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Index

Accreditation, laboratory 101 diffuse catchment sources 128–134, 135 triphosphate (ATP) 111, of recreational 270, 114–115 276, 277 Adenoviruses 69, 72 source identification see Source Adverse health outcomes see Health risks identification Aeration, depuration systems 154, 158 source identifier organisms 70–75 Aeromonas spp. 24, 299 see also Agricultural activities; Faecal Agricultural activities pollution harvesting area pollution 32, 54–55, Animal Product Officers 235, 237–238, 128–134, 135 239, 242 management interventions 271, 287–288 Annapolis Protocol 269–270 recreational pollution 270, 276, Antibiotic resistance analysis (ARA) 58, 277 59, 60, 78 Algae, autochthonous 320 Antibiotic resistance profiles 57, 58–59 Algeria 260 AOAC International 101 American Public Health Association Approved areas (APHA) 150–151 Canada 221, 222–223, 230 Amplified fragment length polymorphisms 259 (AFLP) 57, 63 New Zealand 238, 240–241 Anaerobic bacteria 70–71 42, 94, 149, 198 Animal faecal wastes 53, 54–55, 323 see also Conditionally approved areas

# 2010 World Health Organization (WHO). Safe Management of Shellfish and Harvest Waters. Edited by G. Rees, K. Pond, D. Kay, J. Bartram and J. Santo Domingo. ISBN: 9781843392255. Published by IWA Publishing, London, UK. 332 Safe Management of Shellfish and HarvestWaters

Aquaculture 2, 12 real-time monitoring 114 Canada 219, 222, 224 source identification 70–71 China 249–257 Bacteroidetes 67, 68 New Zealand 235 Batches sanitary surveys prior to establishing avoidance of commingling 188 138–139 depuration 157–158 Scotland 206 documentation 196, 200 Argentina 17 Bathymetry 123 Arkshells 11–12, 13 Beach profiling 270 Artificial neural networks (ANN) 299–300 Best management practices (BMP), Asia 2 agricultural 287–288 production 12 Bifidobacterium 67–68, 70–71 trade 13–16, 18 114 Association of Scottish Shellfish Biosensors 118 Gatherers 212 Biotoxins 320 Astroviruses 170, 298, 303 end product standards 195 Australia, depuration 167–168 monitoring 191, 250–251 Autochthonous bacteria 25–26, 320 related to 40–41 Bivalve Molluscan Shellfish Regulated Bacillus cereus 27 Control Scheme (BMSRCS) Bacillus coli 109–110 (New Zealand) 236–243 see also 260 Bacteria BOX sequences 61 autochthonous 25–26, 320 Bulk bin depuration system 162–163 binding to sediment particles 305–306 Bureau of Quality and Technical decay in coastal environments 303–304 Supervision, China 252, 256 environmental contamination 297–298 faecal indicator 70, 91 74 gastroenteritis due to 24–25, 40 Caliciviruses 24, 33 modelling contamination of Campylobacter 24 shellfish 305 Canada 12, 246–249 post-harvest contamination 27 central competent authority 218, 246 removal by depuration 169–170 control measures 184, 201, 217–231 source identifier 70–71 exports 15, 16, 17, 18, 19, 225, 226 see also Coliforms; Faecal coliforms; imports 226–227 Faecal indicator organisms; monitoring programmes 219–224, 248 specific bacteria shellfish production quantum 219, 247 Bacteriological standards see Micro- Canadian Food Inspection Agency biological standards (CFIA) 218, 220, 224, 225–226, Bacteriological surveys 122, 124 228, 230 (phages) Canadian Shellfish Sanitation Program F þ RNA (FRNA) 7, 70, 172, 175, 298 (CSSP) 218, 219–231, 246 serotyping and genotyping 57, 67 annual classification process overview source identifiers 71–72 221–222 Bacteroides classification of new production areas 16S rDNA assay 60, 67 220–221 phages 67, 72 emergency closure 230 Index 333

