(en)The present invention encompasses recombinant bacteria and immunogenic compositions comprising the bacteria. The immunogenic composition may be used to induce an immune response against C. perfringens.

1.ApplicationNumber: US-68171108-A
1.PublishNumber: US-2011256181-A1
2.Date Publish: 20111020
3.Inventor: CURTISS, III ROY
ZEKARIAS BEREKET
ROLAND KENNETH

4.Inventor Harmonized: CURTISS III ROY(US)
ZEKARIAS BEREKET(US)
ROLAND KENNETH(US)

5.Country: US
6.Claims:
(en)The present invention encompasses recombinant bacteria and immunogenic compositions comprising the bacteria. The immunogenic composition may be used to induce an immune response against C. perfringens.

7.Description:
(en)REFERENCE TO SEQUENCE LISTING
A paper copy of the sequence listing and a computer readable form of the same sequence listing are appended below and herein incorporated by reference. The information recorded in computer readable form is identical to the written sequence listing, according to 37 C.F.R. 1.821 (f).
FIELD OF THE INVENTION
The invention encompasses a recombinant bacterium capable of eliciting an immune response against Clostridium perfringens in a host.
BACKGROUND OF THE INVENTION
C. perfringens is a ubiquitous gram positive, spore-forming, anaerobic organism, found in many environments surrounding poultry production, or other agricultural activities associated with animal rearing, including soil, dust, feces, feed, litter, rodents, and the intestinal contents of asymptomatic animals. The toxins produced by C. perfringens strains cause necrotic enteritis (NE) in severe cases and have the ability, at lower doses, to cause a subclinical necrotic enteritis with thickening of the intestinal mucosa and decreased length of microvili in the ileum. The collective impact of C. perfringens colonization is to reduce the absorptive surface in the intestinal tract with a consequent reduction in the ability of birds, and most likely other animals including humans, to benefit from nutrients in food, resulting in a reduced rate of growth. C. perfringens induces cellulitis and gangrenous dermatitis and is becoming an increasing concern in turkeys as well. Additionally, it is a frequent cause of gas gangrene in humans.
It is interesting to note that the majority of antibiotics added to poultry feed that are most effective as growth promoters are active against gram-positive bacteria, such as Clostridia. In addition, the most prevalently used ionophore anti-coccidial drugs also exhibit anti-clostridial activities. Therefore, C. perfringens infections and NE have been traditionally controlled by addition of Antimicrobial Growth Promoters (AGP) and coccidiostats, to control Eimeria infections, in the animal feed. Large quantities of antimicrobials were used as AGP and as prophylaxis against enteric bacterial pathogens, including C. perfringens. The use of AGP has been condemned due to concerns about increased antibiotic resistance in human pathogens. Consequently, the recent increase in sporadic outbreaks and widespread sub-clinical NE is linked to the withdrawal of AGP. This had been observed initially in Scandinavian countries following the ban on AGP in the early nineties. Furthermore, the decline in use of ionophore coccidiostats, which can prevent C. perfringens lesions, due to the introduction of vaccines to prevent Eimeria infections, has exacerbated the resurgence of NE. Thus, NE is a re-emerging disease and a major threat to the current objective of ‘antimicrobial-free’ poultry farming.
C. perfringens can cause a range of health problems in infected birds, ranging from a subclinical infection which can result in poor feed conversion caused by decreased digestion and adsorption, to necrotic enteritis, resulting in a variety of symptoms including severe depression, decreased appetite, reluctance to move, diarrhea and ruffled feathers, often leading to death. Clinical illness is usually short, with birds often simply found dead. Onset of disease symptoms generally occurs in broilers from two to five weeks of age, coinciding with the disappearance of maternal antibodies. However, NE has also been reported in layers of various ages. Gross lesions typically involve the ileum and jejunum, although cecal lesions can occur. Intestines are friable and distended with gas and fluid and a diphtheritic membrane is often found in the mucosa. Subclinical infection with C. perfringens can lead to economic losses, due to reduced growth rates and poor feed conversion. It is likely that losses due to subclinical infections may constitute a larger problem overall than losses due to acute disease. Occasionally, cholagniohepatitis can result, leading to condemnation losses at slaughter.
In a recent study, the Food Safety and Inspection Service (FSIS) determined Salmonella serotypes isolated from swine, ground turkey, ground beef and broilers in processing plants participating in the Hazard Analysis and Critical Control Point (HACCP) systems for pathogen reduction and found that 87% of the Salmonella isolates were from poultry sources. Using data from the Centers for Disease Control and Prevention collected in 2005, it is evident that some Salmonella serotypes that are most frequently isolated from humans are also very prevalent in poultry, with 8 of the Salmonella serotypes predominantly isolated from poultry being represented in the top 20 serotypes isolated from humans
Hence, there is a need in the art for an inexpensive, effective oral vaccine against C. perfringens for control of both subclinical infections and NE in poultry. However, vaccines that are effective in controlling such infections in poultry might have applications in control of C. perfringens infections in other animal species and even in humans. In addition, such vaccines if they reduced Salmonella infection and colonization in farm animals would benefit food safety by lessening the likelihood for transmission of Salmonella through the food chain to humans.
SUMMARY OF THE INVENTION
One aspect of the invention encompasses a recombinant Salmonella bacterium. The bacterium is capable of the expression of at least one nucleic acid encoding at least one Clostridium perfringens antigen. The bacterium, when administered to a host, typically elicits an immune response against Clostridium perfringens.
Another aspect of the invention encompasses a vaccine composition. The vaccine composition comprises a recombinant bacterium capable of the expression of at least one nucleic acid encoding at least one Clostridium perfringens antigen. The vaccine composition, when administered to a host, when administered to a host, typically elicits an immune response against Clostridium perfringens.
Yet another aspect of the invention is a method of inducing an immune response against Clostridium perfringens. The method comprises administering a composition comprising a recombinant bacterium capable of the expression of at least one nucleic acid encoding at least one Clostridium perfringens antigen to a host.
Other aspects and iterations of the invention are described more thoroughly below.
REFERENCE TO COLOR FIGURES
The application file contains at least one photograph executed in color. Copies of this patent application publication with color photographs will be provided by the Office upon request and payment of the necessary fee.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 depicts the expression of the PlcC antigen by the S. enterica serovar Typhimurium vaccine strain harboring different PlcC expression plasmids. (A) Coomassie blue-stained SDS-PAGE. Lanes: M, molecular mass marker (in kilodaltons) (Bio-Rad, Hercules, Calif.); C, cytoplasmic fraction; P, periplasmic fraction. (B) Western blot of an analogous gel with rabbit anti-PlcC hyperimmune serum. Arrows show PlcC protein bands that also correspond to bands detected by western blotting.
FIG. 2 depicts PlcC vaccine antigen expression plasmids. (A) Plasmid maps for the pYA3977 P trc bla signal peptide sequence (ss) vector, pYA4149 P trc bla ss and bla C-terminal sequence (CT) fusion vector, and pYA4110 P lpp ompA ss vector. (B) The sequences of P trc , P lpp , bla ss, ompA ss, and bla CT. RBS, ribosome binding site (Shine-Dalgarno sequence). Arrows show predicted signal peptide cleavage sites.
FIG. 3 depicts the predicted amino acid sequence and alignment of alpha toxin (PLC) mature protein sequences of strain CP995, an NE isolate, and ATCC 13124. Residues in CP995 that are different from those of ATCC 13124 are indicated. The underlined fragment, amino acids 248 to 370, represents the C-terminal domain (PlcC) of the recombinant vaccine antigen.
FIG. 4 depicts ELISA results of anti-PicC serum IgG (A) and bile IgA (B) responses in chickens immunized with oral RASV or s.c. rPlcC emulsified in 100 μl Freund's complete adjuvant. Five weeks after the primary immunization with either RASV or s.c. rPlcC, all of the chickens were given an s.c. boost injection with 50 μg purified rPlcC protein emulsified in 100 μl incomplete Freund's adjuvant. Arrows point to the time of injection with rPlcC protein. Sera were tested at 1:80 dilutions, and bile samples were tested at 1:100 dilutions. The average absorbance of serum or bile samples from five chickens per group at each time point is shown. Values are indicated, with standard deviations in parentheses, for points that show significant mean differences from results for the RAS control group [χ8914(pYA3493)]. *, P<0.05.
FIG. 5 depicts an immunoblot of C. perfringens culture supernatant and rPlcC with χ8914(pYA3977)-immunized chicken serum. Sera collected at 2 weeks after the boost immunization were pooled and used at a 1:40 dilution. C. perfringens culture supernatant was concentrated in 10% TCA (denaturing condition) or concentrated by filtration to retain the native structure. Protein bands at about 43 kDa (closed arrow) in lanes 2 and 4 show the reactivity of serum antibody with alpha toxin, and lanes 5 and 6 show the reactivity with His-tagged rPlcC (19 kDa). M, molecular mass marker (Invitrogen, Carlsbad, Calif.). Lanes 1 and 3, C. perfringens culture supernatant (without concentration); lane 2, C. perfringens culture supernatant concentrated by 10% TCA precipitation; lane 4, C. perfringens culture supernatant concentrated by the Centricon filtration system; lanes 5 and 6, purified rPlcC protein (open arrow).
FIG. 6 depicts DTH in oral RASV- or s.c. rPlcC-immunized chickens. Four weeks after immunization, chickens were injected with 20 μg purified rPlcC protein in the right leg toe web and with saline in the left leg toe web, and the swellings were measured 48 h later. The difference (diff.) in thickness between the left and right toe webs was calculated. Values are averages from five chickens per group. Bars: 1, RAS control [χ8914(pYA3493)]; 2, RASV-1 [χ8914(pYA3977)]; 3, RASV-2 [χ8914 (pYA4110)]; 4, RASV-3 [χ8914(pYA4149)]; and 5, s.c. rPlcC. An asterisk indicates significant mean differences from results for the control group (P<0.05).
FIG. 7 depicts a graph showing the neutralization of alpha toxin hemolytic activity by serum antibody. Pooled sera from oral RASV- or s.c. rPlcC protein-immunized chickens or control chickens orally immunized with RASV χ8914(pYA3493), collected at 2 weeks after the boost immunization, were tested for the neutralization of alpha toxin in culture supernatant of C. perfringens by measuring the inhibition of hemolysis of rabbit RBCs. The test serum final dilution was 1:20. Alpha toxin was obtained by concentrating the culture supernatant of an overnight culture of C. perfringens. The bars represent averages from five chickens per group.
FIG. 8 depicts indirect immunofluorescence detection of serum antibody binding to the bacterium surface. C. perfringens smears were stained with nonimmunized control chicken serum (A), rPlcC protein injection immunized-chicken serum (B), and RASV-1-primed and rPlcC parenteral boost-immunized chicken serum (C).
FIG. 9 depicts micrographs of gross lesions and lesion histopathology of challenged chickens. (A) Gross lesions with hemorrhagic spots in the jejunum in control RAS-immunized chicken. (B) Jejunum (distal region) showing normal elongated villi. (C) Degeneration and sloughing of apical villus epithelium. (D) Severe necrotic lesion on villi and inflammatory cell infiltration (i.e., widened lamina propria). (E) Higher magnification of villus tip showing clumps of bacteria (arrow) in gut lumen and attached to villus tips, often without a major lesion on the surface epithelium in immunized chickens.
FIG. 10 depicts the optimized plcC sequence.
FIG. 11 depicts diagrams of vectors pYA4531 (A) and pYA4538 (B).
FIG. 12 depicts a western blot showing PlcC synthesis from codon-optimized plcC in recombinant avirulent Salmonella. Lanes: M, Fermentas pre-stained protein ladder; 1, χ9352 (pYA4538-plcC opt) culture A; 2, χ9352 (pYA4538-plcC opt) culture B; 3, χ9352 (pYA4538) vector control; 4, χ9352 (pYA4538) vector control; 5, Purified His-plcC (18 μg); 6, Purified His-plcC (9 μg).
FIG. 13 depicts the optimized netB sequence.
FIG. 14 depicts diagrams of vectors pYA4676 (A) and pYA4677 (B).
FIG. 15 depicts a western blot showing NetB synthesis from codon-optimized plcC in recombinant avirulent Salmonella. Lanes: M, Fermentas pre-stained protein ladder; 1, χ9352 (pYA4531) vector control; 2, χ9352 (pYA4676) clone #1; 3, χ9352 (pYA4676) culture B; 4, χ9352 (pYA4531-netB opt) clone #5 culture A; 5, χ9352 (pYA4531-netB opt) clone #5 culture B; 6, χ9352 (pYA4677) culture A: 7, χ9352 (pYA4677) culture B; 8, χ9352 (pYA4531-netB non-optimized); 9, χ9352 (pYA4531-netB non-optimized).
FIG. 16 depicts the optimized tPFOR sequence.
FIG. 17 depicts the optimized tHP sequence.
FIG. 18 depicts the optimized GDP sequence.
FIG. 19 depicts the optimized FBA sequence.
FIG. 20 depicts a diagram of vector pYA4555.
FIG. 21 depicts a diagram of vector pYA4555+bla SS netB (optimized).
FIG. 22 depicts a diagram of vector pYA4679.



