Genomics’ Role In Global Pathogen Surveillance, Diagnosis

By Bio-IT World Staff 

November 14, 2017 | “Although public health surveillance systems have evolved to meet the changing needs of our global population, we continue to dramatically underestimate our vulnerability to pathogens, both old and new.” So opens a Nature Reviews Genetics article published yesterday by Jennifer Gardy, British Columbia Centre for Disease Control, and Nick Loman, Institute of Microbiology and Infection, University of Birmingham.

Gardy and Loman explore the steps moving us toward a genomics-informed, real-time, global pathogen surveillance system, and the need for such progress (doi:10.1038/nrg.2017.88). Pandemics are not likely to cease—in fact Gardy and Loman quote research that suggests a rising number of emerging human pathogens each decade. And after each new outbreak—most recently the Ebola outbreak in West Africa—groups and commissions “call for enhanced molecular diagnostic and surveillance capacity coupled to data-sharing frameworks,” the authors observe. With technological advances in sequencing, we can begin to expect rapid outbreak response empowered with tools for pathogen genome sequencing and epidemiological analysis and that can be deployed anywhere. We should be able to prepare for outbreaks with portable, in-country genomic diagnostics and routine human, animal and environmental surveillance.

In fact, Gardy and Loman highlight the progress already made on portable sequencers, especially the Oxford Nanopore MinION, which was used in diagnostic tent laboratories during the Ebola epidemic, and has been deployed in other hostile environments including the Arctic and Antarctic.

“Within our increasingly digital landscape, wherein a clinical sample can be transformed into a stream of data for rapid analysis and dissemination in a matter of hours, we face a tremendous opportunity to more proactively respond to disease events,” they write.

But there are challenges along with the opportunities, and the two outline both.

While next-generation sequencing has made great leaps, sequencing in the field still requires a rugged and portable device that can return findings on samples quickly gathered, likely contaminated, with minimal preparation. Clinical metagenomics, though, is expensive, often reserved for lethal, hard-to-diagnose infections.

But as costs come down and our genomic understanding expands, the authors are certain that sequencing will become routine clinical practice driven by, “the additional information afforded by genomics, including the ability to predict virulence or drug resistance phenotypes, the ability to detect polymicrobial infections and phylogenetic reconstruction for outbreak analysis.”

But Gardy and Loman argue that genomics will play a much larger role than just epidemic diagnosis. Genomic epidemiology—including “everything from population dynamics to the reconstruction of individual transmission events within outbreaks”—could help predict and prevent spillover events, track outbreaks, and inform public health messaging.

During the most recent Ebola outbreak, sequencing efforts began months into the epidemic, the authors write. “Had they been deployed earlier, we can only speculate as to their potential impact. Arguably, the most compelling use of early sequencing would have been to provide a definitive Ebola diagnosis in this previously unaffected region of West Africa.”

One Health

In considering future outbreaks, Gardy and Loman believe that genomics should play an important role in the One Health community, an integrated system incorporating human, animal and environmental surveillance.

“Combining genomic data with data streams from enhanced One Health surveillance platforms presents an opportunity to detect the population expansions and/or cross-species transmissions that may precede a human health event,” they write.

For example, instead of expansive animal surveillance, they envision using metagenomics in a One Health surveillance strategy to scanning for zoonotic “jumps”—when a pathogen moves from animals to humans—in selected sentinel human populations, focusing on “hot spots,” or areas with combined wildlife, domestic animals, and human risk factors.

“By combining genomic data generated through these targeted surveillance efforts with phylodynamic approaches, it will be possible to take simple presence or absence signals and derive useful epidemiological insights: signals of population expansion; evidence of transmission within and between animal reservoirs and humans; and epidemiological analysis of a pathogen's early expansion,” they write.