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Food safety: Improving public health

by preventing foodborne diseases

Food from farm to table

National Press Foundation
St. Louis, Missouri
July 22, 2015
Robert Tauxe, MD, MPH
Division of Foodborne, Waterborne and Environmental Diseases
National Center for Emerging and Zoonotic Infectious Diseases
Centers for Disease Control and Prevention

The Centers for Disease Control and Prevention

1946: Malaria Control

in War Areas program
in Atlanta becomes CDC

2012: Building 24 opens

Two complementary health systems

Health care
Outpatient clinics
Primary hospitals
Referral hospitals
Clinical research


Public health
Local health departments

State health departments

National health department
US Public Health Service

and CDC

Foodborne disease prevention involves many partners

Many points for:
At each step,
we have partners in
Industry efforts,
inspection and
enforcement, and

Federal agency roles and responsibilities in

food safety


National disease surveillance
Outbreak detection and

investigation to determine vehicle

and source
Tracks burden and trends
Tools and training for public health

Food safety policies
Inspect, monitor, enforce
Product recall and traceback
Investigation of farm and
production facilities

Problem identification

Problem management

Provide information to guide

Regulation and enforcement

regulatory action

What does CDC do in food safety?

Provide data for decision makers on foodborne diseases:
attribution to sources
Detect and investigate complex outbreaks
Support networks of health departments in states and large cities
Improve public health methods and practices
Build partnerships to improve prevention

The burden of infections from contaminated foods

Each year, 48 million people
become sick (1 in 6 Americans),
128,000 are hospitalized, and
3,000 die
1,000 foodborne outbreaks
reported annually
Major pathogens: $3 billion in
health-related costs each year

Scallan et al (2011) EID 17: 7-15, 16-22.

Attributing illness to foods

Attributing illnesses
to specific foods
helps guide food
safety policy and
Gathered information
from 4,589 outbreaks
reported 1998 2008
Estimated how much
illness came from
each of 17 food types
Painter et al (2013) EID 19: 407-415


Produce was the
dominant source for
driven by norovirus
Meat and poultry was
the dominant source for
fatal illnesses
Online Supplement
Table 4 provides
percentages for each
pathogen and food type

FoodNet: Foodborne Disease Active Surveillance Network

Reports trends in
foodborne infections and
tracks the impact of food
safety policies nationally
Developed: 1995
Because: After the 1993 outbreak due to E. coli O157, USDAs
Food Safety Inspection Service revised meat inspection system.
To tell Congress if E. coli O157 infections were being prevented,
they helped CDC start a new tracking system.
Now: Conducts surveillance for 9 infections and hemolytic
uremic syndrome (HUS), working closely with 10 state health
departments and other federal agencies.
Annual report card on food safety..

FoodNet sentinel sites, 2013

46 million persons (15% of U.S. population)

Progress in prevention, United States, FoodNet,

Since 1996-98,
Vibrio - increased
Salmonella - no change
E. coli O157, and
Listeria have decreased

Since 2006-2008,
only E. coli O157 has
decreased significantly

Improving prevention of foodborne diseases

Reducing the likelihood of contamination with pathogens
Targeting the specific points in production systems where
control needs to be improved
Anticipate new problem points will emerge as landscape
of foods changes
Cycle of continuous adjustment and improvement
Making food production and processing safer
On farms, ranches, orchards
In packing plants, slaughter houses, food factories
In restaurants and private kitchens

Outbreak of foodborne infections

A group of people become ill with the same illness

after eating the same food

More cases of a particular illness than are expected
As a result of eating a particular contaminated food
Can be difficult to detect, investigate and control
Something goes awry somewhere on the food chain
It is not always food. These infections also spread

by other routes

We investigate outbreaks to

Prevent additional cases in the current outbreak

Determine what went wrong in order to prevent

future similar outbreaks

Define high risk foods and gaps in the system

May find a new pathogen or problem
Stimulate further research
Stimulate new processes and regulations

Investigating an outbreak
Detect that an outbreak may be happening
Develop a hypothesis about how transmission

Test the hypothesis 3 lines of investigation
Epidemiological investigation
Source tracing
Culture of suspect food items
The regulatory authorities and the affected company

control and halt the outbreak

Public health surveillance of intestinal

infections in the United States
I feel sick, so I am
going to the doctor
Probably a virus,
but lets send a
sample to the lab

This is an
infection with
Campylobacter bacteria

Public health surveillance of intestinal

infections in the United States
Im glad to know what it is

Campylobacter, eh?
We can treat that, and we
need to report it to the
local health department
I will test it for antibiotic resistance