DETAILED DESCRIPTION OF THE INVENTION
The present invention encompasses a recombinant bacterium capable of eliciting an immune response against C. perfringens . A vaccine composition comprising a recombinant bacterium of the invention may provide economic benefit to the poultry producer by inducing an immune response to C. perfringens . The immune response would result in enhanced feed conversion efficiency and more rapid growth, without the costs or potential human health hazards of using growth-promoting antibiotics. Additionally, the vaccine composition may substantially reduce Salmonella infection of poultry and thus contamination of carcasses and eggs. Therefore, use of the vaccine composition of the invention may contribute to reducing the likelihood of human infection due to Salmonella transmission through the food chain.
I. Recombinant Bacterium
One aspect of the present invention encompasses a recombinant Salmonella bacterium. The bacterium, when administered to a host, typically elicits an immune response against C. perfringens . Generally speaking, the bacterium is capable of the expression of at least one nucleic acid encoding at least one C. perfringens antigen. In some embodiments, the recombinant bacterium is also capable of the regulated expression of a nucleic acid encoding at least one serotype-specific antigen of the bacterium. In exemplary embodiments, the bacterium does not substantially induce an immune response specific to the serotype of the recombinant bacterium.
In exemplary embodiments, a recombinant Salmonella bacterium of the invention is capable of colonizing a host to substantially the same extent as a wild-type bacterium of the same serotype. A bacterium of the invention, however, will preferably be substantially avirulent after colonization.
In some embodiments, the recombinant bacterium may be a Salmonella enterica serovar. In an exemplary embodiment, a bacterium of the invention may be derived from S. Typhimurium, S. Typhi, S. Paratyphi, S. Gallinarum, S. Enteritidis, S. Choleraesius, S. Arizonae, or S. Dublin. In an exemplary embodiment, a bacterium of the invention may be derived from S. Typhimurium, S. Enteriditis, or S. Gallinarum. In all cases, a recombinant bacterium of the invention generally does not comprise any drug resistance nucleic acid sequences or other sequence scars in the chromosomes of the recombinant strain.
(a) Expression of at Least One Serotype-Specific Antigen
In certain embodiments, a recombinant bacterium of the invention may be capable of the regulated expression of a nucleic acid encoding at least one serotype-specific antigen. As used herein, the phrase “serotype-specific antigen” refers to an antigen that elicits an immune response specific for the bacterial vector serotype. In some embodiments, the immune response to a serotype-specific antigen may also recognize closely related strains in the same serogroup, but in a different, but related, serotype. Non-limiting examples of serotype-specific antigens may include LPS O-antigen, one or more components of a flagellum, and Vi capsular antigen. In some embodiments, the expression of at least one, at least two, at least three, or at least four nucleic acid sequences encoding a serotype-specific antigen may be regulated in a bacterium of the invention.
The phrase “regulated expression of a nucleic acid encoding at least one serotype-specific antigen” refers to expression of the nucleic acid encoding a serotype-antigen such that the bacterium does not substantially induce an immune response specific to the bacterial vector serotype. In one embodiment, the expression of the serotype-specific antigen is eliminated. In another embodiment, the expression is substantially reduced. In yet another embodiment, the expression of the serotype-specific antigen is reduced in a temporally controlled manner. For instance, the expression of the serotype-specific antigen may be reduced during growth of the bacterium in a host, but not during in vitro growth.
The expression of a nucleic acid encoding a Salmonella serotype-specific antigen may be measured using standard molecular biology and protein chemistry techniques known to one of skill in the art. As used herein, “substantial reduction” of the expression of a nucleic acid encoding a serotype-specific antigen refers to a reduction of at least about 1% to at least about 99.9% as compared to a Salmonella bacterium in which no attempts have been made to reduce serotype-specific antigen expression. In one embodiment, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by 100% by using a deletion mutation. In other embodiments of the invention, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by at least about 99.9%, 99.5%, 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91% or 90%. In yet other embodiments of the invention, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by at least about 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81% or 80%. In still other embodiments of the invention, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by at least about 75%, 70%, 65%, 60%, 55%, or 50%. In additional embodiments, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by at least about 45%, 40%, 35%, 30%, 25%, or 20%. In yet additional embodiments, the expression of a nucleic acid encoding a serotype-specific antigen is reduced by at least about 15%, 10%, 5%, 4%,3%, 2% or 1%.
Methods of regulating expression of a nucleic acid encoding at least one serotype-specific antigen are discussed in detail below, and in the examples.
i. LPS O-Antigen Expression
In one embodiment, the expression of a nucleic acid encoding the serotype-specific antigen LPS O-antigen is regulated by mutating the pmi nucleic acid sequence, which encodes a phosphomannose isomerase needed for the bacterium to interconvert fructose-6-P and mannose-6-P. In some instances, the bacterium comprises a Δpmi mutation, such as a Δpmi-2426 mutation. A bacterium comprising a Δpmi-2426 mutation, grown in the presence of mannose, is capable of synthesizing a complete LPS O-antigen. But non-phosphorylated mannose, which is the form required for bacterial uptake, is unavailable in vivo. Hence, a bacterium comprising a Δpmi-2426 mutation loses the ability to synthesize LPS O-antigen serotype specific side chains after a few generations of growth in vivo. The LPS that is synthesized comprises a core structure that is substantially similar across many diverse Salmonella serotypes. This results in a bacterium that is capable of eliciting an immune response against at least two Salmonella serotypes without substantially inducing an immune response specific to the serotype of the bacterial vector.
A bacterium of the invention that comprises a Δpmi mutation may also comprise other mutations that ensure that mannose available to the bacterium during in vitro growth is used for LPS O-antigen synthesis. For instance, a bacterium may comprise a Δ(gmd-fcl)-26 mutation. This mutation deletes two nucleic acid sequences that encode enzymes for conversion of GDP-mannose to GDP-fucose. This ensures that mannose available to the bacterium during in vitro growth is used for LPS O-antigen synthesis and not colanic acid production. Similarly, a bacterium may comprise the Δ(wza-wcaM)-8 mutation, which deletes all 19 nucleic acid sequences necessary for colanic acid production, and also precludes conversion of GDP-mannose to GDP-fucose.
In addition to regulating LPS O-antigen synthesis with mannose, the synthesis of LPS O-antigen may be regulated by arabinose, which is also absent in vivo. For instance, a bacterium may comprise the mutation ΔP rfc ::TT araC P BAD rfc. (P stands for promoter and TT stands for transcription terminator.) The rfc (otherwise known as wzy) nucleic acid sequence is necessary for the addition of O-antigen subunits, which typically comprise three or four sugars, in a repeat fashion. When the rfc nucleic acid sequence is absent, only one O-antigen repeat subunit is added to the LPS core polysaccharide. Normally, the serotype-specific O-antigen contains some 50 or so repeats of the O-antigen subunit, catalyzed by the enzyme encoded by the rfc nucleic acid sequence. In the case of a bacterium comprising the ΔP rfc ::TT araC P BAD rfc deletion-insertion mutation, expression of the rfc nucleic acid sequence is dependant on the presence of arabinose that can be supplied during in vitro growth of the strain, but that is absent in vivo. Consequently, rfc expression ceases in vivo, resulting in the cessation of assembly of the O-antigen repeat structure. This reduces the bacterium's ability to induce an immune response against the serotype-specific O-antigen.
Another means to regulate LPS O-antigen expression is to eliminate the function of galE in a recombinant bacterium of the invention. The galE nucleic acid sequence encodes an enzyme for the synthesis of UDP-Gal, which is a substrate for LPS O-antigen, the outer LPS core and colanic acid. Growth of a bacterium comprising a suitable galE mutation in the presence of galactose leads to the synthesis of O-antigen and the LPS core. Non-phosphorylated galactose is unavailable in vivo, however, and in vivo synthesis of UDP-Gal ceases, as does synthesis of the O-antigen and the LPS outer core. One example of a suitable galE mutation is the Δ(galE-ybhC)-851 mutation.
In certain embodiments, a bacterium of the invention may comprise one or more of the Δpmi, ΔP rfc ::TT araC P BAD rfc, and ΔgalE mutations, with or without a Δ(gmd-fcl)-26 or Δ(wza-wcaM)-8 mutation. Such a combination may yield a recombinant bacterium that synthesizes all components of the LPS core and O-antigen side chains when grown in vitro (i.e. in the presence of suitable concentrations of mannose, arabinose and galactose), but that ceases to synthesize the LPS outer core and O-antigen in vivo due to the unavailability of free unphosphorylated mannose, arabinose or galactose. Also, a recombinant bacterium with the inability to synthesize the LPS outer core and/or O-antigen is attenuated, as the bacterium is more susceptible to macrophages and/or complement-mediated cytotoxicity. Additionally, a bacterium with the inability to synthesize the LPS outer core and O-antigen in vivo, induces only a minimal immune response to the serotype-specific LPS O-antigen.
ii. Expression of a Component of a Flagellum
In one embodiment, the expression of a serotype-specific component of a flagellum is regulated by mutating the nucleic acid that encodes FljB or FliC. For instance, a bacterium of the invention may comprise a ΔfljB217 mutation. Alternatively, a bacterium may comprise a ΔfliCl80 mutation. The ΔfljB217 mutation deletes the structural nucleic acid sequence that encodes the Phase II flagellar antigen whereas the ΔfliCl80 mutation deletes the 180 amino acids encoding the antigenically variable serotype-specific domain of the Phase I FliC flagellar antigen. The portion of the flagellar protein that interacts with TLR5 to recruit/stimulate innate immune responses represents the conserved N- and C-terminal regions of the flagellar proteins and this is retained and expressed by strains with the ΔfliCl80 mutation. In addition, the ΔfliCl80 mutation retains the CD4-dependent T-cell epitope. It should be noted, that expression of the Phase I flagellar antigen and not the Phase II flagellar antigen potentiates S. Typhimurium infection of mice. S. Typhimurium recombinant bacteria with the Δpmi-2426, ΔfljB217 and ΔfliC180 mutations, when grown in the absence of mannose, are not agglutinated with antisera specific for the B-group O-antigen or the S. Typhimurium specific anti-flagellar sera. These recombinant bacteria are also non-motile since the FliC180 protein that is synthesized at high levels is not efficiently incorporated into flagella. When these recombinant bacteria are evaluated using HEK293 cells specifically expressing TLR5, the level of NFKB production is about 50% higher than when using a ΔfliB217 F1iC+ strain that assembles flagellin into flagella and exhibits motility (there is no NFKB production by the control ΔfljB217 ΔfliC2426 strain with no flagella). Similarly, recombinant bacteria with the Δ(galE-ybhC)-851, ΔfljB2I7 and ΔfliC180 mutations, when grown in the absence of galactose, are not agglutinated with antisera specific for the B-group O-antigen or the S. Typhimurium specific anti-flagellar sera. These bacteria are also non-motile.
iii. Expression of a Nucleic Acid Encoding the Vi Capsular Antigen
Certain Salmonella strains, such as S. Typhi and S. Dublin, express the Vi capsular antigen. This antigen is serotype-specific, inhibits invasion, and acts to suppress induction of a protective immune response. Consequently, when a recombinant bacterium of the invention is derived from a strain comprising the Vi capsular antigen, one or more nucleic acids encoding the Vi capsular antigen will be deleted such that the Vi capsular antigen is not synthesized.
(b) Expression of at Least One C. Perfringens Antigen
Generally speaking, a recombinant bacterium of the invention is capable of the expression of at least one nucleic acid encoding at least one C. perfringens antigen. As used herein, the phrase “ C. perfringens antigen” refers to an antigen that elicits an immune response against C. perfringens . In an exemplary embodiment, the C. perfringens antigen elicits a protective immune response against C. perfringens. Non-limiting examples of C. perfringens antigens may include PlcC, or NetB (otherwise referred to as CpbX), GDP, PFOR, FBA, HP, or a fragment thereof. In other embodiments, the antigen is NetB, tPFOR, or tHP.
It is not necessary that the nucleic acid encoding a C. perfringens antigen comprise the complete nucleic acid sequence of the antigen. It is only necessary that the C. perfringens antigen sequence used be capable of eliciting an immune response. The antigen may be one that was not found in that exact form in the parent organism. For example, a sequence coding for an antigen comprising 100 amino acid residues may be transferred in part into a recombinant bacterium so that a peptide comprising only 75, 65, 55, 45, 35, 25, 15, or even 10, amino acid residues is produced by the recombinant bacterium. Alternatively, if the amino acid sequence of a particular C. perfringens antigen or fragment thereof is known, it may be possible to chemically synthesize the nucleic acid fragment or analog thereof by means of automated nucleic acid sequence synthesizers, PCR, or the like and introduce said nucleic acid sequence into the appropriate copy number vector.
In certain embodiments, a C. perfringens antigen of the invention may comprise a B cell epitope or a T cell epitope. Alternatively, an antigen to which an immune response is desired may be expressed as a fusion to a carrier protein that contains a strong promiscuous T cell epitope and/or serves as an adjuvant and/or facilitates presentation of the antigen to enhance, in all cases, the immune response to the antigen or its component part. This can be accomplished by methods known in the art. Fusion to tetnus toxin fragment C, CT-B, LT-B and hepatitis virus B core are particularly useful for these purposes, although other epitope presentation systems are well known in the art.
In further embodiments, a nucleic acid sequence encoding an antigen of the invention may comprise a secretion signal. Non-limiting examples of suitable secretion signals may include the bla, dsbA, eltII-B, or ompA secretion signals. In other embodiments, an antigen of the invention may be toxic to the recombinant bacterium.
In another alternative, a recombinant bacterium may comprise a long sequence of nucleic acid encoding several nucleic acid sequence products, one or all of which may be C. perfringens antigens. In some embodiments, the expression of at least one, at least two, at least three, at least four, at least five, at least six, or more nucleic acids encoding C. perfringens antigens is regulated in a bacterium of the invention. These antigens may be encoded by two or more open reading frames operably linked to be expressed coordinately as an operon, wherein each antigen is synthesized independently. Alternatively, the two or more antigens may be encoded by a single open reading frame such that the antigens are synthesized as a fusion protein.
Methods of expressing an antigen in a recombinant bacterium are known in the art. In certain embodiments, vectors, as detailed below, may be used to express an antigen. For more details, see the examples.
In many cases, the high level expression of a nucleic acid sequence encoding an antigen in a bacterium reduces the bacterium's fitness, such that the bacterium grows slowly, is susceptible to stresses encountered in the host, and is generally less able to effectively colonize effector lymphoid tissues. High level expression of a nucleic acid sequence encoding an antigen, however, is highly desirable to maximize induction of an immune response against the antigen. Consequently, the phrase “regulated expression of a nucleic acid encoding at least one C. perfringens antigen” refers to expression of the nucleic acid encoding at least one C. perfringens antigen in a bacterium such that the bacterium is capable of colonizing a host at levels similar to a wild-type bacterium, and yet is still capable of eliciting an immune response against C. perfringens when administered to the host. Methods of regulating expression of at least one C. perfringens antigen are discussed in detail below.
i. Chromosomally Integrated Nucleic Acid Sequence Encoding a Repressor
In one embodiment, the expression of a nucleic acid sequence encoding a C. perfringens antigen is regulated by a chromosomally integrated nucleic acid sequence encoding a repressor and a vector. For instance, a recombinant bacterium of the invention that is capable of the regulated expression of a nucleic acid sequence encoding at least one C. perfringens antigen may comprise, in part, at least one chromosomally integrated nucleic acid sequence encoding a repressor. Typically, the nucleic acid sequence encoding a repressor is operably linked to a regulatable promoter. The nucleic acid sequence encoding a repressor and/or the promoter may be modified from the wild-type nucleic acid sequence so as to optimize the expression level of the nucleic acid sequence encoding the repressor.
Methods of chromosomally integrating a nucleic acid sequence encoding a repressor operably-linked to a regulatable promoter are known in the art and detailed in the examples. Generally speaking, the nucleic acid sequence encoding a repressor should not be integrated into a locus that disrupts colonization of the host by the recombinant bacterium, or attenuates the bacterium. In one embodiment, the nucleic acid sequence encoding a repressor may be integrated into the relA nucleic acid sequence. In another embodiment, the nucleic acid sequence encoding a repressor may be integrated into the endA nucleic acid sequence.
In some embodiments, at least one nucleic acid sequence encoding a repressor is chromosomally integrated. In other embodiments, at least two, or at least three nucleic acid sequences encoding repressors may be chromosomally integrated into the recombinant bacterium. If there is more than one nucleic acid sequence encoding a repressor, each nucleic acid sequence encoding a repressor may be operably linked to a regulatable promoter, such that each promoter is regulated by the same compound or condition. Alternatively, each nucleic acid sequence encoding a repressor may be operably linked to a regulatable promoter, each of which is regulated by a different compound or condition.
A. Repressor
As used herein, “repressor” refers to a biomolecule that represses transcription from one or more promoters. Generally speaking, a suitable repressor of the invention is synthesized in high enough quantities during the in vitro growth of the bacterial strain to repress the transcription of the nucleic acid encoding an antigen of interest on the vector, as detailed below, and not impede the in vitro growth of the strain. Additionally, a suitable repressor will generally be substantially stable, i.e. not subject to proteolytic breakdown. Furthermore, a suitable repressor will be diluted by about half at every cell division after expression of the repressor ceases, such as in a non-permissive environment (e.g. an animal or human host).
The choice of a repressor depends, in part, on the species of the recombinant bacterium used. For instance, the repressor is usually not derived from the same species of bacteria as the recombinant bacterium. For instance, the repressor may be derived from E. coli if the recombinant bacterium is from the genus Salmonella . Alternatively, the repressor may be from a bacteriophage.
