The Microbiology of Safe Food

Cover
Title Page
Contents
Preface to third edition
Preface to second edition
Preface to first edition
Chapter 1 Foodborne infections
	1.1 The microbial world and its relationship to food
	1.2 Origins of safe food production
	1.3 Overview of foodborne illness
	1.4 Public perception of safe food
	1.5 Causes of foodborne illness
	1.6 Food poisoning due to common food commodities
		1.6.1 Milk and milk products
		1.6.2 Meat products
		1.6.3 Fresh produce
		1.6.4 Low-water activity (aw) and low‐moisture foods
	1.7 Host-related issues
	1.8 Hygiene hypothesis
	1.9 Chronic sequelae following foodborne illness
	1.10 The size of the foodborne illness problem
	1.11 The cost of foodborne diseases
	1.12 Changes in antimicrobial resistance of foodborne pathogens
		1.12.1 Bacterial antibiotic resistance in agriculture and aquaculture
		1.12.2 Antibiotics of concern and resistance mechanisms
		1.12.3 Polymyxin and plasmid‐encoded colistin resistance
		1.12.4 Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA)
	1.13 Food safety following natural disasters, and conflict
	1.14 Food microbiology, foodborne diseases and climate change
Chapter 2 Basic aspects
	2.1 The human intestinal tract
	2.2 The normal human intestinal flora
	2.3 Host resistance to foodborne infections
	2.4 Bacterial cell structure
		2.4.1 Morphology
		2.4.2 Cell membrane structure and the Gram stain
		2.4.3 Lipopolysaccharide (LPS, O antigen)
		2.4.4 Flagella (H antigen)
		2.4.5 Capsule (K and Vi antigen)
	2.5 Bacterial toxins and other virulence determinants
		2.5.1 Bacterial endotoxins and exotoxins
		2.5.2 Pathogenicity islands
		2.5.3 Bacterial toxins encoded in bacteriophages
	2.6 Microbial growth cycle
	2.7 Death kinetics
		2.7.1 Expressions
		2.7.2 decimal reduction times (D values) and z values
	2.8 Factors affecting microbial growth
		2.8.1 Intrinsic and extrinsic factors affecting microbial growth
		2.8.2 Water activity
		2.8.3 pH
		2.8.4 Temperature
		2.8.5 Interplay of factors affecting microbial growth in foods
	2.9 Microbial response to stress
		2.9.1 general stress response (GSR)
		2.9.2 pH stress
		2.9.3 Heat shock
		2.9.4 Cold shock
		2.9.5 Osmotic shock
	2.10 Predictive modelling
		2.10.1 Predicting modelling development
		2.10.2 Primary models and the Gompertz and Baranyi equations
		2.10.3 Secondary models
		2.10.4 Tertiary models
		2.10.5 Application of predictive microbial modelling
Chapter 3 Food preservation and spoilage organisms
	3.1 Spoilage micro-organisms
		3.1.1 Spoilage micro-organisms
		3.1.2 Spoilage of dairy products
		3.1.3 Spoilage of meat products
		3.1.4 Fish spoilage
		3.1.5 Egg spoilage
		3.1.6 Cereals and grain
	3.2 Shelf life indicators
		3.2.1 Glucose
		3.2.2 Gluconic and 2-oxogluconic acid
		3.2.3 L- and d-lactic acids, acetic acid and ethanol
		3.2.4 Biologically active amines
		3.2.5 Volatile compounds
		3.2.6 Storage trials
		3.2.7 Challenge tests
		3.2.8 Predictive modelling
	3.3 Methods of preservation and shelf life extension
	3.4 Preservatives
		3.4.1 Organic acids
		3.4.2 Hydrogen peroxide and lactoperoxidase system
		3.4.3 Chelators
		3.4.4 Non-acidic preservatives
		3.4.5 Preservation due to weak acids and low pH
		3.4.6 Biopreservatives
	3.5 Physical methods of preservation
		3.5.1 Preservation by heat treatment
		3.5.2 High-pressure treatment
		3.5.3 Ohmic heating and radio frequency
		3.5.4 Pulsed electric fields
		3.5.5 Ultrasound
		3.5.6 Intense light pulse
		3.5.7 Food irradiation
		3.5.8 Cold plasma and low‐energy electrons for food surface decontamination
	3.6 Packaging
		3.6.1 Reduced oxygen packaging, modified atmosphere packaging and active packaging
