Towards a genomics-informed, real-time, global pathogen surveillance system

Key Points

• Despite the recommendations of many expert groups, public health surveillance systems have not yet improved to the point where emerging infectious threats can be better anticipated. The Ebola and Zika epidemics are the latest to demonstrate that pathogens often spread undetected for some time before being diagnosed in a population.

• Next-generation sequencing, particularly the use of portable genomic sequencers, offers an intriguing solution to the diagnosis and surveillance problems — it enables rapid in situ diagnostics through amplicon-based or metagenomics approaches and creates a stream of genomic data that can reveal critical epidemiological aspects of an outbreak or epidemic's dynamics.

• Genomic epidemiology for rapid outbreak response has demonstrated some early successes in Ebola and Zika, but there are a number of challenges to overcome — some technical and some cultural. Data sharing is one of these, but other ethical and legal issues must be considered.

• The power of a genomic epidemiology approach could be extended by incorporating concepts from digital disease detection and One Health. By coupling sequencing to an enhanced surveillance and response platform, we could take a more anticipatory approach to outbreak prevention and control.

Supplementary information

The online version of this article (doi:10.1038/nrg.2017.88) contains supplementary material, which is available to authorized users.

Abstract

Next-generation sequencing has the potential to support public health surveillance systems to improve the early detection of emerging infectious diseases. This Review delineates the role of genomics in rapid outbreak response and the challenges that need to be tackled for genomics-informed pathogen surveillance to become a global reality.

Supplementary information

The online version of this article (doi:10.1038/nrg.2017.88) contains supplementary material, which is available to authorized users.

Abstract

The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes — now a staple of the public health microbiology laboratory in well-resourced settings — can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.

Supplementary information

The online version of this article (doi:10.1038/nrg.2017.88) contains supplementary material, which is available to authorized users.