public health preparedness and response
Ring the Alarm! How Next-Gen Sequencing Can
Detect the Next Threat
by Sean Page, associate specialist, Public Health Preparedness and Response
For the ever-evolving field of preparedness and
response, public health laboratories (PHLs) must
stay ahead of the next threat by quickly adopting
new technologies. Mass spectrometry, typically
used by chemists, is now making a splash in the
microbiology world where it is being touted as the
next solution to rapidly identify infectious agents. In
the same way, next generation sequencing (NGS) is
quickly making its way into public health and
other laboratories.
NGS could revolutionize biothreat testing through its ability
to determine the agent, modifications to the agent, drug
resistance and other characteristics.
Adopting New Technologies
The US Centers for Disease Control and Prevention (CDC) has supported
NGS as a means to deal with current challenges in outbreak detection
and surveillance. NGS provides a large pool of precise data for identifying
outbreaks compared to the current standard techniques, such as pulsed-field
gel electrophoresis used by PulseNet laboratories. NGS could revolutionize
biothreat testing over the long-term through its ability to determine the agent,
modifications to the agent, drug resistance and other characteristics through a
single test—all while remaining cost-effective. Taking the technology one step
further, NGS could identify an unknown agent and the origins of the outbreak,
leading to a successful investigation.
that Yersinia pestis (the causative agent of plague) and Bacillus anthracis (the
causative agent of anthrax) were part of the normal subway microbiome. In
response to the public outcry that ensued, laboratorians at the University
of California-San Diego reanalyzed the data with appropriate sequencing
methods and revealed that the initial results were invalid due to incorrect
taxonomic classifications. Both studies added to knowledge about the
transmission and expression of microbes in high-traffic built environments.
Reimagining the use of NGS, BioInnovation Solutions SA partnered with the
US Army Medical Research Institute of Infectious Diseases to develop and test
a sequence-based platform for rapid detection and surveillance of filoviruses,
including Ebola and Marburg, from endemic areas. BioInnovation’s platformagnostic technology could enable earlier and quicker detection of known viral
and bacterial pathogens while also discovering new strains. This study could
be a catalyst for deployment of NGS technology to endemic areas as an early
warning system for biothreats.
If There is a Will, There is a Way
Like most new technologies, the initial cost of NGS equipment, reagents and
trained personnel can be high. In order to properly evaluate and interpret the
data, PHLs will need skilled laboratorians with the education and experience
to run testing and analyze the data. Standardization of protocols and analyses
and policies governing data storage will be essential.
Sequencing directly from samples or specimens is still in development.
Currently confirmation of biothreats requires PHLs to grow agents in
culture, which is time-consuming and a barrier to direct detection from
environmental samples. But PHLs, in partnership with academic institutions,
private companies and federal agencies, should actively examine the benefits
of NGS for the detection of biothreats. The path to implementing NGS may
be complex but, like 15 years ago when no PHL performed real-time PCR, it
is not insurmountable. Once more is known about the application of NGS
to detection of biothreats, the US Laboratory Response Network could be a
mechanism for deployment of this technology—providing PHLs access to a
loud and more efficient alarm system.
Beyond Detecting Foodborne Outbreaks
NGS can be essential for studies involving public infrastructure, where precise
identification of pathogens is critical to the daily operation of buildings
and subway systems. A recent metagenomic study of the New York subway
received much attention from major news outlets due to its suggestion
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Reference
BioInnovation Solutions and USAMRIID Develop DNA Sequencing Technology for Rapid Detection and Biosurveillance of
Ebola Virus, prweb, July 14, 2016, Available at http://www.prweb.com/releases/2014/10/prweb12235676.htm
Summer 2016 LAB MATTERS
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