Food microbiology : an introduction

INTRODUCTION
WHO’S ON FIRST?
FOOD MICROBIOLOGY, PAST AND PRESENT
TO THE FUTURE AND BEYOND
INTRODUCTION
FOOD ECOSYSTEMS, HOMEOSTASIS, AND HURDLE TECHNOLOGY
	Foods as Ecosystems
CLASSICAL MICROBIOLOGY AND ITS LIMITATIONS
	Limitations of Detection and Enumeration Methods
	Plate Counts
	Selective, or Differential, Media
	Most-Probable-Number Methods
	Enrichment Techniques
PHYSIOLOGICAL STATES OF BACTERIA
	Introduction
	Injury
	Viable but Nonculturable
QUORUM SENSING AND SIGNAL TRANSDUCTION
	Introduction
	Quorum Sensing
		Examples of Cell Signaling in Foodborne Microbes
	Signal Transduction
	Biofilms
FACTORS THAT INFLUENCE MICROBIAL GROWTH
	Intrinsic Factors
		pH
		Water Activity
	Extrinsic Factors
	Homeostasis and Hurdle Technology
GROWTH KINETICS
MICROBIAL PHYSIOLOGY AND METABOLISM
	Carbon Flow and Substrate-Level Phosphorylation
		The Entner-Doudoroff Pathway Allows Use of Five-Carbon Sugars and Makes One ATP Molecule
		Homolactic Catabolism Makes Only Lactic Acid
		Heterofermentative Catabolism Gives Several End Products
	The TCA Cycle Links Glycolysis to Aerobic Respiration
CONCLUSION
INTRODUCTION
SPORES IN THE FOOD INDUSTRY
Low-Acid Canned Foods
Bacteriology of Sporeformers of Public Health Significance
Heat Resistance of C. botulinum Spores
	Spoilage of Acid and Low-Acid Canned and Vacuum-Packaged Foods by Sporeformers
SPORE BIOLOGY
	Structure
	Macromolecules
	Small Molecules
	Dormancy
	Resistance
	Freezing and Desiccation Resistance
	Pressure Resistance
	γ-Radiation Resistance
	UV Radiation Resistance
	Chemical Resistance
	Heat Resistance
		Sporulation Temperature
		α/β-Type SASP
		Core Water Content and Heat Resistance
THE CYCLE OF SPORULATION AND GERMINATION
	Sporulation
	Activation
	Germination
	Outgrowth
INTRODUCTION
SAMPLE COLLECTION AND PROCESSING
ANALYSIS
	Metabolism-Based Methods
	Surface Testing
INTRODUCTION
SAMPLE PROCESSING
REQUIREMENTS AND VALIDATION OF RAPID METHODS
RAPID METHODS BASED ON TRADITIONAL METHODS
IMMUNOLOGICALLY BASED METHODS
MOLECULAR METHODS
A POTPOURRI OF RAPID METHODS
INTRODUCTION
	The Purpose of Microbiological Criteria
	The Need To Establish Microbiological Criteria
	Definitions
	Who Establishes Microbiological Criteria?
SAMPLING PLANS
	Types of Sampling Plans
		Attributes Sampling Plans
ESTABLISHING LIMITS
INDICATORS OF MICROBIOLOGICAL QUALITY
	Indicator Microorganisms
	Metabolic Products
INDICATORS OF FOODBORNE PATHOGENS AND TOXINS
	Indicator Organisms
	Fecal Coliforms and E. coli
	Metabolic Products
APPLICATION AND SPECIFIC PROPOSALS FOR MICROBIOLOGICAL CRITERIA FOR FOOD AND FOOD INGREDIENTS
CURRENT STATUS
INTRODUCTION
U.S. AGENCIES INVOLVED IN FOOD REGULATION
	The USDA
	The FDA
	The CDC
SURVEILLANCE
WHEN AN OUTBREAK OCCURS
AGROTERRORISM
WHAT’S NEXT?