identification of production/relaying production 11–12, 13, 219, 235 areas 222 relative E. coli contamination 95 interactions between agencies 224–227 trade 13–14, 15, 17, 18 mitigation measures 227–228 Class Aareas, EU 42, 93, 149, 191 monitoring programmes 222–224, 248 Class Bareas, EU 93, 191 product traceability and recall 228–230 Class Bshellfish utilization profiles (CUP) 57, 59 depuration/relaying 150, 194 Casual collecting 2, 4, 8, 46 heat treatment 194–195 legislative controls 184, 189 Class Careas, EU 93, 191 Catchment microbial modelling 272, Class Cshellfish 275–287, 288–289, 323 depuration/relaying 150, 174, 194 linked to nearshore modelling heat treatment 194–195 285–287 Classification of harvesting areas 6–7, using satellite data 277–285, 286 91–92, 186–187 Catchments 124–125 action where results are outside area amended farming practices 271, limits 212–213, 227 287–288 Canada 220–224, 247 holistic concepts 321–322 China 253–255 source apportionment see Source communication to consumers 211 apportionment conditional 124, 150, 198, 242 sources of faecal indicator organisms depuration and relaying thresholds 128–135 149–150 Cattle 27, 54–55, 287–288 European Union 92, 93, 191 Centre for Ecology and Hydrology (CEH) Mediterranean states 258, 259 land cover data 280–281, 283–285 New Zealand 237–239, 240–242, 247 Cerastoderma edule see Cockles primary conflicts 46–47 CFIA see Canadian Food Inspection regular reviews 198, 209, 221–222, Agency 239 Chemical markers, faecal pollution Scotland 207–208, 209–210, 211–212, 74–75 247 tests 114–115 United States 92, 94, 198–199 Chile 12, 17, 19 Clean Water Act (CWA), US 129, 185, China 271–272, 321–322 management controls 249–257, 264 Closed areas 223 production 2, 12, 249, 320 27 shellfish-related outbreaks 40 Coastal environments trade 14–16, 17, 18, 252, 256–257 microbial decay 303–304 China (Province of Taiwan) 16 microbial modelling see Microbial Chlorination modelling in coastal environments depuration systems 147, 164 Cockles ( Cerastoderma edule) sewage discharges 185 Cryptosporidium contamination 23 Cholera 3 depuration 154, 168 Claires 175 production trends 11–12, 13 Clams relative E. coli contamination 95 Cryptosporidium contamination 23 trade 13–14, 17 depuration 160, 168, 200 Codex Alimentarius Commission health risks 22, 33, 40 184–185, 201 334 Safe Management of Shellfish and HarvestWaters

Codex Code of Practice 184–185 CSSP see Canadian Shellfish Sanitation Coliforms Program enumeration methods 110–111 Cyclospora spp. 27, 28 identification 110 Cyprus 259 rapid monitoring 118 Cysts 27, 28 total 91 classification of harvesting areas 94 Degorgeoirs 175 diffuse source pollution 131, 133 Democratic People’s Republic of Korea pre depuration or relaying limits 15, 18 149, 150 16–17 UV disinfection 165 gradient gel electrophoresis see also Escherichia coli; Faecal (DGGE) 62–63 coliforms Department of Fisheries and Oceans Combined sewer overflows (CSO) 126, (DFO), Canada 218, 220, 225, 127, 128, 276, 277 226, 228, 230 Communication 5, 8–9, 188–189, 215, Depuration 5, 8, 31, 145–176, 187 248–249 Canadian controls 223, 228, 229–230 Conditionally approved areas Chinese controls 251, 253, 254, Canada 223, 226, 227–228 255–256 New Zealand 238, 240–241 HACCP approach 166–167, 168, United States 150, 198 173–174 Conditionally restricted areas historical perspective 146–148 New Zealand 238, 241 limitations 42, 146 United States 94, 150, 198 pollution thresholds 149–151 Conditioned zones, Italy 259 process 152–169 Consumers basic principles 152–153 agency interactions 211, 225–226, international perspective 167–169 248–249 parameters 154–158 education 5, 34 preventing re-contamination 157–158 Cooking 34, 42–43, 145 regulation 151–152 see also Heat treatment shellfish suitable for 153–154 Coordination, inter-agency 8–9 regulation 42, 148–152, 193–194, Cost burden, hygiene controls 45–46, 199–200 189, 236 removal of pathogens 169–173 Crassostrea virginica see Oysters Scottish controls 213 Critical control points (CCPs) 168, 173 systems Critical hazard analysis rating (CHAR) commissioning tests 166 168 design 147, 158–163 260 ongoing compliance testing 166–167 Cryptosporidium parvum 27 seawater disinfection 147, 164–166 depuration efficacy 31 Detergents 74 identification 30 Diabetes 25, 34 sources 54, 73 Diffuse source pollution 6, 41, 128–129 Cryptosporidium spp. 27–28 Digital terrain model (DTM) 279–280 contamination of shellfish 23, 27, 28 Dinitrogenase reductase (nifH) gene 68 public health threat 29 Disinfection, water for depuration 147, sources 54, 55, 73 164–166 Index 335

