FROM THE BENCH
With the Help of Automation,
San Diego Rejoins PulseNet
by Kim Krisberg, writer
“Using PFGE, we could look at banding
patterns, but with WGS we can do a full
retina scan,” said Tracy Basler, a molecular
scientist within the San Diego public
health lab. “WGS is a total game-changer.”
In 2012, San Diego’s local public health
lab lost its funding for PulseNet testing,
which meant suspected specimens had
to be sent to the state lab instead. In a
foodborne illness outbreak—when time
is of the essence—it wasn’t an ideal
situation.
Last year, however, with whole genome
sequencing (WGS) becoming the new
gold standard for PulseNet, the lab saw
a chance to get back in the game. In
particular, staff saw a new opportunity
to automate the testing process, allowing
it to leverage its existing resources to
generate even more foodborne illness
data than before and without extra money
or staff. The key? Welcoming the robot
known as Biomek i-Series to the bench.
“Onboarding automation has been a lot
more complicated than we first realized,
but the benefits are tremendous,” said
Syreeta Steele, PhD, assistant laboratory
director at the San Diego Health & Human
Services Agency Public Health Laboratory.
“It’s been extremely beneficial to our
ability to participate in PulseNet.”
A nationwide lab network for detecting,
tracing and solving foodborne illness
outbreaks, PulseNet is a central pillar in
the county’s food safety system. For more
than two decades, the network relied on
pulsed-field gel electrophoresis (PFGE) to
generate the DNA fingerprints that enable
public health detectives to connect the
dots between individual cases of illness
to reveal and track larger outbreaks. But
in 2012, the San Diego lab—a relatively
small lab with a staff of about 30—lost
its funding to continue PFGE testing
for PulseNet, forcing it to turn to the
California Department of Public Health
Microbial Diseases Laboratory (MDL) to fill
in the gap.
But with the shift to WGS—which greatly
amplifies the precision of testing results—
the San Diego lab could automate part of
the testing process and revive its PulseNet
testing and participation.
PublicHealthLabs
@APHL
With the new robot on board, the San
Diego lab has been able to automate the
process of preparing DNA fragments—
typically known as library prep—for
sequencing. The robot does all the prep
work, Basler said, including converting
DNA samples into smaller pieces and
tagging them—a process that would have
otherwise required dedicated lab staff
and hours of hands-on work. Instead,
the robot, which can process up to 96
specimens in a single run, works on its
own over the course of a day, readying
DNA samples for sequencing and eventual
upload to PulseNet.
“Our county is home to about 3 million
people, so any time we had to refer
isolates to MDL, it slowed things down,”
Steele said. With the blessing and support
of the staff at MDL and APHL, the PulseNet
WGS protocols were validated and
implemented. “Now we can test here in
the (local) lab and get results much faster”
Steele reported.
Of course, automation isn’t as easy as
ordering a robot and plugging it in. Basler
said the lab’s new robot required an
incredible amount of fine-tuning to make
sure it could do the prep work as well as a
trained laboratorian would.
“It’s a pretty heavy learning curve,”
she said. “Everything has to be exact—
really perfect—and a lot goes into
the verification phase. It’s quite time-
consuming, but we kept at it. …It takes
a lot of determination and a lot of
repetition, but it’s been well worth it.”
Molecular Scientist Tracy Basler checks samples in the
Biomek-i-Series. Photo: San Diego County PHL
integrating a robot into its WGS process;
next, the lab has plans to expand its use
to prepping Hepatitis C specimens for
CDC’s Global Hepatitis Outbreak and
Surveillance Testing (GHOST) program.
Steele noted that while the San Diego
lab isn’t the first to employ the help of a
robot, the lab has added in enhancements
that free up even more hands-on
staff time. For example, the lab uses a
specialized feeder—what Basler described
as a “giant Pez dispenser”—to replenish
the robot’s pipetting tips when needed.
Such time-saving automation, Basler said,
is the only reason the lab has been able to
rejoin the PulseNet community.
“We’re resource-strapped here and
these are time-intensive processes,
so automation is a huge help when it
comes to efficiency,” Basler said. “Now, we
can respond to and keep up with large
foodborne outbreaks locally… It’s helped
elevate the lab, even though our resources
aren’t changing.” n
DIGITAL EXTRA:
Read more on the PulseNet transition to
whole genome sequencing.
The robot wasn’t purchased just for
foodborne pathogen testing, but to
eventually help automate all of the lab’s
sequencing work, according to Basler.
Re-booting the lab’s participation in
PulseNet was only the lab’s first try at
APHL.org
Summer 2019 LAB MATTERS
17