US20130052227A1 - Hyperblebbing shigella strains - Google Patents

Hyperblebbing shigella strains Download PDF

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US20130052227A1
US20130052227A1 US13/498,723 US201013498723A US2013052227A1 US 20130052227 A1 US20130052227 A1 US 20130052227A1 US 201013498723 A US201013498723 A US 201013498723A US 2013052227 A1 US2013052227 A1 US 2013052227A1
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bacterium
shigella
blebs
protein
seq
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Christiane Gerke
Francesco Berlanda Scorza
Allan Saul
Luana Maggiore
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GSK Vaccines Institue for Global Health SRL
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Novartis Vaccines Institute for Global Health SRL
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K39/025—Enterobacteriales, e.g. Enterobacter
    • A61K39/0283—Shigella
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/12—Antidiarrhoeals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/14—Prodigestives, e.g. acids, enzymes, appetite stimulants, antidyspeptics, tonics, antiflatulents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
    • C07K14/25—Shigella (G)
    • C—CHEMISTRY; METALLURGY
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    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1025—Acyltransferases (2.3)
    • C12N9/1029—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y203/00—Acyltransferases (2.3)
    • C12Y203/01—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K2035/122—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells for inducing tolerance or supression of immune responses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
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    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • This invention is in the field of immunisation against Shigella species.
  • Shigella are Gram-negative non-motile facultative anaerobic bacilli that fall into four serogroups: S. dysenteriae, S. flexneri, S. boydii and S. sonnies . They cause shigellosis (bacillary dysentery).
  • Shigella -caused dysentery is endemic and causes millions of illness episodes in developing countries. For example, there are estimated to be 165 million cases of Shigella diarrhea per year, 99% of which occur in developing countries and 69% of which occur in children under five years of age. The morbidity and mortality due to shigellosis are especially high among children in developing countries.
  • Shigella vaccines were reviewed in ref 1 and have been based on live attenuated strains for oral immunisation, conjugated 0 saccharides for injection, proteosomes (meningococcal outer membrane vesicles with attached Shigella LPS) for intranasal use, invaplexes (subcellular extracts of Shigella including IpaB, IpaC and LPS) for intranasal use, and nuclear protein-ribosomal complexes prepared from msbB ⁇ ve strains with detoxified LPS. Although some of these vaccines have been efficacious in field trials, none protects against multiple Shigella serotypes.
  • Shigella spontaneously release outer membrane blebs during growth due to the turgour pressure of the cell envelope. As disclosed in reference 2, release of the blebs is highly dependent on the bacterial envelope structure.
  • the inventors have used a mutant strain of Shigella in which the Tol-Pal system has been disrupted to disturb the envelope structure. During normal growth these mutant strains release into their culture medium large quantities of blebs which are rich in immunogenic outer membrane proteins, and these blebs can thus be used as immunogens.
  • the invention provides a Shigella bacterium which expresses no more than 4 of TolA, TolB, TolQ, TolR and Pal proteins.
  • At least one protein from the natural five-protein Tol-Pal system is absent, resulting in a bacterium which, during growth in culture medium, releases greater quantities of outer membrane blebs into the medium than the same bacterium expressing all 5 Tol-Pal proteins.
  • TolR is not expressed, but the other four proteins may be expressed.
  • the invention also provides a Shigella bacterium which does not express a TolR protein.
  • the invention also provides a ⁇ tolR strain of Shigella , such as a ⁇ tolR ⁇ galU strain.
  • the invention also provides a Shigella bacterium which expresses TolA, TolB, TolQ, TolR and Pal proteins, wherein the TolA, TolQ, TolR and/or Pal protein (a) is located in the bacterium's inner or outer membrane, and (b) includes one or more amino acid sequence mutation(s) such that, compared to the same bacterium without said mutation(s), the bacterium releases greater quantities of outer membrane blebs when growing in culture medium.
  • the invention also provides a Shigella bacterium in which one or more components of its Tol-Pal system has a modification such that, during growth in culture medium, the bacterium releases greater quantities of outer membrane blebs into the medium than the same bacterium lacking the modification, and which does not express: (i) a native Shigella lipopolysaccharide and/or (ii) a Shigella enteric toxin.
  • the invention also provides a method of preparing a hyperblebbing Shigella bacterium, comprising a step of modifying gene(s) encoding one or more components of a starting bacterium's Tol-Pal system such that the modification causes the bacterium, when grown in culture medium, to release greater quantities of outer membrane blebs into the medium than the starting bacterium, and wherein the modification involves mutating one or more of the starting bacterium's tolA, to1B, tolQ, tolR and/or pal genes.
  • the mutating step may delete the gene.
  • the method may also involve modification of gene(s) encoding a protein required for synthesis of the bacterium's lipopolysaccharide or an enteric toxin.
  • the invention also provides a bleb isolated or obtainable from a bacterium of the invention. These blebs are useful as components of Shigella vaccines.
  • the invention also provides a process for preparing Shigella blebs, comprising a step of separating the blebs from a culture medium comprising bacteria of the invention which have been grown under conditions which permit the release of blebs into the medium by the bacteria.
  • Blebs prepared by this process can be used as components of Shigella vaccines.
  • the invention also provides a culture medium comprising bacteria of the invention which have been grown under conditions which permit the release of blebs into the medium by the bacteria. Blebs may be purified from this culture medium.
  • the invention also provides a composition comprising blebs that, during culture of bacteria of the invention, are released into the culture medium.
  • This composition does not comprise any living and/or whole bacteria.
  • This composition and/or its components can be used for Shigella vaccine preparation.
  • the invention also provides a composition comprising blebs, wherein the blebs are present in the filtrate obtainable after filtration through a 0.22 ⁇ m filter of a culture medium in which a bacterium of the invention has been grown.
  • This composition and/or its components can be used for Shigella vaccine preparation.
  • the invention also provides a Shigella bleb which includes one or more (i.e.
  • n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more).
  • Preferred fragments comprise an epitope from one of SEQ ID NOs: 8 to 67.
  • Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g.
  • the invention also provides a bleb-free immunogenic composition
  • a bleb protein comprising: (a) one or more (e.g.
  • n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more).
  • Preferred fragments comprise an epitope from one of SEQ ID NOs: 8 to 67, and more preferred fragments are immunogenic fragments. Other preferred fragments lack one or more amino acids (e.g.
  • the invention also provides a Shigella bleb which includes one or more (i.e. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
  • n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more).
  • Preferred fragments comprise an epitope from one of SEQ ID NOs: 8 to 136.