Suitable repressors are known in the art, and may include, for instance, LacI of E. coli, C2 encoded by bacteriophage P22, or C1 encoded by bacteriophage λ. Other suitable repressors may be repressors known to regulate the expression of a regulatable nucleic acid sequence, such as nucleic acid sequences involved in the uptake and utilization of sugars. In one embodiment, the repressor is LacI. In another embodiment, the repressor is C2. In yet another embodiment, the repressor is C1.
B. Regulatable Promoter
The chromosomally integrated nucleic acid sequence encoding a repressor is operably linked to a regulatable promoter. The term “promoter”, as used herein, may mean a synthetic or naturally-derived molecule that is capable of conferring, activating or enhancing expression of a nucleic acid. A promoter may comprise one or more specific transcriptional regulatory sequences to further enhance expression and/or to alter the spatial expression and/or temporal expression of a nucleic acid. The term “operably linked,” as used herein, means that expression of a nucleic acid is under the control of a promoter with which it is spatially connected. A promoter may be positioned 5′ (upstream) of the nucleic acid under its control. The distance between the promoter and a nucleic acid to be expressed may be approximately the same as the distance between that promoter and the native nucleic acid sequence it controls. As is known in the art, variation in this distance may be accommodated without loss of promoter function.
The regulated promoter used herein generally allows transcription of the nucleic acid sequence encoding a repressor while in a permissive environment (i.e. in vitro growth), but ceases transcription of the nucleic acid sequence encoding a repressor while in a non-permissive environment (i.e. during growth of the bacterium in an animal or human host). For instance, the promoter may be sensitive to a physical or chemical difference between the permissive and non-permissive environment. Suitable examples of such regulatable promoters are known in the art.
In some embodiments, the promoter may be responsive to the level of arabinose in the environment. Generally speaking, arabinose may be present during the in vitro growth of a bacterium, while typically absent from host tissue. In one embodiment, the promoter is derived from an araC-P BAD system. The araC-P BAD system is a tightly regulated expression system that has been shown to work as a strong promoter induced by the addition of low levels of arabinose. The araC-araBAD promoter is a bidirectional promoter controlling expression of the araBAD nucleic acid sequences in one direction, and the araC nucleic acid sequence in the other direction. For convenience, the portion of the araC-araBAD promoter that mediates expression of the araBAD nucleic acid sequences, and which is controlled by the araC nucleic acid sequence product, is referred to herein as P BAD . For use as described herein, a cassette with the araC nucleic acid sequence and the araC-araBAD promoter may be used. This cassette is referred to herein as araC-P BAD . The AraC protein is both a positive and negative regulator of P BAD . In the presence of arabinose, the AraC protein is a positive regulatory element that allows expression from P BAD . In the absence of arabinose, the AraC protein represses expression from P BAD . This can lead to a 1,200-fold difference in the level of expression from P BAD . Full induction of P BAD transcription also requires binding of the Crp-cAMP complex, which is a key regulator of catabolite repression.
Other enteric bacteria contain arabinose regulatory systems homologous to the araC araBAD system from E. coli. For example, there is homology at the amino acid sequence level between the E. coli and the S. Typhimurium AraC proteins, and less homology at the DNA level. However, there is high specificity in the activity of the AraC proteins. For example, the E. coli AraC protein activates only E. coli P BAD (in the presence of arabinose) and not S. Typhimurium P BAD . Thus, an arabinose regulated promoter may be used in a recombinant bacterium that possesses a similar arabinose operon, without substantial interference between the two, if the promoter and the operon are derived from two different species of bacteria.
Generally speaking, the concentration of arabinose necessary to induce expression is typically less than about 2%. In some embodiments, the concentration is less than about 1.5%, 1%, 0.5%, 0.2%, 0.1%, or 0.05%. In other embodiments, the concentration is 0.05% or below, e.g. about 0.04%, 0.03%, 0.02%, or 0.01%. In an exemplary embodiment, the concentration is about 0.05%.
In other embodiments, the promoter may be responsive to the level of maltose in the environment. Generally speaking, maltose may be present during the in vitro growth of a bacterium, while typically absent from host tissue. The malT nucleic acid encodes MalT, a positive regulator of four maltose-responsive promoters (P PQ , P EFG , P KBM , and P S ). The combination of malT and a mal promoter creates a tightly regulated expression system that has been shown to work as a strong promoter induced by the addition of maltose (6). Unlike the araC-P BAD system, malT is expressed from a promoter (P T ) functionally unconnected to the other mal promoters. P T is not regulated by MalT. The malEFG-malKBM promoter is a bidirectional promoter controlling expression of the malKBM nucleic acid sequences in one direction, and the malEFG nucleic acid sequences in the other direction. For convenience, the portion of the malEFG-malKBM promoter that mediates expression of the malKBM nucleic acid sequence, and which is controlled by the malT nucleic acid sequence product, is referred to herein as P KBM , and the portion of the malEFG-malKBM promoter that mediates expression of the malEFG nucleic acid sequence, and that is controlled by the malT nucleic acid sequence product, is referred to herein as P EFG . Full induction of P KBM requires the presence of the MalT binding sites of P EFG . For use in the vectors and systems described herein, a cassette with the malT nucleic acid sequence and one of the mal promoters may be used. This cassette is referred to herein as malT-P mal . In the presence of maltose, the MalT protein is a positive regulatory element that allows expression from P mal .
In still other embodiments, the promoter may be sensitive to the level of rhamnose in the environment. Analogous to the araC-P BAD system described above, the rhaRS-P rhaB activator-promoter system is tightly regulated by rhamnose. Expression from the rhamnose promoter (P rha ) is induced to high levels by the addition of rhamnose, which is common in bacteria but rarely found in host tissues. The nucleic acid sequences rhaBAD are organized in one operon that is controlled by the P rhaBAD promoter. This promoter is regulated by two activators, RhaS and RhaR, and the corresponding nucleic acid sequences belong to one transcription unit that is located in the opposite direction of the rhaBAD nucleic acid sequences. If L-rhamnose is available, RhaR binds to the P rhaRS promoter and activates the production of RhaR and RhaS. RhaS together with L-rhamnose in turn binds to the P rhaBAD and the P rhaT promoter and activates the transcription of the structural nucleic acid sequences. Full induction of rhaBAD transcription also requires binding of the Crp-cAMP complex, which is a key regulator of catabolite repression.
Although both L-arabinose and L-rhamnose act directly as inducers for expression of regulons for their catabolism, important differences exist in regard to the regulatory mechanisms. L-Arabinose acts as an inducer with the activator AraC in the positive control of the arabinose regulon. However, the L-rhamnose regulon is subject to a regulatory cascade; it is therefore subject to even tighter control than the araC P BAD system. L-Rhamnose acts as an inducer with the activator RhaR for synthesis of RhaS, which in turn acts as an activator in the positive control of the rhamnose regulon. In the present invention, rhamnose may be used to interact with the RhaR protein and then the RhaS protein may activate transcription of a nucleic acid sequence operably-linked to the P rhaBAD promoter.
In still other embodiments, the promoter may be sensitive to the level of xylose in the environment. The xylR-P xylA system is another well-established inducible activator-promoter system. Xylose induces xylose-specific operons (xylE, xylFGHR, and xylAB) regulated by XylR and the cyclic AMP-Crp system. The XylR protein serves as a positive regulator by binding to two distinct regions of the xyl nucleic acid sequence promoters. As with the araC-P BAD system described above, the xylR-P xylAB and/or xylR-P xylFGH regulatory systems may be used in the present invention. In these embodiments, xylR P xylAB xylose interacting with the XyIR protein activates transcription of nucleic acid sequences operably-linked to either of the two P xyl promoters.
The nucleic acid sequences of the promoters detailed herein are known in the art, and methods of operably-linking them to a chromosomally integrated nucleic acid sequence encoding a repressor are known in the art and detailed in the examples.
C. Modification to Optimize Expression
A nucleic acid sequence encoding a repressor and regulatable promoter detailed above, for use in the present invention, may be modified so as to optimize the expression level of the nucleic acid sequence encoding the repressor. The optimal level of expression of the nucleic acid sequence encoding the repressor may be estimated, or may be determined by experimentation. Such a determination should take into consideration whether the repressor acts as a monomer, dimer, trimer, tetramer, or higher multiple, and should also take into consideration the copy number of the vector encoding the antigen of interest, as detailed below. In an exemplary embodiment, the level of expression is optimized so that the repressor is synthesized while in the permissive environment (i.e. in vitro growth) at a level that substantially inhibits the expression of a nucleic acid sequence encoding a C. perfringens antigen, and is substantially not synthesized in a non-permissive environment, thereby allowing expression of the nucleic acid encoding a C. perfringens antigen.
As stated above, the level of expression may be optimized by modifying the nucleic acid sequence encoding the repressor and/or promoter. As used herein, “modify” refers to an alteration of the nucleic acid sequence of the repressor and/or promoter that results in a change in the level of transcription of the nucleic acid sequence encoding the repressor, or that results in a change in the level of synthesis of the repressor. For instance, in one embodiment, modify may refer to altering the start codon of the nucleic acid sequence encoding the repressor. Generally speaking, a GTG or TTG start codon, as opposed to an ATG start codon, may decrease translation efficiency ten-fold. In another embodiment, modify may refer to altering the Shine-Dalgarno (SD) sequence of the nucleic acid sequence encoding the repressor. The SD sequence is a ribosomal binding site generally located 6-7 nucleotides upstream of the start codon. The SD consensus sequence is AGGAGG, and variations of the consensus sequence may alter translation efficiency. In yet another embodiment, modify may refer to altering the distance between the SD sequence and the start codon. In still another embodiment, modify may refer to altering the −35 sequence for RNA polymerase recognition. In a similar embodiment, modify may refer to altering the −10 sequence for RNA polymerase binding. In an additional embodiment, modify may refer to altering the number of nucleotides between the −35 and −10 sequences. In an alternative embodiment, modify may refer to optimizing the codons of the nucleic acid sequence encoding the repressor to alter the level of translation of the mRNA encoding the repressor. For instance, non-A rich codons initially after the start codon of the nucleic acid sequence encoding the repressor may not maximize translation of the mRNA encoding the repressor. Similarly, the codons of the nucleic acid sequence encoding the repressor may be altered so as to mimic the codons from highly synthesized proteins of a particular organism. In a further embodiment, modify may refer to altering the GC content of the nucleic acid sequence encoding the repressor to enhance the stability of expression in Salmonella.
In some embodiments, more than one modification or type of modification may be performed to optimize the expression level of the nucleic acid sequence encoding the repressor. For instance, at least one, two, three, four, five, six, seven, eight, or nine modifications, or types of modifications, may be performed to optimize the expression level of the nucleic acid sequence encoding the repressor.
By way of non-limiting example, when the repressor is LacI, then the nucleic acid sequence of LacI and the promoter may be altered so as to increase the level of LacI synthesis. In one embodiment, the start codon of the LacI repressor may be altered from GTG to ATG. In another embodiment, the SD sequence may be altered from AGGG to AGGA. In yet another embodiment, the codons of lacI may be optimized according to the codon usage for highly synthesized proteins of Salmonella . In a further embodiment, the start codon of lacI may be altered, the SD sequence may be altered, and the codons of lacI may be optimized.
Methods of modifying the nucleic acid sequence encoding the repressor and/or the regulatable promoter are known in the art and detailed in the examples.
D. Transcription Termination Sequence
In some embodiments, the chromosomally integrated nucleic acid sequence encoding the repressor further comprises a transcription termination sequence. A transcription termination sequence may be included to prevent inappropriate expression of nucleic acid sequences adjacent to the chromosomally integrated nucleic acid sequence encoding the repressor and regulatable promoter.
E. Vector
A recombinant bacterium of the invention that is capable of the regulated expression of at least one nucleic acid sequence encoding a C. perfringens antigen may also comprise, in part, a vector. The vector comprises a nucleic acid sequence encoding at least one C. perfringens antigen operably linked to a promoter. The promoter is regulated by the chromosomally encoded repressor, such that the expression of the nucleic acid sequence encoding an antigen is repressed during in vitro growth of the bacterium, but the bacterium is capable of high level synthesis of the antigen in an animal or human host.
As used herein, “vector” refers to an autonomously replicating nucleic acid unit. The present invention can be practiced with any known type of vector, including viral, cosmid, phasmid, and plasmid vectors. The most preferred type of vector is a plasmid vector.
As is well known in the art, plasmids and other vectors may possess a wide array of promoters, multiple cloning sequences, transcription terminators, etc., and vectors may be selected so as to control the level of expression of the nucleic acid sequence encoding an antigen by controlling the relative copy number of the vector. In some instances in which the vector might encode a surface localized adhesin as the antigen, or an antigen capable of stimulating T-cell immunity, it may be preferable to use a vector with a low copy number such as at least two, three, four, five, six, seven, eight, nine, or ten copies per bacterial cell. A non-limiting example of a low copy number vector may be a vector comprising the pSC101 ori.
In other cases, an intermediate copy number vector might be optimal for inducing desired immune responses. For instance, an intermediate copy number vector may have at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 copies per bacterial cell. A non-limiting example of an intermediate copy number vector may be a vector comprising the p15A ori.
In still other cases, a high copy number vector might be optimal for the induction of maximal antibody responses or mucosal immune responses. A high copy number vector may have at least 31, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 copies per bacterial cell. In some embodiments, a high copy number vector may have at least 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, or 400 copies per bacterial cell. Non-limiting examples of high copy number vectors may include a vector comprising the pBR on or the pUC ori.
Additionally, vector copy number may be increased by selecting for mutations that increase plasmid copy number. These mutations may occur in the bacterial chromosome but are more likely to occur in the plasmid vector.
Preferably, vectors used herein do not comprise antibiotic resistance markers to select for maintenance of the vector.
A vector may comprise one or more than one nucleic acid sequences encoding a C. perfringens antigen, whether regulated or not, as detailed above.
F. Promoter Regulated by Repressor
The vector comprises a nucleic acid sequence encoding at least one C. perfringens antigen operably-linked to a promoter regulated by the repressor, encoded by a chromosomally integrated nucleic acid sequence. One of skill in the art would recognize, therefore, that the selection of a repressor dictates, in part, the selection of the promoter operably-linked to a nucleic acid sequence encoding an antigen of interest. For instance, if the repressor is LacI, then the promoter may be selected from the group consisting of LacI responsive promoters, such as P trc , P lac , P T7lac and P tac . If the repressor is C2, then the promoter may be selected from the group consisting of C2 responsive promoters, such as P22 promoters P L and P R . If the repressor is C1, then the promoter may be selected from the group consisting of C1 responsive promoters, such as λ promoters P L and P R .
In each embodiment herein, the promoter regulates expression of a nucleic acid sequence encoding the antigen, such that expression of the nucleic acid sequence encoding an antigen is repressed when the repressor is synthesized (i.e. during in vitro growth of the bacterium), but expression of the nucleic acid sequence encoding an antigen is high when the repressor is not synthesized (i.e. in an animal or human host). Generally speaking, the concentration of the repressor will decrease with every cell division after expression of the nucleic acid sequence encoding the repressor ceases. In some embodiments, the concentration of the repressor decreases enough to allow high level expression of the nucleic acid sequence encoding a C. perfringens antigen after about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 divisions of the bacterium. In an exemplary embodiment, the concentration of the repressor decreases enough to allow high level expression of the nucleic acid sequence encoding a C. perfringens antigen after about 5 divisions of the bacterium in an animal or human host.
In certain embodiments, the promoter may comprise other regulatory elements. For instance, the promoter may comprise lacO if the repressor is LacI. This is the case with the lipoprotein promoter P lpp that is regulated by LacI since it possesses the LacI binding domain lacO.
In one embodiment, the repressor is a LacI repressor and the promoter is P trc .
G. Expression of the Nucleic Acid Sequence Encoding an Antigen
As detailed above, generally speaking the expression of the nucleic acid sequence encoding the C. perfringens antigen should be repressed when the repressor is synthesized. For instance, if the repressor is synthesized during in vitro growth of the bacterium, expression of the nucleic acid sequence encoding the C. perfringens antigen should be repressed. Expression may be “repressed” or “partially repressed” when it is about 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 1%, or even less than 1% of the expression under non-repressed conditions. Thus although the level of expression under conditions of “complete repression” might be exceeding low, it is likely to be detectable using very sensitive methods since repression can never by absolute.
