A long-term goal is to characterize the full range of genetic diversity withinStreptococcus pyogenesas it exists in the world today. Since theemmlocus is subject to strong diversifying selection,emmtype was used as a guide for identifying a genetically diverse set of strains. This report contains a description of multilocus sequence typing based on seven housekeeping loci for 495 isolates representing 158emmtypes, yielding 238 unique combinations of sequence type andemmtype. A genotypic marker for tissue site preference (emmpattern) revealed that only 17% of theemmtypes displayed the marker representing strong preference for infection at the throat and that 39% ofemmtypes had the marker for skin tropism, whereas 41% ofemmtypes harbored the marker for no obvious tissue site preference. As a group, theemmtypes bearing theemmpattern marker indicative of no obvious tissue site preference were far less likely to have two distinctemmtypes associated with the same sequence type than either of the two subpopulations having markers for strong tissue tropisms (P< 0.002). In addition, all genetic diversification events clearly ascribed to a recombinational mechanism involved strains of only two of theemmpattern-defined subpopulations, those representing skin specialists and generalists. The findings suggest that the population genetic structure differs for the tissue-defined subpopulations ofS. pyogenes. The observed differences may partly reflect differential host immune selection pressures.

The FCT regions ofStreptococcus pyogenesstrains encode a variety of cell wall-anchored surface proteins that bind the extracellular matrix of the human host and/or give rise to pilus-like appendages. Strong linkage is evident between transcription-regulatory loci positioned within the FCT andemmregions and theemmpattern genotype marker for preferred infection of the throat or skin. These findings provide a basis for the hypothesis that FCT region gene products contribute to tissue-specific infection. In an initial series of steps to address this possibility, the FCT regions of 13 strains underwent comparative sequence analysis, the gene content of the FCT region was characterized for 113 strains via PCR, and genetic linkage was assessed. A history of extensive recombination within FCT regions was evident. Theemmpattern D-defined skin specialist strains were highly homogenous in their FCT region gene contents, whereas theemmpattern A-C-defined throat specialist strains displayed a greater variety of forms. Most pattern A-C strains harboredprtF1(75%) but lackedcpa(75%). In contrast, the majority ofemmpattern D strains hadcpa(92%) but lackedprtF1(79%). Models based on FCT andemmregion genotypes revealed the most parsimonious pathways of evolution. Using niche-determining candidate genes to infer phylogeny,emmpattern E strains—the so-called generalists, which lack a strong tissue site preference—occupied a transition zone separating most throat specialists from skin specialists. Overall, population genetic analysis supports the possibility that the FCT region gives rise to surface proteins that are largely necessary, but not always sufficient, to confer tissue site preference for infection.

The molecular mechanisms underlying niche adaptation in bacteria are not fully understood. Primary infection by the pathogen group A streptococcus (GAS) takes place at either the throat or the skin of its human host, and GAS strains differ in tissue site preference. Many skin-tropic strains bind host plasminogen via the plasminogen-binding group A streptococcal M protein (PAM) present on the cell surface; inactivation of genes encoding either PAM or streptokinase (a plasminogen activator) leads to loss of virulence at the skin. Unlike PAM, which is present in only a subset of GAS strains, the gene encoding streptokinase (ska) is present in all GAS isolates. In this study, the evolution of the virulence genes known to be involved in skin infection was examined. Most genetic diversity withinskagenes was localized to a region encoding the plasminogen-docking domain (β-domain). The gene encoding PAM displayed strong linkage disequilibrium (P≪ 0.01) with a distinct phylogenetic cluster of theskaβ-domain-encoding region. Yet,skaalleles of distant taxa showed a history of intragenic recombination, and high intrinsic levels of recombination were found among GAS strains having different tissue tropisms. The data suggest that tissue-specific adaptations arise from epistatic coselection of bacterial virulence genes. Additional analysis ofskagenes showed that ∼4% of the codons underwent strong diversifying selection. Horizontal acquisition of oneskalineage from a commensalStreptococcusdonor species was also evident. Together, the data suggest that new phenotypes can be acquired through interspecies recombination between orthologous genes, while constrained functions can be preserved; in this way, orthologous genes may provide a rich and ready source for new phenotypes and thereby play a facilitating role in the emergence of new niche adaptations in bacteria.

Streptococcus pyogenes is a highly prevalent bacterial pathogen, most often giving rise to superficial infections at the throat or skin of its human host. Three genotype-defined subpopulations of strains exhibiting strong tropisms for either the throat or skin (specialists) or having no obvious tissue site preference (generalists) are recognized. Since the microenvironments at the throat and skin are distinct, the signal transduction pathways leading to the control of gene expression may also differ for throat versus skin strains of S. pyogenes . Two loci ( mga and rofA/nra ) encoding global regulators of virulence gene expression are positioned 300 kb apart on the genome; each contains alleles forming two major sequence clusters of ∼25 to 30% divergence that are under balancing selection. Strong linkage disequilibrium is observed between sequence clusters of the transcription regulatory loci and the subpopulations of throat and skin specialists, against a background of high recombination rates among housekeeping genes. A taxonomically distinct commensal species ( Streptococcus dysgalactiae subspecies equisimilus ) shares highly homologous rof alleles. The findings provide strong support for a mechanism underlying niche specialization that involves orthologous replacement of regulatory genes following interspecies horizontal transfer, although the directionality of gene exchange remains unknown.