Fig. 1

Focus of the scoping review on pathogen genomics for public health practice. Different domains in the field of infectious diseases require access to the same pathogen genomic data. Whole-genome sequencing (WGS) has the ability to inform and improve individual patient care, by identifying the species, determining its pathogenic potential, and testing its susceptibility to antimicrobial drugs. WGS also provides data for public health surveillance about the relatedness of the pathogen to other strains to investigate transmission routes, monitor trends over time, and allow the identification and control of outbreaks and new threats. Research is a knowledge driver providing reference data, methods, and a deeper understanding about the underlying biological mechanisms to the other domains. The focus of this scoping review is on the use of WGS as a public health tool, i.e., at the level of the population