Live attenuated bacterial strain and its use as a vaccine

Abstract

Embodiments of the present disclosure relate to a vaccine composition comprising a bacterial strain with a deleted or inactive ntrX gene.

Claims

1. A vaccine composition comprising a bacterial strain selected from the group consisting of an Ehrlichia strain, an Anaplasma strain, a Rickettsia strain, an Orientia strain, a Bartonella strain, and a Brucella strain, with a deleted or inactive ntrX gene.

2. The vaccine composition according to claim 1, wherein said ntrX gene: encodes a NtrX protein having the amino acid sequence of SEQ ID NO: 1 or is an active homologue thereof encoding a NtrX protein having an amino acid sequence with at least 50% of identity with SEQ ID NO: 1.

3. The vaccine composition according to claim 1 wherein: the inactive ntrX gene is an inactive mutant: of a ntrX gene encoding a NtrX protein having the amino acid sequence of SEQ ID NO: 1 or of an active homologue thereof encoding a NtrX protein having an amino acid sequence with at least 50% of identity with SEQ ID NO: 1; or the ntrX gene which is: a ntrX gene encoding a NtrX protein having the amino acid sequence of SEQ ID NO: 1 or an active homologue thereof encoding a NtrX protein having an amino acid sequence with at least 50% of identity with SEQ ID NO: 1 is deleted.

4. The vaccine composition according to claim 1 wherein: the inactive ntrX gene is an inactive mutant of a ntrX gene encoding a NtrX protein having the amino acid sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, and SEQ ID NO: 10 or the ntrX gene encoding a NtrX protein having the amino acid sequence selected from the group consisting of SEQ ID NOT, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, and SEQ ID NO: 10 is deleted.

5. The vaccine composition according to claim 1, wherein said vaccine composition further comprises a pharmaceutically acceptable excipient.

6. The vaccine composition according to claim 1, wherein the bacterial strain is an Alphaproteobacteria strain.

7. The vaccine composition according to claim 1, wherein the bacterial strain is an Ehrlichia strain.

8. The vaccine composition according claim 1, wherein the bacterial strain is selected from the group consisting of: E. canis, E. chaffeensis, E. ewingii, E. muris, and E. ruminantium.

9. A method for producing a vaccine composition for use against a bacterial strain selected from the group consisting of an Ehrlichia strain, an Anaplasma strain, a Rickettsia strain, an Orientia strain, a Bartonella strain, and a Brucella strain, the method comprising: inactivating or deleting the ntrX gene of the bacterial strain, thereby obtaining an attenuated bacterial strain.

10. The method for producing a vaccine composition according to claim 9, wherein the bacterial strain is an Ehrlichia strain.

11. The method for producing a vaccine composition according to claim 9, wherein the bacterial strain is selected from the group consisting of: E. canis, E. chaffeensis, E. ewingii, E. muris, and E. ruminantium.

12. A method of inducing an immune response against a bacterial strain, comprising administering the vaccine composition of claim 1 to a subject in need thereof.

13. The method of claim 12, wherein administering the vaccine composition prevents and/or treats an infection caused by the bacterial strain.

14. The method of claim 12, wherein the bacterial strain is an Ehrlichia strain and the infection caused by the bacterial strain is ehrlichiosis.

Description

FIGURES

(1) FIGS. 1 and 2 show an evidence of gene conversion between ntrX and its inverted duplicate.

(2) FIG. 1 shows an alignment showing the duplicated region (top four rows) of ntrX gene and the matching parental ntrX region (next four rows) in Welgevonden, Gardel and Senegal virulent and attenuated strains and in E. chaffeensis (last row) where there is no inverted duplicate. Alignment positions that show a closer relationship between ntrX and the duplicate within a strain than between strains, including the 4 bp deletion in Senegal strain are bordered by boxes.

(3) FIG. 2 shows a phylogram (left) depicting the expected relationship between ntrX and its duplicate (star) given that it is present in all E. ruminantium strains. The structure of the phylogram is based on the interstrain relationship reconstructed in the maximum likelihood phylogeny (right) by concatenating 54 orthologous ribosomal proteins from the strains and E. chaffeensis.

EXAMPLES

(4) Material and Methods:

