of a Gram-negative bacterium.

Field of the invention

The present invention relates to the fields of medical microbiology and vaccines.

In particular the invention relates to a process for detergent-free preparation of outer membrane vesicles (OMV) of Gram negative bacteria for use in vaccines, to OMV obtainable by said process, and to a pharmaceutical composition comprising such OMV. The present invention further relates to the use of OMV of the present invention as a medicament in particular for use in a method for eliciting an immune response.

Background of the invention

Neisseria meningitidis is a human pathogen that can cause acute meningitis and septicemia, with fatality rates around 15% [Girard et al, 2006]. Serogroup B meningitis accounts for 30-40% of meningitis cases in North America [Sharip et al, 2006; Kaplan et al, 2006] and up to 80% in some European countries [Trotter et al, 2007; Gray et al, 2006], yet a broadly protective vaccine is not available. Effective vaccines against other serogroups have been developed based on capsular polysaccharide conjugated to a carrier protein [Snape et al, 2008]. This approach was not feasible for serogroup B, due to poor immunogenicity [Morley et al, 2001] and concerns for vaccination-induced autoimmunity [Finne et al, 1983]. To date, vaccines based on outer membrane vesicles (OMV) are the only vaccines that successfully controlled serogroup B epidemics with examples in Norway, Cuba, and New Zealand [Bjune et al, 1991; Thornton et al, 2006; Martin et al, 1998; Sierra et al, Fredriksen et al, 1991].

OMV are released from the outer membrane of gram negative bacteria and consist of a phospholipid (PL) bilayer that contains outer membrane proteins, lipopolysacchharide (LPS) and periplasmic constituents [Deatherage et al, 2009]. PorA protein was identified as the major protective antigen in OMV, but is highly variable between the circulating serogroup B strains which complicates vaccine development [Saukkonen et al, 1989; Martin et al, 2006]. For this reason, Rijks Instituut voor Volksgezondheid en Milieu (RIVM), i.e the National Institute for Public Health and the Environment (Bilthoven, The Netherlands) developed an OMV vaccine based on genetically modified N. meningitidis strains that express multiple PorA subtypes. This multivalent OMV vaccine was initially made with 2 trivalent PorA strains, expressing a total of 6 PorA subtypes [van der Ley et al, 1995; Claassen et al, 1996] and provided functional immunogenicity in phase II clinical trials. To ensure sufficient coverage for serogroup B strains circulating globally, a third trivalent strain was added [van den Dobbelsteen et al, 2007].

OMV vaccines are traditionally prepared with detergent extraction (dOMV purification process) to remove LPS and increase vesicle release. The LPS of N. meningitidis is highly toxic, but residual amounts (approx. 1%) are needed to maintain vesicle structure and adjuvate the immune response against PorA [Arigita et al, 2005; Arigita et al, 2003; Steeghs et al, 2004]. With balanced detergent concentrations the dOMV purification process provides these requirements, however there are major disadvantages. Along with LPS, detergent removes PL and also lipoproteins that contribute to immunogenicity, such as factor H binding protein [Koeberling et al, 2009; Koeberling et al, 2008]. The resulting immune response is directed against a specific PorA subtype, without eliciting cross-protection [Morley et al, 2001; van der Voort et al, 1996]. In addition, selective removal of LPS and PL changes the native vesicle structure and promotes aggregation [Hoist et al, 2009; Cametti et al, 2008]. Detergent- treatment is necessary to decrease LPS toxicity, but has detrimental side effects that complicate vaccine development.

Detergent-free OMV purification processes retain all LPS, resulting not only in a preserved native vesicle structure, but also in vaccines that are inherently toxic when used for parenteral immunization [Hoist et al, 2009]. Two detergent-free purification processes have been described. The native OMV (nOMV) process [Zollinger et al 1979; US 6,558,677] comprises similar steps as dOMV, however with a detergent-free extraction step and the supernatant OMV (sOMV) process [Post et al, 2005; Devoe et al, 1973; Hoekstra et al, 1976] utilizes ultrafiltration or ultracentrifugation to purify spontaneously released OMV from the culture supernatant, without extraction. nOMV vaccines produced encouraging results in animals and humans, but high LPS content limited applicability of the vaccine to intranasal administration [Guthrie et al, 2004; Katial et al, 2002; Saunders et al, 1999; Drabick et al, 1999]. Preclinical data on sOMV vaccines is limited to a single study in mice, reporting cross-protection against a panel of serogroup B strains that was not found with dOMV, however potential differences in toxicity and stability were not addressed [Ferrari et al, 2006]. The sOMV process imposes an additional challenge, since it produces OMV yields that are too low for feasible process development [Post et al, 2005; Devoe et al, 1973].

Discovery of lpxLl mutant strains at RIVM Bilthoven [van der Ley et al, 2001] provided a solution for the LPS toxicity issue. Deletion of lpxLl attenuate LPS toxicity, while preserving the adjuvant activity needed for the immune response [Koeberling et al, 2008; van der Ley et al, 2001 ; Fisseha et al, 2005; van de Waterbeemd et al, 2010].

However, for clinical trials or GMP manufacturing of nOMV/sOMV a robust scalable production process is required in which the EDTA extraction step is needed for high yield, but to date causes undesired effects such as bacterial lysis [Prachayasittikul et al, 2010]. DNA release caused by lysis is a problem for large scale production since removal processes such as ultracentrifugation only have limited capacity.

Accordingly, since the processes available to date to prepare sOMV and nOMV either suffer from low yield and/or low purity and/or are limited to laboratory scale, there is a need for improved processes to prepare bacterial OMV, in particular for processes at industrial scale.

Description of the invention

Surprisingly, it has now been demonstrated that OMV can be prepared detergent- free with high yield and high purity in a process that can be performed at any scale.

