Introduction
to Food Microbiology
and
Surveillance for Foodborne Illness
Kali Kniel, Ph.D.
Associate Professor, Microbial Food Safety
Department of Animal and Food Sciences
Foodborne illness (FBI)
• Infection or intoxication caused by transfer of
microbial or chemical contaminants from food or
drinking water to a human
– Over 250 different foodborne diseases and
are constantly changing due to emerging
microorganisms
Food Related Illness and Death in the US
• Centers for Disease Control and Prevention
(CDC), Dr. Elaine Scallan and others, 2011
• 47.8 million cases, of which, an estimated
– 9.4 million illnesses caused by 31 known pathogens
– 38.4 million illnesses caused by unspecified agents
• 128,000 hospitalizations
• 3000 deaths
• Are numbers meaningful?
– Baseline data
– Underreporting/mild disease
Incidence per 100,000 population
Salmonella - National incidence of the top
three serotypes 1970-2001
14
Typhimurium
12
10
8
Enteritidis
6
4
2
Heidelberg
0
1970
1974
1978
1982
1986
1990
1994
1998
Years
4
Outbreaks vs Cases
• Case: an instance of a particular disease
• Outbreak: an incident in which 2 or more cases of a
similar illness result from eating the same food (2 or
more unrelated cases)
– Exception: 1 case of a chemical-related fbi or
Clostridium botulinum poisoning constitutes an
outbreak
Surveillance drives the cycle of public
health prevention
Surveillance
Epidemiologic
investigation
Prevention
Measures
Applied
Targeted
Research
Changes in outbreak scenarios
• Classic “church supper” or Sunday picnic are
now multi-state outbreaks
• Need information to design useful fbi control
programs
Microbiology Basics
• What’s the difference between a bacteria, a
virus, a protozoa, a helminthe, a chemical?
• Which ones may grow in your food? Does that
matter?
• What’s an infection and what is an intoxication?
Bacteriology Basics
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Characterization by spore formation
Characterization by shape
Characterization by Gram stain (1884)
Gram positive (purple)
Gram negative (pink)
Outer membrane
Peptidoglycan
Peptidoglycan
Plasma membrane
Plasma membrane
Periplasmic space
Bacterial Growth
Viral Growth
Parasite Growth
Microbiology Basics
• Factors affecting growth and/or illness
– Nutrients
– pH
– Water availability (Aw)
– Temperature
– Atmosphere
• Manipulate these in terms of Food Preservation & Food Safety
• How?
Process Foods to Enhance Quality & Safety
• What factors can enhance a shelf life and the safety of
the product?
– Pasteurized milk
– Bagged salads
– Packaged deli meats
– Ready to eat sliced apples
• Technologies
– Heat (pasteurization)
– Enhanced packaging films, active packaging
– High pressure processing
Foods Most Often Involved
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Beef-ground beef
Produce
Seafood-fish, shellfish
Other meats
Dairy products
Ready-to-eat (RTE)/Ready-to-heat (RTH)/Ready-to-cook (RTC)
• Why?
Most Common Agents
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Campylobacter
Salmonella
Staphylococus aureus
Escherichia coli O157:H7
Clostridium perfringens
Listeria monocytogenes
Viruses (Norovirus, Hepatitis A)
Protozoa (Cryptosporidium, Cyclospora, Toxoplasma)
Clinical Features
• Transmission
• Pathogenesis
– Host factors
– Organism factors
• Carriers
• Recognizing FBI
– Control and prevention
Symptoms
• Acute symptoms most common
• Often self-limiting
• Chronic sequelae more common
• Diarrhea (5 types), cramps, nausea, fever, vomiting,
body aches
– >3 or 4 loose stools within a 24 hour period
– Warning sign is bloody diarrhea
Factors contributing to outbreaks
• Improper holding temperature
– Danger zone 40-140°F
• Inadequate cooking
• Improper cooling
• Improper reheating
• Poor personal hygiene
• Cross-contamination
• Poor storage practices
Biofilm development
biology.binghamton.edu/davies/research.htm
Factors Affecting Disease
• Microorganism factors
– Gene expression
– Potential for damage or stress to microorganism
– Interaction of microorganism with food
– pH susceptibility
– Interaction with other microorganism
Factors Affecting Disease
• Host factors
– Immunocompromised
– Age
– Pregnancy
– Medications, chemotherapy, diabetes
– Gastric acid
Changing Epidemiology-Agent
• Newly recognized pathogens
– non-O157 shiga-toxin producing E. coli
– Cyclospora cayetanensis
– New variant CJD
• New resistance
– Salmonella Typhimurium DT 104
– Salmonella Newport
– Ciprofloxacin resistant Campylobacter
Foodborne Outbreak Scenarios
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•
Traditional scenario
– usually event associated, or affects a discrete
population
– acute and localized
– high inoculum, high attack rate
Newer scenario
– diffuse and widespread
– low-level contamination of widely distributed food
product
A large outbreak in one place may be
obvious
An outbreak with cases dispersed in many
places may be difficult to detect, unless
We test the pathogens from all the cases, and
We find they are infected with precisely the same
bacterial strain
FB Disease Surveillance
• Disease Prevention and Control
• Knowledge of Disease Causation
• Administrative Guidance
Burden of Illness
http://www.cdc.gov/foodnet/surveillance_pages/burden_pyramid.htm
Foodborne Outbreak Surveillance
• Local Health Departments
– Patient complaints
– Laboratory, HCW CMR reports
• State Health Departments
– Foodborne outbreak reports
– Salmonella serotyping
– PFGE
• Federal Health Agencies (CDC and
regulatory)
– PulseNet and FoodNet
Surveillance
• Passive surveillance occurs when health
agencies are contacted by cases, physicians or
laboratories, which report illnesses or laboratory
results to them.