Conversely, the expression of the nucleic acid sequence encoding the antigen should be high when the expression of the nucleic acid sequence encoding the repressor is repressed. For instance, if the nucleic acid sequence encoding the repressor is not expressed during growth of the recombinant bacterium in the host, the expression of the nucleic acid sequence encoding the antigen should be high. As used herein, “high level” expression refers to expression that is strong enough to elicit an immune response to the antigen. Consequently, the copy number correlating with high level expression can and will vary depending on the antigen and the type of immune response desired. Methods of determining whether an antigen elicits an immune response such as by measuring antibody levels or antigen-dependant T cell populations or antigen-dependant cytokine levels are known in the art, and methods of measuring levels of expression of antigen encoding sequences by measuring levels of mRNA transcribed or by quantitating the level of antigen synthesis are also known in the art. For more details, see the examples.
ii. Other Ways of Regulating at Least One C. Perfringens Antigen
The invention also encompasses other means of regulating the expression of a nucleic acid sequence encoding at least one C. perfringens antigen in a recombinant bacterium. For instance, in one embodiment, the C. perfringens antigen of interest may be encoded on an extra-chromosomal vector. This can be used in the context of a balanced-lethal host-vector system. Alternatively, the nucleotide sequence encoding the antigen of interest may be inserted into the chromosome but have its expression controlled by a regulatable system, e.g., LacI or C2, as with the regulated gene encoding the antigen of interest on an extra-chromosomal vector (e.g., a plasmid).
(c) Attenuation of the Recombinant Bacterium
In each of the above embodiments, a recombinant bacterium of the invention capable of regulated expression may also be attenuated. “Attenuated” refers to the state of the bacterium wherein the bacterium has been weakened from its wild type fitness by some form of recombinant or physical manipulation. This includes altering the genotype of the bacterium to reduce its ability to cause disease. However, the bacterium's ability to colonize the gut (in the case of Salmonella ) and induce immune responses is, preferably, not substantially compromised. For instance, in one embodiment, regulated attenuation allows the recombinant bacterium to express one or more nucleic acids encoding products important for the bacterium to withstand stresses encountered in the host after immunization. This allows efficient invasion and colonization of lymphoid tissues before the recombinant bacterium is regulated to display the attenuated phenotype.
In one embodiment, a recombinant bacterium may be attenuated as described in section I(a)i above, i.e. regulating LPS O-antigen. In another embodiment, a recombinant bacterium may be attenuated as described in section (c)i below. In which case, both regulated attenuation and regulated expression of an enteric antigen encoding sequence may be dependent upon an arabinose regulatable system. Consequently, the concentration of arabinose needed for optimal expression of the regulated enteric antigen encoding sequence may not be the same as the concentration for optimal expression of attenuation. In an exemplary embodiment, the concentration of arabinose for the optimization of both regulated attenuation and regulated expression of sequences encoding antigen will be substantially the same.
Accordingly, the promoter and/or the nucleic acid sequence encoding an attenuation protein may be modified to optimize the system. Methods of modification are detailed above. Briefly, for example, the SD ribosome binding sequence may be altered, and/or the start codon may be altered from ATG to GTG for the nucleic acid sequences fur and phoPQ, so that the production levels of Fur and PhoPQ are optimal for both the regulated attenuation phenotype and the regulated expression when growing strains with a given concentration of arabinose. One of skill in the art will appreciate that other nuceic acid sequences, in addition to fur and phoPQ, may also be altered as described herein in combination with other well-known protocols. In addition, these attenuating nucleic acid sequences may be regulated by other systems using well-established protocols known to one of skill in the art. For example, they may be regulated using with promoters dependent on addition of maltose, rhamnose, or xylose rather than arabinose.
Other methods of attenuation are known in the art. For instance, attenuation may be accomplished by altering (e.g., deleting) native nucleic acid sequences found in the wild type bacterium. For instance, if the bacterium is Salmonella , non-limiting examples of nucleic acid sequences which may be used for attenuation include: a pab nucleic acid sequence, a pur nucleic acid sequence, an aro nucleic acid sequence, asd, a dap nucleic acid sequence, nadA, pncB, galE, pmi, fur, rpsL, ompR, htrA, hemA, cdt, cya, crp, dam, phoP, phoQ, rfc, poxA, galU, mviA, sodC, recA, ssrA, sirA, inv, hilA, rpoE, flgM, tonB, slyA, and any combination thereof. Exemplary attenuating mutations may be aroA, aroC, aroD, cdt, cya, crp, phoP, phoQ, ompR, galE, and htrA.
In certain embodiments, the above nucleic acid sequences may be placed under the control of a sugar regulated promoter wherein the sugar is present during in vitro growth of the recombinant bacterium, but substantially absent within an animal or human host. The cessation in transcription of the nucleic acid sequences listed above would then result in attenuation and the inability of the recombinant bacterium to induce disease symptoms.
The bacterium may also be modified to create a balanced-lethal host-vector system, although other types of systems may also be used (e.g., creating complementation heterozygotes). For the balanced-lethal host-vector system, the bacterium may be modified by manipulating its ability to synthesize various essential constituents needed for synthesis of the rigid peptidoglycan layer of its cell wall. In one example, the constituent is diaminopimelic acid (DAP). Various enzymes are involved in the eventual synthesis of DAP. In one example, the bacterium is modified by using a ΔasdA mutation to eliminate the bacterium's ability to produce β-aspartate semialdehyde dehydrogenase, an enzyme essential for the synthesis of DAP. One of skill in the art can also use the teachings of U.S. Pat. No. 6,872,547 for other types of mutations of nucleic acid sequences that result in the abolition of the synthesis of DAP. These nucleic acid sequences may include, but are not limited to, dapA, dapB, dapC, dapD, dapE, dapF, and asd. Other modifications that may be employed include modifications to a bacterium's ability to synthesize D-alanine or to synthesize D-glutamic acid (e.g., Δmurl mutations), which are both unique constituents of the peptidoglycan layer of the bacterial cell wall.
Yet another balanced-lethal host-vector system comprises modifying the bacterium such that the synthesis of an essential constituent of the rigid layer of the bacterial cell wall is dependent on a nutrient (e.g., arabinose) that can be supplied during the growth of the microorganism. For example, a bacterium may—comprise the ΔP murA :TT araC P BAD murA deletion-insertion mutation. This type of mutation makes synthesis of muramic acid (another unique essential constituent of the peptidoglycan layer of the bacterial cell wall) dependent on the presence of arabinose that can be supplied during growth of the bacterium in vitro.
When arabinose is absent, however, as it is in an animal or human host, the essential constituent of the peptidoglycan layer of the cell wall is not synthesized. This mutation represents an arabinose dependant lethal mutation. In the absence of arabinose, synthesis of muramic acid ceases and lysis of the bacterium occurs because the peptidoglycan layer of the cell wall is not synthesized. It is not possible to generate AmurA mutations because they are lethal. The necessary nutrient, a phosphorylated muramic acid, cannot be exogenously supplied because enteric bacteria cannot take the nutrient up from the media. Recombinant bacteria with a ΔP murA ::TT araC P BAD murA deletion-insertion mutation grown in the presence of arabinose exhibit effective colonization of effector lymphoid tissues after oral vaccination prior to undergoing lysis due to the inability to synthesize muramic acid.
Similarly, various embodiments may comprise the araC P BAD c2 cassette inserted into the asd nucleic acid sequence that encodes aspartate semialdehyde dehydrogenase. Since the araC nucleic acid sequence is transcribed in a direction that could lead to interference in the expression of adjacent nucleic acid sequences and adversely affect vaccine strain performance, a transcription termination (TT) sequence is generally inserted 3′ to the araC nucleic acid sequence. The chromosomal asd nucleic acid sequence is typically inactivated to enable use of plasmid vectors encoding the wild-type asd nucleic acid sequence in the balanced lethal host-vector system. This allows stable maintenance of plasmids in vivo in the absence of any drug resistance attributes that are not permissible in live bacterial vaccines. In some of these embodiments, the wild-type asd nucleic acid sequence may be encoded by the vector described above.
In one embodiment, ΔasdA27::TT araC P BAD c2 has an improved SD sequence and a codon optimized c2 nucleic acid sequence. The C2 repressor synthesized in the presence of arabinose is used to repress nucleic acid sequence expression from P22 P R and P L promoters. In another embodiment, ΔasdA27::TT araC P BAD c2 has the 1104 base-pair asd nucleic acid sequence deleted (1 to 1104, but not including the TAG stop codon) and the 1989 base-pair fragment containing T4 ipIII TT araC P BAD c2 inserted. The c2 nucleic acid sequence in ΔasdA27::TT araC P BAD c2 has a SD sequence that was optimized to TAAGGAGGT. It also has an improved P BAD promoter such that the −10 sequence is improved from TACTGT to TATAAT. Furthermore, it has a codon optimized c2 nucleic acid sequence, in which the second codon was modified from AAT to AAA.
In further embodiments, the bacterium may be attenuated by regulating the murA nucleic acid sequence encoding the first enzyme in muramic acid synthesis and the asd nucleic acid sequence essential for DAP synthesis. These embodiments may comprise the chromosomal deletion-insertion mutations ΔasdA19::TT araC P BAD c2 or □asdA27::TT araC P BAD c2 and ΔP murA7 ::araC P BAD murA or □P murA12 ::TT araC P BAD murA or ΔP murA25 ::TT araC P BAD murA. This host-vector grows in LB broth with 0.1% L-arabinose, but is unable to grow in or on media devoid of arabinose since it undergoes cell wall-less death by lysis. In some embodiments of the invention, the recombinant bacterium may comprise araBAD and araE mutations to preclude breakdown and leakage of internalized arabinose such that asd and murA nucleic acid sequence expression continues for a cell division or two after oral immunization into an environment that is devoid of external arabinose. (For example a strain with the ΔP murA7 ::TT araC P BAD murA deletion-insertion mutation undergoes about two cell divisions and then commences to lyse in media made of mouse or chicken feed or chicken breast meat, unless they are supplemented with arabinose). Either GTG or TTG start codons for the murA and asd nucleic acid sequences are important to decrease translation efficiency on multi-copy plasmids. For instance plasmid vector pYA3681 contains the murA nucleic acid sequence (with altered start codon sequences to decrease translation efficiency) under the control of an araC P BAD promoter. Also the second nucleic acid sequence under the direction of this promoter is the asd nucleic acid sequence (with altered start codon sequences to decrease translation efficiency). The P22 P R promoter is in the anti-sense direction of both the asd nucleic acid sequence and the murA nucleic acid sequence. The P22 P R is repressed by the C2 repressor made during growth of the strain in media with arabinose (due to the ΔasdA19::TT araC P BAD c2 deletion-insertion). However C2 concentration decreases due to cell division in vivo to cause P R directed synthesis of anti-sense mRNA to further block translation of asd and murA mRNA. The araC P BAD sequence is also not from E. coli B/r as originally described but represents a sequence derived from E. coli K-12 strain χ289 with tighter control and less leakiness in the absence of arabinose. In the preferred embodiment, transcription terminators (TT) flank all of the domains for controlled lysis, replication, and expression so that expression in one domain does not affect the activities of another domain. As a safety feature, the plasmid asd nucleic acid sequence does not replace the chromosomal asd mutation since they have a deleted sequence in common, consequently, the E. coli murA nucleic acid sequence was used in the plasmid instead of using the Salmonella murA nucleic acid sequence. The recombinant bacterium of this embodiment is avirulent at oral doses in excess of 10 9 CFU to BALB/c mice. In addition to being fully attenuated, this construction exhibits complete biological containment with no in vivo recombinant bacteria survivors detectable after 21 days and no recombinant bacteria survivors during or after excretion. This property enhances vaccine safety and minimizes the potential for vaccination of individuals not intended for vaccination.
i. Regulated Attenuation
The present invention also encompasses a recombinant bacterium capable of regulated attenuation. Generally speaking, the bacterium comprises a chromosomally integrated regulatable promoter. The promoter replaces the native promoter of, and is operably linked to, at least one nucleic acid sequence encoding an attenuation protein, such that the absence of the function of the protein renders the bacterium attenuated. In some embodiments, the promoter is modified to optimize the regulated attenuation.
In each of the above embodiments described herein, more than one method of attenuation may be used. For instance, a recombinant bacterium of the invention may comprise a regulatable promoter chromosomally integrated so as to replace the native promoter of, and be operably linked to, at least one nucleic acid sequence encoding an attenuation protein, such that the absence of the function of the protein renders the bacterium attenuated, and the bacterium may comprise another method of attenuation detailed in section I above.
A. Attenuation Protein
Herein, “attenuation protein” is meant to be used in its broadest sense to encompass any protein the absence of which attenuates a bacterium. For instance, in some embodiments, an attenuation protein may be a protein that helps protect a bacterium from stresses encountered in the gastrointestinal tract or respiratory tract. Non-limiting examples may be the RpoS, PhoPQ, OmpR, Fur, and Crp proteins. In other embodiments, the protein may be a necessary component of the cell wall of the bacterium, such as the protein encoded by murA. In still other embodiments, the protein may be listed in Section i above.
The native promoter of at least one, two, three, four, five, or more than five attenuation proteins may be replaced by a regulatable promoter as described herein. In one embodiment, the promoter of one of the proteins selected from the group comprising RpoS, PhoPQ, OmpR, Fur, and Crp may be replaced. In another embodiment, the promoter of two, three, four or five of the proteins selected from the group comprising RpoS, PhoPQ, OmpR, Fur, and Crp may be replaced.
If the promoter of more than one attenuation protein is replaced, each promoter may be replaced with a regulatable promoter, such that the expression of each attenuation protein encoding sequence is regulated by the same compound or condition. Alternatively, each promoter may be replaced with a different regulatable promoter, such that the expression of each attenuation protein encoding sequence is regulated by a different compound or condition such as by the sugars arabinose, maltose, rhamnose or xylose.
B. Regulatable Promoter
The native promoter of a nucleic acid encoding an attenuation protein is replaced with a regulatable promoter operably linked to the nucleic acid sequence encoding an attenuation protein. The term “operably linked,” is defined above.
The regulatable promoter used herein generally allows transcription of the nucleic acid sequence encoding the attenuation protein while in a permissive environment (i.e. in vitro growth), but cease transcription of the nucleic acid sequence encoding an attenuation protein while in a non-permissive environment (i.e. during growth of the bacterium in an animal or human host). For instance, the promoter may be responsive to a physical or chemical difference between the permissive and non-permissive environment. Suitable examples of such regulatable promoters are known in the art and detailed above.
In some embodiments, the promoter may be responsive to the level of arabinose in the environment, as described above. In other embodiments, the promoter may be responsive to the level of maltose, rhamnose, or xylose in the environment, as described above. The promoters detailed herein are known in the art, and methods of operably linking them to a nucleic acid sequence encoding an attenuation protein are known in the art.
In certain embodiments, a recombinant bacterium of the invention may comprise any of the following: ΔP fur ::TT araC P BAD fur, ΔP crp ::TT araC P BAD crp, ΔP phoPQ ::TT araC P BAD phoPQ, or a combination thereof. Growth of such strains in the presence of arabinose leads to transcription of the fur, phoPQ, and/or crp nucleic acid sequences, but nucleic acid sequence expression ceases in a host because there is no free arabinose. Attenuation develops as the products of the fur, phoPQ, and/or the crp nucleic acid sequences are diluted at each cell division. Strains with the ΔP fur and/or the ΔP phoPQ mutations are attenuated at oral doses of 10 9 CFU, even in three-week old mice at weaning. Generally speaking, the concentration of arabinose necessary to induce expression is typically less than about 2%. In some embodiments, the concentration is less than about 1.5%, 1%, 0.5%, 0.2%, 0.1%, or 0.05%. In certain embodiments, the concentration may be about 0.04%, 0.03%, 0.02%, or 0.01%. In an exemplary embodiment, the concentration is about 0.05%. Higher concentrations of arabinose or other sugars may lead to acid production during growth that may inhibit desirable cell densities. The inclusion of mutations such as ΔaraBAD or mutations that block the uptake and/or breakdown of maltose, rhamnose, or xylose, however, may prevent such acid production and enable use of higher sugar concentrations with no ill effects.
When the regulatable promoter is responsive to arabinose, the onset of attenuation may be delayed by including additional mutations, such as ΔaraBAD23, which prevents use of arabinose retained in the cell cytoplasm at the time of oral immunization, and/or ΔaraE25 that enhances retention of arabinose. Thus, inclusion of these mutations may be beneficial in at least two ways: first, enabling higher culture densities, and second enabling a further delay in the display of the attenuated phenotype that may result in higher densities in effector lymphoid tissues to further enhance immunogenicity.
C. Modifications
Attenuation of the recombinant bacterium may be optimized by modifying the nucleic acid sequence encoding an attenuation protein and/or promoter. Methods of modifying a promoter and/or a nucleic acid sequence encoding an attenuation protein are the same as those detailed above with respect to repressors in Section (b).
In some embodiments, more than one modification may be performed to optimize the attenuation of the bacterium. For instance, at least one, two, three, four, five, six, seven, eight or nine modifications may be performed to optimize the attenuation of the bacterium.
In various exemplary embodiments of the invention, the SD sequences and/or the start codons for the fur and/or the phoPQ virulence nucleic acid sequences may be altered so that the production levels of these nucleic acid products are optimal for regulated attenuation. FIG. 8 depicts ΔP fur77 ::TT araC P BAD fur, whose start codon is changed from ATG to GTG, and ΔP fur81 ::TT araC P BAD fur, that has a weakened SD sequence as well as the start codon changed from ATG to GTG. FIG. 9 depicts ΔP phopQ173 ::TT araC P BAD phoPQ, that has modifications to the start codon as well as the second codon, which was changed from ATG to GTG. FIG. 9 also depicts ΔP phoPQ177 ::TT araC P BAD phoPQ, wherein the SD sequence has been changed to the weaker AAGG sequence, the start codon was modified, and the second codon was modified from ATG to GTG.
