Patent Publication Number: US-2022218810-A1

Title: New immunogenic compositions

Description:
The present invention relates to new immunogenic compositions and uses in the treatment and prevention of diseases caused by Proteobacteria. 
     RELATED ART 
     Bacterial enteropathogens of the Enterobacteriaceae family account for two of the four key global causes of diarrheal diseases (WHO) and can cause life-threatening invasive disease or severe post-infectious sequela in susceptible individuals (Kirk, M. D. et al. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis.  PLOS Med.  12, e1001921, 2015). As well as causing infections, these strains are very often asymptomatically carried in the intestinal microbiota, as well as gut-draining lymphoid tissues, of livestock, in Europe, which is a major concern in pigs and chickens (Niemann, J.-K. et al. Simultaneous occurrence of  Salmonella enterica, Campylobacter  spp. and  Yersinia enterocolitica  was observed along the pork production chain from farm to meat processing in five conventional fattening pig herds in Lower Saxony.  Berl. Munch. Tierarztl. Wochenschr.  129, 296-303). These infection reservoirs fuel seasonal re-emergence of infections and continuous cycles of infection in young animals. Combined with the on-going requirement for antibiotics in disease management in livestock rearing (WHO), this represents a ticking time bomb with respect to the development of multidrug resistant zoonostic pathogens. There is therefore a pressing need for effective vaccines that block the infectious cycle. 
     A major hurdle to developing such vaccines has been our limited understanding of how protective immunity to bacterial pathogens is actually achieved in the intestine. It has long been known that secretory antibodies, i.e. sIgA, are the major immune component present in the gut lumen of vaccinated animals, and protection is typically mediated by their binding to the O-antigen of lipopolysaccharide (Endt, K. et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal  salmonella  diarrhea.  PLoS Pathog.  6, e1001097 (2010)). However, this protection was observed often to be incomplete and to vary in efficiency depending on the level of exposure. sIgA-O-antigen interactions function by crosslinking cells as the bacteria grow and divide (Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria.  Nature  544, 498-502 (2017). This generates large clumps of bacteria that cannot approach the gut wall, preventing the delivery of virulence factors. However, being enchained in a clump also generates a selective pressure on the luminal enteropathogen population. This drives rapid evolution of vaccine-escape variants of the bacterial strain that no longer bind to vaccine-induced antibodies, accounting for the unsatisfactory percentage protection observed. These pathogen variants typically carry a chemical modification of the O-antigen (Broadbent, S. E., Davies, M. R. &amp; van der Woude, M. W. Phase variation controls expression of  Salmonella  lipopolysaccharide modification genes by a DNA methylation-dependent mechanism.  Mol. Microbiol.  77, 337-53 (2010) and Hauser, E., Junker, E., Helmuth, R. &amp; Malorny, B. Different mutations in the oafA gene lead to loss of O5-antigen expression in  Salmonella enterica  serovar  Typhimurium. J. Appl. Microbiol.  110, 248-53 (2011)). 
     The non-Typhoidal  Salmonella  (NTS) serotypes are a primary cause of foodborne illnesses worldwide. In the U.S. NTS are a leading cause of hospitalization and death due to foodborne illnesses, with  Salmonella enterica  serovar  Typhimurium  (S.Tm) being the most frequent cause. 95% of the total cases of NTS are caused by contaminated food. Unfortunately, absolute protection from infection by enhanced agricultural surveillance is not feasible. The rapid evolution of vaccine-escape variants of Proteobacteria is a major hurdle in vaccine development and explains why there are no successfully licensed vaccines for either human or large-animal use against non-Typhoidal  Salmonella  (NTS) and only very limited options available for pathogenic  E. coli.    
     SUMMARY OF THE INVENTION 
     The present invention relates in particular to an immunogenic composition for Proteobacteria protection and reduced transmission. We have identified Proteobacteria strain combinations, based on the evolutionary trajectory of a serovar during infection of an immune host, that generate an immune response capable of robustly driving bacterial enteropathogens into an evolutionary dead end and reducing the transmission of the bacterium. These inactivated typically oral immunogenic compositions and vaccines, respectively, are easy to apply, cheap to produce, and can be stored long-term without cold-chain requirements making them ideal for application in livestock, or in resource-poor areas. Because these vaccine formulations specifically drive pathogen evolution to loss-of-virulence, according to our knowledge, these are the only immunogenic compositions and vaccine formulations, respectively, capable of breaking the chain of transmission for these types of pathogen. 
     Thus, in a first aspect, the present invention provides for an immunogenic composition comprising at least two or more inactivated serovar-variants of a Proteobacteria strain, wherein each of said two or more inactivated serovar-variants comprises a genetic modification of genes encoding the O-antigen production and modification enzymes, wherein independently each of said genetic modification comprises a glucosylation and/or O-acetylation of the O-antigen. 
     This is distinct to vaccine approaches combining multiple serovars, i.e. which aim to protect against multiple different pathogens in a single vaccine. Instead, these vaccines include multiple variants of a single pathogen serovar, in order to drive the evolution of this pathogen serovar to loss of virulence. 
     In a further aspect, the present invention provides for the inventive immunogenic composition for use as a prophylactic treatment against a disease caused by Proteobacteria in a subject, wherein preferably the subject following treatment contains only a non-transmissible form of said Proteobacteria. 
     In a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of inducing an immune response against a disease caused by Proteobacteria in a subject, wherein said method comprises administrating said immunogenic composition to said subject in need thereof, and wherein preferably administration is by intranasal, intramuscular, subcutaneous, transdermal or sublingual administration. 
     In a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of preventing disease caused by Proteobacteria selected from the group consisting of bacterial gastroenteritis, bacterial enterocolitis, urinary tract infection, mastitis, bacterial pneumonia and bacterial sepsis. 
     In another aspect, the present invention provides for the method of generating the inventive immunogenic composition, wherein said method comprises the following steps:
         i. Administer an inactivated wild type Proteobacterial strain to a subject,   ii. Challenge the subject with the wildtype Proteobacterial strain,   iii. Isolate clones of said Proteobacterial strain from the subject between 2 hours to 7 days post infection,   iv. Identify isolated clones with reduced binding affinity to the wild type Proteobacteria anti-O-antigen antibody,   v. Generate recombinant clones identical to said isolated clones with reduced binding affinity,   vi. Inactivate and combine the recombinant clones with the inactivated wild type Proteobacterial strain,   vii. Repeat steps i-viii, administering the inactivated combined recombinant clones with the inactivated wild-type Proteobacterial strain,   viii. Combine all identified inactivated clones with the inactivated wild type Proteobacteria to produce the immunogenic composition.       

     Further aspects and embodiments of the present invention will become apparent as this description continues. 
    
    
     
