Antibacterial vaccine design using genomics and proteomics

Proteomics in support of immunotherapy: contribution to model-based precision medicine

INTRODUCTION

Proteomics encompasses a wide and expanding range of methods to identify, characterize, and quantify thousands of proteins from a variety of biological samples, including blood samples, tumors, and tissues. Such methods are supportive of various forms of immunotherapy applied to chronic conditions such as allergies, autoimmune diseases, cancers, and infectious diseases.

AREAS COVERED

In support of immunotherapy, proteomics based on mass spectrometry has multiple specific applications related to (i) disease modeling and patient stratification, (ii) antigen/ autoantigen/neoantigen/ allergen identification, (iii) characterization of proteins and monoclonal antibodies used for immunotherapeutic or diagnostic purposes, (iv) identification of biomarkers and companion diagnostics and (v) monitoring by immunoproteomics of immune responses elicited in the course of the disease or following immunotherapy.

EXPERT OPINION

Proteomics contributes as an enabling technology to an evolution of immunotherapy toward a precision medicine approach aiming to better tailor treatments to patients' specificities in multiple disease areas. This trend is favored by a better understanding through multi-omics profiling of both the patient's characteristics, his/her immune status as well as of the features of the immunotherapeutic drug.

Identification of vaccine candidate proteins in Ureaplasma urealyticum causing infertility

BACKGROUND

Ureaplasma urealyticum has gained resistance to number of antibiotics and has been of the greatest concerns nowadays. The treatment options remain extremely low due to the increased levels of intrinsic resistance gained by the pathogen.

AIM

The present study focuses on designing a peptide-based vaccine as there is no vaccine available for the pathogen.

MATERIALS AND METHODS

All the protein sequences of pathogen were collected and examined using various in silico methods to identify the most immunogenic proteins. The study identifies the proteins which are antigenic in nature which induce the immune response, which lends to quick response of immune system on reinfection. The study describes peptide-based vaccine against U. urealyticum using molecular docking and molecular dynamics simulation approach.

RESULTS

The study identifies novel putative vaccine candidate proteins that are antigenic, membrane bound and non-allergenic.

CONCLUSION

The results of the study imply that the vaccine candidate proteins identified may bring about vigorous enduring defensive immunity against U. urealyticum.

The surface lipoproteins of gram-negative bacteria: Protectors and foragers in harsh environments

Gram-negative pathogens are enveloped by an outer membrane that serves as a double-edged sword: On the one hand, it provides a layer of protection for the bacterium from environmental insults, including other bacteria and the host immune system. On the other hand, it restricts movement of vital nutrients into the cell and provides a plethora of antigens that can be detected by host immune systems. One strategy used to overcome these limitations is the decoration of the outer surface of gram-negative bacteria with proteins tethered to the outer membrane through a lipid anchor. These surface lipoproteins (SLPs) fulfill critical roles in immune evasion and nutrient acquisition, but as more bacterial genomes are sequenced, we are beginning to discover their prevalence and their different roles and mechanisms and importantly how we can exploit them as antimicrobial targets. This review will focus on representative SLPs that gram-negative bacteria use to overcome host innate immunity, specifically the areas of nutritional immunity and complement system evasion. We elaborate on the structures of some notable SLPs required for binding target molecules in hosts and how this information can be used alongside bioinformatics to understand mechanisms of binding and in the discovery of new SLPs. This information provides a foundation for the development of therapeutics and the design of vaccine antigens.

Advances and Prospects in Vaccine Development against Enterococci

Enterococci are the second most common Gram-positive pathogen responsible for nosocomial infections. Due to the limited number of new antibiotics that reach the medical practice and the resistance of enterococci to the current antibiotic options, passive and active immunotherapies have emerged as a potential prevention and/or treatment strategy against this opportunistic pathogen. In this review, we explore the pathogenicity of these bacteria and their interaction with the host immune response. We provide an overview of the capsular polysaccharides and surface-associated proteins that have been described as potential antigens in anti-enterococcal vaccine formulations. In addition, we describe the current status in vaccine development against enterococci and address the importance and the current advances toward the development of well-defined vaccines with broad coverage against enterococci.

Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome

Infections by the Burkholderia cepacia complex (Bcc) remain seriously life threatening to cystic fibrosis (CF) patients, and no effective eradication is available. A vaccine to protect patients against Bcc infections is a highly attractive therapeutic option, but none is available. A strategy combining the bioinformatics identification of putative surface-exposed proteins with an experimental approach encompassing the “shaving” of surface-exposed proteins with trypsin followed by peptide identification by liquid chromatography and mass spectrometry is here reported. The methodology allowed the bioinformatics identification of 263 potentially surface-exposed proteins, 16 of them also experimentally identified by the “shaving” approach. Of the proteins identified, 143 have a high probability of containing B-cell epitopes that are surface-exposed. The immunogenicity of three of these proteins was demonstrated using serum samples from Bcc-infected CF patients and Western blotting, validating the usefulness of this methodology in identifying potentially immunogenic surface-exposed proteins that might be used for the development of Bcc-protective vaccines.

