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

Dr Paul Chadwick1,2, Dr Alex Peel1,2, Mr Gary Thirkell2, Dr Bruno Pichon3

1Salford Royal NHS Foundation Trust, Salford, UK,
2The Christie NHS Foundation Trust, Manchester, UK,
3National Infection Service, Public Health England , London, UK


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.


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.


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.


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.


Paul Chadwick graduated from the University of Sheffield in 1987 and trained in medical microbiology in Manchester. He has worked as a consultant at Salford Royal since 1996 and, since 2016, for The Christie hospital where he is the Infection Control Doctor. Dr Chadwick is currently the clinical lead for Microbiology services, Pathology at Wigan and Salford. Dr Chadwick has long standing research interests in the epidemiology, surveillance and control of healthcare-associated infections, including catheter-related blood stream infections in patients receiving parenteral nutrition. Recent research has included collaborative work into molecular diagnosis and management of bloodstream infections.

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