperature after challenge, compared with vaccinated mice (FIG.4I, FIGS.6A-6E). Body weight showed more variance between different immunization groups (which differed by adjuvant), but all immunized groups lost less weight compared with unimmunized mice throughout the study (FIG.4J, FIGS.6A-6E). To compare the overall effect of immunization in protecting against CFT073 challenge, we combined the results from the four groups of immunized mice. Collectively, the immunized mice showed significantly less change in body weight than unimmunized mice (FIG.4K). Further, half of the unimmunized mice died as a result of the challenge, while all vaccinated mice survived (FIG.4L). These results together indicated that the sublingual nanofiber vaccine provided protection against challenge with a human-infecting UPEC strain expressing a single targeted antigen. Example 9 An accessible tablet vaccine formulation raises protective immune responses against UPEC epitopes in mice [000157] Attitudes and perceptions regarding UTIs and resource limitations put constraints on the potential distribution of an anti-UPEC vaccine, particularly outside of wealthy nations. To achieve its most significant impact, a UTI vaccine would likely need to be cost-effective, suggesting the need for heat-stability (to obviate expensive cold chain storage) and simple administration procedures requiring minimal training. We recently developed a procedure for producing tablet vaccines based on self-assembling peptide-polymer nanofibers, which we termed SIMPL (Supramolecular Immunization with Peptides SubLingually) (Kelly, et al. Advanced Healthcare Materials 2021, 10, 2001614, incorporated herein by reference). SIMPL tablets are produced by lyophilization of solutions containing supramolecular nanofibers, sugar excipients, and adjuvant (FIG.7A). [000158] To test the effectiveness of a tablet formulation of an anti-UPEC nanofiber vaccine, we formed tablets containing PEG-Q11(pIreA/pIutA/pIroN/VAC) (FIG.7B). We included either cyclic-di-AMP adjuvant alone or both cyclic-di-AMP and CpG, based on our finding that this adjuvant combination could enhance urinary antibody responses (FIGS.4A- 4L). As a control, we also produced tablets containing PEG-Q11(pIreA/pIutA/pIroN) fibers, which lack the helper T-cell epitope VAC (VACQ11 was replaced with Q11 in the formulation to keep total peptide concentration constant). Sublingual immunization with vaccine tablets performed similarly to the previously used droplet vaccines, raising multivalent responses against all three UPEC B-cell epitopes (FIG.7C). Among tablets with only the cyclic-di-AMP adjuvant, tablets without the VAC epitope raised significantly lower serum antibody responses than those containing the T-cell epitope (FIG.7D). [000159] Interestingly, tablets without VAC did still raise detectable antibody responses against each of the epitopes, indicating that one of pIreA, pIutA, or pIroN may contain a T- cell epitope within its sequence. Putative epitopes within the pIreA sequence have been reported for BALB/c mice (H-2-IAd haplotype), though to our knowledge, T-cell epitopes within these peptides have not been reported for C57BL/6 mice. An in silico prediction we performed using the Consensus method (Wang, et al. BMC Bioinformatics 2010, 11, 1-12; Wang, et al. PLoS Computational Biology 2008, 4, e1000048; each incorporated herein by reference) in the Immune Epitope Database and Analysis Resource (IEDB) did show potentially strong binding sequences to H-2-IAb within the pIreA sequence, which may in part account for the responses seen here. [000160] The highest level of urinary IgG was observed in mice receiving tablets with the VAC epitope and both cyclic-di-AMP and CpG adjuvants, again indicating that adjuvant combinations may be particularly important for stimulation of mucosal responses after sublingual nanofiber immunization (FIG.7E). There was no detectable urinary IgG in mice that received tablets without the VAC epitope. Urinary IgA levels were not significantly different between groups but trended highest for the adjuvant combination group (FIG.7F). [000161] We next tested the protective ability of immune responses elicited by anti-UPEC SIMPL tablets. We challenged mice with a higher-lethality dose of 2x10 8 CFU of CFT073, culturing these bacteria in iron-limited conditions that promote expression of IreA, IutA, and IroN proteins (Hagan, Iron Acquisition by Uropathogenic Escherichia coli: ChuA and Hma Heme Receptors as Virulence Determinants and Vaccine Targets, 2009, incorporated herein by reference) (FIG.7G). Nanofiber tablet vaccines were highly protective even against this increased dose, significantly ameliorating temperature drops and increasing survival (FIGS. 7H-7M, FIGS.8A-8D). Immunization with any