FOOD SAFETY
Building the Next Generation of PulseNet
by Kristy Kubota, manager, PulseNet and Rhodel Bradshaw, specialist, Food Safety
to WGS, while others may not have
resources or volume to conduct real-time
surveillance as efficiently as with PFGE.
During the past year, some laboratories
have had to perform PFGE in tandem with
WGS in order to validate results. This is
costly and requires training personnel
to perform both methods. There is also a
steep learning curve with WGS technology,
and it can be exacerbated at laboratories
with limited IT and bioinformatics
resources. Addressing turnaround time
metrics, automation and upgrading of IT
infrastructures to accommodate storage,
and upload of massive amounts of data to
CDC and NCBI pose additional challenges
for public health laboratories.
Change is never easy. In fact, it can be
daunting, overwhelming and fraught
with difficulty. However, at the same
time, it can be a refreshing experience.
The same can be said for PulseNet’s
national transition from pulse-field gel
electrophoresis (PFGE) to whole genome
sequencing (WGS).
PulseNet is the first national laboratory-
based surveillance program in the United
States to harness the power of WGS, a
technology that can change laboratory
science practice and transform how
outbreaks are detected, investigated
and surveilled.
Traditional vs. Cutting-edge
Traditional subtyping tools like PFGE are
organism-dependent, lack discriminatory
power and require additional testing to
fully identify and characterize pathogens.
WGS is a better subtyping tool for
bacterial, viral or parasitic surveillance.
In addition, with global development
of open-sourced tools and databases,
WGS allows public health scientists
to replace many traditional reference-
based methods. Once laboratories fully
implement and validate WGS, they can
consolidate workflows for identification
and characterization of pathogens,
and clinical diagnostics can evolve
from isolate-based methods to culture-
independent testing. Since current US
surveillance is dependent on isolates,
there is a critical need to develop genomic
databases to respond to the changing
landscape of clinical diagnostics.
Public health laboratories transitioning
PulseNet workflows from PFGE to WGS
face many challenges. One laboratory may
have the capability to easily transition
Collaboration Towards Change
In early 2019 APHL sponsored Joint
PulseNet/OutbreakNet Regional Meetings
in Tampa, San Diego and Omaha to
discuss implementation of WGS for
foodborne surveillance. Roughly 600
laboratory scientists, bioinformaticians,
epidemiologists and environmental
health specialists involved in foodborne
outbreaks and enteric diseases
participated.
Participants from PulseNet laboratories
emphasized quality control and workforce
development as priority needs for WGS
implementation. Evaluation of current
laboratory systems, from the enteric
reference bench to the PulseNet subtyping
laboratory to the IT infrastructure,
were likewise priorities along with
identification of areas to improve
efficiencies. To prepare attendees to
embrace changes in the analysis workflow
for cluster detection, the meetings
included training in BioNumerics 7.6,
Joint Sessions
PulseNet Track Sessions
• PulseNet and OutbreakNet transition to WGS
• Managing New Workflows and Data Integration
• Learning from other nations experiences with
incorporating WGS into food surveillance
• Perspectives fromhigh and low burden states
• Outbreak discussions on utility of WGS
PublicHealthLabs
@APHL
• Guidance for Implementing & Conducting
PulseNet Surveillance Using WGS
• Addressing QA/QC(example: Dry and Wet Lab
Sequence Quality Data and
• BioNumerics Training
APHL.org
which provides WGS analysis tools.
Attendees discussed examples of how
WGS data has supported epidemiological
investigations. In one instance, by using
WGS, investigators were able to show
that the same strain of Salmonella was
responsible for a restaurant-associated
outbreak that occurred over multiple
years. Moving forward, WGS will be
useful in demonstrating such long-term
harborage of pathogens within the
environment as well as trends in the
number of prolonged outbreaks.
According to an internal survey conducted
by APHL and CDC, 93% of attendees rated
meeting content and materials as “good”
or “excellent.” Particularly valuable were
discussions of WGS implementation
from different state perspectives. Many
attendees mentioned that the diversity
of professions represented at the
meeting allowed each to observe how
others handle and share information
on outbreaks. Networking with a range
of professions also produced concrete
results: improvements in SOPs to guide
the transition to WGS.
In January 2019, Listeria monocytogenes
was the first PulseNet pathogen to
fully transition to WGS, and the results
are already promising. Nationally, the
number of listeriosis clusters detected
with WGS has increased, while the
number of cases within a cluster has
decreased. As national surveillance
extends to other PulseNet pathogens, we
should expect to observe similar trends.
Similar opportunities for professionals in
foodborne surveillance to learn from each
other will be vital as PulseNet advances
with implementation of WGS. n
OutbreakNet Track Sessions
• Challenges and Successes surrounding Outbreaks
• Environmental Health Perspectives on Foodborne
Outbreak Investigation
• WGS transition at an Epidemiological and
Environmental Health Science Perspective and
Communication
• SEDRIC Training
Fall 2019 LAB MATTERS
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