With this study we aim to provide new insight into the usefulness for the infection prevention and control team of using whole genome sequencing in the investigation of a suspected Pseudomonas aeruginosa outbreak in an Intensive Care Unit and describe how it compares with current typing methods such as pulsed-field gel electrophoresis and variable number tandem repeat analysis.

Pseudomonas aeruginosa outbreaks in hospital can be time consuming and difficult to investigate. Guidance does not specify which typing technique is most practical or useful for infection prevention and control team (IPCT) to base their decisions on. We aim to provide new insight into the usefulness for the IPCT of using whole genome sequencing (WGS) in the investigation of a suspected Pseudomonas aeruginosa outbreak in an Intensive Care Unit (ICU) and describe how it compares with current typing methods such as pulsed-field gel electrophoresis (PFGE) and variable number tandem repeat (VNTR) analysis. Samples from ICU patients found to have P.aeruginosa underwent VNTR typing and PFGE. Genomic libraries were prepared by Nextera XT (Illumina). WGS was performed using an Illumia MiSeq platform. When routine typing methods were used, both VNTR and PFGE were required to fully determine the potential source of infection and rule out others. WGS provided clarity and unambiguously distinguished the linked isolates this gave the IPCT greater assurance of the transmission route between wash hand basin (WHB) water and two patients supporting the infection prevention and control measures employed. WGS provided detailed information negating the need for further typing. When this data is allied to epidemiological information it can be used by IPCT to understand outbreak situations rapidly and with more certainty. Implementation of this technique in real time would be a major advance in their day-to-day practice and could become a standard of care as it becomes more widespread, portable and reproducible.