Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens

Recent innovations have increased enormously the opportunities for investig ating the molecular basis of bacterial pathogenicity, including the at avai lability of whole-genome sequences, techniques for identifying key virulenc e genes, and the use of microarrays and proteomics. These methods should pr ovide powerful tools for analysing the patterns of gene expression and func tion required for investigating host-microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reduct ionist approach does not adequately address the eclectic and variable outco mes of host-microbe interactions, including evolutionary dynamics and ecolo gical factors. There are difficulties in distinguishing bacterial 'virulenc e' factors from the many determinants that are permissive for pathogenicity , for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and dis cuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies availabl e to us, we are still struggling to come to grips with the question of 'Wha t is a pathogen?'.