Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines
Abstract
:1. Introduction
2. Traditional Vaccine Development
Bacteria | Illness | Intracellular Lifestyles | Bacterial Factors | Host Cells Localization | Incubation Period | Reference |
---|---|---|---|---|---|---|
L. pneumophila Non-spore forming, Gram-negative | Legionnaire’s disease | Intravacuolar pH 6 | Type IV secretion system | Macrophages | 2–10 days | [10] |
M. tuberculosis Non-spore forming, Acid Fast | Tuberculosis | Intravacuolar pH 6.4 | Type VII secretion system | Macrophage, Cytosol, Phagosome | 4–6 weeks | [11] |
S. typhi Rod-shaped, Gram-negative | Typhoid fever | Intravacuolar 5 | Type III secretion system | Macrophages | 10–14 days | [12] |
Brucella spp. Gram-negative coccobacilli | Brucellosis, High fever | Intravacuolar 4 | Type IV secretion system | Neutrophils, Vacuole | 2–4 weeks | [13] |
Listeria monocytogenes (L. monocytogenes) Gram-positive Bacillus | Listeriosis | Intracytosolic | In1A, In1B | Epithelial cells, Cytosol | 1–2 weeks | [14] |
Rickettsia rickettsii (R. rickettsii) Gram-indeterminant coccobacilli | Rocky Mountain spotted fever | Intravacuolar | Type IV secretion system | Monocytes/Macrophages | 2–5 days | [15] |
S. flexneri Non-spore forming, Gram-negative | Enteric disease | Intracytosolic | Type III secretion system | M Cells and Macrophages | 12–96 h | [16] |
M. leprae Acid Fast Bacillus | Leprosy | Intravacuolar | Type VII secretion system | Schwann cells (SCs) | 4–5 years | [17] |
S. typhimurium Non-spore forming, Gram-negative | Indigestion, food poisoning | Intravacuolar pH 5 | Type III secretion system | Macrophage, Vacuole | 12–72 h | [18] |
Chlamydia spp. Gram-indeterminant | Genital and ocular infections | Intravacuolar pH ¼ 7.25 | Type III secretion system | Genital epithelium and conjunctiva, Vacuole, | 1–2 weeks | [19] |
S. aureus Gram-positive | Dermal infection, osteomyelitis, mastitis | Intravascular | Type IV secretion system | Epithelial Cells, Osteoblast, Endosome, Cytosol | 16–18 h | [20] |
S. enterica Gram-negative | Paratyphoid and typhoid | Intravacuolar | Type III secretion system | Macrophage, Modified phagosome, Vacuole | 12–72 h | [21] |
Vaccine Type | Vaccine (Target Bacteria) | Vaccine Status | Reference |
---|---|---|---|
WCA | Q-Vax (C. burnetiid) (Dukoral, Shanchol (V. cholerae) R. rickettsia R. prowazekii O. tsutsugamushi | Licensed Licensed Experimental Experimental Experimental | [23] [24] [25] [26] [25] |
LAVs | BCG (M. tuberculosis) S. enterica spp. BioThrax (B. anthracis) LVS (F. tularensis) Vaxchora (V. cholerae) O. tsutsugamushi R. prowazekii | Licensed Licensed Licensed Licensed Licensed Experimental Experimental | [27] [28] [29] [7] [30] [31] [32] |
Live recombinant bacteria | M. tuberculosis R. rickettsii C. burnetii S. aureus | Experimental Experimental Experimental Experimental | [33] [34] [35] [36] |
subunit vaccines | dTAP combined vaccine (C. tetani) dTAP combined vaccine (B. pertussis) Trumenba (N. meningitidis) rPA102 (B. anthracis) S. aureus Trumenba (N. meningitidis) | Licensed Licensed Licensed clinical trial Experimental Licensed | [37] [38] [39] [40] [41] [42] |
Polysaccharide conjugates | PedvaxHIB, ActHIB, HibTITER (H. influenzae) Prevnar 13, Pneumovax 23 (S. pneumoniae) Menactra, Menveo, Menomune (N. meningitidis) | Licensed Licensed Licensed | [43] [44,45] [46] |
Viral vectors | 85A antigen (M. tuberculosis) | Licensed | [47] |
