In recent years we have studied the relationship between strain genotypes and patient phenotypes in group A Streptococcus (GAS), a model human bacterial pathogen that causes extensive morbidity and mortality worldwide. We have concentrated our efforts on serotype M3 organisms because these strains are common causes of pharyngeal and invasive infections, produce unusually severe invasive infections, and can exhibit epidemic behavior. Our studies have been hindered by the lack of genome-scale phylogenies of multiple GAS strains and whole-genome sequences of multiple serotype M3 strains recovered from individuals with defined clinical phenotypes. To remove some of these impediments, we sequenced to closure the genome of four additional GAS strains and conducted comparative genomic resequencing of 12 contemporary serotype M3 strains representing distinct genotypes and phenotypes. Serotype M3 strains are a single phylogenetic lineage. Strains from asymptomatic throat carriers were significantly less virulent for mice than sterile-site isolates and evolved to a less virulent phenotype by multiple genetic pathways. Strain persistence or extinction between epidemics was strongly associated with presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone significantly underrepresented among necrotizing fasciitis cases has a unique frameshift mutation that truncates MtsR, a transcriptional regulator controlling expression of genes encoding ironacquisition proteins. Expression microarray analysis of this clone confirmed significant alteration in expression of genes encoding iron metabolism proteins. Our analysis provided unprecedented detail about the molecular anatomy of bacterial strain genotypepatient phenotype relationships.carrier ͉ epidemic ͉ genomic resequencing ͉ SNP ͉ phylogeny M icrobial epidemics have repeatedly altered the course of history by decimating human populations, killing domesticated animals, and blighting crops. Despite the impact of these destructive events, we know relatively little about the evolutionary genetic events contributing to bacterial strain emergence and diversification within and between epidemic waves. Also poorly understood is the molecular basis of intraspecies variation in disease phenotype. The recent confluence of genome sequencing and development of high-throughput techniques to interrogate genetic polymorphisms in large samples of strains now permits these topics to be studied at the individual nucleotide level.Group A Streptococcus (GAS) infects humans worldwide and causes an array of diseases ranging from superficial infections such as pharyngitis to fulminant invasive infections characterized by high morbidity and mortality (1, 2). In recent years, we have used serotype M3 GAS strains as model pathogens for studying the molecular processes contributing to clone emergence, epidemic waves, and genotype-phenotype relationships (M protein is a highly polymorphic cell-surface molecule that is antiphagocytic and forms the bas...