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