Bacterial vectors | H. pylori (S. typhimurium) encoding urease A and B subunits Y. enterolica encoding bacterioferritin (B. abortus) L. monocytogenes encoding antigen 85 complex and MPB7MpT51 antigen (M. tuberculosis) | Experimental Experimental Experimental | [48] [49] [50] |
Plasmid DNA | M. tuberculosis (hsp65 from M. leprae) B. anthracis (PA antigen) | Experimental Experimental | [51] [52] |
BGs | Y. pestis S. typhimurium enteritides (BGs expressing flagellin) BGs carrying DNA for N. ghonorhea antigens | Experimental Experimental Experimental | [22] [53] [54] |
OMVs | Bexsero/4CMenB, VA-MENGOC-BC, MeNZB, MenBVac (N. meningitidis serogroup B) B. pertussis BCG C. trachomatis V. cholerae M. smegmatis T. pallidum | Licensed Experimental Experimental Experimental Experimental Experimental Experimental | [55,56,57] [22] [22] [58] [58] [58] [58] |
3. Genomics Revolution
4. Genome-Based Approaches
5. An In-Silico Approach: Reverse Vaccinology (RV)
6. Pan-Genomics Analysis or Comparative Genomics
7. Antigen Prioritization
8. Functional Genomics: Genes Essential for Vaccine Candidates
9. Transcriptomics: Expression Profile Identifies Potential Vaccines
10. Proteomics: A Genomic Complement for Vaccine Development
11. Next-Generation Epitope Mapping and Vaccine Design: Structural Genomics/Vaccinology
12. Synthetic Genomics: The Future of Vaccine Development
13. Conclusions and Future Direction
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Tool Category | Bioinformatics Tool | Description/Web Site |
---|---|---|
General tools | Basic Local Alignment Search Tool (BLAST) | Sequence similarity database http://www.ncbi.nlm.nih.gov/BLAST/ (accessed on 2 September 2022) |
Protein Subcellular Localization Predictor Tool for bacteria (PSORTb) | Bacterial protein subcellular localization (SCL) predictor http://www.psort.org/psortb/ (accessed on 2 September 2022) | |
Signal peptides (SignalP) | Prediction of signal peptides http://www.cbs.dtu.dk/services/SignalP/ (accessed on 2 September 2022) | |
Expert Protein Analysis System (EXPASY) | Translate nucleotide to protein http://www.expasy.org/ (accessed on 2 September 2022) | |
Protein Data Bank (PDB) | Structure of protein http://www.pdb.org/pdb/home/home.do (accessed on 2 September 2022) | |
Protein Variability Server (PVS) | Sequence variability calculator http://imed.med.ucm.es/PVS/ (accessed on 2 September 2022) | |
Allergenic Prediction (AlgPred) | Predicting allergenic proteins and allergenic regions in a protein http://www.imtech.res.in/raghava/algpred/ (accessed on 2 September 2022) | |
T cell epitope prediction | Epitopes Major Histocompatibility Complex (EPIMHC) | MHC-binding peptides and T cell epitopes http://bio.dfci.harvard.edu/epimhc/ (accessed on 2 September 2022) |
Cytotoxic T lymphocytes Predication (CTL PRED) | Direct approach for CTL epitope prediction essential for designing subunit vaccines http://www.imtech.res.in/raghava/ctlpred/ (accessed on 2 September 2022) | |
EpiVax | Epimatrix algorithm http://www.epivax.com/ (accessed on 2 September 2022) | |
Kernel-based Inter-allele peptide binding prediction SyStem (KISS) | SVM-based method KISS http://cbio.ensmp.fr/kiss/ (accessed on 2 September 2022) | |
Protein Predication (ProPred) | Web-based graphical prediction tool for MHC class II binding sites in antigenic protein sequences http://www.imtech.res.in/raghava/propred/ (accessed on 2 September 2022) | |
IMTECH | Quantitative matrix approach http://www.imtech.res.in/raghava/mhc (accessed on 2 September 2022) | |
