the role of microbiological testing and microbiological ......1 the role of microbiological testing...

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The Role of Microbiological Testing and Microbiological

Criteria in an Evolving Regulatory Environment

The Role of Microbiological Testing and Microbiological

Criteria in an Evolving Regulatory Environment

International Commission on Microbiological Standards for Foods

Washington, D.C. October 31, 2005

Robert E. Brackett, Ph.D.Director, Center for Food Safety and Applied Nutrition

Food and Drug Administration

International Commission on Microbiological Standards for Foods

Washington, D.C. October 31, 2005

Robert E. Brackett, Ph.D.Director, Center for Food Safety and Applied Nutrition

Food and Drug Administration

Microbial TestingMicrobial Testing• Why test?

– Safety of “batches”– Investigational sampling– Surveillance – Process control– Quality control/assurance

• Why test?– Safety of “batches”– Investigational sampling– Surveillance – Process control– Quality control/assurance

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Microbial TestingMicrobial Testing• Why test?

– Safety of “batches”– Investigational sampling– Surveillance– Process control– Quality control/assurance

• Why test?– Safety of “batches”– Investigational sampling– Surveillance– Process control– Quality control/assurance

The “Poison Squad”The “Poison Squad”

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Microbial TestingMicrobial Testing

• Microbiological testing is almost always an important component of any integrated program to assure the safety of foods

• Microbiological testing is almost always an important component of any integrated program to assure the safety of foods

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Testing for SafetyTesting for Safety

• Detection and identification• Detection and identification


• Detection and identification– Traditional Plating

• Detection and identification– Traditional Plating

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Traditional Microbiological Plating

Plating on Sorbitol-MacConkey

K-12 Strain 868

Traditional Microbiological Plating

Plating on MUG for β-glucuronidase

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• Detection and identification– Traditional Plating– “Rapid” Tests

• Miniaturized tests• Gene probes• Enzyme-linked immunosorbant assays

(ELISA)• Polymerase Chain Reaction (PCR)• Biosensors

• Detection and identification– Traditional Plating– “Rapid” Tests

• Miniaturized tests• Gene probes• Enzyme-linked immunosorbant assays

(ELISA)• Polymerase Chain Reaction (PCR)• Biosensors

SampleBiologicallysensitivecoatingSensor

Transducer

Output

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• Detection and identification• Enumeration

– Most probable number (MPN)– Plate counts– Instrumental methods

• Flow cytometry– RT-Polymerized Chain Reaction (RT-

PCR)

• Detection and identification• Enumeration

– Most probable number (MPN)– Plate counts– Instrumental methods

• Flow cytometry– RT-Polymerized Chain Reaction (RT-

PCR)

1 2 3 4 5 6 7

Mean Log cfu/gMean Log cfu/g

0.0

0.1

0.2

0.3

0.4

0.5

Pro

babi

lity

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sity

Pro

babi

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What does “the count” mean?

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Testing for SafetyTesting for Safety• Detection and identification• Enumeration• Attribution

– Gram stain– Morphology– Biochemical tests– Immunological

• Serotyping• ELISA

– Molecular• Pulse field gel electrophoresis• Multilocus sequence typing• Cladistic analysis

• Detection and identification• Enumeration• Attribution

– Gram stain– Morphology– Biochemical tests– Immunological

• Serotyping• ELISA

– Molecular• Pulse field gel electrophoresis• Multilocus sequence typing• Cladistic analysis

Outbreak Response:S. Agona in Cereal

Bacteria from the food and patients were the same

Matched using DNA finger print, which is read like a bar code (PulseNet)

PatientPatient FoodFood DifferentDifferentSalmonellaSalmonella

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Microbiological CriteriaMicrobiological Criteria

What are “Criteria”?What are “Criteria”?

