Genome sequencing and annotation Comprehensive identification of virulence gene candidates by various means Bioinformatic prioritization of virulence gene candidates and generation of hypotheses regarding functions of encoded factors Experimental determination of functions of individual virulence factors Integrate knowledge of factors for use in: -eco-evo-systems biology study of pathogen -comparative genomics “Characterization bottleneck” Pathogenomics research overview StepsLimitations (Conserved) hypotheticals and misannotation next-gen sequencing problems with “mobilome” Ongoing curation Protein structure/function prediction Bioinformatic and experimental screens

Andrews-Polymenis et al Vivo

Sassetti and Rubin 2002

Wolfgang et al Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa

rpoS was downregulated in biofilm Whiteley et al Gene expression in Pseudomonas aeruginosa biofilms

Rediers et al. 2005

Valdivia and Falkow 1997 Fluorescence-based isolation of bacterial genes expressed within host cells

Valdivia and Falkow 1997

Chang et al A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae

Lindeberg et al Collmer et al. 2002

Tobe et al An extensive repertoire of type III secretion effectors in Escherichia coli O157

Mazurkiewicz et al Signature-tagged mutagenesis

Mazurkiewicz et al TraSH = Transposon site hybridization 

Mazurkiewicz et al. 2006

Jacobs et al Comprehensive transposon mutant library of Pseudomonas aeruginosa

Jacobs et al. 2003

Comprehensive transposon mutant library of Pseudomonas aeruginosa

Medini et al. 2008

Metzker 2010

Langridge et al. 2009

Sorek and Cossart 2010

Chain et al. 2009

Howe et al. 2008