Application of Pathogen Genomics to Outbreak Investigation

OutbreaksOutbreaks are a risk to public health particularly when pathogenic, hypervirulentHypervirulent, and/or multidrug-resistant organismsMultidrug resistant organisms (MDROsMulti-drug resistant organisms (MDROs)) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbreakOutbreaks detection is essential to implement effective interventions in clinical areas to control and stop further transmission. Advances in the field of whole genome sequencing (WGS)Whole genome sequencing (WGS) have resulted in lowered costs, increased capacity, and improved reproducibility of results. WGSWhole genome sequencing (WGS) now has the potential to revolutionize the investigation and management of outbreaksOutbreaks replacing conventional genotyping and other discrimination systems. Here, we outline specific procedures and protocols to implement WGSWhole genome sequencing (WGS) into investigation of outbreaksOutbreaks in healthcare settings.