		3.6.2 Antimicrobial packaging and nanotechnology
	3.7 Fermented food products
		3.7.1 Fermented milk products
		3.7.2 Fermented meat products
		3.7.3 Fermented vegetables
		3.7.4 Fermented protein foods: shoyu and miso
	3.8 Organisms involved in the production of fermented foods
		3.8.1 Lactic acid bacteria
		3.8.2 Bifidobacterium species
		3.8.3 Other organisms
	3.9 Functional foods: probiotics and gut modulation
		3.9.1 qualified Presumption of Safety (QPS) and Generally Regarded As Safe (GRAS)
		3.9.2 Functional foods and probiotics
		3.9.3 Probiotic studies
		3.9.4 Novel organisms – modulation of gut microbiota
Chapter 4 Bacterial foodborne pathogens
	4.1 Indicator organisms
		4.1.1 Coliforms
		4.1.2 Enterobacteriaceae
		4.1.3 Enterococci
		4.1.4 Bacteriophages
	4.2 Campylobacter jejuni, C. coli and C. lari
		4.2.1 General description
		4.2.2 Campylobacter infections
		4.2.3 Campylobacter jejuni typing
		4.2.4 Virulence factors
		4.2.5 Whole-genome sequence analysis
		4.2.6 Sources and control of Campylobacter jejuni
	4.3 Salmonella serovars
		4.3.1 General description
		4.3.2 Salmonella serotypes
		4.3.3 Infections caused by Salmonella serovars
		4.3.4 Virulence factors of Salmonella serovars
		4.3.5 Whole-genome analysis
		4.3.6 Sources and control of Salmonella serovars
		4.3.7 Salmonella serovar outbreaks
	4.4 Pathogenic E. coli
		4.4.1 General description
		4.4.2 E. coli pathovars
		4.4.3 Infections caused by E. coli pathovars
		4.4.4 Virulence factors
		4.4.5 Whole-genome analysis
		4.4.6 Sources and control of E. coli pathovars
		4.4.7 Outbreaks caused by E. coli pathovars
	4.5 Sh. dysenteriae and Sh. sonnei
		4.5.1 General description
		4.5.2 Shigellosis
		4.5.3 Virulence factors
		4.5.4 Sh. sonnei outbreak
	4.6 Cronobacter species
		4.6.1 General description
		4.6.2 Infections due to Cronobacter species
		4.6.3 Identification and typing methods for Cronobacter species
		4.6.4 Virulence factors
		4.6.5 Sources and control of Cronobacter species
		4.6.6 Cronobacter outbreaks
	4.7 Vibrio cholerae, V. parahaemolyticus and V. vulnificus
		4.7.1 General description
		4.7.2 Infections due to Vibrio species
		4.7.3 Virulence factors
		4.7.4 Sources and control
	4.8 Brucella melitensis, Br. abortus and Br. suis
		4.8.1 General description
		4.8.2 Brucellosis
	4.9 Yersinia enterocolitica
		4.9.1 General description
		4.9.2 Yersiniosis
		4.9.3 Sources and control
		4.9.4 Outbreaks due to Y. enterocolitica
	4.10 Aeromonas hydrophila, A. caviae and A. sobria
		4.10.1 General description
		4.10.2 A. hydrophila gastroenteritis
		4.10.3 Sources and control
	4.11 Plesiomonas shigelloides
		4.11.1 General description
		4.11.2 Plesiomonas infections
		4.11.3 Sources and control
	4.12 Listeria monocytogenes
		4.12.1 General description
		4.12.2 Listeriosis
		4.12.3 Lineages and typing L. monocytogenes
		4.12.4 Virulence factors
		4.12.5 Whole-genome analysis of L. monocytogenes
		4.12.6 Sources and control of L. monocytogenes
		4.12.7 L. monocytogenes outbreaks
	4.13 Staphylococcus aureus
		4.13.1 General description
		4.13.2 Infections associated with St. aureus
		4.13.3 Virulence factors
		4.13.4 Sources and control
	4.14 Clostridium perfringens
		4.14.1 General description
		4.14.2 Cl. perfringens infections
		4.14.3 Sources and control
	4.15 Clostridium botulinum
		4.15.1 General description
		4.15.2 Cl. botulinum intoxication
		4.15.3 Sources and control
	4.16 B. cereus group
		4.16.1 General description
		4.16.2 B. cereus foodborne infections
		4.16.3 Virulence traits
		4.16.4 Sources and control
	4.17 Enterococcus and Streptococcus species
		4.17.1 General description
		4.17.2 E. faecalis and E. faecium
		4.17.3 Streptococcus pyogenes, group A streptococci