Vaccinology: The art of putting together the right ingredients

Historically vaccines were produced using whole attenuated or killed pathogens and still a large proportion of current vaccines utilizes such procedure. However, for safety and quality reasons the development of novel vaccines is preferentially based on the selection and use of specific pathogen components which alone are capable of eliciting protective immune responses against the pathogens they derived from. The big challenge for vaccinologists is how to select the right antigens and to combine them with proper immune stimulatory components (adjuvants) in order to induce protective immunity. This Commentary outlines the authors' view on the current and future strategies for the efficient and rapid identification of the most effective protective antigens and adjuvants. Since efficacious subunit-based vaccines against recalcitrant pathogens are likely to require more than one antigen and/or immune stimulator, this poses the problem of how to make such vaccines economically acceptable. In this regard, the authors also present their view of how bacterial Outer Membrane Vesicles (OMVs) could become a promising platform for the development of future vaccines. The unique properties of OMVs might be exploited in the field of infectious diseases and oncology.

Proteomics in the Study of Bacterial Keratitis

Bacterial keratitis is a serious ocular infection that can cause severe visual loss if treatment is not initiated at an early stage. It is most commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, or Serratia species. Depending on the invading organism, bacterial keratitis can progress rapidly, leading to corneal destruction and potential blindness. Common risk factors for bacterial keratitis include contact lens wear, ocular trauma, ocular surface disease, ocular surgery, lid deformity, chronic use of topical steroids, contaminated ocular medications or solutions, and systemic immunosuppression. The pathogenesis of bacterial keratitis, which depends on the bacterium-host interaction and the virulence of the invading bacterium, is complicated and not completely understood. This review highlights some of the proteomic technologies that have been used to identify virulence factors and the host response to infections of bacterial keratitis in order to understand the disease process and develop improved methods of diagnosis and treatment. Although work in this field is not abundant, proteomic technologies have provided valuable information toward our current knowledge of bacterial keratitis. More studies using global proteomic approaches are warranted because it is an important tool to identify novel targets for intervention and prevention of corneal damage caused by these virulent microorganisms.

Immunization with an autotransporter protein of Orientia tsutsugamushi provides protective immunity against scrub typhus

BACKGROUND

Scrub typhus is an acute febrile disease caused by Orientia tsutsugamushi infection. Recently, the rapid increase of scrub typhus incidence in several countries within the endemic region has become a serious public health issue. Despite the wide range of preventative approaches that have been attempted in the past 70 years, all have failed to develop an effective prophylactic vaccine. Currently, the selection of the proper antigens is one of the critical barriers to generating cross-protective immunity against antigenically-variable strains of O. tsutsugamushi.

METHODOLOGY/PRINCIPAL FINDINGS

We examined the potential role of ScaA protein, an autotransporter protein of O. tsutsugamushi, in bacterial pathogenesis and evaluated the protective attributes of ScaA immunization in lethal O. tsutsugamushi infection in mice. Our findings demonstrate that ScaA functions as a bacterial adhesion factor, and anti-ScaA antibody significantly neutralizes bacterial infection of host cells. In addition, immunization with ScaA not only provides protective immunity against lethal challenges with the homologous strain, but also confers significant protection against heterologous strains when combined with TSA56, a major outer membrane protein of O. tsutsugamushi.

CONCLUSIONS/SIGNIFICANCE

Immunization of ScaA proteins provides protective immunity in mice when challenged with the homologous strain and significantly enhanced protective immunity against infection with heterologous strains. To our knowledge, this is the most promising result of scrub typhus vaccination trials against infection of heterologous strains in mouse models thus far.

[Proteomics in infectious diseases]

Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research.

Immunoproteomic analysis to identify Shiga toxin-producing Escherichia coli outer membrane proteins expressed during human infection

Shiga-toxin producing Escherichia coli (STEC) is the etiologic agent of acute diarrhea, dysentery, and hemolytic-uremic syndrome (HUS). There is no approved vaccine for STEC infection in humans, and antibiotic use is contraindicated, as it promotes Shiga toxin production. In order to identify STEC-associated antigens and immunogenic proteins, outer membrane proteins (OMPs) were extracted from STEC O26:H11, O103, O113:H21, and O157:H7 strains, and commensal E. coli strain HS was used as a control. SDS-PAGE, two-dimensional-PAGE analysis, Western blot assays using sera from pediatric HUS patients and controls, and matrix-assisted laser desorption ionization-tandem time of flight analyses were used to identify 12 immunogenic OMPs, some of which were not reactive with control sera. Importantly, seven of these proteins have not been previously reported to be immunogenic in STEC strains. Among these seven proteins, OmpT and Cah displayed IgG and IgA reactivity with sera from HUS patients. Genes encoding these two proteins were present in a majority of STEC strains. Knowledge of the antigens produced during infection of the host and the immune response to those antigens will be important for future vaccine development.