       DESCRIPTION OF FIGURES 
         FIG. 1A : Graph shows the fecal  Salmonella  Colony Forming Units per gram cecal content (CFU/gcc) of mice that were either vaccinated with 1e10 particles of peracetic acid inactivated wild-type  S. typhimurium  strain SL1344 (PA.STm) or vehicle-only control (PBS). The three test groups of mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 5*10 3 , 5*10 5 , and 5*10 7 . The graph demonstrates protection failure of a wild-type  Salmonella typhimurium  vaccine. 
         FIG. 1B : Graph shows the lymph node  Salmonella  Colony Forming Units per mesenteric lymph node (CFU/mLN) of mice that were either vaccinated with 1e10 particles of peracetic acid inactivated wild-type  S. typhimurium  strain SL1344 (PA.STm) or vehicle-only control (PBS). The three test groups of mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 5*10 3 , 5*10 5 , and 5*10 7 . The graph demonstrates protection failure of a wild-type  Salmonella typhimurium  vaccine. 
         FIG. 1C : Graph shows the amount of Lipocalin2 in feces (ng/g) of mice that were either vaccinated with 1e10 particles of peracetic acid inactivated wild-type  S. typhimurium  strain SL1344 (PA.STm) or vehicle-only control (PBS). The three test groups of mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 5*10 3 , 5*10 5 , and 5*10 7 . The graph demonstrates that inflammation was reduced but still present in wild-type  Salmonella typhimurium  vaccine treated mice. 
         FIG. 1D : Graph shows the log-median fluorescence intensities (MFI) plotted against antibody serial dilutions for each sample from vaccinated mouse and a mouse treated with PBS. From the vaccinated mice, an intestinal lavage was collected. For both the vaccinated (dotted line) and the PBS (straight black line) treated mice, the intestinal supernatants were used to perform serial dilutions. 25 μl of the dilutions (containing intestinal IgA) were incubated with 5*10 5    S. typhimurium . The bacteria were washed and a secondary, fluorescently-labelled anti-IgA antibody. The fluorescence per  S. typhimurium  cell quantifies the bound IgA and was determined by bacterial flow cytometry. This experiment revealed that all vaccinated mice had robust IgA responses against the wild-type  S. typhimurium , i.e. that vaccine failure was not due to failure to induce an intestinal IgA response. 
         FIG. 1E : Graph shows the vaccine-specific intestinal IgA titre production in mice that were vaccinated but developed intestinal inflammation and invasive disease shown in circles with crosses (vaccinated) (unprotected) and in mice that were vaccinated but did not develop intestinal inflammation and invasive disease shown in white circles (vaccinated) (protected). This experiment revealed that all mice had equally robust IgA responses against wild-type  S. typhimurium , despite mouse pathology. 
         FIG. 1F : Graph shows the log-median fluorescence intensities (MFI) of intestinal IgA bound to  S. typhimurium  clones that were isolated from mice that were vaccinated but developed intestinal inflammation and invasive disease shown in circles with crosses (unprotected) and from  S. typhimurium  clones that were isolated from mice that were vaccinated but did not develop intestinal inflammation and invasive disease shown in white circles (protected). This revealed that  S. typhimurium  in the intestines of these vaccinated but unprotected mice no longer bound vaccine-induced IgA—i.e.  S. typhimurium  can escape the IgA response induced by a standard oral vaccine. 
         FIG. 2A : Genome sequencing of  S. typhimurium  clones that were isolated from mice that were vaccinated but developed intestinal inflammation and invasive disease (unprotected). The sequencing revealed a common 7 base-pair contraction in the coding region of the OafA gene, known to encode an Abequose O-acetyl transferase which modifies the  S. typhimurium  O-antigen glycan repeat, the top sequence is the wild type  S. typhimurium  nucleic acid sequence (SEQ ID NO: 1) and amino acid sequence (SEQ ID NO: 45) and the evolved clone is at the bottom with the comparable nucleic acid sequence (SEQ ID NO: 2) and amino acid sequence (SEQ ID NO:46). 
         FIG. 2B : Clones of bacteria that were isolated from mice that were vaccinated but did develop intestinal inflammation and invasive disease (O5−, O5+) were stained with anti-O5 antisera and secondary antibody fluorescent anti-rabbit IgG and compared with  S. typhimurium  wild type stained bacteria (S.Tm WT ). The first graph shows O5 staining of the clean deletion mutant of OafA (S.Tm ΔOafA ) and for wild type  S. typhimurium  (S.Tm WT ). The second graph shows staining of two evolved  S. typhimurium  clones reisolated from infected, vaccinated, but unprotected mice, stained for O5. The graphs show that some  S. typhimurium  clones from vaccinated but unprotected mice had a loss of O5 compared to wild type  S. typhimurium  stained clones (S.Tm WT ), and this was phenotypically identical to deletion of the OafA gene. 
         FIG. 2C : Clones of bacteria that were isolated from mice that were vaccinated but did develop intestinal inflammation and invasive disease (Evolved clone) were stained with anti-O12 antibody and secondary antibody Alexa 647-anti-human IgG and compared with  S. typhimurium  wild type stained bacteria (S.Tm WT ). This identified a second class of clones with apparently bi-stable loss of binding to an anti-O12 typing antibody. The Y-axis represents the % MFI as determined by bacterial flow cytometry. 
         FIG. 3A : Competitive infections assay between mice (n=5) vaccinated with vaccines of O5 serovar (acetylated O-antigen)  S. typhimurium  (O12 locked O5) (PA-S.Tm ΔgtrC ) or mice (n=5) vaccinated with  S. typhimurium  carrying an in-frame deletion of OafA (non-acetylated O-antigen, O4 serovar) (O12 locked O4) (PA-S.Tm ΔoafAΔgtrC ) or mice (n=5) not vaccinated (Naïve) and all were subsequently challenged with a 1:1 ratio of O12 locked O5 and O12 locked O4  S. typhimurium . The Y-axis measures the ratio of O5  S. typhimurium  to O4  S. typhimurium  in feces and the x-axis is the days post infection. The graph shows that in naive mice, both serovars remained at a 1:1 ratio in intestinal content. Mice vaccinated with the inactivated O4 serovar (S.Tm ΔoafAΔgtrC ) had an up to 10 8 -fold over-abundance of the O5 serovar (S.Tm ΔgtrC ) over the O4 serovar and mice vaccinated with the inactivated O5 serovar had an up to 10 8 -fold over abundance of the O4 serovar over the O5 serovar. The graph demonstrates a very strong selective pressure exerted on the  Salmonella typhimurium  O-antigen by vaccine-induced IgA. Black circles represent  S. typhimurium  of naïve vaccinated mice and white circles represent  S. typhimurium  from vaccinated mice. 
         FIG. 3B : The intestinal IgA titre specific for the O5 serovar of  S. typhimurium  was determined by flow cytometry and plotted against the day 4 competitive index (as in  FIG. 3A ). The graph demonstrates a very strong correlation between the strength of the specific IgA response and the selective pressure on the  Salmonella typhimurium  O-antigen by vaccine-induced IgA. White circles represent IgA antibodies from O5 (PA-S.Tm ΔgtrC ) vaccinated mice and white squares represent IgA antibodies from O4 (PA-S.Tm ΔoafAΔgtrC ) vaccinated mice. 
         FIG. 3C : Competitive infections assay between mice (n=10) vaccinated with  S. typhimurium  carrying in frame deletions of GtrC and OafA (non-acetylated O-antigen, cannot glucosylate, O4,O12 locked  serovar) (PA-S.Tm ΔoafAΔgtrC ) or mice (n=5) not vaccinated (Naïve) and all were subsequently challenged with a 1:1 ratio of  S. typhimurium  that has a non-acetylated O-antigen and which cannot glucosylate (O12 locked O4) (S.Tm ΔoafAΔgtrC ) and Serovar O12 O4 (S.Tm ΔoafA ) which can glucosylate the O-antigen. Black circles are naïve mice. White circles are vaccinated mice that did not develop intestinal inflammation and invasive disease (protected). Grey circles are mice that were vaccinated but developed intestinal inflammation and invasive disease (unprotected). The Y-axis measures the ratio of O12 locked  to O12  S. typhimurium  in feces and the x-axis is the days post infection. In Naïve mice both O12O4 and O12 locked O4 survive in equal measure. In vaccinated mice O12 locked O4 dominates in 50% of animals. The assay demonstrated the key role of bistable glucosylation of the O-antigen in escape of IgA-mediated recognition of these bacteria. 
         FIG. 3D : The intestinal IgA titre specific for the O12-2 (glucosylated) serovar of  S. typhimurium  was determined by flow cytometry and plotted against the day 4 competitive index in feces (as in  FIG. 3C ). The graph demonstrates a correlation between the strength of the specific IgA response and the selective pressure on the  Salmonella typhimurium  O-antigen by vaccine-induced IgA. White circles are vaccinated mice and did not develop intestinal inflammation and invasive disease (protected). Grey circles are mice that were vaccinated but developed intestinal inflammation and invasive disease (unprotected). The Y-axis measures  S. typhimurium  competitive index in feces (ratio of O12 locked  to O12  S. typhimurium  in feces at d4 post-infection) and the x-axis measures the anti-O12 locked O4 antibody titre (anti-O12-2 Ab). Out competition of O12-locked strains was only observed in mice with weak O12-2 antibody response. 
         FIG. 4A : Graph shows the  Salmonella  Colony Forming Units per mesenteric lymph node (CFU/mLN) of mice which that were either vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-Mix) or vaccinated with a vehicle-only control PBS (Naive). The mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 1e5. Black circles are unvaccinated (naïve) mice and white circles are vaccinated (PA-Mix) mice. The graph demonstrates that an Evolutionary Trap vaccine (PA-Mix) constructed by combining escape mutants (the four serovar), generated robust vaccine-mediated protection. 
         FIG. 4B : Graph shows the amount of Lipocalin2 in feces (ng/g) of mice that were either vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-Mix) or vaccinated with vehicle-only control PBS (Naive). The mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 1e5. Black circles are unvaccinated (naïve) mice and white circles are vaccinated (PA-Mix) mice. The X-axis is days post infection. The graph shows intestinal inflammation in naive mice versus mice that were vaccinated. The graph demonstrates that an Evolutionary Trap vaccine (PA-Mix), constructed by combining escape mutants (the four serovar), generated robust vaccine-mediated protection from inflammatory disease. 
         FIG. 4C : Graph shows the amount of antibody produced in mice which that were either vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-S.Tm ET ) or vaccinated with wild type  S. typhimurium  (PA-S.Tm WT ). White circles are mice vaccinated with wild type  S. typhimurium  (PA-S.Tm WT ) and circles with black crosses are mice vaccinated with PA-S.Tm ET . At 28 days after the first vaccination, mice receiving the combined vaccine had significantly higher intestinal IgA antibody titres with specificities towards all three serovar variants: O4/O12 (second column), O5/O12-2 (third column) and O4/O12-2 (fourth column) compared to wild type  S. typhimurium  vaccinated mice. The first column was IgA antibody titres with specificities towards O5, O12. 
         FIG. 4D : Graph shows the fraction of  S. typhimurium  clones with a short O-antigen recovered from mice that were either vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-S.Tm ET ) or vaccinated with wild type  S. typhimurium  (PA-S.Tm WT ) or in unvaccinated mice (PBS). The mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 1e5. White squares are vaccinated with wild type  S. typhimurium  (PA-S.Tm WT ) mice and black circles are vaccinated with PA-S.Tm ET  mice. At 4 days post challenge the salmonella clones from the mouse gut were detected by dim staining with the anti-O5 antibody by flow cytometry (% O5-dim—inset graph). Mice receiving the combined vaccine had a significantly higher fraction of  S. typhimurium  with short O-antigens compared to wild type vaccinated and PBS treated mice. 
         FIG. 4E : Gel shows the short O-antigen of  S. typhimurium  recovered from mice that were either vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-S.Tm ET ) or vaccinated with wild type  S. typhimurium  (PA-S.Tm WT ) or in unvaccinated mice (PBS). The mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 1e5. At 4 days post challenge the salmonella clones from the mouse gut were measured for the short O-antigen. The gel contains five control columns, a ladder, a positive control  S. typhimurium  with a constructed short O-antigen (S.Tm wzyB ), clones from wild type  S. typhimurium  vaccinated mice (S.Tm WT ), clones from unvaccinated mice (Mock). The last four columns are clones from mice vaccinated with wild type  S. typhimurium  (PA-S.Tm ET ). The clones from mice that received the combined vaccine PA-S.Tm ET  contained  S. typhimurium  clones with short O-antigens compared to wild type vaccinated and PBS treated mice. 
         FIG. 4F : This graph shows intestinal IgA antibodies from mice which were vaccinated with a 1:1:1:1 mix of 1e10 particles of peracetic acid inactivated  S. typhimurium  strains: Serovar O5, O12, Serovar O4, O12, Serovar O5, O12-2 and Serovar O4, O12-2 (PA-S.Tm ET ). For each intestinal IgA sample, we quantified the ability to bind to  S. typhimurium  with either a short O-antigen (S.Tm wzyB ) (Single repeat) or the wild type  S. typhimurium  (long O-Ag). The single repeat O-antigen resulted in lower binding to vaccine-induced IgA, explaining the emergence of these clones in vaccinated mice. 
         FIG. 5A : The graph shows the mean ratio of GFP signal to OD (fluorescence intensity) measured during the last 100 minutes of incubation of bacteria under stressful conditions (Tris and EDTA), this measured the relative survival of wild-type (expressing GFP) and test bacteria (contributing only to OD) following stress testing. OD and fluorescence values were corrected for the baseline value measured at time 0. The Y-axis is the OD ratio of GFP. The first column measures cell death via OD of  S. typhimurium  producing full length antigen (long O antigen) (S.Tm ΔoafAΔgtrC ) versus a wild type  S. typhimurium  with GFP (S.Tm GFP ). The second column black circles measure cell death via OD of  S. typhimurium  with OAFA GTRC mutant with in-frame deletion mutant for wzyB (S.Tm ΔoafAΔgtrCΔwzyB ) (short O-antigen) versus a wild type  S. typhimurium  with GFP (S.Tm GFP ). The second column cross circles measure cell death via OD of an evolved  S. typhimurium  clone from a vaccinated mouse which carries a genomic deletion including the wzyB gene (S.Tm ΔwzyB ) (short O antigen) versus a wild type  S. typhimurium  with GFP (S.Tm GFP ). Graph demonstrates fitness defects of the short O-antigen mutants and lower survival rate following stressful conditions (Tris and EDTA). 
         FIG. 5B : The graph shows the colony forming units (CFU log 10) measured 1 h after incubation of the bacteria with human serum, this measured the survival of the bacteria following incubation with human complement proteins. The Y-axis is the colony forming units (CFU log 10). The first column measures bacteria count (survival) of  S. typhimurium  with OAFA GTRC mutant producing full length antigen (long O-antigen) (S.Tm ΔoafAΔgtrC ). The second column black circles measure bacteria count (survival) of  S. typhimurium  with OAFA GTRC mutant with in-frame deletion mutant for wzyB (S.Tm ΔoafAΔgtrCΔwzyB ) (short O-antigen). The second column cross circles measure bacteria count (survival) of evolved  S. typhimurium  clone from a vaccinated mouse which carries a genomic deletion including the wzyB gene (S.Tm ΔwzyB ) (short O-antigen). Graph demonstrates fitness defects of the short O-antigen mutants and lower survival rate following incubation with human serum (complement proteins). 
         FIG. 5C : A mouse model which cannot produce antibodies (JH−/−), two mouse models that can produce antibodies (JH+/− and C57BL/6) were vaccinated with  S. typhimurium  with OAFA GTRC mutant (S.Tm ΔoafAΔgtrC ) (long, non-acetylated, no glucosylated O-antigen). A mouse model that can produce antibodies (C57BL/6) was unvaccinated (naïve). All mice were challenged with  S. typhimurium  with a 1:1 ratio of OAFA GTRC mutant producing full length antigen (long O antigen) (S.Tm ΔoafAΔgtrC ) and  S. typhimurium  with OAFA GTRC mutant with in-frame deletion mutant for wzyB (S.Tm ΔoafAΔgtrCΔwzyB ) (short O-antigen). The Y-axis measures the ratio of S.Tm ΔoafAΔgtrCΔwzyB  to S.Tm ΔoafAΔgtrC  in feces. The X-axis is the days post infection. Black triangles are JH−/− vaccinated mice (no antibodies, control for non-immune effects of vaccination) and black circles are C57BL/6 unvaccinated mice, in both cases the long O-antigen bacteria dominated (S.Tm ΔoafAΔgtrC ). White Circles are C57BL/6 vaccinated mice and white triangles are JH+/− vaccinated mice (specific IgA antibodies), in both cases the short O-antigen bacteria dominated (S.Tm ΔoafAΔgtrCΔwzyB ). This demonstrates that specific IgA can strongly select for the evolution of  S. typhimurium  carrying deletions in wzyB, and therefore with a short O-antigen. 
         FIG. 6A : Graph shows the fecal  Salmonella  Colony Forming Units per gram cecal content (CFU/gcc) of mice that were orally challenged with live Long O-antigen  S. typhimurium  (S.Tm ΔoafAΔgtrC ) or live short O-antigen  S. typhimurium  (S.Tm ΔoafAΔgtrCΔwzyB ). These mice acted as donors for fecal-oral transmission to mice in  FIG. 6B . 
         FIG. 6B : Graph shows the fecal  Salmonella  Colony Forming Units per gram cecal content (CFU/gcc) of mice that were fed a high-fat diet and orally infected with one fecal pellet from mice in  FIG. 6A . This demonstrates that short O-antigen S.Tm variants are weakly transmitted to new hosts in a realistic non-typhoidal  Salmonellosis  infection model. 
         FIG. 7 : French Landrace pigs (n=6) received a high dose of peracetic acid-inactivated wild type  Salmonella typhimurium . Blood was collected at the beginning of the trial (“Before”, closed circles), and after 6 weeks of weekly feeding (“After”, open circles). The blood sample was analysed for  S. typhimurium -specific IgG (Y-axis) over a dilution series. In both vaccinated and control pigs, no adverse effects were observed. Therefore the inactivated oral vaccine approach is appropriate for induction of strong antibody-mediated immune responses in domestic pigs. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. 
