The genomes of important human pathogens are under intense scrutiny — the goals being to understand the basis of their virulence and to design more effective antimicrobial drugs. Important steps towards unravelling the secrets of virulence evolution are described in recent articles that report the genome sequences of two microbial pathogens — Yersinia pestis , the agent of plague, and Rickettsia conori , which causes Mediterranean spotted fever. In a third study, which takes a more functional approach, Yinduo Ji et al. have devised a method to find potential virulence genes in Staphylococcus aureus .

The 4.6-Mb genome of Y. pestis seems to be in flux. Parkhill et al. found signs of old genomic expansions — probably a result of horizontal transfer — that preceded the split of Y. pestis from its close cousin Yersinia pseudotuberculosis . This expansion has been followed by the first signs of genome downsizing, associated with a decay of previously active genes into pseudogenes. In part, this seems to reflect a change in the pathogen's lifestyle: the genes necessary for the enteropathogen Y. pseudotuberculosis in its environment within the host's gut, such as adhesion genes, have become pseudogenes in the bloodstream-dwelling Y. pestis. Adaptation to different environments is also reflected in the accumulation of mutations in genes responsible for the uptake and transport of different nutrients in the two species.

Similar studies were conducted by Ogata et al., who sequenced the R. conorii genome (1.2 Mb) and compared it with that of its close relative, Rickettsia prowazekii . These intracellular parasites diverged 40–80 million years ago, so this comparison provided interesting insight into adaptations associated with different intracellular lifestyles. As expected, there seems to be a tendency to streamline the genome. For example, the authors discovered evidence of decaying orthologues — a group of 229 genes in R. conorii had homology to non-coding sequences in R. prowazekii. Nevertheless, some gene families do exist, and they point to processes, such as importing the host cell's ATP, which represent important adaptations of these pathogens.

In an independent approach to identifying essential genes in S. aureus (the sequence of which was published last year), Ji and colleagues subcloned random 200–800-bp fragments of S. aureus DNA into plasmids, downstream of a tetracycline-inducible promoter. Bacteria transformed with these constructs were replica plated and grown in the presence or absence of a tetracycline analogue. This allowed the authors to look for constructs that prevented bacterial growth as a result of induced antisense RNA expression. Of the 600 constructs that were identified, ∼200 contained an open reading frame in an antisense orientation, and 30% of these had no known function. To test whether this approach could be extended to an in vivo context, Ji et al. infected mice with bacteria that contain a construct expressing antisense RNA to a known essential gene. Whereas control mice developed a heavy kidney infection within 72 h, mice induced to express the antisense construct suffered no infection.

Comparative and functional genomics of pathogenic species and their relatives will continue to provide invaluable insights into the evolution of pathogenicity and adaptation. The potential for substantial benefits to human health is tantalizing.