of the three tablet formulations led to 80% survival, compared with just 20% in unimmunized control groups. Example 10 Anti-UPEC sublingual tablet vaccine raises epitope-specific serum and urinary antibodies in rabbits [000162] To further demonstrate the translational potential of anti-UPEC nanofiber vaccines, we sought to use a more representative higher animal model. Compared with mice, rabbits have an oral cavity that is more similar to that of humans. Importantly, the sublingual epithelium is non-keratinized in rabbits and humans (but keratinized in mice), and it contains greater numbers of cell layers in both rabbits and humans than in mice. These differences make rabbits a more desirable model for assessing the potential clinical effectiveness of a sublingually delivered vaccine. Immunization of rabbits with SIMPL tablets containing PEG-Q11(pIreA/pIutA/pIroN/VAC) or PEG-Q11(pIreA/pIutA/pIroN; no VAC) nanofibers and both cyclic-di-AMP and CpG adjuvants elicited epitope-specific antibody responses (FIG.9K, FIG.9L). The full heatmap is shown in FIG.14. Notably, the tablet immunizations were also capable of eliciting epitope-specific IgA responses in urine (FIG. 9I), and the antibodies bound most strongly to CFT073 cultured under iron-limiting uropathogenic conditions (FIG.7N). Finally, to observe the dissolution behavior of the tablets in a simulated clinical setting, we simulated the human oral cavity using 1.0 mL of pooled human saliva heated to body temperature (37°C) (FIG.10). Tablets rapidly dissolved under these conditions, with a median time of 20 seconds. These results indicated the potential feasibility of progressing sublingual tablet vaccines towards clinical translation. Example 11 Sublingual nanofiber vaccine is as effective at preventing UTI as high-dose oral antibiotics [000163] To place the efficacy of the anti-UPEC nanofiber vaccine in context, we compared it with antibiotics, the current gold-standard of treatment for UTIs. We immunized mice with cyclic-di-AMP and CpG adjuvants and either PEG-Q11(PIreA/PIutA/PIroN/VAC) nanofibers or, as a control, PEG-Q11OVA nanofibers. OVA 323-339 is a model epitope that we have previously employed in Q11-based nanofibers for raising sublingual B- and T-cell responses (Kelly, S. H., et al. Biomaterials, 2020, 119903; Kelly, S. H., et al. Advanced healthcare materials 2021, 10, 2001614; each incorporated herein by reference) (FIG.9A). As expected, mice given the anti-UPEC vaccine raised antibody responses against the pIreA, pIutA, and pIroN epitopes, and OVA-immunized mice raised antibody responses against the OVA 323-339 epitope (FIGS.9B-9C, FIGS.11A-11C). We challenged immunized mice transurethrally with 5x10 7 CFU CFT073 to model the route of urinary tract infection, and compared the results with unimmunized mice given repeated, high, daily doses of the oral antibiotic Fosfomycin (FIG.9A). While no mice given the control OVA vaccine survived to 48 hours post-challenge, the vaccine performed similarly to the antibiotic treatment group (FIGS.9D-9E). Notably, both the Fosfomycin-treated and anti-UPEC-immunized groups maintained significantly higher temperatures than mice given the control vaccine (FIG.9F, FIGS.13A-13B). Strikingly, mice given the nanofiber vaccine had significantly less body weight loss than mice treated with Fosfomycin (FIG.9G, FIGS.13A-13B). Weight and temperature curves for individual mice are shown in FIG.12. The lack of efficacy of the control vaccine against OVA demonstrated that the effect of the anti-UPEC nanofiber vaccine was attributable to its antigen-specificity for CFT073, and not non-specific effects due to adjuvants or the nanofibers themselves. Example 12 Anti-UPEC vaccine is minimally disruptive of the microbiome [000164] While antibiotics are highly effective at treating UTIs, there are concerns about their long-term prophylactic usage due to effects on the patient’s microbiome. We tested whether our vaccine strategy would allow for long-term protective responses that were minimally disruptive of the microbiome due to their specificity for uropathogenic E. coli. We collected feces from unimmunized, anti-UPEC immunized, or anti-OVA immunized mice prior to (week 0) and after (week 13) treatment. We also collected feces from the unimmunized group after 3 daily doses of Fosfomycin, prior to transurethral challenge (week 13.5). [000165] The difference between the microbiome composition of antibiotic-treated mice and all other groups was stark. The OTU richness of the microbiome was drastically reduced after antibiotic treatment, while immunization with the anti-UPEC nanofiber vaccine had no effect (FIG.9H). Further, while the Shannon diversity index (a measure of α- diversity) was statistically identical between all non-antibiotic treated