Public health surveillance of intestinal

infections in the United States

Hello Joe hope you are

feeling better
May we ask you some
questions, please?
We want to learn how
you might have caught
this Campylobacter
Weve gotten a lot of
reports like this recently

Local/State Health
Department Level

Campylobacter infections
1.3 million illnesses, 13,000 hospitalizations, and 120
deaths annually in the U.S.
Acquired from different sources
bird and cattle reservoirs
poultry, raw milk, animal contact, surface water
Causes diarrheal illness in humans
bloody and non-bloody diarrhea
Guillain Barr Syndrome (1/1000)

Reported Campylobacter infections,

Alaska, 20002008

Cases mostly in Southcentral Alaska

Mat-Su Valley


Describing the outbreak (first 63 cases)

Age range; 1-79 years, median 47

Female: 49%
White: 88%
Anchorage resident: 73%

Illness features:
91% diarrhea
82% abdominal cramps
21% bloody diarrhea
In all: 98 cases identified
5 hospitalized, 1 with Guillain Barre syndrome
Hypothesis generation: initial interviews
Some spontaneously mentioned eating fresh raw peas
Gardner 2011 Clin Infect Dis 53:26-32

Testing the hypothesis

Case-control study:
67% of persons with Campylobacter ate raw peas
in the week before they got sick, compared to
17% of healthy controls interviewed
p < 0.01
Peas all came from one pea farm
only pea farm in Alaska
in business for many years

The implicated food vehicle

Farm A Peas
Farm A

To process:

Pea harvest scene

Combine with
wash tank

Sandhill Cranes (Grus canadensis)

Testing the hypothesis (contd)

Microbiological findings
Campylobacter identified in samples from
peas in field and in packages,
Sandhill Cranes
Typing indicated outbreak strains similar to wild bird strains
Variety of molecular fingerprints identified
Types found to match
Strains from humans, peas, and cranes

Kwan 2014, Appl Env Microbiol 80:4540-4546

Campylobacter illness from fresh peas

Control efforts
Sept 2008: Harvest halted and peas removed from shelves
Outbreak promptly stopped

2009: Scare-cranes,

Larger label recommending blanching,

Chlorine in water wash tank for harvested peas
Harvest resumed no spike in cases
Through 2014: No recurrence

What was learned

First link between Campylobacter and fresh raw produce
Spread from avian reservoir to food
Controlled by changing washing step on farm to prevent

cross contamination of peas through wash water

General implications for any fresh produce eaten raw
Molecular subtyping useful in proving source

Until recently, foodborne outbreaks were local

Outbreaks detected were typically
Large focal outbreaks
Obvious to the affected persons and local

Often associated with a particular event
Dispersed outbreaks were rarely detected
Fostered impression that foodborne disease was just a

local problem

The changing landscape of foodborne infections

Food industry is becoming more centralized
Food sourcing is going global
Consumer tastes and practices are changing
Rising demand for food that is less processed
Emerging pathogens and unsuspected food hazards
Better surveillance means that we detect more dispersed


A large outbreak in one place may be obvious

Local surveillance will detect this event

An outbreak with cases dispersed in many places

is difficult to detect, unless

We test bacteria from all the cases, and

We find they are infected with the same bacterial strain
We learn by interview they shared an exposure

The spectrum of foodborne disease outbreaks

Local outbreak

Dispersed outbreak

Many cases in one place

Detected by affected group


A few cases in many jurisdictions

Detected by lab-based subtype

Multi-state investigation

Local investigation
Industrial contamination event
Local food handling error
Local solution

Broad implications

Detecting a dispersed outbreak is like finding a

needle in a haystack

National Molecular Subtyping Network for Foodborne Disease Surveillance

Connects cases of
illness nationwide to
identify outbreaks that
would otherwise go
Started: 1996
Because: After 1993 E. coli O157 outbreak (726 cases, 4 deaths),
many clinical labs began testing for E. coli O157. CDC began
PulseNet to detect outbreaks sooner.
Now: National network of public health and food regulatory agency
laboratories that perform standardized molecular subtyping
(fingerprinting) of E. coli O157, Salmonella and Listeria

PulseNet data analysis: Searching for clusters

Cluster of same pattern

PulseNet staff
search for similar
patterns in past 2-4
When a cluster is
identified, they
report it to
States can look at
PulseNet database

Public health surveillance of intestinal

infections in the United States

Hello Joe hope you are

feeling better

Local/State Health
Department Level

May we ask you some

questions, please?
We want to learn how
you might have caught
this Salmonella.