(d) Eliciting an Immune Response Against at Least Two Salmonella Serotypes
A recombinant bacterium of the invention is generally capable of eliciting an immune response against at least two Salmonella serotypes. This may be accomplished, for instance, by eliminating the serotype-specific LPS O-antigen side chains as discussed above. The remaining LPS core will elicit an immune response, inducing the production of antibodies against the LPS core. Since this LPS core is substantially identical in the several thousand Salmonella enterica serotypes, the antibodies potentially provide immunity against several diverse Salmonella enterica serotypes, such as Typhimurium, Heidelberg, Newport, Infantis, Dublin, Hadar, Kentucky, Thompson, Agona, Ohio, Virchow, Typhi, Enteritidis, and Munchen.
In addition, the elimination of the LPS O-antigen provides the host immune system with better access to the outer membrane proteins of the recombinant bacterium, thereby enhancing induction of immune responses against these outer membrane proteins. In some embodiments, as described below, the outer membrane proteins may be upregulated to further enhance host immune responses to these proteins. Non-limiting examples of outer membrane proteins include proteins involved in iron and manganese uptake, as described below. Iron and manganese are essential nutrients for enteric pathogens and the induction of antibodies that inhibit iron and manganese uptake in effect starves the pathogens, conferring protective immunity on the host. Additionally, since these proteins are homologous among the enteric bacteria, such host immune responses provide immunity against multiple Salmonella enterica serotypes.
The elicited immune response may include, but is not limited to, an innate immune response, a humoral immune response and a cell-mediated immune response. In one embodiment, Th2-dependent mucosal and systemic antibody responses to the C. perfringens antigen(s) are observed. Immune responses may be measured by standard immunological assays known to one of skill in the art. In an exemplary embodiment, the immune response is protective.
(e) crp Cassette
In some embodiments, a recombinant bacterium of the invention may also comprise a ΔP crp ::TT araC P BAD crp deletion-insertion mutation. Since the araC P BAD cassette is dependent both on the presence of arabinose and the binding of the catabolite repressor protein Crp, a ΔP crp ::TT araC P BAD crp deletion-insertion mutation may be included as an additional means to reduce expression of any nucleic acid sequence under the control of the P BAD promoter. This means that when the bacterium is grown in a non-permissive environment (i.e. no arabinose) both the repressor itself and the Crp protein cease to be synthesized, consequently eliminating both regulating signals for the araC P BAD regulated nucleic acid sequence. This double shut off of araC P BAD may constitute an additional safety feature ensuring the genetic stability of the desired phenotypes.
Generally speaking, the activity of the Crp protein requires interaction with cAMP, but the addition of glucose, which may inhibit synthesis of cAMP, decreases the ability of the Crp protein to regulate transcription from the araC P BAD promoter. Consequently, to avoid the effect of glucose on cAMP, glucose may be substantially excluded from the growth media, or variants of crp may be isolated that synthesize a Crp protein that is not dependent on cAMP to regulate transcription from P BAD . This strategy may also be used in other systems responsive to Crp, such as the systems responsive to rhamnose and xylose described above.
(f) Reduction in Fluid Secretion
In some embodiments, a recombinant bacterium of the invention may be modified so as to reduce fluid secretion in the host. For instance, the bacterium may comprise the ΔsopB1925 mutation. Alternatively, the bacterium may comprise the ΔmsbB48 mutation. For more details, see the Examples.
(g) Biological Containment
Under certain embodiments, a live recombinant bacterium may possess the potential to survive and multiply if excreted from a host. This leads to the possibility that individuals not electing to be immunized may be exposed to the recombinant bacterium. Consequently, in certain embodiments, a recombinant bacterium of the invention may comprise one or more mutations that decrease, if not preclude, the ability of Salmonella vaccines to persist in the GI tract of animals.
In another embodiment, a recombinant bacterium of the invention may comprise one or more of the Δ(gmd fcl)-26 or Δ(wcaL-wza)-7, ΔagfBAC811 or Δ(P agfD agfG)-4, ΔbcsABZC2118 or ΔbcsEFG2319 and Δ(yshA-yihW)-157 mutations that block synthesis of colanic acid, thin aggregative fimbriae (i.e., curli), cellulose and extracellular polysaccharide, respectively, all of which contribute to biofilm formation. Since the LPS O-antigen also enables biofilm formation, a strain with the Δpmi-2426, ΔP rfc174 ::TT araC P BAD rfc, and Δ(galE-ybhC)-851 mutations with or without a Δ(gmd-fcl)-26 or Δ(wcaM-wza)-8 mutation would be expected to survive less well in nature because of a dependency on the availability of three sugars simultaneously, an unlikely occurrence. Such a strain would thus exhibit a rough phenotype making it less well to survive in soil or even in the intestinal environment. We also have mutations such as ΔyhiR36 that prevents use of DNA as a nutrient, Δ(shdA-ratB)-64, ΔmisL2 and ΔbigA3 that encode four proteins that enable Salmonella to adhere to host extracellular matrix proteins and ΔackA233 that blocks use of acetate. Some of these mutations have been reported to reduce Salmonella persistence in the intestinal tract of calves and in mice, but this is not so in the intestinal track of chickens. We have yet to put all these mutations abolishing abilty to synthesize biofilms, LPS O-antigen, ability to bind to extracellular matrix proteins, and inability to use DNA and acetate as nutrients, but we surmise that such a strain would exhibit a high level of biological containment and be unable to persist in the intestinal tracks of birds or mammals and not survive in the environment if excreted. A further anticipated benefit of such a strain is the further stripping from the vaccine strain cell surface of macromolecules that might mask immunological surveillance of surface localized LPS core and cross reactive outer membrane antigens. Thus we anticipate an enhancement in levels of induced immune responses to expressed antigens. Indeed, vaccine strains with the Δ(wcaM-wza)-8 mutation synthesize five to ten percent more protective antigen and induce similarly higher antibody titers to this antigen. In exemplary embodiments, recombinant bacterium comprising a biological containment mutation are not adversely effected in their virulence or the ability to colonize mice.
In some embodiments, the recombinant bacterium may comprise a method of regulated delayed lysis in vivo that prevents bacterial persistence in vivo and survival if excreted. These mutations include: Δ(gmd-fcl)-26 that precludes synthesis of colanic acid that can protect cells undergoing cell wall-less death from lysing completely and ΔagfBAC811 that blocks synthesis of thin aggregative fimbriae (curli) that are critical for biofilm formation to enable persistent colonization on bile stones in the gall bladder, ΔasdA27::TT araC P BAD c2 insertion-deletion mutation to impose a requirement for the peptidoglycan constituent DAP and ΔP murA12 ::TTaraC P BAD murA insertion-deletion mutation as a conditional-lethal mutation blocking synthesis of the peptidoglycan constituent muramic acid. The latter two mutations are typically complemented by a regulated delayed lysis plasmid vector such as pYA3681 ( FIG. 2 ) that has an arabinose-dependent expression of asdA and murA genes. A recombinant bacterium comprising such mutations grows normally in the presence of arabinose. In vivo, however, the bacterium ceases to express any nucleic acids encoding the AsdA and MurA enzymes, such that synthesis of the peptidoglycan cell wall layer ceases, ultimately resulting in the lysis of the bacterium. This lysis may result in the release of a bolus of antigen specific for an enteric pathogen, thereby serving as a means to enhance induction of immunity against that enteric pathogen while conferring complete biological containment.
II. Vaccine Compositions and Administration
A recombinant bacterium of the invention may be particularly suited for use as a vaccine. Infection of a host with a Salmonella strain typically leads to colonization of the gut-associated lymphoid tissue (GALT) or Peyer's patches, which leads to the induction of a generalized mucosal immune response to the recombinant bacterium. Further penetration of the bacterium into the mesenteric lymph nodes, liver and spleen may augment the induction of systemic and cellular immune responses directed against the bacterium. Thus the use of recombinant Salmonella for oral immunization stimulates all three branches of the immune system, which is particularly important for immunizing against infectious disease agents that colonize on and/or invade through mucosal surfaces.
A recombinant bacterium of the invention may be administered to a host as a vaccine composition. As used herein, a vaccine composition is a composition designed to elicit an immune response to the recombinant bacterium, including any antigens that may be expressed by the bacterium. In an exemplary embodiment, the immune response is protective. As used herein, “protective” means that the immune response contributes to the lessening of any symptoms associated with infection of a host with the pathogen the antigen was derived from or designed to elicit a response against. For example, a protective antigen from a pathogen, such as Mycobacterium, may induce an immune response that helps to ameliorate symptoms associated with Mycobacterium infection or reduce the morbidity and mortality associated with infection with the pathogen. The use of the term “protective” in this invention does not necessarily require that the host is completely protected from the effects of the pathogen.
Immune responses to antigens are well studied and widely reported. A survey of immunology is given by Paul, W E, Stites D et. al. and Ogra P L. et. al. (11-13). Mucosal immunity is also described by Ogra P L et. al. (14).
Vaccine compositions of the present invention may be administered to any host capable of mounting an immune response. Such hosts may include all vertebrates, for example, mammals, including domestic animals, agricultural animals, laboratory animals, and humans, and various species of birds, including domestic birds and birds of agricultural importance, such as chickens and turkeys. Preferably, the host is a warm-blooded animal. The vaccine can be administered as a prophylactic or for treatment purposes.
In exemplary embodiments, the recombinant bacterium is alive when administered to a host in a vaccine composition of the invention. Suitable vaccine composition formulations and methods of administration are detailed below.
(a) Vaccine Composition
A vaccine composition comprising a recombinant bacterium of the invention may optionally comprise one or more possible additives, such as carriers, preservatives, stabilizers, adjuvants, and other substances.
In one embodiment, the vaccine comprises an adjuvant. Adjuvants, such as aluminum hydroxide or aluminum phosphate, are optionally added to increase the ability of the vaccine to trigger, enhance, or prolong an immune response. In exemplary embodiments, the use of a live attenuated recombinant bacterium may act as a natural adjuvant. The vaccine compositions may further comprise additional components known in the art to improve the immune response to a vaccine, such as T cell co-stimulatory molecules or antibodies, such as anti-CTLA4. Additional materials, such as cytokines, chemokines, and bacterial nucleic acid sequences naturally found in bacteria, like CpG, are also potential vaccine adjuvants.
In another embodiment, the vaccine may comprise a pharmaceutical carrier (or excipient). Such a carrier may be any solvent or solid material for encapsulation that is non-toxic to the inoculated host and compatible with the recombinant bacterium. A carrier may give form or consistency, or act as a diluent. Suitable pharmaceutical carriers may include liquid carriers, such as normal saline and other non-toxic salts at or near physiological concentrations, and solid carriers not used for humans, such as talc or sucrose, or animal feed. Carriers may also include stabilizing agents, wetting and emulsifying agents, salts for varying osmolarity, encapsulating agents, buffers, and skin penetration enhancers. Carriers and excipients as well as formulations for parenteral and nonparenteral drug delivery are set forth in Remington's Pharmaceutical Sciences 19th Ed. Mack Publishing (1995). When used for administering via the bronchial tubes, the vaccine is preferably presented in the form of an aerosol.
Care should be taken when using additives so that the live recombinant bacterium is not killed, or have its ability to effectively colonize lymphoid tissues such as the GALT, NALT and BALT compromised by the use of additives. Stabilizers, such as lactose or monosodium glutamate (MSG), may be added to stabilize the vaccine formulation against a variety of conditions, such as temperature variations or a freeze-drying process.
The dosages of a vaccine composition of the invention can and will vary depending on the recombinant bacterium, the regulated antigen, and the intended host, as will be appreciated by one of skill in the art. Generally speaking, the dosage need only be sufficient to elicit a protective immune response in a majority of hosts. Routine experimentation may readily establish the required dosage. Typical initial dosages of vaccine for oral administration could be about 1×10 7 to 1×10 10 CFU depending upon the age of the host to be immunized. Administering multiple dosages may also be used as needed to provide the desired level of protective immunity.
(b) Methods of Administration
In order to stimulate a preferred response of the GALT, NALT or BALT cells, administration of the vaccine composition directly into the gut, nasopharynx, or bronchus is preferred, such as by oral administration, intranasal administration, gastric intubation or in the form of aerosols, although other methods of administering the recombinant bacterium, such as intravenous, intramuscular, subcutaneous injection or intramammary, intrapenial, intrarectal, vaginal administration, or other parenteral routes, are possible.
In some embodiments, these compositions are formulated for administration by injection (e.g., intraperitoneally, intravenously, subcutaneously, intramuscularly, etc.). Accordingly, these compositions are preferably combined with pharmaceutically acceptable vehicles such as saline, Ringer's solution, dextrose solution, and the like.
In an exemplary embodiment, recombinant bacterium may be administered orally. Oral administration of a composition comprising a recombinant bacterium allows for greater ease in disseminating vaccine compositions for infectious agents to a large number of people in need thereof, for example, in Third World countries or during times of biological warfare. In addition, oral administration allows for attachment of the bacterium to, and invasion of, the gut-associated lymphoid tissues (GALT or Peyer's patches) and/or effective colonization of the mesenteric lymph nodes, liver, and spleen. This route of administration thus enhances the induction of mucosal immune responses as well as systemic and cellular immune responses.
In another embodiment, recombinant bacterium may be administered by coarse spray. The vaccines are administered by this whole-body spray route in an amount that is effective in eliciting an immune response, i.e. antibody and/or cellular immunity. Whole-body spray administration is surprisingly effective for vaccines comprising a live avirulent derivative of an enteropathogenic bacteria such as attenuated Salmonella . Spray administration of enteropathogenic bacteria avoids some of the disadvantages of other routes of administrations in that it does not require individual handling of chicks, it can be administered on day-of-hatch, and is easy to use under conditions normally found in commercial poultry production. The effective doses, which elicit an immune response, are roughly comparable to doses that are effective by the oral route of administration, such as administration in the drinking water.
III. Kits
The invention also encompasses kits comprising any one of the compositions above in a suitable aliquot for vaccinating a host in need thereof. In one embodiment, the kit further comprises instructions for use. In other embodiments, the composition is lyophilized such that addition of a hydrating agent (e.g., buffered saline) reconstitutes the composition to generate a vaccine composition ready to administer, preferably orally.
IV. Methods of Use
A further aspect of the invention encompasses methods of using a recombinant bacterium of the invention. For instance, in one embodiment the invention provides a method for modulating a host's immune system. The method comprises administering to the host an effective amount of a composition comprising a recombinant bacterium of the invention. One of skill in the art will appreciate that an effective amount of a composition is an amount that will generate the desired immune response (e.g., mucosal, humoral or cellular). Methods of monitoring a host's immune response are well-known to physicians, veterinarians, and other skilled practitioners. For instance, assays such as ELISA, and ELISPOT may be used. Effectiveness may be determined by monitoring the amount of the antigen of interest remaining in the host, or by measuring a decrease in disease incidence caused by a given pathogen in a host. For certain pathogens, cultures or swabs taken as biological samples from a host may be used to monitor the existence or amount of pathogen in the individual.
In another embodiment, the invention provides a method for eliciting an immune response against a C. perfringens antigen in a host. The method comprises administering to the host an effective amount of a composition comprising a recombinant bacterium of the invention.
In still another embodiment, a recombinant bacterium of the invention may be used in a method for eliciting an immune response against C. perfringens in a host in need thereof. The method comprises administrating to the host an effective amount of a composition comprising a recombinant bacterium as described herein. In a further embodiment, a recombinant bacterium described herein may be used in a method for ameliorating one or more symptoms of C. perfringens infection in a host in need thereof. For instance, a recombinant bacterium may be used to ameliorate one or more symptoms of necrotic enteritis. The method comprises administering an effective amount of a composition comprising a recombinant bacterium as described herein.
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention. Those of skill in the art should, however, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention, therefore all matter set forth or shown in the accompanying drawings is to be interpreted as illustrative and not in a limiting sense.
EXAMPLES
The following examples illustrate various iterations of the invention.
Example 1
Alpha-Toxin Antigen Expressing Recombinant Bacteria
Materials and Methods
Bacterial strains and growth conditions. The bacterial strains used in this study are listed in Table 1. Clostridium perfringens CP995 and JGS4143 strains are type A strains originally isolated from the intestines of NE-affected chickens. CP995 was used for cloning the alpha toxin C-terminal domain, and JGS4143, (a hypervirulent strain), was used in the challenge experiments. Bacteria were grown in chopped meat broth (CMM) or brain heart infusion (BHI) medium with 0.04% D-cycloserine (BBL, Franklin Lakes, N.J.). Tryptose-sulfate- cycloserine (TSC) agar plates with 5% egg yolk (TSC-EY) or 5% sheep blood agar were used for colony differentiation based on lecithinase or hemolytic activity, respectively. Fluid thioglycolate medium (FTG) was used to cultivate large quantities of bacteria for animal inoculation and for bacterial resuscitation from tissue samples. All C. perfringens cultures were grown at 37° C. under anaerobic condition using BBL GasPak systems. Both CP995 and JGS4143 were confirmed to be negative for β 2 toxin by PCR verification.





