Background
The emm typing method targeting the N-terminal region of the emm gene (180bp) is the current ‘gold standard’ for GAS molecular typing. Replacing the current methodology with short read WGS sequencing will enable high-resolution typing, providing highly discriminatory strain relatedness thereby aiding outbreak investigations.
Methods
A total of 1166 isolates submitted between 1st January 2024 and 6th May 2024 to the UKHSA national reference laboratory were selected from 10 common emm types .The emm types were derived by PCR and Sanger sequencing of the emm gene and compared with the emm output derived from the WGS data using MDU-PHL’s emm typing tool (Australia). Sequencing failure observed in samples (n=39) were removed from the analysis. In addition, to help genomic relatedness, MLST data were generated using an in-house tool based on pubMLST’s S.pyogenes database and SNP results with PHEnix pipeline.
Results
The WGS (MDU-PHL) tool showed 98.1% (n=1106) concordance for both the emm type and subtype compared to targeted (Sanger) sequencing. It was not possible to type 0.3% of the samples by both methodologies due to repeat motifs (n=1, identified only by WGS), mixed emm-types (n=1) and contamination (n=1), however 18 samples (1.6%) that were previously untypeable were successfully typed using WGS.
Conclusions
As the WGS data produced strong correlation with the emm types derived by targeted sequencing, this methodology was accepted for routine service as it offers high-resolution data compared to Sanger sequencing along with MLST/SNP data for genomic relatedness and offers the opportunity to type previously intractable samples.