groups, the antibiotic group was highly significantly different from these groups (FIG.9I). To highlight this, we used multidimensional scaling to plot the similarity of each mouse (FIG.9J). The antibiotic mice formed a distinct cluster apart from all other mice. To further probe the differences, we generated a heatmap displaying the relative abundance of microbiome members at the family taxonomic level (FIG.9K). Antibiotic-treated mice had a shift in microbiome composition that included increased levels of the species Bacteroides acidifaciens, Parabacteroides distasonis, Parabacteroides gordonii, and Lactobacillus ruminis, in addition to reduced levels of the species Mucispirillum schaedleri, Ruminococcus gnavus, and Desulfovibrio C21-c20 (FIG.9L, FIG.9M). These results supported the possibility of sublingual vaccines as a safe, long-term prophylactic approach to preventing urinary tract infections. Example 13 Discussion [000166] Detailed herein is the design of an anti-uropathogenic E. coli vaccine that leverages the unique advantages of a sublingual supramolecular nanofiber platform. A single highly co-assembled nanofiber containing a helper T-cell epitope raised simultaneous antibody responses against three UPEC peptide epitopes. Mice immunized with optimized formulations were protected from both systemic and transurethral UPEC challenge and induced minimal changes in the mouse microbiome. [000167] This study presents a strategy with several advantages for progression towards clinical translation. Our vaccine strategy prioritizes safety, a critical consideration for a viable UTI vaccine. The threshold for safety is high for the design of a vaccine against a generally non-life threatening disease. Here, we showed the ability to raise systemic and mucosal responses against peptide UPEC epitopes that have previously been identified as ideal antigenic targets, but which suffered from poor immunogenicity. Two of these epitopes have previously been shown to raise no detectable responses even when adjuvanted with the strong but non-translatable full cholera toxin. In stark contrast, our vaccine raised not only systemic titers, but also epitope-specific antibody responses in urine while using the more favorable nucleotide adjuvants cyclic-di-AMP and CpG. Both classes of adjuvants, cyclic-di- nucleotides (such as AMP) and oligodeoxynucleotides (like CpG) have shown translational promise in clinical trials. [000168] Due to the lack of an established UTI vaccine raising long-term responses in humans, some consequences of such a vaccine are not fully known. A non-specific vaccine is possible that, for example, raises responses that target both UPEC and non-pathogenic E. coli. Approaches that are based on the use of inactivated pathogens or lyophilized microbial proteins may contain epitopes that do not discriminate between pathogenic and non- pathogenic microbes. Given the importance of the microbiota and the damage that can result from continuous use of antibiotics, long-lasting off-target immune responses could have detrimental effects. We showed that nanofiber-generated antibodies bind to a UPEC strain and induce protection without showing any cross-reactivity towards a non-pathogenic E. coli strain. As an additional safeguard, our vaccine raised responses in the urinary tract and blood without eliciting detectable IgA antibodies in the feces, suggesting that there is minimal response in the commensal microbe-rich gastrointestinal tract. Most notably, our vaccine did not induce notable broad changes in the microbiome of mice. In stark contrast, mice treated with the oral antibiotic Fosfomycin had significantly altered microbiome composition. The importance of our vaccine’s ability to raise protective responses without disrupting the microbiome is heightened by evidence suggesting microbiome changes can be passed down generationally. [000169] The sublingual route not only affords the ability to raise systemic and urinary titers, but also provides key logistical benefits. Our tablet formulation has been shown to be heat-stable (Kelly, S. H., et al. Advanced healthcare materials 2021, 10, 2001614, incorporated herein by reference), which may reduce or eliminate the high costs and infrastructure required for cold-chain distribution of a vaccine and enable a far greater global distribution compared to vaccines that are dependent on refrigeration. The limitations of cold chain-dependent vaccine distribution have been acute and prominent during the SARS-CoV- 2 pandemic, heightening awareness of this critical aspect of vaccine development. Additional advantages of sublingual tablet-based vaccination include the potential for self- administration, which could also help to facilitate its adoption. Our tablet vaccine raised responses