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Epidemiology and Diagnosis Allma Mater Studiiorum – Uniiversiità dii Bollogna DOTTORATO DI RICERCA IN Epidemiologia e Controllo delle Zoonosi Ciclo XXIV Settore Concorsuale di afferenza: 07/H3 Settore Scientifico disciplinare: VET/05 TITOLO TESI Evaluation of Microbial Contamination in Bivalve Mollusks: Epidemiology and Diagnosis Presentata da: Marco Grodzki Coordinatore Dottorato Relatore Prof. Giovanni Poglayen Dott.ssa Sara Ciulli Esame finale anno 2012 1 INDEX PAGE ACKNOWLEDGEMENTS 9 INTRODUCTION 10 AIM OF THE THESIS 11 CHAPTER 1 – GENERAL BIOLOGY OF BIVALVE MOLLUSKS AND THEIR ECONOMICAL IMPORTANCE 13 1.1 INTRODUCTION 14 1.2 SHELLFISH ANATOMY 16 1.2.1 SHELL AND MANTLE 16 1.2.2 ADDUCTOR MUSCLE 18 1.2.3 FOOT 20 1.2.4 GILLS 20 1.2.5 DIGESTIVE SYSTEM 23 1.2.6 CIRCULATORY SYSTEM 23 1.3 BIVALVE MOLLUSKS PRODUCTION 24 1.3.1 OYSTERS 25 1.3.1.1 PACIFIC OYSTER (CRASSOSTREA GIGAS) 25 1.3.1.2 AMERICAN OYSTER (CRASSOSTREA VIRGINICA) 26 1.3.1.3 EUROPEAN FLAT OYSTER (OSTREA EDULIS) 26 1.3.2 MUSSELS 27 1.3.2.1 BLUE MUSSELS (MYTILUS EDULIS) 27 1.3.2.2 MEDITERRANEAN MUSSELS (MYTILUS GALLOPROVINCIALIS) 27 1.3.3 CLAMS 27 1.3.3.1 GROOVED CARPET SHELL (RUDITAPES DECUSSATUS) 28 1.3.3.2 JAPANESE CARPET SHELL (RUDITAPES PHILIPPINARUM) 28 CHAPTER 2 – FOOD SAFETY ISSUES RELATED TO CONSUMPTION OF BIVALVE MOLLUSKS 29 2.1 LEGISLATION RELATIVE TO MICROBIOLOGICAL CONTROL OF BIVALVE MOLLUSKS 30 2.1.1 THE MICROBIOLOGICAL CONTROL OF LIVE BIVALVE MOLLUSKS IN THE EUROPEAN UNION 30 2.2 BIVALVE MOLLUSKS AND SANITARY PROBLEMATICS 32 2.2.1 INADEQUACY OF CURRENT EC LEGISLATION CONCERNING BIVALVE MOLLUSKS SAFETY 32 2 2.2.2 SEWAGE CONTAMINATION OF WATER ENVIRONMENT – IMPACT ON SAFETY OF BIVALVE MOLLUSKS 33 2.2.3 IMPACT OF NATURALLY OCCURRING VIBRIO BACTERIA ON BIVALVE MOLLUSK SAFETY 36 2.3 NOROVIRUS GASTROENTERITIS 36 2.3.1 ETIOLOGY 37 2.3.1.1 TAXONOMY 37 2.3.1.2 MORPHOLOGY 38 2.3.1.3 PHYSICAL AND CHEMICAL PROPERTIES 38 2.3.1.3.1 NUCLEIC ACID 39 2.3.1.3.2 PROTEINS 39 2.3.1.3.3 LIPIDS 41 2.3.1.3.4 CARBOHYDRATES 41 2.3.1.4 GENOME ORGANIZATION 41 2.3.1.5 REPLICATION 43 2.3.1.6 ANTIGENIC PROPERTIES 44 2.3.1.7 BIOLOGICAL PROPERTIES 45 2.3.2 PATHOGENESIS 