     Specific Proteobacterial O-antigen modifications can be used to generate vaccines that induce antibodies against the typical serovar-associated O-antigen, and against all escape variants of the serovar-associated O-antigen. We discovered 1) that escape variants can be identified by iterative vaccination and infection in experimental settings and 2) that inducing antibodies against all naturally-arising escape variants is not only critical to make a non-escapable vaccine but also drives evolution of the Proteobacterial target into a dead-end, preventing efficient transmission, i.e. oral vaccines can be used to rationally control bacterial pathogen evolution. This has been specifically demonstrated in  Salmonella enterica  subspecies  enterica  serovar  Typhimurium . Vaccine escape variants were found to carry deletions or epigenetic modifications of O-antigen modifying genes, generating chemical modifications (acetylation, glucosylation) of the O-antigen glycan repeating unit. Rationally combining strains engineered to produce all possible modified O-antigen structures, generates a vaccine which increased the strength of protection per se over the standard wild-type vaccine. Surprisingly vaccination with a combination of these vaccines forces the emergence of a further type of O-antigen variation: production of single-repeat (i.e. very short) O-antigen. Mice which had received the combined vaccine, produced  S. typhimurium  carrying a spontaneous deletion of the O-antigen polymerase (therefore producing very short O-antigens) which outgrew and replaced the wild type  S. typhimurium  cells in the gut. However, this population of  S. typhimurium  with very short O-antigen has a dramatic loss of fitness when these strains are transmitted into naïve hosts, and during environmental phases of the transmission cycle. This breaks the transmission chain of the pathogen in the host population, effectively forcing bacterial evolution into a dead-end. The theory underlining vaccine design to drive pathogens into evolutionary dead ends can be applied to all Proteobacteria as they contain similar polymerized O-antigens and the process of selecting for bacterial escape variants will be identical. The theory underlining vaccine design to drive pathogens into evolutionary dead ends by tracking the evolutionary trajectory of O-antigen modifying enzyme genes and epigenetic variations that modulate O-antigen modifying enzyme gene expression can be applied to all Gammaproteobacteria as they also contain similar polymerized O-antigens and the process of selecting for bacterial escape variants will be identical. 
     Several aspects of the present invention are disclosed herein; the embodiments and preferred embodiments, respectively, mentioned further herein are applicable for each and any of the 8 or further aspects of the present invention disclosed herein, even though not explicitly mentioned. 
     A first aspect of the present invention is an immunogenic composition comprising at least two or more inactivated serovar-variants of a Proteobacteria strain, wherein each of said two or more inactivated serovar-variants comprises a genetic modification of the O-antigen, wherein independently each of said genetic modification comprises a glucosylation and/or O-acetylation of the O-antigen. Thus, each of said two or more inactivated serovar-variants comprises a genetic modification that alters the O-antigen. 
     In one embodiment the present invention provides an immunogenic composition comprising at least two or more inactivated serovar-variants of a Proteobacteria strain, wherein each of said two or more inactivated serovar-variants comprises a genetic modification of the O-antigen modifying genes, wherein independently each of said genetic modification affects enzymes responsible for glucosylation and/or O-acetylation of the O-antigen. 
     In one embodiment the present invention provides an immunogenic composition comprising at least two or more inactivated serovar-variants of a Proteobacteria strain, wherein each of said two or more inactivated serovar-variants comprises a genetic modification of genes involved in the modification of the O-antigen, wherein the genes encode an enzyme responsible for glucosylation and/or O-acetylation of the O-antigen. Thus, each of said two or more inactivated serovar-variants comprises a genetic modification that results in production of altered O-antigen, within a single serovar/serovar group. 
     In one embodiment, the genetic modification of the O-antigen modifying genes in a specific serovar leads to glucosylation, or loss of glucosylation of the O-antigen. In another embodiment of the present invention, the genetic modification of the O-antigen modifying genes leads to O-acetylation, or loss of O-acetylation of the O-antigen. Thus, the genetic modification that alters the O-antigen modifying genes leads to glucosylation of the O-antigen and/or a genetic modification that modifies the O-antigen modifying genes leads to O-acetylation of the O-antigen. 
     In another embodiment, the genetic modification that alters the O-antigen modifying genes generates strains producing all combinations of glucosylated and O-acetylated O-antigen to be combined into one immunogenic composition. 
     In one embodiment, the immunogenic composition additionally comprises the inactivated wild type serovar of said Proteobacteria strain. 
     In another embodiment, the genetic modification of the O-antigen modifying genes, are created by the deletions and/or epigenetic modifications of the O-antigen modifying genes Abequose O-acetyl transferase (OafA gene) and gtrABC operons (gtrC gene). 
     In another embodiment, the immunogenic composition is generated by combining strains carrying the genetic modification of the O-antigen modifying genes, created following deletions and/or epigenetic modifications of the O-antigen modifying genes Abequose O-acetyl transferase (OafA gene) and gtrABC operons (gtrC gene). 
     In another embodiment, the genetic modification of the O-antigen modifying genes, is created following deletions and/or epigenetic modifications of the O-antigen modifying genes of said inactivated serovar. In one embodiment, the O-antigen modifying genes comprise Abequose O-acetyl transferase (OafA gene) and gtrABC operons (gtrC gene). Thus, the genetic modification that alters the O-antigen are created following deletions and/or epigenetic modifications of the O-antigen modifying genes Abequose O-acetyl transferase (OafA gene) and gtrABC operons (gtrC gene). 
     In another embodiment, the immunogenic composition induces in an animal, upon infection with the wild type serovar of said Proteobacteria, the production of a serovar-variant of said Proteobacteria strain with decreased virulence, compared to Proteobacteria strain recovered from animals not exposed to the immunogenic composition, wherein decreased virulence is measured as a decrease in mortality and/or morbidity of the infected animal or animals infected by contact with this animal. 
     “Decreased virulence” in a bacterium refers to altering expression of genes, regulators of virulence, function of proteins associated with virulence, or resistance to host immune mechanisms. Decreased virulence also refers to physical and biochemical manifestations of virulence including those manifestations associated with any step of the bacterial life cycle when it is associated with a host, including without limitation the adherence, invasion, replication, evasion of host defenses, and transmittal to a new host. Decreased bacterial virulence may be manifested in the form of reduced symptoms in a host, and thus may be detected by monitoring the host for a reduced reaction to the bacteria associated therewith. A decrease in virulence may be at least about a 1% reduction, at least about a 10% reduction, at least about a 20% reduction, at least about a 30% reduction, at least about a 40% reduction, at least about a 50% reduction, at least about a 60% reduction, at least about a 70% reduction, at least about a 80% reduction, at least about a 90% reduction, or at least about a 100% reduction of virulence, as measured by any assay known to those of skilled in the art, when measured against a suitable control. 
     In another embodiment, the immunogenic composition induces in an animal, upon infection with the wild type serovar of said proteobacteria, the production of a serovar variant of said proteobacteria strain with a decreased transmission rate, compared to animals not exposed to the immunogenic composition. 
     “Transmission rate” in a bacterium refers to the disease incidence or the number of infected cases. A decrease in transmission rate may be manifested in the form of a reduction or no symptoms in a host, and thus may be detected by monitoring the host for a reduced reaction to the bacteria associated therewith or may be detected by monitoring the level of said bacterial infection or presence of said bacteria in the host. A decrease in transmission rate may be at least about a 1% reduction, at least about a 10% reduction, at least about a 20% reduction, at least about a 30% reduction, at least about a 40% reduction, at least about a 50% reduction, at least about a 60% reduction, at least about a 70% reduction, at least about a 80% reduction, at least about a 90% reduction, or at least about a 100% reduction of transmission, as measured by any assay known to those of skilled in the art, when measured against a suitable control. 
     In another embodiment, the proteobacteria is a specific serovar of  Salmonella  spp or  Escherichia coli . In another embodiment, the proteobacteria is  Salmonella  spp. In another embodiment of the first aspect of the present invention, the proteobacteria is  Escherichia coli.    
     In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica , and wherein preferably said  Salmonella enterica  is  Salmonella enterica  subspecies  enterica . In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica  subspecies  enterica.    
     In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica  subspecies  enterica , wherein said  Salmonella enterica  subspecies  enterica  is selected from the group consisting of: Typhi, Paratyphi A Paratyphi B, Typhimurium, Montevideo, Gallinarium, Anatum, Pullorum, Muenchen, Kentucky, Dublin, Derby, Minnesota and Enteritidis. In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica  subspecies  enterica , wherein said  Salmonella enterica  subspecies  enterica  is a serovar selected from the group of consisting of: Typhi, Paratyphi A Paratyphi B, Typhimurium, Montevideo, Gallinarium, Anatum, Pullorum, Muenchen, Kentucky, Dublin, Derby, Minnesota and Enteritidis. 
     In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica , wherein said  Salmonella enterica  is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium.    
     In another embodiment, the proteobacteria is a specific serovar of  Salmonella enterica  subspecies  enterica  serovar  Typhimurium  strain ATCC SL1344 or ATCC 14028. In another embodiment, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium  strain ATCC SL1344. In another embodiment, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium  strain ATCC 14028 . Salmonella enterica  serovar  Typhimurium  strain ATCC SL1344 or ATCC 14028 are both available from the American Type Culture Collection. It is a common assumption that data obtained with one strain is representative of both the  Typhimurium  serovar and the  S. enterica  species as a whole. 
       Salmonella  as used herein refers to any strain of  Salmonella , including any strain of  Salmonella enterica , including  Salmonella enterica  serovar  Typhimurium . The serovars of  S. enterica  that may be used as the attenuated bacterium of the live compositions described in accordance with various embodiments herein include, without limitation,  Salmonella enterica  serovar  Typhimurium, Salmonella  montevideo,  Salmonella enterica  serovar  Typhi, Salmonella enterica  serovar, Paratyphi B,  Salmonella enterica  serovar Paratyphi C,  Salmonella enterica  serovar Hadar,  Salmonella enterica  serovar  Enteriditis, Salmonella enterica  serovar Kentucky,  Salmonella enterica  serovar In/antis,  Salmonella enterica  serovar Pullorurn,  Salmonella enterica  serovar  Gallinarum, Salmonella enterica  serovar Muenchen,  Salmonella enterica  serovar Anaturn,  Salmonella enterica  serovar Dublin,  Salmonella enterica  serovar Derby,  Salmonella enterica  serovar  Choleraesuis  var. kunzendorf and  Salmonella enterica  serovar minnesota, among other known strains. 
     As used herein, an immunogenic composition is typically and preferably a composition to which a humoral (e.g., antibody) or cellular (e.g., a cytotoxic T cell) response, or, in one embodiment, an innate immune response, is mounted following delivery of said immunogenic composition to a mammal or animal subject. 
     The term “inactivated” refers to a previously virulent or non-virulent bacteria or bacterium that has been irradiated (ultraviolet (UV), X-ray, electron beam or gamma radiation), heated, or chemically treated to inactivate or kill said bacteria or bacterium, while retaining its immunogenicity. In one embodiment, the inactivated bacteria disclosed herein are inactivated by treatment with an inactivating agent. Suitable inactivating agents include beta-propiolactone, binary or beta- or acetyl-ethyleneimine, glutaraldehyde, ozone, peracetic acid and Formalin (formaldehyde). For inactivation by formalin or formaldehyde, formaldehyde is typically mixed with water and methyl alcohol to create formalin. In a preferred embodiment, the inactivating agent is peracetic acid. More preferably, the inactivating agent is peracetic acid and it is used in the range of a final concentration with the bacteria, of between 0.5%-20%, 0.5%-10%, 0.2%-5%, 0.5%-4% or 1%-2%. 
     More particularly, the term “inactivated” in the context of a bacteria means that the bacteria is incapable of replication in vivo or in vitro and, respectively, the term “inactivated” in the context of a bacteria means that the bacteria is incapable of reproduction in vivo or in vitro. For example, the term “inactivated” may refer, in an embodiment, to a bacteria that has been propagated, typically and preferably in vitro, and has then been inactivated using chemical or physical means so that it is no longer capable of replicating. 
     Even more particularly, the term “inactivated” in the context of the present invention means that the bacteria is inactivated by treatment with an inactivating agent, wherein said inactivating agent is preferably peracetic acid, in the manner as described in Example 1 and the referred Moor et al Frontiers in Immunology, (2016) Vol 7, Article 34. 
     The following disclosure of the immunogenic compositions and methods of this invention specifically describes vaccine compositions for prophylactic use against Proteobacteria. The term “vaccine”, as used herein, is a substance used to stimulate the immune response and provide immunity against one or several diseases. 
     The term “wild type  Salmonella ”, as used herein, is in particular directed to an infectious pathogenic  Salmonella , which is particularly capable of infection in swine. 
     “Recombinant”, as applied to a polynucleotide, means that the polynucleotide is the product of various combinations of cloning, restriction or ligation steps, and other procedures that result in a construct that is distinct from a polynucleotide found in nature. A recombinant bacterium is a bacterial cell comprising a recombinant polynucleotide. The terms respectively include replicates of the original polynucleotide construct and progeny of the original bacterial construct. Typical recombinant or genetic engineering steps to generate a recombinant bacterium as referred to herein include bacteriophage transduction or homologous recombination, among other known techniques described in the art. 
     In another embodiment of the immunogenic composition as described herein, the inactivated serovar may be attenuated prior to or after to genetic modification of O-Antigen modifying genes. 
     The terms “genetic modification” refers to any deliberately inserted change in a nucleic acid or protein sequence, such as a deletion of all or part of the O-antigen modifying gene sequences, or an insertion of a sequence into the O-antigen modifying gene sequences or an insertion of a sequence altering expression or function of O-antigen modifying enzymes. 
     “Naturally occurring” means a sequence found in nature and not synthetically prepared or modified. 
     In another embodiment of the immunogenic composition of the present invention, the inactivated serovar-variants are produced via bacteriophage, transduction or homologous recombination. 
     Deletion or insertion in genes involved in determining the O-antigen structure may be engineered using a conventional technique, such as homologous recombination, transposon insertion or bacteriophage transduction. All of these techniques are known in the art. 
     In another embodiment of the present invention, said O-antigens of said  Salmonella enterica  serovar  Typhimurium  (S. Tm) comprise a mannose-rhamnose-galactose-repeat with the modification being (i) in the identity of the mannose-linked di-deoxyhexose, i.e. an O-acetylated Abequose residue (O:4[5] serovar variant) or a non-O-acetylated serotype (O:4 serovar variant) generated by the loss of function of the Abequose O-acetyl transferase OafA, and/or (ii) the galactose residue, i.e. unmodified (O:12-0 serovar variant) or modified by addition of a glucose residue via an α1-4 linkage to the galactose (O:12-2 serovar variant). 
     The following serovar are named in accordance with the Kauffman-White Classification scheme, the system classifies the genus  Salmonella  into serotypes, based on surface antigens. The structures of the O-antigens of said O:4[5],12-0 serovar variant, O:4,12-0 serovar variant, O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant are as follows comprising the depicted genetic modifications of said O-antigens oligosaccharide repeats: 
     
