Emergence of a new, virulent lineage of Methicillin Resistant Staphylococcus aureus revealed by whole genome sequencing

Different hospital-adapted strains of methicillin resistant Staphylococcus aureus (MRSA) have become established across the globe but when a hospital experiences an outbreak of MRSA this is often attributed to poor infection control practice. A new variant of EMRSA-16 (ST36) that appeared in Brighton after 2004 was identified by whole-genome sequencing. The ancestor of this ‘Brighton Outbreak Cluster’ (BOC) is estimated to have arisen in 2004-5. The lineage diversity of EMRSA-16 in Brighton after 2004 was markedly reduced compared with earlier Brighton collections: 22/24 post-2004 EMRSA-16s were BOC compared with 5/14 of EMRSA-16 in the largest comparable genetically-defined cluster among earlier isolates. After 2006, BOC isolates accounted for 78/87 (92%) EMRSA-16 bacteraemia isolates in Brighton. The epidemiology of the outbreak, in which a highly related clone of very recent origin was responsible for the local excess relative to national rates, suggest that bacterial adaptations were responsible for the outbreak rather than or failures in infection control practice. Marked changes in the incidence of infection at a hospital may arise from emergence of new variants of established strains. As whole genome sequencing enters clinical practice this will allow rapid outbreak identification of hospital-associated infection, and support early targeted intervention.