82 FR 44378 - Use of Whole Genome Sequence Analysis To Improve Food Safety and Public Health

DEPARTMENT OF AGRICULTURE
Food Safety and Inspection Service

Federal Register Volume 82, Issue 183 (September 22, 2017)

The Food Safety and Inspection Service (FSIS), with participation from the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), the National Center for Biotechnology Information (NCBI), and other stakeholders is hosting a public meeting to discuss FSIS' and other agencies' practices and plans for collecting and analyzing whole genome sequence (WGS) data of bacteria isolated from official samples, as well as the state of the science and other issues surrounding this technology. WGS analyses can determine sequence relatedness between bacterial isolates with higher resolution than other analytical methods, including pulsed-field gel electrophoresis (PFGE), FSIS' current method of characterizing bacteria. In addition, WGS analyses can characterize genes and other features of bacterial genomes. Currently, FSIS, local, State, and Federal public health and regulatory partners submit WGS data to a Federal public database, readily accessible to Federal and state partners, and other stakeholders, including regulated industry and consumers. Using this common database, Federal food safety partners can share information and collaborate on issues related to food safety and public health. FSIS intends to analyze WGS data using thoroughly vetted and scientifically accepted procedures and standards, along with epidemiological information and industry production and distribution records on amenable product, to carry out its public health mission. Inclusion of WGS analyses in decision-making will enhance foodborne outbreak investigations, as well as general decisions related to the use of data from routine verification sampling of establishments under FSIS jurisdiction. Industry, interested individuals, organizations, and other stakeholders are invited to participate in the meeting and comment on FSIS approaches for using WGS data within a regulatory framework.

[Federal Register Volume 82, Number 183 (Friday, September 22, 2017)]
[Notices]
[Pages 44378-44380]
From the Federal Register Online  [www.thefederalregister.org]
[FR Doc No: 2017-20247]


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DEPARTMENT OF AGRICULTURE

Food Safety and Inspection Service

[Docket No. FSIS-2017-0038]


Use of Whole Genome Sequence Analysis To Improve Food Safety and 
Public Health

AGENCY: Food Safety and Inspection Service, USDA.

ACTION: Notification of public meeting.

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SUMMARY: The Food Safety and Inspection Service (FSIS), with 
participation from the Food and Drug Administration (FDA), the Centers 
for Disease Control and Prevention (CDC), the National Center for 
Biotechnology Information (NCBI), and other stakeholders is hosting a 
public meeting to discuss FSIS' and other agencies' practices and plans 
for collecting and analyzing whole genome sequence (WGS) data of 
bacteria isolated from official samples, as well as the state of the 
science and other issues surrounding this technology. WGS analyses can 
determine sequence relatedness between bacterial isolates with higher 
resolution than other analytical methods, including pulsed-field gel 
electrophoresis (PFGE), FSIS' current method of characterizing 
bacteria. In addition, WGS analyses can characterize genes and other 
features of bacterial genomes. Currently, FSIS, local, State, and 
Federal public health and regulatory partners submit WGS data to a 
Federal public database, readily accessible to Federal and state 
partners, and other stakeholders, including regulated industry and 
consumers. Using this common database, Federal food safety partners can 
share information and collaborate on issues related to food safety and 
public health. FSIS intends to analyze WGS data using thoroughly vetted 
and scientifically accepted procedures and standards, along with 
epidemiological information and industry production and distribution 
records on amenable product, to carry out its public health mission. 
Inclusion of WGS analyses in decision-making will enhance foodborne 
outbreak investigations, as well as general decisions related to the 
use of data from routine verification sampling of establishments under 
FSIS jurisdiction. Industry, interested individuals, organizations, and 
other stakeholders are invited to participate in the meeting and 
comment on FSIS approaches for using WGS data within a regulatory 
framework.

DATES: The public meeting will be held on Thursday and Friday, October 
26 and 27, 2017 from 8:00 a.m. to 4:45 p.m. EST.