       
         
         
             
             
         
       
     
     Preferably, the oligosaccharide repeats within the O-antigen between 10-200 times, further preferably 25-150 times. This is symbolized by the arrows flanking the oligosaccharide and glycan structures, respectively. 
     In another embodiment, the proteobacteria is  Salmonella enterica  serovar  Typhimurium , and wherein said at least 2 inactivated serovar-variants of said proteobacteria strain are selected from the group consisting of O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said inactivated serovar variants comprises a glycan structure, typically and preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises at least 4, preferably exactly 4, inactivated serovar of said proteobacteria strain, and wherein said 4 inactivated serovar are O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said four inactivated serovar variants comprises a glycan structure, typically and preferably oligosaccharide repeats, selected from the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises exactly 4 inactivated serovar variants of said proteobacteria strain, and wherein said 4 inactivated serovar variants are O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said four inactivated serovar comprises a glycan structure of the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated serovar variants O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated serovar variants O:4[5],12-0 serovar variant, and O:4, 12-2 serovar variant and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated serovar variants O:4, 12-0 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated serovar variants are O:4[5],12-0 serovar variant and O:4[5], 12-2 serovar variant and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 2 inactivated serovar variants are O:4, 12-0 serovar variant and O:4[5], 12-2 serovar variant and wherein preferably the O-antigen of said two inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In another embodiment there is the immunogenic composition of the first aspect of the present invention, wherein the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants selected from the group consisting of O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, O:4[5], 12-2 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said three inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, as depicted above. 
     In one embodiment, the O-antigen modifying gene is inserted in the chromosome at a non-naturally occurring site or is present extrachromosomally (plasmid) to enable the proteobacteria to produce or deliver larger amounts of the O-antigen modifying enzymes than would be produced in an unmodified bacterium. 
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants, O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, and O:4[5], 12-2 serovar variant wherein preferably the O-antigen of said three inactivated serovar variants comprises a glycan structure, preferably oligosaccharide repeats, of the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants, O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said three inactivated serovar comprises a glycan structure, preferably oligosaccharide repeats, of the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants are O:4[5],12-0 serovar variant, O:4, 12-2 serovar variant, and O:4[5], 12-2 serovar variant, and wherein preferably the O-antigen of said three inactivated serovar comprises a glycan structure, preferably oligosaccharide repeats, of the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants are O:4,12-0 serovar variant, O:4[5], 12-2 serovar variant, and O:4, 12-2 serovar variant, and wherein preferably the O-antigen of said three inactivated serovar comprises a glycan structure, preferably oligosaccharide repeats, of the following formula: 
     
       
         
         
             
             
         
       
     
     In another embodiment of the immunogenic composition, the proteobacteria is  Salmonella enterica  subspecies  enterica  serovar  Typhimurium , and wherein said composition comprises 3 inactivated serovar variants are O:4[5],12-0 serovar variant, O:4, 12-0 serovar variant, and O:4[5], 12-2 serovar variant and wherein preferably the O-antigen of said three inactivated serovar comprises a glycan structure, preferably oligosaccharide repeats, of the following formula: 
     
       
         
         
             
             
         
       
     