(5) Genomics

(6) DNA Extraction and Purification

(7) Ehrlichia ruminantium Senegal strain passage 7 (80% lysis at day 21 p.i.) and 63 and 64 (80% lysis at day 7 p.i.) were cultured in Bovine Aortic endothelial cells as previously described for Gardel strain (Marcelino et al. 2005). When 80% lysis had occurred, supernatant and cellular debris were collected and centrifuged for 15 minutes at 4,000 g at 4° C. to remove cellular debris. The supernatant was then centrifuged for 30 minutes at 20,000 g at 4° C. in order to collect elementary bodies and remove the supernatant. The pellet was resuspended in 2 ml of cold PBS and homogenized gently then 20 ml of PBS was added to wash it, followed by centrifugation for 30 minutes at 20,000 g at 4° C. The pellet was resuspended in 350 μl PBS and 10 μl of RNase at 10 mg/ml (SIGMA, Lyon, France) and 150 μl of DNase I (Roche, Boulogne-Billancourt, France) were added. The pellet was incubated at 37° C. for 90 minutes and the reaction was stopped by adding 25 μl 0.5M EDTA, pH8. The DNase and Rnase were removed by centrifugation for 15 minutes at 20,000 g at 12° C. followed by a wash with 900 μl of sterile DNase and RNase free water. Cells were centrifuged under the same conditions and the washing step was repeated twice. Lysis of elementary bodies was performed by adding 500 μl of lysis solution (0.1M TRIS-HCl (pH8), 0.15M NaCl, 0.025M EDTA (pH8), 1.5% SDS, 0.3 mg/ml Proteinase K) followed by Incubation for 120 minutes at 55° C. DNA extraction was performed using phenol/chloroform (Perez et al. 1997) as follows: 500 μl of phenol (Eurobio, Courtaboeuf, France) was added to 500 μl of sample and mixed gently to homogenize followed by centrifugation for 5 minutes at 8000 g. The aqueous phase was collected and an equivalent volume of phenol was added before centrifugation for 5 minutes at 8,000 g. The aqueous phase was collected and an equivalent volume of phenol (Eurobiotech, France), chloroform and isoamylalcool (Prolabo, Normapur, France) in 24:24:1 proportion was added and mixed gently. The mixture was centrifuged for 5 minutes at 8,000 g and the aqueous phase collected and mixed gently with an equal volume of chroroform/isoamylalcool in 48:1 proportion. The mixture was centrifuged for 5 minutes at 8,000 g and the supernatant was collected and precipitated in ethanol (Prolabo, Normapur) by adding 2 volumes of absolute ethanol for 1 volume of the collected sample. The sample was stored at 4° C. for one hour in order to obtain a white precipitate which was then centrifuged for 10 minutes at 10,000 g at 10° C. The supernatant was removed and the pellet resuspended in 1 ml of 75% ethanol followed by centrifugation for 5 minutes at 10,000 g. The supernatant was removed and the pellet air dried. The pellet was resuspended in 25 μl of TE buffer (10 mM TRISpH8, 1 mM EDTA pH8). DNAs from Senegal passage 7, 63 and 64 in TE buffer were stored at −20° C. before being used for further sequencing.

(8) Genome Sequencing and Assembly

(9) The genome of the virulent Senegal strain (passage 7) was sequenced using 454 GS FLX technology. The attenuated strain (passage 63 & 64) was sequenced using 454 GS FLX technology and Sanger sequencing. Adapters for the 454 sequences were clipped using NextGen Sequence Workbench v3.2.3 (“NextGen Sequence Workbench” 2015), and reads were clipped for adaptors and quality scores according to the information in the SFF sequence files as well as removing reads less than 25 bp long or those with an average quality score less than 16. Quality trimming was performed for the Sanger sequences using NextGen Sequence Workbench v3.2.3 (“NextGen Sequence Workbench” 2015) with default settings (clip the reads in a 14 bp window until >63% have a quality score>=20) and removing reads less than 25 bp long or those with an average quality score less than 16. The virulent strain was de novo assembled using Mira 4.0.2 (Chevreux, Wetter, and Suhai 1999), resulting in 43 contigs larger than 1 kb. The contigs were ordered according to the previously published Welgevonden strain genome (Collins et al. 2005) using CONTIGuator (Galardini et al. 2011), which mapped 42 of the 43 contigs to the Welgevonden genome. The assembly was checked by realigning the reads onto the concatenated assembly using Bowtie 2 (Langmead and Salzberg 2012) and checking any predicted variants against the Welgevonden genome sequence (Collins et al. 2005). Duplicate reads were removed using Picard (“Picard Tools” 2016), conversion between SAM and BAM formats, sorting and mpileup was done using Samtools (Li et al. 2009) and variants were called using BCFtools (Li et al. 2009) and viewed with Tablet (Milne et al. 2013). Variant calls were manually examined in Tablet (Milne et al. 2013) and the assembly was edited accordingly. The attenuated strain was mapped onto the assembled virulent strain as described for remapping the virulent strain. Indels and SNPs were identified with quality cutoffs of 50 and 20 respectively and manually examined in the read alignment. Both genome assemblies were submitted to Genbank (Accessions MQUJ00000000 for Ehrlichia ruminantium Senegal Virulent, MRDC00000000 for Ehrlichia ruminantium Senegalp63 attenuated).

(10) E. ruminantium RNA Purification for RT-PCR

(11) E. ruminantium Senegal attenuated (passage 63 and 66) and virulent (passage 7 and 11) were inoculated in 25 cm.sup.2 TC flask containing BAE cells as previously described (Marcelino et al. 2005). The medium was changed at 24 h and 72 h for the attenuated strain and at 24 h and every two days, thereafter, for the virulent strain. Cell layers were allowed to reach around 80-90% lysis and were mechanically harvested with a scraper. Re-suspended cells were centrifuged at 4,500×g for 30 minutes at 4° C. Supernatant was discarded and cells were re-suspended in 1 ml PBS. Cells were then centrifuged at 10,000×g for 10 minutes and PBS was removed. Pellets were stored at −70° C. until RNA purification. Cell pellets were allowed to thaw for 5 minutes in ice and RNA was purified using the SV total RNA isolation system (Promega Corporation, Wisconsin, USA). An additional DNAse treatment was added by using the rigorous DNAse treatment with Turbo DNA-free (Ambion, Fisher Scientific, Illkirch, France), which consisted in adding 0.5 μl of the DNAse, incubating for 30 minutes, and repeating this procedure. RNA was immediately stored at −70° C. after inactivation of the DNAse before ntrX RT-PCR.