GLOBAL PERSPECTIVE
“IT TAKES A VILLAGE” AND MAYBE MORE
Outbreak
INTRODUCTION
CHARACTERISTICS OF THE ORGANISM
ENVIRONMENTAL SOURCES
FOODBORNE OUTBREAKS
CHARACTERISTICS OF DISEASE
DOSE
VIRULENCE FACTORS AND MECHANISMS OF PATHOGENICITY
	The Emetic Toxin
	Enterotoxins
	B. cereus as a Medical Pathogen
	The Spore
Outbreak
INTRODUCTION
CHARACTERISTICS OF THE ORGANISM
ENVIRONMENTAL SUSCEPTIBILITY
RESERVOIRS AND FOODBORNE OUTBREAKS
CHARACTERISTICS OF DISEASE
	C. jejuni and C. coli
	Other Campylobacter Species
EPIDEMIOLOGICAL SUBTYPING SYSTEMS USEFUL FOR INVESTIGATING FOODBORNE ILLNESSES
INFECTIVE DOSE AND SUSCEPTIBLE POPULATIONS
VIRULENCE FACTORS AND MECHANISMS OF PATHOGENICITY
	Cell Association and Invasion
	Flagella and Motility
	Toxins
	Other Factors
	Autoimmune Diseases
IMMUNITY
INTRODUCTION
	Botulism
CHARACTERISTICS OF THE DISEASE
TOXIC DOSES
CHARACTERISTICS OF C. BOTULINUM
	Classification
	Tolerance to Preservation Methods
		Low Temperature
		Thermal Inactivation
		pH
		Salt and aw
		Oxygen and Redox Potential
		Preservatives
		Competitive and Growth-Enhancing Microorganisms
		Inactivation by Irradiation
SOURCES OF C. BOTULINUM
	Occurrence of C. botulinum in the Environment
	Occurrence of C. botulinum in Foods
VIRULENCE FACTORS AND MECHANISMS OF PATHOGENICITY
	Structure of the Neurotoxins
	Genetic Regulation of the Neurotoxins
	Mode of Action of the Neurotoxins
INTRODUCTION
	A Spore’s-Eye View of Clostridium perfringens Toxicoinfections
THE FOODBORNE ILLNESS
	Cruel and Unusual Punishment
	Incidence
	Vehicles for C. perfringens Foodborne Illness
	Factors Contributing to C. perfringens Type A Foodborne Illness
	Preventing C. perfringens Type A Foodborne Illness
	Identification of C. perfringens Type A Foodborne Illness Outbreaks
CHARACTERISTICS OF C. PERFRINGENS TYPE A FOODBORNE ILLNESS
INFECTIOUS DOSE FOR C. PERFRINGENS TYPE A FOODBORNE ILLNESS
THE ORGANISM
	Overview
	Classification: Toxin Typing of C. perfringens
	Control of C. perfringens
		Temperature
		Other Factors
RESERVOIRS FOR C. PERFRINGENS TYPE A
VIRULENCE FACTORS CONTRIBUTING TO C. PERFRINGENS TYPE A FOODBORNE ILLNESS
	Heat Resistance
	C. perfringens Enterotoxin
		Evidence that C. perfringens Enterotoxin Is Involved in Foodborne Illness
		Expression and Release of C. perfringens Enterotoxin
		Synthesis of C. perfringens Enterotoxin
		Release of C. perfringens Enterotoxin from C. perfringens
		Biochemistry of C. perfringens Enterotoxin
		C. perfringens Enterotoxin Action on the Gastrointestinal Tract
Outbreak
INTRODUCTION
	Categories of E. coli
		ETEC
		EIEC
		EPEC
		EAEC
		DAEC
		EHEC
CHARACTERISTICS OF E. COLI O157:H7 AND NON-O157 EHEC
	Acid Tolerance
	Antibiotic Resistance
	Inactivation by Heat and Irradiation
RESERVOIRS OF E. COLI O157:H7
	Detection of E. coli O157:H7 and Other EHEC Strains on Farms
	Factors Associated with Bovine Carriage of E. coli O157:H7
	Cattle Model for Infection by E. coli O157:H7
	Domestic Animals and Wildlife
	Humans
DISEASE OUTBREAKS
	Geographic Distribution
	Seasonality of E. coli O157:H7 Infection
	Age of Patients
	Transmission of E. coli O157:H7
	Examples of Foodborne and Waterborne Outbreaks
		The Original Outbreaks