  • Other preferred fragments lack one or more amino acids (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) from the C-terminus and/or one or more amino acids (e.g.
  • 129 proteins have been confirmed as present within blebs of the invention and to be immunoreactive with sera prepared against the blebs.
  • the individual proteins may be used as immunogenic components in purified form, separate from the blebs.
  • a bleb-free immunogenic composition comprising a bleb protein comprising: (a) one or more (e.g.
  • n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more).
  • Preferred fragments comprise an epitope from one of SEQ ID NOs: 8 to 136, and more preferred fragments are immunogenic fragments. Other preferred fragments lack one or more amino acids (e.g.
  • S. flexneri a preferred subset in relation to S. flexneri is the SEQ ID NOs: listed in “Subset 1” beneath Table 1.
  • S. sonnies a preferred subset in relation to S. sonnies is the SEQ ID NOs: listed in “Subset 2” beneath Table 1
  • the Shigella naturally possess a Tol-Pal system which is made up of TolA, TolB, TolQ, TolR and Pal proteins.
  • the natural Tol-Pal system is disrupted, thereby causing the bacterium to release greater quantities of outer membrane blebs into its culture medium during bacterial replication.
  • Various disruptions can be made.
  • At least one of the five Tol-Pal proteins is removed e.g. by deletion or inactivation of the gene encoding the protein.
  • the bacterium may express 0, 1, 2, 3 or 4 of TolA, TolB, TolQ, TolR and Pal proteins. Removal of one of the five proteins can suffice, in which case the bacterium expresses only 4 of these proteins.
  • the TolR protein is removed e.g. by inactivation of a starting strain's tolR gene.
  • the bacterium may be tolA + tolB + tolQ + TolR ⁇ Pat + .
  • the bacterium expresses all five Tol-Pal proteins, but at least one is mutated to cause hyperblebbing.
  • the TolA, TolQ, TolR and/or Pal protein may be mutated such that the protein retains its membrane localisation but its interactions with other members of the Tol-Pal system are disrupted.
  • the bacterium will thus retain TolA, TolQ and TolR as transmembrane proteins in the inner membrane, and Pal protein as a periplasm-facing lipoprotein in the outer membrane, but at least one of the TolA, TolQ, TolR and/or Pal proteins is mutated.
  • the Shigella Bacterium The Shigella Bacterium
  • the invention can be used with any of serogroups S. dysenteriae, S. flexneri, S. boydii and S. sonnies.
  • a Shigella of the invention can advantageously include one or more further changes relative to a wild-type strain. These changes can be used in particular to remove components from the bacterium which would be toxic or undesirable in a human vaccine.
  • a bacterium may not express native Shigella lipopolysaccharide (LPS), thereby reducing endotoxic activity.
  • LPS Shigella lipopolysaccharide
  • Various modifications can be made to prevent synthesis of native LPS, and these may disrupt the native lipid A structure, the oligosaccharide core, or the outer O antigen.
  • reference 3 reports LPS mutants caused by inactivation of the rfe and galU genes
  • reference 4 reports LPS mutants caused by inactivation of yihE, galE, galK, galM and galT.
  • reference 5 reports defective LPS due to mutations in rfc, rfaL, or galU.
  • Reference 6 reports LPS mutants caused by inactivation of msbB1 and msbB2, reducing acylation in lipid A. As shown herein, another LPS mutant with reduced lipid A acylation can be generated by inactivation of htrB [7,8].
  • O antigen in the LPS Absence of O antigen in the LPS is preferred, thereby avoiding serotype-specific responses.
  • S. sonnies the O antigen is absent when the virulence plasmid is removed (see below).
  • the galU gene codes for uridine diphosphoglucose (UDP-glucose) pyrophosphorylase and its inactivation results in synthesis of LPS with no attached O antigen.
  • Inactivation of galU is useful for providing a Shigella without uridine diphosphoglucose pyrophosphorylase activity.
  • Inactivation of rfbF and/or rfbG genes can be used to provide a Shigella without rhamnosyl transferase activity.
  • Inactivation of rfc can be used to provide a Shigella without O antigen polymerase activity.
  • Inactivation of all three of rfbF, rfbG and rfc can provide a useful strain.
  • Absence of hexa-acylated lipid A in the LPS is preferred. Loss of the virulence plasmid (see below) automatically leads to loss of the msbB2 gene, and the chromosomal msbB1 gene can be inactivated, thereby removing myristoyl transferase activity and providing a penta-acylated lipid A in the LPS.
  • Inactivation of the HtrB lauroyl transferase can provide Shigella with mainly tetra-acylated lipid A.
  • Preferred strains have penta- or tetra-acylated LPS.
  • Preferred strains are inactivated for both galU and msbB1 and also lack the virulence plasmid, thereby providing a strain whose LPS is penta-acylated and lacks attached O antigen.
  • Some useful strains have penta- or tetra-acylated LPS which includes attached O antigen. More generally, though, preferred strains have penta- or tetra-acylated LPS which lacks attached O antigen.
  • a S. flexneri strain with tolR, rfbG and htrB knockouts (and, optionally, rfbF and/or rfc inactivation) is useful.
  • a useful S. sonnies strain has a tolR mutation and lacks a virulence plasmid.
  • a bacterium may not express an enteric toxin.
  • a S. flexneri strain (particularly a 2a strain) may not express all of the subunits of Shigella enterotoxin 1 (ShET-1) e.g. the set1A and/or set1B genes can be inactivated.
  • a S. dysenteriae strain may not express both subunits of Shiga toxin e.g. one or both of the stxA and/or stxB genes can be inactivated.
  • a Shigella particularly a S. sonnies or S. flexneri , may not express enterotoxin 2 (ShET-2) e.g. the ospD3 gene may be inactivated, or the virulence plasmid may be absent.
  • Preferred strains encode none of ShET-1, ShET-2 and Shiga toxin.
  • Shigella bacteria of the invention can be prepared conveniently from wild-type or other starting strains using conventional techniques of mutagenesis e.g. see references 9 to 11.
  • the lambda red recombination system is particularly useful with Shigella .
  • Inactivation of a gene can be achieved in various ways e.g. by deletion or mutation in its promoter, by deletion or mutation of its start codon, by introduction of a premature stop codon, by deletion of the complete coding region, by knockout, etc. Isogenic knockout mutants are preferred.
  • mRNA encoding the desired gene is absent and/or its translation is inhibited (e.g. to less than 1% of wild-type levels).
