FOOD SAFETY
PulseNet’s Transition to Whole Genome Sequencing:
Perspectives from the States
By Kristy Kubota, MPH, manager, PulseNet and Rhodel Bradshaw, MPH, specialist, Food Safety
On July 15, 2019, PulseNet, the national
laboratory network that connects bacterial
foodborne illness cases to detect clusters
of illness that might be related as part of
an outbreak, transitioned from pulsed-
field gel electrophoresis (PFGE) to whole
genome sequencing (WGS) as the primary
subtyping method for the network. To make
the WGS transition successful for PulseNet,
it is important that laboratory scientists and
bioinformaticians continually learn from
each other. Providing opportunities to share
knowledge assists in improving workflows,
making the transition more cost-effective
and efficient.
This year, we have presented a series of
articles in Lab Matters, highlighting PulseNet’s
transition to WGS. To complete this series, we
have invited some APHL member laboratories
to share their transition experiences.
Deborah J. Baker
22
LAB MATTERS Fall 2019
Noah C. Hull, PhD, MPH
Wyoming Public Health Laboratory
Noah C. Hull, PhD, MPH, microbiology
laboratories manager
Wanda Manley, MS, senior microbiologist
What are some challenges that low
volume laboratories face with WGS
implementation?
Low volume states are always searching
for the balance point between time and
money. While it may be true that the cost
of sequencing an isolate continues to
drop, the savings are only seen if large
numbers of isolates are being sequenced.
Small-volume state laboratories must
look at the number of isolates received
and determine when they should be
sequenced. Sometimes the turnaround
time may be more important than the
cost per isolate sequenced, particularly
with E. coli and Listeria monocytogenes. If
the low volume laboratory has received
Salmonella isolates, it may be best to batch
those and wait to fill a sequencing run.
Salmonella clusters and outbreaks are
usually detected in the larger volume
states. It is unlikely a cluster would go
undetected if a low volume laboratory
chose not perform a sequencing run
every week. The Wyoming Public Health
Laboratory has completed a cost analysis
to evaluate when it makes sense to
complete a weekly run on the Illumina
iSeq vs. Illumina MiSeq vs. pushing the
run to the following week.
Ryan T. Jepson, M(ASCP)
What are some accomplishments
Wyoming would like to highlight from
the past year?
We have the only sequencing instrument
in the state at this time, and we routinely
offer our services to the Wyoming State
Veterinary Laboratory and the University
of Wyoming. Through this collaboration,
our team has become adept at extracting
and sequencing DNA from organisms
many state public health labs may never
see. Additionally, it is beneficial to include
these isolates on our weekly runs in
order to get the most efficient use of our
flow cell.
Florida Department of Health,
Bureau of Public Health
Laboratories
Marie-Claire Rowlinson, PhD (ABMM),
assistant laboratory director/CLIA laboratory
director
Jason Blanton, PhD, molecular supervisor
What are some challenges that high
volume laboratories face with WGS
implementation?
Florida is a geographically large state
and the third most populous in the US.
We also receive many annual visitors.
Needless to say, Florida has a high burden
of food and waterborne disease with an
estimated 6,000 Salmonella cases every
year. Florida has public health laboratories
in three locations: Jacksonville, Miami
Wanda Manley, MS
PublicHealthLabs
William (Bill) Wolfgang, PhD
@APHL
APHL.org