		4.17.4 Virulence traits
	4.18 Emerging and uncommon foodborne pathogens
		4.18.2 Campylobacter concisus
		4.18.3 EAEC, E. coli O55 and E. coli O26
		4.18.4 Escherichia albertii
		4.18.5 Providencia alcalifaciens
		4.18.6 Clostridium difficile
		4.18.7 Mycobacterium paratuberculosis
		4.18.8 Acinetobacter species
		4.18.9 Nanobacteria
Chapter 5 Foodborne pathogens: viruses, toxins, parasites and prions
	5.1 Foodborne viruses
		5.1.1 Norovirus
		5.1.2 Hepatitis A
		5.1.3 Hepatitis E
		5.1.4 Rotaviruses
		5.1.5 Small round viruses, astroviruses, sapporo-like viruses, adenoviruses and parvoviruses
		5.1.6 Human enteroviruses
	5.2 Seafood and shellfish poisoning
		5.2.1 Ciguatera poisoning
		5.2.2 Scombroid poisoning
		5.2.3 Paralytic shellfish poisoning
		5.2.4 Diarrhoeic shellfish poisoning
		5.2.5 Neurotoxic shellfish poisoning
		5.2.6 Amnesic shellfish poisoning
	5.3 Foodborne parasites: eucaryotes
		5.3.1 Toxoplasma gondii
		5.3.2 Taenia saginata and T. solium
		5.3.3 Echinococcus multilocularis and E. granulosus
		5.3.4 Cyclospora cayetanensis
		5.3.5 Cryptosporidium parvum
		5.3.6 Anisakis simplex
		5.3.7 Trichinella spiralis
	5.4 Mycotoxins
		5.4.1 Aflatoxins
		5.4.2 Ochratoxins
		5.4.3 Fumonisins
		5.4.4 Zearalenone
		5.4.5 Trichothecenes
		5.4.6 Prions and transmissible spongiform encephalopathies
Chapter 6 Methods of detection and characterisation
	6.1 Prologue
	6.2 Conventional methods
		6.2.1 Culture media
		6.2.2 Sublethally injured cells
		6.2.3 Viable but non-culturable bacteria (VBNC)
	6.3 Rapid sampling methods
		6.3.1 Sample preparation
		6.3.2 Separation and concentration of target
	6.4 Rapid end-detection methods
		6.4.1 ELISA and antibody-based detection systems
		6.4.2 Reversed passive latex agglutination
		6.4.3 ATP bioluminescence techniques and hygiene monitoring
		6.4.4 Protein detection
		6.4.5 Flow cytometry
		6.4.6 Biosensors
		6.4.7 Impedance (Conductance) microbiology
	6.5 DNA-based molecular typing and proteomic methods
		6.5.1 Polymerase chain reaction (PCR)
		6.5.2 Microarrays
		6.5.3 Loop-mediated isothermal amplification (LAMP) technique
		6.5.4 Pulsed-field gel electrophoresis (PFGE)
		6.5.5 Restriction fragment length polymorphism (RFLP)
		6.5.6 Amplified fragment length polymorphism (AFLP)
		6.5.7 Random amplification of polymorphic DNA (RAPD)
		6.5.8 Repetitive-element polymerase chain reaction (Rep-PCR)
		6.5.9 Nucleic acid sequence-based amplification (NASBA)
		6.5.10 Multiple-locus variable number tandem (VNTR) repeat analysis
		6.5.11 PCR-probe based serotyping
		6.5.12 Ribotyping
		6.5.13 Matrix-associated laser desorption ionisation – time of flight (MALDI-TOF)
	6.6 Identification and typing methods based on high-throughput DNA sequencing
		6.6.1 Conventional seven-loci MLST
		6.6.2 Genome sequence-based MLST
		6.6.3 CRISPR-cas array typing
		6.6.4 Single nucleotide polymorphism (SNP)-based analysis
	6.7 Specific detection procedures and accreditation
		6.7.1 Aerobic plate count (APC)
		6.7.2 Salmonella serovars
		6.7.3 Campylobacter species
		6.7.4 Enterobacteriaceae and E. coli
		6.7.5 Pathogenic E. coli, including E. coli O157:H7
		6.7.6 Shigella species
		6.7.7 Cronobacter genus
		6.7.8 Aeromonas species
		6.7.9 Arcobacter species
		6.7.10 Listeria monocytogenes
		6.7.11 Staphylococcus aureus
		6.7.12 Clostridium perfringens
		6.7.13 B. cereus, B. subtilis and B. licheniformis
		6.7.14 Mycotoxins
		6.7.15 Viruses
Chapter 7 Microbiological criteria
	7.1 Background to microbiological criteria and end-product testing
	7.2 International commission on microbiological specifications for foods (ICMSF)
	7.3 Codex Alimentarius principles for the establishment and application of microbiological criteria
