FIELD OF THE INVENTION The present invention relates generally to the field of medicine, and Specifically to microbiology, Immunology, vaccines and the prevention of infection by a bacterial pathogen by immunization. BACKGROUND OF THE INVENTION Streptococcus pneumoniae is a leading cause of meningitis, pneumonia, and severe invasive disease in infants and young children throughout the world. The multivalent pneumococcal polysaccharide vaccines have been licensed for many years and have proved valuable in preventing pneumococcal disease in elderly adults and high-risk patients. However, infants and young children respond poorly to 15 most pneumococcal polysaccharides. The 7-valent pneumococcal conjugate vaccine (7vPnC, Prevnar®) was the first of its kind demonstrated to be highly immunogenic and effective against invasive disease and otitis media in infants and young children. This vaccine is now approved in many countries around the world. Prevnar contains the capsular polysaccharides from serotypes 4, 6B, 9V, 14, 180, 19F and 23F, each 20 conjugated to a carrier protein designated CRMigy. Prevnar covers approximately 80-90%, 60-80%, and 40-80% of invasive pneumococcal disease (IPD) in the US, Europe, and other regions of the world, respectively [1,2]. Surveillance data gathered in the years following Prevnar's introduction has clearly demonstrated a reduction of invasive pneumococcal disease in US infants as expected (FIG. 1) [3,4]. Sun/eillance of IPD conducted in US infants prior to the introduction of Prevnar demonstrated that a significant portion of disease due to serogroups 6 and 19 was due to the 6A (approximately one-third) and 19A (approximately one-fourth) serotypes [5,6]. Pneumococcal invasive disease surveillance conducted in the US after licensure of Prevnar suggests that a large burden of disease is still attributable 30 to serotypes 6A and 19A (FIG. 1) [3]. Moreover, these two serotypes account for more cases of invasive disease than serotypes 1, 3, 5, and 7F combined (8.2 vs. 3.3 cases/100,000 children 2 years and under), in addition, serotypes 6A and 19A are 1 associated with higii rates of antibiotic resistance (FIG. 2) [7.8,9]. While it is possible that serogroup cross-protection will result in a decline of serotype 6A and 19A disease as more children are immunized, there is evidence to suggest that there will be a limit to the decline, and a significant burden of disease due to these serotypes ^' 5 will remain (see below). Given the relative burden and importance of invasive pneumococcal disease due to serotypes 1, 3, 5, 6A, 7F, and 19A, adding these serotypes to the Prevnar formulation would increase coverage for invasive disease to >90% in the US and 10 Europe, and as high as 70%-80% in Asia and Latin America. This vaccine would significantly expand coverage beyond that of Prevnar, and provide coverage for 6A and 19A that is not dependent on the limitations of serogroup cross-protection. SUMMARY OF THE INVENTION 15 Accordingly, the present invention provides generally a multivalent immunogenic composition comprising 13 distinct polysaccharide-protein conjugates, wherein each of the conjugates contains a capsular polysaccharide from a different serotype of Streptococcus pneumoniae conjugated to a carrier protein, together with a physiologically acceptable vehicle. Optionally, an adjuvant, such as an aluminum- 20 based adjuvant, is included in the formulation. More specifically, the present invention provides a 13-valent pneumococcal conjugate (13vPnC) composition comprising the seven serotypes in the 7vPnC vaccine (4, 6B, 9V, 14, 18C, 19F and 23F) plus six additional serotypes (1, 3, 5, 6A, 7F and 19A). 25 The present invention also provides a multivalent immunogenic composition, wherein the capsular polysaccharides are from serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F of Streptococcus pneumoniae and the carrier protein is CRM197. 30 The present invention further provides a multivalent immunogenic composition, wherein the capsular polysaccharides are from serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9v, 14, 180, 19A, 19F and 23F of Streptococcus pneumoniae, the carrier protein is CRM197, and the adjuvant is an aluminum-based adjuvant, such as aluminum phosphate, aluminum sulfate and aluminum hydroxide. In a particular embodiment of the invention, the adjuvant is aluminum phosphate. I The present invention also provides a multivalent immunogenic composition, ,' 5 comprising polysaccharide-protein conjugates together with a physiologically acceptable vehicle, wherein each of the conjugates comprises a capsular polysaccharide from a different serotype of Streptococcus pneumoniae conjugated to a carrier protein, and the capsular polysaccharides are prepared from serotype 3 and at least one additional serotype. 10 In one embodiment of this multivalent immunogenic composition, the additional serotype is selected from the group consisting of serotypes 1, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F. In another embodiment, the carrier protein is CRM197. In yet another embodiment, the composition comprises an adjuvant, such 15 as an aluminum-based adjuvant selected from aluminum phosphate, aluminum sulfate and aluminum hydroxide. In a particular embodiment, the adjuvant is aluminum phosphate. The present invention also provides a multivalent immunogenic composition, 20 comprising polysaccharide-protein conjugates together with a physiologically acceptable vehicle, wherein each of the conjugates comprises a capsular polysaccharide from a different serotype of Streptococcus pneumoniae conjugated to a carrier protein, and the capsular polysaccharides are prepared from serotypes 4, 6B, 9V, 14,18C, 19F, 23F and at least one additional serotype. 25 In one embodiment of this multivalent immunogenic composition, the additional serotype is selected from the group consisting of serotypes 1, 3, 5, 6A, 7F, and 19A. In another embodiment, the carrier protein is CRM197. In yet another embodiment, the composition comprises an adjuvant, such as an aluminum-based 30 adjuvant selected from aluminum phosphate, aluminum sulfate and aluminum hydroxide. In a particular embodiment, the adjuvant is aluminum phosphate. 3 The present invention also provides a method of inducing an immune response to a Streptococcus pneumoniae capsular polysaccharide conjugate, comprising administering to a human an immunologically effective amount of any of the immunogenic compositions just described. , 5 The present invention further provides that any of the immunogenic compositions administered is a single 0.5 mL dose formulated to contain: 2 pg of each saccharide, except for 6B at 4 pg; approximately 29 pg CRM197 carrier protein; 0.125 mg of elemental aluminum (0.5 mg aluminum phosphate) adjuvant; and 10 sodium chloride and sodium succinate buffer as excipients. BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 depicts the changes in iPD rates by serotype in US children <2 years of age from baseline (1998/1999) to 2001. 15 FIG. 2 depicts the distribution of pneumococcal isolates with resistance to penicillin (PCN) in children <5 years of age (1998). FIG. 3 depicts the reverse cumulative distribution curves (RCDC) of OPA post-third dose results from the 0118-P16 Prevnar trial. 20 DETAILED DESCRIPTION OF THE INVENTION Inclusion of Prevnar Serotypes 4, 6B, 9V, 14, 18C, 19F, 23F Data from IPD surveillance between 1995-1998 estimated that the seven serotypes in Prevnar were responsible for around 82% of IPD in children <2 years of 25 age [5]. In Northern California, the site of the efficacy trial, the Prevnar serotypes accounted for 90% of all cases of IPD in infants and young children [10]. Since introduction of the Prevnar vaccine in 2000, there has been a significant decrease in the overall IPD rates due to a decrease in disease due to the vaccine serotypes [3,4]. Therefore, there is no justification at this time to remove any of the Prevnar serotypes 30 from the next generation of pneumococcal conjugate vaccines but rather to add serotypes to obtain wider coverage. 4 Inclusion of Serotypes 1, 3, 5 and 7F In the US, the rate of IPD caused by serotype 1 in children under the age of 5 years is <2%, about the same as for each of types 3 and 7F [1,6]. Serotypes 1 and 5 account for higher rates of IPD in US populations at high risk for invasive 5 pneumococcal disease. Specifically, serotype 1 causes 3.5% of IPD in Alaskan native children <2 years of age, and 18% in children 2-4 years of age [11]. Both serotype 1 and serotype 5 significantly cause disease in other parts of the world and in indigenous populations in developed countries [12,13,14]. 