Dispatch centres 251, 255–256 Escherichia coli 7, 24, 109–110 Dispersion models, microbial 301–302 counts Disturbance, during depuration 157 depuration plant testing 166 DNA fingerprinting 58, 61–64 end-product standards 151, 167, 195 Documentation harvesting area classification 42, 93, classified production and relay 240–241, 254–255, 258, 259 areas 192 methods 100, 116–117, 151 shellfish 196–197, 200, 214, 229 pre depuration or relaying limits Domestic animals 54–55 149, 150 see also Animal faecal wastes sampling issues 96, 97–98, 99 Donovan most probable number (MPN) time series data 102 method see Most probable number unreliability 47 (MPN) technique decay in coastal environments 303–304 Drain down, depuration cycle 157, 160 enterohemorrhagic O157 29 Drainage-basin paradigms 321–322 enterotoxigenic (ETEC) 66 as faecal indicator 91 Early warning systems 307–309, 310–311 identification methods 58, 61, 62, 63, 67 Education, consumer 5, 34 modelling contamination of shellfish 305 Egypt 260 modelling in coastal environments 298, Emergency closures see Temporary 299, 300, 306, 307 closures non-faecal sources 55–56 Encephalitozoon spp. 28–29 phages (coliphages) 67, 71 End-product standards real-time monitoring 115, 116–117 China 251, 254–255 source tracking 70, 77, 79 European Union 149, 151, 167, 195–196 species-specific uptake by shellfish United States 149, 200 94–95 see also Microbiological standards Esp PCR assay 66 Ensis spp. see Clams Estuaries, microbial source tracking 79 Enterobacterial repetitive intergenic Eukaryotic cells, markers of faecal consensus (ERIC) sequences 61 pollution 73 Enterococci European Economic Area (EEA) 184 diffuse source pollution 132, 134 European Networks 309 esp gene 66 European Union (EU) modelling in coastal environments agreements with third countries 184, 190 298, 300 classification of harvesting areas 92, non-faecal sources 55–56 93, 191 real-time monitoring technologies depuration and relaying 148–152, 113–114 168–169, 192–193 source identification 58, 70 Directive 91/492/EEC 183–184, 189 Enterocytozoon bieneusi 28–29 early warning systems 308, 309 Enteroviruses, source identification end-product standards 151, 167, 69, 72 195–196 Environment Canada 218, 220, 221, Food Hygiene Regulations 122, 123, 189 222, 230 imports from third countries 184, 190, Environmental Protection Agency (EPA), 197, 257 US 185, 272, 325 legislation 189–197 Enzymatic tests 115–117 Mediterranean states 258–259 336 Safe Management of Shellfish and HarvestWaters

microbiological monitoring 96, 98, 103 non-faecal sources 55–56 production 12 real-time monitoring technologies recreational water management 109–119 270–271 recreational waters 268–270, 272, sanitary profiling 122, 123–124, 135–137 275–276 Shellfish Hygiene Regulations (853/ remediation studies 287–288 2004 and 854/2004) 183–184, 189, samples and sampling 93–99 190–197, 258 sanitary profiling 124–135 Shellfish Waters Directive 186 sewage effluents 127 trade 2, 16–17, 18 source apportionment 275–287 Water Framework Directive (WFD) sources see Sources of microbial 129, 186, 258, 271, 321–322 pollution Export coefficients 129, 130 spatial variations 97 temporal variations 97–98 Faecal coliforms (FC) 7, 91 see also Escherichia coli; Faecal binding to sediment particles 305–306 coliforms; Microbiological counts standards; Source identifier harvesting area classification 42, 94, organisms 223, 240–241 Faecal post depuration or relaying standards binding to sediment particles 305–306 151, 200 decay in coastal environments 303–304 pre depuration/relaying limits 149, modelling in coastal environments 150 298–307 techniques 100, 110–111 modelling input flows 302–303 unreliability 31–32, 47 modelling shellfish contamination 305 decay in coastal environments 304 sources see Sources of microbial diffuse source pollution 131, 133 pollution modelling contamination of shellfish 305 Faecal pollution modelling in coastal environments 298, chemical markers 74–75 299–300, 302–303, 306–307 eukaryotic markers 73–74 non-faecal sources 55–56 events, monitoring 103–104 real-time monitoring 116 importance of preventing 52–53 sample storage 99 remediation studies 287–288 sewage effluents 127 trends 32 see also Escherichia coli see also Animal faecal wastes; Human Faecal indicator organisms (FIOs) 7, 70, faecal wastes; Sewage 91–92 Farming see Agricultural activities diffuse catchments 128–129, 130, methyl ester profiles (FAME) 131–134 59–61 enumeration techniques 100, 110–111, FDA see Food and Drug Administra- 150–151 tion, US identification 109–110 Federal Food, Drug and Cosmetic Act knowledge of ecology 71, 77 1989 197 limitations of current 31–32, 47, 77, Federal Water Pollution Control Act 79–80 see Clean Water Act monitoring see Microbiological Fisheries Act (Canada) 218, 219, 220, 222 monitoring Flow to full treatment 126 Index 337