	7.4 Sampling plans
	7.5 Variables plans
	7.6 Attributes sampling plan
		7.6.1 Two-class plan
		7.6.2 Three-class plan
	7.7 Principles
		7.7.1 Defining a ‘lot’ of food
		7.7.2 Sample unit number
		7.7.3 Operating characteristic curve
		7.7.4 Producer risk and consumer risk
		7.7.5 Stringency of two- and three-class plans, setting n and c
		7.7.6 Setting the values for m and M
	7.8 Microbiological limits
		7.8.1 Definitions
		7.8.2 Limitations of microbiological testing
		7.8.3 Examples of sampling plans
	7.9 Implemented microbiological criteria
		7.9.1 Microbiological criteria in the European Union
		7.9.2 EU Directives specifying microbiological standards for foods
	7.10 UK guidelines for ready-to-eat foods
Chapter 8 Hygienic production practices
	8.1 Contribution of food handlers to foodborne illness
	8.2 Personnel hygiene and training
	8.3 Cleaning
	8.4 Detergents and disinfectants
	8.5 Microbial biofilms
		8.5.1 Microbial biofilm formation
		8.5.2 Bacterial biofilm induction
		8.5.3 Biofilm removal and control
	8.6 Assessment of cleaning and disinfection efficiency
Chapter 9 Food safety management tools
	9.1 The manufacture of hygienic food
	9.2 Microbiological safety of food in world trade
	9.3 Consumer pressure effect on food processing
	9.4 The management of hazards in food in international trade
	9.5 Hazard analysis critical control point (HACCP)
	9.6 Prerequisite programme
	9.7 Outline of HACCP
		9.7.1 Food hazards
		9.7.2 Preparation for HACCP
		9.7.3 Principle 1: hazard analysis (HA)
		9.7.4 Principle 2: critical control points (CCPs)
		9.7.5 Principle 3: critical limits
		9.7.6 Principle 4: CCP monitoring
		9.7.7 Principle 5: corrective actions
		9.7.8 Principle 6: verification
		9.7.9 Principle 7: record keeping
	9.8 Microbiological criteria and HACCP
	9.9 Microbiological hazards and their control
		9.9.1 Sources of microbiological hazards
		9.9.2 Temperature control of microbiological hazards
		9.9.3 Non-temperature control of microbiological hazards
	9.10 HACCP plans
		9.10.1 Production of pasteurised milk
		9.10.2 Swine slaughter in the abattoir
		9.10.3 Chilled food manufacture
		9.10.4 Generic models
	9.11 GMP and GHP
	9.12 Quality systems
	9.13 Total quality management
Chapter 10 Microbiological risk assessment
	10.1 Risk analysis and microbiological risk assessment
	10.2 Origin of MRA
	10.3 MRA – an overview
	10.4 MRA – structure
		10.4.1 Risk assessment
		10.4.2 Risk management
		10.4.3 Risk communication
	10.5 Risk assessment
		10.5.1 Statement of purpose
		10.5.2 Hazard identification
		10.5.3 Exposure assessment
		10.5.4 Hazard characterisation
		10.5.5 Dose–response assessment
		10.5.6 Dose–response models
		10.5.7 Dose and infection
		10.5.8 Risk characterisation
		10.5.9 Production of a formal report
		10.5.10 Triangular distributions and Monte Carlo simulation
	10.6 Risk management
		10.6.1 Risk assessment policy
		10.6.2 Risk profiling
	10.7 Food safety objectives (FSO)
	10.8 Risk communication
	10.9 Future developments in MRA
		10.9.1 International methodology and guidelines
		10.9.2 Risk assessment database
		10.9.3 Training courses and use of resources
Chapter 11 Application of microbiological risk assessment
	11.1 Salmonella serovars
		11.1.1 Salmonella enteritidis in shell eggs and egg products
		11.1.2 Hazard identification and hazard characterisation of Salmonella in broilers and eggs
		11.1.3 Exposure assessment of Salmonella serovars in broilers
		11.1.4 Salmonella serovars in cooked chicken
		11.1.5 Salmonella serovars in cooked patty
		11.1.6 Poultry FARM
		11.1.7 Domestic and Sporadic Human Salmonellosis
	11.2 Campylobacter