• Criterion– Standard: Must meet, regulatory

requirement– Guideline: Should meet, GHP– Specification: Expected to meet,

generally used to describe an agreement between a supplier and a purchaser

• Criterion– Standard: Must meet, regulatory

requirement– Guideline: Should meet, GHP– Specification: Expected to meet,

generally used to describe an agreement between a supplier and a purchaser

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Examples of Microbiological Criteria


• Indicator organisms– Presence or populations of organism

statistically associated with a pathogen• Coliforms, fecal coliforms, E. coli

• Indicator organisms– Presence or populations of organism

statistically associated with a pathogen• Coliforms, fecal coliforms, E. coli



• Indicator organisms• Target pathogens

–None detected • “Zero Tolerance”

–Attribute estimate (e.g. X positive samples in Y total samples)

–Point value limit (e.g. 100 cfu/g)• “Bright Shining Line”

• Indicator organisms• Target pathogens

–None detected • “Zero Tolerance”

–Attribute estimate (e.g. X positive samples in Y total samples)

–Point value limit (e.g. 100 cfu/g)• “Bright Shining Line”

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• Do the criteria have ANY theoretical or demonstrable relationship to public health?




• What qualitative or quantitative values best assure the safety of foods?


• What qualitative or quantitative values best assure the safety of foods?

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1 2 3 4 5 6 7

Mean Log cfu/gMean Log cfu/g

0.0

0.1

0.2

0.3

0.4

0.5

Pro

babi

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sity

Pro

babi

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What does “the count” mean?

UNSAFE

SAFE

Perceived Prediction of Safety

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UNSAFE

Less Safe

Safer

SAFE

Realistic Estimation of Safety

Defining Question

How Does One Choose the “Right” Value?

Defining Question

How Does One Choose the “Right” Value?

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Changes in Philosophy to Assure Safe Foods


• Microbiological Testing for Safety• Microbiological Testing for Safety



• Microbiological Testing for Safety• Preventative Controls• Microbiological Testing for Safety• Preventative Controls

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Preventative ControlsPreventative Controls

• Good Manufacturing/Agricultural Practices– Minimum practices to reasonably

assure sanitation, etc.– Foundation for HACCP

• Good Manufacturing/Agricultural Practices– Minimum practices to reasonably

assure sanitation, etc.– Foundation for HACCP

Preventative ControlsPreventative Controls• Good Manufacturing Principals• Hazard Analysis Critical Control Points

(HACCP)– Focuses on identifying and preventing hazards

from contaminating food – Based on sound science – Permits more efficient and effective government

oversight, – Places responsibility for ensuring food safety

appropriately on the food manufacturer or distributor

– Reduces barriers to international trade.

• Good Manufacturing Principals• Hazard Analysis Critical Control Points

(HACCP)– Focuses on identifying and preventing hazards

from contaminating food – Based on sound science – Permits more efficient and effective government

oversight, – Places responsibility for ensuring food safety

appropriately on the food manufacturer or distributor

– Reduces barriers to international trade.

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Changes in PhilosophyChanges in Philosophy

• Microbiological Testing for Safety• Preventative Controls• “Outcome Based” Food Safety


Changes in PhilosophyChanges in Philosophy• Microbiological Testing for Safety• Preventative Controls• “Outcome Based” Food Safety

– National Public Health Goals


– National Public Health Goals

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Changes in PhilosophyChanges in Philosophy


– National Public Health Goals– Risk Management Framework


– National Public Health Goals– Risk Management Framework

Risk ManagementRisk Management

• It is all about making decisions– Have to establish the level of protection

deemed appropriate to safeguard the public

– That level is both a scientific and a societal decision

– Risk assessment is making it possible to link control measure to pubic health impact

• It is all about making decisions– Have to establish the level of protection

deemed appropriate to safeguard the public

– That level is both a scientific and a societal decision

– Risk assessment is making it possible to link control measure to pubic health impact

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Risk Management ConceptRisk Management Concept

• The degree of “regulatory control” placed on a pathogen-food pair should be a function of the risk to public health

• The degree of “regulatory control” placed on a pathogen-food pair should be a function of the risk to public health

“Outcome Based” Food Safety“Outcome Based” Food Safety

• Quantitative Risk Assessments– Salmonella Enteritidis in Shell Eggs

(USDA/FDA)– Listeria monocytogenes in Ready-to-

Eat Foods (FDA/USDA, WHO)– Vibrio vulnificus in molluscan

shellfish (FDA)– Vibrio parahaemolyticus in seafood

(FDA)

