Genomic Surveillance ofStreptococcus pyogenesStrains Causing Invasive Disease, United States, 2016-2017

Background Streptococcus pyogenesis a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics ofS. pyogeneslineages could inform vaccine development and disease control strategies. Methods We used whole-genome sequencing (WGS) to characterize all invasiveS. pyogenesisolates obtained through the United States Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, includingemmtype, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages withinemmtype. Results Seventy-oneemmtypes were identified from 3873 isolates characterized. Theemmtypes targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies ofemmtypes collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of theerm-positiveemmtypes 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of threeemmtypes (emm49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (P-values < 0.0001). Specific genomic sequence changes were associated with these expanded lineages. Conclusions While the overall population structure of invasiveS. pyogenesisolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.