Lactobacillus acidophilusExpressing Recombinant K99 Adhesive Fimbriae Has an Inhibitory Effect on Adhesion of EnterotoxigenicEscherichia coli

The most common enteric colibacillosis in neonatal and newborns is caused by enterotoxigenic Escherichia coli(ETEC). Colonization of ETEC in the small intestine is associated with adhesions using fimbriae, which is known as a specific adhesion factor and provides highly specific means for anchoring and prerequisite for an infectious agent. In the present study we have engineered Lactobacillus acidophilus to produce recombinant K99 fimbriae, which is used for the colonization to the intestine of pigs. The expression of K99 fimbrial protein was confirmed using SDS-PAGE, immunoblot and agglutination analyses. To evaluate a function of the K99 fimbrial protein, inhibition and competition tests were performed on pre-screened intestinal brush border from pigs. The tests showed that recombinant L. acidophilus, not control L. acidophilus, had a significant inhibitory effect to and competition against K99+ E. coli in a dose dependent manner. In conclusion, we demonstrated that recombinant K99 fimbriae producing L. acidophilus was able to prevent E. coli binding to intestinal brush border.

Identification of potential new protein vaccine candidates through pan-surfomic analysis of pneumococcal clinical isolates from adults

Purified polysaccharide and conjugate vaccines are widely used for preventing infections in adults and in children against the Gram-positive bacterium Streptococcus pneumoniae, a pathogen responsible for high morbidity and mortality rates, especially in developing countries. However, these polysaccharide-based vaccines have some important limitations, such as being serotype-dependent, being subjected to losing efficacy because of serotype replacement and high manufacturing complexity and cost. It is expected that protein-based vaccines will overcome these issues by conferring a broad coverage independent of serotype and lowering production costs. In this study, we have applied the “shaving” proteomic approach, consisting of the LC/MS/MS analysis of peptides generated by protease treatment of live cells, to a collection of 16 pneumococcal clinical isolates from adults, representing the most prevalent strains circulating in Spain during the last years. The set of unique proteins identified in all the isolates, called “pan-surfome”, consisted of 254 proteins, which included most of the protective protein antigens reported so far. In search of new candidates with vaccine potential, we identified 32 that were present in at least 50% of the clinical isolates analyzed. We selected four of them (Spr0012, Spr0328, Spr0561 and SP670_2141), whose protection capacity has not yet been tested, for assaying immunogenicity in human sera. All of them induced the production of IgM antibodies in infected patients, thus indicating that they could enter the pipeline for vaccine studies. The pan-surfomic approach shows its utility in the discovery of new proteins that can elicit protection against infectious microorganisms.

Functional fragments of disorder in outer membrane β barrel proteins

The traditional view of “sequence–structure–function” has been amended by the discovery of intrinsically disordered proteins. Almost 50% of PDB structures are now known to have one or more regions of disorder, which are involved in diverse functions. These regions typically possess low aromatic content and sequence complexity as well as high net charge and flexibility. In this study, we examined the composition and contribution of intrinsic disorder in outer membrane β barrel protein functions. Our systematic analysis to find the dual personality (DP) fragments, which often function by disorder–order transitions, revealed the presence of 61 DP fragments with 234 residues in β barrel trans membrane protein structures. It was found that though the disorder is more prevalent in the periplasmic regions, most of the residues which undergo disorder–order transitions are found in the extracellular regions. For example, the calcium binding sites in BtuB protein are found to undergo disorder to order transition upon binding calcium. The conformational change in the cell receptor binding site of the OpcA protein, which is important in host cell interactions of N. meningitidis, was also found to be due to the disorder–order transitions occurring in the presence of the ligand. The natively disordered nature of DP fragments makes it more appropriate to call them “functional fragments of disorder.” The present study provides insight into the roles played by intrinsically disordered regions in outer membrane protein functions.

The unique structure of Haemophilus influenzae protein E reveals multiple binding sites for host factors

Haemophilus influenzae protein E (PE) is a multifunctional adhesin involved in direct interactions with lung epithelial cells and host proteins, including plasminogen and the extracellular matrix proteins vitronectin and laminin. We recently crystallized PE and successfully collected X-ray diffraction data at 1.8 Å. Here, we solved the structure of a recombinant version of PE and analyzed different functional regions. It is a dimer in solution and in the asymmetric unit of the crystals. The dimer has a structure that resembles a flattened β-barrel. It is, however, not a true β-barrel, as there are differences in both the hydrogen-bonding pattern and the shape. Each monomer consisted of a 6-stranded antiparallel β-sheet with a rigid α-helix at the C terminus tethered to the concave side of the sheet by a disulfide bridge. The laminin/plasminogen binding region (residues 41 to 68) is exposed, while the vitronectin binding region (residues 84 to 108) is partially accessible in the dimer. The dimerized PE explains the simultaneous interaction with laminin and vitronectin. In addition, we found this unique adhesin to be present in many bacterial genera of the family Pasteurellaceae and also orthologues in other, unrelated species (Enterobacter cloacae and Listeria monocytogenes). Peptides corresponding to the surface-exposed regions PE 24 to 37, PE 74 to 89, and PE 134 to 156 were immunogenic in the mouse. Importantly, these peptide-based antibodies also recognized PE at the bacterial surface. Taken together, our detailed structure of PE explains how this important virulence factor of H. influenzae simultaneously interacts with host vitronectin, laminin, or plasminogen, promoting bacterial pathogenesis.