Accordingly, in a first aspect the present invention provides a process for detergent-free preparation of bacterial outer membrane vesicles (OMV) for use in vaccines, said process comprising the steps of:

a) cultivating a population of a Gram-negative bacterium to stationary growth phase; b) at a time point at least about 1 hour after onset of stationary growth phase, incubating the bacteria obtained in a) in a medium adjusted to or having a pH higher than about pH 7.5 or higher than pH 8.0 and a concentration of a metal chelating agent, preferably EDTA, of between about 1 and 100 mM to extract OMV; and, c) recovering the OMV extracted in b), wherein the recovery at least comprises removal of the bacteria from the OMV.

Preferably, the time point after the onset of stationary phase of about 1 hours is a time point of between 1 and 9 hours, more preferably between, 1 and 8 hours, 1 and 7 hours, 1 and 6 hours, 2 and 5 hours, 2 and 4 hours, 2 and 3.5 hours or 2.5 and 3.5 hours. Preferably, in any of the processes according to the invention, the OMV are sterilized, preferably by filter sterilization, preferably using a filter with pores of less than about 0.3 micrometer. Preferably, sterilization is performed during step c); yield loss is greatly decreased due to performing step b) according to the invention. Filter sterilization also referred to as sterile filtration, is herein defined as filtering a compound of interest through a filter, preferably with pores of between about 0.5 and 0.2 micrometer, such that the filtrate comprising the compound of interest does not comprise any microorganism, or that the amount of microorganism in the filtrate is reduced to an acceptably low level.

The term "detergent-free" is herein preferably defined as that no detergent is added and/or used during an extraction step of any of the processes according to the invention; more preferably, no detergent is added and/or used at all during any of the processes according to the invention. If a detergent is used, e.g. as a processing aid in the form of an anti-foam agent, like the anti-foams from Sigma- Aldrich (cat. nr. A6426, A5633, A5757, A8011 or A5758), or molecules with comparable function from other manufacturers, during the cultivation of a population, this is considered to be within the scope of the process according to the invention. It is also possible that in a solution used within a process according to the present invention, small traces of a detergent are inherently present, e.g. traces of a detergent in a complex medium for cultivation; such inherent presence is also considered to be within the scope of the process according to the present invention.

A detergent is herein preferably defined as an agent, preferably a reagent, that has surfactant capacity and, when contacted with the bacterium, has the capacity to extract protein from the bacterium. A detergent can be an anionic, cationic, non-ionic (having a net charge of zero, also known as zwitterionic) or an ethyloxylate. Preferably, an antifoam agent, i.e. an agent that reduces and hinders the formation of foam in industrial process liquids such as the anti-foams from Sigma-Aldrich (cat. nr. A6426, A5633, A5757, A8011 or A5758) is not within the definition of a detergent. Cultivation of a population of a Gram negative bacterium in any of the processes according to the invention may be performed by any method known to the person skilled in the art. A preferred culture medium is a chemically defined medium, preferably such as described in Baart et al., 2007. The temperature may be varied at any temperature such as between about 30 and about 40°C. The pH may be varied at any pH such as at a pH from about 5.5 to 8.5. Preferred culture conditions comprise culturing at about 35 °C at pH 7.2 with aeration. Culture may be performed in several steps, including but not limited to a pre-culture or seed-culture and a main culture. The culture can be performed on any scale, including but not limited to shake flask cultivation, small-scale or large-scale cultivation (including continuous, batch, fed-batch, or solid state cultivation) in laboratory or industrial fermenters. Preferably, the volume of the culture is at least about 10L, more preferably at least about 20L, 40L, 60L 80L, 100L, 200L, 300L, 400L, 500L, 800L, 1500L, 5000L, 10.000L, 20.000L or 40.000L.

A population of a bacterium is herein defined as at least two bacteria, preferably of the same genus and species.

Preferably, the OMV are prepared from a Gram negative bacterium having a genetic modification which causes the bacterium to produce an LPS that is modified to have reduced toxicity. Preferably, the Gram negative bacterium has an LPS with reduced toxicity wherein the LPS (or its Lipid A moiety (LA)) is modified to have reduced toxicity. An LPS that is modified to have reduced toxicity is herein understood as an LPS that is modified to have less toxicity than the toxicity of a corresponding wild-type LPS. Preferably, the modified LPS has less than about 90, 80, 60, 40, 20, 10, 5, 2, 1, 0.5, or 0.2% of the toxicity of the corresponding wild-type LPS. The toxicities of wild-type and various modified LPS's with reduced toxicity may be determined in any suitable assay known in the art. A preferred assay for determining the toxicity, i.e. the biological activity of the LPS is the WEHI test for T F-alpha induction in the MM6 macrophage cell line [Espevik and Niessen, 1986, J.Immunol. Methods 95: 99- 105; Ziegler-Heitbrock et al, 1988, Int. J. Cancer 41 : 456-461].

However, while it is preferred that the LPS of the Gram negative bacterium (or its LA moiety) has reduced toxicity, it is further preferred that the LPS retains at least part of immunostimulatory activity, i.e. adjuvant activity. Thus, the LPS with reduced toxicity of the Gram negative bacterium to be used in the invention preferably has at least about 10, 20, 40, 80, 90 or 100% of the immunostimulatory activity of the corresponding wild-type LPS, whereby the immunostimulatory activity is determined by measuring the production of at least one cytokine or the expression of at least one costimulatory molecule upon co-cultivation of dendritic cells (DC) with the Gram negative bacterium producing the LPS with reduced toxicity as described in Example 3 in WO 2005/107798. The cytokine produced by the DC is preferably selected from IL12, IL10, T F-α, IL6 and IL-Ιβ and the costimulatory molecule expressed by the DC is preferably selected from CD40 and CD86.