not only in mice, but also in rabbits, which possess an oral cavity with key similarities to humans. Safety and efficacy studies in higher animal models may be done, but collectively, the results presented in this study provide a strong indicator of a favorable efficacy and safety profile. [000170] One rationale for the use of the model UPEC strain CFT073 is that it was isolated from a human patient. This indicates that the epitope specificities of the antibodies we raised are clinically significant. How effective our vaccine is against other UPEC strains may be determined. Our multivalent strategy is designed so that most UPEC should express at least one of the three antigenic target proteins (IreA, IutA, IroN). For CFT073, our results suggest that expression of a single target may be sufficient. Expression varies significantly across UPEC, however, so testing our antibodies for binding against a panel of clinical isolates would give a greater indication of the predicted effects on a population level. [000171] We focused on designing a vaccine against UPEC, which cause at least 80% of uncomplicated UTIs. The remaining 20% are caused by several genera of pathogens, including Staphylococcus, Klebsiella, Proteus, and Pseudomonas. Designing a “universal” UTI vaccine would present a challenge, particularly for a safety-focused approach such as this one that relies on peptide epitopes not shared with non-pathogenic microbes. However, the utilization of a supramolecular nanofiber-based vaccine does allow for the possibility of co-assembling a nanofiber containing a large number of epitopes. Example 14 Coil29 and Q11 systems accommodate multiple peptides of interest and Pro-Ala-Ser (PAS) mucoinert modifications [000172] Different epitope peptides of interest bearing the Coil29 or Q11 assembly domains at their C-terminus were synthesized. Coil29 and Q11 variants with PAS modifications were also synthesized. All peptides were synthesized cleanly and were purified with reverse-phase HPLC. These peptides possessed the ability to be intermixed within their respective assembly systems (Q11 peptides together, or Coil29 peptides together, regardless of epitope) to form intermixed nanofibers bearing the epitopes of interest and PAS. The nanofibers were generally well-behaved, showing uniform thickness and lengths of hundreds of nanometers. [000173] Prior work with sublingual immunizations was conducted with Q11 nanofibers, using PEGylation or PASylation to be sublingually immunogenic. However, the Coil29 system in principle possessed several potential advantages, including a non-amyloid structure, control over fiber length, and built-in T-cell epitopes. Mouse models of sublingual immunogenicity showed Coil29 nanofibers did not depend on PASylation for immunogenicity. In studies of mucoadhesion, Coil29 - without PASylation - was highly non- adhesive to mucus. This may reflect the greater hydrophilicity of Coil29 nanofibers with respect to Q11 nanofibers. Both un-modified and OVA-bearing Coil29 nanofibers exhibited this muco-inertness, suggesting that elimination of PAS from this type of nanofiber may still retain good sublingual immunogenicity. [000174] Further studies showed that OVA-Coil29 nanofibers were strongly immunogenic after three doses, raising both significant serum IgG titers (FIG.15, top) and vaginal IgA titers (FIG.15, bottom). Un-PASylated nanofibers displayed a higher IgG titer than those in which half of the peptides were PASylated (FIG.15, top). Both formulations raised vaginal IgA, with a greater but not statistically different magnitude for un-PASylated nanofibers (FIG. 15, bottom). [000175] The efficacy of sublingual immunization platforms for the Coil29 nanofiber system was epitope-dependent. Although Coil29 was immunogenic without any PASylation, a more hydrophobic epitope needed about 50% of the peptides in the nanofiber to be PASylated. Nanofibers with other epitopes were strongly immunogenic even in the absence of PASylation. In aggregate, the findings indicate that while Coil29 nanofibers present an attractive platform for sublingual vaccines against peptide epitopes, there is considerable variation in immunogenicity between various epitopes. PASylation can be utilized to overcome diminished immunogenicity. The physical properties of each epitope, namely hydrophobicity, may influence the mucoadhesivity of the nanofibers, with the most hydrophobic epitopes benefitting from PASylation, as PASylation diminished mucoadhesivity for each epitope studied, and it seems that mucoadhesion correlated with the hydrophobicity index of each peptide. The modularity of both the Q11 and Coil29 systems allows for straightforward adjustment of the degree of PASylation to achieve strong immunogenicity. Example 15 Development of