		11.2.1 C. jejuni risk from fresh chicken
		11.2.2 Risk profile for pathogenic species of Campylobacter in Denmark
		11.2.3 Risk assessment of C. jejuni in broilers
		11.2.4 Campylobacter fluoroquinolone resistance
	11.3 L. monocytogenes
		11.3.1 L. monocytogenes hazard identification and hazard characterisation in ready-to-eat foods
		11.3.2 L. monocytogenes exposure assessment in RTE foods
		11.3.3 Relative risk of L. monocytogenes in selected RTE foods
		11.3.4 L. monocytogenes in European Union trade
		11.3.5 L. monocytogenes in meat balls
		11.3.6 Listeriosis from RTE meat products
	11.4 E. coli O157
		11.4.1 E. coli O157:H7 in ground beef
	11.5 Bacillus cereus
		11.5.1 B. cereus risk assessment
	11.6 Vibrio parahaemolyticus
		11.6.1 Public health impact of V. parahaemolyticus in raw molluscan shellfish
	11.7 Cronobacter species and Salmonella in powdered infant formula (PIF)
	11.8 Viral risk assessments
		11.8.1 Viral contamination of shellfish and coastal waters
Chapter 12 International control of microbiological hazards in foods: regulations and authorities
	12.1 Control of foodborne pathogens
		12.1.1 Control of Salmonella serovars in poultry
		12.1.2 Control of Escherichia coli pathovars and Salmonella serovars in fresh produce
		12.1.3 Control of pathogens in low-moisture foods (LMFs)
	12.2 World Health Organisation (WHO), global food security from accidental and deliberate contamination
		Box 12.1
	12.3 Regulations in international trade of food
	12.4 Codex Alimentarius Commission (CAC)
	12.5 SPS measures, technical barriers to trade (TBT) and the WHO
	12.6 EU legislation
	12.7 International food safety agencies
		12.7.1 European Food Safety Authority (EFSA)
		12.7.2 Food authorities in the United States
Chapter 13 Surveillance and foodborne outbreak investigation
	13.1 Surveillance programmes
		13.1.1 International Food Safety Authorities Network (IFSAN)
		13.1.2 Surveillance systems in the United States
		13.1.3 PulseNet international
		13.1.4 European Centre for Disease Prevention and Control (ECDC) and European surveillance for salmonellosis and shiga toxin-producing E. coli (STEC)
		13.1.5 European food-borne viruses in europe network (FBVE)
		13.1.6 Rapid alert system for food and feed (RASFF)
		13.1.7 Global salm-surv (GSS)
		13.1.8 Surveillance of ready-to-eat foods in the United Kingdom
	13.2 Outbreak investigations
		13.2.1 Preliminary outbreak investigation
		13.2.2 Case definition and data collection
		13.2.3 Data collation and interpretation
	13.3 Social media, crowd sourcing and reporting food poisoning cases
	13.4 Mobile phones and food safety
	13.5 Food terrorism and biocrimes
Chapter 14 Whole-genome sequencing, microbiomes and genomic epidemiology
	14.1 high-throughput DNA sequencing
	14.2 Microbiome analysis
	14.3 Genomic epidemiology
		14.3.1 Whole-genome sequencing for microbial source tracking
		14.3.2 Genome Trakr network (US)
		14.3.3 NCBI pathogen detection site
		14.3.4 Center for Genomic Epidemiology (denmark)
	14.4 Key outbreaks investigated using genomic epidemiology
		14.4.1 Ready-to-eat meat products L. monocytogenes outbreak, canada, 2008
		14.4.2 E. coli O104:H4 outbreak, germany, 2011
		14.4.3 C. jejuni outbreak investigations
		14.4.4 Salmonella enteritidis in eggs, European outbreak, 2014
		14.4.5 Multinational outbreak of Salmonella Agona through infant formula contamination, 2017
		14.4.6 Retrospective Cronobacter sakazakii neonatal intensive care unit outbreak, france, 1994
		14.4.7 L. monocytogenes ST6, polony sausages, south africa, 2017–2018
Glossary of terms
List of abbreviations
Food safety resources on the world wide web
Plates and credits
References
Index
Supplemental Images
EULA