Fluorescence insitu hybridization (FISH) early warning systems 309 30 future projections 31–33 Food alerts 214 human waterborne parasites 27 Food and Agricultural Organization under-reporting 30–31 (FAO)/World Health Organization of unknown aetiology 22–24 (WHO)/Codex Alimentarius viral 24, 40 Commission 184–185 Gene 63–64 Food and Drug Administration, US Geometric mean (GM) levels 94, 96, 149 (USFDA) 197–198 lamblia 27, 28, 30 Chinese export standards 257 Good Practice Guide for the Micro- harvesting area classification 42, 92, 96 biological Monitoring of Bivalve inspection of laboratories 101, 201 Mollusc Production Areas 92, memoranda of understanding 18–19, 123–124 184, 198, 235 17, 258 see also National Shellfish Sanitation Guidelines for Safe Recreational Water Program Environments (GSRWE) 268–270 Food Hygiene Regulations, EU 122, 123, 189 HACCP procedures see Hazard analysis see Industry and critical control point (HACCP) Act 1990 213 procedures (FSA), UK Handling, post-harvest 27 190, 206 Harvesting Food Standards Agency Scotland (FSAS) regulatory controls 192–193, 199 206–216, 246 Scottish controls 213–214 classification of new production areas suspension see Temporary closures 209–210 Harvesting areas communication of control results/ Canada 219 actions 215 classification see Classification of interactions with other agencies 210–212 harvesting areas microbiological monitoring early warning systems 307–309 programmes 207–210 information for consumers 211, 225–226 mitigation measures 212–214 management see Management, strengths and of system harvesting area 215–216 microbiological monitoring 42, 91–106 Food Standards Programme, Joint monitoring 6–7, 44, 191–192 FAO/WHO 184–185 real-time monitoring technologies Fragrance materials 74 109–119 12, 16–17 recording and exchanging information depuration 168 192 management practices 258 regulatory controls 192–193 relaying 175 sanitary profiling 44, 121–140 Funding, official hygiene controls 45–46, Scotland 206, 207 189, 236 temporary closures see Temporary closures Gastroenteritis 21, 22–25 Hazard analysis and critical control point bacterial 24–25, 40 (HACCP) procedures 121–122, 148 depurated shellfish-related 170 codes of practice 185 338 Safe Management of Shellfish and HarvestWaters

depuration systems 166–167, 168, Immunofluorescent antibodies (IFA) 30 173–174 Immunoglobulin A, secretory (sIgA), recreational water management 267 faecal 74 see also Quality Management Plans Immunosuppressed individuals 25, 27 Health Bureaux, local, China 252, 256 India 262–263, 264 Health marks 196–197, 214 Indicator organisms, faecal see Faecal Health Protection Officers 235 indicator organisms Health risks 3–4, 21–34, 320–321 Industry early warning systems 307–309 benefits of sanitary surveys 139 see also Illnesses, shellfish-related funding of official controls 189, 236 Heat treatment 150, 187 importance of source tracking 52–53, 78 Canadian controls 228 interactions with official agencies 8–9, regulation 194–195, 199 188–189, 211–212, 226–227 see also Cooking internal checks 192 Hepatitis Avirus (HAV) 3, 24, 33, 40, 170 risk management 45–46 detection methods 173 Infections, shellfish-vectored see Illnesses, harvesting area monitoring 104–105 shellfish-related heat inactivation 42, 187 Inspection and Quarantine Bureaux, China removal by depuration 171 252, 256–257 removal by relaying 175 International Organization for Standardi- UV disinfection 165 zation (ISO) 101, 102–103, 151 Hong Kong Special Administrative Interstate Shellfish Sanitation Conference, Region (SAR), China 16 US 198 Human faecal wastes 53–54, 323 Intertek Testing Services 252 source identification 70–75, 78 Intravalvular fluid see also Microbial source tracking microbiological monitoring 92 see also Faecal pollution; Sewage microbiological standards 93, 149, 186, Human health risks see Health risks 258–259 Hydrodynamic assessments 123, 124 Iodophore disinfection 166 Hydrodynamic models, microbial Ireland 16, 17 contamination 300–301, 302 Israel 260 Italy 12, 259 Illegal harvesting 32, 34, 253 depuration 169, 194 Illnesses, shellfish-related 3–4, 21–34, trade 16, 17 39–40 autochthonous bacteria 25–26 Japan depurated shellfish 148, 171 production 12 future projections 31–33 shellfish-related outbreaks 40 human waterborne parasites 27–30 trade 2, 14, 15, 17, 18 investigation 211, 243 microbiological monitoring and Kirby-Bauer antibiotic susceptibility 58 103–104 post-harvest bacterial contamination 27 Laboratories prevention 3–4, 33–34, 42–44 accreditation 101 reporting bias 30–31 China 256 sanitization methods 31 regulatory control 201 see also Gastroenteritis see also National reference laboratories Index 339