10 Serotype 1 may also be associated with more severe disease as compared with other pneumococcal serotypes [15]. This observation is based on the difference in rates of case identification between the US and Europe, and the associated difference in medical practice. Overall, the incidence of IPD is lower in Europe than in the US. However, the percent of IPD caused by serotype 1 in Europe is 15 disproportionately higher than in the US (6-7%, vs. 1-2%, respectively). In Europe, blood cultures are obtained predominantly from hospitalized children. In the US, it is routine medical practice to obtain blood cultures in an outpatient setting from children presenting with fever >39°C and elevated white blood cell counts. Given the difference in medical practice, it is postulated that the lower percent of disease 20 caused by serotype 1 in the US may be diluted by higher rates of other serotypes causing milder disease, while the higher percent in Europe reflects more serious disease. In addition, seroepidemiology studies of children with complicated pneumonia demonstrate that serotype 1 is disproportionately represented [16,17,18]. This suggests that inclusion of serotype 1 may reduce the amount of severe 25 pneumococcal disease, as well as, contribute to a total reduction in invasive pneumococcal disease. The addition of serotypes 3 and 7F will increase coverage against IPD in most areas of the world by approximately 3%-7%, and in Asia by around 9%. Thus, 30 an 11-valent vaccine would cover 50% in Asia and around 80% of IPD in all other regions [1,2]. These serotypes are also important with respect to otitis media coverage [19]. In a multinational study of pneumococcal serotypes causing otitis media, Hausdorff et al found serotype 3 to be the 8th most common middle ear fluid 5 ft ; isolate overall [20]. Serotype 3 accounted for up to 8.7% of pneumococcal serotypes associated with otitis media. Thus, the importance of types 3 and 7F in otitis media; as well as in IPD, warrants their inclusion in a pneumococcal conjugate vaccine. 5 However, attempts to produce a multivalent pneumococcal conjugate vaccine that exhibits significant immunogenicity with respect to serotype 3 polysaccharides have been unsuccessful. For example, in a study of the immunogenicity and safety of an 11-valent pneumococcal protein D conjugate vaccine (11-Pn-PD), no priming effect was observed for serotype 3 in infants who had received three doses of the 10 vaccine followed by a booster dose of either the same vaccine or a pneumococcal polysaccharide vaccine (Nurkka et al. (2004) Ped. Inf. Dis. J., 23:1008-1014). In another study, opsonophagocytic assay (OPA) results from infants who had received doses of 11-Pn-PD failed to show antibody responses for serotype 3 at levels comparable to other tested serotypes (Gatchalian e^ al., 17"^ Annual Meeting of the 15 Eur. Soc. Paed. Inf. Dis. (ESPID), Poster No. 4, PI A Poster Session 1, Istanbul Turkey, Mar. 27, 2001). In yet another study, which assessed the efficacy of an 41-Pn-PD in the prevention of acute otitis media, the vaccine did not provide protection against episodes caused by serotype 3 (Prymula et at. www.thelancet.com. Vol. 367: 740-748 (March 4, 2006)). Accordingly, a pneumococcal conjugate vaccine 20 comprising capsular polysaccharides from serotype 3 and capable of eliciting an immunogenic response to serotype 3 polysaccharides provides a significant improvement over the existing state of the art. Inclusion of Serotypes 6A and 19A 25 a. Epidemiology of Serotypes 6A and 19A Surveillance data in the literature suggest that serotypes 6A and 19A account for more invasive pneumococcal disease in US children <2 years of age than serotypes 1, 3, 5, and 7F combined (FIG. 1) [1,5]. In addition, these serotypes are commonly associated with antibiotic resistance (FIG. 2) and play an important role in 30 otitis media [6,19,20]. The ability of the current Prevnar vaccine to protect against disease due to 6A and 19A is not clear. The rationale for inclusion of 6A and 19A components in a 13vPnC vaccine is discussed below. 6 b. Responses to 6A and 19A Induced by 6B and 19F Polysaccharides The licensed unconjugated pneumococcal polysaccharide vaccines (for use in persons at least two years of age) have contained 6A or 6B capsular 5 polysaccharide but not both [21]. Immunogenicity data generated at the time of formulation of the 23-valent pneumococcal polysaccharide vaccine demonstrated that a 6B monovalent vaccine induced antibody to both the 6A and 6B capsules. The data from several trials assessing IgG and opsonophagocytic assay (OPA) responses in a variety of populations with free polysaccharide and with 10 pneumococcal conjugate vaccines suggested that IgG responses to 6A are induced by 6B antigens, but the responses are generally lower, and the OPA activity with 6A organisms is different than with 6B organisms [22,23,24,25]. In addition, subjects responding with high 6B antibody may have little or no activity against 6A. 15 In contrast to the chemical composition of the 6A and 68 capsular polysaccharides where there exists a high degree of similarity, the 19A and 19F capsules are quite different due to the presence of two additional side chains in the 19A polysaccharide. Not surprisingly, immune responses measured in human volunteers immunized with 19F polysaccharide vaccine showed that responses to 20 19F were induced in 80% of subjects, but only 20% of subjects had a response to 19A [26]. Low levels of cross-reactive IgG and OPA responses to serotype 19A after immunization with 19F polysaccharide have also been documented in trials with conjugate vaccines as well [24,26]. 25 Internal data on cross-reactive OPA responses to 6A and 19A have been generated from the 7vPnC bridging trial (D118-P16) conducted in US infants (FIG. 3). These studies are consistent with the findings of others, and demonstrate induction of cross-reactive functional antibody to 6A polysaccharide after immunization with 6B polysaccharide, although at a lower level, and very little functional antibody to 19A 30 after immunization with 19F. 7 Impact of 6B and 19F Immunization on 6A and 19A in Animal Models Animal models have been used to evaluate the potential for cross-protection with polysaccharide immunization. In an otitis media model developed by Giebink et al„ chinchillas were immunized with a tetravalent polysaccharide outer membrane 5 protein (OMP) conjugate vaccine (containing 6B, 14, 19F, 23F saccharides) or placebo [27]. In this trial there appeared to be some cross-protection for 6A; however this did not reach statistical significance and the level of protection was lower than with 6B against otitis media. In this same model there was 100% protection against 19F otitis media, but only 17% protection against 19A otitis media. 10 Saeland et al. used sera from infants immunized with an 8-valent pneumococcal tetanus conjugate vaccine (containing 6B and 19F) to passively immunize mice prior to an intranasal challenge with 6A organisms, in a lung infection model [28]. Of the 59 serum samples, 53% protected mice against bacteremia with 15 68 and 37% protected against 6A. Mice passively immunized with sera from infants immunized with four doses of an 11-valent pneumococcal conjugate vaccine (containing 19F conjugated to tetanus toxoid) were given an intranasal challenge with 19A organisms in the same model [29]. Of 100 mice passively immunized and then challenged, 60 mice had no 19A organisms detected in lung tissue, whereas 20 organisms were identified in ail mice given saline placebo. However, passive immunization did not protect against challenge with 19F organisms in this model; therefore, the relevance of the model for serogroup 19 is questionable. In general these models provide evidence of some biological impact of 68 immunization on 6A organisms although the effect on the heterologous serotype was not as great as that 25 observed with the homologous serotype. The impact of 19F immunization on 19A organisms is not well understood from these models. Impact of 6B and 19F Polysaccharide Conjugate Immunization on 6A and 19A Disease in Efficacy/Effectiveness Trials 30 The number of cases of disease due to the 63, 6A, 19F and 19A serotypes in 7vPnC and 9vPnG (7vPnC plus serotypes 1 and 5) efficacy trials is noted in Table 1 [30,10,31]. The numbers of invasive disease cases are too small to allow any conclusions to be drawn for serotypes 6A and 19A. However, the Finnish otitis 8 media trial generated a large number of pneumococcal isolates [32]. In the per protocol analysis 7vPnC was 84% (95% CI 62%, 93%) efficacious against otitis media due to serotype 6B and 57% (95% CI 24%, 76%) efficacious against otitis media due to serotype 6A (Table 1). In contrast, serotype-specific efficacy witti the 5 7vPnC was not demonstrated for otitis media due to either 19F or 19A. Table 1. Cases of Pneumococcal Disease Due to Serotypes 6B, 6A, 19F, and 19A in Efficacy Trials with tiie TvPnC and 9vPnC Vaccines __ __ j ^ I -^ PnC IContr. PnC jContr. PnC jContr. PnC Icontr. Kaiser Efficacy Trial - 7vPnC ^ j Q ^ 2*13 0 1 Navajo Efficacy Trial - 7vPnC g c < n ^ ■) ^ 0 South African Efficacy Trial -^ 9'i n n •) 1 1 9vPnC HIV (-) (ITT) 1 ^ 1 u u ( o ( South African Efficacy Trial - A -, Q ^n r> i ■> •» 9vPnC HIV (f) (ITT) ^ ^ ^ ^Q ^. i Z i Finnish otitis Media Trial- g* gg ^g* 45 43 53 ^7 26 *Statistically significant efficacy demonstrated 10 From references 30.10 and 33, and personal communications Contr = control ITT = intention to treat analysis PR = per protocol analysis 15 Post-marketing IPD surveillance data is also available from a case-control trial conducted by the Centers for Disease Control to evaluate the effectiveness of Prevnar [33]. Cases of pneumococcal invasive disease occurring in children 3 to 23 months of age were identified in the surveillance laboratories and matched with three 20 control cases by age and zip code. After obtaining consent, medical and immunization history (subjects were considered immunized if they had received at least one dose of Prevnar) was obtained from parents and medical providers for cases and controls. The preliminary results were presented at the 2003 ICAAC meeting and a summary of the findings for 6B, 19F, 19A and 6A disease is presented 25 in Table 2. These data indicate that Prevnar is able to prevent disease due to 6A, although at a level that may be somewhat lower than serotype 6B disease. These data also indicate that the cross-protection for invasive disease due to 19A is limited. 