SIMPL tablets for Coil29 nanofibers [000176] The tabletization process employed in the nanofiber-based sublingual immunotherapy tablets for the β-sheet nanofiber Q11 system was applied to make α-helical Coil29 nanofiber system tablets. The Coil29 system has advantages of being able to tune the length of the nanofibers, as well as having internal T-cell epitopes that may enhance antibody responses, however, it was examined whether the more dynamic helical nanofibers would be stable to the processing steps involved in freeze drying/tabletization and sublingual immunization. The tablets of the α-helical Coil29 nanofiber system showed that the Coil29 peptide assemblies retained their nanofibrillar structure in the presences of various levels of cryoprotectant sugars (FIG.16). After tabletization, they also were sublingually immunogenic with a range of peptide concentration and cryoprotectant sugar concentrations (FIG.17). Coil29 nanofibers also needed lower levels of STING adjuvants, c-di-AMP and cGAMP, as compared to Q11 nanofibers (FIG.18). From these studies, it was observed that the adjuvant dose could be diminished to as low as 1 μg c-di-AMP with equivalent titers to 10 times that dose. *** [000177] The foregoing description of the specific aspects will so fully reveal the general nature of the invention that others can, by applying knowledge within the skill of the art, readily modify and/or adapt for various applications such specific aspects, without undue experimentation, without departing from the general concept of the present disclosure. Therefore, such adaptations and modifications are intended to be within the meaning and range of equivalents of the disclosed aspects, based on the teaching and guidance presented herein. It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance. [000178] The breadth and scope of the present disclosure should not be limited by any of the above-described exemplary aspects, but should be defined only in accordance with the following claims and their equivalents. [000179] All publications, patents, patent applications, and/or other documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication, patent, patent application, and/or other document were individually indicated to be incorporated by reference for all purposes. [000180] For reasons of completeness, various aspects of the invention are set out in the following numbered clauses: [000181] Clause 1. A UPEC conjugate peptide comprising: (i) a self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn); and (ii) at least one UPEC epitope conjugated to a terminus of the self-assembling peptide, wherein the UPEC epitope is selected from pIroN (YLLYSKGNGCPKDITSGGCYLIGNKDLDPE, SEQ ID NO: 80), pIutA (VDDIDYTQQQKIAAGKAISADAIPGGSVD, SEQ ID NO: 81), or pIreA (GIAKAFRAPSIREVSPGFGTLTQGGASIMYGN, SEQ ID NO: 82), or a combination thereof. [000182] Clause 2. The UPEC conjugate peptide of clause 1, wherein each self- assembling peptide forms a beta sheet and comprises a polypeptide having an amino acid sequence selected from QQKFQFQFEQQ (SEQ ID NO: 12), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn). [000183] Clause 3. The UPEC conjugate peptide of clause 1, wherein each self- assembling peptide forms an alpha-helix and comprises a polypeptide having an amino acid sequence of bXXXb (SEQ ID NO: 1), wherein X is independently any amino acid and b is independently any positively charged amino acid. [000184] Clause 4. The UPEC conjugate peptide according to clause 1 or 2, wherein the self-assembling peptide comprises the sequence QQKFQFQFEQQ (SEQ ID NO: 12) or Ac- QQKFQFQFEQQ-NH 2 (SEQ ID NO: 13) or bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid). [000185] Clause 5. The UPEC conjugate peptide of clause 1, 3, or 4, wherein b is independently selected from Arg and Lys. [000186] Clause 6. The UPEC conjugate peptide of clause 1, 3, 4, or 5, wherein bXXXb (SEQ ID NO: 1) is RAYAR (SEQ ID NO: 2) or KAYAK (SEQ ID NO: 3). [000187] Clause 7. The UPEC conjugate peptide of any one of clauses 1 and 3-6, wherein the self-assembling peptide comprises an amino acid sequence of Z n bXXXbZ m (SEQ ID NO: 5), wherein b is independently any positively charged amino acid, Z is independently any amino acid, X is independently any amino acid, n is an integer from 0 to 20, and m is an integer from 0 to 20. [000188] Clause 8. The UPEC conjugate peptide of clause 7, wherein the self-assembling peptide comprises an amino acid sequence selected from QARILEADAEILRAYARILEAHAEILRAQ (Coil29, SEQ ID NO: 6), or QAKILEADAEILKAYAKILEAHAEILKAQ (SEQ ID NO: 7), or ADAEILRAYARILEAHAEILRAQ (SEQ ID NO: 8), or Ac-QARILEADAEILRAYARILEAHAEILRAQ-NH 2 (SEQ ID NO: 9), or Ac- QAKILEADAEILKAYAKILEAHAEILKAQ-NH 2 (SEQ ID NO: 10), or Ac- ADAEILRAYARILEAHAEILRAQ-NH 2 (SEQ ID NO: 