45 2.3.3 SYMPTOMATOLOGY 46 2.3.4 PROPHYLAXIS 47 2.3.5 THERAPY 48 2.4 HEPATITIS CAUSED BY HEPATITIS A VIRUS 49 2.4.1 ETIOLOGY 49 2.4.1.1 TAXONOMY 49 2.4.1.2 MORPHOLOGY 50 2.4.1.3 PHYSICAL AND CHEMICAL PROPERTIES 50 2.4.1.3.1 NUCLEIC ACID 51 2.4.1.3.2 PROTEINS 51 2.4.1.3.3 LIPIDS 52 2.4.1.3.4 CARBOHYDRATES 52 2.4.1.4 GENOME ORGANIZATION 53 2.4.1.5 REPLICATION 54 2.4.1.6 ANTIGENIC PROPERTIES 54 2.4.1.7 BIOLOGICAL PROPERTIES 54 2.4.2 PATHOGENESIS 55 2.4.3 SYMPTOMATOLOGY 55 2.4.4 PROPHYLAXIS 56 3 2.4.5 THERAPY 57 2.5 INFECTION CAUSED BY VIBRIO PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS 57 2.5.1 ETIOLOGY 57 2.5.1.1 TAXONOMY 57 2.5.1.2 PHENOTYPIC AND MOLECULAR CHARACTERISTICS 59 2.5.1.3 GENOME ORGANIZATION 61 2.5.2 PATHOGENESIS 62 2.5.3 SYMPTOMATOLOGY 64 2.5.4 PROPHYLAXIS 66 2.5.5 THERAPY 67 CHAPTER 3 – EPIDEMIOLOGY OF PRINCIPAL VIRAL AND BACTERIAL SHELLFISH- BORNE DISEASES 68 3.1 EPIDEMIOLOGY OF NOROVIRUS GASTROENTERITIS 69 3.1.1 GEOGRAPHIC DISTRIBUTION 69 3.1.2 GENETIC SUSCEPTIBILITY TO NOV INFECTION 73 3.1.3 ENVIRONMENTAL FACTORS LEADING TO NOV EPIDEMICS 73 3.1.4 NOV MUTATION 74 3.1.5 MOLECULAR EPIDEMIOLOGY 78 3.1.6 TRANSMISSION 80 3.1.6.1 NOROVIRUS BIOACCUMULATION IN BIVALVE MOLLUSKS 81 3.1.6.2 NOROVIRUS TRANSMISSION FOLLOWING NATURAL DISASTERS 84 3.2 EPIDEMIOLOGY OF HEPATITIS A 85 3.2.1 GEOGRAPHIC DISTRIBUTION 85 3.2.2 ENVIRONMENTAL FACTORS LEADING TO HAV EPIDEMICS 86 3.2.3 MOLECULAR EPIDEMIOLOGY 88 3.2.4 TRANSMISSION 89 3.3 EPIDEMIOLOGY OF DISEASES DUE TO V. PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS. 90 3.3.1 GEOGRAPHIC DISTRIBUTION 90 3.3.2 ENVIRONMENTAL AND PHYSICAL FACTORS LEADING TO VIBRIO DISEASES 92 3.3.3 TRANSMISSION 92 4 CHAPTER 4 – DIAGNOSIS OF THE PRESENCE OF HUMAN ENTERIC VIRUSES AND VIBRIO BACTERIA IN BIVALVE MOLLUSKS 94 4.1 DETECTION OF HUMAN ENTERIC VIRUSES IN SHELLFISH WITH NON-MOLECULAR METHODS 95 4.2 DETECTION OF HUMAN ENTERIC VIRUSES IN SHELLFISH WITH MOLECULAR METHODS 96 4.2.1 CONCENTRATION OF HUMAN ENTERIC VIRUSES AND NUCLEIC ACID EXTRACTION METHODS 96 4.2.2 THE POLYMERASE CHAIN REACTION 100 4.2.2.1 INTRODUCTION TO PCR 100 4.2.2.2 DIFFERENT PCR METHODS TO ENHANCE THE SENSITIVITY OF PCR REACTION 102 4.2.3 