Genomic approach for analysis of surface proteins in Chlamydia pneumoniae

Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability

In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.

Identification of Subunits for Novel Universal Vaccines against Three Predominant Serogroups and the Emerging O145 among Avian Pathogenic Escherichia coli by Pan-RV Pipeline

Avian pathogenic Escherichia coli, a causative agent of avian colibacillosis, has been causing serious economic losses in the poultry industry. The increase in multidrug-resistant isolates and the complexity of the serotypes of this pathogen, especially the recently reported emergence of a newly predominant serogroup of O145, make the control of this disease difficult. To address this challenge, a high-throughput screening approach, called Pan-RV (Reverse vaccinology based on pangenome analysis), is proposed to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened from the core genome of 127 Avian pathogenic Escherichia coli (APEC) genomes, and six were verified by Western blots using antisera. Overall, our research will provide a foundation for the development of an APEC subunit vaccine against avian colibacillosis. Given the exponential growth of whole-genome sequencing (WGS) data, our Pan-RV pipeline will make screening of bacterial vaccine candidates inexpensive, rapid, and efficient. IMPORTANCE With the emergence of drug resistance and the newly predominant serogroup O145, the control of Avian pathogenic Escherichia coli is facing a serious challenge; an efficient immunological method is urgently needed. Here, for the first time, we propose a high-throughput screening approach to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Importantly, using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened, and three were shown to be immunoreactive with all antisera (covering the four serogroups), thereby providing a foundation for the development of APEC subunit vaccines against avian colibacillosis. Further, our Pan-RV pipeline will provide immunological control strategies for pathogens with complex and variable genetic backgrounds such as Escherichia coli and will make screening of bacterial vaccine candidates more inexpensive, rapid, and efficient.

Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines

Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.

Combing Immunoinformatics with Pangenome Analysis To Design a Multiepitope Subunit Vaccine against Klebsiella pneumoniae K1, K2, K47, and K64

Klebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a leading causative agent of nosocomial infections, mainly infecting patients with immunosuppressive diseases. Capsular (K) serotypes K1, K2, K47, and K64 are commonly associated with higher virulence (hypervirulent Klebsiella pneumoniae), and more threateningly, isolates belonging to the last two K serotypes are also frequently associated with resistance to carbapenem (hypervirulent carbapenem-resistant Klebsiella pneumoniae). The prevalence of these isolates has posed significant threats to human health, and there are no appropriate therapies available against them. Therefore, in this study, a method combining immunoinformatics and pangenome analysis was applied for contriving a multiepitope subunit vaccine against these four threatening serotypes. To obtain cross-protection, 12 predicted conserved antigens were screened from the core genome of 274 complete Klebsiella pneumoniae genomes (KL1, KL2, KL47, and KL64), from which the epitopes of T and B cells were extracted for vaccine construction. In addition, the immunological properties, the interaction with Toll-like receptors, and the stability in a simulative humoral environment were evaluated by immunoinformatics methods, molecular docking, and molecular dynamics simulation. All of these evaluations indicated the potency of this constructed vaccine to be an effective therapeutic agent. Lastly, the cDNA of the designed vaccine was optimized and ligated to pET-28a(+) for expression vector construction. Overall, our research provides a newly cross-protective control strategy against these troublesome pathogens and paves the way for the development of a safe and effective vaccine.

IMPORTANCEKlebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a leading causative agent of nosocomial infections. Among the numerous capsular serotypes, K1, K2, K47, and K64 are commonly associated with higher virulence (hypervirulent K. pneumoniae). More threateningly, the last two serotypes are frequently associated with resistance to carbapenem (hypervirulent carbapenem-resistant K. pneumoniae). However, there is currently no therapeutic agent or vaccine specifically against these isolates. Therefore, development of a vaccine against these pathogens is very essential. In this study, for the first time, a method combining pangenome analysis, reverse vaccinology, and immunoinformatics was applied for contriving a multiepitope subunit vaccine against K. pneumoniae isolates of K1, K2, K47, and K64. Also, the immunological properties of the constructed vaccine were evaluated and its high potency was revealed. Overall, our research will pave the way for the vaccine development against these four threatening capsular serotypes of K. pneumoniae.

Combining pangenome analysis to identify potential cross-protective antigens against avian pathogenic Escherichia coli

AbstractAvian pathogenic Escherichia coli (APEC) is the bacterial pathogen of poultry colibacillosis, which causes significant economic losses to the poultry industry. The lack of an effective vaccine against multiple serotypes and the emergence of multi-resistant isolates have made the control of avian colibacillosis troublesome. To identify conserved potential vaccine candidates, 58 genomes of APEC were obtained (54 sequenced by our laboratory and 4 downloaded from NCBI). A reverse vaccinology (RV) method based on the pangenome - called Pan-RV analysis - was performed in APEC-protective protein mining for the first time. Finally, four proteins were selected, and their immunoreactivity with anti-O1, O2, and O78 serum was verified by western blotting. Our in silico method of analysis will pave the way for rapid screening of vaccine candidates and will lay the foundation for the development of a highly effective subunit vaccine controlling APEC infection.