11). [000189] Clause 9. The UPEC conjugate peptide of any one of clauses 1-8, wherein the at least one UPEC epitope is attached to the C-terminus or the N-terminus of the self- assembling peptide. [000190] Clause 10. The UPEC conjugate peptide of any one of clauses 1-9, wherein 1 to 10 UPEC epitopes are attached to the C-terminus or the N-terminus of the self-assembling peptide. [000191] Clause 11. The UPEC conjugate peptide of any one of clauses 1-10, further comprising: (iii) a PEG molecule or a PAS peptide conjugated to the self-assembling peptide. [000192] Clause 12. The UPEC conjugate peptide of clause 11, wherein the PAS peptide comprises a sequence of Pro-Ala-Ser or comprises the sequence of ASPAAPAPASPAAPAPSAPA (SEQ ID NO: 97), or a peptide having at least 80%, 85%, 90%, or 95% identity thereto. [000193] Clause 13. The UPEC conjugate peptide of clause 11, wherein the PEG molecule comprises PEG-2000. [000194] Clause 14. The UPEC conjugate of any one of clauses 11-13, wherein the PEG molecule or the PAS peptide is conjugated to the self-assembling peptide at the same or the opposite terminus from wherein the UPEC epitope is attached. [000195] Clause 15. The UPEC conjugate peptide of any one of clauses 1-14, further comprising: (iv) at least one linker. [000196] Clause 16. The UPEC conjugate peptide of clause 15, wherein the at least one linker comprises a first linker between the at least one UPEC epitope and the self- assembling peptide, and a second linker between the PEG molecule or the PAS peptide and the self-assembling peptide. [000197] Clause 17. The UPEC conjugate peptide of clause 15 or 16, wherein the at least one linker comprises an amino acid sequence independently selected from SEQ ID NO: 83 (SGSG), SEQ ID NO: 84 ((Ser-Gly) 2 ), SEQ ID NO: 85 (CCCCSGSG), SEQ ID NO: 86 (G n wherein n is an integer from 1 to 10), SEQ ID NO: 87 (GSGS), SEQ ID NO: 88 (SSSS), SEQ ID NO: 89 (GGGS), SEQ ID NO: 90 (GGC), SEQ ID NO: 91 ((GGC) 8 ), SEQ ID NO: 92 ((G 4 S) 3 ), SEQ ID NO: 93 (KSGSG), SEQ ID NO: 94 (KKSGSG), SEQ ID NO: 95 (EAAAK) 2 , and SEQ ID NO: 96 (GGAAY). [000198] Clause 18. The UPEC conjugate peptide of any one of clauses 1-17, wherein the UPEC conjugate peptide comprises a sequence selected from PEG-Q11-pIroN, PEG-Q11- pIutA, or PEG-Q11-pIreA, or a combination thereof. [000199] Clause 19. A nanofiber comprising a plurality of the UPEC conjugate peptide of any one of clauses 1-18, wherein the conjugate peptide self-assembles into the nanofiber. [000200] Clause 20. A nanofiber comprising: (i) at least one UPEC conjugate peptide of any one of clauses 1-19; and (ii) at least one T-cell epitope-conjugate peptide comprising: a self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn); and at least one T- cell epitope conjugated to a terminus of the self-assembling peptide, wherein the at least one T-cell epitope is selected from PADRE and VAC, and wherein PADRE comprises a polypeptide having the amino acid sequence of aKXVAAWTLKAa (SEQ ID NO: 99, wherein “X” comprises cyclohexylalanine and “a” comprises D-alanine), and wherein VAC comprises a polypeptide having the amino acid sequence of QLVFNSISARALKAY (SEQ ID NO: 100). [000201] Clause 21. The nanofiber of clause 20, wherein the T-cell epitope-conjugate peptide further comprises a linker between the T-cell epitope and the self-assembling peptide. [000202] Clause 22. The nanofiber of clause 21, wherein the linker comprises an amino acid sequence selected from SEQ ID NO: 83 (SGSG), SEQ ID NO: 84 ((Ser-Gly) 2 ), SEQ ID NO: 85 (CCCCSGSG), SEQ ID NO: 86 (G n wherein n is an integer from 1 to 10), SEQ ID NO: 87 (GSGS), SEQ ID NO: 88 (SSSS), SEQ ID NO: 89 (GGGS), SEQ ID NO: 90 (GGC), SEQ ID NO: 91 ((GGC) 8 ), SEQ ID NO: 92 ((G 4 S) 3 ), SEQ ID NO: 93 (KSGSG), SEQ ID NO: 94 (KKSGSG), SEQ ID NO: 95 (EAAAK) 2 , and SEQ ID NO: 96 (GGAAY). [000203] Clause 23. The nanofiber of any one of clauses 20-22, wherein the cyclohexylalanine comprises D-alanine. [000204] Clause 24. The nanofiber of any one of clauses 20-23, further comprising: (iii) a plain self-assembling peptide comprising a polypeptide having the amino acid sequence of QQKFQFQFEQQ (SEQ ID NO: 12), bXXXb (SEQ ID NO: 1, wherein X is independently any amino acid and b is independently any positively charged amino acid), FKFEFKFE (SEQ ID NO: 14), KFQFQFE (SEQ ID NO: 15), QQRFQFQFEQQ (SEQ ID NO: 16), QQRFQWQFEQQ (SEQ ID NO: 17), FEFEFKFKFEFEFKFK (SEQ ID NO: 18), QQRFEWEFEQQ (SEQ ID NO: 19), QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine), FKFEFKFEFKFE (SEQ ID NO: 21), FKFQFKFQFKFQ (SEQ ID NO: 22), AEAKAEAKAEAKAEAK (SEQ ID NO: 23), AEAEAKAKAEAEAKAK (SEQ ID NO: 24), AEAEAEAEAKAKAKAK (SEQ ID NO: 25), RADARADARADARADA (SEQ ID NO: 26), RARADADARARADADA (SEQ ID NO: 27), SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28), EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro), WKXKXKXKXK (SEQ ID NO: 30, where X is Val, Ala, Ser, or Pro), KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro), LLLLKKKKKKKKLLLL (SEQ ID NO: 32), VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33), VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34), KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35), VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36), VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37), QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn), QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr), and QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn). [000205] Clause 25. The nanofiber of any one of clauses 20-24, wherein the nanofiber comprises a combination of 10 to 10,000, or 100 to 10,000 peptides comprising UPEC conjugate peptides and T-cell epitope-conjugate peptides. [000206] Clause 26. The nanofiber of any one of clauses 20-24, wherein the nanofiber comprises a combination of 10 to 10,000, or 100 to 10,000 peptides comprising UPEC conjugate peptides, T-cell epitope-conjugate peptides, and plain self-assembling peptides. [000207] Clause 27. The nanofiber of any one of clauses 20-26, wherein at least about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 97.5% of the peptides in the nanofiber are UPEC conjugate peptides. [000208] Clause 28. The nanofiber of any one of clauses 20-27, wherein at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, or 15% of the peptides in the nanofiber are T-cell epitope-conjugate peptides. [000209] Clause 29. The nanofiber of any one of clauses 20-28, wherein the UPEC peptide conjugate and the T-cell epitope-peptide conjugate are present in the nanofiber at a ratio of about 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 12:1, 14:1, 16:1, 18:1, 20:1, 22:1, 24:1, 26:1, 28:1, 30:1, 32:1, 34:1, 36:1, 38:1, or 40:1. [000210] Clause 30. The nanofiber of any one of clauses 20-29, wherein the self- assembling peptide forms a fibril including beta-sheet structures or a fibril having a coiled coil structure. [000211] Clause 31. The nanofiber of any one of clauses 20-29, wherein the self- assembling peptide forms a fibril having a structure of a helical filament formed around a central axis. [000212] Clause 32. The nanofiber of clause 31, wherein the N-terminus of each self- assembling peptide is positioned at the exterior of the helical filament. [000213] Clause 33. The nanofiber of any one of clauses 20-32, wherein the UPEC molecules are exposed on the exterior surface of the nanofiber. [000214] Clause 34. The nanofiber of any one of clauses 20-33, wherein the nanofiber is about 5-30 nm in width. [000215] Clause 35. The nanofiber of any one of clauses 20-34, wherein the nanofiber is about 100 nm to 1 µm, 100 nm to 2 µm, 100 nm to 3 µm, 100 nm to 4 µm, or 100 nm to 5 µm in length. [000216] Clause 36. A pharmaceutical composition comprising: (a) the UPEC conjugate peptide of any one of clauses 1-19 or the nanofiber of any one of clauses 20-35; and (b) a pharmaceutically acceptable carrier, diluent, and/or excipient. [000217] Clause 37. The pharmaceutical composition of clause 36, further comprising: (c) an adjuvant selected from cyclic-di-AMP, CpG, cyclic GMP-AMP (cGAMP), cholera toxin B subunit (CTB), retinoic acid, or heat labile toxin B subunit, or a combination thereof. [000218] Clause 38. The pharmaceutical composition of clause 36 or 37, formulated into a tablet. [000219] Clause 39. The pharmaceutical composition of clause 38, wherein the tablet is a dissolving tablet. [000220] Clause 40. A method of treating a urinary tract infection (UTI), the method comprising administering to a subject a therapeutically effective amount of the UPEC conjugate peptide of any one of clauses 1-19, or the nanofiber of any one of clauses 20-35, or the pharmaceutical composition of any one of clauses 36-39. [000221] Clause 41. A method of treating a bacterial infection, the method comprising administering to a subject a therapeutically effective amount of the UPEC conjugate peptide of any one of clauses 1-19, or the nanofiber of any one of clauses 20-35, or the pharmaceutical composition of any one of clauses 36-39. [000222] Clause 42. The method of clause 40 or 41, wherein the UPEC conjugate peptide or the nanofiber or the pharmaceutical composition is administered sublingually. [000223] Clause 43. The method of any one of clauses 40-42, wherein pathogenic bacteria are reduced. [000224] Clause 44. The method of clause 43, wherein pathogenic bacteria comprise uropathogenic Escherichia coli. [000225] Clause 45. The method of clause 43 or 44, wherein pathogenic bacteria comprise CFT073. [000226] Clause 46. The method of any one of clauses 40-45, wherein