9 Table 2. Preliminary results of a Case Control Trial Performed by the CDC (presented at ICAAC, 2003) ^__ Serotype Informative Sets, n ^^ '^ [ (95% CI) Vacci ne Type, All 115 ^^ Vaccine Related, All 36 (Ss'^SS) Non-Vaccine Type, All 43 (.^otAB) f_ (72, 99) 19F 1Q ''^ 2 (16, 92) 6A 15 ^^ If (53, 97) 19A 16 "^0 I ^f _J (-87, 80) *Vaccine effectiveness comparing vaccinated (>1 dose) vs. unvaccinated, and adjusted for underlying conditions Reference 40 and persohal/confldential communication A published analysis [3] of the use of Prevnar also indicated that serotypes 6B and 19F conferred a nnoderate reduction in IPD caused by serotypes 6A and 19A among children under two years of age (Table 1 in [3]). Disease rates anaong 10 unimmunized adults caused by serotypes 6A, 9A, 9L, 9N, 18A, 18B, 18F, 19A, 19B, 19C, 23A and 23B ("all vaccine-related serotypes") were somewhat reduced (Table 2 in [3]). These data establish that herd immunity from the use of Prevnar in children under two years of age was modest for serotypes 6A and 19A, and provide a basis for the inclusion of serotypes 6A and 19A in the 13vPnC vaccine of this invention. 15 Conclusion for addition of 6A and 19A The post-marketing surveillance data and the case-control study results noted in FIG. 1 and Table 2 with the 7vPnC vaccine suggest that, consistent with the other information on immune responses and performance in the animals models described 20 above, there may be some cross-protection against 6A disease, but to a lesser extent than to 6B disease. Furthermore, it appears the protection against 19A is limited. Therefore, a 13vPnC vaccine containing serotypes 6A and 19A provides coverage that is not dependent on the limitations of serogroup cross-protection by serotypes 6B and 19F. 25 10 Accf3rding!y, the present invention provides a multivalent immunogenic composition comprising 13 distinct polysaccharide-protein conjugates, wherein each of the conjugates contains a different capsular polysaccharide conjugated to a carrier protein, and wherein the capsular polysaccharides are prepared from serotypes 1,3, 5 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F of Streptococcus pneumoniae, together with a physiologically acceptable vehicle. One such carrier protein is the diphtheria toxoid designated CRM197. The immunogenic composition may further comprise an adjuvant, such as an aluminum-based adjuvant, such as aluminum phosphate, aluminum sulfate and aluminum hydroxide. 10 Capsular polysaccharides are prepared by standard techniques known to those skilled in the art. In the present invention, capsular polysaccharides are prepared from serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F of Streptococcus pneumoniae. These pneumococcal conjugates are prepared by 15 separate processes and formulated into a single dosage formulation. For example, in one embodiment, each pneumococcal polysaccharide serotype is grown in a soy-based medium. The Individual polysaccharides are then purified through centrifugation, precipitation, ultra-filtration, and column chromatography. The purified polysaccharides are chemically activated to make the saccharides capable of 20 reacting with the carrier protein. Once activated, each capsular polysaccharide is separately conjugated to a carrier protein to form a glycoconjugate. In one embodiment, each capsular polysaccharide is conjugated to the same carrier protein. In this embodiment, the 25 conjugation is effected by reductive amination. The chemical activation of the polysaccharides and subsequent conjugation to the carrier protein are achieved by conventional means. See, for example, U.S. Pat. Nos. 4,673,574 and 4,902,506 [34,35]. 30 Carrier proteins are preferably proteins that are non-toxic and non-reactogenic and obtainable in sufficient amount and purity. Carrier proteins should be 11 amenable to standard conjugation procedures. In a particular embodiment of the present invention, CRM197 is used as the carrier protein. CRM197 (Wyeth, Sanford, NC) is a non-toxic variant (i.e., toxoid) of diphtheria 5 toxin isolated from cultures of Corynebacterium diphtheria strain C7 (p197) grown in casamino acids and yeast extract-based medium. CRM197 is purified through ultra-filtration, ammonium sulfate precipitation, and ion-exchange chromatography. Alternatively, CRM197 is prepared recombinantly in accordance with U.S. Patent No. 5,614,382, which is hereby incorporated by reference. Other diphtheria toxoids are 10 also suitable for use as carrier proteins. Other suitable carrier proteins include inactivated bacterial toxins such as tetanus toxoid, pertussis toxoid, cholera toxoid (e.g., as described in International Patent Application WO2004/083251 [38]), E coli LT, £ coli ST, and exotoxin A from 15 Pseudomonas aeruginosa. Bacterial outer membrane proteins such as outer membrane complex c (OMPC), porins, transferrin binding proteins, pneumolysin, pneumococcal surface protein A (PspA), pneumococcal adhesin protein (PsaA), C5a peptidase from Group A or Group B streptococcus, or l-iaemophiius infiuenzae protein D, can also be used. Other proteins, such as ovalbumin, keyhole limpet 20 hemocyanin (KLH), bovine serum albumin (BSA) or purified protein derivative of tuberculin (PPD) can also be used as carrier proteins. After conjugation of the capsular polysaccharide to the carrier protein, the polysaccharide-protein conjugates are purified (enriched with respect to the amount 25 of polysaccharide-protein conjugate) by a variety of techniques. These techniques include concentration/diafiltration operations, precipitation/elution, column chromatography, and depth filtration. See examples below. After the individual glycoconjugates are purified, they are compounded to 30 formulate the immunogenic composition of the present invention, which can be used as a vaccine. Formulation of the immunogenic composition of the present invention can be accomplished using art-recognized methods. For instance, the 13 individual pneumococcal conjugates can be formulated with a physiologically acceptable 12 I vehicle to prepare the composition. Examples of such vehicles include, but are not limited to, water, buffered saline, polyols (e.g., glycerol, propylene glycol, liquid polyethylene glycol) and dextrose solutions. 5 In certain embodiments, the immunogenic composition will comprise one or more adjuvants. As defined herein, an "adjuvant" is a substance that serves to enhance the immunogenicity of an immunogenic composition of this invention. Thus, adjuvants are often given to boost the immune response and are well known to the skilled artisan. Suitable adjuvants to enhance effectiveness of the composition 10 include, but are not limited to: (1) aluminum salts (alum), such as aluminum hydroxide, aluminum phosphate, aluminum sulfate, etc.; (2) oil-in-water emulsion formulations (with or without other specific immunostimulating agents such as muramyl peptides (defined below) or bacterial cell 15 wall components), such as, for example, (a) MF59 (PCT Publ. No. WO 90/14837), containing 5% Squalene, 0.5% Tween 80, and 0.5% Span 85 (optionally containing various amounts of MTP-PE (see below, although not required)) formulated into submicron particles using a microfluidizer such as Model 110Y microfiuidizer (Microfluidics, Nevrton, MA), 20 (b) SAP, containing 10% Squalene, 0.4% Tween 80, 5%pluronic-blocked polymer L121, and thr-MDP (see below) either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion, and (c) Ribi™ adjuvant system (RAS), (Corixa, Hamilton, MT) containing 2% Squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the 25 group consisting of 3-O-deaylated monophosphorylipid A (MPL™) described in U.S. Patent No. 4,912,094 (Corixa), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL + CWS (Detox™); (3) saponin adjuvants, such as Quil A or STIMULON™ QS-21 (Antigenics, Framingham, MA) (U:S. Patent No. 5,057,540) may be used or particles generated 30 therefrom such as ISCOMs (immunostimulating complexes); (4) bacterial lipopolysaccharides, synthetic lipid A analogs such as aminoalkyi glucosamine phosphate compounds (AGP), or derivatives or analogs thereof, which are available from Corixa, and which are described in U.S. Patent No. 6,113,918;'one 13 such AGP is 2-[(R)-3-Tetradecanoyloxytetradecanoylamino]ethyl 2-Deoxy-4-0-phosphono-3-0-[(R)-3-tetraciecanoyloxytetradecanoyl]-2-[(R)-3-tetradecanoy!oxytetradecanoylamino]-b-D-glucopyranoside, which is also l solution. The filter was discarded. The polysaccharide was then filtered through a 20 0.2 pm filter. The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafilter and diafiltered with a sodium chloride solution. The partially purified polysaccharide solution was further purified by filtration through a depth filter impregnated with activated carbon. After filtration, the carbon 25 filter was rinsed with a sodium chloride solution. The rinse is combined with the polysaccharide solution, which is then filtered through a 0.2 pm filter. The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafilter and adjusted with a 1M sodium phosphate buffer to achieve a final concentration of 0.0,25 M sodium phosphate. The pH was checked and adjusted to 7.0 + 0.2. 30 The ceramic hydroxyapatite (HA) column was equilibrated with sodium phosphate buffer containing sodium chloride to obtain the appropriate conductivity (<15 pS). The polysaccharide solution was then loaded onto the column. Under these conditions, impurities bound to the resin and the polysaccharide was recovered 19 in the flow-through from the column. The polysaccharide solution was filtered through 0.2|jm inline filters located before and after the column. The polysaccharide solution was concentrated using a 30 kDa MWCO filter. The concentrate was then diafiltered with Water for Injection (WFI). 