Patent Grant
6902906
The invention relates to attenuated bacteria useful in vaccines.
The principle behind vaccination is to induce an immune response in the host thus providing protection against subsequent challenge with a pathogen. This may be achieved by inoculation with a live attenuated strain of the pathogen, i.e. a strain having reduced virulence such that it does not cause the disease caused by the virulent pathogen.
Clasically, live attenuated vaccine strains of bacteria and viruses have been selected using one of two different methodologies. Mutants have been created either by treatment of the organism using mutagenic chemical compounds or by repeated passage of the organism in vitro. However, use of either method gives rise to attenuated strains in which the mode of attenuation is unclear. These strains are particularly difficult to characterise in terms of possible reversion to the wild type strain as attenuation may reflect single (easily reversible) or multiple mutation events. Furthermore, it is difficult to obtain such strains having optimum immunogenic properties because of multiple mutation events, and multiple strains may need to be used to provide protection against the pathogen.
Using modern genetic techniques, it is now possible to construct genetially defined attenuated bacterial strains in which stable attenuating deletions can be created. A number of site directed mutants of Salmonella have been created using this type of technology (2, 4, 5, 9, 12, 16, 17, 18). Mutations in a large number of genes have been reported to be attenuating, including the aro genes (e.g. aroA, aroC, aroD and aroE), pur, htrA, ompR, ompF, ompC, galE, cya, crp and phoP.
Salmonella aroA mutants have now been well characterised and have been shown to be excellent live vaccines against salmonellosis in several animal species. In addition, in order to reduce the chances of a reversion to virulence by a recombination event, mutations have been introduced into two independent genes such as aroA/purA and aroA/aroC. Identical mutations in host adapted strains of Salmonella such as S. typhi (man) and S. dublin (cattle) has also resulted in the creation of a number of candidate single dose vaccines which have proved successful in clinial (8, 11) and field trials (10).
A Salmonella typhimurium strain harboring stable mutations in both ompC and ompF is described in Chatfield et al (1991, ref. 21). When administered orally to BALB/c mice the strain was attenuated, with the 50% lethal dose (LD50) reduced by approximately 1,000-fold. However, the intravenous LD50 was reduced only by approximately 10-fold, demonstrating the importance of the porins in confering on the bacteria the ability to infect by the oral route.
Expression of the ompC and ompF genes is regulated by ompR. Pickard et al (1994, ref. 13) describes the cloning of the ompB operon, comprising the ompR and envZ genes, from a Salmonella typhi Ty2 cosmid bank and characterisation by DNA sequence analysis. The DNA sequence data were used to identify appropriate restriction sites for generating a defined deletion of 517 bp within the open reading frame of the ompR gene. This deletion was introduced by homologous recombination into the chromosomes of two S. typhi strains which already harbored defined deletions in both the aroC and aroD genes. The S. typhi ompR mutants displayed a marked decrease in ompC and ompF porin expression as demonstrated by examination of outer membrane preparations. It was also shown that the ompR-envZ two component regulatory system plays an important role in the regulation of Vi polysaccharide synthesis in S. typhi.
In animal studies, attenuated S. typhimurium has been used as a vehicle for the delivery of heterologous antigens to the immune system (3, 6, 15). This raises the potential of the development of multivalent vaccines for use in man (7).
The invention provides a bacterium attenuated by a non-reverting mutation in each of the aroC gene, the ompF gene and the ompC gene. The invention also provides a vaccine containing the bacterium.
It is believed that the aroC/ompF/ompC combination of mutations gives a vaccine having superior properties. For example, it is believed that the aroC/ompF/ompC combination may be superior to a aroC/ompR combination for two reasons:
Bacteria useful in the Invention
The bacteria that are used to make the vaccines of the invention are generally those that infect by the oral route. The bacteria may be those that invade and grow within eukaryotic cells and/or colonise mucosal surfaces. The bacteria are generally Gram-negative.
