A subtractive proteomics approach for the identification of immunodominant Acinetobacter baumannii vaccine candidate proteins (original) (raw)
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BMC Genomics, 2016
Background: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. Results: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra-and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. Conclusion: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
PROTEOMICS - Clinical Applications, 2014
Acinetobacter baumannii is an important opportunistic pathogen that causes pneumoniae, urinary tract infections, and/or septicemia in immunocompromised patients. This pathogen is frequently associated with nosocomial outbreaks worldwide and has become particularly problematic because of its prevalence and resistance patterns to several antibiotics. In the present study, we used an immunoproteome-based approach to identify immunogenic proteins located on the surface of A. baumannii for the development of a possible immunotherapy against this devastating bacterial infection. Experimental design: Sera from patients with A. baumannii infections (n = 50) and from a control group of healthy individuals (n = 3) were analyzed for reactivity against A. baumannii outer membrane proteins (OMPs) using Western blot analysis. To identify potential immunogenic proteins in A. baumannii, OMPs were separated by 2DE (2D electrophoresis), and reactive Q1 sera from infected patients were randomly selected and divided into two different pools, each containing 15 sera. Finally, MALDI-TOF/TOF mass spectrometric analysis was employed to identify the corresponding proteins. Results: This analysis identified six immunoreactive proteins: OmpA, Omp34kDa, OprC, OprB-like, OXA-23, and ferric siderophore receptor protein. Notably, these proteins are highly abundant on the bacterial surface and involved in virulence, antibiotic resistance, and growth. Conclusions and clinical relevance: Our results support the notion that the proteins identified in the present immunoproteome study could serve as antigen candidates for the development of vaccines and passive immunotherapies against A. baumannii infections.
Frontiers in Microbiology, 2016
Acinetobacter baumannii is emerging as a serious nosocomial pathogen with multidrug resistance that has made it difficult to cure and development of efficacious treatment against this pathogen is direly needed. This has led to investigate vaccine approach to prevent and treat A. baumannii infections. In this work, an outer membrane putative pilus assembly protein, FilF, was predicted as vaccine candidate by in silico analysis of A. baumannii proteome and was found to be conserved among the A. baumannii strains. It was cloned and expressed in E. coli BL21(DE3) and purified by Ni-NTA chromatography. Immunization with FilF generated high antibody titer (>64,000) and provided 50% protection against a standardized lethal dose (10 8 CFU) of A. baumannii in murine pneumonia model. FilF immunization reduced the bacterial load in lungs by 2 and 4 log cycles, 12 and 24 h post infection as compared to adjuvant control; reduced the levels of pro-inflammatory cytokines TNF-α, IL-6, IL-33, IFN-γ, and IL-1β significantly and histology of lung tissue supported the data by showing considerably reduced damage and infiltration of neutrophils in lungs. These results demonstrate the in vivo validation of immunoprotective efficacy of a protein predicted as a vaccine candidate by in silico proteomic analysis and open the possibilities for exploration of a large array of uncharacterized proteins.
Vaccine Research, 2017
Introduction: Acinetobacter baumannii as a Gram-negative coccobacillus has become a major cause of hospital-acquired infections. The virulence factors involved in serum resistance are important targets in the development of an effective vaccine against this pathogen. Our aim in this project was in silico analyses of A. baumannii proteins involved in serum resistance which could potentially be used as efficient vaccines. Methods: Based on computational procedures, we evaluated all A. baumannii proteins involved in serum resistance, namely AbOmpA, PKF, PLD, PBP 7/8, CipA and Tuf SurA1, as vaccine candidates. Subcellular localization, sequence conservation, domain prediction and 3D modelings were analyzed by online tools. Moreover, the prevalence of serum resistance factors in 5 strains of A. baumannii was characterized. The MHC-binding sites of class I and II were detected. Linear and conformational B cell epitopes were analyzed by 2 prediction servers. Results: The MetaLocGramN server showed that AbOmpA, PKF, PBP7/8, phospholipase D, CipA, Tuf and SurA1 were outer membrane protein (56.32%), extracellular protein (58.74%), extracellular protein (52.59%), cytoplasmic protein (45.08%), extracellular protein (53.8%), Cytoplasmic protein (96.36%) and extracellular protein (58.23%), respectively. The OMD of AbOmpA, PKF, PBP7/8 and phospholipase D, CipA, Tuf and SurA1 were 0.060, 0.076, 0.08, 0.101, 0.09, 0.06 and 0.103, respectively. The numbers of immunogenic linear and conformational epitopes with high score (P ≥ 0.6), extracted from beta-barrel of AbOmpA were 6 and 4; whereas these values for PKF were 10 and 4, respectively. Conclusion: The in silico analyses and reverse vaccinology criteria showed that AbOmpA and PKF had better attributes as vaccine targets and they could be considered as promising vaccine candidates against A. baumannii.
