Acanthamoeba spp., 81, 83, 88 persistence and transmission of
actinopods, 83 human pathogens after land adenoviruses, 102, 108–9, 111 application, 318–27 aerobic composting, 332–6 role in contamination of fresh food, aerosol, 329 312–41 Aichi virus (AiV), 102, 107, 335 animal waste treatments, 330–8 aid for trade program, 400 aerobic composting, 332–6 Alexandrium spp., 88 anaerobic digestion, 332 almond processing industry, 246 manure storage, 331–2 Alphitobius diaperinus, 291 regrowth of pathogens in alveolata, 86 composted/digested products, American Type Culture Collection 336–8 (ATCC), 90 antibiotic resistance, 316–17 amoebae, 82–3, 86, 93 antimicrobials, 316–17 amoebozoa, 84, 86 archaeplastida, 84 amplified fragment length and ‘assurance’ activities, 385 polymerisation (AF:P), astrovirus, 102, 108 40 atovaquone, 74 anaerobic digestion, 332 attribute acceptance plans, 261–2 animal manure, 313–15 common practices in applying Bacillus cereus, 357–8 to agricultural fields, bacteria, 316 317–18 impact of composting, 333–5 contamination of produce on farms, bacterial pathogens 327–30 contaminating seeds and sprouts, foodborne pathogens associated 355–60 with, 315–17 bacterial transfers, 166, 171 guidelines on direct application to Balamuthia mandrillaris, 83 cropland, 338–40 Balantidium coli, 83 Index 407
baranyi model, 223, 224, 230 Codex Code of Practice, 384
Baranyi-Ratkowsky model, 224, 227 codex pesticide residue database, 385 batch acceptance, 259 colony forming units (CFU), 166 BAX system real-time (PCR) assay, ‘combimatrix,’ 136 271, 272 comparative exposure assessments, 210, bayesian inference, 209 212, 214 benzalkonium chloride, 86 composting, 331 better Training for Safer Food program, impact on bacteria, spore-formers, 400 parasites and viruses, 333–5 biacore, 134 under suboptimal conditions, 335–6 biofilm, 154, 169 concentrated animal feeding operations biosensors, 134–5 (CAFO), 331 biotyping, 36, 39 confirmatory tests, 270 Bircher-Benner, Max, 352 consumption bradyzoites, 61 raw vegetables, 352–4 British Retail Consortium (BRC), 248, contaminated clothing, 172 384 contamination burden of disease, 204, 215 animal waste treatments, 330–8 attributing to responsible sources, from animal manure, 327–30 204–12 ‘control’ activities, 385 burden of illness, 203–4 control of Y. pseudotuberculosis, 49 butyrate, 8 Convective Interaction Media (CIM), 110 C. jejuni, 326 Council Decision 94/371/EC, 286 cage ban Council Directive 92/117/EEC, 286 Salmonella Enteritidis (SE), 290 coxsackievirus, 102 California Compost Quality Council critical control points (CCPs), 253–4 (CCQC), 337 cross-contamination, 154, 165–9, 171, Campy-Cefex agar, 272 174 Campylobacter, 209–10, 212, 258–9 mitigation options to control campylobacteriosis, 208, 258 L. monocytogenes at retail, Canadian Food Inspection Agency, 175–80 366 Cryptosporidium oocysts, 331 case-control study, 208, 212 Cryptosporidium parvum, 83 cetyltrimethylammonium bromide Culture Collection for Algae and (CTAB), 111 Protozoa (CCAP), 90 Chelex-100, 120 culture methods, 273 Chemical oxygen demand (COD), 396 curing phase, 336 chlorine, 298 cutting boards, 169 CHROMagar Yersinia (CAY), 39 Cyclospora cayetanensis, 83 ciliates, 83 cysts, 334 civil legislation, 385 cytopathic effects (CPE), 117 cleaning and disinfection, 283 climate, 398 Danish Zoonosis Centre, 200 clindamycin, 74 decontamination, 291, 298 code of hygienic practices for fresh deli meat, 152 fruits and vegetables, 385 delicatessen Codex Alimentarius Commission risk assessment of Listeria (Codex), 238, 366 monocytogenes, 173–5 definition of validation, verification Dermanyssus gallinae, 291 and monitoring, 239 diaminodiphenylsulfone, 74 408 Index
