Antibacterial and protective bacteriophage formulations and methods for making and using them

A genetically engineered bacteriophage (“phage”), wherein the bacteriophage genome is altered such that after reproduction in a host cell (optionally a bacterial host cell), or in an in vitro system, the exterior (outer) surface of the bacteriophage comprises:

• (a) at least one non-bacteriophage carbohydrate binding domain (CBD), and optionally the CBD is a mammalian or a human CBD;
• (b) at least one heterologous bacteriophage CBD, wherein optionally the heterologous CBD is a CBD from a different species, genus, family or order of bacteriophage;
• (c) more CBDs than found on a wild type (WT) (comparable) bacteriophage;
• or
• (d) at least one moiety or domain capable of binding to a component of a mucus,
• optionally a mucus of or derived from:
• a mammalian mucus membrane, a gut, a urinary, a reproductive, an animal or an environmental mucus,
• optionally capable of binding to a mucus or mucus-like macromolecule, a mucin, a fatty acid, a phospholipid, a cholesterol, an elastin, a glycoprotein, a mucin glycoprotein or glycan, a mucin protein, a humic acid, a cellulose, a chitin, a high molecular weight (MW) polysaccharide, an N-acetylgalactosamine, an N-acetylglucosamine, a fucose, a galactose, a sialic acid (N-acetylneuraminic acid) a mannose, or any combination thereof,
• and optionally the moiety or domain capable of binding to a component of a mucus directs or targets the phage to a specific region of a mucosal surface that overlaps with a bacterial host range, and optionally the specific region comprises a mucosal surface basal layer, a mucosal surface apical layer, a mucosal surface lumen, a mucus layer, or a mucosal surface having a concentration of between about 0% to 1% mucin, or between about 1% to 5%, or a mucin concentration of between about 1% to 10%,
• and optionally the moiety or domain capable of binding to a component of a mucus directs or that targets the phage to a specific region of a mucosal surface allows the phage to reside or concentrate or persist in a specific region of the mucosal surface that overlaps with a bacterial host range,
• and optionally the phage is adapted to a physico-chemical environment of the mucus or specific region of a mucosal surface, and the physico-chemical environment optionally comprises:
• a pH range of between about 6 to 8, a pH range of between about 4 to 10, a pH range of between about 1 to 12, an ionic concentration of between about 1 mg to 1000 mg, an ionic concentration of between about 1 μg to 1000 gram (g), an ionic concentration of between about 1 pgm (picogram) to 1000 kg, a temperature change of between about 35° C. to 42° C., a temperature change of between about 25° C. to 55° C., or a temperature change of between about 1° C. to 99° C.;
• (e) at least one moiety or domain capable of binding to a protein or peptide, a protein or peptide (optionally an antibody or antigen binding fragment thereof, an antigen, an immunogen, a tolerogen), a glycoprotein, a nucleic acid (optionally an RNA or a DNA), a lipid or cholesterol, a lipopolysaccharide, a mucopolysaccharide, a gel, a hydrogel, a complex fluid, or a combination thereof;
• or
• (f) any combination of (a) to (e),
• and optionally any of (a) to (e) comprises or has structural homology to:
• a C-type lectin, a lectin, a bacteriodetes-associated carbohydrate-binding often N-terminal (BACON) domain, a Brefeldin A-inhibited guanine nucleotide-exchange factor for ADP-ribosylation factor (Big, optionally Big1, Big2, or Big3), a polycystic kidney disease domain (PKD), a Fibronectin type 3 homology domain (Fn3), a HYalin Repeat (HYR) domain, an Ig_2 domain, an immunoglobulin I-set domain, a carbohydrate-adherence domain, a mucus-binding protein, a glycan-binding protein, a protein-binding protein, a mucus-adhering protein or a mucus-adhering glycoprotein.

