Drug Discovery Today  Volume 12, Numbers 11/12  June 2007 REVIEWS ‘The avalanche of genomic data will provide innovative tools to prevent and cure bacterial infections’ The pan-genome: towards a knowledge-based discovery of novel targets for vaccines and antibacterials Alessandro Muzzi, Vega Masignani and Rino Rappuoli Novartis Vaccines, Via Fiorentina 1, 53100 Siena, Italy During the past decade, sequencing of the entire genome of pathogenic bacteria has become a widely used practice in microbiology research. More recently, sequence data from multiple isolates of a single pathogen have provided new insights into the microevolution of a species as well as helping researchers to decipher its virulence mechanisms. The comparison of multiple strains of a single species has resulted in the definition of the species pan-genome, as a measure of the total gene repertoire that can pertain to a given microorganism. This concept can be exploited not only to study the diversity of a species, but also, as we discuss here, to provide the opportunity to use a knowledge-based approach for the development of novel vaccine candidates and new-generation targets for antimicrobials. Introduction After the first complete genome sequence of a free-living organism, Haemophilus influenzae, was determined in 1995 [1], whole-genome sequencing became a standard, rapid method for the study of the biological processes in living forms. During the past decade, the number of available complete genome sequences has grown exponentially and, currently, the most up-to-date genomic databases [2] contain 433 published sequences (42 eukaryotic and 391 prokaryotic); there are 1683 ongoing projects (634 eukaryotic and 1049 prokaryotic), with the chromosomal sequence of pathogenic organisms being the most represented. This increasing amount of sequence data can be used to find new strategies for the discovery of drug targets, diagnostic markers and vaccine candidates. One of the most popular applications of genomic technologies is the reverse vaccinology approach, where the whole genome of a bacterial pathogen is analyzed by computational approaches to predict in silico previously undiscovered vaccine candidates. At the beginning of the genomic era, it was thought that a single representative isolate was sufficient to describe the genetic complexity of a species, and the use of ‘comparative genomics’ was restricted to investigating the diversity among different yet closely related bacteria. More recently, isolates of the same species have been analyzed by subtractive hybridization and comparative genome hybridization (CGH). These studies have shown that intraspecies variation can be as significant as interspecies diversity [3–5]. Comparative genomics studies have revealed that the microbial genome is a dynamic entity shaped by multiple forces, including genome reduction, gene duplication and loss, genome rearrangements, and acquisition of new genes Reviews  KEYNOTE REVIEW ALESSANDRO MUZZI Alessandro Muzzi studied physics at the University of Florence, Italy. In 2000, he joined the Cellular Micro- biology and Bioinformatics Unit at Novartis Vaccines & Diagnostics in Siena, Italy, as a bioinformatics researcher. His research interests focus on bacterial genomics and microarray data analysis as applied to the discovery of targets for vaccine development. VEGA MASIGNANI Vega Masignani received her PhD in Biotechnology with a thesis on the computational approach to the development of a novel Neisseria meningitidis protein-based vaccine. She is currently a senior scientist at the Cellular Microbiology and Bioinformatics Unit of Novartis Vaccines & Diagnostics, carrying out research in the field of computer analysis as applied to microbial pathogenesis. RINO RAPPUOLI Rino Rappuoli is the Global Head of Vaccines Research at Novartis Vaccines & Diagnostics. He is member of the US National Academy of Sciences. He developed the first recombinant bacterial vaccine (against pertussis) and a conjugate vaccine against meningococcus C. Currently, he is involved in the development of a vaccine against group B meningo- coccus using a genome-based approach termed ‘reverse vaccinology,’ and in the development of a vaccine against avian influenza. Corresponding author. Rappuoli, R. (rino.rappuoli@novartis.com) 1359-6446/06/$ - see front matter ß 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.drudis.2007.04.008 www.drugdiscoverytoday.com 429