Antimicrobial Resistance Surveillance and Reporting at Food Safety and Inspection Service (FSIS) - Andrew Hudgens, Microbiologist, Food Safety and Inspection Service, United States Department of Agriculture, from the 2018 NIAA Antibiotic Symposium: New Science & Technology Tools for Antibiotic Stewardship, November 13-15, 2018, Overland Park, KS, USA. More presentations at https://www.youtube.com/playlist?list=PL8ZKJKD9cmEffjOrjbBvQZeN2_SZB_Skc

1. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
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2. Food Safety and Inspection Service:
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Food Safety and Inspection Service
Andrew Hudgens, MPH
Eastern Laboratory – Microbiology Characterization Branch
Office of Public Health Science
Food Safety and Inspection Service, USDA
NIAA’s 8th Annual Antibiotic Symposium November 13-15, 2018
Antimicrobial Resistance Surveillance and
Reporting at Food Safety and Inspection
Service (FSIS)

3. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
Overview
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 Food Safety and Inspection Service (FSIS)
• Mission and Background
• FSIS’s Role in NARMS
• History
 FSIS and Data Analysis
• FSIS and Antimicrobial Resistance (AMR)
• Software Tools
• Outcome of AMR Data
 AMR Driven Investigations
• Linezolid Resistances

4. FSIS and Mission
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Pulsed-Field Gel Electrophoresis
Antimicrobial Susceptibility Testing
Salmonella Molecular Serotyping
Whole Genome Sequencing

5. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
Food Safety and Inspection Service:
National Antimicrobial Resistance Monitoring
System (NARMS)
Food Safety and Inspection Service:
FSIS’s Role in NARMS structure
Source: FDA
Human
Animal
Retail

6. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
1997 2012 2013 2014
Food Safety and Inspection Service:
20151996 2016 2017
ARS FSIS
Food Safety and Inspection Service
NARMS at USDA FSIS: A Collaborative Program
NARMS antimicrobial
susceptibility testing (AST)
on PR/HACCP isolates
conducted by ARS
FSIS conducts
AST for
PR/HACCP and
cecal isolates
FSIS begins WGS
on selected cecal
Salmonella and
Campylobacter
FSIS: WGS for all
Salmonella and
Campylobacter
FSIS PR/HACCP
verification
sampling begins
Cecal sampling
begins: culture,
subtyping, and AST
conducted by
FDA/CVM
FDA: Whole Genome
Sequencing (WGS) for
Salmonella isolates
from cecal samples
FSIS: WGS for all
Salmonella and
Campylobacter
from cecal samples
2018
FSIS: WGS for
select Enterococcus
and E. coli from
cecal samples

7. Food Safety and Inspection Service:
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Samples are collected
from federally inspected
slaughter and processing
plants throughout the
United States
FSIS Sampling Sources
Pathogen Reduction/Hazard
Analysis and Critical Control Point
(PR/HACCP) Program (1997-
Present)
Cecal Sampling Program
(2013-Present)
Food Safety and Inspection Service
Two Sources of Samples from Food Animals
Salmonella - Campylobacter Salmonella – Campylobacter – E.coli – Enterococcus
 The Cecal sampling program is non-regulatory
• Results not used for enforcement but to understand AMR microflora in FSIS products

8. Food Safety and Inspection Service:
Antimicrobial Susceptibility Testing and Interpretation
 FSIS follows NARMS’s semi-automated broth micro dilution
susceptibility testing method as described in NARMS
Interagency Laboratory Manual
https://www.fda.gov/downloads/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/NationalAntimicrobialResistanceM
onitoringSystem/UCM528831.pdf
 Interpretative criteria are defined by NARMS,
• Breakpoints established by the Clinical Laboratory
Standards Institute (CLSI) for Salmonella, E. coli, and
Enterococcus
• Epidemiological cut-off values (ECOFFs) for Campylobacter,
established by the European Committee on AST (EUCAST)
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9. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
FSIS AMR Data: Workflow
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AMR
Genotype
MIC
Results
Transfer of
MIC Results
(operator &
numerical
value)
-Interpretive
Calculations (SIR)
-MDR
Calculations
-NARMS Specific
Fields
-WGS | AMR
Genotype
All AMR raw
and
calculated
values to
produce
interactive
visualizations
Link

10. Food Safety and Inspection Service:
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Food Safety and Inspection Service
AMR at FSIS: The outcome
Antimicrobial Susceptibility Testing
MIC values + CLSI/ECOFF Breakpoints = Interpretation → Phenotype
Whole Genome Sequencing
WGS Data → Genotype
ResFinder
NCBI
PointFinder
Publication of integrated survey
reports that consolidate phenotype
and genotype data from all sources
into an interactive format

11. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
AMR Driven Investigations: Linezolid resistance
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 First identification of Linezolid resistance in the U.S. in
bacteria isolated from food animals
 Linezolid resistance gene optrA in 3 Enterococcus isolates
from cecal content
 An additional linezolid resistance gene cfr identified on the
same plasmid for one of the isolates
 Other resistance markers on these plasmids may indicate
potential co-selection of these plasmids
 Horizontal transmission into bacterial populations that cause
human infections is of concern
Journal of Antimicrobial Chemotherapy, 2018

12. Food Safety and Inspection Service:
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Food Safety and Inspection Service
Acknowledgements
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 USDA FSIS Offices
 USDA ARS
 FDA CVM
 CDC NARMS
 NCBI
 State Laboratories

13. Food Safety and Inspection Service:
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Food Safety and Inspection Service:
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Questions?
One Team, One Purpose
Protecting Public Health and Preventing Foodborne Illness