		Waterborne Outbreaks
		Outbreaks from Apple Cider and Juice
		A Large Multistate Outbreak
		Outbreaks Associated with Vegetables
CHARACTERISTICS OF DISEASE
INFECTIOUS DOSE
MECHANISMS OF PATHOGENICITY
	Attaching and Effacing
	The Locus of Enterocyte Effacement
	The 60-MDa Plasmid (pO157)
	Stxs
		Structure of the Stx Family
		Genetics of Stxs
		Receptors
		Mode of Action of the Stxs
		The Roles of Stxs in Disease
CONCLUSION
Outbreak
INTRODUCTION
CHARACTERISTICS OF THE ORGANISM
	Classification: The Genus Listeria
	Susceptibility to Physical and Chemical Agents
LISTERIOSIS AND SPECIFIC FOODS
	Ready-to-Eat Foods
	Milk Products
	Cheeses
	Meat and Poultry Products
	Seafoods
	Other Foods
	Environmental Sources of L. monocytogenes
	Food-Processing Plants
	Prevalence and the Regulatory Status of L. monocytogenes
	Human Carriers
FOODBORNE OUTBREAKS
CHARACTERISTICS OF DISEASE
INFECTIOUS DOSE
VIRULENCE FACTORS AND MECHANISMS OF PATHOGENICITY
	Pathogenicity of L. monocytogenes
	Specific Genes Mediate Pathogenicity
Outbreak
INTRODUCTION
CHARACTERISTICS OF THE ORGANISM
	Biochemical Identification
	Taxonomy and Nomenclature
	Serological Identification
	Physiology
		Growth and Survival
RESERVOIRS
CHARACTERISTICS OF DISEASE
	Symptoms and Treatment
	Preventative Measures
	Antibiotic Resistance
INFECTIOUS DOSE
PATHOGENICITY AND VIRULENCE FACTORS
	Specific and Nonspecific Human Responses
	Attachment and Invasion
	Growth and Survival within Host Cells
	Virulence Plasmids
	Other Virulence Factors
Outbreak
INTRODUCTION
	Classification and Biochemical Characteristics
	Shigella in Foods
	Survival and Growth in Foods
CHARACTERISTICS OF DISEASE
FOODBORNE OUTBREAKS
VIRULENCE FACTORS
	Genetic Regulation
CONCLUSIONS
Outbreak
CHARACTERISTICS OF THE ORGANISM
	Historical Aspects and General Considerations
	Sources of Staphylococcal Food Contamination
	Resistance to Adverse Environmental Conditions
FOODBORNE OUTBREAKS
	Incidence of Staphylococcal Food Poisoning
	A Typical Large Staphylococcal Food Poisoning Outbreak
CHARACTERISTICS OF DISEASE
TOXIC DOSE
	Toxin Dose Required
MICROBIOLOGY, TOXINS, AND PATHOGENICITY
	Nomenclature, Characteristics, and Distribution of Enterotoxin-Producing Staphylococci
	Introduction to and Nomenclature of the Staphylococcal Enterotoxins: Current Classification Scheme Based on Antigenicity
	Staphylococcal Regulation of Staphylococcal Enterotoxin Expression
		General Considerations
		Molecular Regulation of Staphylococcal Enterotoxin Production
		Regulation of Staphylococcal Enterotoxin Gene Expression
		Other Molecular Aspects of Staphylococcal Enterotoxin Expression
		Toxin Structures
		Staphylococcal Enterotoxin Antigenic Properties
Outbreak
INTRODUCTION
CHARACTERISTICS OF THE ORGANISM
	Epidemiology
CHARACTERISTICS OF DISEASE
SUSCEPTIBILITY TO PHYSICAL AND CHEMICAL TREATMENTS
V. CHOLERAE
	Isolation and Identification
	Reservoirs
	Foodborne Outbreaks
	Characteristics of Disease
	Virulence Mechanisms
V. MIMICUS
	Foodborne Outbreaks
	Characteristics of Disease
	Virulence Factors
V. PARAHAEMOLYTICUS
	Classification
	Reservoirs
	Foodborne Outbreaks
	Characteristics of Disease
	Virulence Mechanisms