Gram negative LPS's having reduced toxicity of the Lipid A moiety but retaining (part of) the adjuvant activity, may e.g. be obtained from genetically modified Gram negative pathogens and as reviewed in WO02/09746. Genetically modified Gram negative pathogens producing LPS with reduced toxicity of the Lipid A moiety but retaining (part of) their adjuvant activity include e.g. Gram negative bacteria having one or more genetic modifications that decrease or knock-out expression of one or more genes selected from the IpxLl and lpxL2 genes or homologues thereof (formerly known as htrB and msbB; see e.g. WOOO/26384; US 5,997,881) and the lipid A 4'- kinase encoding IpxK gene or a homologues thereof (see also below); and genetic modifications that effect the expression of one or more a heterologous IpxE and pagL genes. Preferred genetic modifications are modifications that decrease or knock-out expression of one or more genes selected from the IpxLl and lpxL2 genes or homologues thereof. A preferred LPS with reduced toxicity of the Lipid A moiety but retaining (part of) its adjuvant activity is an LPS described in WOOO/26384 and is an LPS with a lipid A having a reduced number of secondary acyl chains per molecule of LPS compared to the corresponding non-modified LPS molecule and having at least one secondary acyl chain bound to a primary acyl chain at the reducing end of the glucosamine disaccharide; preferably said lipid A has the same number of primary acyl chains as the non-modified LPS molecule and/or said lipid A has a secondary acyl chain on the primary acyl chain at the 2 position of the glucosamine at the reducing end of the glucosamine disaccharide and/or said LPS is an LPS wherein the secondary acyl chain is a lauroyl chain and/or said lipid A has a phosphoethanolamine attached to a phosphate group at the reducing end and/or said lipid A having the molecular structure:

CH,

I ^z CH,

CH, CH,

CH ₃

Stationary growth phase is herein defined as a phase in culture where the growth rate has slowed as a result of nutrient depletion and/or accumulation of toxic products. This phase is e.g. reached as the bacteria begin to exhaust specific nutrient resources that were previously available. The stationary growth phase is preferably a period in culture where the rate of bacterial growth is close or equal to the rate of bacterial death. Preferably, the growth rate of the bacteria has slowed to below 0.1. More preferably, the growth rate of the bacteria has changed from between about 0.3 - 0.5 to below 0.1, even more preferably from about 0.40 ± 0.10 h ^"1 (exponential growth) to 0.00 ± 0.10 h ^"1 (stationary growth). The onset of the stationary growth phase can be determined by the person skilled in the art by any means available, including but not limited to monitoring bacterial growth with timely measuring optical density or dry weight measurements, or by measuring depletion of nutrients such as carbon sources such as glucose, nitrogen sources such as amino acids or ammonium, or by monitoring oxygen consumption or C0 ₂ production Preferably, the onset of the stationary growth phase is defined by determining at least one of the maximum oxygen consumption rate and the maximum C0 ₂ production rate. Preferably therefore, at least one of the maximum oxygen consumption rate and the maximum C0 ₂ production rate are monitored continuously at least during the cultivation step.

The onset of stationary phase may be induced passively, such as in batch culture when a nutrient becomes depleted. The onset of stationary phase may be induced actively, such by depletion of a nutrient from the feed in fed-batch culture, by pH change, or by stopping or reducing the feed or oxygen supply. After the onset of stationary phase, the bacteria are preferably maintained under the same culture conditions as present at the onset of stationary phase, such as temperature, oxygen concentration, stirring, pH etc. Preferably, after the time point at least 1 hour after the onset of stationary growth phase as specified earlier herein, the bacteria or the culture comprising the bacteria is cooled to a temperature of below about 20°C, more preferably below about 15°C, 10°C, 8°C, 6°C, more 5°C, 4°C, 3°C, 2°C, or below about 1°C. When cooled, the bacteria or the culture comprising the bacteria may be stored at the temperature below 20°C as defined here above. The bacteria may be stored at below -20°C, more preferably at below -80°C, -135°C or below -150°C; however, preferably the bacteria or the culture comprising the bacteria is not cooled to a temperature that would cause freezing of (part of) the culture or bacteria, such as e.g. temperatures below 0°C since this could induce lysis of the bacteria.

After the time point at least 1 hour after the onset of stationary growth phase as specified earlier herein, the bacteria obtained are incubated in a medium comprising a metal chelating agent, preferably EDTA, to extract OMV. The metal chelating agent may be any metal chelating agent known to the person skilled in the art. Preferably, the metal chelating agent is one or at least one selected from the group consisting of polyamino carboxylic acids e.g. nitrilotriacetic acid (NTA), diethylene triamine pentaacetic acid (DTP A), ethylene glycol tetraacetic acid (EGTA), l,2-bis(o- aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), ethylenediaminetetraacetic acid (EDTA) Preferably, the metal chelating agent is EDTA. The incubation can be performed at any scale. The invention encompasses that bacteria from several different cultures are incubated in a single medium comprising a metal chelating agent, preferably EDTA, to extract OMV. Preferably, the volume of the incubation is at least about 10L, more preferably at least about 20L, 40L, 60L 80L, 100L, 200L, 300L, 400L, 500L, 800L, 1500L, 5000L, 10.000L, 20.000L or 40.000L. The bacteria may contacted with the medium comprising a metal chelating agent, preferably EDTA, by any means knows to the person skilled in the art. The bacteria may e.g. be separated from the culture medium by centrifugation and then be contacted with the medium comprising a metal chelating agent, preferably EDTA, e.g. by resuspending in the medium comprising a metal chelating agent, preferably EDTA. Preferably, the culture medium is gradually replaced by the medium comprising a metal chelating agent, preferably EDTA. Preferably, the bacteria obtained in the culture are first concentrated by microfiltration. Preferably, the volume of the culture is decreased 2-fold, more preferably 3 -fold, more preferably 4-fold, more preferably 5 -fold, more preferably 6- fold, more preferably 7 fold, more preferably 9-fold, more preferably 10-fold. The concentrated bacterial suspension is then diafiltrated. Preferably the culture medium is gradually replaced with a buffer that has the appropriate pH for extraction. Diafiltration is herein defined as microfiltration with constant volume, wherein a first medium comprising a compound of interest is replaced through continuous dialysis with a second medium, such that the compound of interest after diafiltration is present in the second medium. As such, the medium of the culture medium is thus gradually replaced by another suitable medium, preferably lOOmM Tris-HCl pH 8.6. The concentration and diafiltration may be performed simultaneously or subsequently. When performed simultaneously, the second medium is a medium with the appropriate pH for extraction and comprising a metal chelating agent, preferably EDTA, or a medium buffer with the appropriate pH to which an appropriate amount of a metal chelating agent, preferably EDTA is added directly after diafiltration; preferably, the second medium comprises a buffering agent such as Tris-HCl, at a concentration of between about lOmM to 250mM, with a pH higher than about pH 7.5, preferably as defined below, to which between about 1 mM to lOOmM of a metal chelating agent, preferably EDTA is added. Diafiltration is preferably performed until the first medium has completely been replaced by the second medium; this process may take at least 1 hour - 4 hours, or more. Diafiltration can be performed using any membrane suitable known to the person skilled in the art. Preferably, hollow fiber elements with pore size 0.2 micrometer are used. The medium comprising a metal chelating agent, preferably EDTA, may be any medium suitable for the extraction of OMV. Preferably, the medium does not comprise a detergent. Preferably, the medium comprising a metal chelating agent, preferably EDTA, further comprises a buffering agent or a mixture of buffering agents; examples of buffering agents are, but are not limited to Tris and phosphate. A preferred medium is 100 mM Tris-HCl; pH 8.6 with 10 mM EDTA.