     The chemical structure of O-antigens for the analogous O-antigens in other  Salmonella  species serovars have analogous structural variants or are highly similar with O-antigens variants from  Salmonella enterica Typhimurium  serovars. They typically possess a main chain having a D-Manp-(1--&gt;4)-L-Rhap-(α1--&gt;3)-D-Galp trisaccharide repeat unit and may differ in the configuration (α vs. β) and the position of the polymerization linkage (α1--&gt;2 vs. α1--&gt;6) and the configuration (α vs. β) of the D-Manp-(1--&gt;4)-L-Rhap linkage (Liu et al. FEMS Microbiol Rev 38 (2014) 56-89). 
     In another embodiment of the present invention, the serovar are locked. A locked serovar is a serovar incapable of evolving or switching to another serovar. 
     The terms “nucleic acid sequence”, “polynucleotide,” when used in singular or plural form, generally refers to any nucleic acid sequence, polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as defined herein include, without limitation, single- and double-stranded DNA, DNA including single- and double-stranded regions, single- and double-stranded RNA, and RNA including single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or include single- and double-stranded regions. In general, the term “nucleic acid sequence” embraces all chemically, enzymatically and/or metabolically modified forms of unmodified polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells. 
     The term “percent sequence identity” or “identical” in the context of nucleic acid sequences or chemical or carbohydrate sequences refers to the residues in the two sequences that are the same when aligned for maximum correspondence. The length of sequence identity comparison may be over the full-length of an open reading frame of a gene, protein, subunit, a fragment or carbohydrate. 
     As described herein, the percent identity among the O-antigen modifying genes in proteobacteria and serovars can be about 75%, 80%, 85%, 90%, 95% or over 99%. In other embodiments, the percent identities of the O-antigen modifying genes can be lower than 75%. 
     Identity is readily determined using such algorithms and computer programs as are defined herein at default settings. Alignments are performed using any of a variety of publicly or commercially available Multiple Sequence Alignment Programs, such as “Clustal W”, accessible through Web Servers on the internet. Alternatively, Vector NTI® utilities are also used. There are also a number of algorithms known in the art that can be used to measure nucleotide sequence identity, including those contained in the programs described above. Generally, these programs are used at default settings, although one of skill in the art can alter these settings as needed. Alternatively, one of skill in the art can utilize another algorithm or computer program that provides at least the level of identity or alignment as that provided by the referenced algorithms and programs. The similarities between the sequences can also be defined as the ability to hybridize to the complement of a selected sequence, under stringent conditions. 
     “Isolated” means altered “by the hand of man” from its natural state, i.e., if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or polypeptide naturally present in a living organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein. 
     One skilled in the art may readily reproduce the compositions and methods described herein by use of the elements described herein, which are publicly available from conventional sources. 
     In another embodiment of the inventive immunogenic composition, said composition induces in an animal, upon infection, the release of inflammatory cytokines from macrophages or dendritic cells and an increase in the animal&#39;s innate immune response to the bacterium. 
     In another embodiment the immunogenic composition further comprises a pharmaceutically acceptable excipient. 
     In another embodiment the immunogenic composition described herein further comprises an adjuvant. 
     The immunogenic compositions of the present invention may be further associated with a pharmaceutically acceptable carrier for in vivo delivery. As used herein the term “pharmaceutically acceptable carrier” or “diluent” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with administration to humans or other mammals, or animals, such as avian species. In one embodiment, the diluent is saline or buffered saline. Such pharmaceutically acceptable carriers suitable for use in such a composition are well known to those of skill in the art. Such carriers include, without limitation, and depending upon pH adjustments, buffered water, buffered saline, such as 0.8% saline, phosphate buffer, 0.3% glycine, hyaluronic acid, alcoholic/aqueous solutions, emulsions or suspensions. Other conventionally employed diluents, adjuvants and excipients, may be added in accordance with conventional techniques. Optionally, the pharmaceutical compositions can also contain a mild adjuvant, such as an aluminum salt, e.g., aluminum hydroxide or aluminum phosphate, aqueous suspensions of aluminum and magnesium hydroxides, liposomes, and oil in water emulsions. 
     Carriers can include ethanol, polyols, and suitable mixtures thereof, vegetable oils, and injectable organic esters. Buffers and pH adjusting agents may also be employed. Buffers include, without limitation, salts prepared from an organic acid or base. Representative buffers include, without limitation, organic acid salts, such as salts of citric acid, e.g., citrates, ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid, Tris, trimethanamine hydrochloride, or phosphate buffers. Parenteral carriers can include sodium chloride solution, Ringer&#39;s dextrose, dextrose and sodium chloride, lactated Ringer&#39;s or fixed oils. Intravenous carriers can include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer&#39;s dextrose and the like. Preservatives and other additives such as, for example, antimicrobials, antioxidants, chelating agents, inert gases and the like may also be provided in the pharmaceutical carriers. These compositions are not limited by the selection of the carrier. The preparation of these pharmaceutically acceptable compositions, from the above-described components, having appropriate pH isotonicity, stability and other conventional characteristics is within the skill of the art. 
     The preferred features and embodiments as described above and herein and even though occasionally referred to the first aspect of the present invention apply to any and all subsequent aspects of the present invention described herein. 
     According to a further aspect of the present invention there is provided a method of inducing an immune response against a proteobacteria in a subject in need thereof, the method comprising administering an immunogenic composition described herein to said subject, wherein said composition is administered in an effective amount so as to elicit an immune response to said Proteobacteria. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of inducing an immune response against a proteobacteria in a subject in need thereof, wherein said method comprises administering said inventive immunogenic composition to said subject, and wherein said composition is administered in an effective amount so as to elicit an immune response to said Proteobacteria. 
     According to another aspect of the present invention there is provided a method of treating a subject in need thereof against proteobacteria, the method comprising administering an immunogenic composition described herein to the subject, wherein the subject is preferably thereby resistant to one or more infections by said proteobacteria. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of treating a subject in need thereof against proteobacteria, wherein said method comprises administering said inventive immunogenic composition to the subject, wherein the subject is preferably thereby resistant to one or more infections by said proteobacteria. 
     In a further aspect, the present invention provides for the inventive immunogenic composition for use as a prophylactic treatment against a disease caused by Proteobacteria in a subject, wherein preferably the subject following treatment contains only a non-transmissible form of said Proteobacteria In a further embodiment the subject following treatment contains only a non-transmissible form of said Proteobacteria due to the immunogenic composition driving evolution of the Proteobacteria. 
     According to a still further aspect of the present invention there is provided a method of lessening the severity of symptoms of proteobacteria infection in a subject in need thereof, comprising administering to the subject an effective amount of an immunogenic composition as described herein sufficient to lessen the severity of said symptoms in said subject. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of lessening the severity of symptoms of proteobacteria infection in a subject in need thereof, wherein said method comprises administering to the subject an effective amount of said inventive immunogenic composition sufficient to lessen the severity of said symptoms in said subject. 
     In a further aspect the present invention provides for the inventive immunogenic composition for use in a method of inducing an immune response against a disease caused by Proteobacteria in a subject, wherein said method comprises administrating said immunogenic composition to said subject in need thereof, and wherein preferably said immune response is a protective immune response and wherein preferably administration is by intranasal, intramuscular, subcutaneous, transdermal or sublingual administration. 
     According to another aspect of the present invention there is provided a method of treating a subject in need thereof against proteobacteria, the method comprising administering an immunogenic composition as described herein to the subject, wherein the subject following treatment contains only a non-transmissible form of said proteobacteria. In one embodiment the subject contains only a non-transmissible form of said proteobacteria 12, 24, 48 or 72 hours following treatment. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of lessening the severity of symptoms of proteobacteria infection in a subject in need thereof, wherein said method comprises administering to the subject an effective amount of said inventive immunogenic composition sufficient to lessen the severity of said symptoms in said subject. 
     According to a further aspect of the present invention there is provided a method of vaccinating a subject for a disease caused by proteobacteria, comprising administrating the immunogenic composition as described herein to a subject in need thereof by intranasal, intramuscular, subcutaneous, transdermal or sublingual administration. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of vaccinating a subject for a disease caused by proteobacteria, wherein said method comprises administrating said inventive immunogenic composition to a subject in need thereof by intranasal, intramuscular, subcutaneous, transdermal or sublingual administration. 
     In another embodiment of the inventive methods, said subject is selected from a human and an agricultural animal. 
     In another embodiment of the inventive methods, said agricultural animal is selected from the group consisting of cattle, poultry, swine, horses, sheep and goats. 
     In another embodiment of the inventive methods, said agricultural animal is swine. 
     According to a further aspect of the present invention there is provided an immunogenic composition as described herein, for use in preventing disease caused by proteobacteria selected from the list comprising: bacterial gastroenteritis, bacterial enterocolitis, urinary tract infection, mastitis, bacterial pneumonia, bacterial sepsis. Thus, in a further aspect, the present invention provides for the inventive immunogenic composition for use in a method of preventing disease caused by proteobacteria selected from the list comprising: bacterial gastroenteritis, bacterial enterocolitis, urinary tract infection, mastitis, bacterial pneumonia, bacterial sepsis. 
     In a preferred embodiment, said Proteobacteria is Gammaproteobacteria. In another embodiment, the Proteobacteria may be selected from Enterobacteriaceae, Vibrionaceae, Pseudomonadaceae,  Campylobacter . In another embodiment the Gammaproteobacteria is Enterobacteriaceae and said Enterobacteriaceae is selected from  Salmonella  enteritis,  Escherichia coli, Yersinia pestis, Shigella  spp. 
     Diseases caused by pathogenic Proteobacteria include and are typically and preferably bacterial gastroenteritis, bacterial enterocolitis, urinary tract infection, mastitis, bacterial pneumonia, bacterial sepsis. 
       Salmonella  is a genus of over 2000 serovars and includes organisms that cause a wide range of human and animal diseases. For example,  Salmonella enterica  serovars  Typhimurium  and Enteritidis are the most frequent disease-causing non-typhoidal  Salmonella  (NTS) and cause  salmonellosis —a gastroenteritis which is usually a self-limiting illness in healthy individuals. 
     “Animal” or “subject” as used herein means a mammalian animal, including a human male or female, a veterinary or farm animal, e.g., horses, livestock, cattle, pigs, etc., a domestic animal or pet, e.g., dogs, cats; and animals normally used for clinical research, such as primates, rabbits, and rodents. In one embodiment, the subject is a human. In another embodiment, the subject is a swine. “Animal” as used herein is also meant to include other non-mammals or animal species that are commonly infected by  Salmonella , such as avians or fowl that are used as food products, can be carriers for  Salmonella , and are often the transmitters of the bacterium to humans. 
     According to certain methods, where the intended subject for administration is a swine, or other animal, the composition containing the inactivated and modified proteobacteria described herein may be a composition suitable to be added to a foodstuff. Depending upon the subject selected, type of animal, size, weight, general health, etc., and purpose of treatment, the mode of administration and dosage may be selected by one of skill in the art, e.g., a veterinarian or physician. For example, the mode of administration can be any suitable route: oral, subcutaneous injection, intravenous injection, intramuscular injection, mucosal, intra-arterial, intraperitoneal, parenteral, intradermal, transdermal, nasal, vaginal, or rectal or inhalation routes, among others. The term “oral” refers to administration of a compound or composition to a subject by a route or mode along the alimentary canal, such as by swallowing liquid or solid forms of a composition from the mouth. The doses may be administered as a single dose, multiple doses over a selected time gap, via prime/boosting protocols, etc. 
     When administered as an animal vaccine, e.g., a vaccine and immunogenic composition, respectively, for swine, for example, administration can be by gavage in a carrier. Alternatively, the bacteria can be added to gel beads and mixed with feed. Still alternatively, the bacteria can be sprayed onto the feathers or skin of the animals and inhaled. It is likely also that the bacteria can be lyophilized or otherwise treated and mixed with feed. 
     Similarly the selection of suitable dosages will be within the skill of the art depending upon the subject and course of treatment. Exemplary dosages may be 5×10 6 -5×10 13  colony forming units, e.g., 5×10 5  colony forming units, or 10 10 -10 13  inactivated bacterial particles in 100 microliters to 10 milliliters for, e.g., swine. The selection of the doses and modes of administration and dosage regimens may be selected by one of skill in the art based on the subject to be vaccinated and immunized, respectively, the physical attributes of the subject, the virulence of the bacteria, the route of administration, and other common factors. Those of skill in the art will recognize that the precise dosage may vary from situation to situation and from patient to patient, depending on e.g. age, gender, overall health, various genetic factors, and other variables known to those of skill in the art. Dosages are typically determined e.g. in the course of animal and/or human clinical trials as conducted by skilled medical personnel, e.g. physicians. 
     As used herein, the term “effective amount” means, in the context of the inventive immunogenic composition, an amount of an immunogenic composition capable of inducing an immune response that reduces the incidence of or lessens the severity of infection or incident of disease in an animal. In a preferred embodiment the quantity, delivered by the relevant route is one in which the amount is sufficient to induce a detectable specific antibody response (as determined by bacterial flow cytometry or ELISA) in serum or mucosal secretions. Alternatively, in the context of a therapy, the term “effective amount” refers to the amount of a therapy which is sufficient to reduce or ameliorate the severity or duration of a disease or disorder, or one or more symptoms thereof, prevent the advancement of a disease or disorder, cause the regression of a disease or disorder, prevent the recurrence, development, onset, or progression of one or more symptoms associated with a disease or disorder, or enhance or improve the prophylaxis or treatment of another therapy or therapeutic agent. 
     The volume of a single dose of the immunogenic compositions of this invention will vary by subject and administration route but will be generally within the ranges commonly employed in conventional vaccines and immunogenic compositions, respectively. For example in juvenile swine (4-10 kg) the volume of a single oral dose is preferably between about 0.1 ml and 3 ml, preferably between about 0.2 ml and about 1.5 ml, more preferably between about 0.2 ml and about 0.5 ml at the concentrations of conjugate and adjuvant. 
     The preparation of compositions for use as vaccines and immunogenic compositions, respectively, is known to those of skill in the art. Typically, such compositions are prepared either as liquid solutions or suspensions, however solid forms such as tablets, pills, powders and the like are also contemplated. Solid forms suitable for solution in, or suspension in, liquids prior to administration may also be prepared (e.g. lyophilized, freeze-dried forms, etc.). The preparation may also be emulsified. The active ingredients may be mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredients. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol and the like, or combinations thereof. In addition, the composition may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and the like. If it is desired to administer an oral form of the composition, various thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders and the like may be added. The composition of the present invention may contain any such additional ingredients so as to provide the composition in a form suitable for administration. 
     In addition, the composition may contain adjuvants, many of which are known in the art. For example, adjuvants suitable for use in the invention include but are not limited to: bacterial or microbial derivatives such as non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), Lipid A derivatives, Immunostimulatory oligonucleotides e.g. containing a CpG motif (a dinucleotide sequence containing an unmethylated cytosine linked by a phosphate bond to a guanosine). Double-stranded RNAs and oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory. 
     Recipients of the inventive immunogenic compositions may have never been exposed to the specific proteobacteria for example  Salmonella , or may have been exposed or suspected of having been exposed but be asymptomatic, or may have actual symptoms of disease, and still benefit from administration of the inventive immunogenic composition. Administration of the inventive immunogenic composition may prevent disease symptoms entirely, or may lessen or decrease disease symptoms, the latter outcome being less than ideal but still better than experiencing full-blown disease symptoms. 
     The invention provides methods of vaccinating, or, alternatively, of eliciting an immune response, in a subject in need thereof. The method generally involves identifying a suitable subject, and administering the immunogenic composition as described herein. The method may also encompass follow-up of administration, e.g. by assessing the production of protective antibodies by the subject, or the presence (or lack thereof) of disease symptoms, etc. The immune response that is elicited may be of any type, i.e. any type of antibody may be produced in response to administration, and cell-mediated immunity may also be elicited. 
     The terms “treatment”/“treating” as used herein include: (1) preventing or delaying the appearance of clinical symptoms of the state, disorder or condition developing in a subject that may be afflicted with or predisposed to the state, disorder or condition but does not yet experience or display clinical or subclinical symptoms of the state, disorder or condition; (2) inhibiting the state, disorder or condition (e.g. arresting, reducing or delaying the development of the disease, or a relapse thereof in case of maintenance treatment, of at least one clinical or subclinical symptom thereof); and/or (3) relieving the condition (i.e. causing regression of the state, disorder or condition or at least one of its clinical or subclinical symptoms). The benefit to a patient to be treated is either statistically significant or at least perceptible to the patient or to the physician. However, it will be appreciated that when a medicament is administered to a patient to treat a disease, the outcome may not always be effective treatment. In one embodiment, the terms “treatment”/“treating” as used herein, refer to a therapeutic treatment. In another embodiment, the terms “treatment”/“treating” as used herein, refer to a prophylactic treatment. 
     In addition, the invention provides methods of treating or preventing  Salmonella  infection by a non-typhoid  Salmonella  serovar in a subject, methods of lessening the severity of symptoms of  Salmonella  infection in a subject, and methods of decreasing fecal shedding of  Salmonella  from a subject who is or is likely to be infected with  Salmonella . Each of these methods involves administering to the subject an effective amount of a composition the immunogenic composition described herein and a physiologically acceptable carrier. The amount of the composition is administered is sufficient to elicit an immune response to the at least one  Salmonella  serovar in said subject, thereby of treating or preventing  Salmonella  infection, lessening the severity of symptoms of  Salmonella  infection, decreasing fecal shedding of  Salmonella  and/or decreasing or preventing the transmission of the  Salmonella.    
     Another aspect of the invention contemplates the inventive immunogenic composition for the protection of swine against  Salmonella  infection, wherein said immunogenic composition comprises at least two or more inactivated serovar of  Salmonella  and a pharmaceutically acceptable carrier. 
     Herein, suitable subjects and subjects in need to which compositions of the invention may be administered include animals in need of either prophylactic or treatment for an infection, disease, or condition. 
     The invention provides a method of reducing the incidence of or severity of one or more clinical signs associated with or caused by a  Salmonella  infection, comprising the step of administering an immunogenic composition of the invention as provided herewith, such that the incidence of or the severity of a clinical sign of the  Salmonella  infection is reduced by at least 10%, preferably at least 20%, even more preferred at least 30%, even more preferred at least 50%, even more preferred at least 70%, most preferred at least 100% relative to a subject that has not received the immunogenic composition as provided herein. Such clinical signs include diarrhea shedding and reduction in average daily weight gain. 
     As used herein, “preventative” refers to hindering or stopping a disease or condition before it occurs or while the disease or condition is still in the sub-clinical phase. 
     As used herein, “therapeutic” can refer to treating or curing a disease or condition. 
     According to another aspect of the present invention there is provided a method of generating an immunogenic composition as described herein, comprising the following steps:
         i. Administer an inactivated wild type proteobacterial strain to a subject,   ii. Challenge the subject with the wildtype proteobacterial strain,   iii. Isolate clones of said proteobacterial strain from the subject between 2 hours to 7 days post infection,   iv. Identify isolated clones with reduced binding affinity to the wild type proteobacterial strain anti-O-antigen antibody,   v. Generate recombinant clones identical to said isolated clones with reduced binding affinity,   vi. Inactivate and combine the recombinant clones with the inactivated wild type proteobacterial strain.   vii. Repeat steps i-viii, administering the inactivated combined recombinant clones with the inactivated wild-type proteobacterial strain,   viii. Combine all identified inactivated clones with the inactivated wild type proteobacteria to produce the immunogenic composition.       

