Epidemiological typing using wgs

Typing methods are continuously developing and improving. The methods aim to discriminate different strains beyond the species identification level. The first methods used to detect strain-specific differences were based on phenotypic characteristics within specific species. In the molecular era this changed towards genotypic fragment-based techniques which were quite laborious or sequence-based but having limited resolution. Nevertheless, these methods provided a new way of identifying specific strains and investigating outbreaks. The introduction of whole-genome sequencing (WGS) to the field of bacterial typing and outbreak investigation has set a new standard for discrimination and accuracy as it encompasses a comprehensive view of the bacterial core and accessory genome. In this chapter, we will review the general concepts of typing, as well as the various available typing techniques, and discuss both the advantages and the challenges of using WGS for typing purposes.