Current methods for differentiating isolates of predominant lineages of pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides a high-resolution view of the epidemiology and microevolution of a dominant strain of methicillin-resistant Staphylococcus aureus (MRSA). This approach reveals the global geographic structure within the lineage, its intercontinental transmission through four decades, and the potential to trace person-to-person transmission within a hospital environment. The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology.

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Exposure of Staphylococcus aureus to cell wall inhibitors induces massive overexpression of a number of genes, provided that the VraSR two-component sensory regulatory system is intact. Inactivation of vraS blocks this transcriptional response and also causes a drastic reduction in the levels of resistance to beta-lactam antibiotics and vancomycin. We used an experimental system in which the essential cell wall synthesis gene of S. aureus, pbpB, was put under the control of an isopropyl-␤-D-thiogalactopyranoside-inducible promoter in order to induce reversible perturbations in cell wall synthesis without the use of any cell wall-active inhibitor. Changes in the level of transcription of pbpB were rapidly followed by parallel changes in the vraSR signal, and the abundance of the pbpB transcript was precisely mirrored by the abundance of the transcripts of vraSR and some additional genes that belong to the VraSR regulon. Beta-lactam resistance in S. aureus appears to involve a complex stress response in which VraSR performs the critical role of a sentinel system capable of sensing the perturbation of cell wall synthesis and allowing mobilization of genes that are essential for the generation of a highly resistant phenotype. One of the sites in cell wall synthesis "sensed" by the VraSR system appears to be a step catalyzed by PBP 2.Brief exposure of Staphylococcus aureus to inhibitors of cell wall synthesis invoke an immediate and massive change in the transcription of a unique set of genes, some of which-such as mgtB, murZ, and pbpB-are clearly involved with wall biosynthesis, while others have as yet undefined functions (14,16,31). It was proposed that these genes be referred to as members of a coordinately regulated "cell wall stimulon" (31). A particularly interesting member of this group of genes is vraSR, the DNA sequence of which shows features typical of a two-component sensory regulatory system (14). A careful study by Kuroda and colleagues (14) has demonstrated that transcription of vraSR is a specific response to inhibitors of various stages in wall synthesis: inhibitors of other cellular polymers and/or conditions of stress, such as shifts in temperature, pH, or osmotic pressure, did not alter the transcription of vraSR. Furthermore, and most importantly, the burst of transcription of genes following exposure to cell wall inhibitors was greatly reduced and/or annulled in bacteria in which vraSR was inactivated (14), indicating the essentiality of an intact vraSR system for this response. On the basis of these observations, it was proposed that VraSR functions as a sentinel system capable of detecting conditions that threaten to interrupt the synthesis of the bacterial cell wall. Nevertheless, the precise site(s) of perturbation of wall synthesis "sensed" by this system has just begun to be explored. Recent studies by Boyle-Vavra, Daum, and colleagues have allowed a better definition of the vraSR operon and its mode of induction by cell wall-active antibiotics (2, 3, 32).Kuroda and colleagues (14) also ...