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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).

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introduction to food microbiology and surveillance for foodborne illness

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
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
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
salmonella national incidence of the top three serotypes 1970 2001
Salmonella - National incidence of the top three serotypes 1970-2001




outbreaks vs cases
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









changes in outbreak scenarios
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
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
Bacteriology Basics
  • Characterization by spore formation
  • Characterization by shape
  • Characterization by Gram stain (1884)
  • Gram positive (purple)
  • Gram negative (pink)

Outer membrane



Plasma membrane

Plasma membrane

Periplasmic space

microbiology basics1
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
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
Foods Most Often Involved
  • 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
Most Common Agents
  • Campylobacter
  • Salmonella
  • Staphylococus aureus
  • Escherichia coli O157:H7
  • Clostridium perfringens
  • Listeria monocytogenes
  • Viruses (Norovirus, Hepatitis A)
  • Protozoa (Cryptosporidium, Cyclospora, Toxoplasma)
clinical features
Clinical Features
  • Transmission
  • Pathogenesis
    • Host factors
    • Organism factors
  • Carriers
  • Recognizing FBI
    • Control and prevention
  • 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
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
Biofilm development

factors affecting disease
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 disease1
Factors Affecting Disease
  • Host factors
    • Immunocompromised
    • Age
    • Pregnancy
    • Medications, chemotherapy, diabetes
    • Gastric acid
changing epidemiology agent
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
Foodborne Outbreak Scenarios
  • 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
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
FB Disease Surveillance
  • Disease Prevention and Control
  • Knowledge of Disease Causation
  • Administrative Guidance
burden of illness
Burden of Illness

foodborne outbreak surveillance
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
  • Passivesurveillance occurs when health agencies are contacted by cases, physicians or laboratories, which report illnesses or laboratory results to them.
  • In activesurveillance, 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
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
Notifiable foodborne diseases
  • 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
Objectives of FoodNet
  • Determine the burden of foodborne illness in the United States
  • Monitor trends in the burden of specific foodborne illness over time
  • Attribute the burden of foodborne illness to specific foods and settings
  • Develop and assess interventions to reduce the burden of foodborne illness
  • 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 disease-causing 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
Objectives of PulseNet
  • Detect foodborne disease case clusters by PFGE
  • Allow for real-time communication among state, local health departments, and international partners
  • Facilitate early identification of common source outbreaks
  • 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
DNA Fingerprinting by PFGE ?
  • 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
What is PFGE?









surveillance data limitations
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
The outbreak…
  • So what happens when surveillance indicates that an fbi outbreak is occurring?
initial call
Initial Call
  • Calls from physicians reporting patients with symptoms of fbi
  • Call from Community Health Department
  • Increase in laboratory reports
steps in outbreak investigation
Steps in Outbreak Investigation

1. Verify the Diagnosis

steps in outbreak investigation1
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak

Steps 1 and 2



what could account for the increase in cases1
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
Initial Investigation
  • Any other way to see if there is a relationship between these isolates?
molecular epidemiology
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
steps in outbreak investigation2
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition

Steps 1 and 2



case definition
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 definition1
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 investigation3
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition
  • Descriptive Epidemiology

Steps 1 and 2



characterization of cases
Characterization of Cases

How does this compare this to national data?

What does it tell you?

epidemic curves
Epidemic Curves
  • How to set it up
  • What it tells you
    • Mode of transmission
      • Propagated
      • Common source
    • Timing of exposure
    • Course of exposure
epidemic curves1
Epidemic Curves

Point Source (Also called Common source: point exposure (e.g., Salmonella))

epidemic curves2
Epidemic Curves

Common source: person-to person / propagated exposure

steps in outbreak investigation4
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition
  • Descriptive Epidemiology
  • Develop a hypothesis

Steps 1 and 2



developing a hypothesis
Developing a Hypothesis

Ask questions!!But of whom….And when...

determining the probable period of exposure
Determining the Probable Period of Exposure
  • Mean/Median incubation period
  • Minimum/maximum incubation period
estimating date of exposure
Estimating date of exposure

Maximum incubation

21 days

Probable time of exposure

Minimum incubation

14 days

focus of questionnaire
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

•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
Hypothesis of Investigators
  • Consumption of food x is associated with infection
steps in outbreak investigation5
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition
  • Descriptive epidemiology
  • Develop a hypothesis
  • Test the hypothesis

Steps 1 and 2



pick a control group
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 investigation6
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition
  • Descriptive epidemiology
  • Develop a hypothesis
  • Test the hypothesis
  • Refine hypothesis / Execute additional studies

Steps 1 and 2



refine hypothesis additional studies
Refine Hypothesis/Additional Studies
  • What control measures might you consider at this point?
  • What further studies might you do?
additional studies
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
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 investigation7
Steps in Outbreak Investigation
  • Verify the diagnosis
  • Confirm the outbreak
  • Case definition
  • Descriptive epidemiology
  • Develop a hypothesis
  • Test the hypothesis
  • Refine hypothesis / Execute additional studies
  • Implement control and prevention measures
  • Communicate findings

Steps 1 and 2



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.
  • 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!