Introduction to Food Microbiology

and Surveillance for Foodborne Illness

Kali Kniel, Ph.D.Associate Professor, Microbial Food SafetyDepartment 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

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

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1970 1974 1978 1982 1986 1990 1994 1998

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Typhimurium

Enteritidis

Heidelberg

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

AppliedTargetedResearch

Prevention

Measures

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

• Characterization by spore formation• Characterization by shape• Characterization by Gram stain (1884)• Gram positive (purple)• Gram negative (pink)

Peptidoglycan

Plasma membrane

Periplasmic space

Outer membrane

Peptidoglycan

Plasma membrane

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

• 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

• 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

• 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• 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 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

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 ?

• 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?

LargeFragments

SmallFragments

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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 diagnosis2. Confirm the

outbreak3. 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

• Verify the diagnosis• Confirm the outbreak• Case definition• Descriptive Epidemiology

Steps 1 and 2 are

interchangeable

Characterization of Cases

Age group(years)

GenderTOTAL

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%)

TOTAL 12 (101%) 26 (101%) 38 (100%)

* 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

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

Epidemic Curves

Common source: person-to person / propagated exposure

Steps in Outbreak Investigation

• 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

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Maximum incubation

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Minimum incubation

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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

• 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

• 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

• 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 are

interchangeable

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

• 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 are

interchangeable

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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