Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

A review of reverse vaccinology approaches for the development of vaccines against ticks and tick borne diseases

The field of reverse vaccinology developed as an outcome of the genome sequence revolution. Following the introduction of live vaccinations in the western world by Edward Jenner in 1798 and the coining of the phrase 'vaccine', in 1881 Pasteur developed a rational design for vaccines. Pasteur proposed that in order to make a vaccine that one should 'isolate, inactivate and inject the microorganism' and these basic rules of vaccinology were largely followed for the next 100 years leading to the elimination of several highly infectious diseases. However, new technologies were needed to conquer many pathogens which could not be eliminated using these traditional technologies. Thus increasingly, computers were used to mine genome sequences to rationally design recombinant vaccines. Several vaccines for bacterial and viral diseases (i.e. meningococcus and HIV) have been developed, however the on-going challenge for parasite vaccines has been due to their comparatively larger genomes. Understanding the immune response is important in reverse vaccinology studies as this knowledge will influence how the genome mining is to be conducted. Vaccine candidates for anaplasmosis, cowdriosis, theileriosis, leishmaniasis, malaria, schistosomiasis, and the cattle tick have been identified using reverse vaccinology approaches. Some challenges for parasite vaccine development include the ability to address antigenic variability as well the understanding of the complex interplay between antibody, mucosal and/or T cell immune responses. To understand the complex parasite interactions with the livestock host, there is the limitation where algorithms for epitope mining using the human genome cannot directly be adapted for bovine, for example the prediction of peptide binding to major histocompatibility complex motifs. As the number of genomes for both hosts and parasites increase, the development of new algorithms for pan-genomic mining will continue to impact the future of parasite and ricketsial (and other tick borne pathogens) disease vaccine development.

Antimicrobial susceptibilities and resistance genes of Canadian isolates of Actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia, a severe and highly contagious respiratory disease responsible for economic losses in the swine industry worldwide. Although antimicrobial resistance in A. pleuropneumoniae has been recently reported in different countries, the current situation in Canada is unknown. The aim of the current study was to determine the antimicrobial susceptibilities of 43 strains of A. pleuropneumoniae isolated in Canada. In addition, antimicrobial resistance genes were detected with an oligonucleotide microarray. The impact of biofilm formation on susceptibility to antimicrobials was also evaluated. All isolates were susceptible to ceftiofur, florfenicol, enrofloxacin, erythromycin, clindamycin, trimethoprim/sulfamethoxazole, and tilmicosin. A low level of resistance was observed toward tiamulin, penicillin, and ampicillin as well as danofloxacin. We observed a high level of resistance to chlortetracycline (88.4%) and oxytetracycline (90.7%). The strains showing resistance to tetracycline antimicrobials contained at least one of the following tet genes: tetB, tetO, tetH, or tetC. Five isolates showed multiresistance to penicillins (bla(ROB-1)), streptomycin [aph3'' (strA)], sulfonamides (sulII), and tetracyclines (tetO) antimicrobials whereas three others showed multiresistance to streptomycin [aph3'' (strA)], sulfonamides (sulII), and tetracyclines (tetB, tetO, or tetB/tetH) antimicrobials. To the best of our knowledge, this is the first description of tetC gene in Pasteurellaceae. Finally, cells of A. pleuropneumoniae in a biofilm were 100 to 30,000 times more resistant to antimicrobials than their planktonic counterparts.

2009 pandemic H1N1 influenza virus causes disease and upregulation of genes related to inflammatory and immune responses, cell death, and lipid metabolism in pigs