Emerging and neglected tropical diseases: translational application of proteomics

The challenges of identifying and controlling emerging diseases impact individual health, as well as political, social and economic situations. In this review we discuss the role of proteomics for investigation of pathogen discovery, outbreak investigation, bio-defense, disease control, host-pathogen dynamics and vaccine development of emerging and neglected tropical diseases (NTDs). In the future the discipline of proteomics may help define multiple aspects of emerging and NTDs with respect to personalized medicine and public health.

Designing the next generation of vaccines for global public health

Vaccine research and development are experiencing a renaissance of interest from the global scientific community. There are four major reasons for this: (1) the lack of efficacious treatment for many devastating infections; (2) the emergence of multidrug resistant bacteria; (3) the need for improving the safety of the more traditional licensed vaccines; and finally, (4) the great promise for innovative vaccine design and research with convergence of omics sciences, such as genomics, proteomics, immunomics, and vaccinology. Our first project based on omics was initiated in 2000 and was termed reverse vaccinology. At that time, antigen identification was mainly based on bioinformatic analysis of a singular genome. Since then, omics-guided approaches have been applied to its full potential in several proof-of-concept studies in the industry, with the first reverse vaccinology-derived vaccine now in late stage clinical trials and several vaccines developed by omics in preclinical studies. In the meantime, vaccine discovery and development has been further improved with the support of proteomics, functional genomics, comparative genomics, structural biology, and most recently vaccinomics. We illustrate in this review how omics biotechnologies and integrative biology are expected to accelerate the identification of vaccine candidates against difficult pathogens for which traditional vaccine development has thus far been failing, and how research will provide safer vaccines and improved formulations for immunocompromised patients in the near future. Finally, we present a discussion to situate omics-guided rational vaccine design in the broader context of global public health and how it can benefit citizens in both developed and developing countries.

Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition

Many vaccines have been developed from live attenuated forms of bacterial pathogens or from killed bacterial cells. However, an increased awareness of the potential for transient side-effects following vaccination has prompted an increased emphasis on the use of sub-unit vaccines, rather than those based on whole bacterial cells. The identification of vaccine sub-units is often a lengthy process and bioinformatics approaches have recently been used to identify candidate protein vaccine antigens. Such methods ultimately offer the promise of a more rapid advance towards preclinical studies with vaccines. We have compared the properties of known bacterial vaccine antigens against randomly selected proteins and identified differences in the make-up of these two groups. A computer algorithm that exploits these differences allows the identification of potential vaccine antigen candidates from pathogenic bacteria on the basis of their amino acid composition, a property inherently associated with sub-cellular location.

IMMUNOCAT-a data management system for epitope mapping studies

To enable rationale vaccine design, studies of molecular and cellular mechanisms of immune recognition need to be linked with clinical studies in humans. A major challenge in conducting such translational research studies lies in the management and integration of large amounts and various types of data collected from multiple sources. For this purpose, we have established “IMMUNOCAT”, an interactive data management system for the epitope discovery research projects conducted by our group. The system provides functions to store, query, and analyze clinical and experimental data, enabling efficient, systematic, and integrative data management. We demonstrate how IMMUNOCAT is utilized in a large-scale research contract that aims to identify epitopes in common allergens recognized by T cells from human donors, in order to facilitate the rational design of allergy vaccines. At clinical sites, demographic information and disease history of each enrolled donor are captured, followed by results of an allergen skin test and blood draw. At the laboratory site, T cells derived from blood samples are tested for reactivity against a panel of peptides derived from common human allergens. IMMUNOCAT stores results from these T cell assays along with MHC:peptide binding data, results from RAST tests for antibody titers in donor serum, and the respective donor HLA typing results. Through this system, we are able to perform queries and integrated analyses of the various types of data. This provides a case study for the use of bioinformatics and information management techniques to track and analyze data produced in a translational research study aimed at epitope identification.

Bacterial surface proteins and vaccines

Surface-associated proteins play a key role in bacterial physiology and pathogenesis and are the major targets for vaccine development. Recent advances in defining the proteins associated with, and protruding out of, bacterial cells to a high level of accuracy are substantially contributing to accelerating the process of vaccine target identification and development.

Identification of sortase A (SrtA) substrates in Streptococcus uberis: evidence for an additional hexapeptide (LPXXXD) sorting motif

Sortase (a transamidase) has been shown to be responsible for the covalent attachment of proteins to the bacterial cell wall. Anchoring is effected on secreted proteins containing a specific cell wall motif toward their C-terminus; that for sortase A (SrtA) in Gram-positive bacteria often incorporates the sequence LPXTG. Such surface proteins are often characterized as virulence determinants and play important roles during the establishment and persistence of infection. Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis, which impacts on animal health and welfare and the economics of milk production. Comparison of stringently produced cell wall fractions from S. uberis and an isogenic mutant strain lacking SrtA permitted identification of 9 proteins likely to be covalently anchored at the cell surface. Analysis of these sequences implied the presence of two anchoring motifs for S. uberis, the classical LPXTG motif and an additional LPXXXD motif.

