Subgenomic DNA microarrays were employed to evaluate the expression of the accessory gene regulator (agr locus) as well as multiple virulence-associated genes in Staphylococcus aureus. Gene expression was examined during growth of S. aureus in vitro in standard laboratory medium and rabbit serum and in vivo in subcutaneous chambers implanted in either nonimmune rabbits or rabbits immunized with staphylococcal enterotoxin B. Expression of RNAIII, the effector molecule of the agr locus, was dramatically repressed in serum and in vivo, despite the increased expression of secreted virulence factors sufficient to cause toxic shock syndrome (TSS) in the animals. Statistical analysis and clustering of virulence genes based on their expression profiles in the various experimental conditions demonstrated no positive correlation between the expression of agr and any staphylococcal virulence factors examined. Disruption of the agr locus had only a minimal effect on the expression in vivo of the virulence factors examined. An effect of immunization on the expression of agr and virulence factors was also observed. These results suggest that agr activation is not necessary for development of staphylococcal TSS and that regulatory circuits responding to the in vivo environment override agr activity.A leading cause of nosocomial infections worldwide, Staphylococcus aureus is the etiologic agent of numerous diseases, ranging from relatively benign skin infections to life-threatening illnesses, such as toxic shock syndrome (TSS), septicemia, and osteomyelitis (reviewed in reference 25). Its ability to cause this range of disease is due, in part, to the expression of a wide array of secreted and cell surface-associated virulence factors. The expression of most of these virulence factors has been described as being regulated by the quorum-dependent accessory gene regulator (agr locus). The present model of agr activity and its effect on virulence factor expression is well reviewed elsewhere (15,19). Briefly, the agr locus expresses two primary, divergent transcripts. RNAII (agrBDCA) encodes a two-component system (AgrA-AgrC), recognizing the agrDencoded secreted autoinducing octapeptide (AIP), and AgrB, which is thought to act in the posttranslational processing and secretion of the AIP. The second transcript, RNAIII, acts as the effector molecule of the agr locus. A third, short transcript, RNAI, has been described as encoding AgrA. Upon accumulation in the growth medium of sufficient quantities of the AIP, usually during the transition from the exponential to the stationary phase of growth, signaling via AgrA-AgrC acts to increase transcription of both RNAII and RNAIII. In vitro, this results in the increased expression of secreted virulence factors, including the pyrogenic toxin superantigens and hemolysins, and the repression of numerous surface-associated virulence factors, typified by protein A, which binds the Fc component of immunoglobulin G.Since the identification of agr (20), models of staphylococcal virulence have assig...