ADDRESSES: The meeting will be held at the Jefferson Auditorium in the 
South Building, U.S. Department of Agriculture (USDA), 1400 
Independence Avenue SW., Washington, DC 20250. Attendance is free. Non-
USDA employees must enter through the Wing 5 entrance on Independence 
Avenue. The South Building is a Federal facility and attendees should 
plan to take adequate time to pass through the security screening 
systems. Attendees must show a valid photo ID to enter the building. 
Attendees also must be pre-registered for the meeting and check in 
onsite the day of the meeting. See the pre-registration instructions 
under ``Registration and Meeting Materials.'' Only registered attendees 
will be permitted to enter the building.

FOR FURTHER INFORMATION CONTACT:  Dr. Peter S. Evans, Office of Policy 
and Program Development, Risk Innovations and Management Staff; 
Telephone: (202) 690-6272; Fax: (202) 245-4793; Email: 
[email protected].
    Note that the same week as the WGS public meeting, on October 24 
and 25, 2017, and also in the USDA Jefferson Auditorium, a separate 
interagency public meeting will be held by the National Antimicrobial 
Resistance Monitoring System collaborators. FDA will publish a Federal 
Register Notice to announce this meeting.

SUPPLEMENTARY INFORMATION: 

[[Page 44379]]

I. Background

    FSIS routinely samples meat, poultry and egg products, 
environmental surfaces in slaughter and processing establishments, and 
animal cecal contents for specific microorganisms. FSIS uses 
microbiological test results for a number of purposes: To verify the 
effective implementation of process controls and sanitation programs by 
industry; to help develop pathogen reduction standards for raw products 
and assess whether product meets those standards; and to support 
surveillance, including surveillance related to antimicrobial 
resistance, risk assessment and attribution studies. Sampling results 
may also be used to assign additional sampling or inspection resources 
to establishments or products with higher risk of causing harm to 
consumers. In addition to routine sampling, the Agency may collect 
samples for cause to investigate foodborne illnesses, outbreaks, 
consumer complaints and other non-routine events.
    Due to the rapid advances in DNA sequencing technology, its 
superior resolution, significant reductions in per sample cost, and the 
potential for a single workflow to replace current laboratory subtyping 
methods, WGS analysis is now considered an important tool for routinely 
sub-typing and characterizing bacterial pathogens. Unlike PFGE and 
other DNA-based technologies, which rely on the analysis of 
arrangements of fragments or portions of a genome sequence without 
actually knowing each nucleotide in the sequence arrangement, WGS 
analyses use almost the entire genomic sequence, about 1 to 10 million 
base units for a typical bacterium. WGS provides robust estimates of 
sequence relatedness, based on the presence, absence, substitution and 
arrangement of individual nucleotides in the genomic sequences, thus 
permitting further characterization of individual genes and other 
interesting features of bacterial genomes.
    In 2013, CDC, FDA, FSIS, and the NCBI collaborated with local, 
State, and international partners to implement a pilot study of WGS-
based surveillance for Listeria monocytogenes (Lm).\1\ For the pilot 
study, Lm isolates from patients, food, and domestic food processing 
environments were analyzed using WGS. The resulting analyses were 
routinely made available to CDC epidemiologists and other public health 
and regulatory partners. The availability of WGS analyses transformed 
outbreak surveillance and response: More illness clusters were detected 
(14 clusters detected in the year before the pilot versus 19 and 21 
clusters detected in the two years after implementing WGS). In 
addition, illness clusters were detected sooner, median cluster size 
was markedly reduced, and more outbreaks were resolved by linking Lm 
illness and food sources. This pilot shows the specific improvements 
that can be gained using WGS, as compared to the use of PFGE analyses.
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    \1\ Jackson, B.R., Tarr, C., Strain, E., Jackson, K.A., Conrad, 
A., Carleton, H., . . . Gerner-Smidt, P. (2016). Implementation of 
Nationwide Real-Time Whole-Genome Sequencing to Enhance Listeriosis 
Outbreak Detection and Investigation. Clinical Infectious Diseases, 
Volume 63, Issue 3, 1 August 2016, Pages 380-386, https://doi.org/10.1093/cid/ciw242.
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    FSIS plans to expand its use of WGS analysis to bacteria isolated 
from FSIS sampling projects to aid in accurately identifying and 
responding to outbreaks, conducting efficient traceback, and studying 