  • a Shigella bacterium of the invention may contain a marker gene in place of the inactivated gene e.g an antibiotic resistance marker. This can be achieved using homologous recombination. Preferably, though, unmarked deletions (i.e. deletion without introduction of a marker gene) are used.
  • Virulent Shigella strains possess a 220 kb plasmid that mediates virulence properties.
  • This “virulence plasmid” has been shown to encode the genes for several aspects of Shigella virulence, including adhesins for target epithelial cells, the invasion plasmid antigens, virF, virG, etc.
  • a Shigella of the invention may possess a virulence plasmid but, preferably, it does not possess a virulence plasmid.
  • Absence of the plasmid can stabilise the strain during industrial culture, attenuate the strain by removing virulence factors (thereby increasing safety of manufacture), disrupt the lipopolysaccharide (the biosynthesis genes for the O antigen are on the plasmid in S. sonnies ), avoid the presence of the ShET-2 enterotoxin (encoded by the ospD3 or sen gene on the plasmid), and avoid the presence of msbB2 which is a second copy of the msbB gene responsible for acylation of lipid A.
  • a Shigella of the invention may express one or more heterologous proteins e.g. proteins which are not naturally found in Shigella . If the heterologous protein is an outer membrane protein then blebs from the strain can be used as a delivery system for presenting non- Shigella antigens to the immune system.
  • heterologous proteins e.g. proteins which are not naturally found in Shigella .
  • the heterologous protein is an outer membrane protein then blebs from the strain can be used as a delivery system for presenting non- Shigella antigens to the immune system.
  • Culture conditions for growing Shigella are well known in the art e.g. see references 12 to 14.
  • they may be grown using an organic nitrogen source (such as amino acid mixtures e.g. containing Ala, Arg, Asn, Asp; casamino acids may be used), glycerol as a carbon source, etc.
  • an organic nitrogen source such as amino acid mixtures e.g. containing Ala, Arg, Asn, Asp; casamino acids may be used
  • glycerol as a carbon source
  • Inclusion of L-aspartic acid in the medium is particularly useful and may function as both a nitrogen and carbon source.
  • Shigella of the invention may be grown under iron-limiting conditions as this has been shown to up-regulate iron-regulated proteins which are immunogenic and highly-conserved among Shigella spp.
  • the bacteria may be grown in the presence of a compound such as desferal or 2,2′-dipyridyl or 8-hydroxyquinoline. Under these conditions the bacterium may increase expression of proteins such as the FepA outer membrane receptor, the colicin I receptor (CirA), and/or the ferric siderophore receptor (FhuA).
  • Blebs and Hyperblebbing Shigella bacteria of the invention are, relative to their corresponding wild-type strains, hyperblebbing i.e. they release into their culture medium larger quantities of blebs than the wild-type strain. These blebs are useful as components of Shigella vaccines.
  • the blebs typically have a diameter of 35-120 nm by electron microscopy e.g. 50 nm diameter.
  • the blebs are released spontaneously during bacterial growth and can be purified from the culture medium.
  • the purification ideally involves separating the blebs from living and/or intact Shigella bacteria e.g. by size-based filtration using a filter, such as a 0.22 mm filter, which allows the blebs to pass through but which does not allow intact bacteria to pass through, or by using low speed centrifugation to pellet cells while leaving blebs in suspension.
  • bleb-containing compositions of the invention will generally be substantially free from whole bacteria, whether living or dead.
  • the size of the blebs means that they can readily be separated from whole bacteria by filtration e.g. as typically used for filter sterilisation.
  • blebs will pass through a standard 0.22 mm filters, these can rapidly become clogged by other material, and so it may be useful to perform sequential steps of filter sterilisation through a series of filters of decreasing pore size before using a 0.22 ⁇ m filter. Examples of preceding filters would be those with pore size of 0.8 ⁇ m, 0.45 ⁇ m, etc.
  • Blebs of the invention contain lipids and proteins.
  • the protein content of the blebs has been analysed, and they include the proteins listed in Table 1 and discussed below.
  • Table 1 lists the GenBank name and GI number for 129 proteins which were detected in Shigella blebs of the invention. These 127 proteins may be used as immunogenic components in purified form, separate from blebs. A preferred subset of the 129 is the first 60 in the list (“Subset 3”).
  • Polypeptides can be prepared by various means e.g. by chemical synthesis (at least in part), by digesting longer polypeptides using proteases, by translation from RNA, by purification from cell culture (e.g. from recombinant expression or from Shigella culture). etc. Heterologous expression in an E. coli host is a preferred expression route.
  • Polypeptides of the invention may be attached or immobilised to a solid support.
  • Polypeptides of the invention may comprise a detectable label e.g. a radioactive label, a fluorescent label, or a biotin label. This is particularly useful in immunoassay techniques.
  • Polypeptides can take various forms (e.g. native, fusions, glycosylated, non-glycosylated, lipidated, disulfide bridges, etc.). Polypeptides are preferably Shigella polypeptides.
  • Polypeptides are preferably prepared in substantially pure or substantially isolated form (i.e. substantially free from other Shigella or host cell polypeptides) or substantially isolated form.
  • the polypeptides are provided in a non-naturally occurring environment e.g. they are separated from their naturally-occurring environment.
  • the subject polypeptide is present in a composition that is enriched for the polypeptide as compared to a control.
  • purified polypeptide is provided, whereby purified is meant that the polypeptide is present in a composition that is substantially free of other expressed polypeptides, where by substantially free is meant that less than 50%, usually less than 30% and more usually less than 10% of the composition is made up of other expressed polypeptides.
  • polypeptide refers to amino acid polymers of any length.
  • the polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component.
  • polypeptides containing one or more analogs of an amino acid including, for example, unnatural amino acids, etc.
  • Polypeptides can occur as single chains or associated chains.
  • the invention provides a pharmaceutical composition comprising (a) blebs of the invention and (b) a pharmaceutically acceptable carrier.
  • the invention also provides a process for preparing such a composition, comprising the step of admixing blebs of the invention with a pharmaceutically acceptable carrier.
  • the invention also provides a pharmaceutical composition
  • a pharmaceutical composition comprising (a) the bleb-free immunogenic composition defined above and (b) a pharmaceutically acceptable carrier.
  • the immunogenic composition may include a pharmaceutically acceptable carrier, which can be any substance that does not itself induce the production of antibodies harmful to the patient receiving the composition, and which can be administered without undue toxicity.
  • Pharmaceutically acceptable carriers can include liquids such as water, saline, glycerol and ethanol.
  • auxiliary substances such as wetting or emulsifying agents, pH buffering substances, and the like, can also be present in such vehicles. A thorough discussion of suitable carriers is available in ref. 15.