The bacteria may be from the genera Escherichia, Salmonella, Vibrio, Haemophilus, Neisseria, Yersinia, Bordetella or Brucella. Examples of such bacteria are Escherichia coli—a cause of diarrhoea in humans;
Strains of E. coli and Salmonella are particularly useful in the invention. As well as being vaccines in their own right against infection by Salmonella, attenuated Salmonella can be used as carriers of heterologous antigens from other organisms to the immune system via the oral route. Salmonella are potent immunogens and are able to stimulate systemic and local cellular and antibody responses. Systems for driving expression of heterologous antigens in Salmonella in vivo are known; for example the nirB and htrA promoters are known to be effective drivers of antigen expression in vivo.
The invention may be applied to enterotoxigenic E. coli (“ETEC”). ETEC is a class of E. coli that cause diarrhoea. They colonise the proximal small intestine. A standard ETEC strain is ATCC H10407.
Infections of ETEC are the single most frequent cause of travellers diarrhoea, causing 3-9 million cases per year amongst visitors to developing countries. In endemic areas, ETEC infections are an important cause of dehydrating diarrhoea in infants and young children, resulting in 800,000 deaths a year in the under fives world-wide. In developing countries, the incidence of ETEC infections leading to clinical disease decreases with age, indicating that immunity to ETEC infection can be acquired. In contrast, naive adults from industrialized countries who visit endemic areas are highly susceptible to ETEC infections. However, with prolonged or repeated visits to endemic areas susceptibility to ETEC infections diminishes, suggesting that a live attenuated approach to ETEC vaccination may prove successful.
The inventors chose to work on a non-toxigenic strain of ETEC called E1392/75/2A. E1392/75/2A arose spontaneously from a toxic mutant by deletion of toxin genes. In human studies, oral vaccination with live E1392/75/2A gave 75% protection against challenge with toxin-expressing ETEC from a different serotype. However, approximately 15% of vaccinees experienced diarrhoea as a side effect of the vaccine. The strain needs further attenuation to reduce the side effects before it can be considered as a potential vaccine and the invention gives a means of achieving such attenuation.
Seq Id No. 1 shows the sequence of the E. coli aroC gene, Seq Id No. 3 shows the sequence of the E. coli ompC gene and Seq. Id No. 5 shows the sequence of the E. coli ompF gene.
Further mutations
One or more further mutations may be introduced into the bacteria of the invention to generate strains containing mutations in addition to those in aroC, ompC and ompF. Such a further mutation may be (i) an attenuating mutation in a gene other than aroC, ompC and ompF, (ii) a mutation to provide in vivo selection for cells maintaining a plasmid (e.g. a plasmid expressing a heterologous antigen), or (iii) a mutation to prevent expression of a toxin gene.
The further attenuating mutation may be a mutation that is already known to be attenuating. Such mutations include mutations in aro genes (e.g. aroA, aroD and aroE), pur, htrA, ompR, galE, cya, crp, phoP and surA (see e.g. refs 2, 4, 5, 9, 12, 13, 16, 17 and 18).
A mutation to provide selection for maintenance of a plasmid may be made by mutating a gene that is essential for the bacterium to survive. A plasmid carrying the essential gene is then introduced into the bacterium, so that only cells carrying the plasmid can survive. This may be useful where the plasmid contains, for example, a heterologous antigen to be expressed by the bacterium.
A mutation to prevent expression of a toxin gene may be made to reduce any side-effects caused by vaccination with the bacterium. For example, in the case of vaccination with E. coli strains such as ETEC it may be desirable to mutate the heat labile toxin (LT) or heat stable toxin (ST) genes so that they are not expressed.
The nature of the mutations
The mutations introduced into the bacterial vaccine generally knock-out the function of the gene completely. This may be achieved either by abolishing synthesis of any polypeptide at all from the gene or by making a mutation that results in synthesis of non-functional polypeptide. In order to abolish synthesis of polypeptide, either the entire gene or its 5′-end may be deleted. A deletion or insertion within the coding sequence of a gene may be used to create a gene that synthesises only non-functional polypeptide (e.g. polypeptide that contains only the N-terminal sequence of the wild-type protein).