Elucidation of the outer membrane proteome of Salmonella enterica serovar Typhimurium utilising a lipid-based protein immobilization technique

Background

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of human gastroenteritis worldwide. The outer membrane proteins expressed by S. Typhimurium mediate the process of adhesion and internalisation within the intestinal epithelium of the host thus influencing the progression of disease. Since the outer membrane proteins are surface-exposed, they provide attractive targets for the development of improved antimicrobial agents and vaccines. Various techniques have been developed for their characterisation, but issues such as carryover of cytosolic proteins still remain a problem. In this study we attempted to characterise the surface proteome of S. Typhimurium using Lipid-based Protein Immobilisation technology in the form of LPI™ FlowCells. No detergents are required and no sample clean up is needed prior to downstream analysis. The immobilised proteins can be digested with proteases in multiple steps to increase sequence coverage, and the peptides eluted can be characterised directly by liquid chromatography - tandem mass spectrometry (LC-MS/MS) and identified from mass spectral database searches.

Results

In this study, 54 outer membrane proteins, were identified with two or more peptide hits using a multi-step digest approach. Out of these 28 were lipoproteins, nine were involved in transport and three with enzyme activity These included the transporters BtuB which is responsible for the uptake of vitamin B₁₂, LamB which is involved in the uptake of maltose and maltodextrins and LolB which is involved in the incorporation of lipoproteins in the outer membrane. Other proteins identified included the enzymes MltC which may play a role in cell elongation and division and NlpD which is involved in catabolic processes in cell wall formation as well as proteins involved in virulence such as Lpp1, Lpp2 and OmpX.

Conclusion

Using a multi-step digest approach the LPI™ technique enables the incorporation of a multi-step protease work flow ensuring enough sequence coverage of membrane proteins subsequently leading to the identification of more membrane proteins with higher confidence. Compared to current sub-cellular fractionation procedures and previous published work, the LPI™ technique currently provides the widest coverage of outer membrane proteins identified as demonstrated here for Salmonella Typhimurium.

Proteomics as a probe of microbial pathogenesis and its molecular boundaries

Proteomic technology offers an unprecedented systematic approach to investigate the protein complement of any organism. The field of microbial pathogenesis has greatly benefited from other systems approaches, and the application of proteomics to the study of infectious agents is beginning to emerge. Such applications include unambiguously identifying complete virulence factor inventories, studying the response of both host and pathogen to the infection process and elucidating mechanistic actions of virulence factors as they interface with host cells. This review will highlight examples where proteomic studies have contributed to our understanding of pathogenesis in these areas, with an emphasis on pathogens that employ type III and type IV secretion systems. In addition, we will discuss areas where proteomics may help shape further investigation and discovery in this field.

Identification of uropathogenic Escherichia coli surface proteins by shotgun proteomics

Uropathogenic Escherichia coli (UPEC) cause the majority of uncomplicated urinary tract infections in humans. In the process of identifying candidate antigens for a vaccine, two methods for the identification of the UPEC surface proteome during growth in human urine were investigated. The first approach utilized a protease to 'shave' surface-exposed peptides from the bacterial cell surface and identify them by mass spectrometry. Although this approach has been successfully applied to a Gram-positive pathogen, the adaptation to Gram-negative UPEC resulted in cytoplasmic protein contamination. In a more direct approach, whole-cell bacteria were labeled with a biotin tag to indicate surface-exposed peptides and two-dimensional liquid chromatography-tandem mass spectrometry (2-DLC-MS/MS) was used to identify proteins isolated from the outer membrane. This method discovered 25 predicted outer membrane proteins expressed by UPEC while growing in human urine. Nine of the 25 predicted outer membrane proteins were part of iron transport systems or putative iron-regulated virulence proteins, indicating the importance of iron acquisition during growth in urine. One of the iron transport proteins identified, Hma, appears to be a promising vaccine candidate is being further investigated. The method described here presents a system to rapidly identify the outer membrane proteome of bacteria, which may prove valuable in vaccine development.

Surfome analysis as a fast track to vaccine discovery: identification of a novel protective antigen for Group B Streptococcus hypervirulent strain COH1

Safe recombinant vaccines, based on a small number of antigenic proteins, are emerging as the most attractive, cost-effective solution against infectious diseases. In the present work, we confirmed previous data from our laboratory showing that whole viable bacterial cell treatment with proteases followed by the identification of released peptides by mass spectrometry is the method of choice for the rapid and reliable identification of vaccine candidates in Gram-positive bacteria. When applied to the Group B Streptococcus COH1 strain, 43 surface-associated proteins were identified, including all the protective antigens described in the literature as well as a new protective antigen, the cell wall-anchored protein SAN_1485 belonging to the serine-rich repeat protein family. This strategy overcomes the difficulties so far encountered in the identification of novel vaccine candidates and speeds up the entire vaccine discovery process by reducing the number of recombinant proteins to be tested in the animal model.

New ways to identify novel bacterial antigens for vaccine development

This article provides an overview of developments in approaches to identify novel bacterial components for use in recombinant subunit vaccines. In particular it describes the processes involved in "reverse vaccinology", and some associated complementary technologies such as proteomics that can be used in the identification of new and potentially useful vaccine antigens. Results obtained from the application of these new methods are forming a basis for a new generation of vaccines for use in the control of bacterial infections of humans and animals.