Preferably, the medium comprising a metal chelating agent, preferably EDTA, has a concentration of metal chelating agent, preferably EDTA of between about 1 and lOOmM. Preferably, the concentration is between about 1 and 50 mM, more preferably between about 1 and 25 mM, 2 and 25 mM, 3 and 25 mM, 4 and 25 mM, 5 and 25 mM, or 5 and 20 mM, and most preferably between about 5 and 15 mM such as about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 and 15 mM. Preferably, the metal chelating agent is one as defined earlier herein, more preferably, the metal chelating agent is EDTA. Preferably, the medium has the preferred value of the concentration of metal chelating agent, preferably EDTA, after the bacteria have been contacted with the medium. The concentration of metal chelating agent, preferably EDTA, of the medium may be adjusted. Adjustment may take place during any time of contacting the bacteria with the medium or during incubation of the bacteria in the medium, and may be performed more than once and may be performed continuously and/or automatically. The person skilled in the art knows how to adjust the metal chelating agent concentration of a medium, e.g. by measuring the metal chelating agent concentration and by adding an appropriate amount of metal chelating agent, either as a solid or as a solution. When the metal chelating agent is EDTA, the EDTA may be in any form, e.g. as acid or as one of the EDTA salts known to the person skilled in the art, or as mixture of several forms of EDTA.

Preferably, the medium comprising a metal chelating agent, preferably EDTA, has a pH higher than about pH 7.5. Preferably, the pH of the medium a metal chelating agent, preferably EDTA is higher than about pH 7.6, pH 7.7, pH 7.8, pH 7.9, pH 8.0, pH 8.1, pH 8.2, pH 8.3, pH 8.4, pH 8.5, pH 8.6, pH 8.7, pH 8.9, pH 9.0, pH 9.1, pH 9.2, pH 9.3, pH 9.4 or pH 9.5. More preferably, the pH of the medium is between about pH 7.5 and pH 9.5, more preferably between about pH 8.0 and pH 9.0, more preferably between about pH 8.2 and pH 8.8, more preferably between about pH 8.4 and pH 8.7. Most preferably, the pH of the medium comprising a metal chelating agent, preferably EDTA is about pH 8.6. Preferably the pH is at the preferred value after the bacteria have been contacted with the medium comprising a metal chelating agent, preferably EDTA. The pH of the medium a comprising metal chelating agent, preferably EDTA may be adjusted. Adjustment may take place during any time of contacting the bacteria with the medium or during incubation of the bacteria in the medium, and may be performed more than once and may be performed continuously and/or automatically. The person skilled in the art knows how to adjust pH of a medium, e.g. by measuring the pH and adding a suitable acid or base to the medium comprising a metal chelating agent, preferably EDTA.

A preferred medium for the extraction of the OMV is a medium with pH higher than about pH 7.5 and wherein the concentration of the metal chelating agent, preferably EDTA, is between about 5 to 15mM; more preferably, the pH is about pH 8.6 and the concentration of the metal chelating agent, preferably EDTA, is between about 5 to 15mM; preferably, the medium comprises Tris-HCl, e.g. 100 mM as a buffering agent.

After incubation of the bacteria in a medium comprising a metal chelating agent, preferably EDTA to extract the OMV, the OMV are recovered by at least removing the bacteria from the OMV. Removal of the bacteria from the OMV may be performed by any means known to the person skilled in the art. Examples of methods for removal are, but are not limited to: filtration with 0.5-0.2 μπι pore size, centrifugation, or any other method for (spontaneous) sedimentation of bacteria. A preferred method to remove the bacteria from the OMV is by batch or continuous centrifugation, depending on the scale of the process, e.g. batch centrifugation for volumes up to about 100L and continuous centrifugation for volumes above about 100L.

After recovery or simultaneously with recovery, the OMV preparation may be purified. Purification may comprise any methods known to the person skilled in the art. Preferably at least one method from the following group is applied: ultrafiltration as described earlier herein and/or diafiltration to exchange the medium, e. g. to remove the metal chelating agent from the extraction medium and/or to concentrate the OMV preparation; degradation of nucleic acids such as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which may be performed enzymatically using one or more suitable nucleases, preferably using Benzonase® (Merck, the Netherlands); clarification by filtration, preferably using a filter with a pore size of between about 0.5μΜ and 1.0 μΜ; gel filtration (such as Size Exclusion Chromatography; Sepharose 6 Fast Flow column material; OMV are recovered from the void volume of the column); sterile filtration as described earlier herein. Preferably, at least sterile filtration is applied. Preferably, more than one purification method is applied. Preferably, the following methods are consecutively applied: ultrafiltration (e.g. 100 or 300 kDa cutoff), diafiltration (e.g. 100 or 300 kDa cut-off), enzymatic degradation of nucleic acids, clarification, gel filtration and sterile filtration, although not necessarily in this order. A preferred process according to the invention does not include ultracentrifugation.