Laundry brighteners 74 interactions with other agencies 210, Lead agencies 8 211, 212, 224–225 Lebanon 260 microbiological monitoring Legislative and regulatory approaches programmes 207, 208, 209 183–202 mitigation measures 212, 213–214 Canada 201, 217–231 LTIIa PCR assay 66 China 249–257 –luciferase reaction 114–115 depuration and relaying 148–152 developing agenda 324–326 Malaysia 2, 13–14, 16 European Union 189–197 Malta 259 general principles 186–189 Management, harvesting area 4–5, 41–44 India 262–263 challenges 320–321 interactions with other legislation current practices 42–43, 245–264 185–186 developing agenda 324–326 Mediterranean states 257–262 new tools and approaches 46–48, new tools and approaches 46–48, 321–324 321–324 see also Legislative and regulatory New Zealand 201, 233–234 approaches; Official control outside the EU and USA 201 monitoring programmes principal systems 184–185 Mediterranean states 257–262, 263–264 Scotland 205–216 EU member 258–259 United States 197–201 non-EU 260–262 see also Management, harvesting area; Membrane filtration method 100, 110 Official control monitoring Meteorological evaluation 123 programmes Methanobrevibacter spp. 68 Libraries, microbial source 57–58, 64 Microbial decay, coastal environments Library dependent source tracking 303–304 methods (LDMs) 56, 57–65 Microbial modelling in coastal environ- genotypic methods 58, 61–64 ments 298–307, 310, 324, 325–326 limitations and critical issues 64–65 applications 306–307 phenotypic methods 58–61 parameters 302–306 Library independent source tracking process-based dynamic models 300–302 methods (LIMs) 56, 57, 65–69, 80 statistical models 299–300 culture dependent 66–67 Microbial source tracking (MST) 45, culture independent 67–69 52–80, 288, 323 limitations and critical issues 69 definition 52 Libyan Arab Jamahiriya 260–261 developed and developing countries spp. 25 76–78 disease, pre-existing 25, 34 human vs animal differentiation 53–56 Livestock faeces 27, 54–55 importance 52–53 see also Agricultural activities; Animal methods 52, 56–76, 80 faecal wastes availability in developing countries Loading parameters, depuration systems 77–78 154–155 library dependent (LDMs) 56, 57–65 Local food authorities (LFA) 207, 215–216 library independent (LIMs) 56, 57, communication of control results/ 65–69, 80 actions 215 selection 75–76 340 Safe Management of Shellfish and HarvestWaters

targeted organisms 70–75 Mitochondrial genes 73 targeted sampling 75 261 Microbiological monitoring 40, 42, 44, Monitoring 6–7, 44, 191–192 91–106 microbiological see Microbiological analytical tolerance 102–103, 104 monitoring China 250–251 non-microbiological 105–106 data interpretation 101–103 programmes, official control see Official indicator organisms see Faecal indicator control monitoring programmes organisms real-time technologies 109–119 interaction with mitigation strategies targeting peak risk episodes 325 105, 212–213 261 interaction with other monitoring 17, 261 strategies 105–106 Most probable number (MPN) technique New Zealand 240 100, 103, 110 pathogens 104–105 MST see Microbial source tracking real-time technologies 109–119 Multi-layer depuration system 161 relation to pollution and illness events Multiple antibiotic resistance (MAR) 58 103–104 Multivariate regression systems, water research gaps 106 quality prediction 274–275 sample matrix 93–96 Mussels ( Mytilus spp.) sampling methods 98–99 depuration 147, 154–155, 200 sampling plans 96–98 international overview 168, 169 seawater 45, 93–94, 95–96 system design 160, 161, 162–163 shellfish 42, 45, 46–47, 94–95, 96 health risks 33 time series data sets 101–102 pathogens contaminating 23, 28 Microbiological standards production 11–12, 13, 219, 235 action when results are outside limits relative E. coli contamination 95 212–213, 227 relaying 147 depuration and relaying thresholds trade 13, 14, 15, 16, 17 149–151 depuration system validation 167, 200 National Interdepartmental Shellfish end-products see End-product standards Committee (NISC) 225 harvesting areas 42, 93, 94, 223, National reference laboratories 240–241, 254–255, 258–259 China 256 recreational waters 268–270 UK 212, 213, 215, 216 see also Faecal indicator organisms National Shellfish Sanitation Program Microbiological testing (NSSP), US 184, 197–201 accreditation and proficiency testing 101 depuration and relaying 148, 149, depuration system checks 166–167 150–151, 168 methods 100 harvesting area classification 92, 94 monitoring programmes 99–101 microbiological testing methods validation of alternative methods 100, 103 100–101 sanitary surveys 122–123, 124, 135–137 Microsporidia 28–29, 30 Nearshore modelling 289, 324 Mitigation measures 187, 248–249 catchment modelling linked to 285–287 Canada 227–228 see also Microbial modelling in coastal Scotland 212–214 environments Index 341

