Food-Borne Pathogens

Surveillance Networks 253 1980 as a result of the international awareness of the socioeconomic impacts of the increase of food-borne diseases. The Food and Agricultural Organization (FAO) of the United Nations/WHO Collaborating Center manages this program for Research and Training in Food Hygiene and Zoonoses under the responsibil- ity of the WHO European Centre for Environment and Health in Rome. The main objective of the program has been to provide information for the prevention and control of food-borne diseases in the region. Particular objectives include: 1. Identification of the causes and epidemiology of food-borne diseases in Europe. 2. Distribution of relevant information on surveillance. 3. Collaboration with national authorities in the identification of priorities in the establishment or reinforcement of their systems of prevention and control of food- borne diseases. Since its establishment in 1980, interest in the program has grown continually, reaching 51 countries at the end of 1998. The program is particularly interested in inviting all the countries in the WHO-EURO region to provide them with support in their efforts to reinforce their surveillance system. The system includes the fol- lowing countries: Albania, Andorra, Armenia, Austria, Azerbaijan, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Hungary, Iceland, Ireland, Israel, Italy, Kazakhstan, Kyrgyzstan, Latvia, Lithuania, Luxembourg, Malta, Monaco, the Netherlands, Norway, Poland, Portugal, Republic of Moldova, Romania, Russian Federation, Slovak Republic, Slovenia, Spain, Sweden, Switzerland, the former Yugoslav Republic of Macedonia, Turkey, Turkmenistan, Ukraine, United Kingdom, Uzbekistan, and Yugoslavia. Each participating coun- try designates a national contact point, usually at the health ministry, who collects and reports official data on food-borne outbreaks and other relevant information. The program compiles and reports the data. Country reports include: • General information on the surveillance systems in each country. • Data from statutory notification. • Information on epidemiologic investigated outbreaks. • Additional information. The general information section includes a description of the official sur- veillance and reporting system in the corresponding country. Statutory notification presents data from the official notification system in the countries. In a number of countries these data refer only to the number of cases notified to the health agencies with or without laboratory confirmation and without any further epidemiologic background information. The section on epidemiologically investigated outbreaks includes informa- tion on:

254 Molnar et al. • Number of affected people. • Causal agents. • Incriminated foods. • Place where food was contaminated, acquired, or consumed. • Factors contributing to the outbreak. This information is frequently based on the reports of laboratories involved in the investigation of food-borne incidents. Finally, the section of additional information may include comments from the national contact points and, when available, links to the participating coun- tries’ related Web sites with information on actual figures or trends in food- borne diseases. 2.2. FoodNet Estimates of the magnitude of food-borne illness in the United States have been imprecise. To quantify, better understand, and more precisely monitor food-borne illness, since 1996 the Food-Borne Diseases Active Surveillance Network (FoodNet) has collected data to monitor nine food-borne diseases in selected US sites (7). The Centers for Disease Control and Prevention (CDC) is actively involved in preventing food-borne disease. The CDC’s principal role in the interagency national Food Safety Initiative has been to enhance surveillance for and investigation of infections that are often food-borne. FoodNet is the principal food-borne disease component of the CDC’s Emerging Infections Program (EIP). FoodNet is a collaborative project among participating EIP sites, the US Department of Agriculture (USDA), and the US Food and Drug Administration (FDA) (8). The objectives of FoodNet are: (1) to describe the epidemiology of new and emerging bacterial, parasitic, and viral food-borne diseases of national impor- tance; (2) to more precisely determine the frequency and severity of food-borne diseases in the United States; and (3) to determine the proportion of food-borne disease caused by eating specific foods. FoodNet provides a precise measure of the laboratory-diagnosed cases of food- borne illness and performs additional surveys and studies to interpret trends over time. The FoodNet data indicate a decline in several of the major bacterial and par- asitic causes of food-borne illnesses and temporal variations in diagnostic prac- tices. The trends also may reflect implementation of disease prevention efforts. Laboratory-based surveillance programs such as FoodNet have significant lim- itations. The criterion for inclusion in the study is simply the physician’s decision to send a stool culture. Many enrolled cases may have had mild diarrheal illness- es that did not truly merit obtaining stool cultures; conversely, it is highly likely that the stool cultures were never sent on the majority of cases with bacterial enteropathogens. It is impossible in studies such as these to determine the rate of