DETECTION OF NOROVIRUS IN BIVALVE MOLLUSKS WITH PCR TECHNIQUES 106 4.2.4 DETECTION OF HAV IN BIVALVE MOLLUSKS WITH PCR TECHNIQUES 108 4.3 DETECTION OF V. PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS WITH CULTURAL AND MOLECULAR METHODS 108 CHAPTER 5 –SURVEY ON MICROBIAL CONTAMINATION BY VIBRIO PARAHAEMOLYTICUS, VIBRIO CHOLERAE, VIBRIO VULNIFICUS, NOROVIRUS AND HAV IN BIVALVE MOLLUSKS IN ITALY 112 5.1 MATERIALS AND METHODS 113 5.1.1 SAMPLING OF BIVALVE MOLLUSKS 113 5.1.2 RESEARCH OF VIBRIO PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS 117 5.1.2.1 PROCESSING OF BIVALVE MOLLUSKS 117 5.1.2.2 ISOLATION OF BACTERIAL STRAINS AND BIOCHEMICAL SCREENING 117 5.1.2.3 MOLECULAR IDENTIFICATION OF VIBRIO STRAINS 123 5.1.2.3.1 PREPARATION OF COLONIES 124 5.1.2.3.2 AMPLIFICATION OF TARGET GENES WITH MULTIPLEX PCR 124 5.1.2.3.2.1 IDENTIFICATION OF V. PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS STRAINS TO SPECIES LEVEL 125 5.1.2.3.2.2 RESEARCH OF VIRULENCE GENES FOR V. PARAHAEMOLYTICUS 126 5.1.2.3.2.3 RESEARCH OF VIRULENCE GENES FOR V. CHOLERAE 127 5.1.2.4 GEL ELECTROPHORESIS AND VISUALIZATION OF RESULTS 128 5.1.3 RESEARCH OF VIRUSES 128 5.1.3.1 DISSECTION OF SHELLFISH DIGESTIVE TISSUES 128 5.1.3.2 PROCESSING OF SHELLFISH DIGESTIVE TISSUES 128 5.1.3.3 NUCLEIC ACID EXTRACTION 129 5.1.3.4 RESEARCH OF NOROVIRUS BY RT-PCR 129 5.1.3.4.1 PRIMERS SELECTION 130 5 5.1.3.4.2 RT-SEMINESTED PCR FOR RESEARCH OF NOROVIRUS 131 5.1.3.4.3 GEL ELECTROPHORESIS AND VISUALIZATION OF RESULTS 131 5.1.3.5 RESEARCH OF NOROVIRUS BY RRT-PCR 132 5.1.3.6 RESEARCH OF HEPATITIS A VIRUS 133 5.1.3.6.1 PRIMERS SELECTION 133 5.1.3.6.2 RT-SEMINESTED PCR FOR RESEARCH OF HEPATITIS A VIRUS 133 5.1.3.6.3 GEL ELECTROPHORESIS AND VISUALIZATION OF RESULTS 135 5.1.4 SEQUENCING OF POSITIVE SAMPLES 135 5.1.4.1 PURIFICATION OF POSITIVE PCR PRODUCTS 135 5.1.4.2 SEQUENCING REACTION 135 5.1.4.3 PURIFICATION OF SEQUENCING REACTION 136 5.1.4.4 SEQUENCING 136 5.1.5 ANALYSIS OF SEQUENCES 137 5.1.5.1 VISUALIZATION AND CORRECTION OF SEQUENCES 137 5.1.5.2 ALIGNMENT OF SEQUENCES AND CONSTRUCTION OF A PHYLOGENETIC TREE 137 5.2 RESULTS 137 5.2.1 DETECTION OF V. PARAHAEMOLYTICUS, V. CHOLERAE AND V. VULNIFICUS 