(12) RT-PCR of ntrX

(13) The expression of the ntrX in the virulent (passage 7 and 11) and attenuated (passage 63 and 66) Senegal strains was determined using the primers ntrX qRT F1 (5′-GGAAAGATTGTATATTTCTG-3′) (SEQ ID NO: 21) and ntrX qRT2 R1 (5′-ACCAGTAATGAGTATACGAC-3′) (SEQ ID NO: 22) that amplify a 517 bp piece of the ntrX gene. Amplifications were done using the OneStep RT-PCR kit (QIAgen, California, USA) with the following conditions: one Reverse transcriptase cycle at 50° C. for 30 minutes, a denaturating cycle at 95° C. for 15 minutes for activation of HotStart Taq, 35 cycles with a denaturating step 95° C. for 1 minute, an annealing step at 50° C. for 1 minute, and an amplification step at 72° C. for 1 minute, followed by an amplification cycle of 72° C. for 10 minutes. DNA from E. ruminantium Senegal passage 6 was used as positive control. Products were run in agarose gel and bands were visualized with SYBR safe.

(14) Distance of E. Muds and Senegal Strain Intergenic Regions

(15) The Senegal strain genome was aligned to the Ehrlichia muris genome using Mauve 2.3.1 (Darling et al. 2004) and intergenic regions were output from the alignment based on the E. muris annotation. Distances were calculated between the aligned intergenic regions using the TN93 model (Tamura and Nei 1993) in the APE package (Paradis, Claude, and Strimmer 2004) in R version 3.2.3 (R Core Team 2015) where at least 30 bases could be aligned, resulting in 364 intergenic distances between Senegal strain and E. muris. The distance between the ntrX gene from E. muris and the duplicate from Senegal strain was measured in the same way for comparison with the intergenic regions.

(16) Vaccination

(17) Preparation of the Inoculum

(18) A. Preparation of the Purified Supernatant

(19) As soon as 80% of lysis of cells is reached with a synchronous infection corresponding to 5 days of culture of Senegal passage 68, the supernatant with the cellular debris was passed in a syringe 26 G3/8. The totality of the supernatant was collected and centrifuged for 15 minutes at 3000 rpm. Then, the supernatant was recovered without removing the cellular pellet.

(20) 500 μl of the supernatant was tested in order to evaluate the viability of the sample. One part of the purified supernatant has been used to infect endothelial cell TC flask in order to control the infectivity of the inoculum 14 ml were at 4° C. before inoculation.

(21) B. Evaluation of the Viability Using the LIVE/DEAD BacLight™ Bacterial Viability Kits (ThermoFisher Scientific)

(22) The purified supernatant was washed in 15 ml of physiological serum and then centrifuged 30 min at 20,000 g at 4° C. It has been suspended again in 500 μl of physiological serum, passed in a syringe. 1.5 μl of Syto9 and Propidium Iodide was added. It was incubated 15 min then counted on a slide and passed in a flow cytometer. It was counted in a Neubeaur chamber in triplicate 8 squares each time. The final concentration was obtained by multiplication by the factor 1.6*10.sup.5. There was no dilution factor.

(23) Infection of the Animals

(24) Naïve goats were injected intravenously with the following doses of elementary bodies of live attenuated Senegal strain passage 64. The calibrated doses which reproduce natural challenge for virulent strain (between 10 and 12 days before hyperthermia and dead between day 12 and 15 after infection) is comprised between 3×10.sup.4 an 9×10.sup.4 live elementary bodies per goat (Vachiery et al, 2006). For this experiment, we decided to use a lethal dose and ten times the lethal dose using 9×10.sup.4 and 9×10.sup.5 live elementary bodies per goat.

(25) TABLE-US-00003 Goat Challenge Doses (Live elementary number body number) 0615 9 10.sup.4 0636 9 10.sup.4 0803 9 10.sup.5

(26) Preparation of inoculum depending on the viabilities and concentrations which were found.

(27) Viability

(28) From the cell culture supernatant we measured 5.89×10.sup.6 elementary bodies/ml on neaubeaur counting cell. The percentage of viability was measured by flow cytometry and we obtained 40% of viability. The number of live elementary bodies was 2.35×10.sup.6 CE live/ml. The supernatant was diluted in fresh cell culture medium to get 9×10.sup.4 and 9×10.sup.5 elementary bodies in a final volume of 2 ml.

(29) Monitoring of Animals;

(30) Clinical signs were checked every day in order to score the severity of the disease. A serology targeting MAP-1 antibodies was done one time a week and one blood sample were taken daily.

(31) Results:

(32) Virulent and Attenuated Senegal Strains Genomic Differences: SNPs and Indels

(33) The variants found between the virulent and attenuated strains are shown in Table below.