V. VULNIFICUS
	Classification
	Susceptibility to Control Methods
	Reservoirs
	Foodborne Outbreaks
	Characteristics of Disease
	Virulence Mechanisms
V. FLUVIALIS, V. FURNISSII, V. HOLLISAE, AND V. ALGINOLYTICUS
Outbreak
INTRODUCTION
	Characteristics of the Organism
	Classification
	Susceptibility and Tolerance
CHARACTERISTICS OF INFECTION
RESERVOIRS
FOODBORNE OUTBREAKS
MECHANISMS OF PATHOGENICITY
	Pathological Changes
VIRULENCE DETERMINANTS
	Chromosomal Determinants of Virulence
	Other Virulence Determinants
	Pathogenesis of Yersinia-Induced Autoimmunity
INTRODUCTION
THE BIOCHEMICAL FOUNDATION OF FOOD FERMENTATION
	Catabolic Pathways
	Genetics of Lactic Acid Bacteria
DAIRY FERMENTATIONS
	Starter Cultures
	Production of Aroma Compounds
VEGETABLE FERMENTATIONS
	Ingredients and Additives Used during Fermentations
	Sauerkraut Fermentation
	Pickle Fermentation
MEAT FERMENTATIONS
INTRODUCTION
FERMENTATIONS THAT USE YEAST
	Bread
	Beer
	Wine
VINEGAR FERMENTATION
COCOA AND COFFEE FERMENTATIONS
	Cocoa
	Coffee
FERMENTED FOODS OF NON-WESTERN SOCIETIES
INTRODUCTION
MEAT, POULTRY, AND SEAFOOD PRODUCTS
	Origin of the Microbiota in Meat
	Origin of the Microbiota in Poultry
	Origins of the Microbiota in Finfish
	Origins of the Microbiota in Shellfish
	Bacterial Attachment to Food and Food Contact Surfaces
	Microbial Progression during Storage
	Muscle Tissue as a Growth Medium
		Composition and Spoilage of Red Meats
		Composition and Spoilage of Poultry Muscle
		Composition and Spoilage of Finfish
		Composition and Spoilage of Shellfish
	Factors Influencing Spoilage
		Proteolytic and Lipolytic Activities
		Spoilage of Adipose Tissue
		Spoilage under Anaerobic Conditions
		Other Meat Characteristics Associated with Spoilage
		Comminuted Products
		Cooked Products
		Processed Products
	Control of Spoilage of Muscle Foods
MILK AND DAIRY PRODUCTS
	Milk and Dairy Products as Growth Media
		Milk
		Dairy Products
	Psychrotrophic Spoilage
		Psychrotrophic Bacteria in Milk
		Control of Product Defects Associated with Psychrotrophic Bacteria
	Spoilage by Fermentative Nonsporeformers
		Defects of Fluid Milk Products
		Defects in Cheese
		Control of Defects Caused by Lactic Acid and Coliform Bacteria
	Spore-Forming Bacteria
		Defects in Fluid Milk Products
		Defects in Cheese
	Yeasts and Molds
SPOILAGE OF PRODUCE AND GRAINS
	Types of Spoilage
	Mechanisms of Spoilage
	Influence of Physiological State
	Microbiological Spoilage of Vegetables
		Microbiota of Organically Grown Vegetables
		Spoilage Microbiota
	Microbiological Spoilage of Fruits
		Normal and Spoilage Microbiota
	Microbiological Spoilage of Grains and Grain Products
		Natural Microbiota
		Effects of Processing
		Types of Spoilage
INTRODUCTION
ISOLATION, ENUMERATION, AND IDENTIFICATION
ASPERGILLUS SPECIES
	A. flavus and A. parasiticus
		Detection and Identification
		Aflatoxins
	Other Toxigenic Aspergilli
PENICILLIUM SPECIES
	Significant Penicillium Mycotoxins
FUSARIA AND TOXIGENIC MOLDS OTHER THAN ASPERGILLI AND PENICILLIA
	Toxigenic Fusarium Species
	Detection and Quantitation of Fusarium Toxins
	Other Toxic Molds
Outbreak
INTRODUCTION
PROTOZOA
	Cryptosporidium spp.