• Quantitative Risk Assessments– Salmonella Enteritidis in Shell Eggs

(USDA/FDA)– Listeria monocytogenes in Ready-to-

Eat Foods (FDA/USDA, WHO)– Vibrio vulnificus in molluscan

shellfish (FDA)– Vibrio parahaemolyticus in seafood

(FDA)

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Impact of Risk Analysis Framework


• Being able to better link food safety activities to public health outcomes via risk assessments has allowed:– New concepts to be considered

• Food Safety Objective (FSO)• Appropriate Level of Protection (ALOP)• Performance Objective (PO)

• Being able to better link food safety activities to public health outcomes via risk assessments has allowed:– New concepts to be considered

• Food Safety Objective (FSO)• Appropriate Level of Protection (ALOP)• Performance Objective (PO)

Food Safety ObjectiveFood Safety Objective

• An FSO can be viewed an a “bright shining line”

• By definition–Below is safe–Above is not safe

• PO is the equivalent at a specified point earlier in the food chain

• An FSO can be viewed an a “bright shining line”

• By definition–Below is safe–Above is not safe

• PO is the equivalent at a specified point earlier in the food chain

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• Being able to better link food safety activities to public health outcomes via risk assessments has allowed:– New concepts to be considered – Old concepts to be put on a more scientific

basis• Performance criteria• Process criteria• Product criteria• Microbiological criteria

• Being able to better link food safety activities to public health outcomes via risk assessments has allowed:– New concepts to be considered – Old concepts to be put on a more scientific

basis• Performance criteria• Process criteria• Product criteria• Microbiological criteria

The Evolving Regulatory Environment


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• Massive and Revolutionary changes are occurring which affect Regulatory Policy

• Massive and Revolutionary changes are occurring which affect Regulatory Policy

Change #1Changes in Philosophy

Change #1Changes in Philosophy

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Past PhilosophyPast Philosophy• Command and control

– Pasteurized Milk Ordinance (PMO) –1924

– Low-Acid Canned Foods – 1973, 1979– Acidified Foods – 1979– Infant Formula Quality Control

Procedures - 1982– Current Good Manufacturing Practice

- 1986

• Command and control– Pasteurized Milk Ordinance (PMO) –

1924– Low-Acid Canned Foods – 1973, 1979– Acidified Foods – 1979– Infant Formula Quality Control

Procedures - 1982– Current Good Manufacturing Practice

- 1986

New PhilosophyNew Philosophy• End results

–Preventative technologies–Food Safety Objectives

• End results–Preventative technologies–Food Safety Objectives

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New PhilosophyNew Philosophy• Performance standards

–Focusing less on howoutcomes are achieve

–Focusing more on IS the outcome achieved • If the food safe?

• Performance standards–Focusing less on howoutcomes are achieve

–Focusing more on IS the outcome achieved • If the food safe?

New PhilosophyNew Philosophy• Creativity on the part of

the industry–Take risks in developing new

technologies–Providing the scientific rationale

and data for new processes• Importance of microbiological

testing

• Creativity on the part of the industry–Take risks in developing new

technologies–Providing the scientific rationale

and data for new processes• Importance of microbiological

testing

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Change #2Changes in Knowledge

Change #2Changes in Knowledge

Changes in KnowledgeChanges in Knowledge

• Genetics• Genetics

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Reference Strain Collection

History of Microbial IdentificationHistory of Microbial Identification• Detection at Genus Level• Detection at Genus Level

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History of Microbial IdentificationHistory of Microbial Identification• Detection at Genus Level• Detection at Species Level• Detection at Genus Level• Detection at Species Level

History of Microbial IdentificationHistory of Microbial Identification• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level

• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level

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History of Microbial IdentificationHistory of Microbial Identification• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level• Detection at Serotype or Serovar

Level

• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level• Detection at Serotype or Serovar

Level

History of Microbial IdentificationHistory of Microbial Identification• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level• Detection at Serotype or Serovar

Level• Detection at Molecular Level

• Detection at Genus Level• Detection at Species Level• Detection at Subspecies Level• Detection at Serotype or Serovar

Level• Detection at Molecular Level

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• Genetics• Pathogenicity/Virulence

