Genome sequencing of group A Streptococcus (GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the emm gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the emm28 gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the emm28 gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (mefA, ermB, and ermTR) was analyzed by PCR, and less than 2% of the strains were positive.Research on group A Streptococcus (GAS) host-pathogen interactions has been aided greatly by the recent publication of genome sequences from serotype M1, M3, M6, and M18 strains (1,5,16,38,48,51). The availability of multiple genome sequences has also increased our understanding of GAS molecular population genetics, species diversity, and strain variation within and between M-protein serotypes. The majority of differences in gene content between strains are located in 35-to 45-kb insertions corresponding to prophages, prophage-like elements, and other exogenous sequences (1-6, 16, 38, 48, 51) (for simplicity, the term prophage will be used to refer to prophages or prophage-like elements). The genome of each sequenced GAS strain is polylysogenic, and 23 distinct prophages have been described (1-6, 16, 38, 48, 51). Twenty of these 23 prophages encode one or two proven or putative extracellular virulence factors, including pyrogenic toxin superantigens (speA, speC, speH, speI, speK, speL, speM, and ssa), DNases (spd1, spd3, spd4, sdn, and sda), a phospholipase A 2 (slaA), macrolide resistance (mefA), and a novel cell surface protein of unknown function (1-5, 16, 37, 38, 48, 51).The contribution of serotype M28 GAS strains to human morbidity and mortality has often been underappreciated in part because serotypes such as M1 and M3 att...