• In active surveillance, the health agencies
regularly contact physicians and laboratories to
make sure that reportable diseases have been
reported and required clinical specimens or
isolates have been forwarded to state
laboratories for further analysis.
Disease Reporting
• Passive surveillance system
• Mandatory disease reporting to LHD
• LHD case follow-up and further investigation if
needed
• LHD transmit data to DHS to CDC
• For select agents, must report immediately
Notifiable foodborne diseases
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Food Net - Foodborne Diseases Active Surveillance Network (CDC, USDA, FDA)
Salmonella, Shigella, Campylobacter, Escherichia coli O157, Listeria
monocytogenes, Yersinia enterocolitica, Vibrio and Cryptosporidium and
Cyclospora
Objectives of FoodNet
1.
Determine the burden of foodborne illness in the United
States
2.
Monitor trends in the burden of specific foodborne
illness over time
3.
Attribute the burden of foodborne illness to specific
foods and settings
4.
Develop and assess interventions to reduce the burden
of foodborne illness
PulseNet
• A national network of public health
and food regulatory agency laboratories coordinated CDC.
– The network consists of: state health departments, local health
departments, and federal agencies (USDA/FSIS, FDA).
• PulseNet participants perform standardized molecular
subtyping (or “fingerprinting”) of foodborne diseasecausing bacteria by pulsed-field gel electrophoresis
(PFGE).
• PFGE can be used to distinguish strains of organisms at
the DNA level. DNA “fingerprints,” or patterns, are
submitted electronically to a dynamic database at the
CDC. These databases are available on-demand to
participants—this allows for rapid comparison of the
patterns
Objectives of PulseNet
1. Detect foodborne disease case clusters by PFGE
2. Allow for real-time communication among state, local
health departments, and international partners
3. Facilitate early identification of common source
outbreaks
4. Help food regulatory agencies identify areas where
implementation of new measures are likely to increase
the safety of our food supply
DNA Fingerprinting by PFGE ?
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Isolates are obtained from patients, food, etc
DNA is isolated
DNA is cut into fragments with an enzyme
DNA fragments loaded into a gel matrix and are separated
using an electric field
What is PFGE?
Large
Fragments
Small
Fragments
3
1
4
2
Surveillance Data Limitations
• Many but not all foodborne pathogens are reportable
diseases to the local health dept from physicians &
laboratories
• Underreporting issues
– Estimated that for every 1 case of Salmonella that is
diagnosed, 38 cases are undiagnosed
• Not all reported cases are foodborne
– Person to person, animal contact, water
The outbreak…
• So what happens when surveillance indicates that an fbi
outbreak is occurring?
Initial Call
• Calls from physicians reporting patients with
symptoms of fbi
• Call from Community Health Department
• Increase in laboratory reports
Steps in Outbreak Investigation
1. Verify the Diagnosis
Steps in Outbreak Investigation
1. Verify the diagnosis
2. Confirm the outbreak
Steps 1 and 2
are
interchangeable
What could account for the increase in
cases?
What could account for the increase in
cases?
Real increase
• Increase in population
size
• Changes in population
characteristics
• Random variation
• Outbreak
Artificial increase
• Increased
examination of
stools
• New testing protocol
• Changes in
reporting
procedures
Initial Investigation
• Any other way to see if there is a relationship between
these isolates?
Molecular Epidemiology
• DNA fingerprinting
• Pulsed Field Gel Electrophoresis (PFGE) most common
in outbreak investigations
• A cluster of isolates with the same PFGE pattern
suggests they arose from the same parent (same
source)
• Still need an epidemiologic investigation
PFGE pattern of E. coli Isolates
Steps in Outbreak Investigation
1. Verify the diagnosis
2. Confirm the outbreak
3. Case definition
Steps 1 and 2
are
interchangeable
Case Definition
• Outbreak investigation definition:
1. what symptoms
2. where
3. onset of symptoms (dates)
4. stool culture or PFGE pattern
• Advantages? Disadvantages?
E. coli O157:H7 isolated from a stool culture or development of
hemolytic-uremic syndrome in a school-age child resident of the
county with gastrointestinal symptoms beginning between
November 3 and November 8, 2009.