Degradation of nucleic acids using benzonase is preferably performed in a buffer of pH 8.4 +/- 0.4, comprising between about 0.1 to 10U benzonase/ml and between about 1 to lOmM of Mg ²⁺ , at 4°C to 37°C for 1 to 20 hours.

Preferably, in any of the processes according to the invention, the population of a Gram-negative bacterium comprises a species of Neisseria, Bordetella, Haemophilus, Actinobacillus or Pasteurella; more preferably a species of Neisseria or Bordetella; even more preferably, the population of a Gram-negative bacterium comprises a Neisseria lactamica, a Neisseria gonorrheae, a Neisseria meningitidis, a Bordetella pertussis, or a Pasteurella multocida; even more preferably a Neisseria meningitidis, preferably a serogroup B Neisseria meningitidis or a Bordetella pertussis.

Preferably, the population of a Gram-negative bacterium comprises a Gram- negative bacterium having one or more mutations to decrease or knock-out expression of a gene product. Preferably, the gene product is selected from the group consisting of cps, ctrA, ctrB, ctrC, ctrD, exbB, exbD, firpB, galE, htrB, msbB, lpbB, lpxK, lpxLl, nmb0033, op A, opC, rmpM, phoP, pilC, pmrE, pmrF, porA, porB, siaA, siaB, siaC, said, synA, synB, sync, tbpA and tbpB, or homologues thereof; many of these mutations are reviewed in WO02/09746. Preferably, the gene product is selected from the group consisting of cps, lipid A biosynthesis gene products including lpxLl, rmpM, porA, porB and opA. Preferably, the Gram-negative bacterium has at least mutations to decrease or knock-out expression of lpxLl, preferably such as described in WO00/26384. Preferably, the Gram-negative bacterium has at least mutations to decrease or knock-out expression of both lpxLl and rmpM. Preferably, lpxLl has at least about 30% sequence identity, more preferably at least about 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% sequence identity with the amino acid sequence of SEQ ID NO: 1. Most preferably, lpxLl is identical to the amino acid sequence of SEQ ID NO: 1.

Preferably, rpmM has at least about 30% sequence identity, more preferably at least about 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%), 97%), 98%), or 99% sequence identity with the amino acid sequence of SEQ ID NO: 2. Most preferably, rpmM is identical to the amino acid sequence of SEQ ID NO: 2.

Preferably, the Gram-negative bacterium is a Neisseria meningitidis strain that is a replicate or derivative of Neisseria meningitidis serogroup B isolate H44/76 [Holten et al, 1979; van den Dobbelsteen et al, 2007].

It is understood that replicates and/or derivatives of any strain according to the invention are encompassed by the invention. The term "replicate" refers to the biological material that represents a substantially unmodified copy of the material, such as material produced by growth of micro-organisms, e.g. growth of bacteria in culture media. The term "derivative" refers to material created from the biological material and which is substantially modified to have new properties, for example caused by heritable changes in the genetic material. These changes can either occur spontaneously or be the result of applied chemical and/or physical agents (e.g. mutagenesis agents) and/or by recombinant DNA techniques as known in the art. When referring to a strain "derived" from another strain, it is understood that both "replicates" of that strain, as well as "derivatives" of the strain are encompassed, as long as the derived strain can be used to elicit an immune response against the Gram negative bacterium used in the method of the invention, such as e.g. Neisseria meningitidis.

Percentage of identity is herein preferably determined by calculating the ratio of the number of identical nucleotides/amino acids in the sequence divided by the length of the total nucleotides/amino acids minus the lengths of any gaps. DNA multiple sequence alignment was herein performed using any suitable sequence alignment software package available to a person skilled in the art. The minimal length of a relevant amino acid sequence showing 30% or higher identity level should preferably be about 40 amino acids, more preferably about 50, 70, 100, 150, 170, 200, 210, 220, 230, 240 or more amino acids, and in case of lpxLl more preferably about 50, 70, 100, 150, 170, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 295 or more amino acids. Preferably, the sequence identity is calculated over the entire sequence of SEQ ID NO: 1 or 2.

Expression will herein be understood to include any step involved in the production of a polypeptide including, but not limited to transcription, post- transcriptional modification, translation, post-translational modification, and secretion.

To decrease or knock-out expression a gene product defined earlier herein, the person skilled in the art has a plethora of well-known tools available. It is routine practice for the person skilled in the art to choose an adequate strategy to introduce a suitable modification in a polynucleotide in order to decrease or knock-out expression of a functional gene product. For example, methods for in vitro mutagenesis are described in Sambrook et al. (Molecular cloning, A laboratory Manual, 2 ^nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1989). Corresponding methods are also available commercially in the form of kits (e.g., Quikchange site-directed mutagenesis kit by Stratagene, La Jolla, USA). Deletion of a polynucleotide may, for example, be accomplished by the gene replacement technology that is well known to the skilled person.

Preferably, the population of a Gram-negative bacterium comprises multiple species of Gram-negative bacteria such that multiple serotypes of antigen are expressed and finally end up in the OMV preparation. More preferably, a species of Gram- negative bacteria expresses multiple serotypes of an antigen. When the population of bacteria comprises a Neisseria meningitidis, the population preferably comprises a Neisseria meningitidis expressing multiple serotypes of porA antigen; more preferably, the population of bacteria comprises multiple species of Neisseria meningitidis, each species expressing multiple serotypes of porA antigen. Preferably, the population of a Gram-negative bacterium comprises three trivalent PorA Neisseria meningitidis strains, expressing a total of 9 PorA subtypes [van der Ley et al, 1995; Claassen et al, 1996; van den Dobbelsteen et al, 2007].

