The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression.

Gene transfer and homologous recombination in Streptococcus pyogenes has the potential to 21 trigger the emergence of pandemic lineages, as exemplified by lineages of emm1 and emm89 22 that emerged in the 1980s and 2000s respectively. Although near-identical replacement gene 23 transfer events in the nga (NADase) and slo (Streptolysin O) loci conferring high expression 24 of these toxins underpinned the success of these lineages, extension to other emm-genotype 25 lineages is unreported. The emergent emm89 lineage was characterised by five regions of 26 homologous recombination additional to nga/slo, including complete loss of the hyaluronic 27 acid capsule synthesis locus hasABC, a genetic trait replicated in two other leading emm 28 types and recapitulated by other emm types by inactivating mutations. We hypothesised that 29 other leading genotypes may have undergone similar recombination events. We analysed a 30 longitudinal dataset of genomes from 344 clinical invasive disease isolates representative of 31 locations across England, dating from 2001 to 2011, and an international collection of S. 32 pyogenes genomes representing 54 different genotypes, and found frequent evidence of 33 recombination events at the nga-slo locus predicted to confer higher toxin expression. We 34 identified multiple associations between recombination at this locus and inactivating 35 mutations within hasA/B, suggesting convergent evolutionary pathways in successful 36 genotypes. This included common genotypes emm28 and emm87. The combination of no or 37 low capsule, and high expression of nga and slo, may underpin the success of many emergent 38 S. pyogenes lineages of different genotypes, triggering new pandemics and could change the 39 way S. pyogenes causes disease