Ongoing emergence of M1UK lineage among invasive group A streptococcus isolates in 2020 and use of allele-specific PCR

Background An increasing burden of invasive group A streptococcal infections is reported in multiple countries, notably England, where scarlet fever cases are also abundant. In England, increased scarlet fever and invasive infections have been associated with emergence of a sublineage of emm1 Streptococcus pyogenes that expresses increased SpeA scarlet fever erythrogenic toxin. Wider surveillance for toxigenic Streptococcus pyogenes lineage M1UK is much needed however, to date, lineage assignment has required genome sequencing limiting surveillance to those centres with access to such facilities. Methods To circumvent the requirement for genome sequencing, an allele-specific PCR was developed to distinguish M1UK from other emm1 strains. Additional PCR assays were developed to distinguish M1UK from two intermediate lineages that were detected previously. The assay was evaluated using DNA from genome-sequenced upper respiratory tract emm1 S. pyogenes strains and a further set of 16 genome-sequenced invasive S. pyogenes isolates that included the two intermediate lineages. The assay was then applied to DNA from all 305 invasive emm1 isolates that had been submitted to the reference laboratory in the one pear period Jan 1-Dec 31 2020, in order to assign lineage. Results The allele specific PCR was 100% accurate when compared with genome sequencing, correctly identifying M1UK, two intermediate sublineages, and other emm1 strains. The assay demonstrated the M1UK lineage to be dominant among emm1 invasive isolates in England, representing 278/305 (91%) of invasive emm1 isolates by end of 2020. Implications Emm1 S. pyogenes have a prominent role in invasive infections; any emm1 lineage that demonstrates enhanced fitness within the population is of public health concern. The allele specific PCR provides a readily available method to subtype emm1 isolates and does not require access to complex sequencing facilities. The data confirm that the M1UK lineage has persisted and further expanded in England underlining the importance of wider global surveillance.