(34) TABLE-US-00004 TABLE Days for lysis of virulent and attenuated Senegal strain passages Passage Days to lyse Virulence 4 5 Virulent 4 8 Virulent 4 >8 Virulent 4 >10 Virulent 5 6 Virulent 5 >7 Virulent 5 5 Virulent 6 14 Virulent 6 14 Virulent 6 >7 Virulent 6 7 Virulent 6 >5 Virulent 7 4 Virulent 7 4 Virulent 7 6 Virulent 7 6 Virulent 8 6 Virulent 8a 6 Virulent 8b 6 Attenuated 65 4 Attenuated 68 5 Attenuated 69 5 Attenuated 70 5 Attenuated 70 4 Attenuated 71 4 Attenuated 73 4 Attenuated 74 4 Attenuated 74 4 Attenuated 75 5 Attenuated 75 4 Attenuated 76 4 Attenuated

(35) We identified only two SNPs and three indels between the virulent and attenuated Senegal strains. The SNPs occur in the glyA (ERGA_CDS_07110 ortholog), a serine hydroxymethyltransferase involved in the interconversion of serine and glycine as well as tetrahydrofolate production, and the ERGA_CDS_07720 ortholog, a putative M16 protease. Both SNPs are non-synonymous. The indels occur in a hypothetical gene (ERGA_CDS_01780 ortholog), the response regulator of the putative nitrogen-sensing two-component system, ntrX (ERGA_CDS_06840 ortholog) and map1-2 (ERGA_CDS_09130 ortholog), a member of the map1 family of outer membrane proteins. The hypothetical gene and ntrX both contain a 4 bp deletion, while the map1-2 gene contains a 2 bp insertion. The map1-2 gene appears to be a pseudogene in the virulent Senegal strain and the result of the insertion is to restore the open reading frame of the gene in the attenuated strain, making it a possible gain of function mutation. The hypothetical protein contains a Patatin domain and has sequence similarity to other patatin-like phospholipase family proteins that have lipolytic activity (Banerji and Flieger 2004).

(36) Candidate Mutations for Senegal Strain Attenuation

(37) The two nonsynonymous SNPs and the three indels identified between the virulent and attenuated Senegal strains provide a small number of candidates to explain the attenuation process in this strain.

(38) The glyA gene is involved in the interconversion of serine and glycine, and is necessary for virulence in Salmonella Typhimurium and Brucella species (Köhler et al. 2002; Xiang, Zheng, and He 2006; Jelsbak et al. 2014). However, the attenuation in Brucella suis was obtained by Tn5 insertion to knock out the gene, and in the case of the SNP in our data, the protein is still probably produced. The substituted amino acid lies near the end of the protein (position 388/421) and outside of any predicted domains. An alignment of glyA in several Rickettsial species shows that while most of the protein is well conserved, the portion where the mutation occurs is variable across the species suggesting that the region is not vital for protein function.

(39) The map1-2 gene is a member of a multigene family of Major Antigenic Proteins in the Anaplasmataceae, Pfam PF01617 (Dunning Hotopp et al. 2006), which are surface exposed and have been identified as potential vaccine targets (Bekker et al. 2002). Some members of these map genes have been experimentally characterized as porins (Huang et al. 2007) and are suspected to be involved in host cell adhesion (Garcia-Garcia et al. 2004; Park, Choi, and Dumler 2003). Thus, its mutation appears to be a potential candidate for attenuation. However, a study of the map1-2 gene in several different strains of E. ruminantium failed to provide evidence of transcription of this gene in any of the strains they tested (Senegal virulent and attenuated, Gardel, Welgevonden and Sankat 430) in either ticks or bovine endothelial cells (Bekker et al. 2002). A different study did however report the transcription of the map1-2 gene in Welgevonden (van Heerden et al. 2004). The map1-2 gene contains a 2 bp deletion in the Senegal virulent strain (presumably rendering it non-functional) that is reverted in the attenuated strain. Curiously, the deletion is not present in a previous study using a different isolate of the virulent Senegal strain (Bekker et al. 2005). Examination of the reads covering this indel in our data revealed that they fully support the deletion in the virulent Senegal, while it is not present in any reads in the attenuated strain. This result suggests that this deletion may be unique to the virulent strain sequenced in this study. The lack of detectable transcription of the gene in some strains (Bekker et al. 2002) and the fact that the complete map1-2 sequence is present in several other virulent strains of E. ruminantium including another Senegal isolate makes the reversion insertion unlikely to be the cause of attenuation of the Senegal strain.

(40) The patatin domain-containing protein (ERGA_CDS_01780 ortholog) may play a role in the virulence of E. ruminantium, as patatin-like phospholipase proteins are putatively involved in host cell entry in Rickettsia (Rahman et al. 2010). Phospholipase proteins have been identified as virulence factors secreted by the Type III secretion system in Pseudomonas aeruginosa (ExoU), and the Type IV-B secretion system in Legionella pneumophiHa (VipD) (Rahman et al. 2010). Bacterial pathogens also tend to contain more patatin-like-proteins than non-pathogens (Banerji and Flieger 2004), suggesting possible roles in virulence. However, their presence in non-pathogens also shows that patatins are not always involved in virulence functions. The indel in the attenuated strain is close to, but outside of the predicted patatin domain, suggesting that the phospholipase activity might be maintained, but making the result of the indel unsure in terms of its effect on the function of the protein. Proteolysis can play roles in virulence at various levels in bacterial pathogens (Frees, Brøndsted, and Ingmer 2013), and although we could find no evidence for a known role of proteases from the M16 family in bacterial virulence, proteases from this family in Toxoplasma gondii have been suggested to play a possible role in host invasion by the parasite (Laliberté and Carruthers 2011).

