title: Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery.
abstract: New generation vaccines are in demand to include only the key antigens sufficient to confer protective immunity among the plethora of pathogen molecules. In the last decade, large-scale genomics-based technologies have emerged. Among them, the Reverse Vaccinology approach was successfully applied to the development of an innovative vaccine against Neisseria meningitidis serogroup B, now available on the market with the commercial name BEXSERO® (Novartis Vaccines). The limiting step of such approaches is the number of antigens to be tested in in vivo models. Several laboratories have been trying to refine the original approach in order to get to the identification of the relevant antigens straight from the genome. Here we report a new bioinformatics tool that moves a first step in this direction. The tool has been developed by identifying structural/functional features recurring in known bacterial protective antigens, the so called "Protectome space," and using such "protective signatures" for protective antigen discovery. In particular, we applied this new approach to Staphylococcus aureus and Group B Streptococcus and we show that not only already known protective antigens were re-discovered, but also two new protective antigens were identified.
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Emrah
authors.initials: E
authors.lastname: Altindis
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Cozzi
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Benedetta
authors.initials: B
authors.lastname: Di Palo
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Necchi
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Ravi P
authors.initials: RP
authors.lastname: Mishra
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Maria Rita
authors.initials: MR
authors.lastname: Fontana
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Soriani
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Bagnoli
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Maione
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy guido.grandi@unitn.it.
authors.forename: Guido
authors.initials: G
authors.lastname: Grandi
authors.affiliation: From the ‡Research Department, Novartis Vaccines and Diagnostics, 53100 Siena, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Liberatori
mesh_terms: D015720:5'-Nucleotidase / Q000378:metabolism; D000818:Animals; D001426:Bacterial Proteins / Q000276:immunology; D001428:Bacterial Vaccines / Q000276:immunology*; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D004195:Disease Models, Animal; D005260:Female; D051379:Mice; D038541:Neisseria meningitidis, Serogroup B / Q000276:immunology; D021382:Protein Sorting Signals; D020543:Proteome / Q000276:immunology*; D015203:Reproducibility of Results; D013211:Staphylococcus aureus / Q000276:immunology; D013292:Streptococcus agalactiae / Q000276:immunology
chemical_list: D001426:Bacterial Proteins; D001428:Bacterial Vaccines; D021382:Protein Sorting Signals; D020543:Proteome; D015720:5'-Nucleotidase