TABLE 1



Bacterial strains and plasmids used in this study




Strain or plasmid
Genotype and/or characteristics



Strains


S. enterica serovar
ΔpabA1516 ΔpabB232 ΔasdA16; vaccine vector


Typhimurium


χ8914

E. coli χ6097
F − araD139 Δ(proAB-lac) λ-φ80dlacZΔM15 rpsL ΔasdA4 Δ(zhf-2::Tn10) thi-1; contains


pYA232 (Tc r , lacI q ); used for cloning and propagation of plasmid


C. perfringens

Type A, NE Isolate

CP995

JGS4143
Type A, NE isolate, virulent strain

Plasmids

pYA3493
P trc , asd, pBRori, bla SS; parent plasmid vector

pYA3620
P trc , asd, pBRori, bla SS, bla CT; parent plasmid vector pYA3493 with bla C-terminal


fusions

pYA4101
P trc , asd, pBRori, ompA SS; parent plasmid vector with OmpA signal peptide fusion

pYA3977
375-bp DNA encoding PlcC in pYA3493 PlcC expression plasmid

pYA4110
375-bp DNA encoding PlcC in pYA4101 PlcC expression plasmid

pYA4149
375-bp DNA encoding PlcC in pYA3620 PlcC expression plasmid

pYA3910
375-bp DNA encoding PlcC in pBAD/HisB vector; used for His-tagged PlcC (rPlcC)