Proteomic approaches for discovery of new targets for vaccine and therapeutics against visceral leishmaniasis

Visceral leishmaniasis (VL) is the most devastating type caused by Leishmania donovani, Leishmania infantum, and Leishmania chagasi. The therapeutic mainstay is still based on the antiquated pentavalent antimonial against which resistance is now increasing. Unfortunately, due to the digenetic life cycle of parasite, there is significant antigenic diversity. There is an urgent need to develop novel drug/vaccine targets against VL for which the primary goal should be to identify and characterize the structural and functional proteins. Proteomics, being widely employed in the study of Leishmania seems to be a suitable strategy as the availability of annotated sequenced genome of Leishmania major has opened the door for dissection of both protein expression/regulation and function. Advances in clinical proteomic technologies have enable to enhance our mechanistic understanding of virulence/pathogenicity/host-pathogen interactions, drug resistance thereby defining novel therapeutic/vaccine targets. Expression proteomics exploits the differential expression of leishmanial proteins as biomarkers for application towards early diagnosis. Further using immunoproteomics efforts were also focused on evaluating responses to define parasite T-cell epitopes as vaccine/diagnostic targets. This review has highlighted some of the relevant developments in the rapidly emerging field of leishmanial proteomics and focus on its future applications in drug and vaccine discovery against VL.

Monitoring FET flow control and wall adsorption of charged fluorescent dye molecules in nanochannels integrated into a multiple internal reflection infrared waveguide

Using Si as the substrate, we have fabricated multiple internal reflection infrared waveguides embedded with a parallel array of nanofluidic channels. The channel width is maintained substantially below the mid-infrared wavelength to minimize infrared scattering from the channel structure and to ensure total internal reflection at the channel bottom. A Pyrex slide is anodically bonded to the top of the waveguide to seal the nanochannels, while simultaneously enabling optical access in the visible range from the top. The Si channel bottom and sidewalls are thermally oxidized to provide an electrically insulating barrier, and the Si substrate surrounding the insulating SiO(2) layer is selectively doped to function as a gate. For fluidic field effect transistor (FET) control, a DC potential is applied to the gate to manipulate the surface charge on SiO(2) channel bottom and sidewalls and therefore their zeta-potential. Depending on the polarity and magnitude, the gate potential can accelerate, decelerate, or reverse the flow. Here, we demonstrate that this nanofluidic infrared waveguide can be used to monitor the FET flow control of charged, fluorescent dye molecules during electroosmosis by multiple internal reflection Fourier transform infrared spectroscopy. Laser scanning confocal fluorescence microscopy is simultaneously used to provide a comparison and verification of the IR analysis. Using the infrared technique, we probe the vibrational modes of dye molecules, as well as those of the solvent. The observed infrared absorbance accounts for the amount of dye molecules advancing or retracting in the nanochannels, as well as adsorbing to and desorbing from the channel bottom and sidewalls.

Quantitative profile of the uropathogenic Escherichia coli outer membrane proteome during growth in human urine

Outer membrane proteins (OMPs) of microbial pathogens are critical components that mediate direct interactions between microbes and their surrounding environment. Consequently, the study of OMPs is integral to furthering the understanding of host-pathogen interactions and to identifying key targets for development of improved antimicrobial agents and vaccines. In this study, we used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and tandem mass spectrometry to characterize the uropathogenic Escherichia coli (UPEC) outer membrane subproteome; 30 individual OMPs present on the bacterial surface during growth in human urine were identified. Fluorescence difference gel electrophoresis was used to identify quantitative changes in levels of UPEC strain CFT073 OMPs during growth in urine; six known receptors for iron compounds were induced in this environment, i.e., ChuA, IutA, FhuA, IroN, IreA, and Iha. A seventh putative iron compound receptor, encoded by CFT073 open reading frame (ORF) c2482, was also identified and found to be induced in urine. Further, the induction of these seven iron receptors in human urine and during defined iron limitation was verified by using quantitative real-time PCR (qPCR). An eighth iron receptor, fepA, displayed similar induction levels under these conditions as measured by qPCR but was not identified by 2D-PAGE. Addition of 10 microM FeCl(2) to human urine repressed the transcription of all eight iron receptor genes. A number of fecal-commensal, intestinal pathogenic, and uropathogenic E. coli strains all displayed similar growth rates in human urine, showing that the ability to grow in urine per se is not a urovirulence trait. Thus, human urine is an iron-limiting environment and UPEC enriches its outer membrane with iron receptors to contend with this iron limitation.