There exists limited information about whether adaptation is needed for cross-species transmission of the 2009 pandemic H1N1 influenza virus (pH1N1). Here, we compare the pathogenesis of two pH1N1 viruses, one derived from a human patient (A/CA/04/09 [CA09]) and the other from swine (A/swine/Alberta/25/2009 [Alb09]), with that of the 1918-like classical swine influenza virus (A/swine/Iowa/1930 [IA30]) in the pig model. Both pH1N1 isolates induced clinical symptoms such as coughing, sneezing, decreased activity, fever, and labored breathing in challenged pigs, but IA30 virus did not cause any clinical symptoms except fever. Although both the pH1N1 viruses and the IA30 virus caused lung lesions, the pH1N1 viruses were shed from the nasal cavities of challenged pigs whereas the IA30 virus was not. Global gene expression analysis indicated that transcriptional responses of the viruses were distinct. pH1N1-infected pigs had an upregulation of genes related to inflammatory and immune responses at day 3 postinfection that was not seen in the IA30 infection, and expression levels of genes related to cell death and lipid metabolism at day 5 postinfection were markedly different from those of IA30 infection. These results indicate that both pH1N1 isolates are more virulent due in part to differences in the host transcriptional response during acute infection. Our study also indicates that pH1N1 does not need prior adaptation to infect pigs, has a high potential to be maintained in naïve swine populations, and might reassort with currently circulating swine influenza viruses.

Genomic differences between Actinobacillus pleuropneumoniae serotypes 5b and 3 and their distribution and transcription among 15 serotypes

The development of serotyping-based diagnostic methods and multivalent vaccines has been significantly hampered due to the limited information available on the genetic differences among the 15 currently known serotypes of Actinobacillus pleuropneumoniae. In this study, using the GenomeComp informatics software, differential genes were screened and identified between the complete genome sequences of the serotypes 5b (L20 strain, highly virulent) and 3 (JL03 strain, weakly virulent), 84 presented uniquely in strain L20, while 57 were only found in JL03 strain. Of these, 75 encode putative proteins and 66 encode hypothetical proteins, including phage-related proteins, Apx toxin, capsular polysaccharide biosynthesis proteins, ATP-binding cassette (ABC) transporters, Clp-like proteases, fimbrial protein (Flp), various glycosyltransferases, methylases, integrases, and other proteins related to virulence. To confirm and further characterize the differential genes, we carefully selected 34 proven or putative virulence genes which were extremely useful on researching into detection and vaccine of A. pleuropneumoniae, and investigated the distribution and transcription of these genes among the 15 serotypes through polymerase chain reaction, reverse transcriptase- polymerase chain reaction and sequencing, and different distribution and transcription patterns of the differential genes in each serotype were first found and described. These information of these differential genes among the 15 serotypes of A. pleuropneumoniae may greatly serve as an indicator for future research on the pathogenic mechanisms of different serotypes, serotyping-based diagnostic methods, and multivalent vaccines.

Genome-wide evidence for positive selection and recombination in Actinobacillus pleuropneumoniae

Background

Actinobacillus pleuropneumoniae is an economically important animal pathogen that causes contagious pleuropneumonia in pigs. Currently, the molecular evolutionary trajectories for this pathogenic bacterium remain to require a better elucidation under the help of comparative genomics data. For this reason, we employed a comparative phylogenomic approach to obtain a comprehensive understanding of roles of natural selective pressure and homologous recombination during adaptation of this pathogen to its swine host.

Results

In this study, 12 A. pleuropneumoniae genomes were used to carry out a phylogenomic analyses. We identified 1,587 orthologous core genes as an initial data set for the estimation of genetic recombination and positive selection. Based on the analyses of four recombination tests, 23% of the core genome of A. pleuropneumoniae showed strong signals for intragenic homologous recombination. Furthermore, the selection analyses indicated that 57 genes were undergoing significant positive selection. Extensive function properties underlying these positively selected genes demonstrated that genes coding for products relevant to bacterial surface structures and pathogenesis are prone to natural selective pressure, presumably due to their potential roles in the avoidance of the porcine immune system.

Conclusions

Overall, substantial genetic evidence was shown to indicate that recombination and positive selection indeed play a crucial role in the adaptive evolution of A. pleuropneumoniae. The genome-wide profile of positively selected genes and/or amino acid residues will provide valuable targets for further research into the mechanisms of immune evasion and host-pathogen interactions for this serious swine pathogen.

Immunoproteomic analysis of bacterial proteins of Actinobacillus pleuropneumoniae serotype 1

Background

Actinobacillus pleuropneumoniae (APP) is one of the most important swine pathogens worldwide. Identification and characterization of novel antigenic APP vaccine candidates are underway. In the present study, we use an immunoproteomic approach to identify APP protein antigens that may elicit an immune response in serotype 1 naturally infected swine and serotype 1 virulent strain S259-immunized rabbits.

