This prospective study was established to develop and evaluate methods to harness pathogen sequencing in the clinical microbiology environment. We describe new insights into the clinical benefits of using whole-genome sequencing (WGS) for outbreak investigation with solutions for the practical barriers to implementation in clinical settings.


Surveillance software (ICNet) and statistical process control charts (SPCs) detected potential outbreaks of meticillin-resistant (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE), Enterobacteriaceae producing extended spectrum β-lactamases (ESBLs), Listeriaspp. and optrAgene positive enterococci. Isolates were sent to reference laboratories for conventional typing and the Infection Group, School of Medicine, University of St Andrews for WGS (Illumina Inc, San Diego, CA, USA) and bioinformatic data analysis.


Over 400 isolates have been sequenced to date. WGS replaced multiple typing techniques in a ICU outbreak. It confirmed two patient’s Listeria spp. isolates were indistinguishable prompting hospital kitchen inspections, identified a patient to be carrying two strains of VRE and confirmed that vancomycin-sensitive Enterococcus faecium isolates related to a VRE cluster. We observed five main barriers to implementing WGS (infrastructure, performance/quality assessment of data, isolate selection, clinical result interpretation and database management).


WGS is beneficial in outbreaks of uncommon organisms and when conventional typing cannot show whether isolates are linked or not. Identifying barriers assisted us in developing a clinical decision aid that can be used by clinicians when applying WGS to outbreak investigations.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.

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