  • compositions of the invention may be prepared in various forms.
  • the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared.
  • the composition may be prepared for topical administration e.g. as an ointment, cream or powder.
  • the composition be prepared for oral administration e.g. as a tablet or capsule, or as a syrup (optionally flavoured).
  • the composition may be prepared for pulmonary administration e.g. as an inhaler, using a fine powder or a spray.
  • the composition may be prepared as a suppository or pessary.
  • the composition may be prepared for nasal, aural or ocular administration e.g. as drops.
  • composition is preferably sterile. It is preferably pyrogen-free. It is preferably buffered e.g. at between pH 6 and pH 8, generally around pH 7. Compositions of the invention may be isotonic with respect to humans.
  • Immunogenic compositions comprise an immunologically effective amount of immunogen, as well as any other of other specified components, as needed.
  • immunologically effective amount it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, age, the taxonomic group of individual to be treated (e.g. non-human primate, primate, etc.), the capacity of the individual's immune system to synthesise antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials.
  • compositions of the invention will generally be between 10 and 500 ⁇ g/ml, preferably between 25 and 200 ⁇ g/ml, and more preferably about 50 ⁇ g/ml or about 100 ⁇ g/ml (expressed in terms of total protein in the blebs).
  • a dosage volume of 0.5 ml is typical for injection.
  • composition may be administered in conjunction with other immunoregulatory agents.
  • Adjuvants which may be used in compositions of the invention (particularly in bleb-free compositions) include, but are not limited to:
  • Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminium salts and calcium salts.
  • the invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulphates, etc. [e.g. see chapters 8 & 9 of ref. 19], or mixtures of different mineral compounds, with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption being preferred.
  • the mineral containing compositions may also be formulated as a particle of metal salt.
  • aluminium hydroxide typically aluminium oxyhydroxide salts, which are usually at least partially crystalline.
  • Aluminium oxyhydroxide which can be represented by the formula AlO (OH)
  • IR infrared
  • the degree of crystallinity of an aluminium hydroxide adjuvant is reflected by the width of the diffraction band at half height (WHH), with poorly-crystalline particles showing greater line broadening due to smaller crystallite sizes.
  • aluminium hydroxide adjuvants The surface area increases as WHH increases, and adjuvants with higher WHH values have been seen to have greater capacity for antigen adsorption.
  • a fibrous morphology e.g. as seen in transmission electron micrographs
  • the pI of aluminium hydroxide adjuvants is typically about 11 i.e. the adjuvant itself has a positive surface charge at physiological pH.
  • Adsorptive capacities of between 1.8-2.6 mg protein per mg Al +++ at pH 7.4 have been reported for aluminium hydroxide adjuvants.
  • the adjuvants known as “aluminium phosphate” are typically aluminium hydroxyphosphates, often also containing a small amount of sulfate (i.e. aluminium hydroxyphosphate sulfate). They may be obtained by precipitation, and the reaction conditions and concentrations during precipitation influence the degree of substitution of phosphate for hydroxyl in the salt. Hydroxyphosphates generally have a PO 4 /Al molar ratio between 0.3 and 1.2. Hydroxyphosphates can be distinguished from strict AlPO 4 by the presence of hydroxyl groups. For example, an IR spectrum band at 3164 cm ⁇ 1 (e.g. at 200° C.) indicates the presence of structural hydroxyls [ch. 9 of ref. 19].
  • the PO 4 /Al 3+ molar ratio of an aluminium phosphate adjuvant will generally be between 0.3 and 1.2, preferably between 0.8 and 1.2, and more preferably 0.95+0.1.
  • the aluminium phosphate will generally be amorphous, particularly for hydroxyphosphate salts.
  • a typical adjuvant is amorphous aluminium hydroxyphosphate with PO 4 /Al molar ratio between 0.84 and 0.92, included at 0.6 mg Al 3+ /ml.
  • the aluminium phosphate will generally be particulate (e.g. plate-like morphology as seen in transmission electron micrographs). Typical diameters of the particles are in the range 0.5-20 ⁇ m (e.g. about 5-10 ⁇ m) after any antigen adsorption.
  • Adsorptive capacities of between 0.7-1.5 mg protein per mg Al +++ at pH 7.4 have been reported for aluminium phosphate adjuvants.
  • Suspensions of aluminium salts used to prepare compositions of the invention may contain a buffer (e.g. a phosphate or a histidine or a Tris buffer), but this is not always necessary.
  • the suspensions are preferably sterile and pyrogen-free.
  • a suspension may include free aqueous phosphate ions e.g.
  • the suspensions may also comprise sodium chloride.
  • an adjuvant component includes a mixture of both an aluminium hydroxide and an aluminium phosphate.
  • there may be more aluminium phosphate than hydroxide e.g. a weight ratio of at least 2:1 e.g. >5:1, >6:1, >7:1, >8:1, >9:1, etc.
  • the concentration of Al +++ in a composition for administration to a patient is preferably less than 10 mg/ml e.g. ⁇ 5 mg/ml, ⁇ 4 mg/ml, ⁇ 3 mg/ml, ⁇ 2 mg/ml, ⁇ 1 mg/ml, etc.
  • a preferred range is between 0.3 and 1 mg/ml.
  • a maximum of ⁇ 0.85mg/dose is preferred.
  • Oil emulsion compositions suitable for use as adjuvants in the invention include squalene-water emulsions, such as MF59 [Chapter 10 of ref. 19; see also ref. 16] (5% Squalene, 0.5% Tween 80, and 0.5% Span 85, formulated into submicron particles using a microfluidizer). Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used.
  • CFA Complete Freund's adjuvant
  • IFA incomplete Freund's adjuvant
  • oin-in-water emulsions typically include at least one oil and at least one surfactant, with the oil(s) and surfactant(s) being biodegradable (metabolisable) and biocompatible.
  • the oil droplets in the emulsion are generally less than 5 ⁇ m in diameter, and advantageously the emulsion comprises oil droplets with a sub-micron diameter, with these small sizes being achieved with a microfluidiser to provide stable emulsions. Droplets with a size less than 220 nm are preferred as they can be subjected to filter sterilization.
  • the invention can be used with oils such as those from an animal (such as fish) or vegetable source.
  • Sources for vegetable oils include nuts, seeds and grains. Peanut oil, soybean oil, coconut oil, and olive oil, the most commonly available, exemplify the nut oils.
