Real-time whole genome sequencing to control an outbreak of Streptococcus pyogenes at a UK Specialist Orthopaedic Hospital

Following the death of a patient from Streptococcus pyogenes bacteraemia an outbreak investigation was conducted. Upon screening of 4 patients and 179 staff, 12 isolates of Group A Streptococcus (GAS) were identified. Emm-typing demonstrated that 6 of these isolates were emm 1.0, including the index case isolate and 5 healthcare workers. Whole genomic sequence (WGS) analysis was undertaken on these 6 emm 1.0 isolates. Five were indistinguishable by single-nucleotide polymorphism (SNP) analysis, with a 0 SNP distance, and one had one SNP difference, supporting the hypothesis of recent local transmission. All GAS positive healthcare workers were offered treatment with penicillin or clindamycin and did not return to duty until they were asymptomatic. No further cases were identified. The increased molecular discrimination of WGS confirmed the clustering of these cases but was unable to establish the directionality of spread, limited by low potential transmission and exposure period. This case demonstrates the clinical utility of WGS in managing outbreaks of invasive GAS in real time.