Establishing whole genome sequencing at the core of epidemiological surveillance

Over the last two decades, genome sequencing has become an important tool for understanding and tracking the spread of pathogens. Genomic epidemiology is now a preferred method of surveillance and recent years have seen pathogen sequencing at an unprecedented scale, pushing the underlying technologies to the limit. This has brought major innovations and opportunities to public attention, as well as identifying new research areas. However, major challenges remain in public health settings. These include: incorporating new sequencing technologies and data types for real-time surveillance; developing platforms and nomenclatures for genome-based typing and epidemiology; understanding pathogen evolution and the emergence of virulence and antimicrobial resistance; contextualizing knowledge of clinical microbiology with One Health ecological genomics. In this collection, we bring together recent studies that are establishing pathogen genomics as a major part of contemporary disease control efforts.