Promiscuous EPitope-based VACcine (PEPVAC) | Prediction of promiscuous epitopes http://immunax.dfci.harvard.edu/PEPVAC/ (accessed on 2 September 2022) | |
RANKPEP | Predicts peptide binders to MHCI and MHCII http://bio.dfci.harvard.edu/Tools/rankpep.html (accessed on 2 September 2022) | |
SYFPEITHI | Database for searching and T cell epitope prediction http://www.syfpeithi.de/ (accessed on 2 September 2022) | |
Immune Epitope Database (IEDB) | Identification of novel B and T cell epitopes in proteins of interest http://www.immuneepitope.org/ (accessed on 2 September 2022) | |
NetCTL 1.2 Server | Verified Prediction of CTL epitopes in protein sequences http://www.cbs.dtu.dk/services/NetCTL/ (accessed on 2 September 2022) | |
Major Histocompatibility Complex Predication (MHCPred) | A quantitative T cell epitope prediction server http://www.ddg-pharmfac.net/mhcpred/MHCPred/ (accessed on 2 September 2022) | |
NetMHC 3.0 | Predicts peptide binding to variety of different HLA alleles http://www.cbs.dtu.dk/services/NetMHC/ (accessed on 2 September 2022) | |
Support Vector machine-based method form MHC (SVMHC) | Prediction of MHC-binding peptides https://abi.inf.uni-tuebingen.de/Services/SVMHC (accessed on 2 September 2022) | |
EpiJen | Multistep algorithm for T cell epitope prediction http://www.ddg-pharmfac.net/epijen/EpiJen/ (accessed on 2 September 2022) | |
Major Histocompatibility Complex Binding and Non-binding peptides (MHCBN) | Information about MHC binders, MHC non-binder, TAP binders, TAP non-binders, and T cell epitopes http://www.imtech.res.in/raghava/mhcbn/ (accessed on 2 September 2022) | |
B cell epitope tools | B-cell epitopes predication 2.0 (BepiPred 2.0) | Continuous B cell epitope identification http://www.cbs.dtu.dk/services/BepiPred/ (accessed on 2 September 2022) |
B-cell predication (Bcepred) | Continuous B cell epitope identification http://crdd.osdd.net/raghava/bcepred/ (accessed on 2 September 2022) | |
B-cell Epitope prediction using Support vector machine Tool (BEST) | Continuous B cell epitope identification http://biomine.cs.vcu.edu/datasets/BEST/ (accessed on 2 September 2022) | |
Continuous B-cell Epitopes Pro (COBEpro) | Predictions on short peptide fragments http://scratch.proteomics.ics.uci.edu/ (accessed on 2 September 2022) | |
Conformational B-cell Epitope predication (CBTOPE) | Prediction of conformational B cell epitope http://crdd.osdd.net/raghava/cbtope/submit.php (accessed on 2 September 2022) | |
DiscoTope 2.0 | Discontinuous B cell epitopes prediction http://www.cbs.dtu.dk/services/DiscoTope/ (accessed on 2 September 2022) | |
Peptide epitope (Pepitope) | Continuous and discontinuous B cell epitopes prediction http://pepitope.tau.ac.il/ (accessed on 2 September 2022) | |
Epitopia | Continuous and discontinuous B cell epitope prediction http://epitopia.tau.ac.il/ (accessed on 2 September 2022) | |
DiscoTope 1.2 Server | Uses 3D structure of protein to forecast discontinuous B cell epitopes http://www.cbs.dtu.dk/services/DiscoTope/ (accessed on 2 September 2022) | |
Linear B-cell epitopes (LBtope) | Accurate method for linear B cell epitopes (https://webs.iiitd.edu.in/raghava/lbtope/ (accessed on 2 September 2022) | |
Ellipsoid and Protrusion (ElliPro) | Method used for continuous and discontinuous B cell epitopes prediction http://www.pepitope.tau.ac.il/ (accessed on 2 September 2022) | |
Artificial neural network-based B-cell epitope prediction (ABCpred) | Predicting linear B cell epitopes (https://webs.iiitd.edu.in/raghava/abcpred/ (accessed on 2 September 2022) | |
