The Microbiology of Safe Food [3 ed.] 1119405017, 9781119405016

Table of contents :
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