Shoe-leather Molecular Epidemiology:

Genomics, Metagenomics, and the Future of

Foodborne Disease Surveillance

Molly Freeman, PhD

PulseNet USA
(slides courtesy of John Besser, PhD)
Foodborne Disease Surveillance

sur·veil·lance; sərˈvāləns/noun

Public health surveillance

is the systematic collection,
analysis and interpretation
of health data
Foodborne Disease Surveillance

sur·veil·lance; sərˈvāləns/noun

 Outbreak detection and

investigation
 Monitor burden, trends,
and attribution
 Foodborne Illness in the U.S.

 Each year, 1 out of 6

Americans gets sick
from foodborne
disease and 3,000 die
as a result

“That's an unacceptable price to pay for

contaminations that are mostly preventable.”
– Kathleen Sebelius, Secretary of Health and Human Services
 How are Outbreaks Detected?

1. Notification (usually events)

2. Laboratory-based (pathogen-
specific) surveillance
“Event-driven” Outbreaks

 Usually localized
 Usually due to unsafe
food preparation
 Best way to discover
new PATHOGENS
Pathogen-specific Surveillance

 Often widely
dispersed
 Fastest, most effective
way to discover food
production and
distribution problems
(not detected before
consumption)
Shoe-leather Molecular Epidemiology

 Past and Present (PFGE)

 The very near future (genomics

and new cluster analysis tools)

 The slightly more distant

future (metagenomics)
87 Labs in the PulseNet USA Network
PulseNet Groups Together Cases Most Likely
to Share a Cause for Their Illnesses
PulseNet Groups Together Cases Most Likely
to Share a Cause for Their Illnesses
 Onset Dates of Escherichia coli O157:H7 Cases Submitted
to MDH Clinical Laboratory Section, Minnesota, 1995
(n=183)

18

16

14
Number of Cases

12

10

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Onset Date
 Onset Dates of Escherichia coli O157:H7 Cases Submitted
to MDH Clinical Laboratory Section, Minnesota, 1995
(n=183)

18

16

14
Number of Cases

12

10

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec

Onset Date
Consequences of PFGE Case Definitions

 Outbreaks detected
and resolved faster,
with fewer cases
 Stimulate incremental
safety improvements
2013 PulseNet-triggered or Enhanced Outbreak Investigations
2014 PulseNet-triggered or Enhanced Outbreak Investigations
National Cluster Investigations:
30 – 60 clusters monitored per week

Local
investigations:
~ 1,500/year
 Food Safety Improvements Triggered
by PulseNet Investigations

Ready-to-eat &
“ready-to cook” foods Beef
Peanut products
Eggs Cheese
and dairy

Vine Spices
Deli meats vegetables Tree nuts
Leafy
greens

Mellon

Poultry
Sprouts
Flour
Shoe-leather Molecular Epidemiology

 Past and Present (PFGE)

 The very near future (genomics

and new cluster analysis tools)

 The slightly more distant

future (metagenomics)
Shoe-leather Molecular Epidemiology
Listeriosis Incidence and Outbreak
Recognition in the U.S.

Listeria
initiative

PulseNet era
begins
Listeriosis Incidence and Outbreak
Recognition in the U.S.

1 2012 2013 2014 2015 2016 2017 2018

Listeria
initiative NGS
PulseNet era
begins era?
Nationwide Real-time Genomics-based Surveillance
Pilot for Listeria monocytogenes Infections

 Sequence and investigate all

U.S. cases of Listeriosis
(~800 per year)
 WGS in parallel with PFGE
 ~15 PFGE and 17 WGS clusters
investigated (5 months)
 Long-term Laboratory-based
Surveillance Strategy
1. Preserve cultures 2. Prepare for the future 3. Metagenomics
working on pure cultures No cultures
Current
methods 250 STEC genomes
study Bigs.db
(serotyping, AST, Applied Maths
PFGE, MLVA etc.)

Real-time WGS surveillance

CIDT Working groups:

Whole genome of listeriosis

1. Overarching WG
2. Regulatory WG
sequencing Proof of concept

(WGS)
Global Microbial Identifier
3. PHL/Funding/Best Practices WG (GMI)
4. CIDT panel evaluation WG
5. Industry WG
Retrospective
WGS studies:
V. cholerae, Salmonella, Listeria
E. coli, Campylobacter
100k Foodborne pathogens

Metagenomics
sequencing study

Communication:
White papers, Meetings
Presentations, Publications LRN metagenomics
studies
Why Whole Genome Sequencing (WGS)?

 High resolution, scalable

case definitions
 Universal
 Provides additional
information
 Typing Methods (example: STEC)

PFGE MLVA WGS

Strain 5 – 20 5-7 DNA loci • 3,500 loci

measuring “bands” • 4,600,000 bases
units
Information Subtype • Subtype • Hi Res Subtype
derived • Evolutionary • Evolutionary
relationships relationships
• Virulence
• Antimicrobial
susceptibility
Shoe-leather Molecular Epidemiology

 Past and Present (PFGE)

 The very near future (genomics

and new cluster analysis tools)

 The slightly more distant

future (metagenomics)
Conclusion: John’s prediction

Metagenomics will be
changing how we do
business in foodborne
and waterborne
disease surveillance
in 10 years or less
 Alice Comments on our Expanding
Understanding of Microbial Genetics

from Alice in Wonderland