emm1 increases in scarlet fever outbreaks. Increase of emm1 isolates among group A Streptococcus strains causing scarlet fever during 2011-2015 in Shanghai, China

Large outbreaks of scarlet fever caused by emm12 group A Streptococcus (GAS) occurred in China in 2011. Since then, scarlet fever has been epidemic annually, but there are no continuous surveillance data on the molecular epidemiological characterization of the GAS isolates. This study aimed to figure out the dynamic prevalence and diversity of GAS population and to explore the pathogen-associated spread mechanism. Epidemiological data of scarlet fever in Shanghai during 2011–2015 were obtained from the National Notifiable Infectious Disease Surveillance System. Throat swabs of patients with scarlet fever were cultured, and GAS carriage surveillance was performed in schools. A total of 1,568 GAS isolates were collected for analysis, and 39 emm1 isolates were performed Illumina sequencing. This continuous study showed that the annual incidence of culture-confirmed scarlet fever was 7.5-19.4/100,000-person-year in Shanghai during 2011-2015, with an average GAS carriage rate being 7.6% in school-age children. With predominance of emm12 (61.8%, 897/1451) in patient isolates, the proportion of emm1 GAS strains increased from 3.8% in 2011 to 48.6% in 2014, and they harbored a superantigen profile different from emm12 isolates. Two predominant clones, SH001-emm12 and SH002-emm1, circulated in 66.9% of scarlet fever cases and 50% of carriers. GAS isolates showed high frequencies (>95%) of resistance to macrolides (ermB) and tetracycline (tetM). Genomic analysis showed emm1 isolates in China constituted distinct clads, harboring characteristic mobile genetic elements. GAS population causing scarlet fever in China is changing. Ongoing surveillance is warranted to monitor the dynamic changes of GAS emm type, predominant clone, and superantigen profile.