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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
Testing for SafetyTesting for Safety
• 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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Testing for SafetyTesting for Safety
• 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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Testing for SafetyTesting for Safety
• 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
den
sity
Pro
babi
lity
den
sity
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
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
Examples of Microbiological Criteria
Examples of Microbiological Criteria
• 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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Microbiological CriteriaMicrobiological Criteria
• Do the criteria have ANY theoretical or demonstrable
relationship to public health?
• Do the criteria have ANY theoretical or demonstrable
relationship to public health?
Microbiological CriteriaMicrobiological Criteria
• Do the criteria have ANY theoretical or demonstrable
relationship to public health?
• What qualitative or quantitative values best assure the safety
of foods?
• Do the criteria have ANY theoretical or demonstrable
relationship to public health?
• 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
lity
den
sity
Pro
babi
lity
den
sity
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
Changes in Philosophy to Assure Safe Foods
• Microbiological Testing for Safety• Microbiological Testing
for Safety
Changes in Philosophy to Assure Safe Foods
Changes in Philosophy to Assure Safe Foods
• 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
• 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
• Microbiological Testing for Safety• Preventative Controls•
“Outcome Based” Food Safety
– National Public Health Goals
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Changes in PhilosophyChanges in Philosophy
• Microbiological Testing for Safety• Preventative Controls•
“Outcome Based” Food Safety
– National Public Health Goals– Risk Management Framework
• Microbiological Testing for Safety• Preventative Controls•
“Outcome Based” Food Safety
– 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
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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Impact of Risk Analysis Framework
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 – 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
The Evolving Regulatory Environment
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The Evolving Regulatory Environment
The Evolving Regulatory Environment
• 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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Changes in KnowledgeChanges in Knowledge
• 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
Changes in KnowledgeChanges in Knowledge
• 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
Emergence of Foodborne Pathogens
• 1942– Staphylococcus aureus– Salmonella– Clostridium
botulinum– Streptococci
• 1942– Staphylococcus aureus– Salmonella– Clostridium
botulinum– Streptococci
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Emergence of Foodborne Pathogens
Emergence of Foodborne Pathogens
– 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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Changes in SocietyChanges in Society
• 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
Changes in SocietyChanges in Society
• Technology• Human Demographics and Behavior• Technology• Human
Demographics and Behavior
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Changes in SocietyChanges in Society
• 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
Changes in SocietyChanges in Society
Consumers are eating different foods
Consumers are eating different foods
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Changes in SocietyChanges in Society
20%-25% of the Population is At Risk
Changes in SocietyChanges in Society
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
Changes in SocietyChanges in Society
• 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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40
42
44
46
48
2003 2004 2005 200636
38
40
42
44
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48
2003 2004 2005 2006Travel Year
Arr
ival
s (m
illio
ns)
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Changes in SocietyChanges in Society
• Technology• Demographics• Travel• Business
– International trade– Economic development and land use
• Consolidation of production and processing facilities
• Technology• Demographics• Travel• Business
– International trade– Economic development and land use
• Consolidation of production and processing facilities
Changes in SocietyChanges in Society
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
– International trade– Economic development and land use
• Consolidation of production and processing facilities
• Technology• Demographics• Travel• Business
– International trade– Economic development and land use
• Consolidation of production and processing facilities
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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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Future TrendsFuture Trends
• 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
Future TrendsFuture Trends
• 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