5 The diafiltered polysaccharide solution was filtered through a 0.2 [jm membrane filter into polypropylene bottles. Samples were removed for release testing and the purified polysaccharide was stored frozen at -25° ± 5°C. Characterization 10 The 1H-NMR.data was consistent with the chemical structure by the assignment of signals assigned to the protons of the polysaccharide molecule. The 1H-NMR spectrum showed a series of well-resolved signals (protons from the methyl group) for the quantitation of the 0-acetyl functional group in the polysaccharide. The identity of the monovalent polysaccharide was confirmed by 15 countercurrent Immunoelectrophoresis using specific antisera. High performance gel filtration chromatography coupled with refractive index and multiangle laser light scattering (MALLS) detectors was used in conjunction with the sample concentration to calculate the molecular weight. Size exclusion chromatography media (CL-4B) was used to profile the relative 20 molecular size distribution of the polysaccharide. Example 2 Preparation of Serotype 1 Pneumococcal Saccharide - CRIWig? Conjugate Activation and Coniuaation 25 Containers of purified polysaccharide were thawed and combined in a reaction vessel. To the vessel, 0.2 M sodium carbonate, pH 9.0 was added for partial deacetylation (hydrolysis) for 3 hours at 50°C. The reaction was cooled to 20°C and neutralization was performed by 0.2 M acetic acid. Oxidation in the presence of sodium periodafe was perfomied by incubation at 2-8''C, and the mixture 30 was stirred for 15-21 hours. 20 The activation reaction mixture was concentrated and diafiltered 10x with 0.9% NaCI using a 30K IVIWCO membrane. The retentate was 0.2 pm filtered. The activated saccharide was filled into 100 mL glass lyophilization bottles and shell- frozen at -75°C and lyophilized. 5 "Shell-freezing" is a method for preparing samples for lyophilization (freeze- drying). Flasks are automatically rotated by motor driven rollers in a refrigerated bath containing alcohol or any other appropriate fluid. A thin coating of product is evenly frozen around the inside "shell" of a flask, permitting a greater volume of material to be safely processed during each freeze-drying run. These automatic, refrigerated 10 units provide a simple and efficient means of pre-freezing many flasks at a time, producing the desired coatings inside, and providing sufficient surface area for efficient freeze-drying. Bottles of lyophilized material were brought to room temperature and resuspended in CRM197 solution at a saccharide/protein ratio of 2:1. To the 15 saccharide/protein mixture 1M sodium phosphate buffer was added to a final 0.2M ionic strength and a pH of 7.5, then sodium cyanoborohydride was added. The reaction was incubated at 23°C for 18 hours, followed by a second incubation at 37°C for 72 hours. Following the cyanoborohydride incubations, the reaction mixture was diluted with cold saline followed by the addition of IM sodium carbonate to 20 adjust the reaction mixture to pH 9.0. Unreacted aldehydes were quenched by addition of sodium borohydride by Incubation at 23°C for 3-6 hours. The reaction mixture was diluted 2-fold with saline and transferred through a 0.45 - 5 pm prefilter into a retentate vessel. The reaction mixture is diafiltered 30x with 0.15 M phosphate buffer, pH 6, and 20x with saline. The retentate was filtered 25 through a 0.2 pm filter, The conjugate solution was diluted to a target of 0.5 mg/mL in 0.9% saline, and then sterile filtered into final bulk concentrate (FBC) containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. 30 Characterization Size exclusion chromatography media (CL-4B) was used to profile the relative molecular size distribution of the conjugate. 21 'l The identity of tlie conjugate was confirmed by tine slot-blot assay using specific antisera. Tlie sacctiaride and protein concentrations were determined by tiie uronic acid and Lowry assays, respectively. Tine ratio of saccinaride to protein in ttie 5 covaiently bonded conjugate complex was obtained by the calculation: pg/mL saccharide Ratio = pg/mL protein 0-acetyl content was measured by the Hestrin method {Hestrin et. al., J. Biol. 10 Chem. 1949, 180, p. 249). The ratio of 0-acetyl concentration to total saccharide concentration gave pmoles of 0-acetyl per mg of saccharide. Example 3 Preparation of S. Pneumoniae Capsular Polysaccharide Serotype 3 15 Preparation of Master and Working Cell Banks S. pneumoniae serotype 3 was obtained from Dr. Robert Austrian, University of Pennsylvania, Philadelphia, Pennsylvania. For preparation of the cell bank system, see Example 1. Fermentation and Harvesting 20 Cultures from the working cell bank were used to inoculate seed bottles containing soy-based medium. The bottles were incubated at 36°C ± 2° C without agitation until growth requirements were met. A seed bottle was used to inoculate a seed fermentor containing soy-based medium. A pH of about 7.0 was maintained with sterile sodium carbonate solution. After the target optical density was reached, 25 the seed fermentor was used to inoculate an intermediate seed fermentor. After the target optical density was reached, the intermediate seed fermentor was used to inoculate the production fermentor. The pH was maintained with sterile sodium carbonate solution. The fermentation was terminated after the working volume of the fermentor was reached. An appropriate amount of sterile 12% sodium deoxycholate 30 was added to the culture to lyse the bacterial ceils and release cell-associated polysaccharide. After lysing, the fermentor contents were cooled. The pH of the lysed culture broth was adjusted to approximately pH 6.6 with acetic acid. The lysate 22 was clarified by continuous flow centrifugation followed by depth filtration and 0.45 pm microfiltration. ! Purification 5 The purification of the pneumococcal polysaccharide consisted of several concentration/diafiltration operations, precipitation/elution, column chromatography, and depth filtration steps. All procedures were performed at room temperature unless otherwise specified. Clarified broth from the fermentor cultures of S. pneumoniae serotype 3 were 10 concentrated and diafiltered using a 100 kDa MWCO filter. Diafiltration was accomplished using sodium phosphate buffer at neutral pH. Diafiltration removed the low molecular weight medium components from the higher molecular weight biopolymers such as nucleic acid, protein and polysaccharide. Prior to the addition of hexadecyltrlmethyl ammonium bromide (HB), a 15 calculated volume of a NaCI stock solution was added to the concentrated and diafiltered polysaccharide solution to give a final concentration of 0.25 M NaCI. The polysaccharide was then precipitated by adding HB from a stock solution to give a final concentration of 1% HB (w/v). The polysaccharide/HB precipitate was captured on a depth filter and the filtrate was discarded. The polysaccharide precipitate was 20 resolubilized and eluted by recirculating a sodium chloride solution through the precipitate-containing depth filter. The filters were then rinsed with additional sodium chloride solution. Sodium iodide (Nal) was added to the polysaccharide solution from a stock Nal solution to achieve a final concentration of 0.5% to precipitate HB. The 25 precipitate was removed by depth filtration. The filtrate contained the target polysaccharide. The precipitation vessel and the filter were rinsed with a NaCI/Nal solution and the rinse was combined with the partially purified polysaccharide solution. The filter was discarded. The polysaccharide was then filtered through a 0.2 pm filter. 30 The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafilter and diafiltered with a sodium chloride solution. The partially purified polysaccharide solution was further purified by filtration through a depth filter impregnated with activated carbon. After filtration, the carbon 23 filter was rinsed wittn a sodium cfiloride solution. The rinse was combined with the polysaccharide solution, which was then filtered through a 0.2 pm filter. The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafilter and adjusted with a 1M sodium phosphate buffer to achieve a final concentration of 5 0.0251V! sodium phosphate. The pH was checked and adjusted to 7.0 ± 0.2. The ceramic hydroxyapatite (HA) column was equilibrated with sodium phosphate buffer containing sodium chloride to obtain the appropriate conductivity (15 pS). The polysaccharide solution was then loaded onto the column. Under these conditions, impurities bound to the resin and the polysaccharide was recovered in the 10 flow-through from the column. The polysaccharide was flushed through the column with buffer and was filtered through a 0.2pm filter. The polysaccharide solution was concentrated using a 30 kDa MWCO filter. The concentrate was then diafiltered with WFI. The diafiltered polysaccharide solution was filtered through a 0.2 pm 15 membrane filter into stainless steel containers. Samples were removed for release testing and the purified polysaccharide was stored frozen at -25° ± 5''C. Characterization The 1H-NMR data was consistent with the chemical structure by the 20 assignment of signals assigned to the protons of the polysaccharide molecule. The identity • of the monovalent polysaccharide was confirmed by countercurrent Immunoelectrophoresis using specific antisera. High performance gel filtration chromatography, coupled with refractive index and multiangle laser light scattering (MALLS) detectors, was used in conjunction with 25 the sample concentration to calculate the molecular weight. Size exclusion chromatography media (CL-4B) was used to profile the relative molecular size distribution of the polysaccharide. 