diarrhoea, 38, 358, 359 European Union
STEC-associated, 363 Salmonella Enteritidis (SE), diarrhoeal toxin, 357 281–2 direct sequencing, 123–4 sprouts consumption, 353 disability-adjusted life year (DALY), excavata, 84, 86 204 exclusivity, 270 DNA enzyme immunoassay (DEIA), excystment, 82 122 feline calicivirus (FCV), 104, 130 E. coli, 397 fenugreek seeds, 364 E. coli O157, 354–5, 363 flagellates, 83 E. coli O157:H7, 3, 222, 265, 319, 326, fluorescent microscopy, 397 328 food business operator (FBO), 369 nontoxigenic, 326 food classification system, 205 E. coli VTEC, 397 food disease surveillance, 198–201 eggs categorization, 198–200 albumen, 284 surveillance components, potential treatments, 297–9 collaborations and Salmonella Enteritidis (SE), 282–5 communication flow, 200 washing, 297 evidence for policy to prevent and emetic toxin, 357 control foodborne diseases, encephalitis, 72 203–12 encystment, 82 attributing the burden of disease enrichment, 269 to sources, 204–12 Entamoeba histolytica, 83 estimating true burden of Enteroaggregative E. coli (EAggEC), foodborne diseases, 203–4 363 source attribution to inform risk Enterobacter aerogenes, 166 management, 197–216 Enterobacteriacea, 34, 270–1, 273 future trends, 214–16 environmental pollution, 315 requirements to improve enzyme-linked immunosorbent assay foodborne diseases surveillance (ELISA), 68 systems, 202 epidemiological approaches, 205, 208, role of typing of foodborne 214 pathogens, 201–3 EspADB gene, 5 usefulness and applicability of ethidium monoazide (EMA), 138 source attribution methods, EU Commission Regulation No. 212–14 208/2013, 368 food hygiene, 178 EU Commission Regulation No. food parasite 209/2013, 368–9 Toxoplasma gondii, 59–74 EU Commission Regulation No. biology, genetics and genomics, 210/2013, 369 67–8 EU Commission Regulation No. diagnosis, 68–9 211/2013, 369–70 epidemiology, 69–70 EU Council Directive 1999/74/EC, future trends, 74 290 morphology, structure and life European Centre for Disease cycle, 61–7 Prevention and Control pathogenesis and clinical features, (ECDC), 214 70–3 European Food Safety Authority treatment and prevention, 73–4 (EFSA), 214 food safety, 149–50 Index 409
Food Safety and Inspection Service foodborne illness, 258
(FSIS), 20, 151, 173 consumption of sprouts, 360–5 food safety controls foodborne pathogens, 205 reassessment or revalidation, 243–4 non-O157 Shiga toxin-producing validation, 245–6 E. coli, 3–21 almond processing, 246 animal reservoirs, 8–10 low-acid canned foods, 245–6 detection, 20–2 food safety criteria, 260 interventions for control in cattle, food safety management system 16–19 (FSMS), 379 interventions for control in improvement, 392–7 produce, 15–16 assessment of current system, outbreaks, 10–14 393–5 resistance to stress, 19–20 sampling and testing for transmission to humans, 14–15 verification, 396–7 virulence, 4–8 water use, quality and treatment in role of free-living protozoa in fresh produce supply chain, protection of, 81–95 395–6 Yersinia, 33–51 key definitions, 387 control, 44–9 Food Safety Modernization Act detection and identification (FSMA), 313, 330, 338 methods, 38–40 Food Safety Objective (FSO), 262 evolution, genome, taxonomy and food safety outcomes, 240 pathogenicity, 35–8 food safety policy, 197 future trends, 49–51 food safety standards history and background, 34–5 fresh produce supply chain, 379–401 molecular epidemiology, 