Results

Proteins from total cell lysates of serotype 1 APP were separated by two-dimensional electrophoresis (2DE). Western blot analysis revealed 21 immunoreactive protein spots separated in the pH 4-7 range and 4 spots in the pH 7-11 range with the convalescent sera from swine; we found 5 immunoreactive protein spots that separated in the pH 4-7 range and 2 in the pH 7-11 range with hyperimmune sera from S259-immunized rabbits. The proteins included the known antigens ApxIIA, protective surface antigen D15, outer membrane proteins P5, subunit NqrA. The remaining antigens are being reported as immunoreactive proteins in APP for the first time, to our knowledge.

Conclusions

We identified a total of 42 immunoreactive proteins of the APP serotype 1 virulent strain S259 which represented 32 different proteins, including some novel immunoreactive factors which could be researched as vaccine candidates.

Proteomic and immunoproteomic characterization of a DIVA subunit vaccine against Actinobacillus pleuropneumoniae

Background

Protection of pigs by vaccination against Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is hampered by the presence of 15 different serotypes. A DIVA subunit vaccine comprised of detergent-released proteins from A. pleuropneumoniae serotypes 1, 2 and 5 has been developed and shown to protect pigs from clinical symptoms upon homologous and heterologous challenge. This vaccine has not been characterized in-depth so far. Thus we performed i) mass spectrometry in order to identify the exact protein content of the vaccine and ii) cross-serotype 2-D immunoblotting in order to discover cross-reactive antigens. By these approaches we expected to gain results enabling us to argue about the reasons for the efficacy of the analyzed vaccine.

Results

We identified 75 different proteins in the vaccine. Using the PSORTb algorithm these proteins were classified according to their cellular localization. Highly enriched proteins are outer membrane-associated lipoproteins like OmlA and TbpB, integral outer membrane proteins like FrpB, TbpA, OmpA1, OmpA2, HgbA and OmpP2, and secreted Apx toxins. The subunit vaccine also contained large amounts of the ApxIVA toxin so far thought to be expressed only during infection. Applying two-dimensional difference gel electrophoresis (2-D DIGE) we showed different isoforms and variations in expression levels of several proteins among the strains used for vaccine production. For detection of cross-reactive antigens we used detergent released proteins of serotype 7. Sera of pigs vaccinated with the detergent-released proteins of serotypes 1, 2, and 5 detected seven different proteins of serotype 7, and convalescent sera of pigs surviving experimental infection with serotype 7 reacted with 13 different proteins of the detergent-released proteins of A. pleuropneumoniae serotypes 1, 2, and 5.

Conclusions

A detergent extraction-based subunit vaccine of A. pleuropneumoniae was characterized by mass spectrometry. It contained a large variety of immunogenic and virulence associated proteins, among them the ApxIVA toxin. The identification of differences in expression as well as isoform variation between the serotypes implied the importance of combining proteins of different serotypes for vaccine generation. This finding was supported by immunoblotting showing the induction of cross-reactive antibodies against several surface associated proteins in immunized animals.

Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs

Background

Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, namely capsular polysaccharides, RTX toxins, LPS and many iron acquisition systems. In order to identify genes that are expressed in vivo during a natural infection, we undertook transcript profiling experiments with an A. pleuropneumoniae DNA microarray, after recovery of bacterial mRNAs from serotype 5b-infected porcine lungs. AppChip2 contains 2033 PCR amplicons based on the genomic sequence of App serotype 5b strain L20, representing more than 95% of ORFs greater than 160 bp in length.

Results

Transcriptional profiling of A. pleuropneumoniae recovered from the lung of a pig suffering from a natural infection or following growth of the bacterial isolate in BHI medium was performed. An RNA extraction protocol combining beadbeating and hot-acid-phenol was developed in order to maximize bacterial mRNA yields and quality following total RNA extraction from lung lesions. Nearly all A. pleuropneumoniae transcripts could be detected on our microarrays, and 150 genes were deemed differentially expressed in vivo during the acute phase of the infection. Our results indicate that, for example, gene apxIVA from an operon coding for RTX toxin ApxIV is highly up-regulated in vivo, and that two genes from the operon coding for type IV fimbriae (APL_0878 and APL_0879) were also up-regulated. These transcriptional profiling data, combined with previous comparative genomic hybridizations performed by our group, revealed that 66 out of the 72 up-regulated genes are conserved amongst all serotypes and that 3 of them code for products that are predicted outer membrane proteins (genes irp and APL_0959, predicted to code for a TonB-dependent receptor and a filamentous hemagglutinin/adhesin respectively) or lipoproteins (gene APL_0920). Only 4 of 72 up-regulated genes had previously been identified in controled experimental infections.