30 24 < Example 4 Preparation of Serotype 3 Pneumococcal Saccharide - CRM197 Conjugate Activation and Coniuqation Containers of purified serotype 3 saccharide were thawed and combined in a 5 reaction vessel. To the vessel, WF! and 2M acetic acid were added to a final concentration of 0.2M and 2mg/mL saccharide. The temperature of the solution was raised to 85°C for one hour to hydrolyze the polysaccharide. The reaction was cooled to ^ZSX and 1M magnesium chloride was added to a final concentration of 0.1 M. Oxidation in the presence of sodium periodate was performed by incubation 10 for 16-24 hours at 23°C. The activation reaction mixture was concentrated and diafiltered 10x with WFI using a 100K MWCO membrane. The retentate was filtered through a 0.2-|jm filter. For compounding, 0.2M sodium phosphate, pH 7.0, was added to the activated saccharide to a final concentration of 10mM and a pH of 6.0-6.5. CRM197 15 carrier protein was mixed with the saccharide solution to a ratio of 2g of saccharide per 1g of CRM197. The combined saccharide/protein solution was filled into 100 mL glass lyophilization bottles with a 50mL target fill, shell-frozen at -75''C, and lyophilized. Bottles of co-lyophilized saccharide/protein material were brought to room 20 temperature and resuspended in 0.1 M sodium phosphate buffer, pH 7.0, to a final saccharide concentration of 20 mg/mL. The pH was adjusted to 6.5 and then a 0.5 molar equivalent of sodium cyanoborohydride was added. The reaction was incubated at 37°C for 48 hours. Following the cyanoborohydride incubation, the reaction mixture was diluted with cold 5mM succinate/0.9% saline buffer. Unreacted 25 aldehydes were quenched by the addition of sodium borohydride and incubation at 23°C for 3-6 hours. The reaction mixture was transferred through a 0.45-5 pm prefilter into a retentate vessel. I The reaction mixture was diafiltered 30x with 0.1M phosphate buffer (pH 9), 20x with 0.15M phosphate butter (pH 6), and 20x with 5mM succinate/0.9% saline. 30 The retentate was filtered through a 0.2-pm filter. 25 i I . .' ! The conjugate solution was diluted to a sacciiaride target of 0.5 mg/mL, and then sterile filtered into FBC containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. Characterization 5 Size exclusion chromatography media (CL-4B) was used to profile the relative molecular size distribution of the conjugate. The identity of the conjugate was confirmed by the slot-blot assay using specific antisera. The saccharide and protein concentrations were determined by the Anthrone 10 and Lowry assays, respectively. The ratio of saccharide to protein in the covalently bonded conjugate complex was obtained by the calculation: Ijg/mL saccharide 15 . Ratio = yg/mL protein Example 5 Preparation of S. Pneumoniae Capsular Polysaccharide Serotype 5 20 S. pneumoniae serotype 5 was obtained from Dr. Gerald Schlffman of the State University of New York, Brooklyn, New York. For preparation of the cell bank system, see Example 1. For fermentation, harvesting, purification and characterization of the polysaccharide, see Example 1. 2S Alternate' Fermentation Process Cultures from the working cell bank were used to inoculate seed bottles containing a soy-based medium and a 10mM sterile NaHCOa solution. The bottles were incubated at 36°C + 2° C without agitation until growth requirements were met. 30 A seed bottle was used to inoculate a seed fermentor containing soy-based medium and a lOmM sterile NaHCOa solution. A pH of about 7.0 was maintained with 3N NaOH. After the target optical density was reached, the seed fermentor was used to inoculate the production fermentor containing soy-based medium with a lOmM I 26 NaHCOa concentration. The pH was naaintained with 3N NaOH. The fermentation was terminated after cessation of growth or when the working volume of the fermentor was reached. An appropriate amount of sterile 12% sodium deoxycholate was added to the culture to obtain a 0.12% concentration in the broth, to lyse the ■ 5 bacterial cells and release cell-associated polysaccharide. After lysing, the fermentor contents were held, with agitation, for a time interval between 8 and 24 hours at a temperature between TO. and IS^C to assure that complete cellular lysis and polysaccharide release had occurred. Agitation during this hold period prevented lysate sediment from settling on the fermentor walls and pH probe, thereby allowing 10 the pH probe integrity to be maintained. Next, the pH of the lysed culture broth was adjusted to approximately pH 4.5 with 50% acetic acid. After a hold time without agitation, for a time interval between 12 and 24 hours at a temperature between 15°C and 25°C, a significant portion of the previously soluble proteins dropped out of solution as a solid precipitate with little loss or degradation of the polysaccharide, 15 which remained in solution. The solution with the precipitate was then clarified by continuous flow centrifugation followed by depth filtration and 0.45 pm microfiltration. Example 6 Preparation of Serotype 5 Pneumococcal Saccharide - CRM197 Conjugate 20 Activation and Coniuqation Containers of serotype 5 saccharide were thawed and combined in a reaction vessel. To the vessel, 0.1 M sodium acetate, pH 4.7, was added followed by oxidation in the presence of sodium periodate by incubation for 16-22 hours at 23°C. The activation reaction mixture was concentrated and diafiltered 10x with WFI 25 using a 100K MWCO membrane. The retentate was filtered through a 0.2 pm filter. The serotype 5 activated saccharide was combined with CRM197 at a ratio of 0.8:1. The combined saccharide/protein solution was filled into 100 mL glass iyophilization bottles (50 mL target fill), shell-frozen at -75°C, and co-lyophilized. Bottles of co-lyophilized material were brought to room temperature and 30 resuspended in 0.1 M sodium phosphate, pH 7.5, and sodium cyanoborohydride was added. The reaction was incubated at 30°C for 72 hours, followed by a second addition of cyanoborohydride and incubated at 30°C for 20-28 hours. 27 Following the cyanoborohydride incubations, the reaction mixture was diluted 2-fold with saline and transferred through a 0.45-5 pm prefilter into a retentate vessel. The reaction mixture was diafiitered 30x with 0.01 M phosphate buffer, pH 8, 20x with 0.15M phosphate buffer, pH 6, and 20x with saline. The retentate was filtered 5 through a 0.2 [am filter. The conjugate solution was diluted to a saccharide target of 0.5 mg/mL, and then sterile filtered into FBC containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. For the characterization of the conjugate, see Example 2. 10 Example 7 Preparation of S. Pneumoniae Capsular Polysaccharide Serotype 6A S. pneumoniae serotype 6A was obtained from Dr. Gerald Schiffman of the State University of New York, Brooklyn, New York. For preparation of the cell bank 15 system, see Example 1. For fermentation, harvesting and purification of the polysaccharide, see Example 1, except that during purification, the 30 kDa MWCO concentration step, prior to the chromatography step, is omitted. Example 8 20 Preparation of Serotype 6A Pneumococcal Saccharide - CRM197 Conjugate Activation and Conjugation Serotype 6A polysaccharide is a high molecular weight polymer that had to be reduced in size prior to oxidation. Containers of serotype 6A saccharide were 25 thawed and combined in a reaction vessel. To the vessel, 2 iVI acetic acid was added to a final concentration of 0.1 M for hydrolysis for 1.5 hours at 60°C. The reaction was cooled to 23°C and neutralization was performed by adjusting the reaction mixture with 1 M NaOH to pH 6. Oxidation in the presence of sodium periodate was peri'ormed by incubation at 23°C for 14-22 hours. 30 The activation reaction mixture was concentrated and diafiitered 10x with WFl using a 100K MWCO membrane. The retentate was filtered through a 0.2 pm filter. Serotype 6A was compounded with sucrose and filled into 100 mL glass lyophilization bottles (50mL target fill) and shell-frozen at -75°C and lyophiiized. 28 Bottles of lyophilized material were brought to room temperature and resuspended in dimethylsuifoxide (DMSO) at a saccharide/protein ratio of 1:1. After addition of sodium cyanoborohydride, tlie reaction mixture was incubated at 23°C for 18 hours. Following the cyanoborohydride incubation, the reaction mixture was 5 diluted with cold saline. Unreacted aldehydes were quenched by addition of sodium borohydride by incubation at 23°C for 3-20 hours. The diluted reaction mixture was transferred through a 5 pm prefilter into a retentate vessel. The reaction mixture was diafiltered 10x with 0.9% NaCI and 30x with succinate-buffered NaCI. The retentate was filtered through a 0.2 pm filter. 10 The conjugate solution was diluted to a saccharide target of 0.5 mg/mL, and then sterile filtered into FBC containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. For the characterization of the conjugate, see Example 2. 15 Example 9 Preparation of S. Pneumoniae Capsular Polysaccharide Serotype 7F S. pneumoniae serotype 7F was obtained from Dr. Gerald Schiffman of the State University of New York, Brooklyn, New York. For preparation of the ceil bank system, and for fermentation and harvesting of the polysaccharide, see Example 3. 