A synthetic bacteriophage (“phage”) or phagemid, wherein the exterior (outer) surface of the bacteriophage or phagemid comprises:

• (a) (i) at least one non-bacteriophage carbohydrate binding domain (CBD), wherein optionally the CBD is a mammalian or a human CBD;
• (ii) at least one bacteriophage carbohydrate binding domain (CBD),
• (iii) at least as many CBDs found on a wild type (WT) (comparable) bacteriophage;
• (iv) more CBDs than found on a wild type (WT) bacteriophage;
• (v) at least one moiety or domain capable of binding to a component of a mucus,
• optionally a mucus of or derived from:
• a mammalian mucus membrane, a gut, a urinary, a reproductive, an animal or an environmental mucus,
• optionally capable of binding to a mucus or mucus-like macromolecule, a mucin, a fatty acid, a phospholipid, a cholesterol, an elastin, a glycoprotein, a mucin glycoprotein or glycan, a mucin protein, a humic acid, a cellulose, a chitin, a high molecular weight (MW) polysaccharide, an N-acetylgalactosamine, an N-acetylglucosamine, a fucose, a galactose, a sialic acid (N-acetylneuraminic acid) a mannose, or any combination thereof,
• and optionally the moiety or domain capable of binding to a component of a mucus directs or targets the phage or phagemid to a specific region of a mucosal surface that overlaps with a bacterial host range, and optionally the specific region comprises a mucosal surface basal layer, a mucosal surface apical layer, a mucosal surface lumen, a mucus layer, or a mucosal surface having a concentration of between about 0% to 1% mucin, or between about 1% to 5%, or a mucin concentration of between about 1% to 10%,
• and optionally the moiety or domain capable of binding to a component of a mucus directs or that targets the phage or phagemid to a specific region of a mucosal surface allows the phage or phagemid to reside or concentrate or persist in a specific region of the mucosal surface that overlaps with a bacterial host range,
• and optionally the phage is adapted to a physico-chemical environment of the mucus or specific region of a mucosal surface, and the physico-chemical environment optionally comprises:
• a pH range of between about 6 to 8, a pH range of between about 4 to 10, a pH range of between about 1 to 12, an ionic concentration of between about 1 mg to 1000 mg, an ionic concentration of between about 1 μg to 1000 g, an ionic concentration of between about 1 pgm to 1000 kg, a temperature change of between about 35° C. to 42° C., a temperature change of between about 25° C. to 55° C., or a temperature change of between about 1° C. to 99° C.;
• (vi) at least one moiety or domain capable of binding to a protein or peptide, a protein or peptide (optionally an antibody or antigen binding fragment thereof, an antigen, an immunogen, a tolerogen), a glycoprotein, a nucleic acid (optionally an RNA or a DNA), a lipid or cholesterol, a lipopolysaccharide, a mucopolysaccharide, a gel, a hydrogel, a complex fluid, or a combination thereof;
• or
• (vii) any combination of (i) to (vi),
• and optionally any of (i) to (vi) comprises or has structural homology to:
• a C-type lectin, a lectin, a bacteriodetes-associated carbohydrate-binding often N-terminal (BACON) domain, a Brefeldin A-Inhibited Guanine nucleotide-exchange factor for ADP-ribosylation factor (Big, optionally Big1, Big2, or Big3), a polycystic kidney disease domain (PKD), a Fibronectin type 3 homology domain (Fn3), a HYalin Repeat (HYR) domain, an Ig_2 domain, an immunoglobulin I-set domain, a carbohydrate-adherence domain, a mucus-binding protein, a glycan-binding protein, a protein-binding protein, a mucus-adhering protein or a mucus-adhering glycoprotein;
• or
• (b) the synthetic bacteriophage or phagemid of (a), wherein the synthetic bacteriophage or phagemid is or comprises:
• a synthetic phage-like particle, a phage-like microsphere, a bacteriophage particle, a prophage, a bacteriophage capsid, a protein shell, a nanoparticle, lytic phage, a temperate phage, a myoviridae, a siphoviridae, a podoviridae, a claudoviralaes, a DNA containing particle, an RNA containing particle, a replicative particle, a non-replicative particle or an equivalent thereof.