Whole genome sequencing service : investigating healthcare associated infections

Abstract

Advances in the field of whole genome sequencing (WGS) have resulted in lowered costs, increased capacity and improved reproducibility of results. WGS now has the potential to revolutionise the investigation and management of healthcare-associated infection (HAI) outbreaks replacing conventional typing systems. The main objective of this work was to establish a WGS service for the investigation of suspected HAI outbreaks that could confirm or refute outbreaks in real-time in the National Health Service (NHS). WGS results were compared to conventional typing results and the practical barriers and clinical benefits associated with implementing this technology in a clinical environment were identified. Over a five year period a WGS service was used to investigate twenty one suspected outbreaks. The challenges of establishing a WGS service fell into six main areas: infrastructure; performance and quality assessment of data and processing; pipelines and management of reference databases; when to use WGS; clinical interpretation of results and finally when to use increased WGS discriminatory power in outbreak investigations. The clinical benefits of translating genomics into clinical practice comprised five themes: WGS can provide results with greater granularity than routine typing methods; genomic analysis can enhance the detection of “alert organisms’”; WGS can replace the need for multiple tests allowing streamlining of clinical microbiology services; genomic analysis can be used to rule out outbreaks and therefore minimise disruption to healthcare services; WGS can be utilised to investigate new resistance mechanisms. Identifying these practical barriers and clinical benefits informed the development of a clinical decision aid to assist staff on how best to utilise a WGS service. Implementing WGS as a standard of care in real-time was found to be a major advance in day-to-day IPC practice which is particularly relevant in view of the global threat we face with increasing antimicrobial resistance (AMR) and limited treatment options.