  • Jojoba oil can be used e.g. obtained from the jojoba bean. Seed oils include safflower oil, cottonseed oil, sunflower seed oil, sesame seed oil and the like. In the grain group, corn oil is the most readily available, but the oil of other cereal grains such as wheat, oats, rye, rice, teff, triticale and the like may also be used.
  • 6-10 carbon fatty acid esters of glycerol and 1,2-propanediol may be prepared by hydrolysis, separation and esterification of the appropriate materials starting from the nut and seed oils.
  • Fats and oils from mammalian milk are metabolizable and may therefore be used in the practice of this invention.
  • the procedures for separation, purification, saponification and other means necessary for obtaining pure oils from animal sources are well known in the art.
  • Most fish contain metabolizable oils which may be readily recovered. For example, cod liver oil, shark liver oils, and whale oil such as spermaceti exemplify several of the fish oils which may be used herein.
  • a number of branched chain oils are synthesized biochemically in 5-carbon isoprene units and are generally referred to as terpenoids.
  • Shark liver oil contains a branched, unsaturated terpenoid known as squalene, 2,6,10,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaene.
  • Other preferred oils are the tocopherols (see below). Oil in water emulsions comprising sqlauene are particularly preferred. Mixtures of oils can be used.
  • Surfactants can be classified by their ‘HLB’ (hydrophile/lipophile balance). Preferred surfactants of the invention have a HLB of at least 10, preferably at least 15, and more preferably at least 16.
  • the invention can be used with surfactants including, but not limited to: the polyoxyethylene sorbitan esters surfactants (commonly referred to as the Tweens), especially polysorbate 20 and polysorbate 80; copolymers of ethylene oxide (EO), propylene oxide (PO), and/or butylene oxide (BO), sold under the DOWFAXTM tradename, such as linear EO/PO block copolymers; octoxynols, which can vary in the number of repeating ethoxy (oxy-1,2-ethanediyl) groups, with octoxynol-9 (Triton X-100, or t-octylphenoxypolyethoxyethanol) being of particular interest; (octylphenoxy)polyethoxyethanol
  • Preferred surfactants for including in the emulsion are Tween 80 (polyoxyethylene sorbitan monooleate), Span 85 (sorbitan trioleate), lecithin and Triton X-100.
  • detergents such as Tween 80 may contribute to the thermal stability seen in the examples below.
  • Mixtures of surfactants can be used e.g. Tween 80/Span 85 mixtures.
  • a combination of a polyoxyethylene sorbitan ester such as polyoxyethylene sorbitan monooleate (Tween 80) and an octoxynol such as t-octylphenoxypolyethoxyethanol (Triton X-100) is also suitable.
  • Another useful combination comprises laureth 9 plus a polyoxyethylene sorbitan ester and/or an octoxynol.
  • Preferred amounts of surfactants are: polyoxyethylene sorbitan esters (such as Tween 80) 0.01 to 1%, in particular about 0.1%; octyl- or nonylphenoxy polyoxyethanols (such as Triton X-100, or other detergents in the Triton series) 0.001 to 0.1%, in particular 0.005 to 0.02%; polyoxyethylene ethers (such as laureth 9) 0.1 to 20%, preferably 0.1 to 10% and in particular 0.1 to 1% or about 0.5%.
  • polyoxyethylene sorbitan esters such as Tween 80
  • octyl- or nonylphenoxy polyoxyethanols such as Triton X-100, or other detergents in the Triton series
  • polyoxyethylene ethers such as laureth 9
  • oil-in-water emulsion adjuvants useful with the invention include, but are not limited to:
  • Antigens and adjuvants in a composition will typically be in admixture at the time of delivery to a patient.
  • the emulsions may be mixed with antigen during manufacture, or extemporaneously, at the time of delivery.
  • the adjuvant and antigen may be kept separately in a packaged or distributed vaccine, ready for final formulation at the time of use.
  • the antigen will generally be in an aqueous form, such that the vaccine is finally prepared by mixing two liquids.
  • the volume ratio of the two liquids for mixing can vary (e.g. between 5:1 and 1:5) but is generally about 1:1.
  • Saponin formulations may also be used as adjuvants in the invention.
  • Saponins are a heterogeneous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponin from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponin can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria officianalis (soap root).
  • Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs. QS21 is marketed as StimulonTM.
  • Saponin compositions have been purified using HPLC and RP-HPLC. Specific purified fractions using these techniques have been identified, including QS7, QS17, QS18, QS21, QH-A, QH-B and QH-C.
  • the saponin is QS21.
  • a method of production of QS21 is disclosed in ref. 28.
  • Saponin formulations may also comprise a sterol, such as cholesterol [29].
  • ISCOMs immunostimulating complexs
  • phospholipid such as phosphatidylethanolamine or phosphatidylcholine.
  • Any known saponin can be used in ISCOMs.
  • the ISCOM includes one or more of QuilA, QHA & QHC.
  • the ISCOMS may be devoid of additional detergent [32].
  • Adjuvants suitable for use in the invention include bacterial or microbial derivatives such as non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), Lipid A derivatives, immunostimulatory oligonucleotides and ADP-ribosylating toxins and detoxified derivatives thereof.
  • LPS enterobacterial lipopolysaccharide
  • Lipid A derivatives Lipid A derivatives
  • immunostimulatory oligonucleotides and ADP-ribosylating toxins and detoxified derivatives thereof.
  • Non-toxic derivatives of LPS include monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL).
  • 3dMPL is a mixture of 3 de-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains.
  • a preferred “small particle” form of 3 De-O-acylated monophosphoryl lipid A is disclosed in ref. 35. Such “small particles” of 3dMPL are small enough to be sterile filtered through a 0.22 ⁇ m membrane [35].
  • Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529 [36,37].
  • Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174.
  • OM-174 is described for example in refs. 38 & 39.
  • Immunostimulatory oligonucleotides suitable for use as adjuvants in the invention include nucleotide sequences containing a CpG motif (a dinucleotide sequence containing an unmethylated cytosine linked by a phosphate bond to a guanosine). Double-stranded RNAs and oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
  • the CpG's can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded.
  • References 40, 41 and 42 disclose possible analog substitutions e.g. replacement of guanosine with 2′-deoxy-7-deazaguanosine.
  • the adjuvant effect of CpG oligonucleotides is further discussed in refs. 43-48.
  • the CpG sequence may be directed to TLR9, such as the motif GTCGTT or TTCGTT [49].
  • the CpG sequence may be specific for inducing a Th1 immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN.
  • CpG-A and CpG-B ODNs are discussed in refs. 50-52.
  • the CpG is a CpG-A ODN.