Chlamydia abortus OmcB protein is essential for adhesion to host cells

Chlamydia abortus (C. abortus) is one of the most important zoonotic pathogens, causing a number of serious diseases. The adhesion of C. abortus to host cells is the first and crucial step in the process of infection. Outer membrane protein 2 (OmcB) is the second most abundant outer membrane protein. It has been shown to be an important adhesin of Chlamydia trachomatis and Chlamydia pneumoniae. In the present study, the OmcB gene of C. abortus was cloned and expressed in Escherichia coli, and the recombinant OmcB protein with His-tag was used to prepare polyclonal antibodies. Infectivity inhibition assays carried out with C. abortus in the presence of recombinant OmcB showed a considerable reduction (∼50%) in infectivity. Using anti-OmcB serum in infectivity inhibition assays resulted in a 30% reduction in infectivity. Anti-OmcB serum and recombinant OmcB protein in infection inhibition assays showed that OmcB is a surface-exposed protein that functions as an adhesin. The constructed deletion variant of the OmcB motif for infection inhibition assays showed that the first XBBXBX motif of the C. abortus OmcB protein is essential for binding to host cells.

Genomic Analysis of Pasteurella atlantica Provides Insight on Its Virulence Factors and Phylogeny and Highlights the Potential of Reverse Vaccinology in Aquaculture

Pasteurellosis in farmed lumpsuckers, Cyclopterus lumpus, has emerged as a serious disease in Norwegian aquaculture in recent years. Genomic characterization of the causative agent is essential in understanding the biology of the bacteria involved and in devising an efficient preventive strategy. The genomes of two clinical Pasteurella atlantica isolates were sequenced (≈2.3 Mbp), and phylogenetic analysis confirmed their position as a novel species within the Pasteurellaceae. In silico analyses revealed 11 genomic islands and 5 prophages, highlighting the potential of mobile elements as driving forces in the evolution of this species. The previously documented pathogenicity of P. atlantica is strongly supported by the current study, and 17 target genes were recognized as putative primary drivers of pathogenicity. The expression level of a predicted vaccine target, an uncharacterized adhesin protein, was significantly increased in both broth culture and following the exposure of P. atlantica to lumpsucker head kidney leucocytes. Based on in silico and functional analyses, the strongest gene target candidates will be prioritized in future vaccine development efforts to prevent future pasteurellosis outbreaks.

A primary Chlamydia trachomatis genital infection of rhesus macaques identifies new immunodominant B-cell antigens

To identify immunodominant antigens that elicit a humoral immune response following a primary and a secondary genital infection, rhesus monkeys were inoculated cervically with Chlamydia trachomatis serovar D. Serum samples were collected and probed with a protein microarray expressing 864/894 (96.4%) of the open reading frames of the C. trachomatis serovar D genome. The antibody response to the primary infection was analyzed in 72 serum samples from 12 inoculated monkeys. The following criteria were utilized to identify immunodominant antigens: proteins found to be recognized by at least 75% (9/12) of the infected monkeys with at least 15% elevations in signal intensity from week 0 to week 8 post infection. All infected monkeys developed Chlamydia specific serum antibodies. Eight proteins satisfied the selection criteria for immunodominant antigens: CT242 (OmpH-like protein), CT541 (mip), CT681 (ompA), CT381 (artJ), CT443 (omcB), CT119 (incA), CT486 (fliY), and CT110 (groEL). Of these, three antigens, CT119, CT486 and CT381, were not previously identified as immunodominant antigens using non-human primate sera. Following the secondary infection, the antibody responses to the eight immunodominant antigens were analyzed and found to be quite different in intensity and duration to the primary infection. In conclusion, these eight immunodominant antigens can now be tested for their ability to identify individuals with a primary C. trachomatis genital infection and to design vaccine strategies to protect against a primary infection with this pathogen.

Insights Into a Chlamydia pneumoniae-Specific Gene Cluster of Membrane Binding Proteins

Chlamydia pneumoniae is an obligate intracellular pathogen that causes diseases of the upper and lower respiratory tract and is linked to a number of severe and chronic conditions. Here, we describe a large, C. pneumoniae-specific cluster of 13 genes (termed mbp1-13) that encode highly homologous chlamydial proteins sharing the capacity to bind to membranes. The gene cluster is localized on the chromosome between the highly diverse adhesin-encoding pmp genes pmp15 and pmp14. Comparison of human clinical isolates to the predicted ancestral koala isolate indicates that the cluster was acquired in the ancestor and was adapted / modified during evolution. SNPs and IN/DELs within the cluster are specific to isolates taken from different human tissues and show an ongoing adaptation. Most of the cluster proteins harbor one or two domains of unknown function (DUF575 and DUF562). During ectopic expression in human cells these DUF domains are crucial for the association of cluster proteins to the endo-membrane system. Especially DUF575 which harbors a predicted transmembrane domain is important for binding to the membrane, while presence of the DUF562 seems to be of regulatory function. For Mbp1, founding member of the cluster that exhibits a very limited sequence identity to the human Rab36 protein, we found a specific binding to vesicles carrying the early endosomal marker PtdIns(3)P and the endosomal Rab GTPases Rab11 and Rab14. This binding is dependent on a predicted transmembrane domain with an α-helical / β-strand secondary structure, as the mutant version Mbp1mut, which lacks the β-strand secondary structure, shows a reduced association to PtdIns(3)P-positive membranes carrying Rab11 and Rab14. Furthermore, we could not only show that Mbp1 associates with Rab36, but found this specific Rab protein to be recruited to the early C. pneumoniae inclusion. Detection of endogenous Mbp1 and Mbp4 reveal a colocalization to the chlamydial outer membrane protein Momp on EBs. The same colocalization pattern with Momp was observed when we ectopically expressed Mbp4 in C. trachomatis. Thus, we identified a C. pneumoniae-specific cluster of 13 membrane binding proteins (Mbps) localizing to the bacterial outer membrane system.

Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach

Klebsiella pneumoniae is declared as antibiotic resistant by WHO, with the critical urgency of developing novel antimicrobial therapeutics as drug resistance is the second most dangerous threat after terrorism. Besides many attempts still, there is no effective vaccine available against K. pneumoniae. By utilizing all the available proteomic data we prioritized the novel proteins ideal for vaccine development using bioinformatics tools and techniques. Among the huge data, eight proteins passed all the barriers and were considered ideal candidates for vaccine development. These include: copper silver efflux system outer membrane protein (CusC), outer membrane porin protein (OmpN), Fe⁺⁺ enterobactin transporter substrate binding protein (fepB), zinc transporter substrate binding protein (ZnuA), ribonuclease HI, tellurite resistant methyltransferase (the B), and two uncharacterized hypothetical proteins (WP_002918223 and WP_002892366). These proteins were also subjected to epitope analysis and were found best for developing subunit vaccine against K. pneumoniae. The study shows that the potential vaccine targets are sufficiently efficient being virulent, of outer membranous origin and can be proposed for the DNA third-generation vaccines development that would help to cope up infections caused by multidrug-resistant K. pneumoniae.

In silico Design of a Multivalent Vaccine Against Candida albicans

Invasive candidiasis (IC) is the most common nosocomial infection and a leading cause of mycoses-related deaths. High-systemic toxicity and emergence of antifungal-resistant species warrant the development of newer preventive approaches against IC. Here, we have adopted an immunotherapeutic peptide vaccine-based approach, to enhance the body's immune response against invasive candida infections. Using computational tools, we screened the entire candida proteome (6030 proteins) and identified the most immunodominant HLA class I, HLA class II and B- cell epitopes. By further immunoinformatic analyses for enhanced vaccine efficacy, we selected the 18- most promising epitopes, which were joined together using molecular linkers to create a multivalent recombinant protein against Candida albicans (mvPC). To increase mvPC's immunogenicity, we added a synthetic adjuvant (RS09) to the mvPC design. The selected mvPC epitopes are homologous against all currently available annotated reference sequences of 22 C. albicans strains, thus offering a higher coverage and greater protective response. A major advantage of the current vaccine approach is mvPC's multivalent nature (recognizing multiple-epitopes), which is likely to provide enhanced protection against complex candida antigens. Here, we describe the computational analyses leading to mvPC design.

PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome

Background

A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology.

Results

We have designed an integrative computational pipeline term as “PanRV” that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.

Conclusion

The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2713-9) contains supplementary material, which is available to authorized users.

Proteomics, Bioinformatics and Structure-Function Antigen Mining For Gonorrhea Vaccines

Expanding efforts to develop preventive gonorrhea vaccines is critical because of the serious health consequences combined with the prevalence and the dire possibility of untreatable gonorrhea. Reverse vaccinology, which includes genome and proteome mining, has proven successful in the discovery of vaccine candidates against many pathogenic bacteria. Here, we describe proteomic applications including comprehensive, quantitative proteomic platforms and immunoproteomics coupled with broad-ranging bioinformatics that have been applied for antigen mining to develop gonorrhea vaccine(s). We further focus on outlining the vaccine candidate decision tree, describe the structure-function of novel proteome-derived antigens as well as ways to gain insights into their roles in the cell envelope, and underscore new lessons learned about the fascinating biology of Neisseria gonorrhoeae.

A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen

Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and ROP18, which are T. gondii virulence determinants. The chance of randomly selecting a ROP protein was 0.2% given 8263 sequences. We conclude that the approach described is a valuable addition to other in silico approaches to identify vaccines candidates worthy of laboratory validation and could be adapted for other apicomplexan parasite species (with appropriate data).

BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design against Burkholderia pseudomallei

Due to significant advances in computational biology, protein prediction, together with antigen and epitope design, have rapidly moved from conventional methods, based on experimental approaches, to in silico-based bioinformatics methods. In this context, we report a reverse vaccinology study that identified a panel of 104 candidate antigens from the Gram-negative bacterial pathogen Burkholderia pseudomallei, which is responsible for the disease melioidosis. B. pseudomallei can cause fatal sepsis in endemic populations in the tropical regions of the world and treatment with antibiotics is mostly ineffective. With the aim of identifying potential vaccine candidates, we report the experimental validation of predicted antigen and type I fimbrial subunit, BPSL1626, which we show is able to recognize and bind human antibodies from the sera of Burkholderia infected patients and to stimulate T-lymphocytes in vitro. The prerequisite for a melioidosis vaccine, in fact, is that both antibody- and cell-mediated immune responses must be triggered. In order to reveal potential antigenic regions of the protein that may aid immunogen re-design, we also report the crystal structure of BPSL1626 at 1.9 Å resolution on which structure-based epitope predictions were based. Overall, our data suggest that BPSL1626 and three epitope regions here-identified can represent viable candidates as potential antigenic molecules.

In silico prediction of T- and B-cell epitopes in PmpD: First step towards to the design of a Chlamydia trachomatis vaccine

BACKGROUND

Chlamydia trachomatis is the most common sexually transmitted bacterial infection globally. Currently, there are no vaccines available despite the efforts made to develop a protective one. Polymorphic membrane protein D (PmpD) is an attractive immunogen candidate as it is conserved among strains and it is target of neutralizing antibodies. However, its high molecular weight and its complex structure make it difficult to handle by recombinant DNA techniques. Our aim is to predict B-cell and T-cell epitopes of PmpD.