the environmental harborage and movement of pathogens in regulated 
establishments. All WGS data will continue to be uploaded to a Federal 
database that is readily accessible to all food safety and public 
health partners and stakeholders, including consumers. Additionally, 
FSIS will analyze WGS data from FSIS samples and other food, 
environmental, and clinical samples contributed by other sources and 
organizations.
    Additionally, FSIS has begun to analyze WGS data to identify 
specific genes associated with characteristics of public health 
concern. In collaboration with Federal partners, FSIS uses an 
antimicrobial resistance (AMR) gene database to identify genes 
associated with emerging resistance to beta-lactamase, colistin, 
linezolid and other critically important antibiotics. In partnership 
with the National Antimicrobial Resistance Monitoring System (NARMS), 
FSIS is searching for additional genes linked to AMR within the genomes 
of bacteria recovered from FSIS-regulated and other product samples. 
Notably, FSIS and the Agricultural Research Service reported WGS 
analyses of an E. coli from the cecal contents of swine which contained 
a recently discovered resistance gene to the antibiotic colistin.\2\
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    \2\ Meinersmann, R.J., Ladely, S.R., Bono, J.L., Plumblee, J.R., 
Hall, M.C., Genzlinger, L.L., & Cook, K.L. (2016). Complete Genome 
Sequence of a Colistin Resistance Gene (mcr-1)-Bearing Isolate of 
Escherichia coli from the United States. Genome Announc, 4(6). 
http://genomea.asm.org/content/4/6/e01283-16.full.
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    In summary, FSIS expects that the application of WGS analyses will 
enhance Agency resource allocation and decision-making. From our Lm WGS 
pilot experience, it is anticipated that the application of WGS 
analyses will lead to greater efficiencies, by consolidating laboratory 
workflows into a single step for bacterial characterization. In 
addition, FSIS and partners will use WGS in conjunction with 
epidemiologic and traceback evidence to identify the sources of 
outbreaks more expeditiously and to potentially prevent such events by 
putting in place preventive actions, informed by WGS analyses. Also, 
FSIS and other public health partners may identify genes associated 
with virulence, AMR, and other characteristics of concern, as well as 
newly emerging pathogen sub-types that were previously 
indistinguishable from routinely isolated bacteria.
    With the increase in application of WGS, PFGE and other sub-typing 
methods are expected to be phased out by FSIS and its public health 
partners, and consequently it will be important to build WGS capacity 
to perform sequencing and develop analyses to adequately support the 
respective regulatory frameworks. To address this, FSIS, with speakers 
from FDA, CDC, NCBI, academic institutions and the domestic and 
international partners, is hosting a public meeting to discuss these 
concepts in greater detail. An agenda will be published online before 
the public meeting. General topics will include:
     WGS technology: The global and local perspective and 
advantages and limitations;
     Collaboration and data sharing among Federal and non-
Federal entities;
     Information on the GenomeTrakr and PulseNet databases;
     International standards for WGS;
     Information on the equivalency of methods used by 
different agencies and stakeholders;
     Communicating WGS results to stakeholders; and
     Transitioning from PFGE to WGS in PulseNet.

II. Registration and Meeting Materials

    There is no fee to register for the public meeting, but pre-
registration is mandatory for participants attending in-person. On-site 
registration will not be permitted. Early registration is recommended 
as space is limited. All attendees must register online at http://www.fsis.usda.gov/wps/portal/fsis/newsroom/meetings. Attendees 
requiring a sign language interpreter or other special accommodations 
should notify Ms. Evelyn Arce via telephone: 202-418-8903 or email: 
[email protected].
    As stated above, FSIS will finalize an agenda on or before the 
meeting dates

[[Page 44380]]

and post it on the FSIS Web page at http://www.fsis.usda.gov/meetings.

III. Public Comments and Participation in Meetings

Public Comments: Oral Comments

    Stakeholders will have an opportunity to provide oral comments 
during the public meeting. Due to the anticipated high level of 
interest in the opportunity to make public comments and the limited 
time available to do so, FSIS will do its best to accommodate all 
persons who wish to express an opinion. FSIS encourages persons and 
groups who have similar interests to consolidate their information for 
presentation by a single representative.

