Precision epidemiology for infectious disease control

Abstract

Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This includes the use of genome-based approaches to inform molecular diagnosis and individual-level treatment regimens. In addition, advances in the speed and granularity of pathogen genome generation have improved the capability to track and understand pathogen transmission, leading to potential improvements in the design and implementation of population-level public health interventions. In this Perspective, we outline several trends that are driving the development of precision epidemiology of infectious disease and their implications for scientists' ability to respond to outbreaks.

Fig. 1. Pathogen sequencing during infectious disease outbreaks can inform precise interventions.

Technological advances are enabling the broad application of pathogen genome sequencing for our response to outbreaks of infectious disease. Whole-genome sequencing of many pathogens can now be done directly from clinical samples and in near real time during an outbreak. By analyzing these genomes and their metadata in the context of other sequences generated from the same outbreak, as well as previously characterized variants, researchers can inform individual- and population-level intervention strategies to minimize the burden of infectious diseases. We term the collective approach—sequencing, analysis, and response—as precision epidemiology.