The mutations are non-reverting mutations. These are mutations that show essentially no reversion back to the wild-type when the bacterium is used as a vaccine. Such mutations include insertions and deletions. Insertions and deletions are preferably large, typically at least 10 nucleotides in length, for example from 10 to 600 nucleotides. Preferably, the whole coding sequence is deleted.
The bacterium used in the vaccine preferably contains only defined mutations, i.e. mutations which are characterised. It is clearly undesirable to use a bacterium which has uncharacterised mutations in its genome as a vaccine because there would be a risk that the uncharacterised mutations may confer properties on the bacterium that cause undesirable side-effects.
The attenuating mutations may be introduced by methods well known to those skilled in the art (see ref. 14). Appropriate methods include cloning the DNA sequence of the wild-type gene into a vector, e.g. a plasmid, and inserting a selectable marker into the cloned DNA sequence or deleting a part of the DNA sequence, resulting in its inactivation. A deletion may be introduced by, for example, cutting the DNA sequence using restriction enzymes that cut at two points in or just outside the coding sequence and ligating together the two ends in the remaining sequence. A plasmid carrying the inactivated DNA sequence can be transformed into the bacterium by known techniques such as electroporation and conjugation. It is then possible by suitable selection to identify a mutant wherein the inactivated DNA sequence has recombined into the chromosome of the bacterium and the wild-type DNA sequence has been rendered non-functional by homologous recombination.
Expression of heterologous antigens
The attenuated bacterium of the invention may be genetically engineered to express an antigen that is not expressed by the native bacterium (a “heterologous antigen”), so that the attenuated bacterium acts as a carrier of the heterologous antigen. The antigen may be from another organism, so that the vaccine provides protection against the other organism. A multivalent vaccine may be produced which not only provides immunity against the virulent parent of the attenuated bacterium but also provides immunity against the other organism. Furthermore, the attenuated bacterium may be engineered to express more than one heterologous antigen, in which case the heterologous antigens may be from the same or different organisms.
The heterologous antigen may be a complete protein or a part of a protein containing an epitope. The antigen may be from another bacterium, a virus, a yeast or a fungus. More especially, the antigenic sequence may be from E. coli (e.g. ETEC), tetanus, hepatitis A, B or C virus, human rhinovirus such as type 2 or type 14, herpes simplex virus, poliovirus type 2 or 3, foot-and-mouth disease virus, influenza virus, coxsackie virus or Chlamydia trachomatis. Useful antigens include non-toxic components of E. coli heat labile toxin, E. coli K88 antigens, ETEC colonization factor antigens, P.69 protein from B. pertussis and tetanus toxin fragment C.
The ETEC colonization factors and components thereof are prime candidates for expression as heterologous antigens. To instigate diarrhoeal disease, pathogenic strains of ETEC must be able to colonize the intestine and elaborate enterotoxins. For most strains of ETEC colonization factors (CF) that are required for adhesion to the intestinal mucosa have been identified. In almost all cases CFs are expressed as fimbrae on the outer surface of the bacteria. A large number of CFs have been identified, the most prevalent being CFAI, CRAII (includes CS1, CS2, CS3) and CFAIV (includes CS4, CS5, CS6).
A vaccine to ETEC will ideally give protection against a range of colonization factor antigens to ensure that protection against different strains is obtained. In order to achieve this, it would be possible to express several colonization factors in one strain. Alternatively, the same attenuations could be made in a range of different ETEC strains, each with a different colonization factor. This would involve deleting the toxins from such strains.
The DNA encoding the heterologous antigen is expressed from a promoter that is active in vivo. Two promoters that have been shown to work well in Salmonella are the nirB promoter (19, 20) and the htrA promoter (20). For expression of the ETEC colonization factor antigens, the wild-type promoters could be used.
A DNA construct comprising the promoter operably linked to DNA encoding the heterologous antigen may be made and transformed into the attenuated bacterium using conventional techniques. Transformants containing the DNA construct may be selected, for example by screening for a selectable marker on the construct. Bacteria containing the construct may be grown in vitro before being formulated for administration to the host for vaccination purposes.
