The use of genomics in microbial vaccine development

Vaccination is one of the most effective tools for the prevention of infectious diseases. The availability of complete genome sequences, together with the progression of high-throughput technologies such as functional and structural genomics, has led to a new paradigm in vaccine development. Pan-genomic reverse vaccinology, with the comparison of sequence data from multiple isolates of the same species of a pathogen, increases the opportunity of the identification of novel vaccine candidates. Overall, the conventional empiric approach to vaccine development is being replaced by vaccine design. The recent development of synthetic genomics may provide a further opportunity to design vaccines.

[1]  James Theiler,et al.  Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants , 2007, Nature Medicine.

[2]  R. Nogarotto,et al.  Genomic Approach for Analysis of Surface Proteins in Chlamydia pneumoniae , 2002, Infection and Immunity.

[3]  Christian Drosten,et al.  Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome , 2003, Science.

[4]  J F Hocquette,et al.  Where are we in genomics? , 2005, Journal of physiology and pharmacology : an official journal of the Polish Physiological Society.

[5]  J. Venter,et al.  Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. , 2000, Science.

[6]  H. Tettelin,et al.  Identification of a Universal Group B Streptococcus Vaccine by Multiple Genome Screen , 2005, Science.

[7]  N. Ariel,et al.  Search for Potential Vaccine Candidate Open Reading Frames in the Bacillus anthracis Virulence Plasmid pXO1: In Silico and In Vitro Screening , 2002, Infection and Immunity.

[8]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Betts.  Transcriptomics and Proteomics: Tools for the Identification of Novel Drug Targets and Vaccine Candidates for Tuberculosis , 2002, IUBMB life.

[10]  S. Salzberg,et al.  The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria , 2003, Nature.

[11]  Rino Rappuoli,et al.  Post‐genomic vaccine development , 2006, FEBS letters.

[12]  R. Rappuoli,et al.  A universal vaccine for serogroup B meningococcus. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Daniel C. Douek,et al.  The Rational Design of an AIDS Vaccine , 2006, Cell.

[15]  Evan Powell,et al.  Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome , 2007, Journal of bacteriology.

[16]  J. Mattick,et al.  Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis. , 2001, Vaccine.

[17]  G. Bensi,et al.  Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome , 2006, Nature Biotechnology.

[18]  N. Bergman,et al.  Transcriptional Profiling of Bacillus anthracis during Infection of Host Macrophages , 2007, Infection and Immunity.

[19]  R. Rappuoli,et al.  The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials. , 2007, Drug discovery today.

[20]  A. Shafferman,et al.  Identification of In Vivo-Expressed Immunogenic Proteins by Serological Proteome Analysis of the Bacillus anthracis Secretome , 2007, Infection and Immunity.

[21]  Anne S De Groot,et al.  Immunomics: discovering new targets for vaccines and therapeutics. , 2006, Drug discovery today.

[22]  Ren Zhang,et al.  The impact of comparative genomics on infectious disease research. , 2006, Microbes and infection.

[23]  Peter F. Hallin,et al.  Ten years of bacterial genome sequencing: comparative-genomics-based discoveries , 2006, Functional & Integrative Genomics.

[24]  J. Weber,et al.  Transcriptome Analysis of Neisseria meningitidis during Infection , 2003, Journal of bacteriology.

[25]  Z. Younossi,et al.  Hepatitis C: an update on the silent epidemic. , 2000, Journal of clinical gastroenterology.

[26]  Liang Tong,et al.  Conserved Surface Features Form the Double-stranded RNA Binding Site of Non-structural Protein 1 (NS1) from Influenza A and B Viruses* , 2007, Journal of Biological Chemistry.

[27]  C. Fraser,et al.  Application of microbial genomic science to advanced therapeutics. , 2005, Annual review of medicine.

[28]  Gary J. Nabel,et al.  A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice , 2004, Nature.

[29]  B. Barrell,et al.  Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity. , 2001, Genome research.

[30]  R. Rappuoli,et al.  Reverse vaccinology: a genome-based approach for vaccine development , 2002, Expert opinion on biological therapy.

[31]  Rino Rappuoli,et al.  Reverse Vaccinology and Genomics , 2003, Science.

[32]  L. Huber,et al.  Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis , 2002, Proteomics.

[33]  P. Martelli,et al.  Postgenomics of Neisseria meningitidis for vaccines development , 2007, Expert review of proteomics.

[34]  W. Wimley,et al.  Viroporin potential of the lentivirus lytic peptide (LLP) domains of the HIV-1 gp41 protein , 2007, Virology Journal.

[35]  A. Mccarthy.  Development , 1996, Current Opinion in Neurobiology.

[36]  H. Mizoguchi,et al.  Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray , 2004, Journal of bacteriology.

[37]  I. Outschoorn,et al.  Current status of meningococcal group B vaccine candidates: capsular or noncapsular? , 1994, Clinical Microbiology Reviews.

[38]  Georgios S. Vernikos.  Genome watch: Overtake in reverse gear , 2008, Nature Reviews Microbiology.

[39]  Pamela G. Guren,et al.  Candidates , 1982, Otolaryngology–Head and Neck Surgery.

[40]  Claudio Donati,et al.  Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. , 2006, Current opinion in microbiology.

[41]  Steven E Brenner,et al.  The Impact of Structural Genomics: Expectations and Outcomes , 2005, Science.

[42]  A. Ljungh,et al.  Identification of novel immunogenic proteins of Helicobacter pylori by proteome technology. , 2002, Journal of immunological methods.

[43]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[44]  Matthew N Davies,et al.  Harnessing bioinformatics to discover new vaccines. , 2007, Drug discovery today.

[45]  R. Rappuoli.  From Pasteur to genomics: progress and challenges in infectious diseases , 2004, Nature Medicine.

[46]  Theresa M. Wizemann,et al.  Use of a Whole Genome Approach To Identify Vaccine Molecules Affording Protection against Streptococcus pneumoniae Infection , 2001, Infection and Immunity.

[47]  R. Rappuoli,et al.  Genome-derived vaccines , 2004, Expert review of vaccines.

[48]  Adeline R. Whitney,et al.  Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[49]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[50]  R. Zagursky,et al.  Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. , 2000, Vaccine.

[51]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[52]  A. Ko,et al.  Surfaceome of Leptospira spp , 2005, Infection and Immunity.

[53]  D. K. Kaushik,et al.  Developing Antibacterial Vaccines in Genomics and Proteomics Era , 2008, Scandinavian journal of immunology.

[54]  S. Salzberg,et al.  Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. , 2000, Science.

[55]  R. Zuerner,et al.  Genomics and vaccine development. , 2007, Revue scientifique et technique.

[56]  R. Rappuoli,et al.  Subunit S1 of pertussis toxin: mapping of the regions essential for ADP-ribosyltransferase activity. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[57]  H. Tettelin,et al.  Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays , 2002, Nature Biotechnology.

[58]  P. Williams,et al.  A Functional Gene Array for Detection of Bacterial Virulence Elements , 2007, PloS one.

[59]  P. Schrotz-King,et al.  Streptococcus pneumoniae: proteomics of surface proteins for vaccine development. , 2008, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[60]  Kate E. Jones,et al.  Global trends in emerging infectious diseases , 2008, Nature.