This is a rare type of Salmonella.

We dont see this type very often.
Lets check the PulseNet database

Public health surveillance of intestinal

infections in the United States

Local/State Health
Department Level

Level = CDC

In the last week,

we have reports of several
people in our state
with similar illness.
We are starting to investigate them

We have seen 4 Salmonella with the

same fingerprint recently. It also looks
like there are cases in other states that
have the same rare type.
Maybe it is bigger than just one state

Public health surveillance of intestinal

infections in the United States

Local/State Health
Department Level

Level = CDC
Well hold a conference
call with all the states that have
cases. Let us know if your
interviews give any clues

We usually get about 15 of these

per year in the US, so to have
20 reported in the last week
around the country is concerning

Salmonella infections
1.2 million illnesses, 23,000 hospitalizations, and 450
deaths annually in the U.S.
Acquired from many different sources
Many animal reservoirs
Poultry, meat, fresh produce, eggs, raw milk,
animal contact
Causes diarrheal illness in humans
blood stream infections
severe focal infections
Many serotypes: Enteritidis, Typhimurium, Newport and
Heidelberg are most common

This story begins in 2012 - Salmonella Heidelberg

May 2012 April 2013

134 cases confirmed (1 pattern)
13 states (mostly WA and OR)
Linked to Foster Farms chicken
from WA plant
Raw chicken advisory
With changes at plant, outbreak
stopped cases below baseline

55% female
Median age 21 years
31% hospitalized
No deaths
2/14 tested were multidrug resistant, including

New cluster detected in 2013

June 17, 2013:
PulseNet detected a new cluster of Salmonella
Heidelberg illnesses in Western states with a different
rare PulseNet pattern

Initial interviews with ill persons:

7 of 8 reported eating chicken
2 of 3 reported eating Foster Farms brand chicken
Routine retail meat testing:
Salmonella Heidelberg with same rare pattern in a
retail poultry sample from Foster Farms

The outbreak expands

Continued surveillance identifies more cases

7 different PulseNet patterns linked to this outbreak

(Including one from 2012 outbreak)

Patterns included when

Significant increase above expected baseline
Similar geographic distribution
Ill persons with these patterns reporting having eaten
chicken, specifically Foster Farms brand
Pattern identified in Foster Farms chicken

Some patterns resistant to antibiotics

October 8, 2013:
Results of patient interviews (n=132)



# Exposed/
# Observed











Foster Farms

FoodNet Pop Survey*

Percent Exposed


*Foodborne Diseases Active Surveillance Network (FoodNet)

Population Survey: national food consumption survey

Assessment at slaughter facilities (USDA-FSIS)

FSIS traceback led to 3 Foster Farm facilities in California

FSIS was unable to link illnesses to one specific facility,

product, or production period

Routine regulatory sampling of whole carcasses did not

exceed Salmonella performance limits: <5% positive

Testing at 3 facilities in California

Salmonella Heidelberg was found in variety of chicken parts
at 3 facilities (variety of parts)
Strains with 6 of 7 outbreak patterns

October 7, 2013: USDA-FSIS issued a Public Health Alert

October 11, 2013: Company began process improvements

Outbreak summary

March 1, 13 July 31, 14

634 cases confirmed
29 states & Puerto Rico
Lull in December 2013
Finally ended in July 2014

49% female
Median age 18 years
38% hospitalized
13% blood infections
No deaths

What was learned?

Large outbreak traced to raw chicken simultaneously from

several plants in same company over many months

Routine testing of whole carcasses had not revealed a


Multiple PulseNet patterns likely came in on live birds from

farms (and likely from their parents)

Finally controlled by extensive changes in processing that

reduced contamination of
live birds on farms
chicken parts (breasts, thighs, drumsticks, etc.)

What can we do to improve prevention?