20 For an alternate fermentation and harvesting process, see the alternate process described in Example 1. Purification The purification of the pneumococcal polysaccharide consisted of several 25 concentration/diafiltration operations, precipitation/elution, column chromatography, and depth filtration steps. All procedures were performed at room temperature unless otherv\/ise specified. Clarified broth from fermentor cultures of S. pneumoniae serotype 7F were concentrated and diafiltered using a 100 kDa MWCO filter. Diafiltration was 30 accomplished using sodium phosphate buffer at neutral pH. Diafiltration removed the low molecular weight medium components from the higher molecular weight biopolymers such as nucleic acid, protein and polysaccharide. 29 Serotype 7F does not form a precipitate with HB. instead, impurities were precipitated from tlie concentrated and diafiltered solution by adding the HB from a stocl< solution to a final concentration of 1 % HB. The precipitate was captured on a depth filter and the filter was discarded. The polysaccharide was contained in the ■ 5 filtrate. Sodium iodide (Nal) was added to the polysaccharide solution from a stock Nai solution to achieve a final concentration of 0.5% to precipitate HB. The precipitate was removed by depth filtration. The filtrate contained the target polysaccharide. The precipitation vessel and the filter were rinsed with a NaCI/Nal 10 solution and the rinses were combined with the partially purified polysaccharide solution. The filter was discarded. The polysaccharide was then filtered through a 0.2pm filter. The polysaccharide solution was concentrated on a 30 l testing and the purified polysaccharide was stored at 2° - 8°C. For characterization of the polysaccharide, see Example 3. 30 Example 10 Preparation of Serotype 7F Pneumococcal Saccharide - CRMi97 Conjugate Activation and Conjugation 5 Oxidation in the presence of sodium periodate was performed by incubation for 16-24 hrs at 23°C. Tiie activation reaction mixture was concentrated and diafiltered 10x witln 10mM NaOAc, pH 4.5, using a 100K iMWCO membrane. The retentate was filtered through a 0.2 pm filter. 10 Serotype 7F was filled into 100 mL glass lyophilization bottles (50 mL target fill) and shell-frozQn at -75°C and lyophilized. Bottles of lyophilized serotype 7F and CRM197 were brought to room temperature and resuspended in DMSO at a saccharide/protein ratio of 1.5:1. After the addition of sodium cyanoborohydride, the reaction was incubated at 23''C for 8- 15 10 hours. Unreacted aldehydes were quenched by the addition of sodium borohydride by incubation at 23°C for 16 hours. The reaction mixture was diluted 10-fold with cold saline and transferred through a 5 pm prefilter into a retentate vessel. The reaction mixture was diafiltered lOx with 0.9% saline and 30x with succinate-buffered saline. The retentate was 20 filtered through a 0.2 pm filter. The conjugate solution was diluted to a saccharide target of 0.5 mg/mL 0.9% saline, and then sterile filtered into FBC containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. For characterization of the conjugate, see Example 4. 25 31 Example 11 Preparation of S. Pneumoniae Capsular Polysaccharide Serotype 19A 5 S. pneumoniae serotype 19A was obtained from Dr. Gerald Schiffman of the State University of New York, Brool<:iyn, New York. For preparation of ttie cell bank systenn, see Example 1. For fermentation, harvesting and purification of the polysaccharide, see Example 7. For characterization, see Example 3. 10 Example 12 Preparation of Serotype 19A Pneumococcal Saccharide - CRM197 Conjugate Activation and Coniugation Containers of serotype 19A saccharide were thawed and combined in a reaction vessel. Sodium acetate was added to 10 mM (pH 5.0) and oxidation was 15 carried out in the presence of sodium periodate by incubation for 16-24 hrs at 23°C. The activation reaction mixture was concentrated and diafiltered 1Dx with 10mM acetate, pH 5.0, using a 100K MWCO membrane. The retentate was filtered through a 0.2 ym filter. The activated, saccharide was compounded with sucrose followed by the 20 addition of CRM197. The serotype 19A activated saccharide and CRMig? mixture (0.8:1 ratio) was filled into 100 mL glass lyophilization bottles (50 mL target fill) and shell-frozen at -75°C and lyophilized. Bottles of lyophilized material were brought to room temperature and resuspended in DMSO. To the saccharide/protein mixture, sodium 25 cyanoborohydride (100 mg/ml) was added. The reaction was incubated at 23°C for 15 hours. Following the cyanoborohydride incubation, unreacted aldehydes were quenched by the addition of sodium borohydride by incubation at 23°C for 3-20 hours. The reaction mixture was diluted 10-fold with cold saline and transferred 30 through a 5 pm prefilter into a retentate vessel. The reaction mixture was diafiltered 10x with 0.9% NaCI, 0.45-pm filtered, and 30x with diafiltration using 5mM succinate/ 0.9% NaCI buffer, pH 6. The retentate was filtered through a 0.2 pm filter. 32 ft The conjugate solution was diluted to a target of 0.5 mg/mL using 5mM succinate/0.9% saline, and then sterile filtered into FBC containers in a Class 100 hood. The conjugate was stored at 2 - 8°C. For characterization of the conjugate, see Example 4, 5 Example 13 Preparation of S. Pneumoniae Capsular Polysaccharide Serotypes 4, 6B, 9V, 14,18C, 19F and 23F 10 Preparation of the S. pneumoniae Seed Culture S. pneumoniae serotypes 4, 6B, 9V, 18C, 19F and 23F were obtained from Dr. Gerald Schiffman, State University of New York, Brooklyn, New York. S. pneumoniae serotype 14 was obtained from the ATCC, strain 6314. Separately, one vial of each of the desired serotypes of Streptococcus 15 pneumoniae was used to start a fermentation batch. Two bottles containing a soy-based medium and phenol red were adjusted to a pH range of 7.4 + 0.2 using sodium carbonate, and the required volume of 50% dextrose/1% magnesium sulfate solution was then added to the bottles. The two bottles were inoculated with different amounts of seed. The bottles were incubated at 36° ± 2°C until the medium turned 20 yellow. Following incubation, samples were removed from each bottle and tested for optical density (OD) (0.3 to 0.9) and pH (4.6 to 5.5). One of the two.bottles was selected for inoculation of the seed fermentor. Soy-based medium was transferred to the seed fermentor and sterilized. Then a volume of 50% dextrose/1 % magnesium sulfate solution was added to the 25 fermentor. The pH and agitation of the seed fermentor were monitored and controlled (pH 6.7 to 7.4). The temperature was maintained at 36'' ± 2°C. The seed inoculum (bottle), was aseptically connected to the seed fermentor and the inoculum was transferred. The fermentor was maintained in pH control and samples were periodically removed and tested for OD and pH. When the desired OD of 0.5 at 600 30 nm was reached, the intermediate fermentor was inoculated with the fermentation broth from the seed fermentor. Soy-based medium was transferred to the intermediate fermentor and sterilized. Then a volume of 50% dextrose/1% magnesium sulfate solution was 33 i . "' i added to the fermentor. The pH and agitation of the intermediate fermentor were monitored and controlled (pH 6.7 to 7.4). The temperature was maintained at 36° ± 2°C. The contents of the seed fermentor were transferred to the intermediate fermentor. The fermentor was maintained in pH control and samples were 5 periodically removed and tested for OD and pH. When the desired OD of 0.5 at 600 nm was reached, the production fermentor was inoculated with the fermentation broth from the intermediate fermentor. Soy-based medium was transferred to the production fermentor and sterilized. Then a volume of 50% dextrose/1% magnesium sulfate solution was 10 added to the fermentor. The pH and agitation of the production fermentor were monitored and controlled (pH 6.7 to 7.4). The temperature was maintained at 36° ± 2°C. The fermentor was maintained in pH control and samples were periodically removed and tested for OD and pH, until the femnentation was complete. Deoxycholate sodium was added to the fermentor to a final concentration of 15 approximately 0.12% w/v. The culture was mixed for a minimum of thirty minutes and the temperature set point was reduced to 10°C. The culture was incubated overnight and following confirmation of inactivation, the pH of the culture was adjusted to between 6.4 and 6.8, as necessary, with 50% acetic acid. The temperature of the fermentor was increased to 20° ± 5°C and the contents were 20 transferred to the clarification hold tank. The contents of the clarification hold tank (including the cellular debris) were processed through a centrifuge at a flow rate between 25 and 600 liters per hour (except Serotype 4, wherein the cell debris was discarded and the flow rate tightened to between 25 and 250 liters per hour), Samples of the supernatant were removed 25 and tested for OD. The desired OD during the centrifugation was < 0.15. Initially, the supernatant was recirculated through a depth filter assembly until an OD of 0.05 ± 0.03 was achieved. Then the supernatant was passed through the depth filter assembly and through a 0.45 |j,m membrane filter to the filtrate hold tank. Subsequently, the product was transferred through closed pipes to the 30 purification area for processing. All of the above operations (centrifugation, filtration and transfer) were performed between 10°C to 30°C. 34 For an alternate fermentation and harvesting process for serotypes 4 and 