  • the CpG oligonucleotide is constructed so that the 5′ end is accessible for receptor recognition.
  • two CpG oligonucleotide sequences may be attached at their 3′ ends to form “inunomers”. See, for example, refs. 53-55.
  • an adjuvant used with the invention may comprise a mixture of (i) an oligonucleotide (e.g. between 15-40 nucleotides) including at least one (and preferably multiple) CpI motifs (i.e. a cytosine linked to an inosine to form a dinucleotide), and (ii) a polycationic polymer, such as an oligopeptide (e.g. between 5-20 amino acids) including at least one (and preferably multiple) Lys-Arg-Lys tripeptide sequence(s).
  • an oligonucleotide e.g. between 15-40 nucleotides
  • CpI motifs i.e. a cytosine linked to an inosine to form a dinucleotide
  • a polycationic polymer such as an oligopeptide (e.g. between 5-20 amino acids) including at least one (and preferably multiple) Lys-Arg-Lys tripeptide sequence(s).
  • the oligonucleotide may be a deoxynucleotide comprising 26-mer sequence 5′-(IC) 13 -3′ (SEQ ID NO: 7).
  • the polycationic polymer may be a peptide comprising 11-mer amino acid sequence KLKLLLLLKLK (SEQ ID NO: 6). This combination of SEQ ID NOs: 6 and 7 provides the IC-31TM adjuvant.
  • Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the invention.
  • the protein is derived from E. coli ( E. coli heat labile enterotoxin “LT”), cholera (“CT”), or pertussis (“PT”).
  • LT E. coli heat labile enterotoxin
  • CT cholera
  • PT pertussis
  • the use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in ref. 59 and as parenteral adjuvants in ref. 60.
  • the toxin or toxoid is preferably in the form of a holotoxin, comprising both A and B subunits.
  • the A subunit contains a detoxifying mutation; preferably the B subunit is not mutated.
  • the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LT-G192.
  • LT-K63 LT-K63
  • LT-R72 LT-G192.
  • a useful CT mutant is or CT-E29H [69].
  • Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in ref. 70, specifically incorporated herein by reference in its entirety.
  • Human immunomodulators suitable for use as adjuvants in the invention include cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 [71], etc.) [72], interferons (e.g. interferon-y), macrophage colony stimulating factor, and tumor necrosis factor.
  • cytokines such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 [71], etc.) [72], interferons (e.g. interferon-y), macrophage colony stimulating factor, and tumor necrosis factor.
  • interferons e.g. interferon-y
  • macrophage colony stimulating factor e.g. interferon-y
  • tumor necrosis factor e.g. tumor necrosis factor.
  • a preferred immunomodulator is IL-12.
  • Bioadhesives and mucoadhesives may also be used as adjuvants in the invention.
  • Suitable bioadhesives include esterified hyaluronic acid microspheres [73] or mucoadhesives such as cross-linked derivatives of poly(acrylic acid), polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the invention [74].
  • Microparticles may also be used as adjuvants in the invention.
  • Microparticles i.e. a particle of ⁇ A 100 nm to ⁇ 150 ⁇ m in diameter, more preferably ⁇ 200 nm to ⁇ 30 ⁇ m in diameter, and most preferably ⁇ 500 nm to ⁇ 10 ⁇ m in diameter
  • materials that are biodegradable and non-toxic e.g. a poly( ⁇ -hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.
  • a negatively-charged surface e.g. with SDS
  • a positively-charged surface e.g. with a cationic detergent, such as CTAB
  • liposome formulations suitable for use as adjuvants are described in refs. 75-77.
  • Imiquamod and its homologues e.g. “Resiquimod 3M”
  • Resiquimod 3M Imiquamod and its homologues
  • the invention may also comprise combinations of aspects of one or more of the adjuvants identified above.
  • the following adjuvant compositions may be used in the invention: (1) a saponin and an oil-in-water emulsion [80]; (2) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL) [81]; (3) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g.
  • RibiTM adjuvant system (RAS), (Ribi Immunochem) containing 2% squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (DetoxTM); and (8) one or more mineral salts (such as an aluminum salt)+a non-toxic derivative of LPS (such as 3dMPL).
  • MPL monophosphorylipid A
  • TDM trehalose dimycolate
  • CWS cell wall skeleton
  • LPS such as 3dMPL
  • An aluminium hydroxide adjuvant is useful, and antigens are generally adsorbed to this salt.
  • Oil-in-water emulsions comprising squalene, with submicron oil droplets, are also preferred, particularly in the elderly.
  • Useful adjuvant combinations include combinations of Th1 and Th2 adjuvants such as CpG & an aluminium salt, or resiquimod & an aluminium salt.
  • a combination of an aluminium salt and 3dMPL may be used.
  • the invention also provides a method for raising an antibody response in a mammal, comprising administering an immunogenic composition of the invention to the mammal.
  • the antibody response is preferably a protective antibody response.
  • the invention also provides compositions of the invention for use in such methods.
  • the invention also provides a method for protecting a mammal against a Shigella infection and/or disease (e.g. against shigellosis, Reiter's syndrome, and/or hemolytic uremic syndrome), comprising administering to the mammal an immunogenic composition of the invention.
  • a Shigella infection and/or disease e.g. against shigellosis, Reiter's syndrome, and/or hemolytic uremic syndrome
  • the invention provides compositions of the invention for use as medicaments (e.g. as immunogenic compositions or as vaccines). It also provides the use of vesicles of the invention in the manufacture of a medicament for preventing a Shigella infection in a mammal e.g. for preventing shigellosis, Reiter's syndrome, and/or hemolytic uremic syndrome. It also provides the use of a bleb protein (as defined above) in the manufacture of a bleb-free medicament for preventing a Shigella infection in a mammal e.g. for preventing shigellosis.
  • the mammal is preferably a human.
  • the human may be an adult or, preferably, a child.
  • the vaccine is for prophylactic use, the human is preferably a child (e.g. a toddler or infant); where the vaccine is for therapeutic use, the human is preferably an adult.
  • a vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc.
  • the uses and methods are particularly useful for preventing/treating diseases including, but not limited to, shigellosis, Reiter's syndrome, and/or hemolytic uremic syndrome
  • Efficacy of therapeutic treatment can be tested by monitoring Shigella infection after administration of the composition of the invention.
  • Efficacy of prophylactic treatment can be tested by monitoring immune responses against immunogenic proteins in the blebs or other antigens after administration of the composition.