The Gram-negative bacterium, which preferably is a Neisseria meningitidis strain that is a replicate or derivative of Neisseria meningitidis serogroup B isolate H44/76, may express an antigen foreign to said Gram-negative bacterium. OMV prepared according to the invention prepared from said Gram-negative bacterium will comprise said foreign antigen. As such, the OMV according to the invention can be used as a vehicle with adjuvant activity and can conveniently be used for the treatment diseases or conditions associated with said foreign antigen. The antigen foreign to the Gram- negative bacterium may be any antigen and may be one or at least one selected from the group consisting of Nad A protein, heparin binding protein, Q fever surface antigen, a Chlamydia antigen, pertactin, pertussis toxin, 92kDa antigen, fim2, fim3, dermonecrotic toxin, factor H binding protein, polysaccharides from Neisseria meningitis serogroup A, C, W135 or Y, Chlamydia surface antigen, diphtheria toxoid, attenuated or inactivated polio virus, tetanus toxiod, Haemophilus influenzae b polysaccharide or auto-antigens associated with diseases where an autoimmune response may be involved such as e.g. Alzheimers disease and tumor antigens.

The foreign antigen may be expressed by any means known to the person skilled in the art; preferably the foreign antigen is targeted to the OMV. Preferably, the foreign antigen or a part thereof is fused to or comprised in Neisseria meningitidis serogroup B porA or a part thereof.

Within the scope of the invention, it is possible to culture or otherwise provide several species of Gram-negative bacteria, each expressing a single or multiple antigen serotype and to extract OMV simultaneously from one or more pooled populations of said bacteria. It is also within the scope of the present invention to extract the OMV separately from populations of bacteria and then preferably pool the preparations of OMV. It is further within the scope of the invention that different species Gram- negative bacteria are cultivated together in a single, mixed population or separately in individual populations or even in a combination of individual and mixed populations.

The OMV preparation obtained by any of the processes according to the present invention can conveniently be stored for future use, either in lyophilized form or in solution, or frozen in solution. In any of the processes according to the present invention, one or several compounds may be added to the OMV preparation such as a (colloidal) stabilizer, such as sucrose, in order to prevent aggregation and/or a preservative such as thiomersal in order to prevent microbial growth.

The OMV preparation obtained by any of the processes according to the present invention can conveniently be used for the preparation of a medicament, preferably a medicament for the treatment of meningitis, preferably said medicament is a vaccine against Neisseria meningitidis infection. Accordingly, any of the processes according to the present invention, may further comprise the step of combining the OMV with a pharmaceutically accepted excipient, such as a carrier, an adjuvant, a stabilizing agent, an osmotic agent, a buffering agent and/or a dispersing agent. In addition, in any of the processes according to the present invention, the OMV may be combined with a another antigen to prepare a mixed vaccine, preferably with antigens comprising outer membrane proteins from Neisseria meningitis serogroup B or from other gram-negative pathogens, including but nor limited to NadA protein, heparin binding protein, Q fever surface antigen, pertactin, pertussis toxin, 92kDa antigen, fim2, fim3, dermonecrotic toxin, factor H binding protein, polysaccharides from Neisseria meningitis serogroup A, C, W135 or Y preferably conjugated to a suitable pharmaceutically accepted carrier protein, Chlamydia surface antigen, diphtheria toxoid, attenuated or inactivated polio virus, tetanus toxiod, Haemophilus influenzae b polysaccharide, preferably conjugated to a suitable pharmaceutically accepted carrier protein.

Vaccination is applied for the prophylactic protection against pathogens or for the treatment of diseases following pathogenic infection.

Adjuvants are herein defined to include any substance or compound that, when used in combination with an antigen, to immunize a subject, preferably a mammal, preferably a human, stimulates the immune system, thereby provoking, enhancing or facilitating the immune response against the antigen, preferably without generating a specific immune response to the adjuvant itself. Preferred adjuvants enhance the immune response against a given antigen by at least a factor of 1.5, 2, 2.5, 5, 10 or 20, as compared to the immune response generated against the antigen under the same conditions but in the absence of the adjuvant. Tests for determining the statistical average enhancement of the immune response against a given antigen as produced by an adjuvant in a group of animals or humans over a corresponding control group are available in the art. The adjuvant preferably is capable of enhancing the immune response against at least two different antigens.

The pharmaceutical carrier can be any compatible, non-toxic substance suitable to deliver the active ingredients, to the subject. Pharmaceutically acceptable carriers for intranasal delivery are exemplified by water, buffered saline solutions, glycerin, polysorbate 20, cremophor EL, and an aqueous mixture of caprylic/capric glyceride, and may be buffered to provide a neutral pH environment. Pharmaceutically acceptable carriers for parenteral delivery are exemplified by sterile buffered 0.9% NaCl or 5% glucose optionally supplemented with a 20% albumin. Preparations for parental administration must be sterile. The parental route for administration of the active ingredients is in accord with known methods, e.g. injection or infusion by subcutaneous, intravenous, intraperitoneal, intramuscular, intraarterial or intralesional routes. The compositions according to the invention are preferably administered by bolus injection. For oral administration, the active ingredient can be administered in liquid dosage forms, such as elixirs, syrups, and suspensions. Liquid dosage forms for oral administration can contain coloring and flavoring to increase patient acceptance. Methods for preparing parenterally, orally or intranasally administrable compositions are well known in the art and described in more detail in various sources, including, for example, Remington's Pharmaceutical Science (15th ed., Mack Publishing, Easton, PA, 1980) (incorporated by reference in its entirety for all purposes).

In a second aspect, the present invention provides OMV obtainable by any one of the processes according to first aspect of the present invention. Preferably, said OMV is the directly derived product of any one of the processes according to the first aspect of the present invention.

The OMV preparation obtainable by any of the processes according to the present invention can conveniently be used for the preparation of a medicament, preferably a medicament for the treatment of meningitis, preferably said medicament is a vaccine against Neisseria meningitidis infection. Preferably, said OMV preparation is the directly derived product of any one of the processes according to the first aspect of the present invention. Accordingly, the present invention provides a pharmaceutical composition comprising OMV obtainable by any of the processes according to the present invention and pharmaceutically acceptable excipient, such as a carrier, an adjuvant, a stabilizing agent, an osmotic agent, a buffering agent and/or a dispersing agent, as described earlier herein. Preferably, said OMV is the directly derived product of any one of the processes according to the first aspect of the present invention. Since the present invention provides for OMV comprising adjuvant activity itself, a preferred pharmaceutical composition does not comprise an additional adjuvant other than the OMV comprising adjuvant activity.

