Genomic sequencing of a national emm66 group A streptococci (GAS) outbreak among people who inject drugs and homeless, England and Wales January 2016-May 2017

An outbreak of an uncommon type, emm66.0 of group A streptococcus (GAS) infection, was investigated in England and Wales in a population that included a high proportion of people who were homeless or injected drugs between January 2016 and May 2017. Whole genome sequences, antimicrobial resistance, and BEAST and network analyses were performed on emm66 GAS isolates received at the national reference laboratory, between January 2005 and February 2017 (n=55). Forty one isolates (including 32 outbreak cases) located to a single emm66.0 clade (average SNP difference: 6.6; range 0-16 SNPs) in comparison with SNP average 5,876, range 93 to >8,000 SNPs for sporadic isolates. Geographical clustering was observed (2.6 average SNPs difference within towns) and antibiotic resistance was not detected in the outbreak clone. No common source of infection was identified. WGS confirmed expansion of an emm66.0 clone in a hard-to-reach population, enabled refinement of the initial case definition and targeting services to prevent further cases.