Driven by million-fold improvements in biotechnology, biology is increasingly shifting towards high-resolution, quantitative approaches to study the molecular dynamics of entire populations. One exciting application enabled by this new era of biology is the "digital immune system". It would work in much the same way as an adaptive, biological immune system: by observing the microbial landscape, detecting potential threats, and neutralizing them before they spread beyond control. With the potential to have an enormous impact on public health, it is time to integrate the necessary biotechnology, computational, and organizational systems to seed the development of a global, sequencing-based pathogen surveillance system.