expression







































S. enterica serovar Typhimurium x8914, containing defined attenuating deletions of the pabA and pabB genes, was used as the vaccine vector. χ8914 is derived from a highly virulent S. enterica serovar Typhimurium strain (χ3761). χ8914 has an oral 50% lethal dose of greater than 1×10 9 CFU for 1-day-old chicks, whereas the 50% lethal dose for the wild-type χ3761 is 3×10 3 CFU. χ8914 also has a deletion in the gene encoding aspartate β-semialdehyde dehydrogenase (asd), which renders it deficient in the synthesis of diaminopimelic acid (DAP). Since DAP is an obligate component of the cell wall peptidoglycan, in the absence of exogenously supplied DAP the growth of χ8914 strictly depends on the complementation of the asd mutation with the vaccine antigen expression plasmid that carries the Salmonella asd gene. This dependence on Asd + plasmid complementation is the basis for the balanced lethal host-vector system, which abrogates the need for antibiotic resistance markers. Bacteria were grown at 37° C. in Luria-Bertani (LB) culture medium containing 0.1% dextrose. When required, 50 μg/ml DAP was added.
Cloning of the C. perfringens pkC gene. C. perfringens DNA was isolated from a bacterial lysate prepared from colonies grown overnight on TSC agar plates. Bacteria were suspended in 150 μl 0.5 M NaOH, pH 8.5, incubated for 30 min at room temperature, and diluted with 25 μl Tris-Cl, pH 7.4, and 425 μl water. A 375-bp region of the alpha toxin gene (plc) encoding the carboxy-terminal end of the alpha toxin (amino acids 248 to 370) was PCR amplified from the CP995 lysate using standard PCR conditions with the following primer sequences: 5′-CGGAATTCGATCCATCAGTTGGAAAGAATGTA-3′ (SEQ ID NO:1) and 5′-CCGAAGCTTATTATTTTATATTATAAGTTGAATTTCC-3′ (SEQ ID NO:2). For the sequence analysis of the complete alpha toxin gene from CP995, primers binding to flanking regions of plc, 5′ AGTTTAACAATTTAGAGTGGGTAAGGTTAGATGTG 3′ (SEQ ID NO:3) and 5′ GCCAGCTCCTAGGAATCCTGAAATTATATCTAC 3′ (SEQ ID NO:4), were used.
rPlcC protein preparation. The PCR product of plcC, the alpha toxin C-terminal domain-encoding sequence, was first cloned into the pBAD/HisB plasmid vector (Invitrogen, Carlsbad, Calif.) for the expression of a His-tagged recombinant PlcC (rPlcC) protein. The plasmid pYA3910 (pBADHisB containing plcC) (Table 1) was electroporated into competent Escherichia coli Top10 cells (Invitrogen, Carlsbad, Calif.). The expression of His-tagged rPlcC in the Top10 cells (pYA3910) was induced by adding 0.02% L -arabinose into early-log-phase growing bacteria. Bacteria were harvested from a 250-ml culture at an optical density at 600 nm (OD 600 ) of 1.2 by centrifugation at 5,000×g for 15 min. The cell pellet was resuspended in 40 ml cell lysis solution (Sigma, St. Louis, Mo.), which contains lysozyme (0.2 mg/ml), benzonase (50 U/ml), and protease inhibitors. Following 15 min of incubation at room temperature in the lytic solution, the bacterial suspension was briefly sonicated (2 min) to ensure cell disruption. Insoluble material was removed by centrifugation at 16,000×g for 10 min. The supernatant containing His-tagged protein was loaded onto 0.8- by 4-cm chromatography columns (Bio-Rad, Hercules, Calif.) packed with nickel-Sepharose gel (6%) (Sigma, St. Louis, Mo.). The affinity gel matrix was washed with 50 mM NaH 2 PO 4 , pH 8.0, 0.3 M NaCl solution before and after the bacterial lysate was loaded. Proteins were eluted with 200 mM C 3 H 4 N 2 (imidazole) in the washing solution. The elute was desalted and concentrated by a Centricon filtration system using 5,000 (5K) and 50K nominal molecular weight membranes (Millipore, Billerica, Mass.). Protein was analyzed by electrophoresis on a 12% Tris-Bis gel (see FIG. 1 ) and by Western blotting using 6-HisG antibody (Invitrogen, Carlsbad, Calif.). The protein concentration was determined by a Bradford assay using bovine serum albumin as the standard. To produce rabbit anti-PlcC antibody, two rabbits were injected subcutaneously (s.c.) with 100 μg rPlcC protein emulsified in Freund's adjuvant. The rabbits were immunized three times, with 2-week intervals between injections, and the antiserum was tested for specific reactivity against rPlcC by immunoblot analysis (see FIG. 1 ).
Plasmids for PlcC expression in the S. enterica serovar Typhimurium vaccine strain. Three different recombinant gene expression plasmids, pYA3493, pYA3620, and pYA4101, were used for the expression of PlcC by the S. enterica serovar Typhimurium vaccine strain (Table 1). The plasmids contain a modified P trc or P lpp promoter and a signal peptide sequence from E. coli class A β-lactamase (bla) or the outer membrane protein A (ompA) at the translation start site for the cloned antigen ( FIG. 2 ). The P trc or P lpp promoter directs the constitutive expression of the recombinant PlcC in Salmonella . The signal peptides target the protein for secretion by the type II secretion pathway into the periplasm, with subsequent release into the culture supernatant. In addition to the β-lactamase signal peptide sequence, pYA3620 also has the β-lactamase C-terminal protein-coding sequence at the 3′ end of the recombinant gene. Such a fusion of the C-terminal peptide sequence of β-lactamase to the recombinant protein has been reported to facilitate the transport of recombinant protein across membranes. PlcC expression plasmids pYA3977, pYA4110, and pYA4149 (Table 1) were propagated, and PlcC expression was confirmed first in E. coli strain χ6097. Protein expression in χ6097 was induced by 0.5 mM isopropyl-β- D -thiogalactopyranoside. Once PlcC expression was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis, the plasmids were recovered from E. coli and introduced into competent χ8914 by electroporation. As a vaccine control strain (designated the RAS control), the parent plasmid pYA3493 was similarly introduced into χ8914. To verify plasmid stability, the vaccine strain harboring the expression plasmid was grown for more than 50 generations under nonselective conditions (i.e., in the presence of DAP) and then was tested for growth on medium without DAP.
Expression of PlcC protein by the S. enterica serovar Typhimurium vaccine vector. RASV strains were grown overnight in 5 ml LB broth. The next day, cultures were inoculated into 100 ml LB broth and grown with aeration at 200 rpm until the culture reached an OD 600 of 0.8. To test the expression of rPlcC as a cytoplasmic soluble protein, 1 ml of the culture was transferred to a microcentrifuge tube and centrifuged for 3 min at 14,000×g, and the pellet was resuspended in 500 μl Tris-HCl buffer (50 mM Tris-HCl, 100 mM NaCl, pH 7.2, 10 mM β-mercaptoethanol, and 2 mM phenylmethylsulfonyl fluoride). Bacteria were lysed by sonication, and insoluble protein was removed by centrifugation at 14,000×g for 2 min. The supernatant was tested for rPlcC. To evaluate PlcC protein localization in the periplasm and secretion into culture supernatant, bacteria were harvested from a 100-ml culture by centrifugation at 4,000×g for 15 min at 4° C. Subcellular fractionation for periplasm contents was performed using the lysozyme digestion of the bacterial pellet by osmotic shock with sucrose as previously described. The culture supernatant was filtered through a 0.22-μm filter and concentrated by precipitation overnight at 4° C. in a 10% trichloroacetic acid (TCA) solution. The protein samples were analyzed by SDS-PAGE and Western blotting. Specific protein bands with the predicted molecular masses were distinguished by the Coomassie blue staining of the SDS-PAGE and the immunoblots using rabbit anti-PlcC hyperimmune serum. The amount of PlcC expression was estimated from the SDS-PAGE bands based on comparisons of their densitometry data to those of a known concentration of bovine serum albumin. To ensure the absence of cell lysis that could confound the secreted proteins recovered from culture supernatants and to control the preparation of periplasmic protein, β-galactosidase was used as a cytoplasm protein marker. The MudJ allele (atrB13::MudJ) was inserted into the S. enterica serovar Typhimurium vaccine strain [χ8914(pYA3977)] chromosome by transduction. β-Galactosidase production by the χ8914(pYA3977) atrB13::MudJ construct was used as a cytoplasm protein marker. The culture supernatant, periplasm, and cytoplasm fractions from this construct were analyzed by Western blotting using anti-β-galactosidase antibody (Sigma, St. Louis, Mo.).
RASV inoculum preparation. RASV strains from −80° C. stock were spread on LB agar. Five colonies were inoculated into 5 ml broth and grown statically overnight at 37° C. The following day, the whole culture was inoculated into 100 ml prewarmed LB broth in a 500-ml culture flask and grown with constant shaking at 200 rpm to an OD 600 of 0.8 (about 5 h of culture). Bacteria were harvested by centrifugation at 4,000×g for 15 min at room temperature, and the pellet was resuspended in buffered saline with 1% gelatin (BSG) solution. The volume of the bacterial culture and BSG for resuspension was calculated to yield a bacterial concentration of 2×10 9 CFU/ml. Chickens were inoculated orally with 0.5 ml of the suspension, which contained 1×10 9 CFU.
Chicken immunization. One-day-old Cornish×Rock chicks were purchased from McMurray Hatchery (Webster City, Iowa). On arrival three chicks were euthanized, and samples of internal organs were aseptically collected to test for S. enterica serovar Typhimurium infection by bacterial culture on MacConkey agar plates. Chicks were divided into separate Horsfall isolators, with 10 chicks per Horsfall. On the second day (3 days of age), all chicks, except for those of one group, were orally inoculated (using an oral gavage needle) with 0.5 ml bacterial suspension containing 10 9 CFU of either RASVs or the RAS control strain [χ8914(pYA3493)]. To facilitate the passage of the inoculum to the intestines, chickens were deprived of feed and water for 8 h prior to inoculation, and feed and water were returned 1 h after the RASV inoculation. Ten days later, a similar second dose was given as a boost immunization. One group of chickens was injected s.c. in the neck with 50 μg rPlcC protein in a 100-μl suspension of complete Freund's adjuvant. These chickens received a boost immunization 14 days later with the same dose but with incomplete Freund's adjuvant.
In a prior experiment, chickens were immunized with two doses of RASV χ8914(pYA3977), χ8914(pYA4110), or χ8914(pYA3493) and by s.c. rPlcC injection, and 5 weeks later (7 weeks of age) all the chickens were given a late boost immunization with rPlcC by s.c. injection. The chickens were administered 50 μg protein in a 100-μl volume suspension emulsified in incomplete Freund's adjuvant. This experiment, oral RASV priming followed by a parenteral protein boost immunization, was carried out to evaluate the effect of primary immunization with RASV ora subunit vaccine on antibody titers. RASV-3 was not included in this experiment.
Chickens were fed an antibiotic-free corn-based starter diet or a wheat/barley-based grower's diet (Purina Mills, St. Louis, Mo.). Feed and water were provided ad libitum. In the first week, chicks were reared at a brooding temperature of 32° C. with 24 h of light. Subsequently, the cage temperature was kept at 25° C. and the light schedule modified to 16 h of light and 8 h of dark.
All of the animal experiments detailed above were conducted with the permission and under the guidelines of the Arizona State University Institutional Animal Care and Use Committee.
Clostridium perfringens challenge. Two weeks after RASV immunization, the chicken feed was replaced by a wheat- and barley-based formulated growers' diet, which has higher crude protein and neutral fiber content. After 1 week on the grower diet, chickens were challenged by oral inoculation and repeated infection through contaminated feed with C. perfringens strain JGS4143. On the first day of the challenge, chickens were orally gavaged with 2 ml of an overnight culture of C. perfringens in CMM. Contaminated feed was prepared by mixing an overnight culture with feed as formerly described. Briefly, C. perfringens was grown in 10 ml CMM broth for 18 h at 37° C., which then was inoculated into 1 liter of FTG and grown for 18 h. The FTG culture was mixed with feed at a wt/vol ratio of 1:1. The bacterial feed mix was freshly prepared twice per day and was provided to the chickens for four consecutive days. The average number of bacteria in the 18-h FTG culture was 1×10 9 CFU/ml, and shortly after being mixed with feed, 10 7 CFU/g feed was recovered, which declined to 10 2 to 10 3 CFU/g feed after 10 h on the feeder. One day after the end of the challenge infection, five birds were euthanized by CO 2 inhalation for postmortem examination. The remaining five chickens were used for delayed-type hypersensitivity (DTH) assays and euthanized five days later. Individual body weights were measured before and after challenge infections.
S. enterica serovar Typhimurium vaccine strain and C. perfringens isolation from chickens. One week after RASV boost immunization, cloacal swabs were collected for bacteriology to assess RASV shedding. Dilutions of cloacal swabs were spread on MacConkey agar plates with 1% lactose. The RASV strain was identified by PCR on randomly selected S. enterica serovar Typhimurium colonies using primers that anneal to plcC and the promoter region of the expression plasmid. The cloacal swab preparations also were spread on TSC-EY agar plates and incubated in an anaerobic jar to identify lecithinase-positive ( C. perfringens ) colonies. After challenge infection with C. perfringens , segments of the ileum and cecum with the intestinal contents were aseptically collected and homogenized in BSG. Tissue homogenates were diluted in BSG and spread on MacConkey agar plates for S. enterica serovar Typhimurium detection and on TSC agar plates for C. perfringens detection.
Measuring antibody responses. Blood samples were collected weekly by wing vein puncture, and bile samples were collected during autopsy. Serum immunoglobulin G (IgG) and bile IgA responses were measured by indirect enzyme-linked immunosorbent assay (ELISA). Briefly, microtiter plates (Nunc, Roskilde, Denmark) were coated with 10 μ/ml (1 μg/well) of purified rPlcC protein diluted in coating solution (Na 2 CO 3 , 1.6 g; NaHCO 3 , 2.9 g; NaN 3 , 0.2 g; all in 1 liter distilled H 2 O). Plates were incubated overnight at 4° C., dried, and washed in phosphate-buffered saline (PBS)-0.2% Tween 20 (washing solution). Nonspecific binding was blocked by using Sea Block blocking buffer (Pierce, Rockford, Ill.) for 1 h at 37° C. Test samples (serum or bile) were twofold diluted in blocking buffer, added in duplicate, and incubated at 37° C. with agitation. After repeat washes, biotinylated goat anti-chicken IgG or IgA heavy plus light chain antibody (Bethyl Laboratories, Montgomery, Tex.) was added (1:5,000 dilution) and incubated for 1 h at 37° C. Plates were washed, streptavidin-horseradish peroxidase solution (Southern Biotech, Birmingham, Ala.) (1:5,000 dilution) was added, and the plates were incubated for an extra 1 h at 37° C. Peroxidase activity and color development were detected by 2-2′-azino-di-(3-ethylbenzthiazoline sulfuric acid) (ABTS) substrate (Sigma, St. Louis, Mo.) containing 0.03% H 2 O 2 in citrate buffer, pH 4.35. Plates were incubated for 10 min at 37° C. for color development, and the reaction was stopped with 1% SDS solution. The OD of each well's contents was measured at 405 nm using a microplate reader (Molecular Devices, Sunnyvale, Calif.). A volume of 100 μl/well of the test samples, antibodies, or washing solutions was used in each steps. The antibody response in the serum also was tested by the immunoblot analysis of immunized chicken sera against alpha toxin obtained from concentrated culture supernatant of C. perfringens and rPlcC proteins.
Alpha toxin neutralization test. The neutralization of alpha toxin by serum antibody was determined by the inhibition of red blood cell (RBC) hemolysis by alpha toxin. RBCs were prepared by washing samples of freshly collected rabbit blood twice in PBS and diluting them to 2% (vol/vol) in PBS containing 3 mM CaCl 2 . Alpha toxin was obtained from the supernatant of a C. perfringens culture grown overnight by sequential filtration through 100- and 10-kDa Amicon Ultra filters (Millipore, Billerica, Mass.). The enzymatic activity of the culture supernatant concentrate was evaluated and quantified using a phosphatidylcholine-phospholipase C assay kit (Invitrogen, Carlsbad, Calif.). The concentrated culture supernatant was diluted in PBS containing 0.1 mM CaCl 2 , and 100-μl aliquots containing an estimated 250 ng protein (about 200 U) were distributed into a 96-well dilution plate. Purified recombinant alpha toxin (250 ng) (Sigma, St. Louis, Mo.) was included as a control. Test sera (pooled serum samples) were twofold diluted in PBS (1:10, 1:20, and 1:40), and 100 μl was added into wells. Control wells contained either serum with no toxin or alpha toxin alone. Well contents were mixed and incubated for 1 h at 37° C. with slow agitation. After 1 h, 100 μl of the 2% RBC solution was added into each well. After incubation for 2 h at 37° C., plates were chilled for 15 min at 4° C. and briefly centrifuged at 500×g to sediment intact cells (i.e., RBCs). The absorbance of well contents was measured at 540 nm using a microtiter plate reader. As a reference, 100% RBC lysis was obtained by adding 50 μl of 1% Triton X-100 to wells containing serum and RBCs, while 100% lysis inhibition was recorded from wells without alpha toxin. The hemolysis or inhibition of cell lysis was expressed as the percent difference of the absorbance of wells with test sample, and control wells with half-diluted alpha toxin without a test sample.
DTH assay. Four weeks after the RASV boost immunization and 3 days after the challenge infection, five chickens per group were injected intradermally with 20 μg of the rPlcC protein in 50 μl saline into the left footpad at the toe web between the first and second digits. The right foot was injected with sterile saline as a negative control. The thickness of the toe web was measured with a digital micrometric caliper at 48 and 72 h after antigen or saline injection. Data were expressed as the difference between results for the left foot and the right foot (control).
Serum bacteriostatic (growth inhibition) assay. Sera from immunized or control chickens were filtered through 0.45-μm pore filters, decomplemented by being heated at 56° C. in a water bath for 30 min, and added into the CMM broth culture at 1:20 and 1:40 final dilutions. A volume of 100 μl overnight culture of C. perfringens diluted to a concentration of 10 5 CFU per ml was added into 1 ml of culture medium containing serum, and the cultures were incubated anaerobically at 37° C. The growth of bacteria was monitored by the culture OD, and the number of CFU was monitored by plating serial dilutions on TSC-EY agar plates at 12 and 18 h.
Immunofluorescence microscopy. An indirect immunofluorescence test was performed to determine if antibody against PlcC binds to the bacterial cell surface. Formalin-inactivated bacteria or a fresh colony of C. perfringens from an overnight TSC-EY plate was spread on microscope slides. The formalin inactivation of bacteria was carried out by incubating washed bacterial cells (from a 24-h culture of JGS4143 in BHI broth) in 3 mM formaldehyde solution in PBS for 2 h at 37° C., followed by overnight incubation at room temperature with slow agitation. The suspension (10 ml) was centrifuged at 5,000×g for 15 min, and the pellet was washed twice and resuspended in PBS. Live cells were spread on slides from colonies and were killed and fixed by being heated. Slides were dried and covered with PBS containing 1% bovine serum albumin and incubated for 1 h at room temperature in a humidified box. The blocking solution was removed, and 200 μl of the test serum from immunized or control chickens diluted 1:50 in PBS was spread onto the slide and covered with a coverslip. Slides were incubated overnight at 4° C. After being washed with PBS-0.1% Tween 20, goat anti-chicken IgG antibody conjugated with fluorescein isothiocyanate (Southern Biotech, Birmingham, Ala.) was added, and the solution was incubated for an extra 2 h at room temperature. Slides then were washed three times in PBS-0.1% Tween 20, dried, and observed under a fluorescence microscope.