Conclusions

These genes that we have identified as up-regulated in vivo, conserved across serotypes and coding for potential outer membrane proteins represent potential candidates for the development of a cross-protective vaccine against porcine pleuropneumonia.

Genomic differences between Actinobacillus pleuropneumoniae serotypes 1 and 3 and the diversity distribution among 15 serotypes

The limited information on the genetic differences among the 15 currently known serotypes of Actinobacillus pleuropneumoniae has significantly hampered the development of typing-based diagnostic methods and multivalent vaccines. In this study, we compared the genomic differences between A. pleuropneumoniae strains CVCC259 (serotype 1) and CVCC261 (serotype 3) by representational difference analysis. Of the eight differential DNA sequences in the CVCC259 strain and 11 differential DNA sequences in the CVCC261 strain that we identified, seven represent known virulent genes, 10 encode putative proteins, and two encode hypothetical proteins. We also investigated the distribution of these 19 sequences among the 15 serotypes, and each serotype showed a different distribution pattern. The autotransporter adhesin occurred as a novel putative virulence factor in serotypes 1, 5, 7, 8, 9, and 11. Notably, the presence of wzm and wzt in serotypes 1, 9, and 11 and the diverse distribution of wzz and wzy in the other serotypes suggest the presence of different O-antigen biosynthesis pathways among serotypes. The information on the differential distribution of these DNA sequences in the 15 serotypes of A. pleuropneumoniae may contribute to future research on the pathogenic mechanisms of different serotypes, typing-based diagnosis methods, and multivalent vaccines.

malT knockout mutation invokes a stringent type gene-expression profile in Actinobacillus pleuropneumoniae in bronchoalveolar fluid

Background

Actinobacillus pleuropneumoniae causes contagious pleuropneumonia, an economically important disease of commercially reared pigs throughout the world. To cause this disease, A. pleuropneumoniae must rapidly overcome porcine pulmonary innate immune defenses. Since bronchoalveolar fluid (BALF) contains many of the innate immune and other components found in the lungs, we examined the gene expression of a virulent serovar 1 strain of A. pleuropneumoniae after exposure to concentrated BALF for 30 min.

Results

In reverse transcription PCR differential display (RT-PCR DD) experiments, A. pleuropneumoniae CM5 exposed to BALF up-regulated, among other genes, a gene predicted to encode LamB, an outer-membrane transport protein of the maltose regulon. To determine the role of the lamB and other genes of the maltose regulon in the pathogenesis of A. pleuropneumoniae, knockout mutations were created in the lamB and malT genes, the latter being the positive transcriptional regulator of the maltose regulon. Relative to the lamB mutant and the wild type, the malT mutant had a significant (P < 0.05) decrease in growth rate and an increased sensitivity to fresh porcine serum and high concentrations (more than 0.5 M) of sodium chloride. In DNA microarray experiments, the BALF-exposed malT mutant exhibited a gene-expression profile resembling that of a stringent type gene-expression profile seen in bacteria facing amino acid or carbon starvation. Genes encoding proteins for protein synthesis, energy metabolism, and DNA replication were down-regulated, while genes involved in stringent response (e.g., relA), amino acid and nucleotide biosynthesis, biofilm formation, DNA transformation, and stress response were up-regulated.

Conclusion

These results suggest that MalT may be involved in protection against some stressors and in the transport of one or more essential nutrients in BALF. Moreover, if MalT is directly or indirectly linked to the stringent response, an important global mechanism of bacterial persistence and virulence in many bacterial pathogens, it might play a role in A. pleuropneumoniae pathogenesis.

Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae

Biofilm formation is an important virulence trait of many bacterial pathogens. It has been reported in the literature that only two of the reference strains of the swine pathogen Actinobacillus pleuropneumoniae, representing serotypes 5b and 11, were able to form biofilm in vitro. In this study, we compared biofilm formation by the serotype 1 reference strain S4074 of A. pleuropneumoniae grown in five different culture media. We observed that strain S4074 of A. pleuropneumoniae is able to form biofilms after growth in one of the culture conditions tested brain heart infusion (BHI medium, supplier B). Confocal laser scanning microscopy using a fluorescent probe specific to the poly-N-acetylglucosamine (PGA) polysaccharide further confirmed biofilm formation. In accordance, biofilm formation was susceptible to dispersin B, a PGA hydrolase. Transcriptional profiles of A. pleuropneumoniae S4074 following growth in BHI-B, which allowed a robust biofilm formation, and in BHI-A, in which only a slight biofilm formation was observed, were compared. Genes such as tadC, tadD, genes with homology to autotransporter adhesins as well as genes pgaABC involved in PGA biosynthesis and genes involved in zinc transport were up-regulated after growth in BHI-B. Interestingly, biofilm formation was inhibited by zinc, which was found to be more present in BHI-A (no or slight biofilm) than in BHI-B. We also observed biofilm formation in reference strains representing serotypes 3, 4, 5a, 12 and 14 as well as in 20 of the 37 fresh field isolates tested. Our data indicate that A. pleuropneumoniae has the ability to form biofilms under appropriate growth conditions and transition from a biofilm-positive to a biofilm-negative phenotype was reversible.

Immunoproteomic analysis of outer membrane proteins and extracellular proteins of Actinobacillus pleuropneumoniae JL03 serotype 3

Background

Actinobacillus pleuropneumoniae is the causative agent of porcine contagious pleuropneumonia, a highly contagious respiratory infection in pigs, and all the 15 serotypes are able to cause disease. Current vaccines including subunit vaccines could not provide satisfactory protection against A. pleuropneumoniae. In this study, the immunoproteomic approach was applied to the analysis of extracellular and outer membrane proteins of A. pleuropneumoniae JL03 serotype 3 for the identification of novel immunogenic proteins for A. pleuropneumoniae.

Results

A total of 30 immunogenic proteins were identified from outer membrane and extracellular proteins of JL03 serotype 3, of which 6 were known antigens and 24 were novel immunogenic proteins for A. pleuropneumoniae.

Conclusion

These data provide information about novel immunogenic proteins for A. pleuropneumoniae serotype 3, and are expected to aid in development of novel vaccines against A. pleuropneumoniae.

New plasmid tools for genetic analysis of Actinobacillus pleuropneumoniae and other pasteurellaceae

We have generated a set of plasmids, based on the mobilizable shuttle vector pMIDG100, which can be used as tools for genetic manipulation of Actinobacillus pleuropneumoniae and other members of the Pasteurellaceae. A tandem reporter plasmid, pMC-Tandem, carrying promoterless xylE and gfpmut3 genes downstream of a multiple-cloning site (MCS), can be used for identification of transcriptional regulators and conditions which favor gene expression from different cloned promoters. The ability to detect transcriptional regulators using the tandem reporter system was validated in A. pleuropneumoniae using the cloned rpoE (sigma(E)) promoter (P). The resulting plasmid, pMCrpoEP, was used to identify a mutant defective in production of RseA, the negative regulator of sigma(E), among a bank of random transposon mutants, as well as to detect induction of sigma(E) following exposure of A. pleuropneumoniae to ethanol or heat shock. pMCsodCP, carrying the cloned sodC promoter of A. pleuropneumoniae, was functional in A. pleuropneumoniae, Haemophilus influenzae, Haemophilus parasuis, Mannheimia haemolytica, and Pasteurella multocida. Two general expression vectors, pMK-Express and pMC-Express, which differ in their antibiotic resistance markers (kanamycin and chloramphenicol, respectively), were constructed for the Pasteurellaceae. Both plasmids have the A. pleuropneumoniae sodC promoter upstream of the gfpmut3 gene and an extended MCS. Replacement of gfpmut3 with a gene of interest allows complementation and heterologous gene expression, as evidenced by expression of the Haemophilus ducreyi nadV gene in A. pleuropneumoniae, rendering the latter NAD independent.