(41) Consequently, the only attenuation candidate is the ntrX gene containing the 4 bp deletion because it is the response regulator of one of only three two-component systems in E. ruminantium that are responsible for global regulation of various bacterial systems (Cheng et al. 2006; Kumagai et al. 2006; Cheng, Lin, and Rikihisa 2014). Two-component systems are involved in sensing of environmental or cellular signals and the downstream expression of genes, allowing bacteria to coordinate their gene expression in response to their environment or cellular state. During infection, bacterial pathogens need to efficiently coordinate their metabolic activities with their virulence to allow for maximization of their growth and successful attack on the host cells, while avoiding host defences. Signals such as the availability of nutrients or metabolites may inform the bacteria of the optimal time to produce virulence factors, and the regulation of many bacterial virulence factors is linked with nutrient availability (Somerville and Proctor 2009; Barbier, Nicolas, and Letesson 2011). NtrX lies at the crossroads of environmental sensing and gene expression and is therefore the ideal candidate to explain attenuation because perturbations to the NtrY/X system are likely to have major consequences for the growth, survival and the coordination of bacterial metabolism and virulence. Furthermore, ntrX as the attenuator explains the apparently biased nature of attenuation in the Senegal strain as compared to other E. ruminantium strains due to its genomic context, which will be discussed later.

(42) The ntrX Gene is Disrupted by Segmental Gene Conversion from a Nearby Inverted Partial ntrX Duplication in Attenuated Senegal Strain

(43) A segment of the ntrX gene has been duplicated in all E. ruminantium genomes for which there is available genome sequence data. The duplicated section is inverted and covers 421 bp close to the 5′ end of ntrX (not including the start codon), and lies roughly 2 kb downstream of the ntrX gene itself. The alignment between the ntrX and the duplicate region reveals that the 4 bp deletion identified in the ntrX gene in the Senegal attenuated strain is also present in the duplicated segment in both the attenuated and virulent strains of Senegal, but not in any of the other strains. The 4 bp deletion in ntrX in the attenuated strain causes a frameshift between the domain regions for the response regulator receiver domain and the sigma factor interaction domain, which introduces a stop codon that disrupts the gene. There are also seven other mutations across the sequenced strains between ntrX and its duplicate that exhibit a pattern that is incongruent with the expected phylogeny. At these residues, the ntrX gene and its duplicate are more similar within a strain than they are to their orthologous positions in the other strains, a pattern that indicates gene conversion (FIGS. 1 and 2).

(44) TABLE-US-00005 SEQ ID NO: Nucleic acid sequences of regions shown at figure 1 Welgevonden 12 CTAATAATGATATATTAGGTGTGATAATTATATCACTAAATTAGCAGTTGATGGTTTATCCGCGATCAAGATG Duplicate GCTTATGAAAAAGAGCCTGATGTTGTATTATTGGATATATGGTTAAGAGGATCTGATATTGATGGATTAAGT GTACTGGAAAAGCTTAAAGAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGCCA CTGCTGTAAAGTCTCTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAAGT TAGTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAG GATTATGAAATAGTCGGTAACTCCCCTGTTATACGTAATTTGAGAAGTATGGTTAATAA Gardel 13 CTAATAATGATATATTAAGTGATGATAATTATGTCACTAAATTAGCAGTTGATGGTTTATCCGCGATCAAGAT Duplicate GGCTTATGAAAAAGAGCCTGATGTTGTATTATTGGATATATGGTTAAGAGGATCTGATATTGATGGATTAAG TGTACTGGAGAAGCTTAAAGAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGCC ACTGCTGTAAAGTCTCTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAAG TTAGTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAG GATTATGAAATAGTCGGTAACTCCCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Senegal 14 CTAATAATGATATATTAGGCAATGATAATTATGTAACCAAATTAGCAGTTGATTATTTATGAAAAAGAGCCTG Virulent ATGTTGTATTATTGGATATATAGTTAAAGAGGATCTGATATTGATGGATTAAGCGTACTGGAAAAGCTTAAA Duplicate GAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGCTACTGCTGTAAAGTCTTTGC ATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAAGTTGTAAAGAGAGCTATAGA GTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAGGATTATGAGATAGTGGGTAACTC GCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Senegal 15 CTAATAATGATATATTAGGCAATGATAATTATGTAACCAAATTAGCAGTTGATTATTTATGAAAAAGAGCCTG Attenuated ATGTTGTATTATTGGATATATAGTTAAAGAGGATCTGATATTGATGGATTAAGCGTACTGGAAAAGCTTAAA Duplicate GAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGCTACTGCTGTAAAGTCTTTGC ATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAAGTTGTAAAGAGAGCTATAGA GTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAGGATTATGAGATAGTGGGTAACTC GCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Welgevonden 16 CTAATAAAAGATATATTAAGTGATGATAATTATGTCACTAAATTAGCAGTTGATGGTTTATCCGCGATCAAGA ntrX TGGCTTATGAAAAAGAGCCTGATGTTGTATTATTAGATATATGGTTAAGAGGATCTGATATTGATGGATTAAG TGTACTGGAAAAGCTTAAAGAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGCC ACTGCTGTAAAGTCTCTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAAG TTAGTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAG GATTATGAAATAGTCGGTAACTCCCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Gardel ntrX 17 CTAATAAAAGATATATTAAGTGATGATAATTATGTCACTAAATTAGCAGTTGATGGTTTATCCGCGATCAAGA TGGCTTATGAAAAAGAGCCTGATGTTGTATTATTGGATATATGGTTAAGAGGATCTGATATTGATGGATTAA GTGTACTGGAGAAGCTTAAAGAAAGGTATCCTTATTTGCCTGTTATTATGATTAGTGGGCATGGTAATATTGC CACTGCTGTAAAGTCTCTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAA GTTAGTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGA GGATTATGAAATAGTCGGTAACTCCCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Senegal 18 CTAATAAAAGATATATTAAGTGATGATAATTATGTCACTAAATTAGCAGTTGATGGTTTATCTGCGATCAAGA Virulent ntrX TGGCTTATGAAAAAGAGCCTGATGTTGTATTATTGGATATATGGTTAAGAGGATCTGATATTGATGGATTAA GCGTACTGGAAAAGCTTAAAGAAAGGTATCCTTATTTACCTGTTATTATGATTAGTGGGCATGGTAATATTGC TACTGCTGTAAAGTCTTTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAA GTTAGTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGA GGATTATGAGATAGTGGGTAACTCGCCTGTTATACGTAATTTGAGAAGTATGATTAATAA Senegal 19 CTAATAAAAGATATATTAAGTGATGATAATTATGTCACTAAATTAGCAGTTGATGGTTTATCTGCGATCAAGA Attenuated TGGCTTATGAAAAAGAGCCTGATGTTGTATTATTGGATATATGGTTAAGAGGATCTGATATTGATGGATTAA ntrX GCGTACTGGAAAAGCTTAAAGAAAGGTATCCTTATTTACCTGTTATTATGATTAGTGGGCATGGTAATATTGC TACTGCTGTAAAGTCTTTGCATATGGGTGCTTATGATTATATAGAAAAGCCTTTTACAGAAGGAAGATTAAA GTTGTAAAGAGAGCTATAGAGTCTGGTAGATTACGTAGAGAAAATGATGAGTTGAAATCAGCATTTGAGGA TTATGAGATAGTGGGTAACTCGCCTGTTATACGTAATTTGAGAAGTATGATTAATAA E. chaffeensis 20 TTAATAAAGGATATATTAAGTGATGATAATTATGTCACAAAATTAGCAGTTGATGGGTTGTCTGCTATTAAGA ntrX TGGCTTATGAGAAAGAACCAGATGTTGTTTTACTAGATATATGGTTAAAAGGATCAGATATTGATGGGTTAA GTGTTTTAGAGAAACTAAAGGAAAGGTATCCATATTTACCTGTGATTATGATTAGTGGACATGGTAATATTGC TACTGCTGTGAAGTCTTTGCACATGGGAGCTTATGATTATATAGAGAAACCTTTTACAGAAGGTAGATTAAA GTTAGTAGTTAAGAGAGCGATAGAATCTGGTAGATTGCGTAGAGAAAATGACGAATTAAAATCAACATTTGA AGATTACGAAATAGTTGGCAACTCTCCTGTAATAAAAAATCTAAGGAGTATGATTAATAA

