FOOD SAFETY
and Tampa. Next generation sequencing
for bacterial organisms is performed in
Jacksonville, which can create challenges
with coordination. Florida has overcome
this [challenge] through training and
outreach. Our current protocol is for all
three laboratories to receive isolates
and for Miami and Tampa to confirm
identifications and make DNA. The
DNA is then shipped to Jacksonville for
sequencing. The major limitation for
Florida is funding to support sequencing
of all PulseNet isolates that are
received, despite the laboratory having
the capability and capacity (staffing,
equipment, skills) to sequence all isolates.
Remaining challenges include attracting
and retaining skilled staff. Florida has
worked closely with academic institutions
to recruit laboratory scientists.”
What are some accomplishments Florida
would like to highlight from the past
year?
Florida has successfully filled two key
positions in the last few months. One is
dedicated to bringing on an NGS method
for genotyping and determination of drug
resistance in HIV, and the other will serve
as the regional bioinformatics resource
lead. Both positions will assist Florida
in increasing sequencing capabilities
in many areas of the laboratory for
diagnostics as well as surveillance. To
date in 2019, Florida has sequenced
3,535 bacterial isolates. To build on this
momentum, in 2020, we hope to increase
this number and bring on sequencing
more routinely for tuberculosis, HIV,
Legionella and other outbreak or multi-
drug resistant organisms.
New York Department of Health-
Wadsworth Center State Hygienic Laboratory at the
University of Iowa
William (Bill) Wolfgang, PhD, research
scientist Michael A. Pentella, PhD, D(ABMM),
laboratory director
Deborah J. Baker, research scientist Ryan T. Jepson, M(ASCP), microbiology
supervisor
What are some challenges that
laboratories in the northeast face with
WGS implementation?
All laboratories in the northeast are in
various stages of implementing WGS but
have encountered challenges, which are
likely not unique to the region. We sent
around a survey in May and gathered the
following information related to these
challenges:
Funding: No labs received enough funding
to sequence all of their isolates. A few labs
think they will be able to make up the
difference with other funds. As an Area
Lab, we did not receive requested funds to
host another small local meeting, which
we found very beneficial this year.
Prioritization: Almost every lab is thinking
about or implementing prioritization
schemes in the expectation of not being
able to sequence all isolates.
Calculation engine: All labs have had
various difficulties with the CDC
calculation engine.
Improving efficiency: Labs are looking at
ways to improve efficiency as a means of
stretching funding.
Frustration: There is definitely some
frustration with implementation among
the labs. Issues range from reorganization
of workflow, database challenges and
struggles to maintain turnaround time.
What are some accomplishments the
northeast area laboratories would like to
highlight from the past year?
All laboratories within the region have
FastQ certified personnel and all but one
are analysis certified.
PublicHealthLabs
@APHL
APHL.org
Gina Kline, clinical laboratory technical
specialist
What are some challenges that Iowa
faces with WGS implementation?
In general, the State Hygienic Laboratory
(SHL) is pleased with the conversion
process. The gaps and challenges that we
continue to encounter involve electronic
communications, especially uploading
files and error messages. Troubleshooting
problems is very time consuming and
issues may take days to resolve. The time
it takes to upload files is a significant
concern; when uploads fail, it is difficult
to pinpoint the source of the error. Recent
one-on-one Skype meetings between
SHL and PulseNet staff have been very
helpful. Increased validation of the
electronic communication processes
before implementation would have
benefitted us.
What are some accomplishments
Iowa would like to highlight from the
past year?
SHL has successfully performed WGS
of all Salmonella, E. coli and Listeria in
real-time since 2016. In February 2018,
the Iowa Foodborne Rapid Response
Team quickly identified chicken salad
as the source of a multistate Salmonella
Typhimurium outbreak. For the first time,
SHL relied on WGS results to match the
Salmonella isolated from the patient to
the Salmonella recovered from the chicken
salad. This outbreak proved to SHL and
its public health partners that whole-
genome sequencing could provide a faster
turnaround time than PFGE. n
Fall 2019 LAB MATTERS
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