METHOD

A sequence (Genbank AAK69391.2) having 99-100% identity with various serovars of C. trachomatis was used for predictions. NetMHC and NetMHCII were used for T-cell epitope linked to MHC I or MHC II alleles prediction, respectively. BepiPred predicted linear B-cell epitopes. For three dimensional epitopes, PmpD was homology-modeled by Raptor X. Surface epitopes were predicted on its globular structure using DiscoTope.

RESULTS

NetMHC predicted 271 T-cell epitopes of 9-12aa with weak affinity, and 70 with strong affinity to MHC I molecules. NetMHCII predicted 2903 T-cell epitopes of 15aa with weak affinity, and 742 with strong affinity to MHC II molecules. Twenty four linear B-cell epitopes were predicted. Raptor X was able to model 91% of the three-dimensional structure whereas 57 residues of discontinuous epitopes were suggested by DiscoTope. Six regions containing B-cell and T-cell epitopes were identified by at least two predictors.

CONCLUSIONS

PmpD has potential B-cell and T-cell epitopes distributed throughout the sequence. Thus, several fragments were identified as valuable candidates for subunit vaccines against C. trachomatis.

Comparative proteomic analysis of Xanthomonas citri ssp. citri periplasmic proteins reveals changes in cellular envelope metabolism during in vitro pathogenicity induction

Citrus canker is a plant disease caused by Gram-negative bacteria from the genus Xanthomonas. The most virulent species is Xanthomonas citri ssp. citri (XAC), which attacks a wide range of citrus hosts. Differential proteomic analysis of the periplasm-enriched fraction was performed for XAC cells grown in pathogenicity-inducing (XAM-M) and pathogenicity-non-inducing (nutrient broth) media using two-dimensional electrophoresis combined with liquid chromatography-tandem mass spectrometry. Amongst the 40 proteins identified, transglycosylase was detected in a highly abundant spot in XAC cells grown under inducing condition. Additional up-regulated proteins related to cellular envelope metabolism included glucose-1-phosphate thymidylyltransferase, dTDP-4-dehydrorhamnose-3,5-epimerase and peptidyl-prolyl cis-trans-isomerase. Phosphoglucomutase and superoxide dismutase proteins, known to be involved in pathogenicity in other Xanthomonas species or organisms, were also detected. Western blot and quantitative real-time polymerase chain reaction analyses for transglycosylase and superoxide dismutase confirmed that these proteins were up-regulated under inducing condition, consistent with the proteomic results. Multiple spots for the 60-kDa chaperonin and glyceraldehyde-3-phosphate dehydrogenase were identified, suggesting the presence of post-translational modifications. We propose that substantial alterations in cellular envelope metabolism occur during the XAC infectious process, which are related to several aspects, from defence against reactive oxygen species to exopolysaccharide synthesis. Our results provide new candidates for virulence-related proteins, whose abundance correlates with the induction of pathogenicity and virulence genes, such as hrpD6, hrpG, hrpB7, hpa1 and hrpX. The results present new potential targets against XAC to be investigated in further functional studies.

Immunoprotective potential of BamA, the outer membrane protein assembly factor, against MDR Acinetobacter baumannii

Acinetobacter baumannii infections are responsible for major health problems in immunocompromised patients particularly in intensive care units. Due to rapid acquisition of and also inherent drug resistance, a vaccine is an effective treatment option against this pathogen. BamA, an outer membrane β-barrel assembly protein, was identified in A. baumannii as potential vaccine candidate by in silico analysis. The immunoprotective efficacy of this highly conserved protein was investigated against a virulent multidrug resistant clinical isolate using murine pneumonia model. Recombinant BamA elicited a high IgG antibody titer (160000) in mice. Opsonophagocytic killing assay showed non-neutrilizing, opsonizing antibodies with combinatorial bactericidal activity of antibodies and complement components. Active and passive immunization protected 80 and 60% mice respectively against intranasal challenge with lethal dose (10⁹ CFU) of virulent A. baumannii along with efficient clearance of bacteria in mice lungs and reduction in levels of pro-inflammatory cytokines viz. TNF-α, IL-6 and IL-1β in sera and lung tissue homogenate. Increase in levels of IL-10, an anti-inflammatory cytokine and reduction of neutrophils in lungs facilitated the control of infection. This study demonstrates the potential of BamA as effective vaccine candidate and a promising target for antibody-based therapy to protect against MDR A. baumannii infections.

Towards developing a vaccine for rheumatic heart disease

Rheumatic heart disease (RHD) is the most serious manifestations of rheumatic fever, which is caused by group A Streptococcus (GAS or Streptococcus pyogenes) infection. RHD is an auto immune sequelae of GAS pharyngitis, rather than the direct bacterial infection of the heart, which leads to chronic heart valve damage. Although antibiotics like penicillin are effective against GAS infection, improper medical care such as poor patient compliance, overcrowding, poverty, and repeated exposure to GAS, leads to acute rheumatic fever and RHD. Thus, efforts have been put forth towards developing a vaccine. However, a potential global vaccine is yet to be identified due to the widespread diversity of S. pyogenes strains and cross reactivity of streptococcal proteins with host tissues. In this review, we discuss the available vaccine targets of S. pyogenes and the significance of in silico approaches in designing a vaccine for RHD.

VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

Background

With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases. A pipeline, VacSol, is designed here based on a similar approach to predict putative vaccine candidates both rapidly and efficiently.

