Genetically Diverse Group A Streptococci from Children in Far-Western Nepal Share High Genetic Relatedness with Isolates from Other Countries

The genetic diversity of group A streptococci (GAS) throughout much of the world has not been adequately explored. To assess genetic variation among GAS in western Nepal, 120 noninvasive GAS, collected from eight different villages, were genetically characterized usingemm typing,sof sequencing, and multilocus sequence typing (MLST). A high level of genetic diversity was observed among these isolates, with 51 genotypes based upon 51 multilocus sequence types (STs), 45emm sequence types, and 28sof sequence types. On the basis of shared ST-emm andsof -emm associations, 40 of the 51 genotypes were identical or highly related to genotypes characterized from locations outside of Nepal, even though most of theemm sequence and clonal types are rare among GAS within the United States. When analyzing all known STs highly related to Nepal STs, only one example of similar STs shared between asof PCR-positive strain and asof PCR-negative strain was observed. Since previous data indicate free exchange of MLST loci betweensof -positive andsof -negative strains, there is possibly selection against the expansion of subclones resulting from horizontal transfers ofsof oremm genes betweensof -positive andsof -negative strains. All 45emm types encountered in Nepal have also been documented from other countries. These data, together with data encompassing the past decade ofemm type surveillance, support the possibility that most existing GASemm types have been discovered. Similarly, since most (40/51) strain types were highly related to strains found elsewhere, it is likely that a major fraction of the existing GAS clonal complexes have been discovered.