6B, see tiie alternate process described in Example 1. Purification 5 The purification of each pneumococcal polysaccharide consisted of several concentration/diafiltration operations, precipitation/elution, column chromatography, and depth filtration steps. All procedures were performed at room temperature unless otherwise specified. Clarified broth from the fermentor cultures of the desired S. pneumoniae 10 serotype was concentrated and diafiltered using a 100 kDa MWCO filter. Diafiltration was accomplished using sodium phosphate buffer at pH < 9.0. Diafiltration removed the low molecular weight medium components from the higher molecular weight biopolymers such as nucleic acid, protein and polysaccharide. The polysaccharide was precipitated from the concentrated and diafiltered 15 solution by adding HB from a stock solution to give a final concentration of 1 % HB (w/v) (except Serotype 23F, which had a final concentration of 2.5%). The ' polysaccharide/HB precipitate was captured on a depth filter and the filtrate was discarded. (Note: Serotype 14 does not precipitate; therefore the filtrate was retained.) The polysaccharide precipitate was resolubilized and eluted by 20 recirculating a sodium chloride solution through the precipitate-containing depth filter. The filters were then rinsed with additional sodium chloride solution. Sodium iodide (Nal) was added to the polysaccharide solution from a stock Nal solution to achieve a final concentration of 0.5% to precipitate HB (except for Serotype 6B, which had a final concentration of 0.25%). The precipitate was 25 removed by depth filtration. The filtrate contained the target polysaccharide. The ■ filter was discarded. The polysaccharide was then filtered through a 0.2pm filter. The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafilter and diafiltered with a sodium chloride solution. The partially purified polysaccharide solution was further purified by filtration 30 through a depth filter impregnated with activated carbon. After filtration, the carbon filter was rinsed with a sodium chloride solution. The rinse was combined with the polysaccharide solution, which was then filtered through a 0.2pm filter. 35 The polysaccharide solution was concentrated on a 30 kDa MWCO ultrafiiter and the filter was rinsed with a sodium chloride solution. The pH was checked and adjusted to 7.0 ± 0..3. The ceramic hydroxyapatite (HA) column was equilibrated with sodium 5 phosphate buffer containing sodium chloride until the pH is 7.0 ± 0.3 and the conductivity was 26 + 4yS. The polysaccharide solution was then loaded onto the column. Under these conditions, impurities bound to the resin and the polysaccharide was .recovered in the flow through from the column. The polysaccharide solution was filtered through a 0.2pm filter. 10 The polysaccharide solution was concentrated using a 30 kDa MWCO filter. The concentrate was then diafiltered with WFI until the conductivity was < 15pS. The diafiltered polysaccharide solution was filtered through a 0.2pm membrane filter into bulk containers and stored at 2-8°C. 15 Example 14 Preparation of Pneumococcal Saccharide - CRIVI197 Conjugates For Serotypes 4, 6B, 9V, 14,18C, 19F and 23F Activation Process 20 The different serotype saccharides follow different pathways for activation (hydrolysis or no hydrolysis prior to activation) and conjugation (aqueous or DMSO reactions) as described in this example. Polysaccharide was transferred from the bulk containers to the reactor vessel. The polysaccharide was then diluted in WFI and sodium phosphate to a final 25 concentration range of 1.6 - 2.4 mg/mL. Step 1. For serotypes 6B, 9V, 14, 19F and 23F, pH was adjusted to pH 6.0 ± 0.3. For serotype 4, hydrochloric acid (0.01 M final acid concentration) was added 30 and the solution was incubated for 25 - 35 minutes at 45° ± 2°C. Hydrolysis was stopped by cooling to 21 - 25°C and adding 1M sodium phosphate to a target of pH 6.7 ± 0.2. An in-process test was done to confirm an appropriate level of depyruvylation. 36 For serotype 18C, glacial acetic acid (0.2 M final acid concentration) was added and the solution was incubated for 205 - 215 minutes at 94° ± Z'C. Temperature was then decreased to 21 - 25°C and 1 - 2 M sodium phosphate was added to a target of pH 6.8 ±0.2. 5 • Step 2: Periodate Reaction The required sodium periodate molar equivalents for pneumococcal saccharide activation was determined using total saccharide content (except for serotype 4). For serotype 4, a ratio of 0.8-1.2 moles of sodium periodate per mole of saccharide was 10 used. With thorough mixing, the oxidation reaction was allowed to proceed between 16 to 20 hours at 21 - 25°C for all serotypes except 19F for which the temperature was<15''C. Step 3: Ultrafiltration 15 The oxidized saccharide was concentrated and diafiltered with WFI (0.01 M sodium phosphate buffer pH 6.0 for serotype 19F) on a 100 kDa MWCO ultrafilter (5 kDa ultrafilter for 18C). The permeate was discarded and the retentate was filtered through a 0.22 |a,m filter. 20 Step 4: Lyophilization For serotypes 4, 9V, and 14 the concentrated saccharide was mixed with CRMig7 carrier protein, filled into glass bottles, shell-frozen and stored at < -65°C. The frozen concentrated saccharide-CRMigr was lyophilized and then stored at -25° ± 5°C. 25 For serotypes 6B, 19F, and 23F a specified amount of sucrose was added which was calculated to achieve a 5% ± 3% sucrose concentration in the conjugation reaction mixture. Serotype 18C did not require sucrose addition. The concentrated saccharide was then filled into glass bottles, shell-frozen and stored at < -65°C. The frozen concentrated saccharide was lyophilized and then stored at -25° ± 5°C. 30 Conjugation Process Two conjugation processes were used: aqueous conjugation for serotypes 4, 9V, 14 and 18C, and DMSO conjugation for serotypes 6B, 19F and 23F. 37 Aqueous Conjugation • Step 1: Dissolution For serotypes 4, 9V and 14, the lyophilized activated saccliaride-CRMi97 mixture . 5 was thawed and equilibrated at room temperature. The lyophilized activated saccharide-CRMi97 was then reconstituted in 0.1 M sodium phosphate buffer at a typical ratio of: • 1L of buffer per 16 - 24 g of saccharide for serotype 4 and 9V • 1L of buffer per 6 -10 g of saccharide for serotype 14 10 The reaction mixture was incubated at 37° ± 2°C until total dissolution for the serotype 9V and at 23° ±2°C for serotypes 4 and 14. For serotype "ISC, the lyophilized saccharide was reconstituted in a solution of CRMi97 in 1M dibasic sodium phosphate at a typical ratio of 0.11 L of sodium 15 phosphate per 1 L of CRM197 solution. The reaction mixture (8-12 g/L saccharide concentration) was incubated at 23° + 2°C until total dissolution. The pH was tested as an in-process control at this stage. Step 2: Conjugation Reaction 20 For serotypes 4 and 9V, the conjugation reaction was initiated by adding the sodium cyanoborohydride solution (100 mg/mL) to achieve 1.0 - 1.4 moles sodium cyanoborohydride per mole of saccharide. The reaction mixture was incubated for 44 - 52 hours at 37° + 2°C. The temperature was then reduced to 23° + 2°C and sodium chloride 0.9% was added to the reactor. Sodium borohydride solution (100 25 mg/mL) was added to achieve 1.8- 2.2 molar equivalents, of sodium borohydride per mole saccharide. The mixture was incubated for 3 - 6 hours at 23° ± 2°C. The mixture was diluted with sodium chloride 0,9% and the reactor was rinsed. The diluted conjugation mixture was filtered using a 1.2 jum pre-filter into a holding vessel. For serotypes 14 and 18C, the conjugation reaction was initiated by adding the 30 cyanoborohydride solution (100 mg/mL) to achieve 1.0 - 1.4 moles of sodium cyanoborohydride per mole of saccharide. The reaction mixture was incubated for 12-24 hours at 23° ± 2°C. The temperature was increased to 37° ± 2°C and the reaction was incubated for 72 - 96 hours. The temperature was then reduced to 23° 38 ± 2°C and 0.9% sodium chloride was added to the reactor. Sodium borohydride solution (100mg/mL) was added to achieve 1.8 - 2.2 moiar equivalents of sodium borohydride per mole of saccharide. The mixture was incubated for 3 - 6 hours at 23° ± 2°C. The mixture was diluted with 0.9% sodium chloride and the reactor was 5 rinsed. The diluted conjugation mixture was then filtered using a 1.2 [a.m pre-filter into a holding vessel. Step 3: Ultrafiltration 100 kDa The diluted conjugation mixture was concentrated and diafiltrated on a 100 kDa 10 MWCO ultrafilter with either a minimum of 15 volumes (serotype 4) or 40 volumes (serotypes 9V, 14; and 18C) of 0.9% sodium chloride. The permeate was discarded. For serotype 4, the retentate was filtered through a 0.45fj,m filter. An in-process control (saccharide content) was performed at this step. 15 Step 4: HA Column Purification This step was only performed for the serotype 4 conjugate. The HA column was first neutralized using 0.5M sodium phosphate buffer (pH 7.0 ± 0.3) and then equilibrated with 0.9% sodium chloride. The filtered retentate 20 (serotype 4) was loaded onto the column at a flow rate of 1.0 L/min. The column was washed with 0.9% sodium chloride at a flow rate of < 2.0 L/min. The product was then eluted with 0.5M sodium phosphate buffer at a flow rate of < 2.0 L/min. The HA fraction was then concentrated and diafiltered on a 100 kDa MWCO membrane with a minimum of 20 volumes of 0.9% sodium chloride. The permeate 25 was discarded. Step 5: Sterile Filtration The retentate after the 100 kDa MWCO diafiltration was filtered through a 0.22nm filter. In-process controls (saccharide content, free protein, free saccharide 30 and cyanide) were performed on the filtered product. In-process controls on filtered retentate were performed to determine whether additional concentration, diafiltration, and/or dilution were needed to meet FBC targets. These and additional tests were repeated in FBC samples. 