     In one embodiment wherein step viii. combine all identified inactivated serovar variants with the inactivated wild type proteobacteria to produce the immunogenic composition capable of manipulating Proteobacterial evolution. 
     In a preferred embodiment, the method as described in the aforementioned aspect comprises the use of bacteriophage transduction or homologous recombination to generate the recombinant clones. 
     EXAMPLES 
     The present invention provides the following examples which are not limiting. 
     Example 1 
     Mice Vaccinated with Inactivated Wild Type  Salmonella enterica  Serovar  Typhimurium  ( S. typhimurium ) are Weakly Protected from Wild-Type  S. typhimurium  Challenge Due to the Emergence of Vaccine-Escape Variants 
     Generation of Inactivated Oral Vaccines. 
     Peracetic acid killed vaccines were produced as previously described in Moor et al. Frontiers in Immunology (2016) Vol 7, Article 34. Briefly, bacteria were grown overnight to late stationary phase, harvested by centrifugation and resuspended to a density of 10 9 -10 10  per ml in sterile PBS. Peracetic acid (Sigma-Aldrich) was added to a final concentration of 1%. The suspension was mixed thoroughly and incubated for 60 min at room temperature. Bacteria were washed once in 40 ml of sterile 10×PBS and subsequently three times in 50 ml sterile 1×PBS. The final pellet was resuspended to yield a density of 10 11  particles per ml in sterile PBS (determined by OD600) and stored at 4° C. for up to three weeks. As a quality control, each batch of vaccine was tested before use by inoculating 100 μl of the killed vaccine (one vaccine dose) into 300 ml LB and incubating over night at 37° C. with aeration. Vaccine lots were released for use only when a negative enrichment culture had been confirmed. 
     Vaccination and Challenge of Mice 
     All animal experiments were approved by the legal authorities (licenses 223/2010, 222/2013 and 193/2016; Kantonales Veterinäramt Zürich, Switzerland) and performed according to the legal and ethical requirements. Vaccinations were administered between 5 and 6 weeks of age, and males and females were randomized between groups to obtain identical ratios wherever possible. Mice received either 1e10 particles of peracetic acid inactivated wild-type  S. typhimurium  strain SL1344 (“WT vaccine”,  Salmonella enterica  serovar  Typhimurium  strain SL1344 is available from the American Type Culture Collection) or vehicle-only control once per week per os for 4 weeks. At 28 days after the first vaccination, infections were carried out as described in Barthel, M. et al Pretreatment of mice with streptomycin provides a  Salmonella enterica  serovar  Typhimurium  colitis model that allows analysis of both pathogen and host,  Infect. Immun.  71, 2839-58 (2003). In order to allow reproducible gut colonization, mice were orally pretreated 24 h before infection with 25 mg streptomycin. Strains were cultivated overnight separately in LB containing the 50 μg/ml streptomycin. Subcultures were prepared before infections by diluting overnight cultures 1:20 in fresh LB without antibiotic and incubation 4 h at 37° C. Mice were orally challenged with live wild-type  S. typhimurium  strain SL1344 with an inoculum size of 5*10 3 , 5*10 5 , and 5*10 7 . 
     Analysis of the  S. typhimurium  and the Antibody Produced in Mice Following Challenge with Wild-Type  S. typhimurium  Strain SL1344 
     Fecal, mesenteric ( FIG. 1A ) and lymph node ( FIG. 1B )  Salmonella  Colony Forming Units (CFU) were quantified over 2 days by plating on Mackonkey agar (Oxoid) containing relevant antibiotics. 
     Intestinal inflammation was quantified by measuring Lipocalin2 in feces by ELISA (R&amp;D) in accordance with the manufacturer&#39;s instructions ( FIG. 1C ). 
       S. typhimurium  clones were reisolated from the feces (by picking colonies from plates) of vaccinated protected and unprotected mice. These were cultivated and used as targets to titre intestinal IgA from intestinal lavages of vaccinated and unvaccinated mice by bacterial flow cytometry. 
     Specific antibody titers in mouse intestinal washes were measured by flow cytometry as described previously in Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria.  Nature  544, 498-502 (2017) and Moor, K. et al. Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry as described in  Nat. Protoc.  11, 1531-1553 (2016). 
     Determining Antibody Titres by Bacterial Flow Cytometry 
     Bacterial targets (the antigens against which antibodies are to be titered) were grown to late stationary phase or the required OD, and then gently pelleted for 2 min at 3000 g. The pellet was washed with sterile-filtered 1% BSA/PBS before resuspending at a density of approximately 10 7  bacteria per ml. 
     To prepare mouse IgA for analysis, intestinal washes were collected by flushing the small intestine with 5 ml PBS and centrifugation at 16000 g for 30 min. aliquots of the supernatants were stored at −20° C. until analysis. For analysis, aliquots of intestinal washes were thawed, and centrifuged at 16000 g for 10 min. Supernatants were used to perform serial dilutions. 25 μl of the dilutions were incubated with 25 μl bacterial suspension at 4° C. for 1 h. Bacteria were washed twice with 200 μl FACS buffer before resuspending in 25 μl FACS buffer containing monoclonal FITC-anti-mouse IgA (BD Pharmingen, 10 μg/ml) or Brilliant violet 421-anti-IgA (BD Pharmingen). After 1 h of incubation, bacteria were washed once with FACS buffer and resuspended in 300 μl FACS buffer for acquisition on FACS LSRII of Beckman Coulter Cytoflex S using FSC and SSC parameters in logarithmic mode. Data were analysed using FloJo (Treestar). After gating on bacterial particles, log-median fluorescence intensities (MFI) were plotted against antibody concentrations for each sample and 4-parameter logistic curves were fitted using Prism (Graphpad, USA). Titers were calculated from these curves as the inverse of the antibody concentration giving an above-background signal. 
     Results 
     This experiment revealed that all mice had robust IgA responses against the wild-type  S. typhimurium  ( FIG. 1D ). However, some mice developed intestinal inflammation and invasive disease despite a robust vaccination response, in  FIG. 1E  it was shown that the unprotected vaccinated mice had similar antibody production to vaccinated protected mice. When  S. typhimurium  clones from vaccinated but unprotected mice were used to detect specific IgA in intestinal lavages, this revealed that  S. typhimurium  in the intestines of these mice no longer bound vaccine-induced IgA—i.e.  S. typhimurium  can escape the IgA response induced by a standard oral vaccine ( FIG. 1F ). 
     Example 2 
     Characterization of  Salmonella  Variants with Weak Binding to Standard Vaccine-Induced sIgA 
     To establish the nature of IgA escape, we first carried out Genome resequencing of  S. typhimurium  clones from vaccinated but unprotected mice. 
     Genome Resequencing 
     The genomes of S.Tm wt  and evolved derivatives ( Salmonella  variants/clones) were fully sequenced by the Miseq system (2×300 bp reads, Illumina, San Diego, Calif.) operated at the Functional Genomic Center in Zurich. The sequence of S.Tm SL1344 (NC_016810.1) was used as reference. Quality check, reads trimming, alignments, SNPs and indels calling were performed using the bioinformatics software CLC Workbench (Qiagen). 
     Results 
     Genome sequencing revealed a common 7 base-pair contraction in the coding region of the OafA gene, known to encode an Abequose O-acetyl transferase which modifies the  S. typhimurium  O-antigen glycan repeat ( FIG. 2A ). Acetylation of the O-antigen Abequose converts a serovar O4 strain into a serovar O5 strain. We therefore serotyped the reisolated clones by bacterial flow cytometry ( FIG. 2B ). 
     Serotyping by Bacterial Flow Cytometry 
     1 μl of these enrichments or of primary cultures, or 1 μl of fresh feces or cecal content suspension (as above) was stained with STA5 (human recombinant monoclonal IgG2 anti-O12, Moor et al. Nature 2017) and Rabbit anti- Salmonella  O5 (Difco). After incubation at 4° C. for 30 min, bacteria were washed once with PBS/1% BSA and resuspended in appropriate secondary reagents (Alexa 647-anti-human IgG, Jackson Immunoresearch, Brilliant Violet 421-anti-Rabbit IgG, Biolegend). This was incubated for 10-60 min before cells were washed and resuspended for acquisition on a BD LSRII or Beckman Coulter Cytoflex S. 
     Results 
     This confirmed loss of O5 on some clones ( FIG. 2B ). 
     During this flow cytometry based serotyping, a second class of clones were also identified with apparently bi-stable loss of binding to an anti-O12 typing antibody ( FIG. 2C ). Genome sequencing of these clones revealed no consistent mutational pattern (data not shown). We therefore carried out methylation analysis of the genome of these strains ( FIG. 2D —heatmap of methylation of the promoter of the GtrABC operon). 
     DNA Methylation Analysis 
     For REC-Seq (restriction enzyme cleavage-sequencing) we followed the same procedure described by Ardissone, S. et al. Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria.  PLoS Genet.  12, e1006499 (2016). In brief, 1 μg of genomic DNA from each S.Tm was cleaved with MboI, a blocked (5′biotinylated) specific adaptor was ligated to the ends and the ligated fragments were then sheared to an average size of 150-400 bp (Fasteris SA, Geneva, CH). Illumina adaptors were then ligated to the sheared ends followed by deep-sequencing using a HiSeq Illumina sequencer, the 50 bp single end reads were quality controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). To remove contaminating sequences, the reads were split according to the MboI consensus motif (5′-{circumflex over ( )}GATC-3′) considered as a barcode sequence using fastx_toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --exact). A large part of the reads (60%) were rejected and 40% kept for remapping to the reference genomes with bwa mem (Li, H. &amp; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform.  Bioinformatics  25, 1754-1760 (2009)) and samtools (Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.  Bioinformatics  27, 2987-93 (2011)) to generate a sorted bam file. The bam file was further filtered to remove low mapping quality reads (keeping AS&gt;=45) and split by orientation (alignmentFlag 0 or 16) with bamtools (Barnett, D. W., Garrison, E. K., Quinlan, A. R., Stromberg, M. P. &amp; Marth, G. T. BamTools: a C++ API and toolkit for analyzing and managing BAM files.  Bioinformatics  27, 1691-2 (2011)). The reads were counted at 5′ positions using Bedtools (Quinlan, A. R. &amp; Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features.  Bioinformatics  26, 841-2 (2010)) (bedtools genomecov -d -5). Both orientation count files were combined into a bed file at each identified 5′-GATC-3′ motif using a homemade PERL script. The MboI positions in the bed file were associated with the closest gene using Bedtools closest (Quinlan, A. R. &amp; Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features.  Bioinformatics  26, 841-2 (2010)) and the gff3 file of the reference genomes (Kersey, P. J. et al. Ensembl Genomes 2016: more genomes, more complexity.  Nucleic Acids Res.  44, D574-D580 (2016)). The final bed file was converted to an MS Excel sheet with a homemade script. The counts were loaded in RStudio 1.1.442 (RStudio, Inc., Boston, M. RStudio: Integrated Development for R. Available at: https://www.rstudio.com/) with R version 3.4.4 (R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Available at: https://www.r-project.org/about.html) and analysed with the DESeq2 1.18.1 package (Love, M. I., Huber, W. &amp; Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 . Genome Biol.  15, 550 (2014)) comparing the reference strain with the 3 evolved strains considered as replicates. The counts are analysed by genome position rather than by gene. The positions are considered significantly differentially methylated upon an adjusted p-value &lt;0.05. 
     Results 
     Of the 2607 GATC positions, only 4 were found significantly differentially methylated, and they are all located in the promoter of the gtrABC operon, which encodes a glucosyl transferase system known to add glucose to the galactose of the  S. typhimurium  O-antigen repeat. H1 NMR analysis of purified O-antigen from the reisolated clones confirmed the presence of this glucose in their O-antigen. 
     Therefore the  S. typhimurium  strain we were using has two methods to escape standard vaccine-induced IgA: by mutation of a hypervariable tandem repeat it can inactivate the gene for an O-acetyl transferase, removing an acetyl group from the O-antigen repeats, and by epigenetic modification it can turn on expression of a glucosyl transferase adding a glucose to the O-antigen repeats (Broadbent, S. E., Davies, M. R. &amp; van der Woude, M. W. Phase variation controls expression of  Salmonella  lipopolysaccharide modification genes by a DNA methylation-dependent mechanism.  Mol. Microbiol.  77, 337-53 (2010)). Combining these two mechanisms generates four chemically different O-antigens with the serovar variant notations O:4[5], 12-0, O: 4, O12-0, O:4[5], 12-2 and O:4, 12-2. Here we discovered the four bacterial escape variants that lead to loss of binding to antibodies induced by a wild type  Salmonella  vaccine. 
     Example 3 
     Strength of Vaccine-Mediated Selective Pressure on O-Antigen Structure. 
     In order to confirm that the intestinal antibodies of  Salmonella  infected mice, confer a major selective pressure for the emergence of these modifications, we carried out competitive infections. 
