FROM THE BENCH
A Small Lab Makes a Big Push Towards Whole-
Genome Sequencing for Foodborne Pathogens
By Jill Sakai, writer
As the US Centers for Disease Control
and Prevention (CDC) and PulseNet
move to establish whole-genome
sequencing (WGS) rather than pulsed-
field gel electrophoresis (PFGE) as the
gold standard for foodborne disease
surveillance and identification efforts,
public health laboratories must adapt to
changing technology, workflows, analysis
and reporting methods.
WGS offers superior precision and
specificity for bacterial identification and
molecular characterization, as well as the
opportunity to consolidate workflows for
serotyping, antibiotic resistance, virulence
factors and more, said Kristy Kubota, MPH,
PulseNet manager for APHL. The change
also reflects advances in the diagnostics
industry.
“We’re seeing a shift in how clinical
laboratories are testing patients for
foodborne diseases such as E. coli and
Salmonella, and they’re using molecular
methods that do not yield isolates,”
Kubota said. “As the clinical diagnostics
industry moves away from isolates
toward genomics, we need to change our
surveillance so that we can be prepared
for an era when there are no more
isolates. One way to do that is to develop
genomics-based testing on the public
health side.”
Technological and scientific advances
are driving sequencing costs down,
making WGS more feasible to implement
on a public health level. However, the
shift can still be a challenge, especially
for labs with constrained resources or
limited expertise in advanced sequencing
methods and analysis. Even in the face
of such barriers, the Maine State Health
and Environmental Testing Laboratory
has shown in the past three years how a
smaller public health lab can successfully
adopt WGS for surveillance and outbreak
detection.
24
LAB MATTERS Fall 2019
E. coli
Charting a New Course
CDC’s push to eliminate PFGE started
the conversation in Maine about moving
to WGS. “We were kind of reluctant
at the beginning to bring it on,” said
Nicholas Matluk, MS, MB, (ASCP)CM the
lab’s Clinical Laboratory Improvement
Amendments (CLIA) microbiology
supervisor and technical supervisor. “It is
a very expensive technique compared to
PFGE, and Maine is a low-incidence state
for everything, including all the foodborne
diseases.”
Then he attended the 2016 American
Society for Microbiology meeting in
Boston, MA, where several WGS seminars
and trainings showed him the platform’s
potential to streamline multiple tests and
workflows. “I saw that if we could use this
for more than just foodborne pathogens,
we would get bigger bang for our buck and
make it cheaper down the line,” Matluk
said.
That approach can be especially
important to lower the barrier for
laboratories with fewer resources to draw
on, said Joel Sevinsky, PhD, a consultant
in public health bioinformatics. “The real
promise of WGS is in the expansion of
these technologies into other organisms
and other programs. That’s where we’re
really going to see cost and turnaround
times going down. But it’s been difficult,”
he said. “One of the real challenges is
getting labs to adopt these technologies
for more than just what’s required.”
That’s one reason Maine’s efforts stand
out. “Maine has transitioned a lot of their
traditional testing to WGS testing. They
validated it, they’re reporting results,
they’re even thinking about moving in the
direction of metagenomics,” said Sevinsky.
“They ended up accomplishing this
transition out of necessity. They were a
small lab, trying to reduce costs and trying
to get more for less. And they saw WGS as
a way of doing that.”
PublicHealthLabs
@APHL
APHL.org