40 benefits and concerns relating to sources, sporadic cases and implementation, 388–92 outbreaks, 40–4 building trust in supply chain, foodborne viruses, 102–12 380–4 biosensors, 134–5 importance of training and risk challenges in detection, 103–4 communication, 399–401 confirmation of RNA-amplified improving food safety products, 122–5 management system, 393–7 direct sequencing, 123–4 key terminology, 384–8 hybridization, 122 overview of standards along the nested RT-PCR, 124–5 fresh produce supply chain, 386 restriction digestion, 122–3 summary of different outbreaks detection methods, 118–19 associated with leafy vegetables, animal cell-culture based 381–3 infectivity assays, 118–19 future trends, 397–9 immunological methods, 119 food safety systems molecular approaches for validating, 239–43 detection, 119 Food Standards Agency of Australia detection of infectious vs and New Zealand (FSANZ), noninfectious viruses using 367 molecular based assays, 138–9 food workers methodologies for sampling and Listeria monocytogenes, 170–3, 178 concentration, 109–12 Foodborne Disease Burden sampling, 109–10 Epidemiological Reference virus concentration, 110 Group (FERG), 213 microarrays, 135–6 410 Index
molecular amplification and significance of bacteria–protozoa
detection, 119–20, 120–2 interactions for food safety, multiplex RT-PCR, 121–2 90–4 reverse-transcriptase polymerase fresh food chain reaction (RT-PCR), role of animal manure in 120–1 contamination of fresh food, molecular-based detection methods, 312–41 117–39 animal waste treatments, 330–8 next-generation sequencing applying animal manure to approaches, 136–8 agricultural fields, 317–18 nucleic acid sequence-based contamination of produce on amplification, 131–2 farms, 327–30 real-time reverse-transcriptase foodborne pathogens associated polymerase chain reaction with animal manure, 315–17 approaches, 125–31 guidelines on direct application to reverse transcription loop-mediated cropland, 338–40 isothermal amplification assay, persistence and transmission of 132–4 human pathogens after land RNA extraction and purification, application, 318–27 119–20 fresh meat types of virus, 104–9 developments in sampling and adenoviruses, 108–9 test methods for pathogens, Aichi virus, 107 257–75 astrovirus, 108 current US and EU methods of hepatitis A virus, 105–6 sample testing, 271–4 hepatitis E virus, 106–7 future trends, 274–5 human noroviruses, 104–5 HACCP systems, 262–7 other human enteroviruses, 109 principles and limitations of parvoviruses, 109 sample testing, 267–71 rotavirus, 107–8 sampling plans, 259–62 sapoviruses, 105–6 fresh produce FP7 Veg-i-Trade, 380, 388, 392, 400 modelling spread of pathogen overview of microbiological results contamination, 220–34 of sampling fresh produce and case study on pathogen growth, production environment 224–8 enteric E. coli as hygiene indicator, Listeria monocytogenes 394 contamination of minced tuna, pathogens in leafy greens, 394 229–33 quality assurance recommendations, pathogen growth behaviour, 221–3 395 modelling bacterial behaviour in/ free-living protozoa, 84 on fresh produce, 223 drinking water and food, 87–8 related bacterial pathogens, 221–2 ecological importance, 84–5 fresh produce supply chain food-related environments, 85–7 benefits and concerns relating to interactions with bacteria, 89–90, implementation, 388–92 91–3 impact of organization and occurrence in natural habitats and context on adoption of anthropogenic environment, standards, 391–2 85 impact on structure and role in protection of foodborne governance of supply chain, pathogens, 81–95 390–1 Index 411
