A laboratory-developed extraction free real-time PCR for Group A Streptococcus in throat swabs: greater detection and faster results.

Aim: This work describes the validation of an in-house extraction free real-time polymerase chain reaction (PCR) for the detection of Group A Streptococcus (GAS) in throat swabs collected in gel amies.

Method: Throat swabs received by the laboratory were prospectively tested by routine bacterial culture and an in-house PCR assay targeting the GAS SpeB gene with a multiplexed RNaseP internal control. Samples with discrepant culture/PCR results had additional testing using the commercial Xpert Group A Strep PCR assay (Cepheid). Post introduction of the in-house GAS PCR the comparative laboratory turn-around time between PCR and historic culture results was determined.

Results: Of the 1,093 throat swabs included in the final analysis, GAS was detected by culture and GAS PCR in 262 (24.0%) and 319 (29.2%) respectively. The overall, positive and negative agreement of the GAS PCR with culture was 94.2%, 98.9% and 92.8% respectively. Of the 63 discordant samples, one (33.3%) of three culture positive/in-house PCR negative samples and 56 (93.3%) of 60 culture negative/in-house PCR positive samples were GAS positive on the Xpert Group A Strep assay. Median turn-around time from laboratory receipt to result decreased from 44 to 16 hours with the introduction of the GAS PCR into routine practice. Forty-five percent of samples came from European patients and 25% from persons aged over 30 years, suggesting over-testing in persons at low risk of GAS pharyngitis complications.

Conclusion: The in-house GAS PCR provided greater and faster detection of GAS from throat swabs compared to culture. However, throat swabbing for GAS needs to be better targeted to those populations at high risk of post-GAS pharyngitis complications.