Formulation of the vaccine
The vaccine may be formulated using known techniques for formulating attenuated bacterial vaccines. The vaccine is advantageously presented for oral administration, for example in a lyophilised encapsulated form. Such capsules may be provided with an enteric coating comprising, example, EUDRAGIT “S” (Trade Mark) anionic polymer of methacrylic acid and methacrylates with a —COOH group, EUDRAGIT “L” (Trade Mark) anionic polymer of methacrylic acid and methacrylates with a —COOH group, cellulose acetate, cellulose phthalate or hydroxypropylmethyl cellulose. These capsules may be used as such, or alternatively, the lyophilised material may be reconstituted prior to administration, e.g. as a suspension. Reconstitution is advantageously effected in a buffer at a suitable pH to ensure the viability the bacteria. In order to protect the attenuated bacteria and the vaccine from gastric acidity, a sodium bicarbonate preparation is advantageously administered before each administration of the vaccine. Alternatively, the vaccine may be prepared for parenteral administration, intranasal administration or intramuscular administration.
The vaccine may be used in the vaccination of a mammalian host, particularly a human host but also an animal host. An infection caused by a microorganism, especially a pathogen, may therefore be prevented by administering an effective dose of a vaccine prepared according to the invention. The dosage employed will ultimately be at the discretion of the physician, but will be dependent on various factors including the size and weight of the host and the type of vaccine formulated. However, a dosage comprising the oral administration of from 107 to 1011 bacteria per dose may be convenient for a 70 kg adult human host.
The Examples described in this section serve to illustrate the invention.
Design of deletions and construction of plasmids pCVDΔAroC, pCVDΔOmpC and pCVDΔOmpF
Deletions were designated to remove the entire open reading frame of the target gene. Using the E. coli genome sequence as a template, PCR primers were designed to amplify fragments of 500-600 base pairs flanking the target open reading frame (see Table 1 for primer sequences). Splicing by overlap extension using PCR was used to fuse the two flanking sequences, creating a PCR product with the entire gene deleted (FIG. 1). The wild-type sequences around the deletion site and the predicted sequences after deletion are depicted in FIG. 2.
For each gene two different restriction sites were introduced into the splice region (see Table 2 below). These were used for identification of deletion clones. The PCR primers at either end of the PCR fragment introduced unique restriction sites that were used to clone the fragment into the multiple cloning site of pCVD442 (FIG. 3).
PCR products were gel purified using a Qiagen (Trade Name) gel extraction kit and digested with the relevant restriction enzymes prior to ligation to the suicide plasmid pCVD442(22) digested with the same enzyme and treated with alkaline phosphatase to prevent vector self-ligation (FIG. 3). The ligation mix was transformed into SY327λpir and plated on L-Ampicillin (100 μg/ml) plates. Plasmids from Ampicillin resistant transformants were screened for the presence of the deletion cassettes by restriction digestion. The following plasmids were generated:
The suicide plasmid pCVD442 can only replicate in cells harboring the pir gene. On introduction into non-pir strains, pCVD442 is unable to replicate, and the Ampicillin resistance conferred by the plasmid can only be maintained if the plasmid is integrated in the chromosome by a single homologous recombination event. The plasmid also has a sacB gene, encoding levan sucrase, which is toxic to gram negative bacteria in the presence of sucrose. This can be used to select clones that have undergone a second recombination event, in which the suicide plasmid is excised. Such cells will be resistant to sucrose, but Ampicillin sensitive.
Construction and characterisation of ΔAroCΔOmpCΔOmpF strain
This section outlines the chronology of construction and history of a ΔAroCΔOmpCΔOmpF strain. In the section, “ETEC” refers specifically to strain E1392/75/2A or its derivatives.
ΔAroCΔOmpCΔOmpF deletions were introduced into E1392/75/2A in the following order: ΔAroC-ΔAroCΔOmpC-ΔAroCΔOmpCΔOmpF
Construction of ETECΔAroC
Conjugation was used to introduce pCVDΔOmpF into E1392/75/2AΔAroCΔOmpC.
