Ongoing emergence of M1UKlineage among invasive group A streptococcus isolates in 2020 and use of allele-specific PCR

SummaryBackgroundAn 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 ofemm1Streptococcus pyogenesthat expresses increased SpeA scarlet fever erythrogenic toxin. Wider surveillance for toxigenicStreptococcus pyogeneslineage M1UKis much needed however, to date, lineage assignment has required genome sequencing limiting surveillance to those centres with access to such facilities.MethodsTo circumvent the requirement for genome sequencing, an allele-specific PCR was developed to distinguish M1UKfrom otheremm1 strains. Additional PCR assays were developed to distinguish M1UKfrom two intermediate lineages that were detected previously. The assay was evaluated using DNA from genome-sequenced upper respiratory tractemm1S. pyogenesstrains and a further set of 16 genome-sequenced invasiveS. pyogenesisolates that included the two intermediate lineages. The assay was then applied to DNA from all 305 invasiveemm1 isolates that had been submitted to the reference laboratory in the one pear period Jan 1-Dec 31 2020, in order to assign lineage.ResultsThe allele specific PCR was 100% accurate when compared with genome sequencing, correctly identifying M1UK, two intermediate sublineages, and otheremm1 strains. The assay demonstrated the M1UKlineage to be dominant amongemm1 invasive isolates in England, representing 278/305 (91%) of invasiveemm1 isolates by end of 2020.ImplicationsEmm1S. pyogeneshave a prominent role in invasive infections; anyemm1 lineage that demonstrates enhanced fitness within the population is of public health concern. The allele specific PCR provides a readily available method to subtypeemm1 isolates and does not require access to complex sequencing facilities. The data confirm that the M1UKlineage has persisted and further expanded in England underlining the importance of wider global surveillance.