     To quantify the selective advantage of gain or loss of an acetyl group, we vaccinated mice, as described in Example 1, with vaccines constructed from O:4[5] serovar (acetylated O-antigen)  S. typhimurium  or from  S. typhimurium  carrying an in-frame deletion of OafA (non-acetylated O-antigen, O:4 serovar variant). On day 28, we carried out infectious challenges as described in Experiment 1, with the following modifications: 
     In order to specifically assay the effect of acetylation in the absence of glucosylation, we competed  S. typhimurium  carrying an in-frame deletion in GtrC (acetylated O-antigen, cannot glucosylate) (O:4[5], 12-0 serovar) with  S. typhimurium  carrying in frame deletions of GtrC and OafA (non-acetylated O-antigen, cannot glucosylate) (O:4,12-0 serovar). The strains were mixed 1:1 prior to oral infection and carried different antibiotic resistances to all identification by differential plating. In naive or mock-vaccinated mice, the strains remain at a ratio of 1:1 in the intestinal content over 4 days of infection. 
     Results 
     In naive mice, both serovars remained at a 1:1 ratio in intestinal content ( FIG. 3A ). However, mice vaccinated with the inactivated O:4 serovar had an up to 10 8 -fold over-abundance of the O:4[5] serovar over the O:4 serovar ( FIG. 3A ). Conversely, Mice vaccinated with the inactivated O:4[5] serovar had an up to 10 8 -fold overabundance of the O:4 serovar over the O:4[5] serovar ( FIG. 3A ). This selective pressure correlated strongly with the magnitude of the specific antibody response, determined by bacterial flow cytometry as in Example 1 ( FIG. 3B ). The assay demonstrated the key role the O-antigen-targeting IgA plays in negatively selecting  S. typhimurium  in the gut lumen. In vaccinated mice, the presence of specific antibodies against either the acetylated O-antigen or the non-acetylated O-antigen, results in up to 1e8-fold out-competition by the non-recognised strain, indicating a very strong negative selection of the antibody-targeted strain and a huge benefit of mutation and vaccine escape. 
     Testing the Selective Advantage of O12/O12-2 Epigenetic Switching 
     An identical experiment was carried out to assess the role of glucosylation. Mice were vaccinated with  S. typhimurium  carrying in frame deletions of gtrC and oafA (non-acetylated O-antigen, cannot glucosylate, O:4, 12-0 serovar) or with vehicle alone. Mice were challenged with a 1:1 mixture of  S. typhimurium  locked into the O:12-0 serovar by genetic deletion of gtrC and  S. typhimurium  that could switch to the O:12-2 serovar (O12 locked O4) on an O:4 background as was done in Example 1. 
     Results 
     Mice in which the vaccine-induced IgA bound poorly to the O:4,12-2 serovar demonstrated an up to 10 6 -fold over-representation of  S. typhimurium  able to turn on their glucosylation system, over  S. typhimurium  genetically incapable of doing this ( FIG. 3C ). The assay demonstrated the key role of glucosylation of the O-antigen in IgA-mediated recognition of these bacteria. In vaccinated mice, the presence of specific antibodies against either the glucosylated O-antigen or the non-glucosylated O-antigen, results in up to 1e6-fold out-competition by the non-recognised strain ( FIG. 3C ), indicating a very strong negative selection of the antibody-targeted strain and a huge benefit of mutation and vaccine escape. Out competition of O:12-0-locked strains was only observed in mice with weak O:12-2-binding antibody response as shown in  FIG. 3D . 
     Together these experiments demonstrate the very strong selection of  S. typhimurium  surface carbohydrates by vaccine-induced IgA. 
     Example 4 
     Generation of an Evolutionary Trap Vaccine 
     By inducing IgA responses capable of recognising all of the O-antigen escape variants, we discovered that it would be possible to generate improved vaccine-mediated protection. To do this, four new strains of  S. typhimurium  were constructed: 
     1)  S. typhimurium  carrying an in frame deletion of gtrC (acetylated O-antigen, cannot glucosylate) (Serovar O:4[5], 12-0) 
     2)  S. typhimurium  carrying in frame deletions of gtrC and oafA (non-acetylated O-antigen, cannot glucosylate) (Serovar O:4, 12-0) 
     3)  S. typhimurium  carrying an in frame deletion of gtrC and a plasmid expressing the gtrABC operon under the control of a constitutive promoter (acetylated, glucosylated O-antigen) (Serovar O:4[5], 12-2) 
     4)  S. typhimurium  carrying in frame deletions of gtrC and oafA, and a plasmid carrying the gtrABC operon under the control of a constitutive promoter (non-acetylated, glucosylated O-antigen) (Serovar O:4, 12-2) 
     Peracetic acid-inactivated vaccines were constructed from these strains and were combined at a 1:1:1:1 ratio for oral delivery, as with our standard vaccine. 
     At 28 days after the first vaccination, mice receiving the combined vaccine had significantly higher intestinal IgA antibody titres with specificities towards all four serovar variants O:4,12-0, O:4[5],12-0, O:4,12-2 and O:4[5], 12-2, as determined by bacterial flow cytometry compared to unvaccinated mice ( FIG. 4C ). 
     The mice were then orally challenged as described in example 1 with wild-type  S. typhimurium . This generated robust vaccine-mediated protection, as determined by lymph node invasion of  S. typhimurium  in naive mice versus mice that were vaccinated ( FIG. 4A ) and intestinal inflammation in naive mice versus mice that were vaccinated ( FIG. 4B ). However, closer examination of the mice revealed a third evolutionary event along with acetylation and glucosylation modifications of the O-antigen; in mice receiving the combined vaccine:  S. typhimurium  clones reisolated from the intestinal content of these mice produced only a very short variant of the O-antigen, demonstrated using bacterial flow cytometry in  FIG. 4D , and using polyacrylamide gel electrophoresis (using standard techniques) of purified lipopolysaccharide ( FIG. 4E ). Resequencing of these clones (as performed in example 2) revealed a large deletion between inverted repeats in the genome that removes the O-antigen polymerase wzyB. Thus these clones produce only a single repeat of the O-antigen. This loss of O-antigen resulted in lower binding to vaccine-induced IgA, explaining the emergence of these clones in vaccinated mice ( FIG. 4F ). 
     The Significance of Selection of wzyB Mutant Clones 
     The O-antigen is normally hundreds of repeats long (i.e. contains around 400 sugar residues polymerized into a chain). This forms a thick dense hydrophilic layer around the outside of a gram negative bacterium Mostowy, R. J. &amp; Holt, K. E. Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating.  Trends Microbiol.  26, 1008-1021 (2018). Chlebicz, A. &amp; Śliżewska, K. Campylobacteriosis, Salmonellosis, Yersiniosis, and Listeriosis as Zoonotic Foodborne Diseases: A Review.  Int. J. Environ. Res. Public Health  15, 863 (2018). Liu, B. et al. Structural diversity in  Salmonella  O antigens and its genetic basis.  FEMS Microbiol. Rev.  38, 56-89 (2014). When wzyB is missing, only 4 sugar residues are present in each chain making a very weak hydrophilic barrier and increasing susceptibility to complement- and pore-forming antimicrobial-mediated lysis as well as poor resistance to outer membrane stressors such as altered salt concentrations of bile acids (Murray, G. L., Attridge, S. R. &amp; Morona, R. Altering the length of the lipopolysaccharide O antigen has an impact on the interaction of  Salmonella enterica  serovar  Typhimurium  with macrophages and complement.  J. Bacteriol.  188, 2735-9 (2006). Rojas, E. R. et al. The outer membrane is an essential load-bearing element in Gram-negative bacteria.  Nature  559, 617-621 (2018)). 
     This was demonstrated in vitro: 
     Test 1 
     Stress Testing 
     Single or 1:1 mixture of wzyB mutant serovar with wild type S.Tm LB subcultures were diluted 1000 times in 200 μl of media distributed in 96 well Black side microplates (Costar). To measure growth and competitions in stressful conditions that specifically destabilize the outer membrane of S.Tm, a mixture of Tris and EDTA (Sigma) was diluted to final concentration (4 mM Tris, 0.4 mM EDTA) in LB. The lid-closed microplates were incubated at 37° C. with fast and continuous shaking in a microplate reader (Synergy H4, BioTek Instruments). The optical density was measured at 600 nm and the green fluorescence using 491 nm excitation and 512 nm emission filter wavelengths every 10 minutes for 18 hours. The outcome of competitions was determined by calculating mean OD and fluorescence intensity measured during the last 100 minutes of incubation, this measured the survival of the bacteria following stress testing. OD and fluorescence values were corrected for the baseline value measured at time 0. 
     Test 2 
     Test Complement Resistant. 
     Serovar WT and Wzyb mutants were added to human serum. If the bacteria are susceptible to complement proteins of the immune system the bacteria would be lysed. Complement proteins are destroyed with heat inactivation of the human serum and this was used as a control. 
     Overnight LB cultures were washed three times in PBS, OD adjusted to 0.5 and incubated with human serum obtained from Unispital Basel (3 volumes of culture for 1 volume of serum) at 37° C. for 1 hour. Heat inactivated (56° C., 30 min) serum was used as control treatment. Surviving bacteria were enumerated by plating on non-selective LB agar plates. For this, dilutions were prepared in PBS immediately after incubation. 
     Results 
     WzyB-mutant clones were much more sensitive to membrane-stress-induced cell death (FIG.  5 A). Additionally, Complement proteins in the serum were much more effective at killing wzyB “single repeat O-antigen” mutant S.tm than wild type S.Tm ( FIG. 5B ). 
     We also carried out in vivo competition assays with an in-frame deletion mutant for wzyB versus on a background of oafA and gtrC deletion (short O antigen) versus a oafA and gtrC mutant producing full length antigen (long O antigen), in wild-type  S. typhimurium  in vaccinated and naive mice, as in Example 1. We discovered that loss of full-length O-antigen is a major fitness disadvantage for  S. typhimurium  in naive animals, but is strongly selected for in vaccinated mice ( FIG. 5C ). JH−/− is a mouse model that does not produce antibodies and JH+/− is the negative control mouse which can produce antibodies. The WzyB-deletion mutants are more weakly recognized by vaccine-induced antibodies due to a decrease in O-antigen present per cell ( FIG. 4F ), which in turn promotes propagation. Therefore our evolutionary trap vaccine forces the emergence of  S. typhimurium  genotypes that are detrimental for transmission and for infection of unvaccinated animals. 
     This will be a huge benefit for disease control in high-transmission settings such as farm animal rearing, as this is the only type of vaccination against Enterobacterial pathogens that is capable of decreasing transmission efficiency. 
     Test 3 
     This was also tested for transmission into a realistic non-Typhoidal  Salmonellosis  model based on infecting high-fat diet fed mice. 
     Streptomycin-treated mice were infected with either oafA, gtrC-double mutant  S. typhimurium  (long O-antigen) or the oafA, gtrC, wzyB-triple mutant strain (short O-antigen). At 24 h post-infection, feces were collected and used to infect a cohort of high-fat diet-treated mice (one fecal pellet transferred per mouse, equivalent to an oral dose of 1e7-1e8 S.Tm). The fecal load of S. Tm in recipient mice was determined by selective plating for 4 days after infection. 
     Results 
     Fecal-oral transmission from mice carrying the short O-antigen mutant of S.Tm resulted in significantly lower colonization of recipient animals than transmission of the long O-antigen S.Tm strain as shown in  FIG. 6 . This indicates that emergence of wzyB-mutant strains in animals vaccinated with the combined immunogenic oral vaccine will decrease S.Tm transmission in realistic settings. 
     Example 4 
     Toxicity and Proof-of-Principle Trial 
     French Landrace pigs (n=6) received the peracetic acid-inactivated wild type  Salmonella typhimurium . The vaccine was prepared as explained in Example 1 above and either packed into enteric capsules, or fed as a paste mixed with palatable foodstuff (tinned sardine). The pigs received the vaccine by voluntary oral delivery once per week from the age of 4 weeks to 10 weeks. Pigs received orally 1e13 particles of peracetic acid inactivated wild-type  S. typhimurium  strain SL1344 in each vaccine dose (i.e. maximum proposed dosing). 
     A blood sample was taken before the vaccination at 4 weeks of age and after vaccination at 10 weeks of age. The blood sample was analysed for  S. typhimurium -specific IgG by flow cytometry. The secondary antibodies used in detection for flow cytometry were goat-anti pig IgG Fc antisera (biotin conjugate, 1:200, Serotec) followed by a Streptavidin-Allophycocyanin conjugate at 1 μg/ml (Biolegend). 
     Results 
       FIG. 7  provides the results and demonstrates that Peracetic acid-inactivated oral vaccines safely induce antibody responses in domestic pigs. No adverse effects were recorded, and all animals gained weight as expected and all internal organs were macroscopically and histologically confirmed healthy at euthanasia (10 weeks of age), indicating that the vaccine is well-tolerated. 
     All strains and plasmids are listed below in table 1. All primers used in the examples are listed in table 2. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
             