The pharmaceutical composition may be used as a vaccine. The vaccine may be used for immunization (raising an immune response) or vaccination of a subject, preferably a mammal, preferably a human. In the pharmaceutical composition, the OMV may be combined with another antigen to prepare a mixed vaccine, i.e. in combination with vaccines against Neisseria meningitidis serogroup A, C, W135, Y, pneumococcal disease, diphtheria, whooping cough, polio, RSV, or tetanus The present invention further provides an OMV obtainable by any of the processes according to the present invention for use as a medicament, preferably in the treatment of meningitis. Preferably, said medicament is a vaccine against Neisseria meningitidis infection. Preferably, said OMV is the directly derived product of any one of the processes according to the first aspect of the present invention.

The present invention further provides the use of an OMV obtainable by any of the processes according to the present invention for the preparation of a medicament, preferably for the treatment of meningitis. Preferably, said medicament is a vaccine against Neisseria meningitidis infection. Preferably, said OMV is the directly derived product of any one of the processes according to the first aspect of the present invention.

The present invention further provides a process for eliciting in a subject an immune reaction, preferably against Neisseria meningitidis, comprising administering to said subject OMV obtainable by any of the processes according to the present invention or administering to said subject a pharmaceutical composition according to the invention, preferably a vaccine against Neisseria meningitidis infection. Preferably, said OMV is the directly derived product of any one of the processes according to the first aspect of the present invention.

The present invention further provides the use of the OMV according to the invention or a pharmaceutical composition according to the invention for eliciting in a subject an immune reaction, preferably against Neisseria meningitidis, comprising administering to said subject OMV according to the invention or a pharmaceutical composition according to the invention.

In this document and in its claims, the verb "to comprise" and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article "a" or "an" thus usually means "at least one". The word "about" or "approximately" when used in association with a numerical value (e.g. about 10) preferably means that the value may be the given value (of 10) more or less 0.1% of the value.

The sequence information as provided herein should not be so narrowly construed as to require inclusion of erroneously identified bases. The skilled person is capable of identifying such erroneously identified bases and knows how to correct for such errors. In case of sequence errors, the sequence of the polypeptide obtainable by expression of the gene present in Neisseria meningitidis serogroup B isolate H44/76 containing the nucleic acid sequence coding for the polypeptide should prevail.

All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.

The present invention is further described by the following example which should not be construed as limiting the scope of the invention.

Unless stated otherwise, the practice of the invention will employ standard conventional methods of molecular biology, virology, microbiology or biochemistry. Such techniques are described in Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual (2 ^nd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press; in Sambrook and Russell (2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, NY; in Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current Protocols, USA; and in Volumes I and II of Brown (1998) Molecular Biology LabFax, Second Edition, Academic Press (UK); Oligonucleotide Synthesis (N. Gait editor); Nucleic Acid Hybridization (Hames and Higgins, eds.). Description of the figures

Figure 1. Typical PorA content of trivalent bulk OMV from the three different trivalent RL NonaMen strains, together expressing the same 9 PorA subtypes as the HP

NonaMen strains [van den Dobbelsteen et al, 2007], but with additional deletions in rmpM and IpxLl genes. Depicted are trivalent bulk OMV from strains RL16215, RL10124 and RL1416, respectively, containing the PorA at approximately 41 kDa. Typical PorA content of RL NonaMen trivalent bulk OMV is between 60-80% of total protein content.

Figure 2. Functional immunogenicity in rabbits of RL NonaMen vaccines at 2 different doses (7.5 and 15 μg/PorA), with and without A1P04 adjuvant. Pre-immunisation sera were taken at D=0 and post-immunisation sera were taken after three immunisations. All three vaccines gave significantly higher bactericidal titres at D=43 than at D=0, but no significant dose or adjuvant related effects were observed. This indicated that RL 7.5 μg/PorA contains sufficient antigen and that there is no need for the use of adjuvants when the vaccine is made with the process described herein.

Sequences

Table 1. Sequences as set forth in the Sequence Listing

SEQ ID NO: SEQ type Gene product

1 Polypeptide Neisseria meningitidis IpxLl

2 Polypeptide Neisseria meningitidis rpmM

Examples

Example 1 : Scalable manufacturing of nonavalent OMV vaccine against Neisseria meningitidis serotype B with improved yield and purity

The example below was performed with 40 L production culture, but is fully scalable to at least 800 L.

Three different Neisseria meningitidis serogroup B strains, originating from strain H44/76 [Fredriksen et al 1991] with additional deletions in cps, porB, rmpM and IpxLl genes [Van de Waterbeemd et al 2010] and each expressing 3 unique PorA subtypes [Van den Dobbelsteen et al 2007], namely:

Pl .7,16 / PI .5-1,2-2 / PI .19,15-1 for strain RL16.2.15;

PI .5-2,10 / P12-1, 13 / P1.7-2,4 for strain RL10.12.4 and

Pl .22,14 / PI .7-1,1 / PI .18-1,3,6 for strain RL14.1.6,

were stored at -135°C as master seed lots. Master seed lots were thawed and expanded in shake flasks with 150mL chemically defined medium [Baart et al 2007], divided in aliquots during exponential growth and stored at -135°C after addition of glycerol to obtain working seed lots.

A primary preculture shake flask with chemically defined growth medium (Baart et al., 2007) was inoculated with a frozen working seed lot to provide an identical starting point for each production batch. During exponential growth the entire primary preculture was used to inoculate a secondary preculture, grown in 3 L chemically defined growth medium [Baart et al., 2007] in a bioreactor. During growth of the secondary preculture, temperature was controlled at 35°C and dissolved oxygen concentration was controlled at 30% with variable stirring speed and addition of pure oxygen to the headspace airflow. During exponential growth, 1L of biomass from the secondary preculture was transferred to 40 L chemically defined growth medium (Baart et al., 2007). The production culture was grown in a bioreactor with controlled temperature at 35°C, controlled pH at 7.2 with phosphoric acid and an anti-foam agent. Dissolved oxygen concentration was controlled at 30% with a combination of variable stirring speed and variable sparger airflow.