Case Definition
• Advantages:
– Lab confirmation increases specificity of case definition
• Reduces misclassification; maximizes power to detect source.
• Disadvantages:
– Lab confirmation
• Excludes patients who didn’t see MD, were not examined, or no
PFGE.
• Decreases the sensitivity of the case definition
• Possibly leads to a misrepresentation of case characteristics.
– Limiting cases to certain area
• excludes visitors who became infected; inhibits recognition of
extension of outbreak into other states.
– Dates reasonable?
• Could limit the number of secondary cases included in the study
Steps in Outbreak Investigation
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Verify the diagnosis
Confirm the outbreak
Case definition
Descriptive Epidemiology
Steps 1 and 2
are
interchangeable
Characterization of Cases
Age group
(years)
Gender
TOTAL
Male
Female
0-9
2 (17%)*
2 (8%)
4 (11%)
10-19
2 (17%)
3 (12%)
5 (13%)
20-39
3 (25%)
9 (35%)
12 (32%)
40-59
2 (17%)
8 (31%)
10 (26%)
60+
3 (25%)
4 (15%)
7 (18%)
12 (101%)
26 (101%)
38 (100%)
TOTAL
* percentages refer to column totals.
How does this compare this to national data?
What does it tell you?
Epidemic Curve
Epidemic Curves
• How to set it up
• What it tells you
– Mode of transmission
• Propagated
• Common source
– Timing of exposure
– Course of exposure
Epidemic Curves
Point Source (Also called Common source: point exposure
(e.g., Salmonella))
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Cases
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2
1
0
1
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4
5
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Days
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Epidemic Curves
Common source: person-to person / propagated exposure
Steps in Outbreak Investigation
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Verify the diagnosis
Confirm the outbreak
Case definition
Descriptive
Epidemiology
Develop a hypothesis
Steps 1 and 2
are
interchangeable
Developing a Hypothesis
Ask questions!!
But of whom….
And when...
Determining the Probable Period of
Exposure
• Mean/Median incubation period
• Minimum/maximum incubation period
Estimating date of exposure
Maximum incubation
21 days
Probable time of exposure
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Cases
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Minimum incubation
1
14 days
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3
5
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Days
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Focus of Questionnaire
• Demographic information
• Clinical details of the illness with date of onset,
duration, and severity of symptoms
– visits to health care providers or hospitals, and laboratory
results
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A complete food history in the last 7 days
Water exposure in the last 7 days
Exposure to other ill persons in the last 7 days
Exposure to children in day care in the last 7 days
Exposure to a farm or farm animals in the last 7 days
Travel outside the immediate area in the last 7 days
Hypothesis of Investigators
• Consumption of food x is associated with infection
Steps in Outbreak Investigation
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Verify the diagnosis
Confirm the outbreak
Case definition
Descriptive
epidemiology
Develop a hypothesis
Test the hypothesis
Steps 1 and 2
are
interchangeable
Pick a Control Group
• 1-2 controls selected for every
case
• Matched to the case by:
– Age group
• (0-<2 years, 2-<5 years, 5-<12 years,
12-<18 years, 18-<60 years, and 60+
years)
– Gender
• Random digit dialing
• Neighborhood controls
• Other patients of same physician
Steps in Outbreak Investigation
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Verify the diagnosis
Steps 1 and 2
Confirm the outbreak
are
interchangeable
Case definition
Descriptive epidemiology
Develop a hypothesis
Test the hypothesis
Refine hypothesis / Execute additional
studies
Refine Hypothesis/Additional Studies
• What control measures might you consider at
this point?
• What further studies might you do?
Additional Studies
• Culture implicated sprouts
• Parts of the traceback study
– distributor, processor, and producer;
examination of the chain of production from
the farm to the table
• Applied research on microbial contaminant
What Interventions are Needed?
1) The immediate problem with this
implicated food/water
2) The larger issue of this food/water as
vehicles for pathogenic
Steps in Outbreak Investigation
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Verify the diagnosis
Steps 1 and 2
are
Confirm the outbreak
interchangeable
Case definition
Descriptive epidemiology
Develop a hypothesis
Test the hypothesis
Refine hypothesis / Execute additional studies
Implement control and prevention measures
Communicate findings
Communicate Findings
• Halt distribution and remove from the marketplace
• Hold meetings for public health officials to explain
routes of contamination
• Public television and radio announcements about the
risk of contaminated foods and recommending
persons at high risk for complications not eat the
food/water
• Government regulatory agencies should begin working
with the implicated industry to identify ways to make
food safer for human consumption.
Conclusion
• Many steps involved in the process to investigate
foodborne illness outbreaks.
• Begins with an understanding of the chemical, physical,
and microbial hazards.
• There are many players involved in this process
– From ensuring food safety
– To investigating
– And implementing control measures
• Makes a great learning system for discussing principles
of food safety, microbiology, epidemiology, and so much
more!
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References: www.slideshare.net
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