7) Sucrose resistant colonies were screened for ΔompF gene by PCR with primers TT1/TT2. The sequences of the primers are given in Table 1 below. The screened colonies were grown overnight on L-Agar. 3 colonies out of 47 had the ΔompF gene with no evidence of the wild-type ompF gene.
10) The colonies were microbanked and one colony was chosen as a master stock.
11) For permanent storage, a bead from the master stock was inoculated into 1 ml L-broth, grown for 4 hr with shaking at 37° C. and used to make agar slopes which were used to make freeze dried stocks. The freeze dried stock of E1392/75/ 2AΔaroCΔompCΔompF was designated PTL003. 20 ml of L-broth was added to the rest of the 1 ml culture and the culture was incubated overnight at 30° C. 1 ml of the overnight culture was transferred to each of three cryovials and stored in liquid nitrogen.
Characterisation of E1392/75/2AΔAroCΔOmpCΔompF
Strain PTL003 was deposited on Sep. 3, 2001 under accession number 01090302 with the European Collection of Cell Cultures (ECACC), CAMR, Salisbury, Wiltshire SP4 OJG, United Kingdom.
Table 1—PCR primers (SEQ ID NOS: 7-28, respectively)
The study was designed to evaluate a candidate live attenuated vaccine strain of enterotoxigenic E. coli, namely the ΔaroC/ΔompC/ΔompF PTL003 described above.
Preparation of the vaccine seed lots
The bacterial strain was plated onto MacConkey agar for purity and for confirmation of identity, and 5 colonies used to inoculate a flask containing 200 ml of luria broth. After 8 hours incubation at +37° C., 30 ml of sterile glycerol was added to the broth culture and aliquots prepared (1 ml per vial). One hundred such vials were frozen at −70° C. These vials constituted the seed lot for the vaccine strain.
Purity of the seed lot was ensured by selecting ten random vials, and testing them for bacterial purity and freedom from fungi. An additional three vials were tested to determine the number of bacteria in the vials using standard plate count methods with serial dilutions of the culture broth.
Preparation of the vaccine
The vaccine was prepared fresh prior to each vaccination and all steps in the preparation of the inoculum carried out in a safety cabinet. The day prior to vaccination, 0.2 ml was spread onto the surface of luria agar plates using sterile cotton swabs to prepare the lawn of bacteria. The same culture broth was streaked onto MacConkey and luria agar plates for purity. The agar plates were incubated at 37° C. for 18 hours in a sealed container with tamper-resistant indicator tape to ensure that the plates were not tampered with during incubation. After incubation, the lawn of bacteria was harvested with 5 ml of sterile phosphate buffered saline (PBS), and the optical density of the suspension measured. The appropriate volume of this suspension, corresponding to the desired dose, was then placed into unit dose bottles with 30 ml of bicarbonate buffer and administered to the volunteers. An extra dose of vaccine was prepared and left in the laboratory, and immediately after the volunteers had been vaccinated the actual number of bacteria in each dose of vaccine was validated using standard colony count procedures with ten fold dilutions of vaccine.
The procedure for diluting the bacteria was established during preliminary studies using lawn cultures prepared and incubated exactly as done for the vaccine preparations administered to volunteers. Suspensions were made and the number of viable bacteria enumerated by colony counts of serial dilutions and related to the determined optical density. Based on these preliminary studies, a standard procedure was developed for preparing and validating the correct dilutions of bacteria in order to give the doses stated.
Preparation of buffer
A buffer consisting of sodium bicarbonate in water was used. For each dose of vaccine 150 ml of deionised water containing 2 gram of sodium bicarbonate was prepared and filter sterilised. 30 ml of the buffer was placed into 50 ml sterile vials and the dose of vaccine bacteria was added to these vials. The remaining 120 ml of buffer was placed into separate sterile bottles. At the time of vaccination, the volunteers were first administered 120 ml of buffer, then a minute later, 30 ml of buffer containing the vaccine.
Vaccination schedule
Groups of volunteers were studied in a dose escalation manner. The first group of volunteers received a dose of approximately 5×107 bacteria, the second a dose of approximately 5×109 and the third group a dose of approximately 5×108.