Stationary growth phase set in as determined by periodical OD measurement. The complete 40L production culture was subsequently harvested by transferring into a stirred tank after 3 hours of stationary growth, to ensure an optimal balance between OMV yield and DNA release caused by bacterial lysis. The harvested production culture was first cooled to 20°C and the volume was then reduced from 40 L to 6 L, using microfiltration with hollow fiber units (0.2 μπι pore size). The concentrated harvest was diafiltrated with 2 volumes (12 L) 100 mM Tris-HCl buffer at pH 8.6 to adjust biomass pH to pH 8.4±0.4 Concentrated lOOmM EDTA solution was added to a final concentration of 10 mM to initiate OMV extraction followed by incubation for30 min. at 20°C in a stirred a tank at 100 rpm. Biomass was separated from the OMV extract with parallel batch centrifugation at semi-high-speed (6 buckets of 1 L; 30 min.; 4°C; 20.000x g); supernatant was retained. Batch centrifugation can be replaced with continuous centrifugation, if desired, for production at industrial scale. Supernatants were pooled and any residual pathogens or other particles were removed by depth filtration through a unit with a pore size narrowing from initially 0.5 μπι to a final pore size of 0.2 μπι.

The pathogen-free OMV extract was either stored at 4°C for several weeks or was used directly for downstream processing. Volume was first reduced 12-fold to 0.5 L using ultrafiltration with 100 kDa cut-off and then diafiltrated with 2 volumes (1 L) lOOmM Tris-HCl buffer pH 8.6 to remove EDTA. Any genomic DNA present in the crude OMV was digested into fragments of less than 1000 bp using 1000 U/L (final concentration) Benzonase (Merck) in the presence of Mg ²⁺ cofactor (incubation at 21°C for 18 hours). Any precipitates that may have formed during the Benzonase treatment were removed with a clarification filter (1.2-0.5 μπι), before purifying the crude OMV on a gel filtration column that was packed with Sepharose 6 Fast Flow material (GE Healthcare) to remove DNA and small molecules from the OMV and allow a buffer change to storage buffer (10 mM Tris-HCl pH 7.4 with 3% (w/v) sucrose). Trivalent bulk OMV was then sterilized by filtration through a unit with 0.2 μπι pore size and diluted to 1 mg/mL trivalent PorA with storage buffer (10 mM Tris-HCl pH7.4 and 3% (w/v) sucrose). At this concentration, the bulk OMV could be safely stored at 4°C for at least 6 months without loss of quality (Table 2).

The yield improvement obtained by harvesting the production culture at 3 hours after onset of stationary growth phase and performing the OMV extraction at pH 8.6 was 2.7-fold and could even be increased to 6.3-fold (Table 3), if harvest was delayed until 9 hours after onset of stationary growth and process modifications for improved DNA removal capacity were implemented (i.e. by using 10000 U/L Benzonase; The overall yield of the process described above was 30 ± 4 mg trivalent PorA per liter production culture (the equivalent of 1338 human doses of 7.5 μg per PorA subtype). This PorA yield was obtained with an overall downstream process efficiency of 33 ± 7%. Sterile filtration was included in this calculation and it is emphasized that the described process results in high filtration efficiency and reproducibility (92% ± 4%, Table 4) when compared to reference processes. The reference processes either used a preservative [thiomersalate; Fredriksen et al 1991 and Claasen et al 1996] to prevent yield loss associated with sterile filtration, or included process steps with mechanic shearing to reduce OMV size and improve efficiency [RIVM 2007 NonaMen: Van den Dobbelsteen et al 2007 and Zollinger et al 2010]. In addition, trivalent bulk OMV from the strains mentioned above had improved PorA purity compared to OMV from other strains and processes [Zollinger et al 2010, US6558677 (Figure 5); Fredriksen et al 1991]. Typical trivalent PorA content was 60-80% of total protein content (Figure 2). Despite the high LPS content, low toxicity was observed. This was enabled by the IpxLl deletion which attenuates LPS toxicity [Van de Waterbeemd et al 2010].

Trivalent bulk OMV from three strains listed previously was mixed proportionally to create nonavalent bulk OMV and consecutively diluted with storage buffer to a final concentration of 0.135 mg/mL nonavalent PorA (7.5 μg per PorA subtype per dose; no adjuvant) and 0.270 mg/mL nonavalent PorA (15 μg per PorA subtype per dose; both with and without A1P0 ₄ adjuvant). The three different vaccines were subdivided in 0.5 mL aliquots and stored at 4°C until parenteral administration in rabbits on day 1, 15 and 29.

All OMV vaccines gave significantly higher bactericidal titres at D=43 than at D=0, but no significant dose or adjuvant related effects were observed. This indicated that RL 7.5 μg/PorA contained sufficient antigen and that there is no need for the use of adjuvants when the vaccine is made with the process according to the present invention. In addition the OMV vaccines induced cross-protection based on other antigens than PorA alone, as indicated by the high bactericidal titres against AporA strain HI5 (Figure 2). Table 2: Analysis of the different trivalent OMV during long-term storage.

Table 3: OMV and DNA yields obtained with different setpoints for harvest (in hours after onset of stationary growth) and pH (of the EDTA extraction buffer). Results were calculated with predictive models, obtained from the outcome of an experimental design study. In results #1 to #3, harvest and pH setpoints were optimized for the lowest (#1) or highest (#2) possible OMV yield and for the highest OMV yield with a restriction on DNA yield (#3). Results #4 to #8 were obtained with predefined setpoints for harvest and a fixed pH setpoint. Yield is defined in mg/L crude OMV extract.

Table 4: Sterile filtration efficiency of three consecutive bulk OMV batches. Minor losses were observed (<10%), which were mainly caused by the dead volume of the sterile filter.

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