Results

VacSol, a new pipeline introduced here, is a highly scalable, multi-mode, and configurable software designed to automate the high throughput in silico vaccine candidate prediction process for the identification of putative vaccine candidates against the proteome of bacterial pathogens. Vaccine candidates are screened using integrated, well-known and robust algorithms/tools for proteome analysis, and the results from the VacSol software are presented in five different formats by taking proteome sequence as input in FASTA file format. The utility of VacSol is tested and compared with published data and using the Helicobacter pylori 26695 reference strain as a benchmark.

Conclusion

VacSol rapidly and efficiently screens the whole bacterial pathogen proteome to identify a few predicted putative vaccine candidate proteins. This pipeline has the potential to save computational costs and time by efficiently reducing false positive candidate hits. VacSol results do not depend on any universal set of rules and may vary based on the provided input. It is freely available to download from: https://sourceforge.net/projects/vacsol/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1540-0) contains supplementary material, which is available to authorized users.

The Chlamydia pneumoniae Adhesin Pmp21 Forms Oligomers with Adhesive Properties

Chlamydiae sp. are obligate intracellular pathogens that cause a variety of diseases in humans. The adhesion of Chlamydiae to the eukaryotic host cell is a pivotal step in pathogenesis. The adhesin family of polymorphic membrane proteins (Pmp) in Chlamydia pneumoniae consists of 21 members. Pmp21 binds to the epidermal growth factor receptor (EGFR). Pmps contain large numbers of FXXN (where X is any amino acid) and GGA(I/L/V) motifs. At least two of these motifs are crucial for adhesion by certain Pmp21 fragments. Here we describe how the two FXXN motifs in Pmp21-D (D-Wt), a domain of Pmp21, influence its self-interaction, folding, and adhesive capacities. Refolded D-Wt molecules form oligomers with high sedimentation values (8-85 S). These oligomers take the form of elongated protofibrils, which exhibit Thioflavin T fluorescence, like the amyloid protein fragment β42. A mutant version of Pmp21-D (D-Mt), with FXXN motifs replaced by SXXV, shows a markedly reduced capacity to form oligomers. Secondary-structure assays revealed that monomers of both variants exist predominantly as random coils, whereas the oligomers form predominantly β-sheets. Adhesion studies revealed that oligomers of D-Wt (D-Wt-O) mediate significantly enhanced binding to human epithelial cells relative to D-Mt-O and monomeric protein species. Moreover, D-Wt-O binds EGFR more efficiently than D-Wt monomers. Importantly, pretreatment of human cells with D-Wt-O reduces infectivity upon subsequent challenge with C. pneumoniae more effectively than all other protein species. Hence, the FXXN motif in D-Wt induces the formation of β-sheet-rich oligomeric protofibrils, which are important for adhesion to, and subsequent infection of human cells.

Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis

The obligate intracellular developmental cycle of Chlamydia trachomatis presents significant challenges in defining its proteome. In this study we have applied quantitative proteomics to both the intracellular reticulate body (RB) and the extracellular elementary body (EB) from C. trachomatis. We used C. trachomatis L2 as a model chlamydial isolate for our study since it has a high infectivity:particle ratio and there is an excellent quality genome sequence. EBs and RBs (>99% pure) were quantified by chromosomal and plasmid copy number using PCR, from which the concentrations of chlamydial proteins per bacterial cell/genome were determined. RBs harvested at 15h post infection (PI) were purified by three successive rounds of gradient centrifugation. This is the earliest possible time to obtain purified RBs, free from host cell components in quantity, within the constraints of the technology. EBs were purified at 48h PI. We then used two-dimensional reverse phase UPLC to fractionate RB or EB peptides before mass spectroscopic analysis, providing absolute amount estimates of chlamydial proteins. The ability to express the data as molecules per cell gave ranking in both abundance and energy requirements for synthesis, allowing meaningful identification of rate-limiting components. The study assigned 562 proteins with high confidence and provided absolute estimates of protein concentration for 489 proteins. Interestingly, the data showed an increase in TTS capacity at 15h PI. Most of the enzymes involved in peptidoglycan biosynthesis were detected along with high levels of muramidase (in EBs) suggesting breakdown of peptidoglycan occurs in the non-dividing form of the microorganism. All the genome-encoded enzymes for glycolysis, pentose phosphate pathway and tricarboxylic acid cycle were identified and quantified; these data supported the observation that the EB is metabolically active. The availability of detailed, accurate quantitative proteomic data will be invaluable for investigations into gene regulation and function.

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

Chlamydia pneumoniae acute liver infection affects hepatic cholesterol and triglyceride metabolism in mice

OBJECTIVE

Chlamydia pneumoniae has been linked to atherosclerosis, strictly associated with hyperlipidemia. The liver plays a central role in the regulation of lipid metabolism. Since in animal models C. pneumoniae can be found at hepatic level, this study aims to elucidate whether C. pneumoniae infection accelerates atherosclerosis by affecting lipid metabolism.

METHODS

Thirty Balb/c mice were challenged intra-peritoneally with C. pneumoniae elementary bodies and thirty with Chlamydia trachomatis, serovar D. Thirty mice were injected with sucrose-phosphate-glutamate buffer, as negative controls. Seven days after infection, liver samples were examined both for presence of chlamydia and expression of genes involved in inflammation and lipid metabolism.