Netherlands see also Legislative and regulatory depuration 162–163, 169 approaches; Management, trade 16, 17 harvesting area New Zealand 233–244, 246–249, 263 Oocysts 27, 28 central competent authority 234, 246 Ostrea edulis see Oysters early warning systems 308–309 , dissolved, depuration systems 154 exports 14, 15, 16, 17, 19 Oysters management and regulatory approach causes of contamination 32 201, 235–243, 247–248, 322, 325 depuration 154–155, 160, 162, 167–168, shellfish production quantum 235, 247 169, 172, 200 New Zealand Food Safety Authority health risks 22, 24–25, 26, 33, 40 (NZFSA) 234, 246, 248 prevention of human illness 42, 43 90% compliance levels 94, 96, 103,149,150 production 11–12, 13, 219, 235 No-take zones 44 relative E. coli contamination 95 see also Prohibited areas relaying 146–147, 175 NordVal validation protocol 101 trade 14, 15, 16, 18 24, 45 Ozonation 147, 165–166 decay in coastal environments 304 detection methods 173 Packing 199 harvesting area monitoring 104–105 Parasites, human waterborne 27–30 heat inactivation 42–43 Parvoviruses 170 modelling in coastal environments 307 Pathogens 320 real-time monitoring 113 decay in coastal environments 304 removal by depuration 171, 172–173 end-product standards 167 removal by relaying 175 harvesting area monitoring 104–105 sanitary profiling 138 human faecal wastes 54 sewage effluents 126 management 42, 243 North Korea see Democratic People’s real-time monitoring technologies Republic of Korea 109–119 Norwalk-like viruses (NLVs) 21–22, 24, 33 removal by depuration 169–173 see also Noroviruses sanitary surveys 137–138 NSSP see National Shellfish Sanitation see also Bacteria; Viruses Program PCR see Polymerase chain reaction Pectens 13 Oceanic and Fisheries Bureaux, local, Peru 17 China 252, 255–256 Phages see Bacteriophages Official control monitoring programmes Pigs 55 184–201 Plesiomonas shigellosis 21–22, 24, 320 Canada 219–224, 248 Point sources of faecal pollution 5, 41, China 249–257 126–128, 135 funding 45–46, 189, 236 Polymerase chain reaction (PCR) India 262–263 esp assay 66 Mediterranean states 257–262 host-specific assays 57, 66, 67–68 minimum requirements 47 LTIIa and STII assays 66 New Zealand 233–244, 248 real-time quantitative (qPCR) 111, primary conflicts 46–47 112–114, 117–118 Scotland 205–216, 248 repetitive (rep-PCR) 57, 60, 61–62 342 Safe Management of Shellfish and HarvestWaters

tetracycline resistance (tetr )assays 69 microbial contamination models 299 virus detection 173 recreational water management studies Post-harvest contamination 27 275–276, 277 Post-harvest quality management 40 sanitary profiling and 130–135 Poultry 55, 118 sewage discharges and 126, 127, 128 Pre-harvest interventions 40–49 Random amplification of polymorphic Pregnancy 27 DNA (RAPD) 57, 63 Product recall procedures 214, 229–230 Raw shellfish 32–33, 34, 321 Product traceability see Traceability health risks 22–24, 26, 29 Production Real-time monitoring technologies areas see Harvesting areas 109–119, 325 Canada 219, 247 chemiluminescence 114–115 global 2, 11–12, 13, 320 enzymatic methods 115–117 New Zealand 235, 247 molecular methods 112–114 Scotland 246–247 Real-time prediction of water quality Proficiency testing, laboratory 101 7, 273–275 Prohibited areas 44 Recreational waters 267–289 Canada 224 current developments 270–288 New Zealand 242–243 guidelines development 268–270 United States 94, 198 linked catchment and nearshore Protozoan parasites, waterborne 27–30 modelling 285–287 identification methods 29–30 real-time prediction of water quality source identification 73 273–275 Public Health (Shell Fish) Regulations remediation of faecal indicator fluxes 1934 183 287–288 Public health risks see Health risks source apportionment studies 275–285 Public Health Service Act 1944 197 Regional Interdepartmental Shellfish Pulsed field gel electrophoresis (PFGE) Committee (RISC) 225 57, 62 Regulatory approaches see Legislative and Purification, controlled see Depuration regulatory approaches Relaying 5, 8, 145–146, 174–175, 187 Quahogs 168 Canadian controls 222, 223, 228 Quality Management Plans (QMPs) 226, Chinese controls 253, 254 227, 229 documentation 196 Quantitative microbial source apportion- historical perspective 146–148 ment (QMSA) 125, 128 regulation 148–152, 194 see also Source apportionment Relaying areas 194 Quantitative polymerase chain reaction classification 191 (qPCR) 111, 112–114, 117–118 monitoring 191 Quantitative reverse transcriptase recording and exchanging information polymerase chain reaction 192 (RT-qPCR) 113 Remediation studies 287–288 Quantitative risk analysis (QRA) 44 Remote approved areas, New Zealand 238, 240–241 Rainfall 48 Renal disease 25, 34 diffuse source pollution and 129, Repetitive extragenic palindromic (REP) 131–134 sequences 61 Index 343