(45) NtrX is Expressed in Senegal Virulent Strain but not in the Attenuated Strain

(46) To confirm the pseudogenisation of ntrX in the attenuated strain, we performed a RT-PCR on RNA samples from the virulent (passage 7 and 11) and avirulent (passage 63 and 66) strains. RT-PCR resulted in the amplification of a 517 bp in one (Senegal passage 11 and not Senegal passage 7) of the two virulent samples confirming the expression of ntrX. No band was observed in either of the samples from the attenuated strain indicating that ntrX gene is not expressed in the attenuated Senegal strain.

(47) Vaccination with the Attenuated Strain

(48) After inoculation, the goats infected with the attenuated strain suffered from a slight hyperthermia with no other clinical signs and all survived even with 10-fold lethal dose of challenge. Consequently, the mutant E. ruminantium passage 64 is attenuated.

(49) 100% of goats infected with the attenuated strain and which were submitted to a challenge with the virulent strain (E. ruminantium passage 7) survived, whereas all the control goats, which were submitted to a challenge with the virulent strain without having been previously infected with the attenuated strain, died.

(50) These results show that a E. ruminantium with an inactive or deleted ntrX gene provides an efficient vaccine against ehrlichiosis.

(51) Owing to the very high conservation degree of the ntrX gene in the Anaplasmataceae family (see table 1), these results apply to the other strains of the Anaplasmataceae family.