Proteomic approach for identification and characterization of novel immunostimulatory proteins from soluble antigens of Leishmania donovani promastigotes

Visceral leishmaniasis (VL) caused by Leishmania donovani is a major parasitic disease prevalent in endemic regions of Bihar in India. In the absence of good chemotherapeutic options, there is a need to develop an effective vaccine against VL which should be dependent on the generation of a T helper type 1 (Th1) immune response. We have shown that soluble proteins from promastigote of a new clinical isolate of L. donovani (2001) ranging from 68 to 97.4 kDa (F2 fraction), induce Th1 responses in the peripheral blood mononuclear cells of cured Leishmania patients and hamsters and also showed significant prophylactic potential. To understand the nature of F2 proteins, it was further characterized using 2-DE, MALDI-TOF and MALDI-TOF/TOF-MS. In all, 63 spots were cut from a CBB stained gel for analysis and data was retrieved for 52 spots. A total of 33 proteins were identified including six hypothetical/unknown proteins. Major immunostimulatory proteins were identified as elongation factor-2, p45, heat shock protein (HSP)70, HSP83, aldolase, enolase, triosephosphate isomerase, protein disulfideisomerase and calreticulin. This study substantiates the usefulness of proteomics in characterizing a complex protein fraction (F2) map of soluble L. donovani promastigote antigen identified as Th1 stimulatory for its potential as vaccine targets against VL.

Technologies for bacterial surface proteomics

Proteins from bacterial membranes are notoriously difficult to analyze using the traditional technologies encompassed under the term 'proteomics'. This is because of several factors, including the comparatively low abundance of most membrane proteins within a complex mixture containing cytoplasmic metabolic enzymes, the poor solubility of membrane components such as phospholipids, lipopolysaccharides and peptidoglycans, and the inherent hydrophobicity of many integral membrane proteins that contain up to 15 transmembrane-spanning regions. Recent advances in gel-based and chromatographic separations, coupled with protein and peptide labelling and the exquisite sensitivity of mass spectrometry, are finally beginning to overcome these problems. New technologies in membrane proteomics enable comparative analysis of these recalcitrant proteins from bacteria under a variety of biological conditions.

Post-genomic vaccine development

For over a century, vaccines were developed according to Pasteur's principles of isolating, inactivating and injecting the causative agent of an infectious disease. The availability of a complete microbial genome sequence in 1995 marked the beginning of a genomic era that has allowed scientists to change the paradigm and approach vaccine development starting from genomic information, a process named reverse vaccinology. This can be considered as one of the most powerful examples of how genomic information can be used to develop therapeutic interventions, which were difficult or impossible to tackle with conventional approaches. As the genomic era progressed, it became apparent that multi-strain genome analysis is fundamental to the design of universal vaccines. In the post-genomic era, the next challenge of the vaccine biologist will be the merging of the vaccinology with structural biology.

The impact of genomics on vaccine design

After 200 years of practice, vaccinology has gained new perspectives for preventing infectious diseases. Sequencing of complete bacterial genomes led to the development of new large-scale technologies, such as bioinformatics, proteomics and DNA microarrays. By examining genetic content, as well as transcription and expression profiles, a more detailed understanding of bacterial pathogenesis can be reached. Moreover, the whole-genome perspective is expected to provide an instrumental contribution to vaccine development, particularly to target those pathogens for which the traditional approaches have failed so far. In this review, we describe how genomic approaches can be used to identify novel vaccine candidates or create safer live-attenuated vaccines.

Screening the whole genome of a pathogen in vivo for individual protective antigens

We report the results of a general protocol that was used to screen the whole genome of Chlamydophila abortus, type strain B577 (formerly Chlamydia psittaci strain B577), in a mouse pneumonia model. Genetic immunization was used to functionally test the genes of C. abortus as vaccines in a mouse challenge system. Nine gene fragments were isolated that conferred protection, with five protecting as effectively as the live-vaccine positive control. Bioinformatics approaches were unable to reconstruct isolation of these antigens. These results suggest that pathogen genomes can be functionally screened for vaccine candidate antigens in a mouse model to reveal new classes of vaccine candidate antigens that may have therapeutic efficacy across host species, disease manifestations, and delivery platforms.

Biotechnology and vaccines: application of functional genomics to Neisseria meningitidis and other bacterial pathogens

Since its introduction, vaccinology has been very effective in preventing infectious diseases. However, in several cases, the conventional approach to identify protective antigens, based on biochemical, immunological and microbiological methods, has failed to deliver successful vaccine candidates against major bacterial pathogens. The recent development of powerful biotechnological tools applied to genome-based approaches has revolutionized vaccine development, biological research and clinical diagnostics. The availability of a genome provides an inclusive virtual catalogue of all the potential antigens from which it is possible to select the molecules that are likely to be more effective. Here, we describe the use of "reverse vaccinology", which has been successful in the identification of potential vaccines candidates against Neisseria meningitidis serogroup B and review the use of functional genomics approaches as DNA microarrays, proteomics and comparative genome analysis for the identification of virulence factors and novel vaccine candidates. In addition, we describe the potential of these powerful technologies in understanding the pathogenesis of various bacteria.

DNA microarrays — techniques and applications in microbial systems

Genome projects produce a huge amount of sequence information. As a result, the focus of genomics research is turning toward deduction of functional information about newly discovered genes. Thus structural genomics paves the way for a new discipline called functional genomics by providing the information required for microarray manufacture. Microarray technology is the result of automation and miniaturization in the detection of differential gene expression. By using this technology one can make a parallel analysis of RNA abundance and DNA homology for thousands of genes in a single experiment. Over the past several years, this unique technology has been used to explore hundreds transcriptional patterns and genome differences for a variety of microbial species. Applications of microarrays extend beyond the boundaries of basic biology into diagnostics, environmental monitoring, pharmacology, toxicology and biotechnology. We describe comprehensive nature of DNA microarray technology with emphasis on fabrication of DNA microarrays and application of this technology in biological environment with primary accent on microbial systems.