            
               
                   
                   
                 Relevant 
                   
               
               
                 Strains 
                 Background 
                 genotype 
                 Source 
               
               
                   
               
               
                 
                   S. Tm 
                 
                 SL1344 
                 Wild-Type 
                 American 
               
               
                   
                 14028 
                 (ATCC) 
                 Type Culture 
               
               
                   
                   
                 Wild-Type 
                 Collection 
               
               
                   
                   
                 (ATCC) 
                 Hoiseth, 
               
               
                   
                   
                   
                 
                   Nature 1981 
                 
               
               
                 
                   S. Tm 
                   oafA 
                 
                 SL1344 
                 ΔoafA 
                 Constructed 
               
               
                   
                   
                 Tag1::aphT 
                 from SL1344 
               
               
                   
                   
                   
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   gtrC 
                 
                 SL1344 
                 gtrC(a)::cat 
                 Constructed 
               
               
                   
                   
                   
                 from SL1344 
               
               
                   
                   
                   
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   gtrA 
                 
                 SL1344 
                 gtrA(a)::cat 
                 Constructed 
               
               
                   
                   
                   
                 from SL1344 
               
               
                   
                   
                   
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   oafA gtrC 
                 
                 SL1344 
                 ΔoafA 
                 Constructed 
               
               
                   
                   
                 gtrC(a)::cat 
                 from SL1344 
               
               
                   
                   
                   
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   oafA gtrC kan 
                 
                 SL1344 
                 ΔoafA 
                 Constructed 
               
               
                   
                   
                 gtrC(a)Tag1::aphT 
                 from SL1344 
               
               
                   
                   
                   
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   oafA gtrC wzyB 
                 
                 SB300 
                 ΔoafA 
                 Constructed 
               
               
                   
                   
                 gtrC(a) 
                 from SL1344 
               
               
                   
                   
                 wzyB::cat 
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   oafA ΔGT 
                 
                 SB300 
                 ΔoafA ΔgtrB(a) 
                 Constructed 
               
               
                   
                   
                 ΔgtrB(b) 
                 from SL1344 
               
               
                   
                   
                 ΔSTM0712-0723 
                 using 
               
               
                   
                   
                 Δwca-wza 
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                 
                   S. Tm 
                   oafA gtrC pGtrABC 
                 
                 SL1344 
                 ΔoafA 
                 Constructed 
               
               
                   
                   
                 gtrC(a)::cat 
                 from SL1344 
               
               
                   
                   
                 pGtrABC 
                 using 
               
               
                   
                   
                   
                 primers in 
               
               
                   
                   
                   
                 table 2 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                   
                   
                 Relevant 
                   
               
               
                 Plasmids 
                 Backbone 
                 genotype 
                 Reference 
               
               
                   
               
               
                 pM965 
                 pSC101 
                 P rpsM -gfp 
                 Addgene Stecher, 
               
               
                   
                   
                   
                 
                   Infection and 
                 
               
               
                   
                   
                   
                 
                   Immunity 2004 
                 
               
               
                 pGtrABC 
                 pM965 
                 P rpsM -gtrABC(a) 
                 Constructed 
               
               
                   
                   
                   
                 from pM965 
               
               
                   
                   
                   
                 using primers 
               
               
                   
                   
                   
                 in table 2 
               
               
                 pKD46 
                 Used for 
                   
                 Addgene 
               
               
                   
                 strain 
                   
                 
                   Datsenko 
                 
               
               
                   
                 construction 
                   
                 
                   PNAS 2000 
                 
               
               
                 pCP20 
                 Used for 
                   
                 Addgene 
               
               
                   
                 strain 
                   
                 
                   Datsenko 
                 
               
               
                   
                 construction 
                   
                 
                   PNAS 2000 
                 
               
               
                 pKD3 
                 Used for 
                   
                 Addgene 
               
               
                   
                 strain 
                   
                 
                   Datsenko 
                 
               
               
                   
                 construction 
                   
                 
                   PNAS 2000 
                 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
             
               
                 TABLE 2  
               
             
            
               
                   
               
               
                 Primer_ 
                   
               
            
           
           
               
               
               
            
               
                 name 
                 Sequence 
                 Purpose 
               
               
                   
               
               
                 oafA_Seq_ 
                 CCGCCATAGTTACGTTTTG (SEQ ID NO: 3) 
                 Sequencing of oafA 
               
               
                 up 
                   
                   
               
               
                 oafA_Seq_ 
                 AAGCTATACACATAAAATAATTTGC (SEQ ID NO: 4) 
                   
               
               
                 dw 
                   
                   
               
               
                 oafA_IntSeq1_ 
                 AGTACTTGATTTTTATATTGCAAG (SEQ ID NO: 5) 
                   
               
               
                 up 
                   
                   
               
               
                 oafA_IntSeq2_ 
                 GAGGTTTATGGGATAGTCC (SEQ ID NO: 6) 
                   
               
               
                 up 
                   
                   
               
               
                 oafA_IntSeq3_ 
                 GCCTGATATTTGCTTCCTC (SEQ ID NO: 7) 
                   
               
               
                 up 
                   
                   
               
               
                 oafA_IntSeq4_ 
                 CCGTAATCTGAGAGATAATGA (SEQ ID NO: 8) 
                   
               
               
                 up 
                   
                   
               
               
                   
               
               
                 Del_oafA_ 
                 AATTATAGGTAAAAAATGATCTACAAGAAATTCAGACTCGTG 
                 In frame deletion oafA 
               
               
                 up 
                 TGTAGGCTGGAGCTGCTTC (SEQ ID NO: 9) 
                   
               
               
                 Del_oafA_ 
                 GGCAAGCCCCTCTGTTTATTTTGAAATCTGCTTTTTCACTCA 
                   
               
               
                 dw 
                 TATGAATATCCTCCTTAG (SEQ ID NO: 10) 
                   
               
               
                   
               
               
                 Ver_oafA_ 
                 ATGTAGTTGATGTAACAGGTC (SEQ ID NO: 11) 
                 Deletion verification oafA 
               
               
                 up 
                   
                   
               
               
                 Ver_oafA_ 
                 ATGCCCCATCAGAAAAGCT (SEQ ID NO: 12) 
                   
               
               
                 dw 
                   
                   
               
               
                   
               
               
                 Ver_  
                 ATTGGTGTGATAAATCCTATTG (SEQ ID NO: 13) 
                 Deletion verification gtrC(a) 
               
               
                 STM0558_up 
                   
                   
               
               
                 Ver_ 
                 GCTATCAGCCTGATATGCG (SEQ ID NO: 14) 
                   
               
               
                 STM0558_dw 
                   
                   
               
               
                   
               
               
                 Ver_ 
                 GTAATCATCAGAGTGAATAGG (SEQ ID NO: 15) 
                 Deletion verification gtrC(b) 
               
               
                 TM4205_up 
                   
                   
               
               
                 Ver_ 
                 CGCAATTAGCCTTATTTGCG (SEQ ID NO: 16 
                   
               
               
                 STM4205_dw 
                   
                   
               
               
                   
               
               
                 Del_wca_ 
                 TAAAAATAGCGGTACTTACCCTCCCCGCTTCGGCAGCGAAT 
                 Deletion cluster wca-wza 
               
               
                 wza_up 
                 GTGTAGGCTGGAGCTGCTTC (SEQ ID NO: 17) 
                   
               
               
                 Dewca_ 
                 AGTGATAAATAATCAATGATGAAATCCAAAATGAAATTGACA 
                   
               
               
                 wza_71w 
                 TATGAATATCCTCCTTAG (SEQ ID NO: 18) 
                   
               
               
                   
               
               
                 Ver_wca_ 
                 CCATAACATTAAGTATGAACAACT (SEQ ID NO: 19) 
                 Verification deletion cluster  
               
               
                 wza_up 
                   
                 wca-wza 
               
               
                 Ver_wca_ 
                 AAGCCGCTATTTAAATTGCACA (SEQ ID NO: 20) 
                   
               
               
                 wza_dw 
                   
                   
               
               
                   
               
               
                 Del_0712- 
                 TGATGGATTTGTTTTGTGAAAAGAAAATATCTTACGCAAGTG 
                 Deletion cluster SaltsV1_0712 
               
               
                 23_up 
                 TGTAGGCTGGAGCTGCTTC (SEQ ID NO: 21) 
                 to SaltsV1_0723 
               
               
                 Del_0712- 
                 GGAATTAAATGACGCTTAGTTATATTTTGCCCAAAATTTTCA 
                   
               
               
                 23_dw 
                 TATGAATATCCTCCTTAG (SEQ ID NO: 22) 
                   
               
               
                   
               
               
                 Ver_0712- 
                 ATTAAACTCATCTGATCAGTGAT (SEQ ID NO: 23) 
                 Verification deletion cluster  
               
               
                 23_up 
                   
                 SaltsV1_0712 to SaltsV1_0723 
               
               
                 Ver_0712- 
                 GGCGAGCGCCCAATAAT (SEQ ID NO: 24) 
                   
               
               
                 23_dw 
                   
                   
               
               
                   
               
               
                 Del_0559_ 
                 CGACTAACGAGATTTTCATTTCGCATCCCTAAAGACAATGT 
                 In frame deletion gtrA(a) 
               
               
                 up 
                 GTGTAGGCTGGAGCTGCTTC (SEQ ID NO: 25) 
                   
               
               
                 Del_0559_ 
                 CCGCTGATTTTCATAATGTTGAAGTTATTCGCTAAGTACACA 
                   
               
               
                 dw 
                 TATGAATATCCTCCTTAG (SEQ ID NO: 26) 
                   
               
               
                   
               
               
                 Ver_0559_ 
                 TAGAAAATAGGTATCGTGGCT (SEQ ID NO: 27) 
                 Verification deletion gtrA(a) 
               
               
                 up 
                   
                   
               
               
                 Ver_0559_ 
                 GTAGTGCTACACTCCAGAC (SEQ ID NO: 28) 
                   
               
               
                 dw 
                   
                   
               
               
                   
               
               
                 Del_gtrC_ 
                 ATAATTAAGAATGAGAAGAAAAATGGTTAACAATAGATTATG 
                 In frame deletion gtrC(a) 
               
               
                 up 
                 TGTAGGCTGGAGCTGCTTC (SEQ ID NO: 29) 
                   
               
               
                 Del_gtrC_ 
                 TACATGAATGTTATTTAATTATTTCCGTAATATTCTCATTCAT 
                   
               
               
                 dw 
                 ATGAATATCCTCCTTAG (SEQ ID NO: 30) 
                   
               
               
                   
               
               
                 Ver_gtrC_ 
                 CGCCCGTTACCCATTGG (SEQ ID NO: 31) 
                 Verification deletion gtrC(a) 
               
               
                 up 
                   
                   
               
               
                 Ver_gtrC_ 
                 TTGATAGGAATAGGTATTCTTGG (SEQ ID NO: 32) 
                   
               
               
                 dw 
                   
                   
               
               
                   
               
               
                 Del_wzyB_ 
                 TTCTAAAGGCTCTATATGCTTATAATTTCATACATTGCATTAT 
                 In frame deletion wzyB 
               
               
                 up 
                 GC T GTGCAGGCTGGAGCTGCTTC (SEQ ID NO: 33) 
                   
               
               
                 Del_wzyB_ 
                 TTGCCGCCGTATAACTTATTTATTGTTTCTTAGTAAAACGAA 
                   
               
               
                 dw 
                 TCTCATATGAATATCCTCCTTAG (SEQ ID NO: 34) 
                   
               
               
                   
               
               
                 Ver_wzyB_ 
                 CCAACAAGCTTTACAGGAAC (SEQ ID NO: 35) 
                 Verification deletion wzyB 
               
               
                 up 
                   
                   
               
               
                 Ver_wzyB_ 
                 GATTCAGAATATCTTGCCAGA (SEQ ID NO: 36) 
                   
               
               
                 dw 
                   
                   
               
               
                   
               
               
                 Pstl_  
                 ATCGTACTGCAGATGTTGAAGTTATTCGCTAAGTA (SEQ ID 
                 Cloning gtrABC(a) 
               
               
                 Gtr57.59_up 
                 NO: 37) 
                   
               
               
                 EcoRV_ 
                 GTAATCGATATCGGCGGGGAACATTAATTATAC (SEQ ID 
                   
               
               
                 Gtr57.59_dw 
                 NO: 38) 
                   
               
               
                   
               
               
                 SeqInt1_ 
                 CATACATCCTCTATTACTCATC (SEQ ID NO: 39) 
                 Sequencing PrpsM-gtrABC(a) 
               
               
                 gtrABC 
                   
                   
               
               
                 SeqInt2_ 
                 ATCTCTTGTAGTTGTATTAATTTCT (SEQ ID NO: 40) 
                   
               
               
                 gtrABC 
                   
                   
               
               
                 SeqInt3_ 
                 TAATTAAGAATGAGAAGAAAAATGGT (SEQ ID NO: 41) 
                   
               
               
                 gtrABC 
                   
                   
               
               
                 SeqInt4_ 
                 GGTGCTGGCTAAGCGC (SEQ ID NO: 42) 
                   
               
               
                 gtrABC 
                   
                   
               
               
                 SeqInt5_ 
                 CAGCTGTCTTACGCTTCAT (SEQ ID NO: 43) 
                   
               
               
                 gtrABC 
                   
                   
               
               
                 SeqInt6_ 
                 ATCAGCCTGATATGCGGATT (SEQ ID NO: 44) 
                   
               
               
                 gtrABC