We have a problem with Salmonella in poultry

Much is likely coming down from parent and grandparent birds
Control programs exist for Salmonella that harm birds
Should be expanded to include Salmonella that harm humans

We have a problem with poultry parts (and ground poultry)

Regulatory focus has been exclusively on whole carcasses

Most consumers buy parts
Parts more likely to be contaminated (25% vs <5%)
New USDA performance standards for parts, ground poultry

We have a problem with antibiotic resistance

Particularly with resistance to drugs important in human medicine
Need judicious use in parent and grandparent birds as well

Multistate foodborne outbreaks reported to CDC

PulseNet begins

Isolates uploaded to PulseNet and clusters identified,


Novel foods implicated in outbreaks since 2006 in

the United States

Bagged spinach
Carrot juice
Peanut butter
Broccoli powder on a snack food
Dry dog food
Frozen pot pies
Canned chili sauce
Hot peppers
White and black pepper
Raw cookie dough (flour?)
Fenugreek sprouts
Pine nuts
Raw scraped tuna
Pomegranate anils
Cashew nut cheese
Chia sprout powder
Caramel-dipped apples

21 (100%) were found

as a result of multi-state
17 (81%) are produce
9 (43%) are imported

Multistate outbreaks point to risk of contamination

early in food production
Local outbreaks: often follow a local breakdown in food safety
Multistate outbreaks: often reflect contamination early in

production, that is then distributed widely

Contamination as a result of
Transmission from mother animal to baby
Poor practices in an another country
Contamination of an added ingredient
Contamination in a processing or packing facility
Using a contaminated ingredient
Addressing those may make many foods safer

If detecting a
dispersed outbreak
is like finding a
needle in the
would a bigger
magnet help?

The Opportunity

Sequencing the entire DNA of a bacterium is

becoming practical for routine use
Cost ~ $100: Subtype, virulence, resistance in one test
2013: Began proof-of-concept project: Whole genome
sequencing with enhanced surveillance for Listeria
For each case: 3,000,000 base pairs and 300 questions
Collaboration among CDC, FDA, USDA, and NCBI and the
state public health departments
International collaboration: Developing and refining the
informatics pipelines with partners in four other countries
Now evaluating in parallel with Pulsenet PFGE. Needs
Robust platform for sharing data (data pipelines)
New analytic tools for public health use
Sequencing equipment and training

Using whole genome sequencing in surveillance

Listeria pilot project, September 2013 present:
Sept 2013 : Sequencing all Listeria monocytogenes

isolates in close to real time

Collaboration: Clinical isolates at CDC (~800/year), food

isolates at FDA (~800 year), data stored with NIH

Results through June 2015:
Pre PulseNet: 1 outbreak every 3 years, average size = 60 cases
PulseNet : 3 outbreaks/year, average size = 8 cases
WGS Pilot: 9 outbreaks/year, average size 4 cases

New food vehicles for Listeria:

Stone fruits
Caramel apples
Ice cream

Listeria monocytogenes

Reported: ~ 750 cases per year

Estimated: 1650 infections/year,
1500 hospitalized, and 260 deaths
A invasive bacterial pathogen
Rare but serious infections in people
at high risk
Pregnant women -> fetus
Found in moist cool environments
Grows at low temperatures
Transmitted by
Processed meats
Soft cheeses
Produce (e.g. cantaloupe)

Listeria and Blue Bell Ice Cream: Cluster #1

South Carolina Health Dept found L

mono with several PulseNet patterns
in Blue Bell ice cream products made
in Texas.

PulseNet: 5 cases, 4 patterns, in

patients hospitalized at one Kansas
hospital (Jan 2014 Jan 2015)

3 of the 4 patterns also found in

Scoops institutional Ice Cream
product, made in Texas plant

CDC recommends that consumers

do not eat products that Blue Bell

Creameries removed from the

market, and institutions and

retailers should not serve or sell

All 5 patients ate that product

WGS: strains from people and ice
cream are nearly indentical
All from one production line halted,
product withdrawn, and then recalled,
and CDC advised public

Listeria and Blue Bell Ice Cream: Cluster #2

CDC recommends that consumers

do not eat any Blue Bell brand
products made at the Oklahoma
production facility, nor any recalled
products, and that retailers and
institutions not serve or sell them

Testing other Blue Bell Ice Cream

products at KS hospital, that were
made in Oklahoma plant, also found
Listeria with a rare PulseNet pattern

Same rare pattern found in 5

patients in Texas, OK, and AZ over
5 years (2010 2014)

WGS confirmed nearly identical

Patients hospitalized before Listeria

infection began

Exposure to ice cream uncertain,

though their hospitals got Blue Bell
ice cream products from OK plant

Same strain found in several

products at Oklahoma plant

Listeria and Blue Bell ice cream:

stopping the outbreak

10 cases in 2 clusters, with 3 deaths

2 DNA types, from 2 ice cream plants

Stretched over time and space

o 1 cluster: 1 year in 1 hospital
o 1 cluster: 5 years in 3 states

FDA and CDC shared findings with

company, which led to:
o Stopping all production and
recalling all product

CDC warned
o Public, with web-updates, social
media, media outreach
o All health care facilities
o All public health departments