Biotechnology to improve health in developing countries -- a review

The growing health disparities between the developing and the developed world call for urgent action from the scientific community. Science and technology have in the past played a vital role in improving public health. Today, with the tremendous potential of genomics and other advances in the life sciences, the contribution of science to improve public health and reduce global health disparities is more pertinent than ever before. Yet the benefits of modern medicine still have not reached millions of people in developing countries. It is crucial to recognize that science and technology can be used very effectively in partnership with public health practices in developing countries and can enhance their efficacy. The fight to improve global health needs, in addition to effective public health measures, requires rapid and efficient diagnostic tools; new vaccines and drugs, efficient delivery methods and novel approaches to therapeutics; and low-cost restoration of water, soil and other natural resources. In 2002, the University of Toronto published a report on the "Top 10 Biotechnologies for Improving Health in Developing Countries". Here we review these new and emerging biotechnologies and explore how they can be used to support the goals of developing countries in improving health.

L’analyse protéomique : concepts, réalités et perspectives en thérapeutique

The present paper aims at clarifying some important aspects of proteomics, i.e. the large scale analysis of proteins. To this purpose, the main types of proteomic analyses are presented, i.e. those aiming at determining expression levels and those aiming at unravelling protein-protein interactions networks. Their performances and limitations are outlined, as well as their potential applications in biomedicine, to give an reasoned view of the current state of the art.

Vaccines against bacterial meningitis

Meningitis remains an important cause of morbidity and mortality among children >5 years of age and is especially prevalent in developing countries. Effective routine immunization against Hib, pneumococcus and serogroupC meningococcus has had a significant impact on both invasive disease and carriage caused by these encapsulated bacteria. The major challenge in prevention of meningitis remains the delivery of vaccines worldwide, especially to resource-poor regions with the greatest disease burden.

Genome-based bioinformatic selection of chromosomal Bacillus anthracis putative vaccine candidates coupled with proteomic identification of surface-associated antigens

Bacillus anthracis (Ames strain) chromosome-derived open reading frames (ORFs), predicted to code for surface exposed or virulence related proteins, were selected as B. anthracis-specific vaccine candidates by a multistep computational screen of the entire draft chromosome sequence (February 2001 version, 460 contigs, The Institute for Genomic Research, Rockville, Md.). The selection procedure combined preliminary annotation (sequence similarity searches and domain assignments), prediction of cellular localization, taxonomical and functional screen and additional filtering criteria (size, number of paralogs). The reductive strategy, combined with manual curation, resulted in selection of 240 candidate ORFs encoding proteins with putative known function, as well as 280 proteins of unknown function. Proteomic analysis of two-dimensional gels of a B. anthracis membrane fraction, verified the expression of some gene products. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analyses allowed identification of 38 spots cross-reacting with sera from B. anthracis immunized animals. These spots were found to represent eight in vivo immunogens, comprising of EA1, Sap, and 6 proteins whose expression and immunogenicity was not reported before. Five of these 8 immunogens were preselected by the bioinformatic analysis (EA1, Sap, 2 novel SLH proteins and peroxiredoxin/AhpC), as vaccine candidates. This study demonstrates that a combination of the bioinformatic and proteomic strategies may be useful in promoting the development of next generation anthrax vaccine.

Bioinformatics: how it is being used to identify bacterial vaccine candidates

Genomic sequencing has provided a tremendous amount of information that can be useful in vaccine target identification. The sheer volume of information available necessitates the use of new research disciplines and techniques. Using bioinformatics, researchers sift through available data to identify appropriate candidates for biological analysis. This review provides an overview of available bioinformatic techniques for vaccine candidate identification and a few examples of how these techniques are being applied to specific bacterial pathogens.

Rational antibacterial vaccine design through genomic technologies

After 200 years of practice, vaccinology has proved to be very effective in preventing infectious diseases. However, several human and animal pathogens exist for which vaccines have not yet been discovered. As for other fields of medical sciences, it is expected that vaccinology will greatly benefit from the emerging genomics technologies such as bioinformatics, proteomics and DNA microarrays. In this review, the potential of these technologies will be illustrated taking into account part of the research activities currently in progress in our laboratories. In particular, I will describe the identification of new vaccine candidates against Meningococcus B through high-throughput cloning and expression of meningococcal antigens selected by: (i) in silico analysis of genome sequence; and (ii) transcriptome analysis of bacteria adherent to epithelial cells. In addition, I will show how the combination of high-throughput cloning and expression technology with two-dimensional gel/mass spectrometry led us to the elucidation of Chlamydia pneumoniae surface protein subproteome and to the identification of potential vaccine candidates.

The future of meningitis vaccines

Without effective vaccines meningitis remains a substantial worldwide threat with major health-care implications. A number of advances have been made in vaccine design and implementation over the last decade, with new vaccine initiatives providing substantial promise for the future reduction of global disease burden.