agr is a global regulatory system in the staphylococci, operating by a classical two-component signaling module and controlling the expression of most of the genes encoding extracellular virulence factors. As it is autoinduced by a peptide, encoded within the locus, that is the ligand for the signal receptor, it is a sensor of population density or a quorum sensor and is the only known quorum-sensing system in the genus. agr is conserved throughout the staphylococci but has diverged along lines that appear to parallel speciation and subspeciation within the genus. This divergence has given rise to a novel type of interstrain and interspecies cross-inhibition that represents a fundamental aspect of the organism's biology and may be a predominant feature of the evolutionary forces that have driven it. We present evidence, using a newly developed, luciferasebased agr typing scheme, that the evolutionary divergence of the agr system was an early event in the evolution of the staphylococci and long preceded the development of the nucleotide polymorphisms presently used for genotyping. These polymorphisms developed, for the most part, within different agr groups; mobile genetic elements appear also to have diffused recently and, with a few notable exceptions, have come to reside largely indiscriminately within the several agr groups.The agr operon encodes a global regulatory system in the staphylococci, central to the biology of the organism (reviewed by Novick) (36). It controls a large set of genes, including most of those encoding extracellular virulence factors and many others encoding cytoplasmic proteins with catabolic and other functions. agr is highly conserved throughout the staphylococci but has diverged in a way that closely parallels speciation and subspeciation within the genus. This divergence has given rise to a novel type of interstrain and interspecies cross-inhibition that may represent the selective forces that have driven its evolution.agr operates by a classical two-component signaling module (Fig. 1A). It is autoinduced by a peptide, encoded within the locus, that is the ligand for the histidine kinase component of the signaling module. agr is therefore a sensor of population density or a quorum sensor. The agr variants represent specificity groups that determine the response to cognate or heterologous autoinducing peptides (AIPs). Although an AIP always activates its cognate agr locus, it competitively crossinhibits agr activation in most heterologous combinations. This cross-inhibition results in a novel type of bacterial interference in which the expression of accessory genes, but not growth, is blocked. This interference has potential therapeutic implications that are presently under investigation. In Staphylococcus aureus there are four known agr specificity groups, characterized by major sequence variations in a central region of the locus that encodes the AIP, the enzyme that processes it, and the receptor domain of the histidine kinase (7,19,21). The sequences flanking this central variab...