Listeria monocytogenes infections and ice cream

Prevention lessons learned
Novel food vehicle: Ice cream not linked to Listeria infection before 2015
Two processing facilities contaminated with 2 different strains
Highly dispersed in space and time: stretched over 3 states and 5 years
WGS increased confidence that cases and product were truly related
Action stopped the outbreak and saved lives could have been indefinite
Industry needs rigorous sanitation, monitoring and preventive controls
Key is environmental monitoring for Listeria in ice cream factories

Changes in our public health surveillance system for

foodborne disease continue to drive improvement
1996 2013: PulseNet molecular subtype-based surveillance

E. coli O157/STEC, Salmonella, Listeria, Shigella, Campylobacter

More multistate outbreaks
Solving smaller outbreaks
Growing variety of food vehicles

2013 - Future: Whole genome sequence-based surveillance

Proof-of-concept project with Listeria, with testing at CDC

More outbreaks, smaller outbreaks, more new food vehicles
Finding unsuspected gaps in food safety
Next is Shiga toxin producing E. coli, then Salmonella
Expanding technology to states:
Rolling out new software platform to states this summer
Have developed algorithms for reading information from sequence
Pilot with 10 states that have sequencers and training

Future foodborne outbreaks more likely to be

Dispersed in space: Multi-state, multi-national

Dispersed in time: Multi-year
Detected by sequence-based surveillance
Detected as contaminated product first
Associated with
fresh produce and minimally processed foods
imported foods
novel food vehicles
novel routes and pathways of contamination

Could 2015 be a tipping point for improving

foodborne disease prevention?

USDA/FSIS: Implementing new performance standards for

poultry parts, ground poultry, for Salmonella and

FDA: Will; publish new regulations under FSMA for

Preventive Controls = Processed foods
Produce Safety
Foreign Supplier Verification

Companies imposing new requirements for suppliers,

making fod safety part of corporate culture

Consumers demanding food that is responsibly produced

There is a small
cloud on the

Wanderer above the Sea of Fog

C. D. Friedrich

Tsunami warning: A coming challenge

Rapid culture-independent
diagnostic tests

GI Pathogen Panel
15 targets,
five hours

culture independent
diagnostic platforms

BioFire FilmArray
22 targets,
one hour

The challenge: Culture versus cultureindependent diagnostic tests

Clinical laboratory

Public health laboratory

Culture on petri dish

PulseNet fingerprints

diagnostic test platform

No PulseNet fingerprints,
No serotype, no antibiotic
susceptibilty test, no DNA sequence

The challenge: Culture versus cultureindependent diagnostic tests

Clinical laboratory

Public health laboratory

Culture on petri dish

PulseNet fingerprints

Reflex culture

diagnostic test platform

No PulseNet fingerprints,
No serotype, no antibiotic
susceptibilty test, no DNA sequence

Culture-independent diagnostic tests: Challenges to

public health programs

Public health currently depends on the isolate to:

Track cases and trends accurately
Detect and investigate outbreaks
Take public health action
Estimate the overall burden
Track changes in antimicrobial resistance

Meeting the challenge to public health of

culture-independent diagnostic tests

Short term: Preserve access to isolates:

Work with FDA, CMS and medical testing industry
Reflex culture of positive specimens to confirm them
In clinical labs or public health labs

Medium term: Build public health lab capacity to handle

sequencebased information

Long term: Develop assays for public health that are themselves
Selective amplification around diagnostic regions of genome?
Single cell sorting and sequencing?
Of use in food matrices as well?

Culture-independent diagnostic tests: Opportunities

If diagnosis and reporting were faster:
Patients could remember better what they ate
Faster detection, intervention
If more infections could be diagnosed (correctly):
We might find more infections than by culture
We could track diseases we miss now (norovirus, other
E. coli infections)
If the right gene targets are incorporated into the new tests:
Antibiotic susceptibility data
Subtyping data $900 Disposable DNA sequencer
Available in gene sequence obtained in single clinical
Transmitted instantly to public health

Foodborne diseases in the 21st century

A continuing challenge to public health
New hazards, new foods, new solutions
Better public health surveillance pushes systemic change
Investigating outbreaks and learning from them means
greater opportunity to prevent them
Laboratory-based surveillance methods must evolve as
we move to a post-isolate era
More than ever, food safety is local and global at the
same time

Thank you

The findings and conclusions in this presentation are those

of the author and do not necessarily represent the views of
the Centers for Disease Control and Prevention