Global epidemiological comparison of Streptococcus pyogenes emm-types associated with pharyngitis and pharyngeal carriage.

Objectives To test the prevailing dogma that S. pyogenes emm-types that cause pharyngitis are the same as those associated with carriage, using a global dataset. Methods Drawing on our systematic review of the global distribution of S. pyogenes emm-types and emm-clusters from 1990 to 2023, we compared the distribution and diversity of strains associated with pharyngitis and pharyngeal carriage, in the context of local United Nations Development Programme Human Development Index (HDI) values. Results We included 20 222 isolates from 71 studies done in 34 countries, with the vast majority of carriage strain data from studies in ‘Low HDI’ settings (550/1293; 43%). There was higher emm-type diversity for carriage than pharyngitis strains (Simpson Reciprocal Index of diversity 28.9 vs 11.4). Compared to pharyngitis strains, carriage emm-types were disproportionately from emm-clusters E and D, usually described as ‘generalist’ or ‘skin’ strains. Conclusions A limited number of studies have compared S. pyogenes strains from cases of pharyngitis compared to carriage. Our understanding of strains associated with carriage is poorest for high-income settings. In low and medium HDI countries, we found greater strain associated with pharyngeal carriage than pharyngitis. Improving our understanding of S. pyogenes carriage epidemiology in the pre-vaccine era will help to decipher direct and potential indirect effects of vaccines.