	Cyclospora cayetanensis
	Toxoplasma gondii
	Giardia intestinalis
	Other Protozoa of Interest
HELMINTHS
	Roundworms (Nematodes)
		Trichinella spiralis
		Ascaris lumbricoides
		Anisakis
	Tapeworms (Cestodes)
		Taenia spp.
		Diphyllobothrium latum
	Flukes (Trematodes)
		Fasciola hepatica
DETECTION
PREVENTATIVE MEASURES
INTRODUCTION
VIRUSES
	Elementary Virology
	Viruses as Agents of Foodborne Illness
		Intervention
		Noroviruses
		Hepatitis A
		Food Relatedness of Other Viruses
		Are Specific Food Commodities More at Risk?
	Bacteriophages in the Dairy Industry
	Beneficial Uses of Viruses
		Bacterial Detection
		Bacterial Control
PRIONS
	A Short History of the Prion
	Prion Biology
INTRODUCTION
FACTORS THAT AFFECT ANTIMICROBIAL ACTIVITY
ORGANIC ACIDS
PARABENZOIC ACIDS
NITRITES
PHOSPHATES
SODIUM CHLORIDE
WATER ACTIVITY
DISINFECTANTS
	Sulfites
	Chlorine
	Quaternary Ammonium Compounds
	Peroxides
	Ozone
NATURALLY OCCURRING ANTIMICROBIALS
	Lysozyme
	Lactoferrin and Other Iron-Binding Proteins
	Avidin
	Spices and Their Essential Oils
	Onions and Garlic
	Isothiocyanates
	Phenolic Compounds
	Phage Therapy
INTRODUCTION
BIOPRESERVATION BY CONTROLLED ACIDIFICATION
BACTERIOCINS
	General Characteristics
	Bacteriocin Applications in Foods
		Bacteriocin-producing starter cultures can improve the safety of fermented foods
		Organization of bacteriocin genes: a generic operon
		Bacteriocin action
		Legal status
PROBIOTIC BACTERIA
	The Human GI Tract Is a Microbial Ecosystem
INTRODUCTION
PHYSICAL DEHYDRATION PROCESSES
	Drying
	Freeze-Drying
COOL STORAGE
	Controlled-Atmosphere Storage
	Modified-Atmosphere Packaging
FREEZING AND FROZEN STORAGE
PRESERVATION BY HEAT TREATMENTS
	Technological Fundamentals
	Thermobacteriology
	Calculating Heat Processes for Foods
	Heat Resistance?
INTRODUCTION
ACCEPTANCE
HIGH-PRESSURE PROCESSING
OZONE
ULTRAVIOLET LIGHT
PULSED ELECTRIC FIELDS AND PULSED LIGHT
OSCILLATING MAGNETIC FIELDS
ULTRASOUND
CONCLUSIONS
INTRODUCTION
FOOD SAFETY OBJECTIVES
GOOD MANUFACTURING PRACTICES
	General Provisions (Subpart A)
	Buildings and Facilities (Subpart B)
	Equipment (Subpart C)
	Production and Process Controls (Subpart E)
	DALs (Subpart G)
SANITATION
	SSOPs
	HACCP
		Background
		HACCP Basics
		HACCP: Beyond the Food Processor
		HACCP Established for Specific Food Industries
FOOD SAFETY MODERNIZATION ACT
CONCLUSIONS
Consider the source of the information
	What is the medium of publication?
	Who is the source of the information?
	Which organizations do the authors represent?
	If the information is on a web page, what type of web page is it?
Be quantitative
Understand what the numbers mean
Compare the number with a reference value you know and understand
	Is a given number a lot or a little?
Compare information with data from other sources
Follow the money
When in doubt, doubt