Proteasomal cleavage (Pcleavage) | Proteasomal cleavage site identification (https://webs.iiitd.edu.in/raghava/pcleavage/ (accessed on 2 September 2022) | |
A database for B-Cells Epitopes (BCIPEP) | B cell epitope validation http://www.imtech.res.in/raghava/bcipep/index.html (accessed on 2 September 2022) |
Bacteria | Disease | Techniques | Vaccine Status |
---|---|---|---|
C. pneumoniae | Pneumonia, meningitis, middle ear infections | Reverse vaccinology Proteomics Pan-genomic | Discovery/pre-clinical |
B. anthracis | Anthrax | Reverse vaccinology CGH microarray Microarray Proteomics Immunoproteomics Antigen prioritization | Discovery/pre-clinical |
R. prowazekii | Epidemic typhus, also called louse-borne typhus | Reverse vaccinology Proteomics Pan-genomic | Discovery/pre-clinical |
M. tuberculosis | Tuberculosis | Reverse vaccinology Structural genomics/vaccinology Synthetic genomics Antigen prioritization Pan-genomic | Discovery/pre-clinical |
H. pylori | Ulcer, atrophic gastritis, adenocarcinoma, lymphoma | Reverse vaccinology Immunoproteomics Pan-genomic | Discovery/pre-clinical |
P. gingivalis | Periodontitis | Reverse vaccinology | Discovery/pre-clinical |
N.meningitidis serogroup B | Bacterial meningitis and septicemia | Reverse vaccinology Microarray Proteomics | Phase II clinical trials |
Brucella | Brucellosis | Proteomics | Discovery/pre-clinical |
L. monocytogenes | Invasive foodborne infections. | Proteomics | Phase 1 clinical trials |
Bacteria | Developed Vaccine/Antigen Identified by Pan-Genomics | References |
---|---|---|
N. meningitidis | 4CMenB (Bexsero®) vaccine | [141] |
C. pneumoniae | LcrE antigen | [102] |
Brucella | RV web-based vaccine design program (VaxiJen), that identified O-sialoglycoprotein endopeptidase; 32 OMPs (Omp2b, Omp25, Omp31-1, TonB, adhesins, and adhesin-like proteins (FlgE and FlgK) | [142] |
S. agalactiae | GBS322 (SAG0032, Sip protein), GBS67 (SAG1408), GBS80 | [95] |
(SAG0645), GBS104 (SAG0649) proteins | [143] | |
HMW pilus-based vaccine | [144] | |
S. pneumoniae | Sp36, Sp46, Sp91, Sp101, and Sp128/130 protective antigens (cell wall anchor) | [89] |
RrgB321 (fusion protein of three RrgB variants) | [145] | |
S. pyogenes (GAS) | Cpa, MI_128, and MI_130 (Recombinant pilus protein) | [96] |
Protective antigen Spy0416 | [146] | |
L. pneumophila | Q5ZVG4, Q5ZRZ1, Q5ZWE6, Q5ZT09, and Q5ZUZ8 | [134] |
M.tuberculosis | PE/PPE, plcC | [124] |
ESAT-6 antigen and diacylglycerol acyltransferase | [129] |
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Share and Cite
Khan, M.A.; Amin, A.; Farid, A.; Ullah, A.; Waris, A.; Shinwari, K.; Hussain, Y.; Alsharif, K.F.; Alzahrani, K.J.; Khan, H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2023, 15, 152. https://doi.org/10.3390/pharmaceutics15010152
Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics. 2023; 15(1):152. https://doi.org/10.3390/pharmaceutics15010152
Chicago/Turabian StyleKhan, Muhammad Ajmal, Aftab Amin, Awais Farid, Amin Ullah, Abdul Waris, Khyber Shinwari, Yaseen Hussain, Khalaf F. Alsharif, Khalid J. Alzahrani, and Haroon Khan. 2023. "Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines" Pharmaceutics 15, no. 1: 152. https://doi.org/10.3390/pharmaceutics15010152
APA StyleKhan, M. A., Amin, A., Farid, A., Ullah, A., Waris, A., Shinwari, K., Hussain, Y., Alsharif, K. F., Alzahrani, K. J., & Khan, H. (2023). Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics, 15(1), 152. https://doi.org/10.3390/pharmaceutics15010152