RESULTS

C. pneumoniae was isolated from 26 liver homogenates, whereas C. trachomatis was never re-cultivated (P < 0.001). C. pneumoniae infected mice showed significantly increased serum cholesterol and triglycerides levels compared both with negative controls (P < 0.001 and P = 0.0197, respectively) and C. trachomatis infected mice (P < 0.001). Liver bile acids were significantly reduced in C. pneumoniae compared to controls and C. trachomatis infected mice. In C. pneumoniae infected livers, cholesterol 7α-hydroxylase (Cyp7a1) and low-density lipoprotein receptor (Ldlr) mRNA levels were reduced, while inducible degrader of the low-density lipoprotein receptor (Idol) expression was increased. Hypertriglyceridemia was associated to reduced expression of hepatic carnitine palmitoyltransferase-1a (Cpt1a) and medium chain acyl-Coenzyme A dehydrogenase (Acadm). Pro-inflammatory cytokines gene expression was increased compared to negative controls. Conversely, in C. trachomatis infected animals, normal serum lipid levels were associated with elevated pro-inflammatory cytokines gene expression, linked to only a mild disturbance of lipid regulatory genes.

CONCLUSION

Our results indicate that C. pneumoniae mouse liver infection induces dyslipidemic effects with significant modifications of genes involved in lipid metabolism.

OmpA family proteins and Pmp-like autotransporter: new adhesins of Waddlia chondrophila

Waddlia chondrophila is a obligate intracellular bacterium belonging to the Chlamydiales order, a clade that also includes the well-known classical Chlamydia responsible for a number of severe human and animal diseases. Waddlia is an emerging pathogen associated with adverse pregnancy outcomes in humans and abortion in ruminants. Adhesion to the host cell is an essential prerequisite for survival of every strict intracellular bacteria and, in classical Chlamydia, this step is partially mediated by polymorphic outer membrane proteins (Pmps), a family of highly diverse autotransporters that represent about 15% of the bacterial coding capacity. Waddlia chondrophila genome however only encodes one putative Pmp-like protein. Using a proteomic approach, we identified several bacterial proteins potentially implicated in the adhesion process and we characterized their expression during the replication cycle of the bacteria. In addition, we demonstrated that the Waddlia Pmp-like autotransporter as well as OmpA2 and OmpA3, two members of the extended Waddlia OmpA protein family, exhibit adhesive properties on epithelial cells. We hypothesize that the large diversity of the OmpA protein family is linked to the wide host range of these bacteria that are able to enter and multiply in various host cells ranging from protozoa to mammalian and fish cells.

Nonclassically secreted proteins as possible antigens for vaccine development: a reverse vaccinology approach

Reverse vaccinology strategies have already been applied to a variety of microorganisms and have contributed significantly to vaccine development. However, most of the studies focused on an individual organism or on proteins with signature sequence motifs commonly found in known secreted proteins from bacteria. In this work, we applied a reverse vaccinology strategy based on conservation, virulence, and nonclassically surface exposure criterions to identify potential antigens in two microorganisms with significant degree of genomic plasticity among isolates (Streptococcus pneumoniae and Leptospira spp.), which imposes a major limitation to the production of a multistrain component vaccine. PSORTb 3.0.2 was run to predict the subcellular localization of the proteins. OrthoMCL was run to identify groups of the most conserved proteins between strains. Virulence prediction was done for the most conserved proteins, and SecretomeP was run to predict the nonclassically secreted proteins among the potential virulence factors. Based on the above criteria, we identified 37 proteins conserved between 16 genomes of S. pneumoniae and 12 proteins conserved between 5 leptospiral genomes as potential vaccine candidates.

Enhancing in silico protein-based vaccine discovery for eukaryotic pathogens using predicted peptide-MHC binding and peptide conservation scores

Given thousands of proteins constituting a eukaryotic pathogen, the principal objective for a high-throughput in silico vaccine discovery pipeline is to select those proteins worthy of laboratory validation. Accurate prediction of T-cell epitopes on protein antigens is one crucial piece of evidence that would aid in this selection. Prediction of peptides recognised by T-cell receptors have to date proved to be of insufficient accuracy. The in silico approach is consequently reliant on an indirect method, which involves the prediction of peptides binding to major histocompatibility complex (MHC) molecules. There is no guarantee nevertheless that predicted peptide-MHC complexes will be presented by antigen-presenting cells and/or recognised by cognate T-cell receptors. The aim of this study was to determine if predicted peptide-MHC binding scores could provide contributing evidence to establish a protein's potential as a vaccine. Using T-Cell MHC class I binding prediction tools provided by the Immune Epitope Database and Analysis Resource, peptide binding affinity to 76 common MHC I alleles were predicted for 160 Toxoplasma gondii proteins: 75 taken from published studies represented proteins known or expected to induce T-cell immune responses and 85 considered less likely vaccine candidates. The results show there is no universal set of rules that can be applied directly to binding scores to distinguish a vaccine from a non-vaccine candidate. We present, however, two proposed strategies exploiting binding scores that provide supporting evidence that a protein is likely to induce a T-cell immune response-one using random forest (a machine learning algorithm) with a 72% sensitivity and 82.4% specificity and the other, using amino acid conservation scores with a 74.6% sensitivity and 70.5% specificity when applied to the 160 benchmark proteins. More importantly, the binding score strategies are valuable evidence contributors to the overall in silico vaccine discovery pool of evidence.

Discovering a vaccine against neosporosis using computers: is it feasible?

A vaccine is urgently needed to prevent cattle neosporosis. This infectious disease is caused by the parasite Neospora caninum, a complex biological system with multifaceted life cycles. An in silico vaccine discovery approach attempts to transform digital abstractions of this system into adequate knowledge to predict candidates. Researchers need current information to implement such an approach, such as understanding evasion mechanisms of the immune system, type of immune response to elicit, availability of data and prediction programs, and statistical models to analyze predictions. Taken together, an in silico approach involves assembly of an intricate jigsaw of interdisciplinary and interdependent knowledge. In this review, we focus on the approach influencing vaccine development against Neospora caninum, which can be generalized to other pathogenic apicomplexans.