  • Immunogenicity of compositions of the invention can be determined by administering them to test subjects (e.g. children 12-16 months age) and then determining standard serological parameters. These immune responses will generally be determined around 4 weeks after administration of the composition, and compared to values determined before administration of the composition. Where more than one dose of the composition is administered, more than one post-administration determination may be made.
  • compositions of the invention will generally be administered directly to a patient.
  • Direct delivery may be accomplished by parenteral injection (e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly, or to the interstitial space of a tissue), or by rectal, oral, vaginal, topical, transdermal, intranasal, ocular, aural, pulmonary or other mucosal administration.
  • Intramuscular administration to the thigh or the upper arm is preferred.
  • Injection may be via a needle (e.g. a hypodermic needle), but needle-free injection may alternatively be used.
  • a typical intramuscular dose is about 0.5 ml.
  • the invention may be used to elicit systemic and/or mucosal immunity.
  • Dosage treatment can be a single dose schedule or a multiple dose schedule. Multiple doses may be used in a primary immunisation schedule and/or in a booster immunisation schedule. A primary dose schedule may be followed by a booster dose schedule. Suitable timing between priming doses (e.g. between 4-16 weeks), and between priming and boosting, can be routinely determined.
  • composition “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
  • references to a percentage sequence identity between two amino acid sequences means that, when aligned, that percentage of amino acids are the same in comparing the two sequences.
  • This alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in section 7.7.18 of reference 84.
  • a preferred alignment is determined by the Smith-Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62.
  • the Smith-Waterman homology search algorithm is well known and is disclosed in reference 85.
  • GI numbering is used above.
  • a GI number, or “GenInfo Identifier”, is a series of digits assigned consecutively to each sequence record processed by NCBI when sequences are added to its databases. The GI number bears no resemblance to the accession number of the sequence record.
  • a sequence is updated (e.g. for correction, or to add more annotation or information) then it receives a new GI number. Thus the sequence associated with a given GI number is never changed.
  • this epitope may be a B-cell epitope and/or a T-cell epitope.
  • Such epitopes can be identified empirically (e.g. using PEPSCAN [86,87] or similar methods), or they can be predicted (e.g. using the Jameson-Wolf antigenic index [88], matrix-based approaches [89], MAPITOPE [90], TEPITOPE [91,92], neural networks [93], OptiMer & EpiMer [94, 95], ADEPT [96], Tsites [97], hydrophilicity [98], antigenic index [99] or the methods disclosed in references 100-101, etc.).
  • Epitopes are the parts of an antigen that are recognised by and bind to the antigen binding sites of antibodies or T-cell receptors, and they may also be referred to as “antigenic determinants”.
  • FIG. 1 shows an electron micrograph of blebs of the invention purified from culture.
  • FIG. 2 shows 2D SDS-PAGE of blebs from S. sonnies ⁇ tolR ⁇ galU.
  • FIG. 3 shows LPS of blebs in various indicated strains, stained with anti-core antibody.
  • FIG. 4 shows an immunoblot of 2D-separated proteins of blebs using serum from immunised mice.
  • FIG. 5 shows SDS-PAGE of bacteria grown in different conditions.
  • FIG. 6 shows adsorbed proteins in blebs. Lanes from left to right: 1) protein molecular weight marker, 2) Ss OMB 10 ⁇ g, 3) Ss OMB 2 ⁇ g, 4) Ss OMB 10 ⁇ g adsorbed on alum for 1 month.
  • FIG. 7 shows FACS data for indicated strains.
  • the tolR gene of wild-type S. sonnies 53G was deleted using the k Red system [11,102]. Competent cells transformed with the ⁇ Red plasmids are prepared and then transformed with a linear fragment designed to swap the tolR gene for an antibiotic resistance gene by homologous recombination. Clones that have integrated the fragment into the chromosome are selected by resistance to the antibiotic and deletion of the tolR is verified by PCR or other techniques. The temperature sensitive ⁇ Red plasmids can then be removed by growth of the new clones at 37° C.
  • the galU gene was also deleted in a similar way, to provide a ⁇ galU single mutant and a ⁇ tolR ⁇ galU double mutant. Blebs released by mutants are confirmed to have a defective LPS lacking 0 antigen.
  • a ⁇ tolR ⁇ msbB double mutant strain with modified LPS is prepared in the same way.
  • the virulence plasmid has also been removed from the ⁇ tolR and ⁇ tolR ⁇ msbB strains.
  • the tolR gene of S. flexneri was deleted using the ⁇ Red system as described above for S. sonnies. O antigen biosynthesis in S. flexneri was abolished by deletion of a chromosomal fragment comprising the complete rfbG gene and as well as parts of dbF and rfc, resulting in activation of all three genes. The deletion was generated using the ⁇ Red system and is abbreviated as ⁇ rfbG.
  • a ⁇ tolR ⁇ rfbG double mutant has been generated in the same way.
  • a ⁇ tolR ⁇ htrB double mutant containing modified LPS has been generated in the same way.
  • the virulence plasmid has also been removed from these strains.
  • Fermentation of the double mutant ⁇ tolR ⁇ galU strain was run under the following conditions: pH 7.1, 37° C., dissolved oxygen maintained at 30% saturation by controlling agitation and setting maximum aeration.
  • the pH was controlled by addition of 4M ammonium hydroxide.
  • the foam was controlled by addition of 10% PPG during the run.
  • the medium consisted of the following components: KH 2 PO 4 5 g/l, K 2 HPO 4 20 g/l and yeast extract 30 g/l. After the medium was sterilized by autoclaving, glycerol 15 g/l and MgSO 4 2 mM were added prior to inoculation.
  • the culture inoculum was 5% of the fermentor volume. The fermentation process took approximately 13 hours and cell concentration was measured as optical density at 600 nm.
  • the fermentation process of the S. sonnies ⁇ tolR ⁇ msbB double mutant strain was performed with defined medium: glycerol 30 g/l, KH 2 PO 4 13.3 g/l, (NH 4 ) 2 HPO 4 4 g/l, MgSO 4 ⁇ 7H 2 O (1M) 2 ml, citric acid 1.7 g/l, CoCl 2 ⁇ 6H 2 O 2.5 mg/l, MnCl 2 ⁇ 4H 2 O 15 mg/l, CuCl 2 ⁇ 2H 2 O 1.5 mg/l, H 3 BO 3 3 mg/l, Na 2 MoO 4 ⁇ 2H 2 O 2.5 mg/l, Zn(CH 3 COO) 2 ⁇ 2H 2 O 13 mg/l, ferric citrate 2 ⁇ M, thiamine 50 mg/l, nicotinic acid 10 mg/l, L-acid aspartic 2.5 g/l.