Pathological examination. Autopsies were performed 24 h after the last day (i.e., the fourth day) of the challenge infections. The whole intestines were examined for gross lesions such as hemorrhagic spots, mucosal paleness or discoloration, swelling, feebleness of the intestinal wall, and the nature of the contents. Tissue samples of the duodenum, midjejunum, and ileum from similar segments (i.e., located at identical distances from the Meckel diverticulum mark) were collected in buffered 4% formaldehyde for histopathology. Sections of the intestinal tissues were stained with hematoxylin and eosin and were examined for microscopic lesions of enteritis and tissue morphological alterations. Villus epithelial degeneration, sloughing, and inflammatory leukocyte infiltration into lamina propria and submucosa were examined, as was villus shortening. The severity and distribution of lesions were graded semiquantitatively by using a scale (0 to 5) that considers the severity and distribution of the lesions based on prior knowledge of normal histology and severe NE lesions. The scores were given as follows: 0, no lesion; 1, scattered mild degeneration of villus tip epithelium; 2, mild degeneration detected uniformly in several microscopic fields; 3, moderate necrotic lesions with epithelial sloughing, degeneration, and leukocyte infiltrations; 4, severe epithelial degeneration and necrosis dispersed in several microscopic fields; and 5, severe and frequent necrotic lesions, often with villus shortening or atrophy.
Statistical analysis. The differences in body weights were evaluated by two-way analysis of variance with the Bonferroni posttest method. One-way analysis of variance and the Bonferroni posttest were used to compare the differences in ELISA (absorbance) and DTH data. A P value of less than 0.05 was considered significant. The analyses were performed using the GraphPad Prism program.
Amino acid sequence of alpha toxin. The primary structure of alpha toxin from NE isolate CP995 shows 98% sequence identity to the type A reference strain ATCC 13124 (GenBank accession no. M24904), with a few amino acid substitutions (Leu 16 to Thr, Lys 17 to Gln, Ala 174 to Asp, Thr 177 to Pro, Ser 335 to Pro, Gly 363 to Arg, and Asn 364 to Lys) and a deletion of Ile 21 ( FIG. 3 ). Except for the absence of Ile 21 , the amino acid substitutions at the specific sites are common variations among type A isolates from humans and animals. These variations do not affect alpha toxin's phospholipase C and hemolytic activities or hinder the neutralizing ability of C terminus-specific antibody against alpha toxin.
PlcC expression in S. enterica serovar Typhimurium vaccine vector. The expression of the PlcC protein in the S. enterica serovar Typhimurium vaccine strain was detected on the SDS-PAGE gel stained with Coomassie blue ( FIG. 1 ). High levels of PlcC expression were obtained with all three plasmid constructs. The PlcC protein concentration was estimated at roughly 100 ng/μl bacterial lysate, as measured by a densitometry analysis that compared the results to those for a standard concentration of bovine serum albumin (ChemiDoc XRS; Bio-Rad, Hercules, Calif.). PlcC was effectively secreted by the S. enterica serovar Typhimurium vaccine strains through a type II secretion system. The fusion with the OmpA or Bla signal peptide sufficiently enabled the transport of PlcC into the periplasm, which then was secreted across the outer membrane into the culture supernatant. No β-galactosidase was detected in the culture supernatant of the RASV χ8914 (pYA9977)atrB13::MudJ strain, thus indicating that bacterial lysis had not occurred.
The molecular masses of PlcC expressed from the three constructs appear different due to differences in the sizes of the signal peptides, the linker amino acids, and the β-lactamase C-terminal fusion in pYA4149 constructs ( FIG. 2 ). Accordingly, the molecular mass of PlcC was 16 kDa in χ8914(pYA3977), 14 kDa in χ8914(pYA4110), and 18 kDa in χ8914(pYA4149). The molecular mass of the His-tagged rPlcC was 19 kDa.
Antibody responses in immunized chickens. RASV-immunized chickens generally had low serum antibody responses, as measured by ELISA, at serum dilutions as low as 1:40. Unexpectedly, chickens that received s.c. immunization with rPlcC also showed a low serum IgG response similar to that of RASV-immunized chickens. Formerly, we tested whether RASV or rPlcC immunization gives some priming effect when followed by a boost protein immunization at a later time point. When the chickens were injected with 50 μg of purified rPlcC protein 5 weeks after the primary immunization (i.e., at 7 weeks of age), chickens that first were immunized with RASV developed a significant and rapid increase in antibody titers (i.e., in comparison to the typical response pattern), whereas those immunized with rPlcC injection had low titers compared to those of the RASV groups ( FIG. 4A ). The rPlcC-immunized chickens had a higher initial bile IgA titer, which abruptly declined after the final boost with rPlcC. In the RASV-immunized chickens, the IgA titers increased significantly after the rPlcC boost ( FIG. 4B ). This strong antibody response in the RASV prime and protein boost approach shows that although there were low levels of serum antibody titers generated by the primary immunization, RASV stimulates an immune reaction that produces a better memory response than repeated immunization with protein alone.
Because our goal is to develop an oral RASV, we immunized a second group of birds with RASV and performed a more complete evaluation of immune responses and C. perfringens challenge to assess the protective efficacy. Sera from the RASV-immunized chickens were tested by Western blotting on SDS-PAGE-separated rPlcC and the whole alpha toxin, and both PlcC protein and the complete alpha toxin obtained from the culture supernatant of C. perfringens were detected ( FIG. 5 ). This confirmed the presence of serum antibody responses in RASV-immunized chickens. Sera from the RASV- or rPlcC-vaccinated chickens reacted positively with the whole alpha toxin, whether it was denatured by TCA precipitation or not (i.e., concentrated by filtration) prior to separation on SDS-PAGE.
DTH reaction. RASV-immunized chickens showed an increase in DTH responses compared to those of the chickens inoculated with the control S. enterica serovar Typhimurium vector strain ( FIG. 6 ). The highest DTH reaction level (P<0.05) was induced in chickens immunized with χ8914(pYA4110) or s.c. rPlcC at 48 h after PlcC injection. At 72 h after PlcC injection, the DTH responses in all immunized chickens were similar to each other and were higher than those of the control chickens (P>0.05). The role of cell-mediated immunity in NE is not clear; however, since S. enterica serovar Typhimurium replicates intracellularly within antigen-presenting cells, it presumably facilitates the delivery of recombinant antigens by the endogenous antigen presentation pathway to prime CD4 + T cells and the cell-mediated response. DTH is commonly used as an index for cellular responses.
Alpha toxin neutralization. Toxin neutralization by serum antibody was measured as a function of alpha toxin-induced RBC lysis. Pooled sera from chickens immunized with RASV or rPlcC inhibited the hemolytic effect of the alpha toxin in a C. perfringens culture supernatant ( FIG. 7 ). The highest level of RBC lysis inhibition was observed with sera from birds vaccinated with rPlcC and RASV-3 [χ8914(pYA4149)], with inhibitions of 76 and 71%, respectively. The sera from chickens immunized with the other RASVs (RASV-1 and RASV-2) also showed more than 50% reductions in RBC lysis compared to that of the RAS-immunized (control) chicken serum. These results indicate the presence of alpha toxin-neutralizing antibodies in RASV-immunized chickens.
C. perfringens growth inhibition by immunized chicken serum. Decomplemented sera from immunized chickens inhibited the proliferation of C. perfringens growth in culture (Table 2). Bacterial growth in cultures containing serum from either RASV- or rPlcC-immunized chickens was suppressed by up to 1,000-fold compared to that of cultures with serum from control nonimmunized chickens.
Immunofluorescence microscopy. Antibodies binding to bacterial surface proteins or capsules are known to inhibit bacterial growth and to facilitate opsonophagocytosis. To investigate the inhibitory effects of the sera from immunized chickens, we evaluated the possibility of surface binding by serum antibody by using an indirect immunofluorescence assay. Remarkably, serum antibody against PlcC from immunized chickens showed binding to the surface of whole bacteria ( FIG. 8 ). Higher levels of fluorescence were frequently detected at bacterial poles.
Isolation of the RASV strain and C. perfringens from chickens. The S. enterica serovar Typhimurium vaccine strain was readily detected in cloacal swabs collected 1 week after the boost immunization and in the intestinal segments (from the ileum and cecum) collected during autopsy at 3 weeks after immunization. The average S. enterica serovar Typhimurium numbers in cloacal swabs were 1×10 4 CFU/g of fecal material, and 3 weeks later the numbers in the ileum and in the cecum were, on average, 1×10 2 and 1×10 4 CFU per gram of tissue, respectively. No S. enterica serovar Typhimurium was detected in the liver or spleen at 3 weeks after immunization.
C. perfringens could not be detected from cloacal swab samples collected prior to the challenge infection. Usually, a small number of C. perfringens (resident flora) cells are identified by culture from healthy young birds, especially in birds reared under experimental conditions. After the challenge infection, generally smaller numbers of C. perfringens were detected from intestines, even at 1 day after the challenge infection. The average numbers of C. perfringens cells detected in the intestines were less than 1×10 3 and 1×10 5 CFU/g in the ileum and cecum, respectively. Five days after the end of the challenge infection, the numbers in cecum declined to less than 10 3 CFU/g, and none could be recovered from the ileum. The numbers of C. perfringens cells recovered were highly variable among chickens in all groups, and there was no correlation between the number of bacteria isolated from an intestinal segment and lesion development.
Intestinal mucosal lesion development after challenge infection. Gross lesions with mucoid intestinal luminal content, feeble intestinal walls, mucosal edema, and hemorrhagic spots were found in the duodenum and proximal jejunum of nonimmunized chickens ( FIG. 9A ). Overall, few chickens showed overt gross lesions and diarrhea. Histopathology lesions such as hyperemia of the lamina propria, villus tip epithelium degeneration, villus shortening, disruption of the structural integrity of enterocytes with the basement membrane, and inflammatory leukocyte infiltration were observed mainly in the jejunum. These lesions were observed 1 day after challenge predominantly in nonimmunized chickens. The hematoxylin- and eosin-stained sections also revealed clusters of C. perfringens in the intestinal lumen and mucosal surfaces that were seldom attached to epithelial surfaces ( FIG. 9E ). Sites with bacterial clumps often depicted a mild defect of the epithelial surface and microvilli mostly in nonimmunized or control RAS-immunized chickens. The lesions were severe and more frequent in nonimmunized (control) chickens, while immunized chickens had minimal lesions in a few chickens (Table 3). The histopathological lesions had receded by 4 days after challenge. RASV-immunized chickens showed significantly higher percentages of body weight gain at 10 days after challenge with C. perfringens compared to the average body weight gain for nonimmunized chickens (Table 3).
A subunit vaccine consisting of the C-terminal domain of alpha toxin (PlcC) protects mice against gas gangrene. However, no injectable PlcC subunit vaccine or live attenuated S. enterica serovar Typhimurium-delivered PlcC vaccine to induce protective immunity against C. perfringens type A strain-caused enteric disease has been evaluated before. The current study showed that an RASV expressing PlcC or an rPlcC subunit vaccine induced toxin-neutralizing antibodies and reduced intestinal lesion development and body weight loss in chickens challenged with virulent C. perfringens. Formerly, many investigators showed protection against NE by vaccination with a toxoid vaccine that consisted of an inactivated whole alpha toxin. The delivery of such a vaccine by repeated parenteral injections is not a feasible approach in commercial broilers and layers.
The expression of C. perfringens genes in Salmonella can be problematic and lead to strain instability due to the low G+C content in the DNA of C. perfringens (24-27%) compared to the G+C content of Salmonella (50-53%). In addition, the codon usage in C. perfringens is different from Salmonella , which can lead to poor expression due to the presence of codons in the coding sequences that are rare in highly expressed genes of Salmonella . We have optimized the sequence of plcC for codon usage and G+C content ( FIG. 10 ). The G+C content was increased from 30% to 45%. We cloned this modified gene into Asd+expression vector pYA4538 ( FIG. 11B ), fusing the optimized plcC gene to the dsbA signal sequence. The plasmid was moved into Salmonella vaccine strain χ9352 (Δpmi-2426 Δ(gmd-fcl)-26 ΔP fur77 ::TT araC P BAD fur ΔP crp527 ::TT araC P BAD crp ΔasdA21::TTaraC P BAD c2 ΔaraE25 ΔaraBAD23 ΔrelA198::araC P BAD lac/TT) and expression of the fusion protein was confirmed by western blot ( FIG. 12 ). We are performing immunological evaluations using Salmonella vaccine strain χ9352 or χ9345 (Δpmi-2426 Δ(gmd-fcl)-26 ΔP fur77 ::TT araC P BAD fur ΔP crp527 ::TT araC P BAD crp ΔasdA18::TTaraC P BAD c2 ΔaraE25 ΔaraBAD23 ΔrelA198::araCP BAD lacITT) carrying these plasmids.
Example 2
NetB Antigen Expressing Recombinant Bacteria
The netB gene encodes a protein that shows limited homology with C. perfringens β-toxin. It is found primarily in C. perfringens isolated from birds suffering from necrotic enteritis, but not from healthy animals. NetB is cytotoxic to chicken leghorn male hepatoma cells in vitro and it is required for the induction of necrotic enteritis symptoms in chickens. We have cloned the naturally occurring netB gene into a number of our Asd+ expression vectors and are performing immunological evaluations on Salmonella vaccine strains carrying these plasmids.
We have optimized the nucleic acid sequence of netB for codon usage and G+C content to allow optimal expression in Salmonella ( FIG. 13 ). The G+C content in the optimized sequence was increased from 27% to 45%. The optimized nucleic acid sequence was cloned into Asd + gene expression vectors pYA4531 ( FIG. 11A ) and pYA4538 ( FIG. 11B ), fused to the signal sequences for eltII-B and dsbA, respectively, to yield plasmids pYA4676 ( FIG. 14A ) and pYA4677 ( FIG. 14B ). These plasmids were introduced into Salmonella vaccine strain χ9352 and expression of NetB was confirmed by western blot ( FIG. 15 ). We are performing immunological evaluations. The optimized netB gene is being inserted into plasmid vectors pYA3493 and pYA3620.
Example 3
Additional Protective Antigens for Expression in Recombinant Attenuated Salmonella Vaccines
Additional C. perfringens antigens that provide protection against necrotic enteritis when administered to chickens by injection into muscle tissue or when delivered by attenuated Salmonella include glyceraldehyde 3-phosphate dehydrogenase (GDP), pyruvate:ferredoxin oxidoreductase (PFOR), truncated pyruvate:ferredoxin oxidoreductase (tPFOR), fructose 1,6-biphosphate aldolase (FBA), a hypothetical protein (HP), and a truncated form of hypothetical protein (tHP). We have optimized the nucleic acid sequences for the genes encoding tPFOR ( FIG. 16 ), tHP ( FIG. 17 ), GDP ( FIG. 18 ) or FBA ( FIG. 19 ) for codon usage and G+C content for expression in Salmonella . The optimized genes are fused to a secretion signal such as bla SS, ompA SS, bla SS+CT, eltII-B SS or dsbA SS by cloning the optimized gene into AsdA+ expression plasmid pYA3493, pYA4101, pYA3620, pYA4531 or pYA4538, respectively and expressed in an attenuated S. Typhimurium strain such as χ9352.
Example 4
Expression of Two or More Antigens in a Single Salmonella Vaccine Strain
The incorporation of two or more antigens encoded by genes that have been optimized for G+C content and codon usage for expression in Salmonella , into the vaccine may provide enhanced protection against necrotic enteritis caused by C. perfringens . In one example, a bla SS-plcC fusion gene and a bla SS-netB fusion gene are cloned into the same Asd+ plasmid vector as an operon fusion. Expression is driven from a single, regulatable promoter, such as the P trc promoter. Both genes are expressed in the same attenuated Δasd Salmonella strain in amounts adequate to induce a protective immune response. In another example, each gene is transcribed from its own, regulatable promoter.
In another embodiment, each gene is cloned into a different expression plasmid, one with an Asd+ selectable marker and the other with a different selectable marker, such as DadB+. The bla SS netB (optimized) fusion protein is cloned into DadB+ expression vector pYA4555 ( FIG. 20 ) to yield pYA4555+ bla SS netB (optimized) ( FIG. 21 ). In this plasmid, the bla SS netB (optimized) gene is transcribed from the regulatable P22 P L promoter. Plasmid pYA4555+ bla SS netB (optimized) and plasmid pYA4679 ( FIG. 22 ) are introduced into strain such as χ9590 (Δpmi-2426 Δ(gmd-fcl)-26 ΔP fur81 ::TT araC P BAD fur ΔP crp527 ::TT araC P BAD crp ΔasdA27::TT araC P BAD c2 ΔaraE25 ΔaraBAD23 ΔrelA198::araC P BAD lacI TT ΔsopB1925 ΔagfBAC811 Δalr-3 ΔdadB4), which carries deletions in the asdA, alr-3 and dadB4 genes, allowing for selection of both AsdA+ plasmids and DadB+ plasmids. In addition, this strain produces both the C2 repressor and the LacI repressor, each transcribed from its own arabinose-regulated P BAD promoter, providing regulatable expression of netB from the P22 P L promoter (pYA4555 +bla SS netB (optimized)) and plcC from the P trc promoter (pYA4679), respectively. Two antigens, PlcC and NetB are synthesized in a single bacterium in amounts adequate to induce an immune response against C. perfringens . Other attenuated Salmonella strains that can support the presence of two plasmids may also be used. Other plasmid selectable markers that are used include murA, aroA, aroC, aroD, ilvC or ilvE. Plasmids carrying these markers are maintained in strains carrying a deletion of the selectable marker gene.
We recently constructed derivatives of χ9590 with various types of rec mutations to investigate possible difficulties in the stable maintenance of two plasmids specifying two different protective antigens and with either the AsdA+ or DadB+ selective marker but with some DNA sequences in common due to using the same P trc promoter, termination sequence and pBR ori. Although we determined that recombination between plasmids as well as within plasmids was exceedingly rare (frequency of no more than 10 −3 after full growth of a culture for some 30 generations), we found even greater stability in the χ9590 derivative strain χ9760 that has the ΔrecF126 allele in which recombination between plasmids was reduced another 10-fold. The inclusion of the ΔrecF126 deletion mutation in the wild-type S. Typhimurium UK-1 strain χ3761 has no effect on virulence having the same LD 50 . We will therefore include the ΔrecF126 mutation in strains to maintain multiple plasmids specifying synthesis and delivery of multiple protective antigens from Clostridium perfringens.
In other embodiments, the genes for other protective antigens are codon-optimized and optimized for G+C content are used. The genes encoding tPFOR ( FIG. 16 ), tHP ( FIG. 17 ), GDP ( FIG. 18 ) or FBA ( FIG. 19 ) are cloned into separate plasmids or as operon fusions or as protein fusions and are expressed from one or more plasmids.
In another embodiment, one plasmid carries an operon fusion of two antigens, such as plcC and netB, and another plasmid directs the synthesis of a third antigen, such as tPFOR.
Example 5
Expression of One or More Antigens Host-Adapted Salmonella
Clostridium perfringens causes necrotizing enteritis in the small intestines of a variety of species, including cattle (Jejunal hemorrhagic syndrome, necrotic enteritis), swine and even humans, which occurs sporadically in underdeveloped countries. Some factors that predispose to C. perfringens induced necrotic enteritis include protozoan and helminth infections. C. perfringens type A, associated diarrhea is one of the top 5 causes of food borne bacterial diarrheal disease ranked by CDC in the U.S. α-toxin is particularly responsible for sublethal effects on enterocytes that could lead to malabsorption and stunting in children in developing countries. Studies also show the possible etiologic significance of early intestinal C. perfringens colonization and development of necrotizing enterocolitis in newborns. Therefore, it may be advantageous to formulate this vaccine for use in other species. Host-adapted Salmonella may be attenuated and further modified for this purpose as described above. Attenuated Salmonella Typhi and Salmonella Paratyphi A can be used as the antigen delivery vector for a human vaccine, attenuated Salmonella Choleraesuis can be used for a swine vaccine and attenuated Salmonella Dublin can be used for a bovine vaccine. In addition, attenuated Salmonella Gallinarum may be used for a poultry vaccine.