Use of whole genome sequencing to resolve a surgical ward cluster of meticillin-resistant Staphylococcus aureus.

Abstract

Introduction: Whole genome sequencing (WGS) has been proposed to replace spa typing and pulsed field gel electrophoresis (PFGE) for the investigation of Staphylococcus aureus clusters, but its place has yet to be established for routine outbreak analyses. A cluster of meticillin-resistant Staphylococcus aureus (MRSA) isolates provided an opportunity to compare typing methods for resolving suspected linked cases. Methods: A cluster of MRSA colonisations occurred over six weeks on a surgical ward. It was established that isolates from seven patients were linked in both time and place, with all patients staying in one of two bays. There were no common links in terms of theatres, procedures or theatre staff. Six isolates were typed using spa typing and PFGE by the National Infection Service. In addition, isolates were genome sequenced and their genetic relatedness was assessed using SnapperDB, a single nucleotide polymorphisms (SNP) based typing method. Results: Spa typing, PFGE and genome clustering provided concordant results and linked six isolates to two independent events of transmission of the EMRSA15 strain. However, while SNP addresses showed that all isolates belonged to a single monophyletic clade (within 25 SNP distance), isolates formed two distinct sub-clades of triplets, each clustered within 5 SNP distance. Comparison with genome sequences of local EMRSA15 isolates suggested the presence of an endemic strain, probably introduced several years ago. Conclusion: WGS provided valuable support to the ascertainment of a cluster in a hospital setting. Routine WGS testing of S. aureus would provide strong evidence for effective management of incidents.