importance of factors at farmer validating food safety systems,
and country level, 390 239–43 requirements from farmers, 389 validation of food controls, 245–6 food safety standards, 379–401 verification of food safety FSIS Microbiology Laboratory management system activities, Guidebook (MLG), 21 246–8 testing for pathogens, 262–7, 274–5 ‘gene melting pot, 94 heat-shock response, 336 General Food Law Regulation (EC) heliozoa, 83 178/2002, 385 helminths, 316 Giardia lamblia, 83 hemolytic uremic syndrome (HUS), 3 Global Food Safety Initiative (GFSI), hemorrhagic colitis (HC), 3 239 hepatitis A virus (HAV), 102, 105–6 validation and verification, 248–9 hepatitis E virus (HEV), 102, 106–7 definition, 248–9 highly active antiretroviral therapy global microbial identifier genomic (HAART), 73 epidemiological database, 215 human illness source attribution, GlobalG.A.P., 385, 388 204 Globotriaosylceramide (Gb3), 6 human noroviruses (HNoV), 102, GloGerm, 165 104–5 good agricultural practices (GAPs), human salmonellosis 366 outbreaks in Europe, 293–4 Good hygiene practice (GHP), 366, outbreaks outside Europe, 294–6 388 hybridization, 122 good manufacturing practice (GMP), hydrogen peroxide, 298 366, 388 hygiene practice manual, 365 granulomatous amoebic encephalitis, hypochlorites, 176 88 guanidiniumisothiocyanate (GuSCN), illumina sequencing, 123, 137 119 immunomagnetic separation (IMS), 22, Gymnodinium spp, 88 112, 129, 269–70, 397 immunosorbent agglutination test haemolytic uremic syndrome (HUS), (IAA), 68 359, 363, 364, 369 in-plant validation, 242–3 hand washing, 171–2, 178 indirect fluorescent antibody assay Hartmannella vermiformis, 81 (IFA), 68 Hazard Analysis and Critical Control indirect haemagglutination test Points (HACCP), 365, 367, (IHAT), 68 385 integrated surveillance, 199 developments in validation and internal amplification control (IAC), verification methods for food 120 safety systems, 238–53 internalins, 151 critical control points and International Food Safety (IFS), prerequisite programs, 240–53 384 future trends, 249–50 intervention studies, 210–11 Global Food Safety Initiative intimin, 7, 271 (GFSI) perspective, 248–9 iodine, 298 reassessment or revalidation of ion torrent sequencing, 123 food safety controls, 243–4 irgasan-ticarcillin-potassium chlorate system design, 242 (ITC), 39 system execution, 242 ISO 6579:2002, 272 412 Index
ISO 22000, 248 risk assessment in delicatessen, 173–5
isolation, 269 transfer dynamics, 162–70 modelling using two or more Jameson effect, 229, 233 inanimate objects, 169–70 review of cross-contamination, keratitis, 88 165–9 listeriosis, 150–4, 222 labels, 385 epidemiology, 152–4 laboratory-based surveillance, 199 Listeria detection, characterization lagoons, 314 and subtyping, 150–1 latex agglutination test (LAT), 68 selected outbreaks, 155–6 laying flocks locus of enterocyte effacement (LEE), Salmonella Enteritidis (SE), 363 282–5 loopamp kit, 133 importance of ‘sell by’ dates for low-acid canned foods industry, 245–6 eggs, 284–5 persistence in eggs, 283–4 macrogamont, 65 Leafy Green Marketing Agreement manure storage, 331–2 (LGMA), 337 mastigophora, 82 Lebensreform, 352 mathematical modelling, 242 LEE (locus of enterocyte effacement), maximum residue limits (MRLs), 384, 6 388 Legionella pneumophila, 81 mealworm beetle larvae see Legionnaires’ disease, 81 Alphitobius diaperinus Leishmania spp., 83 merozoites, 65 Light Cycler SYBR green-based mesophilic phase, 333 RT-qPCR assay, 125 microbial subtyping, 