39 As necessary, the filtered conjugate was diluted with 0.9% sodium ctiloride in order to acl-iieve a final concentration of less than 0.55 g/L. Release tests for saccharide content, protein content and saccharide:protein ratio were performed at this stage. 5 Finally, the conjugate was filtered (0.22 iim) and filled into 10 L stainless steel canisters at a typical quantity of 2.64 g/canister. At this stage, yield, saccharide content, protein content, pH, saccharide:protein ratio and lysine content were performed as in-process controls. Release testing (appearance, free protein, free saccharide, endotoxin, molecular size determination, residual cyanide, saccharide 10 identity, CRlVligr identity) was performed at this stage. DMSO Conjugation Step I: Dissolution The lyophilized activated saccharide serotypes 6B, 19F, 23F and the lyophilized 15 CRMi97 carrier protein were equilibrated at room temperature and reconstituted in DMSO. The dissolution concentration typically ranged from 2-3 grams of saccharide (2-2.5 g protein) per liter of DMSO. Step II: Conjugation Reaction ■ 20 The activated saccharide and CRMi^y carrier protein were mixed for 60 - 75 minutes at 23° ± 2°C at a ratio range of 0.6 g - 1.0 g saccharide/g CRM197 for serotypes 6B and 19F or 1.2 to 1.8 g saccharide/g CRM197 for serotype 23F. The conjugation reaction was initiated by adding the sodium cyanoborohydride solution (lOOmg/mL) at a ratio of 0.8 - 1.2 molar equivalents of sodium 25 cyanoborohydride to one mole activated saccharide. WFI was added to the reaction mixture to a target of 1% (v/v) and the mixture was incubated for over 40 hours at 23° ± 2°C. Sodium borohydride solution, 100 mg/mL (typical 1.8 - 2.2 molar equivalents sodium borohydride per mole activated saccharide) and WFI (target 5% v/v) were 30 added to the reaction and the mixture was incubated for 3 - 6 hours at 23° ± 2°C. This procedure reduced any unreacted aldehydes present on the saccharides. Then the reaction mixture was transferred to a dilution tanl< containing 0.9% sodium chloride at <15°C. 40 ^, : step III: 100 kDa Ultrafiltration The diluted conjugate mixture was filtered through a 1.2 jam filter and concentrated and diafiltered on a 100 kDa MWCO membrane with a minimum of 15 5 volumes of 0.9% sodium chloride (0.01 M sodium phosphate/0.05M NaCI buffer was used for serotype 23F). The permeate was discarded. The retentate was filtered through a 0.45 |j,m filter. An in-process saccharide content sample was taken at this stage. 10 Step IV: DEAE Column Purification This step was only performed for serotype 23F. The DEAE column was equilibrated with 0.01 M sodium phosphate/0.05M sodium chloride buffer. The filtered retentate (serotype 23F) was loaded onto the column and washed with 0.01 M sodium phosphate/O.OSM sodium chloride buffer. 15 The column was then washed with 0.01 M sodium phosphate/0.9% NaCI buffer. The product was then eluted with 0.01 M sodium phosphate/0.5M sodium chloride buffer. Step V: 100 kDa Ultrafiltration The retentate from 6B and 19F was concentrated and diafiltered with at least 30 volumes of 0.9% sodium chloride. The permeate was discarded. 20 The eluate from serotype 23F was concentrated and diafiltered with a minimum of 20 volumes of 0.9% sodium chloride. The permeate was discarded. Step VI: Sterile Filtration The retentate after the 100 kDa MWCO dialfiltration was filtered through 0.22 p.m 25 filter. In-process controls (saccharide content, free protein, free saccharide, residual DMSO.and residual cyanide) were performed on the filtered product. In-process controls on filtered retentate were performed to determine whether additional concentration, diafiltration, and/or dilution were needed to meet FBC targets. These and additional tests were repeated in FBC samples. 30 As necessary, the filtered conjugate was diluted with 0.9% sodium chloride to achieve a final concentration of less than 0.55 g/L. Release tests for saccharide content, protein content and saccharidetprotein ratio were performed at this stage. 41 Finally, the conjugate was filtered (0.22 (j,m) and filled into 10 L stainless steel canisters at a quantity df 2.64 g/canister. At this stage, yield, saccharide content, protein content, pH, saccharide:protein ratio and lysine content were performed as in-process controls. Release testing (appearance, free protein, free saccharide, 5 endotoxin, molecular size determination, residual cyanide, residual DMSO, saccharide identity and CRM197 identity) was performed at this stage. Example 15 Formulation of a Multivalent Pneumococcal Conjugate Vaccine 10 The final bulk concentrates of the 13 conjugates contain 0.85% sodium chloride. Type 3, 6A, 7F and 19A bulk concentrates also contain 5 mM sodium succinate buffer at pH 5.8. The required volumes of bulk concentrates were calculated based "on the batch volume and the bulk saccharide concentrations. After 80% of the 0.85% sodium chloride (physiological saline) and the required amount of 15 succinate buffer were added to the pre-labeied formulation vessel, bulk concentrates were added. The preparation was then sterile filtered through a 0.22 |jm membrane into a second container by using a Millipore Durapore membrane filter unit. The first container was washed with the remaining 20% of 0.85% sodium chloride and the solution was passed through the same filter and collected into the second container. ,20 The formulated bulk was mixed gently during and following the addition of bulk aluminum phosphate. The pH was checked and adjusted if necessary. The formulated bulk product was stored at 2-8°C. The formulated bulk pr6duct was filled into Type 1 borosilicate glass syringes obtained from Becton Dickinson. The vaccine was monitored at regular intervals for 25 turbidity to ensure the uniformity of the filling operation. The filled vaccine (Final Product) was stored at 2-8°C. Example 16 Immunogenicity of the 13-Valent Conjugate Vaccine To date, the preclinical studies performed on the 13vPnC vaccine have been 30 in rabbits. Studies #HT01-0021 and #HT01-0036 were designed to independently examine the effect of chemical conjugation of capsular polysaccharides (PSs) from S. pneumoniae to CRM197 and the effect of aluminum phosphate (AIPO4) adjuvant on the immune response to the 13vPnC vaccine in rabbits. These effects were 42 characterized by antigen-specific ELISA for serum IgG concentrations and for antibody function by opsonopliagocytic assay (OPA). Study #HT01-0021 Study #HT01-0021 examined \he ability of the 13vPnC vaccine with AIPO4 5 adjuvant to elicit vaccine serotype-specific immune responses. The pneumococcal serotypes represented in the 13vPnC vaccine include types 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F and 23F. Secondary objectives included an evaluation of the l m -^, 2 ^-^ O w -—- „_, c 5 "■So §■ I ^ ! ;$ ^ ,-^ . , . ■ iO "° c co'csTio'orj^fSS'cM^oo'csrs So o II « ^ s ^t c — ^ S O O « 2 Q.- S . ■ E- flJo'SSoO O «;(• NJ- O CM '^ "^ O O O O^S DiOKS^ '^ "^ o d 1-^ d rd d ■r^ -t-: T-: ^gf = C J " g 53-.J-.0 O O O O O ~ in K^ O O O 0"oX E«:5-SO O O O O O g '& VZ O O O 03 ^ ■<- O S m r^ CD O O OmP 3^ ■^ooo^r:oggf::3oooo-ofe "^•^ o >, in Table 4. S. pneumoniae OPA GMTs for NZW Rabbit Serum Pools Following Immunization with Two Doses of 13-valent Pneumococcal Glycoconjugate - ^ WeekO Week 4 wKwkO ^eekO Week 4 ^^^'° Serotype WK4.WKU Wk4:WkO 1 <8 64 16 <8 64 16 3 <8 8 2 <8 16 4 4 <8 16 4 <8 32 8 5 <8 128 32 <8 512 128 6A 8 128 16 8 512 64 6B <8 256 64 8 ■ 1,024 128 7F 8 64 8 8 • 128 16 9V 8 64 8 8 128 18 14 16 32 2 16 32 2 18C 8 . 256 32 <6 256 64 19A <8 256 64 <8 1,024 256 19F <8 128 32 <8 512 128 23F 8 64 8 <8 256 64 A: Pools consisted of equal volumes of serum from individual rabbits within a treatment group (n=12) 5 Study #HT01-0036 Study #HT01-0036 compared rabbit immune responses to the polysacciiarides (PSs) contained in the vaccine, after immunization with the 13vPnC vaccine with or without conjugation to the CRMig? protein. New Zealand White 10 rabbits were immunized intramuscularly at week 0 and week 2 with a dose of 2.2 |xg of each PS (except 4.4 ^g of 6B). Animals received one of three vaccine preparations: (a) 13vPnC (PS directly conjugated to CRM197), (b) 13vPnPS, (free PS) or (c) ISvPnPS + CRM197 (free PS mixed with CRM197). All vaccine preparations contained AIPO4 as the adjuvant at 125 |ag/dose. 15 Serotype specific Immune responses for all vaccine preparations were evaluated in an IgG ELISA and complement-mediated OPA measuring functional antibody. The immune responses were compared between the treatment groups. Table 5 presents GMT data obtained from week 4 bleeds analyzed in antigen specific IgG ELISAs. Additional analyses show the ratio of GMT values at week 4 to 20 week 0. The data .indicate that the conjugate vaccine preparation elicited greater serum IgG titers than free PS or free PS + CRMigr vaccine. With the exception of S. 46 pneumoniae type 14, the 13vPnC vaccine was able to induce functional antibodies to tiie representative strains of S. pneumoniae in an OPA (Table 6). After two immunizations with either the 13vPnPS or 13vPnPS + CRM197 vaccine, neither could induce OPA titers > 8-fold at week 4 relative to week 0 for 10 out of the 13 serotypes 5 measured (Table 6). 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