REFERENCES

(52) Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present application. Atack, John M., Yogitha N. Srikhanta, Karrera Y. Djoko, Jessica P. Welch, Norain H. M. Hasri, Christopher T. Steichen, Rachel N. Vanden Hoven, et al. 2013. “Characterization of an ntrX Mutant of Neisseria gonorrhoeae Reveals a Response Regulator That Controls Expression of Respiratory Enzymes in Oxidase-Positive Proteobacteria.” Journal of Bacteriology 195 (11): 2632-41. doi:10.1128/JB.02062-12. Banerji, Sangeeta, and Antje Flieger. 2004. “Patatin-like Proteins: A New Family of Lipolytic Enzymes Present in Bacteria?” Microbiology (Reading, England) 150 (Pt 3): 522-25. doi: 10.1099/mic.0.26957-0. Bekker, Cornells P. J., Lesley Bell-Sakyi, Edith A. Paxton, Dominique Martinez, Albert Bensaid, and Frans Jongejan. 2002. “Transcriptional Analysis of the Major Antigenic Protein 1 Multigene Family of Cowdria ruminantium.” Gene 285 (1-2): 193-201. Bekker, Cornells P. J., Milagros Postigo, Amar Taoufik, Lesley Bell-Sakyi, Conchita Ferraz, Dominique Martinez, and Frans Jongejan. 2005. “Transcription Analysis of the Major Antigenic Protein 1 Multigene Family of Three In Vitro-Cultured Ehrlichia ruminantium Isolates.” Journal of Bacteriology 187 (14): 4782-91. doi: 10.1128/JB. 187.14.4782-4791.2005. Camus, E., and N. Barre. 1988. “[Diagnosis of headwater from brain ecrasement].” Revue Cheng, Zhihui, Yumi Kumagai, Mingqun Lin, Chunbin Zhang, and Yasuko Rikihisa. 2006. “Intra-Leukocyte Expression of Two-Component Systems in Ehrlichia Chaffeensis and Anaplasma Phagocytophilum and Effects of the Histidine Kinase Inhibitor Closantel.” Cellular Microbiology 8 (8): 1241-52. doi:10.1111/j.1462-5822.2006.00704.x. Cheng, Zhihui, Mingqun Lin, and Yasuko Rikihisa. 2014. “Ehrlichia Chaffeensis Proliferation Begins with NtrY/NtrX and PutA/GInA Upregulation and CtrA Degradation Induced by Proline and Glutamine Uptake.” mBio 5 (6). doi: 10.1128/mBio.02141-14. Chevreux, B., T. Wetter, and S. Suhai. 1999. “Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.” In Proceedings of the German Conference on Bioinformatics, 99:45-56. Collins, Nicola E., Junita Liebenberg, Etienne P. de Villiers, Kelly A. Brayton, Elmarié Louw, Alri Pretorius, F. Erika Faber, et al. 2005. “The Genome of the Headwater Agent Ehrlichia ruminantium Contains Multiple Tandem Repeats of Actively Variable Copy Number.” Proceedings of the National Academy of Sciences of the United States of America 102 (3): 838-43. doi:10.1073/pnas.0406633102. Darling, Aaron C. E., Bob Mau, Frederick R. Blattner, and Nicole T. Perna. 2004. “Mauve: Multiple Alignment of Conserved Genomic Sequence with Rearrangements.” Genome Research 14 (7): 1394-1403. doi:10.1101/gr.2289704. Dunning Hotopp, Julie C., Mingqun Lin, Ramana Madupu, Jonathan Crabtree, Samuel V. Angiuoli, Jonathan A. Eisen, Jonathan Eisen, et al. 2006. “Comparative Genomics of Emerging Human Ehrlichiosis Agents.” PLoS Genetics 2 (2): e21. doi: 10.1371/journal.pgen.0020021. Frees, Dorte, Lone Brandsted, and Hanne Ingmer. 2013. “Bacterial Proteases and Virulence.” Sub-Cellular Biochemistry 66: 161-92. doi:10.1007/978-94-007-5940-4_7. Frutos, Roger, Alain Viari, Conchita Ferraz, Anne Morgat, Sophie Eychenie, Yane Kandassamy, Isabelle Chantal, et al. 2006. “Comparative Genomic Analysis of Three Strains of Ehrlichia ruminantium Reveals an Active Process of Genome Size Plasticity.” Journal of Bacteriology 188 (7): 2533-42. doi: 10.1128/JB. 188.7.2533-2542.2006. Galardini, Marco, Emanuele G. Biondi, Marco Bazzicalupo, and Alessio Mengoni. 2011. “CONTIGuator: A Bacterial Genomes Finishing Tool for Structural Insights on Draft Genomes.” Source Code for Biology and Medicine 6: 11. doi: 10.1186/1751-0473-6-11. Garcia-Garcia, Jose C., José de la Fuente, Gianna Bell-Eunice, EdmourF. Blouin, and Katherine M. Kocan. 2004. “Glycosylation of Anaplasma Marginale Major Surface Protein 1a and Its Putative Role in Adhesion to Tick Cells.” Infection and Immunity 72 (5): 3022-30. doi:10.1128/IAI.72.5.3022-3030.2004. Jansen, Gunther, Lena L. Crummenerl, Felix Gilbert, Timm Mohr, Roxana Pfefferkorn, Robert Thänert, Philip Rosenstiel, and Hinrich Schulenburg. 2015. “Evolutionary Transition from Pathogenicity to Commensalism: Global Regulator Mutations Mediate Fitness Gains through Virulence Attenuation.” Molecular Biology and Evolution 32 (11): 2883-96. doi: 10.1093/molbev/msv160. Jelsbak, Lotte, Hassan Hartman, Casper Schroll, Jesper T. Rosenkrantz, Sebastien Lemire, Inke Wallrodt, Line E. Thomsen, et al. 2014. “Identification of Metabolic Pathways Essential for Fitness of Salmonella Typhimurium In Vivo.” PLoS ONE 9 (7): e101869. doi:10.1371/journal.pone.0101869. Jongejan, F. 1991. “Protective Immunity to Headwater (Cowdria ruminantium Infection) Is Acquired after Vaccination with in Vitro-Attenuated Rickettsiae.” Infection and Immunity 59 (2): 729-31. Köhler, Stephan, Vincent Foulongne, Safia Ouahrani-Bettache, Gisèle Bourg, Jacques Teyssier, Michel Ramuz, and Jean-Pierre Liautard. 