Background: Conventional PCR and sequencing-based methods for emm typing are time consuming (>72 hours) for outbreak situations and costly for resource-limited settings. We tested a multiplex real-time PCR scheme to quickly (<24 hours) identify 20 common emm types in the USA to type GAS strains from recent nursing home outbreaks.
Methods: The method included 5 quadriplexed assays designed to identify 20 emm types including emm1, emm2, emm3, emm4, emm6, emm11, emm12, emm28, emm49, emm59, emm75, emm76, emm77, emm81, emm82, emm83, emm87, emm89, emm92, and emm118. GAS outbreak isolates received from nursing homes in 15 states (2018-2021) were analyzed. We determined emm type for a subset of isolates using whole-genome sequencing (WGS) to confirm PCR results.
Results: The method identified emm type for 351 of 384 (92.5%) isolates; 33 (8.5%) were non-typeable and belonged to emm types not included in the scheme. Of 20 emm types included, 18 types were identified, including emm1 (8.5%), emm89 (16.5%), emm82 (11.9%), emm77 (7.1%), and emm75 (6.8%). We observed 100% concordance for emm type by real-time PCR with WGS in a subset of 132 isolates.
Conclusions: The real-time PCR emm typing approach quickly identified types of outbreak GAS isolates from nursing homes and greatly assisted in expedient guidance of response efforts. A limitation is that the method does not identify emm subtypes. While this method targets the most prevalent emm types in the USA, many of these types are also common in other countries making this method useful for additional geographic regions.