Revolutionising Public Health Reference Microbiology using Whole Genome Sequencing: Salmonella as an exemplar

Advances in whole genome sequencing (WGS) platforms and DNA library preparation have led to the development of methods for high throughput sequencing of bacterial genomes at a relatively low cost (Loman et al. 2012; Medini et al. 2008). WGS offers unprecedented resolution for determining degrees of relatedness between strains of bacterial pathogens and has proven a powerful tool for microbial population studies and epidemiological investigations (Harris et al. 2010; Lienau et al. 2011; Holt et al. 2009; Ashton, Peters, et al. 2015). The potential utility of WGS to public health microbiology has been highlighted previously (Koser et al. 2012; Kwong et al. 2013; Reuter et al. 2013; Joensen et al. 2014; Nair et al. 2014; Bakker et al. 2014; D Auria et al. 2014). Here we report, for the first time, the routine use of WGS as the primary test for identification, surveillance and outbreak investigation by a national reference laboratory. We present data on how this has revolutionised public health microbiology for one of the most common bacterial pathogens in the United Kingdom, the Salmonellae.