Repetitive polymerase chain reaction annual reviews 123, 221–222, 239, (rep-PCR) 57, 60, 61–62 247–248 Republic of Korea (South Korea) aquaculture sites 138–139 production 12 assessment of input fluxes 125–135 trade 14, 15, 16, 18, 19 Canada 221, 247–248 Restricted areas catchment context 124–125 Canada 223, 226, 227–228 China 255 conditionally see Conditionally contents of aprofile 135–137 restricted areas international application 122–124 New Zealand 238, 241 New Zealand 237–239, 247–248 United States 94, 150, 198 pathogens 137–138 Restriction fragment length polymor- Scotland 208, 247–248 phisms (RFLPs) 62 Sanitization methods, post-harvest see Rhodococcus coprophilus 71 Treatment processes, post-harvest Ribotyping 57, 62 Satellite data, catchment delivery Risk assessment 102, 138, 248 modelling 277–285, 286 recreational waters 268 Scallops Risk management 44–46 production 11–12, 13, 219, 235 recreational waters 270 trade 13, 14, 15, 16, 17, 18 72–73, 175 Science, requirements 47–48 Ruditapes spp. see Clams Scotland 205–216, 246–249 Russian Federation 15 central competent authority 206, 246 recreational water management 273 Saccostrea commercialis see Oysters shellfish production quantum 206, 207, Salinity, depuration systems 155–156 246–247 enterica, phage typing 67 see also Food Standards Agency Salmonella spp. 24, 91–92, 263 Scotland; modelling in coastal environments 299 Scottish Environmental Protection Agency product standards 167, 195, 251, (SEPA) 212, 215, 273 258, 259 Scottish Fish Hygiene Working Group removal by depuration 170 210 Salmonella typhi 24–25 Seasonal patterns Sample stations 240 diffuse source pollution 129 Samples 240 sanitary profiling and 130–135 storage 99 Vibrio spp. infections 26 transport 98–99 viral contamination 172 Sampling Seawater methods 98–99 disinfection, depuration systems 147, plans 96–98 164–166 randomised 98 enumeration of indicator organisms 100 seawater 93–94, 95–96 microbiological monitoring 45, 93–94, shellfish 94–95, 96 95–96 spatial effects 97 microbiological standards 94, 149, 150, targeted 75, 98 223, 240–241, 251, 258 temporal effects 97–98 parameters, depuration systems Sanitary profiling (surveys) 6, 44, 155–157, 172 121–140, 191, 247–248, 322 quality, depuration systems 158 344 Safe Management of Shellfish and HarvestWaters

recycling, depuration systems 158 Shucking 199 sampling methods 98–99 Signs, real-time prediction 273 Secretory immunoglobulin A(sIgA), Singapore 13–14, 16, 19 faecal 74 16S rDNA assays 60, 67–68 Sediment particles, binding of micro- 259 organisms 305–306 Small round structured viruses (SRSV) Septicaemia, Vibrio vulnificus 25–26 see Noroviruses Sewage Sodium thiosulphate 164 bacterial and viral gastroenteritis related Source apportionment 275–287 to 22–25 linked catchment and nearshore discharges 126–128, 135 modelling 285–287 faecal indicator organisms 127 quantitative microbial (QMSA) management 43, 242–243 125, 128 pollution, legislative controls 185–186 satellite data for catchment delivery treatment 43, 126 modelling 277–285, 286 deficiencies 32, 54 Source identification 5–6, 51–80 recreational water management 275, microbial see Microbial source tracking 276, 277 non-microbial methods 73–75, 79 types 125 Source identifier organisms 70–75, 79–80 see also Human faecal wastes; Sources bacteria 70–71 of microbial pollution limitations of current 79–80 SGS-CSTC Standards Technical Services non-microbial alternatives 73–75, 79 Co., Ltd 252 protozoa 73 Shallow tank depuration system 159, 160 viruses 71–73 Shellfish Hygiene Directive (91/492/EEC) see also Faecal indicator organisms 183–184, 189 Source management 43 Shellfish Hygiene Regulations (853/2004 Source protection 43 and 854/2004), EU 183–184, 189, Source tracking see Source identification 190–197, 258 Sources of microbial pollution 5–6, 41–42, Shellfish tissues (flesh) 124 enumeration of indicator organisms 100 diffuse (non-point) 6, 41, 128–129, 130, microbiological monitoring 42, 45, 131–134, 135 46–47, 94–95, 96 identification see Source identification microbiological standards 93, 149, 150, intermittent 6, 41 240–241, 251, 254–255, 258–259 point 5, 41, 126–128, 135 real-time monitoring technologies South Korea see Republic of Korea 109–119 12 sampling methods 98–99 depuration 168 species differences in contamination trade 16, 17 94–95 Spatial variations, faecal indicator bacteria Shellfish Waters Directive 2006/113/EC counts 97 186 Spores, microsporidian 28–29 Shellfish:water ratio, depuration systems Stack depuration systems 161–162, 163 155 Standards, microbiological see Micro- Shigella spp. 24, 251 biological standards Ships, discharges from 43, 54, 243 Stanols, faecal 74 Shoreline surveys 122, 123 Staphylococcus aureus 27 Index 345

