Prospective whole genome sequencing for national surveillance of Listeria monocytogenes in Australia

Whole genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here, we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approach using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem repeat analysis (MLVA), binary typing and serotyping. Initially 423 L. monocytogenes isolates underwent WGS and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary and serotyping results inferred in silico from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable by our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, providing a greater level of discrimination to conventional typing for inferring linkage to point source outbreaks. A risk based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows WGS could be adopted for prospective L. monocytogenes surveillance, and investigated for other pathogens relevant to public health.