GENOMIC SEQUENCE INVESTIGATION STREPTOCOCCUS PYOGENES CLUSTERS IN ENGLAND (2010-2015).

Streptococcus pyogenes is associated with mild to severe infections affecting skin and soft tissues, the respiratory tract and may cause disseminated infections. The elderly, postpartum mothers and neonates are at the highest risks of developing severe and/or invasive diseases. Clusters of S. pyogenes infection can lead to a poor clinical outcome for affected patients, hence require effective patient management and infection control measures to be implemented to reduce transmission via patients, healthcare workers and the environment. In cases where epidemiological information suggests a link, conventional typing may not always differentiate isolates from others obtained from unrelated clusters. The genomic sequences of 134 S. pyogenes isolates from 21 clusters of invasive infection in nursing care homes, care of the elderly hospital wards or maternity wards submitted to the Reference Laboratory from 2010-2015 were analysed within clusters and compared to background isolates from geographically distinct clusters of S. pyogenes infection. Genomic sequence analysis provided greater discrimination than emm sequence typing combined with MLST analysis for all clusters. Genomic sequences from epidemiologically linked isolates from patients, staff and healthcare environmental settings were highly conserved, differing by as few as 0 to 1 SNP in some cases and mirrored geographical data. Healthcare workers (HCW) were found to be colonized with the outbreak strain in 7 of the 21 clusters investigated. For four clusters, environmental isolate(s) indistinguishable or with limited SNP differences to the isolates from infected patients were detected indicating environmental colonization/contamination is common. A total of 10 isolates were excluded from epidemiological outbreaks using genomic SNP analysis that would have been included if analysis was reliant on emm typing & MLST alone.