Identification of Novel Vaccine Candidates against Multidrug-Resistant Acinetobacter baumannii
PLoS ONE, 2013
Acinetobacter baumannii is an emerging opportunistic bacterium associated with nosocomial infections in intensive care units. The alarming increase in infections caused by A. baumannii is strongly associated with enhanced resistance to antibiotics, in particular carbapenems. This, together with the lack of a licensed vaccine, has translated into significant economic, logistic and health impacts to health care facilities. In this study, we combined reverse vaccinology and proteomics to identify surface-exposed and secreted antigens from A. baumannii. Using in silico prediction tools and comparative genome analysis in combination with in vitro proteomic approaches, we identified 42 antigens that could be used as potential vaccine targets. Considering the paucity of effective antibiotics available to treat multidrug-resistant A. baumannii infections, these vaccine targets may serve as a framework for the development of a broadly protective multi-component vaccine, an outcome that would have a major impact on the burden of A. baumannii infections in intensive care units across the globe.
The bacterial species Acinetobacter baumannii is a major cause of hospital acquired infection throughout the world and it is increasing public health concern. Infection caused by multidrug resistant A. baumannii is currently among the most difficult to treat due to propensity to acquire mobile genetic element. To date there is no vaccine or specific drug available for its treatment, this necessitate the need for the identification of therapeutic target enzyme and vaccine. Pharmacogenomic and computational biology represent an attractive alternative approach for the identification of common drug target and peptide-vaccine candidates in the pathogen. Vaccine designing is shifted from entire pathogen or whole antigen to peptide or epitope based-vaccines that are specific, safe and easy to produce. Comparative genomic approach was used to identify conserved protein signatures among five genomes. Three outer membrane proteins conserved among the genomes with high vaxijen scores were used to produce both B-cell and T-cell mediated immunity. Propred and propred1 were used to predict promiscuos helper T-Lymphocytes (HTL), Cytotoxic T-Lymphocyte (CTL) epitopes and MHCPred for their binding affinity.Three T-cell epitopes derived from identified B-cells bind to maximum number of MHC class I and class II alleles and specifically bind to HLA alleles such as DRB1*0101 and DRB1*0401.The epitopes are YEKLAAGPS, FYTSQPEDS and YVTGNPLGL with high potential to induce humoral and cell mediated immune responses. These predicted epitopes (small peptide) might be promising candidates for vaccine design against A. baumannii infection, though experimental validation.
Proteomics for development of vaccine
Journal of …, 2011
The success of genome projects has provided us with a vast amount of information on genes of many pathogenic species and has raised hopes for rapid progress in combating infectious diseases, both by construction of new effective vaccines and by creating a new generation of therapeutic drugs. Proteomics, a strategy complementary to the genomic-based approach, when combined with immunomics (looking for immunogenic proteins) and vaccinomics (characterization of host response to immunization), delivers valuable information on pathogen-host cell interaction. It also speeds the identification and detailed characterization of new antigens, which are potential candidates for vaccine development. This review begins with an overview of the global status of vaccinology based on WHO data. The main part of this review describes the impact of proteomic strategies on advancements in constructing effective antibacterial, antiviral and anticancer vaccines. Diverse aspects of disease mechanisms and disease preventions have been investigated by proteomics.
2021
Acinetobacter baumannii (A. baumannii), an opportunistic, gram-negative pathogen, has evoked the interest of the medical community throughout the world because of its ability to cause nosocomial infections, majorly infecting those in intensive care units. It has also drawn the attention of researchers due to its evolving immune evasion strategies and increased drug resistance. The emergence of multi-drug-resistant-strains has urged the need to explore novel therapeutic options as an alternative to antibiotics. Due to the upsurge in antibiotic resistance mechanisms exhibited by A. baumannii, the current therapeutic strategies are rendered less effective. The aim of this study is to explore novel therapeutic alternatives against A. baumannii to control the ailed infection. In this study, a computational framework is employed involving, pan genomics, subtractive proteomics and reverse vaccinology strategies to identify core promiscuous vaccine candidates. Two chimeric vaccine construct...
International Journal of Peptide Research and Therapeutics, 2019
Acinetobacter baumannii is a well-recognized cause of nosocomial infections. This organism is recognized to be among the most difficult antimicrobial-resistant gram-negative bacilli to control and treat. One of the main challenges we face is Carbapenem resistance in A. baumannii. Carbapenem resistance in A. baumannii associated with the loss of an outer membrane protein designated CarO (Carbapenem resistance outer membrane protein). This protein is a membrane porin of A. baumannii. Using specific antibodies against this protein exert a bacteriostatic or bactericidal effect in vitro. Attempts should be made to discover peptides that could mimic protein epitopes and possess the same immunogenicity as the complete protein. Subsequently, bioinformatics methods for epitope prediction have been developed leading to synthesis of such peptides that are important for development of vaccine. This study provides a basis for the design of pathogen specifically, B cell epitope-based vaccine that is targeted to diseases caused by A. baumannii in the global human population. A combination of available bioinformatics tools are used to understand and characterize the Baumannii Acinetobactin utilization structure of A. baumannii and appropriate selection regions as effective B cell epitopes and functional exposed amino acids. In conclusion, amino acids 19-158 were selected as vaccine candidate.