Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America

Clonal emergence is a major driver for changes in bacterial disease epidemiology. Recently, it has been proposed that episodic emergence of novel, hypervirulent clones of group A Streptococcus (GAS) results from horizontal gene transfer (HGT) and recombination events leading to increased expression of the cytotoxins Nga (NADase) and SLO (streptolysin O). We previously described a gene fusion event involving the gene encoding the GAS M protein (emm) and an adjacent M-like protein (enn) in the emm4 GAS population, a GAS emm type that lacks the hyaluronic acid capsule. Using whole genome sequencing of a temporally and geographically diverse set of 1,127 isolates, we discovered that the North American emm4 GAS population has undergone clonal replacement with emergent GAS strains completely replacing historical isolates by 2017. Emergent emm4 GAS strains were defined by a handful of small genetic variations, including the emm-enn gene fusion, and showed a marked in vitro growth defect compared to historical strains. In contrast to other previously described GAS clonal emergence events, emergent emm4 GAS lacked significant HGT events and showed no significant increase in transcript levels of nga/slo toxin gene via RNA sequencing and quantitative real-time PCR analysis relative to historic strains. Despite the in vitro growth differences, emergent emm4 GAS strains demonstrated hypervirulence in mouse and ex vivo growth in human blood compared to historical strains. Thus, these data detail the emergence and dissemination of a hypervirulent acapsular GAS clone defined by small genetic variation thereby defining a novel model for GAS strain replacement. Overall design: Comparison of transcriptomes between emm4 group A Streptococcus subpopulations