137 5.2.2 DETECTION OF NOV AND HAV 140 5.2.3 ANALYSIS OF NOV AND HAV SEQUENCES 143 5.3 DISCUSSION 147 CHAPTER 6 – BIOACCUMULATION OF NOROVIRUS BY DIFFERENT SPECIES OF BIVALVE MOLLUSKS 156 6.1 MATERIALS AND METHODS 157 6.1.1 BIOACCUMULATION EXPERIMENTS 157 6.1.1.1 CONDITIONS OF THE EXPERIMENTS 157 6.1.1.2 PREPARATION OF VIRAL SOLUTIONS 158 6.1.1.3 ANALYZED BIOACCUMULATION EXPERIMENTS 159 6.1.2 ANALYSIS OF BIOACCUMULATED BIVALVE MOLLUSKS 160 6.1.2.1 DISSECTION OF TISSUES AND HEMOLYMPH COLLECTION 160 6.1.2.2 PROCESSING OF SHELLFISH TISSUES 163 6.1.2.3 NUCLEIC ACID EXTRACTION 164 6.1.2.4 RRT-PCR AMPLIFICATION 167 6.1.2.4.1 SELECTION OF PRIMERS AND PROBES 167 6.1.2.4.2 RRT-PCR CONDITIONS 168 6.1.3 ANALYSIS OF RESULTS 169 6 6.1.3.1 QUANTIFICATION OF VIRAL NUCLEIC ACIDS 169 6.1.3.2 ANALYSIS OF VIRAL INTAKE BY DIFFERENT SHELLFISH TISSUES 170 6.2 RESULTS 170 6.2.1 BIOACCUMULATION NO. 1 (APRIL 2011) 170 6.2.2 BIOACCUMULATION NO. 2 (MAY 2011) 172 6.2.3 BIOACCUMULATION NO. 3 (NOVEMBER 2011) 173 6.2.4 BIOACCUMULATION NO. 4 (JANUARY 2012) 176 6.2.5 BIOACCUMULATION NO. 5 (FEBRUARY 2012) 179 6.2.6 SUMMARY 179 6.3 DISCUSSION 183 CHAPTER 7 – EVALUATION OF VIRAL CONTAMINATION IN BIVALVE MOLLUSKS FOLLOWING XYNTHIA TEMPEST 188 7.1 MATERIALS AND METHODS 189 7.1.1 DYNAMICS OF XYNTHIA TEMPEST 189 7.1.2 CONSEQUENCES OF THE TEMPEST 190 7.1.3 RESEARCH OF HUMAN ENTERIC VIRUSES IN THE AREAS HIT BY XYNTHIA 191 7.1.3.1 SAMPLING OF BIVALVE MOLLUSKS 191 7.1.3.2 DISSECTION OF SHELLFISH DIGESTIVE TISSUE 194 7.1.3.3 PROCESSING OF DIGESTIVE TISSUE SAMPLES 194 7.1.3.4 NUCLEIC ACID EXTRACTION 195 7.1.4 SELECTION OF TARGET VIRUSES 196 7.1.4.1 NOROVIRUS 196 7.1.4.2 SAPOVIRUS 197 7.1.4.3 HEPATITIS A VIRUS 197 7.1.4.4 HEPATITIS E VIRUS 198 7.1.4.5 ENTEROVIRUS 199 7.1.4.6 ROTAVIRUS 199 7.1.4.7 AICHI VIRUS 200 7.1.5 SELECTION OF PRIMERS AND PROBES FOR DETECTION OF SELECTED VIRUSES 200 7.1.6 RRTPCR AMPLIFICATION 201 7.1.7 VIRUS DETECTION AND QUANTIFICATION, ANALYSIS OF RESULTS 202 7.2 RESULTS 203 7.2.1 E.COLI ANALYSIS 203 7.2.2 VIRAL CONTAMINATION OF SHELLFISH SAMPLES 204 7 7.3 DISCUSSION 207 FINAL CONSIDERATIONS 209 BIBLIOGRAPHY 210 APPENDIX 1.
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