– Identification of virulence factors– Role of extrachromosomal elements

• Plasmids– What turns virulence genes “off” or

“on”• Quorum sensing

• Genetics• Pathogenicity/Virulence

– Identification of virulence factors– Role of extrachromosomal elements

• Plasmids– What turns virulence genes “off” or

“on”• Quorum sensing


• Genetics• Pathogenicity/Virulence• Ecology

• Genetics• Pathogenicity/Virulence• Ecology

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Attachment and Survival of E. coli O157:H7 on Cut Lettuce

Attachment and Survival of E. coli O157:H7 on Cut Lettuce

Internalization of PathogensInternalization of Pathogens

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Changes in KnowledgeChanges in Knowledge• Genetics• Pathogenicity/Virulence• Ecology• Growth and Survival in “Extreme”

Environments– Microbial adaptation and change

• Unrestricted use of antibiotics• Resistance to food processing technologies

– Acid, redox potential, sanitizer, preservative adaptation

• Genetics• Pathogenicity/Virulence• Ecology• Growth and Survival in “Extreme”

Environments– Microbial adaptation and change

• Unrestricted use of antibiotics• Resistance to food processing technologies

– Acid, redox potential, sanitizer, preservative adaptation

Changes in KnowledgeChanges in Knowledge• Genetics• Pathogenicity/Virulence• Ecology• Growth and Survival in “Extreme” Environments

• New Foodborne Pathogens• New, more virulent strains

– E. coli O157:H7, S. Typhimurium DT104, S.Enteritidis PT2

• Genetics• Pathogenicity/Virulence• Ecology• Growth and Survival in “Extreme” Environments

• New Foodborne Pathogens• New, more virulent strains

– E. coli O157:H7, S. Typhimurium DT104, S.Enteritidis PT2

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Emergence of Foodborne Pathogens


• 1942– Staphylococcus aureus– Salmonella– Clostridium botulinum– Streptococci

• 1942– Staphylococcus aureus– Salmonella– Clostridium botulinum– Streptococci

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– Yersinia enterocolita– Enterobacter sakazakii– Norwalk and Norwalk-

like viruses– Rotavirus– Cryptosporidium parvum– Giardia lamblia– Toxoplasma gondii– Bovine spongiform

encephalopathy prion

– Yersinia enterocolita– Enterobacter sakazakii– Norwalk and Norwalk-

like viruses– Rotavirus– Cryptosporidium parvum– Giardia lamblia– Toxoplasma gondii– Bovine spongiform

encephalopathy prion

– Campylobacter jejuni– Clostridium

botulinum (infant)– E. coli 0157:H7– Listeria

monocytogenes– Salmonella Enteritidis– Vibrio cholerae (Latin

America)– Vibrio vulnificus

– Campylobacter jejuni– Clostridium

botulinum (infant)– E. coli 0157:H7– Listeria

monocytogenes– Salmonella Enteritidis– Vibrio cholerae (Latin

America)– Vibrio vulnificus

New or Non-traditional Foods Associated With Recent

Outbreaks

New or Non-traditional Foods Associated With Recent

Outbreaks

• Mangos • Puffer fish • Almonds • Potatoes • Soft cheese• Mamey• Infant formula • Dry Cereal

• Mangos • Puffer fish • Almonds • Potatoes • Soft cheese• Mamey• Infant formula • Dry Cereal

• Seed/bean sprouts• Eggs• Salsa• Bean dip• Cantaloupe• Fruit juices• Berries

• Seed/bean sprouts• Eggs• Salsa• Bean dip• Cantaloupe• Fruit juices• Berries

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Change #3Changes in Society

Change #3Changes in Society

Changes in SocietyChanges in Society

• Technology• Technology

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• Technology– Processing technology

• Aseptic • High pressure

– Transportation• Air freight• Refrigerated/MA trucking

– Packaging• Extended shelf-life

• Technology– Processing technology

• Aseptic • High pressure

– Transportation• Air freight• Refrigerated/MA trucking

– Packaging• Extended shelf-life


• Technology• Human Demographics and Behavior• Technology• Human Demographics and Behavior

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• Technology• Human Demographics and Behavior

– Age– Increased reliance on medicines– Purchasing and eating habits– Migrations to urban centers

• Technology• Human Demographics and Behavior

– Age– Increased reliance on medicines– Purchasing and eating habits– Migrations to urban centers


Consumers are eating different foods

Consumers are eating different foods

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20%-25% of the Population is At Risk


