Multilocus Sequence Typing ofStreptococcus pyogenesRepresenting Most KnownemmTypes and Distinctions among Subpopulation Genetic Structures

Abstract

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.