All subtypes of the Pmp adhesin family are implicated in chlamydial virulence and show species-specific function

The bacterial pathogens Chlamydia trachomatis and C. pneumoniae are obligate intracellular parasites, cause a number of serious diseases, and can infect various cell types in humans. Chlamydial infections are probably initiated by binding of the bacterial outer membrane protein OmcB to host cell glycosaminoglycans (GAGs). Here, we show that all nine members of the polymorphic membrane protein (Pmp) family of C. trachomatis mediate adhesion to human epithelial and endothelial cells. Importantly, exposure of infectious particles to soluble recombinant Pmps blocks subsequent infection, thus implicating an important function of the entire protein family in the infection process. Analogous experiments with pairs of recombinant Pmps or a combination of Pmp and OmcB revealed that all Pmps probably act in an adhesion pathway that is distinct from the OmcB-GAG pathway. Finally, we provide evidence that the Pmps of C. trachomatis and C. pneumoniae exhibit species and tissue specificity. These findings argue for the involvement of C. trachomatis Pmps in the initial phase of infection and suggest that they may interact with a receptor other than the epidermal growth factor receptor recently identified for their counterparts in C. pneumoniae.

Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology

We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of protein candidates determined by a set of machine learning algorithms. Vacceed has the potential to save time and money by reducing the number of false candidates allocated for laboratory validation. Vacceed, if required, can also predict protein sequences from the pathogen's genome.

AVAILABILITY AND IMPLEMENTATION

Vacceed is tested on Linux and can be freely downloaded from https://github.com/sgoodswe/vacceed/releases (includes a worked example with sample data). Vacceed User Guide can be obtained from https://github.com/sgoodswe/vacceed.

Identification of Sphingomyelinase on the Surface of Chlamydia pneumoniae: Possible Role in the Entry into Its Host Cells

We have recently suggested a novel mechanism, autoendocytosis, for the entry of certain microbes into their hosts, with a key role played by the sphingomyelinase-catalyzed topical conversion of sphingomyelin to ceramide, the differences in the biophysical properties of these two lipids providing the driving force. The only requirement for such microbes to utilize this mechanism is that they should have a catalytically active SMase on their outer surface while the target cells should expose sphingomyelin in the external leaflet of their plasma membrane. In pursuit of possible microbial candidates, which could utilize this putative mechanism, we conducted a sequence similarity search for SMase. Because of the intriguing cellular and biochemical characteristics of the poorly understood entry of Chlamydia into its host cells these microbes were of particular interest. SMase activity was measured in vitro from isolated C. pneumoniae elementary bodies (EB) and in the lysate from E. coli cells transfected with a plasmid expressing CPn0300 protein having sequence similarity to SMase. Finally, pretreatment of host cells with exogenous SMase resulting in loss plasma membrane sphingomyelin attenuated attachment of EB.

Designing vaccines for the twenty-first century society

The history of vaccination clearly demonstrates that vaccines have been highly successful in preventing infectious diseases, reducing significantly the incidence of childhood diseases and mortality. However, many infections are still not preventable with the currently available vaccines and they represent a major cause of mortality worldwide. In the twenty-first century, the innovation brought by novel technologies in antigen discovery and formulation together with a deeper knowledge of the human immune responses are paving the way for the development of new vaccines. Final goal will be to rationally design effective vaccines where conventional approaches have failed.

In silico approach for the identification of immunological properties of enolase from Trypanosoma cruzi and its possible usefulness as vaccine in Chagas disease

Nowadays, Chagas disease is a major health problem in Latin America that has been disseminated also into non-endemic countries. Currently, a vaccine against Chagas disease does not exist. In the present study, the gene encoding Trypanosoma cruzi enolase (TcENO) was amplified, cloned, and sequenced and the recombinant protein was purified. We used in silico and an experimental assay to investigate the immunological role of TcENO. The in silico assays showed that TcENO sequence contains characteristic motifs of enolase; additionally, a transmembranal region was identified, and this could indicate the potential membrane localization of TcENO. Moreover, both B lymphocyte and cytotoxic T lymphocytes (CTL) predicted epitopes were localized; these results suggest the possibility that TcENO can develop both humoral and cellular immune responses. Furthermore, the presence of antibodies was verified by western blot assays, showing that the purified recombinant protein was detected by sera from experimentally infected mice and sera of patients with Chagas disease. These results indicate that TcENO is immunogenic and could be used as a vaccine candidate.

Genome-derived vaccines

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

Characterization of the interaction between the chlamydial adhesin OmcB and the human host cell

In a previous study, we reported that the OmcB protein from Chlamydia pneumoniae mediates adhesion of the infectious elementary body to human HEp-2 cells by interacting with heparin/heparan sulfate-like glycosaminoglycans (GAGs) via basic amino acids located in the first of a pair of XBBXBX heparin-binding motifs (K. Moelleken and J. H. Hegemann, Mol. Microbiol. 67:403-419, 2008). In the present study, we show that the basic amino acid at position 57 (arginine) in the first XBBXBX motif, the basic amino acid at position 61 (arginine) in the second motif, and another amino acid (lysine 69) C terminal to it play key roles in the interaction. In addition, we show that discrimination between heparin-dependent and -independent adhesion by C. trachomatis OmcBs is entirely dependent on three variable amino acids in the so-called variable domain C terminal to the conserved XBBXBX motif. Here, the predicted conformational change in the secondary structure induced by the proline at position 66 seems to be crucial for heparin recognition. Finally, we performed neutralization experiments using different anti-heparan sulfate antibodies to gain insight into the nature of the GAGs recognized by OmcB. The results suggest that C. trachomatis serovar L2 OmcB interacts with 6-O-sulfated domains of heparan sulfate, while C. pneumoniae OmcB apparently interacts with domains of heparan sulfate harboring a diverse subset of O-sulfations.