209 limit of detection (LOD), 270 approach, 212 liquid electrochemiluminescence microbiological criteria, 387–8 (ECL) hybridization, 122 microbiological hazards Listeria-like organisms (LLOs), 151 seeds and sprouts, 354–5 Listeria monocytogenes, 222, 358 microgamont, 65 contamination of minced tuna, MLG, 271–3 229–33 modified agglutination test (MAT), growth modelling, 229–33 68 mitigation options to control cross- molecular amplification and detection contamination, 175–80 multiplex RT-PCR, 121–2 selected activities to control molecular typing methods, 201, 203 L. monocytogenes in food most probable number (MPN) method, settings, 177 229 observed growth on lettuce, 227 moulting, 292 presence and prevalence in retail multi-locus-sequence-typing (MLST), operations, 154, 157–62 203, 209–10 reducing cross-contamination in food multiple-locus variable number tandem retail operations, 149–81 repeat analysis (MLVA), 203 food safety, 149–50 Multiplex RT-PCR, 121–2 future trends, 180–1 murine norovirus, 104, 120 listeriosis, 150–4 mitigation options to control Naegleria fowleri, 83 cross-contamination, 175–80 NASBA electroluminescence role of food workers, 170–3 (NASBA-ECL) assay, 132 Index 413
National Advisory Committee on the outbreaks
Microbiological Criteria associated with leafy vegetables, (NACMCF), 238 381–3 National control programme (NCP), foodborne illness associated with 287, 288 consumption of sprouts, 360–5 National Poultry Improvement Plan human salmonellosis, 293–6 (NPIP), 295 ozone, 298 nested RT-PCR, 124–5 niches, 162 Paramecium, 83 no formal surveillance, 198 parasites non-O157 Shiga toxin-producing impact of composting, 333–5 E. coli, 3–21 parvoviruses, 109 animal reservoirs, 8–10 pathogen contamination detection, 20–2 modelling in fresh produce, 220–34 interventions for control in cattle, case study on pathogen growth, 16–19 224–8 interventions for control in produce, Listeria monocytogenes 15–16 contamination of minced tuna, outbreaks, 10–14 229–33 resistance to stress, 19–20 pathogen growth behaviour, 221–3 transmission to humans, 14–15 pathogen growth virulence, 4–8 predicting growth on lettuce, 224–8 non-O157 STEC virulence genes, pathogen–host relationship, 284 5–8 pathogen internalization, 328 serogroups and serotypes pathogen regrowth, 336–7 associated with human disease, pathogens 4–5 in fresh meat, developments in Nordic Committee on Food Analysis sampling and test methods, (1987) method, 39 257–75 NoroChip, 135 current US and EU methods of norovirus (NoV), 397 sample testing, 271–4 human, 102 future trends, 274–5 northern hybridization, 122 HACCP systems, 262–7 notational analysis, 165 principles and limitations of nucleic acid sequence-based sample testing, 267–71 amplification, 131–2 sampling plans, 259–62 NucliSens Basic Kit, 132 PCR-restriction fragment length polymorphism (RFLP), 122 obligate endobionts, 89 pesticide residue monitoring, 396–7 occurrence approaches, 209–10 phenotypic methods, 201 oligotrophic soil environment, 325 plaque forming units (PFU), 118 one-health framework, 199 Plasmodium spp., 83 oocysts, 66, 334 plastic bag technique, 45 open reading frames (ORF), 106 polymerase chain reaction methods, 38 operating characteristic (OC) curve, pontiac fever, 81 261–2 poultry red mite see Dermanyssus two-class attributes acceptance plans, gallinae 263 predictive microbiology, 221 Operational Prerequisite Programs prepatent periods, 66 (OPRPs), 239 prerequisite programs (PRPs), 239, opisthokonta, 84 253–4 414 Index
process performance, 259, 262, 264 risk assessments, 152