More Food Prepared Outside the Home

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Changes in the U.S. PopulationChanges in the U.S. Population

• 17% of population is 60 or older– 4% of the population is 80 or older

• 64% of the adult population is overweight

• 5% of infants and young children and 2% of adults have food allergies

• 44% of the non-institutionalized population reports taking one or more prescription medications during the last month

• 17% of population is 60 or older– 4% of the population is 80 or older

• 64% of the adult population is overweight

• 5% of infants and young children and 2% of adults have food allergies

• 44% of the non-institutionalized population reports taking one or more prescription medications during the last month


• Technology• Demographics• Travel and Tourism

• Technology• Demographics• Travel and Tourism

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Global TravelGlobal Travel

• International travel is a at an all time high and is expected to increase– Business– Tourism

• Travelers will be exposed to new types of organisms– E.g. Cyclosporiasis

• Once rare illnesses could become endemic in home country

• International travel is a at an all time high and is expected to increase– Business– Tourism

• Travelers will be exposed to new types of organisms– E.g. Cyclosporiasis

• Once rare illnesses could become endemic in home country

Forecast of Inbound Travel to U.S.Forecast of Inbound Travel to U.S.

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42

44

46

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2003 2004 2005 200636

38

40

42

44

46

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2003 2004 2005 2006Travel Year

Arr

ival

s (m

illio

ns)

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• Technology• Demographics• Travel• Business

– International trade– Economic development and land use

• Consolidation of production and processing facilities





More Food Now Comes From Distant Places

More Food Now Comes From Distant Places

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Imported Food Line EntriesImported Food Line EntriesFood Import Line Entries

02,000,0004,000,0006,000,0008,000,000

10,000,00012,000,00014,000,000

1990

1992

1994

1996

1998

2000

2002

2004

2006

*

Year*Estimates (2005 and 2006)

Changes in SocietyChanges in Society• Technology• Demographics• Travel• Business






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Future Trends Affecting the Regulatory Environment?

Future Trends Affecting the Regulatory Environment?

Future TrendsFuture Trends

• Enhanced role of epidemiology– Role of traditional microbiological

testing?

• Enhanced role of epidemiology– Role of traditional microbiological

testing?

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• Enhanced role of epidemiology• Better attribution

– Use of molecular biology to match outbreak strains to facility/line

– Identification of “hot” strains

• Enhanced role of epidemiology• Better attribution

– Use of molecular biology to match outbreak strains to facility/line

– Identification of “hot” strains


• Enhanced role of epidemiology• Better attribution• Importance of International

Agreements– NAFTA-North America Free Trade

Agreement– GATT-General Agreements on Tariffs

and Trade• SPS-Sanitary and Phytosanitary

Measures Provisions

• Enhanced role of epidemiology• Better attribution• Importance of International

Agreements– NAFTA-North America Free Trade

Agreement– GATT-General Agreements on Tariffs

and Trade• SPS-Sanitary and Phytosanitary

Measures Provisions

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• Harmonization– International Standards and

Regulations– Methods of Analysis– Codex Alimentarius Commission

• Standardizing body

• Harmonization– International Standards and

Regulations– Methods of Analysis– Codex Alimentarius Commission

• Standardizing body

Global TradeGlobal Trade

• Harmonization• Increased importance of International

Scientific Bodies– Joint Expert Committee on Food

Additives (JECFA)– Joint Expert Meetings on

Microbiological Risk Assessment (JEMRA)

• Harmonization• Increased importance of International

Scientific Bodies– Joint Expert Committee on Food

Additives (JECFA)– Joint Expert Meetings on

Microbiological Risk Assessment (JEMRA)

Global TradeGlobal Trade

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SummarySummary• Microbiological Testing will Continue to

be a Fundamental Regulatory Tool• Scientific and Social Changes will

Impact the Role of Microbiological Testing– Changes in philosophy– Changes in knowledge– Changes in society

• Both Technology and the Regulatory Environment will change in response

• Microbiological Testing will Continue to be a Fundamental Regulatory Tool

• Scientific and Social Changes will Impact the Role of Microbiological Testing– Changes in philosophy– Changes in knowledge– Changes in society

• Both Technology and the Regulatory Environment will change in response

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