The volunteers were given Ciprofloxacin 500 mg BID for three days beginning on day 4. They were discharged on day 6, having had a haematology and chemistry screen for safety. Serum was saved for antibody measurement.
On days 9 and 14 the volunteers returned for follow-up outpatient visits at which time an interval history was done and a blood sample was obtained for serolodical assays. In total, blood (40 ml) was collected for serology three times, prior to vaccination and on day 9 and day 14 after vaccination.
Laboratory Assay Procedures
Up to two faecal specimens were cultured each day while the volunteers were in hospital. For qualitative cultures, a faecal swab was placed into Cary Blair transport media and taken to the laboratory where it was inoculated directly onto MacConkey agar and onto MacConkey agar containing antibiotics selective for the vaccine strain. Up to five colonies were shown to be agglutinated using antisera specific for the vaccine strain. For quantitative culture (first specimen each day only) faecal specimens were weighed and diluted in PBS, with serial 10-fold dilutions up to 10—4, and then 100 μl of each dilution was spread onto MacConkey agar with antibiotics. Suspected colonies were confirmed by agglutination with anti-O serum.
Serum was collected and saved for subsequent assay for antibody against CFA II antigens by ELISA and bactericidal antibody against the vaccine strain.
Peripheral blood mononuclear cells were separated from whole blood collected into citrate and washed. These cells were cultured at a density of 107 cells per ml in RPMI tissue culture medium at 37° C. for 48 hours. After 48 hours the supernatant was transferred to a cryovial and frozen at −20° C. until it could be assayed for IgG and IgA antibody to CFA II by ELISA.
Results:
No symptoms were seen at all actual doses of 6.8×107 and 3.7×108 cfu. At the higher dose of 4.7×109 ⅙ volunteers experienced diarrhoea and 2/6 had mild abdominal cramps. Bacterial shedding was seen in all volunteers at the 5×109 cfu dose level form day 1 post vaccination until, as per protocol, ciprofloxacin was started on day 4 after vaccination. This indicates good intestinal colonisation, which is indicative of the potential to induce a good immune response. At the two lower doses, vaccine strain was recovered from all volunteers on at least one time point following vaccination but the duration of the excretion was reduced compared to that seen at the highest dose.
At the time of filing the application, the analysis of the immune responses generated by the vaccine was incomplete. However, the IgA anti-CFA II responses in the culture supernatants of PBMNC purified from the blood of recipients of the highest dose of vaccine at day 0 (before vaccination) and days 7 and 10 post vaccination have been analysed (see FIG. 7). Supernatants were analysed by ELISA on assay plates coated with purified CFA II antigen. The OD values observed from the day 7 and day 10 samples were significantly higher than those from the pre-vaccination samples, demonstrating the induction of a specific IgA response at these time points. As expected, the responses show a peak at day 7 and are reduced at day 10, consistent with the homing of primed IgA secreting B-cells from the blood to the mucosal effector sites of the Gut Associated Lymphoid Tissue.
The attenuated live strain of ETEC (ΔaroC/ΔompC/ΔompF) has been shown to be well tolerated in healthy adult volunteers and to colonise the intestine in a manner consistent with its utility as an oral vaccine to protect against travellers diarrhoea. It has also been demonstrated to elicit a specific mucosal immune response.
| Number | Date | Country | Kind |
|---|---|---|---|
| 9806449 | Mar 1998 | GB | national |
This application is a national phase application of International Patent Appln. No. PCT/GB99/00935, filed Mar. 25, 1999 and designating the U.S.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/GB99/00935 | 3/25/1999 | WO | 00 | 1/31/2001 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO99/49026 | 9/30/1999 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 5683700 | Charles et al. | Nov 1997 | A |
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| 0 322 237 | Jun 1989 | EP |
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| 0 524 205 | Jan 1993 | EP |
| 9115572 | Oct 1991 | WO |
| 9215689 | Sep 1992 | WO |
| WO 9215689 | Sep 1992 | WO |