non-pathogenic bacteria are not reduced. [000227] Clause 47. The method of any one of clauses 40-46, wherein the microbiome in the colon is maintained. [000228] Clause 48. The method of any one of clauses 40-47, wherein the microbiome in the colon statistically maintains a Shannon Diversity Index. SEQUENCES SEQ ID NO: 1 bXXXb wherein X is independently any amino acid, and b is independently any positively charged amino acid. SEQ ID NO: 2 RAYAR SEQ ID NO: 3 KAYAK SEQ ID NO: 4 RXXXR wherein X is any amino acid. SEQ ID NO: 5 Z n bXXXbZ m wherein b is independently any positively charged amino acid, Z is independently any amino acid, X is independently any amino acid, n is an integer from 0 to 20, and m is an integer from 0 to 20. SEQ ID NO: 6 Coil29 QARILEADAEILRAYARILEAHAEILRAQ SEQ ID NO: 7 QAKILEADAEILKAYAKILEAHAEILKAQ SEQ ID NO: 8 Coil23 ADAEILRAYARILEAHAEILRAQ SEQ ID NO: 9 Ac-QARILEADAEILRAYARILEAHAEILRAQ-NH 2 SEQ ID NO: 10 Ac-QAKILEADAEILKAYAKILEAHAEILKAQ-NH 2 SEQ ID NO: 11 Ac-ADAEILRAYARILEAHAEILRAQ-NH 2 SEQ ID NO: 12 Q11 QQKFQFQFEQQ SEQ ID NO: 13 Ac-QQKFQFQFEQQ-NH 2 FKFEFKFE (SEQ ID NO: 14) KFQFQFE (SEQ ID NO: 15) QQRFQFQFEQQ (SEQ ID NO: 16) QQRFQWQFEQQ (SEQ ID NO: 17) FEFEFKFKFEFEFKFK (SEQ ID NO: 18) QQRFEWEFEQQ (SEQ ID NO: 19) QQXFXWXFQQQ (SEQ ID NO: 20, where X is ornithine) FKFEFKFEFKFE (SEQ ID NO: 21) FKFQFKFQFKFQ (SEQ ID NO: 22) AEAKAEAKAEAKAEAK (SEQ ID NO: 23) AEAEAKAKAEAEAKAK (SEQ ID NO: 24) AEAEAEAEAKAKAKAK (SEQ ID NO: 25) RADARADARADARADA (SEQ ID NO: 26) RARADADARARADADA (SEQ ID NO: 27) SGRGYBLGGQGAGAAAAAGGAGQGGYGGLGSQG (SEQ ID NO: 28) EWEXEXEXEX (SEQ ID NO: 29, where X is Val, Ala, Ser, or Pro) WKXKXKXKXK (SEQ ID NO: 30 , where X is Val, Ala, Ser, or Pro) KWKVKVKVKVKVKVK (SEQ ID NO: 31, where X is Val, A, Ser, or Pro) LLLLKKKKKKKKLLLL (SEQ ID NO: 32) VKVKVKVKVDPPTKVKVKVKV (SEQ ID NO: 33) VKVKVKVKVDPPTKVKTKVKV (SEQ ID NO: 34) KVKVKVKVKDPPSVKVKVKVK (SEQ ID NO: 35) VKVKVKVKVDPPSKVKVKVKV (SEQ ID NO: 36) VKVKVKTKVDPPTKVKTKVKV (SEQ ID NO: 37) QQKFxFQFEQQ (SEQ ID NO: 38, wherein x is Glu, Asp, or Asn) QQKFQxQFEQQ (SEQ ID NO: 39, wherein x is Trp or Tyr) QQKFQFxFEQQ (SEQ ID NO: 40, wherein x is Glu, Asp, or Asn) VEVKVEVKV (SEQ ID NO: 41) VEVKVEVKVEVK (SEQ ID NO: 42) VVVAAAEEE (SEQ ID NO: 43) VEVEVEVEVEVEVEVEVEVE (SEQ ID NO: 44) CGNKRTRGC (SEQ ID NO: 45) VKVKVKVKVDPPTKVEVKVKV (SEQ ID NO: 46) LRKKLGKA (SEQ ID NO: 47) VVVVVVKK (SEQ ID NO: 48) AEAKAEAKAEAKAEAK (SEQ ID NO: 49) AEAKAEAK (SEQ ID NO: 50) AEAEAEAEAKAK (SEQ ID NO: 51) AEAEAKAK (SEQ ID NO: 52) AEAEAKAKAEAEAKAK (SEQ ID NO: 53) RADARADARADARADA (SEQ ID NO: 54) RADARGDARADARGDA (SEQ ID NO: 55) RADARADA (SEQ ID NO: 56) RARADADARARADADA (SEQ ID NO: 57) RARADADA (SEQ ID NO: 58) RARARARADADADADA (SEQ ID NO: 59) ADADADADARARARAR (SEQ ID NO: 60) DADADADARARARARA (SEQ ID NO: 61) RAEARAEARAEARAEA (SEQ ID NO: 62) RAEARAEA (SEQ ID NO: 63) KAKAKAKAEAEAEAEA (SEQ ID NO: 64) AEAEAEAEAKAKAKAK (SEQ ID NO: 65) KADAKADAKADAKADA (SEQ ID NO: 66) KADAKADA (SEQ ID NO: 67) AEAEAHAHAEAEAHAHA (SEQ ID NO: 68) AEAEAHAHA (SEQ ID NO: 69) HEHEHKHKHEHEHKHK (SEQ ID NO: 70) HEHEHKHK (SEQ ID NO: 71) FEFEFKFKFEFEFKFK (SEQ ID NO: 72) FEFKFEFK (SEQ ID NO: 73) LELELKLKLELELKLK (SEQ ID NO: 74) LELELKLK (SEQ ID NO: 75) KFDLKKDLKLDL (SEQ ID NO: 76) FKFEFKFF (SEQ ID NO: 77) FEFEFKFK (SEQ ID NO: 78) RFRFRFRFRFRFRFRFRFRF (SEQ ID NO: 79) SEQ ID NO: 80 UPEC epitope, pIroN YLLYSKGNGCPKDITSGGCYLIGNKDLDPE SEQ ID NO: 81 UPEC epitope, pIutA VDDIDYTQQQKIAAGKAISADAIPGGSVD SEQ ID NO: 82 UPEC epitope, pIreA GIAKAFRAPSIREVSPGFGTLTQGGASIMYGN SEQ ID NO: 83 Linker SGSG SEQ ID NO: 84 Linker (Ser-Gly) 2 SEQ ID NO: 85 Linker CCCCSGSG SEQ ID NO: 86 Linker G n wherein n is an integer from 1 to 10 SEQ ID NO: 87 Linker GSGS SEQ ID NO: 88 Linker SSSS SEQ ID NO: 89 Linker GGGS SEQ ID NO: 90 Linker GGC SEQ ID NO: 91 Linker (GGC) 8 SEQ ID NO: 92 Linker (G 4 S) 3 SEQ ID NO: 93 Linker KSGSG SEQ ID NO: 94 Linker KKSGSG SEQ ID NO: 95 Linker (EAAAK) 2 SEQ ID NO: 96 Linker GGAAY SEQ ID NO: 97 PAS peptide ASPAAPAPASPAAPAPSAPA SEQ ID NO: 98 PAS peptide H 2 N-ASPAAPAPASPAAPAPSAPA-NH 2 SEQ ID NO; 99 PADRE molecule aKXVAAWTLKAa, wherein “X” comprises cyclohexylalanine and “a” comprises D-alanine SEQ ID NO: 100 VAC molecule QLVFNSISARALKAY SEQ ID NO: 101 mPEG 2000 -pIroN-Q11 mPEG 2000 -SGSG-QQKFQFQFEQQ-SGSG-YLLYSKGNGCPKDITSGGCYLIGNKDLDPE- NH 2 SEQ ID NO: 102 mPEG 2000 -pIutA-Q11 mPEG 2000 -SGSG-QQKFQFQFEQQ-SGSG- VDDIDYTQQQKIAAGKAISADAIPGGSVD- NH 2 SEQ ID NO: 103 mPEG 2000 -pIreA-Q11 mPEG 2000 -SGSG-QQKFQFQFEQQ-SGSG- GIAKAFRAPSIREVSPGFGTLTQGGASIMYGN-NH 2 SEQ ID NO: 104 PADRE-Q11 H 2 N-aKXVAAWTLKAa-SGSG-QQKFQFQFEQQ-NH 2 SEQ ID NO: 105 VAC-Q11 H 2 N-QLVFNSISARALKAY-SGSG-QQKFQFQFEQQ-NH 2 SEQ ID NO: 106 PADRE-Q11 aKXVAAWTLKAa-SGSG-QQKFQFQFEQQ SEQ ID NO: 107 VAC-Q11 QLVFNSISARALKAY-SGSG-QQKFQFQFEQQ
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