  • defined medium glycerol 30 g/l, KH 2 PO 4 13.3 g/l,
  • Vesicles produced in the fermentation broth were purified using two consecutive TFF (tangential flow filtration) steps: micro-filtration at 0.22 ⁇ m and then a second micro-filtration at 0.1 ⁇ m.
  • TFF tangential flow filtration
  • the vesicles were separated from biomass by TFF through a 0.22 ⁇ m pore size cassette.
  • the biomass was first concentrated 4-fold and, after five diafiltration steps against PBS, the vesicles were collected in the filtrate.
  • the filtrate from the 0.22 ⁇ m TFF was further micro-filtered trough a 0.1 ⁇ m cut-off cassette, in order to purify the vesicles from soluble proteins.
  • the vesicles could not pass through the filter cassette.
  • the retentate containing the vesicles was collected.
  • the final purified product was observed with TEM ( FIG. 1 ).
  • the blebs have a homogenous size of about 50 nm in diameter.
  • Blebs from S. flexneri mutants were purified in the same way after growing the various strains in yeast extract medium as used for S. sonnies
  • blebs are essentially pure outer membranes. Unlike conventional outer membrane vesicles (OMV) derived by disruption of the outer membrane, the blebs conserve lipophilic proteins and are essentially free of cytoplasmic and inner membrane components.
  • OMV outer membrane vesicles
  • Blebs from S. sonnies and S. flexneri strains were denatured with a detergent and proteins were identified with a LC-MS/MS approach.
  • blebs were separated with SDS page or 2D gel electrophoresis ( FIG. 2 ). Visible bands and spots were excised from the gel and proteins identified via protein mass fingerprint. The relative amount of different proteins was studied with densitometer analysis of SDS-PAGE bands or spots from the 2D gel.
  • FIG. 3 shows a shift in LPS mobility in the ⁇ galU mutant strain compared to wildtype Shigella and E. coli (all strains are in a ⁇ tolR background).
  • a second proteomic approach based on surface digestion, was used to characterize exposed portions of membrane proteins.
  • a set of proteins was identified as reactive with sera from mice immunized with the blebs and many of these have been found to be conserved in a large panel of strains. Little is known about the structure of most integral outer membrane proteins.
  • the surfome of blebs was investigated by treatment with a protease and recovery and identification via LC-MS/MS of released peptides. As blebs should represent the surface of the whole living bacterial cell, this map should be representative of exposed proteins on the surface of S. sonnies.
  • mice immunised with the blebs from the ⁇ tolR ⁇ galU strain produce serum which reacts with a 2D gel of the blebs as shown in FIG. 4 .
  • the blebs are immunogenic.
  • adjuvant aluminium hydroxide or Freund's complete.
  • a classical ELISA method was performed to analyze IgG production in sera obtained from immunization studies. Sera from all groups of mice demonstrated a high level production of bleb-specific IgG. No significant differences in IgG production were detected when blebs were used alone or in combination with an adjuvant. Tthe group immunized with the lower dose of 2 ⁇ g showed the same level of bleb-specific IgG as the group immunized with 10 ⁇ g, showing that a low dose vaccine may be achievable i.e. more doses per dollar. Blebs from other S. sonnies as well as S. flexneri strains were similarly immunogenic.
  • Sera raised against the blebs were tested for reactivity with three different bacteria: S. sonnies G53, S. flexneri 2a 2457T or S. flexneri 5 M90T.
  • the samples were than stained with a labeled secondary Ab and were analyzed by flow cytometry. As shown in FIG. 7 , the S. sonnies and S. flexneri strains cross-react with the sera.
  • the bleb approach has a strong potential to produce effective and low-cost vaccines and can be extended to different Shigella strains towards a broad spectrum vaccine.
  • Blebs were combined with aluminium hydroxide (2 mg/ml) for adsorption.
  • the adsorbed material was stored at 4° C. for 1 day, 1 week or 1 month.
  • the blebs were toatlyl adsorbed after 1 day and there was no evidence of desorption even after 1 month ( FIG. 6 ).
  • FIG. 5 shows proteins expressed by Shigella grown under various conditions.
  • the bacteria were grown in the presence of 200 ⁇ M FeSO 4 whereas in lane 5 the culture had 200 ⁇ M dypiridyl.
  • the inset shows that three proteins are up-regulated under the iron-limiting conditions. These three proteins were identified as the FepA outer membrane receptor (GI 74311118), the colicin I receptor (GI 74312677), and the putative ferric siderophore receptor (GI 74313972). These proteins are well-conserved among Shigella spp. and enterobacteriaceae and are potentially highly immunogenic. Thus growth of Shigella under iron-limiting conditions can lead to the release of blebs which are, compared to normal growth conditions, enriched for these proteins.
  • SEQ ID NOs: 70, 71, 73, 74, 76, 111, 112, 114-129 & 131-135 were identified from S. sonnies ⁇ tolR blebs.
  • SEQ ID NOs: 8-15 & 17-58 were identified from S. sonnies ⁇ tolR ⁇ galU blebs.
  • SEQ ID NOs: 83, 94, 97 & 107 were identified from S. flexneri ⁇ tolR blebs.
  • SEQ ID NOs: 68, 69, 72, 75, 77-82, 84-93, 95, 96, 98-106, 108-10, 113, 130 & 136 were identified from S. flexneri ⁇ tolR ⁇ rfbG blebs.
  • SEQ ID NOs: 60-67 were identified from surface digestion of S. sonnies.
  • Subset 1 SEQ ID NOs: 68, 69, 72, 75, 77-110, 113, 130 & 136.
  • Subset 2 SEQ ID NOs: 8-15, 17-58, 60-67, 70, 71, 73, 74, 76, 111, 112, 114-129 & 131-135.
  • Subset 3 SEQ ID NOs: 1-60.
  • SEQ ID NO: 18 is the same as SEQ ID NO: 5; SEQ ID NO: 33 is the same as SEQ ID NO: 2; SEQ ID NOs: 9 & 16 are related ( ⁇ 97% identity); SEQ ID NOs: 23 & 59 are related ( ⁇ 98% identity).
  • Vaccine Adjuvants Preparation Methods and Research Protocols (Volume 42 of Methods in Molecular Medicine series). ISBN: 1-59259-083-7. Ed. O'Hagan.

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US10188722B2 (en) 2008-09-18 2019-01-29 Aviex Technologies Llc Live bacterial vaccines resistant to carbon dioxide (CO2), acidic pH and/or osmolarity for viral infection prophylaxis or treatment
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