2002. “The Analysis of the Intramacrophagic Virulome of Brucella Suis Deciphers the Environment Encountered by the Pathogen inside the Macrophage Host Cell.” Proceedings of the National Academy of Sciences of the United States of America 99 (24): 15711-16. doi: 10.1073/pnas.232454299. Kumagai, Yumi, Zhihui Cheng, Mingqun Lin, and Yasuko Rikihisa. 2006. “Biochemical Activities of Three Pairs of Ehrlichia Chaffeensis Two-Component Regulatory System Proteins Involved in Inhibition of Lysosomal Fusion.” Infection and Immunity 74 (9): 5014-22. doi: 10.1128/IAI.00735-06. Laliberté, Julie, and Vern B. Carruthers. 2011. “Toxoplasma Gondii Toxolysin 4 is an Extensively Processed Putative Metalloproteinase Secreted from Micronemes.” Molecular and Biochemical Parasitology 177 (1): 49-56. doi:10.1016/j.molbiopara.2011.01.009. Langmead, Ben, and Steven L. Salzberg. 2012. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9 (4): 357-59. doi: 10.1038/nmeth. 1923. Li, Heng, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics (Oxford, England) 25 (16): 2078-79. doi:10.1093/bioinformatics/btp352. Marcelino, Isabel, Celia Verissimo, Marcos F. Q. Sousa, Manuel J. T. Carrondo, and Paula M. Alves. 2005. “Characterization of Ehrlichia ruminantium Replication and Release Kinetics in Endothelial Cell Cultures.” Veterinary Microbiology 110 (1-2): 87-96. doi:10.1016/j.vetmic.2005.07.012. Milne, lain, Gordon Stephen, Micha Bayer, Peter J. A. Cock, Leighton Pritchard, Linda Cardie, Paul D. Shaw, and David Marshall. 2013. “Using Tablet for Visual Exploration of Second-Generation Sequencing Data.” Briefings in Bioinformatics 14 (2): 193-202. doi: 10.1093/bib/bbs012. Nene, Vishvanath, and Chittaranjan Kole. 2008. Genome Mapping and Genomics in Animal-Associated Microbes. Springer Science & Business Media. Park, Jinho, Kyoung Seong Choi, and J. Stephen Dumler. 2003. “Major Surface Protein 2 of Anaplasma Phagocytophilum Facilitates Adherence to Granulocytes.” Infection and Immunity 71 (7): 4018-25. doi:10.1128/IAI.71.7.4018-4025.2003. Parkinson, J. S., and E. C. Kofoid. 1992. “Communication Modules in Bacterial Signaling Proteins.” Annual Review of Genetics 26: 71-112. doi: 10.1146/annurev.ge.26.120192.000443. Paradis, Emmanuel, Julien Claude, and Korbinian Strimmer. 2004. “APE: Analyses of Phylogenetics and Evolution in R Language.” Bioinformatics 20 (2): 289-90. doi: 10.1093/bioinformatics/btg412. Pilet, Héloïse, Nathalie Vachiéry, Moez Berrich, Rim Bouchouicha, Benoît Durand, Ludovic Pruneau, Valérie Pinarello, et al. 2012. “A New Typing Technique for the Rickettsiales Ehrlichia ruminantium: Multiple-Locus Variable Number Tandem Repeat Analysis.” Journal of Microbiological Methods 88 (2): 205-11. doi:10.1016/j.mimet.2011.11.011. Rahman, M. Sayeedur, Nicole C. Ammerman, Khandra T. Sears, Shane M. Ceraul, and Abdu F. Azad. 2010. “Functional Characterization of a Phospholipase A2 Homolog from Rickettsia Typhi.” Journal of Bacteriology 192 (13): 3294-3303. doi: 10.1128/JB.00155-10. Tanner, Jennifer R., Laam Li, Sebastien P. Faucher, and Ann Karen C. Brassinga. 2016. “The CpxRA Two-Component System Contributes to Legionella Pneumophila Virulence.” Molecular Microbiology, March, n/a-n/a. doi: 10.1111/mmi. 13365. Tamura, K., and M. Nei. 1993. “Estimation of the Number of Nucleotide Substitutions in the Control Region of Mitochondrial DNA in Humans and Chimpanzees.” Molecular Biology and Evolution 10 (3): 512-26. Vachiery N., Lefrançois, T., Esteves, I., Molia, S., Sheikboudou, C., Kandassamy Y., Martinez, D., Optimisation of the inactivated vaccine dose against headwater and in vitro quantification of Ehrlichia ruminantium challenge material. 2006. Vaccine, 24: 4747-4756. Van Heerden H1, Steyn H C, Allsopp M T, Zweygarth E, Josemans A I, Allsopp B A. 2004 “Characterization of the pCS20 region of different Ehrlichia ruminantium isolates.” Vet Microbiol. 101 (4):279-91. Xiang, Zuoshuang, Wenjie Zheng, and Yongqun He. 2006. “BBP: Brucella Genome Annotation with Literature Mining and Curation.” BMC Bioinformatics 7: 347. doi: 10.1186/1471-2105-7-347. Zweygarth, Erich, Antoinette I. Josemans, M. Fransie Van Strijp, Laura Lopez-Rebollar, Mirinda Van Kleef, and Basil A. Allsopp. 2005. “An Attenuated Ehrlichia ruminantium (Welgevonden Stock) Vaccine Protects Small Ruminants against Virulent Headwater Challenge.” Vaccine 23 (14): 1695-1702. doi: 10.1016/j.vaccine.2004.09.030.