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

Background

Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs.

Results

A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset.

Conclusions

Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html

Imaging of the skeletal muscle metastases

Preclinical Research

Copyright 2011 Wiley-Liss, Inc., A Wiley CompanyThis article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.

Omics technologies include genomics, transcriptomics, proteomics, metabolomics, and immunomics. These technologies have been used in vaccine research, which can be summarized using the term “vaccinomics.” These omics technologies combined with advanced bioinformatics analysis form the core of “systems vaccinology.” Omics technologies provide powerful methods in vaccine target identification. The genomics‐based reverse vaccinology starts with predicting vaccine protein candidates through in silico bioinformatics analysis of genome sequences. The VIOLIN Vaxign vaccine design program (http://www.violinet.org/vaxign) is the first web‐based vaccine target prediction software based on the reverse vaccinology strategy. Systematic transcriptomics and proteomics analyses facilitate rational vaccine target identification by detesting genome‐wide gene expression profiles. Immunomics is the study of the set of antigens recognized by host immune systems and has also been used for efficient vaccine target prediction. With the large amount of omics data available, it is necessary to integrate various vaccine data using ontologies, including the Gene Ontology (GO) and Vaccine Ontology (VO), for more efficient vaccine target prediction and assessment. All these omics technologies combined with advanced bioinformatics analysis methods for a systems biology‐based vaccine target prediction strategy. This article reviews the various omics technologies and how they can be used in vaccine target identification.

Recombinant outer membrane vesicles carrying Chlamydia muridarum HtrA induce antibodies that neutralize chlamydial infection in vitro

BACKGROUND

Outer membrane vesicles (OMVs) are spheroid particles released by all Gram-negative bacteria as a result of the budding out of the outer membrane. Since they carry many of the bacterial surface-associated proteins and feature a potent built-in adjuvanticity, OMVs are being utilized as vaccines, some of which commercially available. Recently, methods for manipulating the protein content of OMVs have been proposed, thus making OMVs a promising platform for recombinant, multivalent vaccines development.

METHODS

Chlamydia muridarum DO serine protease HtrA, an antigen which stimulates strong humoral and cellular responses in mice and humans, was expressed in Escherichia coli fused to the OmpA leader sequence to deliver it to the OMV compartment. Purified OMVs carrying HtrA (CM rHtrA-OMV) were analyzed for their capacity to induce antibodies capable of neutralizing Chlamydia infection of LLC-MK2 cells in vitro.

RESULTS

CM rHtrA-OMV immunization in mice induced antibodies that neutralize Chlamydial invasion as judged by an in vitro infectivity assay. This was remarkably different from what observed with an enzymatically functional recombinant HtrA expressed in, and purified from the E. coli cytoplasm (CM rHtrA). The difference in functionality between anti-CM rHtrA and anti-CM rHtrA-OMV antibodies was associated to a different pattern of protein epitopes recognition. The epitope recognition profile of anti-CM HtrA-OMV antibodies was similar to that induced in mice during Chlamydial infection.

CONCLUSIONS

When expressed in OMVs HtrA appears to assume a conformation similar to the native one and this results in the elicitation of functional immune responses. These data further support the potentiality of OMVs as vaccine platform.

Vaccines, reverse vaccinology, and bacterial pathogenesis

Advances in genomics and innovative strategies such as reverse vaccinology have changed the concepts and approaches to vaccine candidate selection and design. Genome mining and blind selection of novel antigens provide a novel route to investigate the mechanisms that underpin pathogenesis. The resulting lists of novel candidates are revealing new aspects of pathogenesis of target organisms, which in turn drives the rational design of optimal vaccine antigens. Here we use the discovery, characterization, and exploitation of fHbp, a vaccine candidate and key virulence factor of meningococcus, as an illustrative case in point. Applying genomic approaches to study both the pathogen and host will ultimately increase our fundamental understanding of pathogen biology, mechanisms responsible for the development of protective immunity, and guide next-generation vaccine design.

Identification of the immunogenic spore and vegetative proteins of Bacillus anthracis vaccine strain A16R

Immunoproteomics was used to screen the immunogenic spore and vegetative proteins of Bacillus anthracis vaccine strain A16R. The spore and vegetative proteins were separated by 2D gel electrophoresis and transferred to polyvinylidene difluoride membranes, and then western blotting was performed with rabbit immune serum against B.anthracis live spores. Immunogenic spots were cut and digested by trypsin. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry was performed to identify the proteins. As a result, 11 and 45 immunogenic proteins were identified in the spores and vegetative cells, respectively; 26 of which have not been reported previously. To verify their immunogenicity, 12 of the identified proteins were selected to be expressed, and the immune sera from the mice vaccinated by the 12 expressed proteins, except BA0887, had a specific western blot band with the A16R whole cellular lytic proteins. Some of these immunogenic proteins might be used as novel vaccine candidates themselves or for enhancing the protective efficacy of a protective-antigen-based vaccine.