Statistical models 299–300 Transportation Sterols, faecal 74 harvested shellfish 27, 193, 196–197, STII PCR assay 66 199 Storage microbiological samples 98–99 samples 99 Treatment processes, post-harvest 8, 31, shellfish 193, 199 145–146, 187 Storm tank overflows (STO) 126, 127, Canadian controls 227–228 128, 276, 277 regulatory requirements 93, 94 Streptococci 258 Scottish controls 213 Syrian Arab Republic 261 see also Depuration; Heat treatment; Relaying Tapes spp. see Clams Tropical waters 7, 77 Targeted sampling 75, 98 17, 261 Temperature Turbidity, depuration systems 156–157 depuration systems 156, 158–159, 172 17, 261–262 harvested shellfish 199 Typhoid fever 24–25, 183, 218 relaying systems 175 depuration and 146, 147, 169–170 Temporal variations, faecal indicator bacteria counts 97–98 Ultraviolet (UV) irradiation 147, 164–165, Temporary closures 187 275 Canada 230, 238–239, 243, 247 Uncertainty, analytical 102–103 China 253 United Kingdom (UK) European Union 192, 213, 214, 215 depuration 147, 148, 155–156, 160–163, New Zealand 242, 247 169, 170, 193–194 United States 198 exports 16, 17 Temporary Regulation on Monitoring recreational water management 271, and Management for Hygiene of 273–275 the Bivalve Cultivation Environ- regulation 183, 190, 192–194 ment (TRMMHBCE), China source apportionment studies 275–287 251–256 see also Scotland Tetracycline resistance (tetr )assays 69 United States of America (USA) Thailand 263 adverse health outcomes 21–25 production 12 classification of harvesting areas 92, 94, trade 2, 13–14, 17, 18 124, 198–199 Total Maximum Daily Load (TMDL) depuration and relaying 146–152, 168, assessment 271–272 199–200 see Biotoxins legislation 184, 197–198 Toxoplasma gondii 27, 28 management of harvesting areas 42 Traceability, product 188, 196 microbiological monitoring 96, 98, 101 Canada 228–230 National Shellfish Sanitation Program Scotland 214 see National Shellfish Sanitation Trade 2, 13–19 Program global 11, 13 production 12 regional 13–18 recreational water management regulations 18–19 271–272, 274 Training, official control officers 216 trade 16, 17, 18–19 Transmissive stages, persistence 32 water pollution legislation 185 346 Safe Management of Shellfish and HarvestWaters

Validation, microbiological testing management interventions 42–43 methods 100–101 modelling contamination of shellfish Venerupis spp. see Clams 305 Venus spp. see Clams modelling in coastal environments 299, Vertical stack depuration systems 302–303, 307 161–162, 163 removal by depuration 148, 151–152, 25, 26, 262 170–173 Vibrio parahaemolyticus 25, 26, 40 removal by relaying 175 microbiological standards 251, 258 source identifier 71–73 prevention of human illness 42 see also specific viruses real-time monitoring 113 research in India 262 Wastewater Vibrio spp. 21–22, 33, 320 discharge of unprocessed 32, 54 harvesting area monitoring 104–105 gastroenteritis related to 22–25 human illness 25–26 sources of faecal pollution 53–54 Vibrio vulnificus 25–26, 34, 262, 320 treatment 32, 41, 43, 54 Viet Nam 17, 18 Water see Seawater Viruses 40 Water flow, depuration systems 155, 160 binding to sediment particles 305–306 Water Framework Directive (WFD), EU causing gastroenteritis 24 129, 186, 258, 271, 321–322 decay in coastal environments 303, 304 Water quality management 40–43 detection methods 173 Waters, harvesting see Harvesting areas end-product standards 167 Wild harvesting 2, 12 environmental contamination 297–298 Canada 219, 224 faecal wastes 53, 54 New Zealand 247 identification 68–69 Wildlife 55