Public Comments: Written Comments

    Any Stakeholder wishing to submit written comments prior to the 
meeting may do so, and may also submit comments after the meeting, 
using any of the following methods: Electronically--go to http://www.regulations.gov and follow the online instructions for submitting 
comments; Mail, including CD-ROMS--send to Docket Clerk, USDA, FSIS 
Docket Room, 1400 Independence Avenue SW., Patriots Plaza III, Mailstop 
3782, Room 8-163A, Washington, DC 20250-3700; Hand- or courier-
delivered items--deliver to the Docket Clerk, USDA, FSIS Docket Room at 
Patriots Plaza III, 355 E Street SW., Room 8-164, Washington, DC 20250, 
between 8:00 a.m. and 4:30 p.m., Monday through Friday.
    All items submitted by mail or electronic mail must include the 
Agency name and docket number FSIS-2017-0038. Written comments received 
in response to this docket will be made available for public inspection 
and posted without change, including any personal information, to 
http://www.regulations.gov. For access to background documents or 
written comments received, go to the FSIS Docket Room at Patriots Plaza 
III, 355 E Street SW., Room 8-164, Washington, DC 20250, 8:30 a.m. and 
4:30 p.m., Monday through Friday.
    Question-and-Answer Periods: Time has been allotted for audience 
questions after most presentations delivered during the meeting. 
Participants will have the opportunity to ask questions via a 
microphone in the auditorium.

IV. Transcripts

    The transcript of the proceedings from the public meeting will 
become part of the administrative record. As soon as the meeting 
transcripts are available they will be accessible on the FSIS Web site 
at http://www.fsis.usda.gov/wps/portal/fsis/newsroom/meetings. The 
transcripts may also be viewed at the FSIS Docket Room at the addressed 
listed above.

Additional Public Notification

    Public awareness of all segments of rulemaking and policy 
development is important. Consequently, FSIS will announce this Federal 
Register publication online through the FSIS Web page located at: 
http://www.fsis.usda.gov/federal-register.
    FSIS also will make copies of this publication available through 
the FSIS Constituent Update, which is used to provide information 
regarding FSIS policies, procedures, regulations, Federal Register 
notices, FSIS public meetings, and other types of information that 
could affect or would be of interest to our constituents and 
stakeholders. The Constituent Update is available on the FSIS Web page. 
Through the Web page, FSIS is able to provide information to a much 
broader, more diverse audience. In addition, FSIS offers an email 
subscription service which provides automatic and customized access to 
selected food safety news and information. This service is available 
at: http://www.fsis.usda.gov/subscribe. Options range from recalls to 
export information, regulations, directives, and notices. Customers can 
add or delete subscriptions themselves, and have the option to password 
protect their accounts.

USDA Non-Discrimination Statement

    No agency, officer, or employee of the USDA shall, on the grounds 
of race, color, national origin, religion, sex, gender identity, sexual 
orientation, disability, age, marital status, family/parental status, 
income derived from a public assistance program, or political beliefs, 
exclude from participation in, deny the benefits of, or subject to 
discrimination, any person in the United States under any program or 
activity conducted by the USDA.

How To File a Complaint of Discrimination

    To file a complaint of discrimination, complete the USDA Program 
Discrimination Complaint Form, which may be accessed online at: http://www.ocio.usda.gov/sites/default/files/docs/2012/Complain_combined_6_8_12.pdf, or write a letter signed by you or your 
authorized representative.
    Send your completed complaint form or letter to USDA by mail, fax, 
or email:
    Mail: U.S. Department of Agriculture, Director, Office of 
Adjudication, 1400 Independence Avenue SW., Washington, DC 20250-9410.
    Fax: (202) 690-7442.
    Email: [email protected].
    Persons with disabilities who require alternative means for 
communication (Braille, large print, audiotape, etc.), should contact 
USDA's TARGET Center at (202) 720-2600 (voice and TDD).

    Done at Washington, DC, on: September 19, 2017.
Paul Kiecker,
Acting Administrator.
[FR Doc. 2017-20247 Filed 9-21-17; 8:45 am]
 BILLING CODE 3410-DM-P