Surveillance Networks 255 missed or inappropriate cases. Because microbiology laboratories report the cul- ture results, cases are usually not linked to clinical information. Most surveillance programs attempt to obtain data retrospectively only on patients with positive cul- ture results, leading to clinical information that is incomplete and of questionable accuracy. Despite these limitations, laboratory-based disease surveillance pro- grams are relatively inexpensive and provide a wealth of information about trends in food-borne illnesses (9). One such program of particular relevance to emer- gency physicians is the EMERGEncy IDNet. 2.2.1. EMERGEncy IDNet This program has collected data on patients with acute diarrheal illnesses, as well as other infections disease presentations (10,11). Although providing a supplement to programs such as FoodNet, these efforts are more labor-intensive and more expensive on a case-by-case basis and are more limited in scope than county- and state-based disease surveillance efforts (4). 2.3. PulseNet In 1995, the CDC, with the assistance of the Association of Public Health Laboratories (APHL), selected the state public health laboratories in Massachusetts, Minnesota, Texas, and Washington as area laboratories for a national molecular subtyping network for food-borne bacterial disease surveil- lance. This network later became known as PulseNet. PulseNet, which began in 1996 with 10 laboratories typing a single pathogen (Escherichia coli O157:H7), now includes 46 state and 2 local public health laboratories and the food safety lab- oratories of the FDA and the USDA. Four food-borne pathogens (E. coli O157:H7, nontyphoidal Salmonella serotypes, Listeria monocytogenes, and Shigella) are being subtyped, and other bacterial, viral, and parasitic organisms will be added. A national database of pulsed-field gel electrophoresis (PFGE) patterns is being assembled for food-borne bacterial pathogens. These databases reside on the PulseNet server at the CDC. For each bacterial pathogen, the normalized PFGE pattern is associated with a pattern database and the database of epidemi- ological and clinical information for isolates. Standardized protocols for food- borne bacterial pathogens were developed in priority order based on the ability of PFGE to discriminate among strains of the organism and the epidemiological utility of the resulting data. Standardized PFGE protocols have been developed for E. coli O157:H7, Salmonella enterica serotype Typhimurium, L. monocyto- genes, and Shigella species. 2.3.1. Role of PulseNet in Outbreak Investigations PulseNet plays several roles in detecting, investigating, and controlling out- breaks. Identification by PulseNet of an increase in a specific subtype of a

256 Molnar et al. pathogen may be an early indication of an outbreak. PFGE patterns submitted to the national database by participating laboratories may link apparently unre- lated cases that are geographically dispersed. Rapid sharing of PFGE subtyping data through PulseNet plays a critical role in linking apparently unrelated out- breaks and identifying a common vehicle. Although PulseNet has proven invaluable in detecting food-borne disease outbreaks and facilitating their investigation, molecular subtyping is an adjunct to epidemiologic investigation and not a replacement for it (12). 2.4. Enter-net Funded by the European Commission, Enter-net (formerly Salm-net) is an international surveillance system for Salmonella infections (including data on antibiotic resistance) and E. coli O157 infections. Microbiologists and epi- demiologists responsible for national laboratory-based surveillance of these pathogens in 15 European countries form the Enter-net network (13). Enter-net participants are working toward a common set of laboratory protocols, includ- ing procedures for serotyping, phage typing, and toxin typing. They report dis- ease cases to the international Enter-net database on a regular basis, through the Internet, by using standardized data fields. Every year, the participants from each member country attend a workshop to discuss technical issues and princi- ples of collaboration. Potential conflicts addressed at workshops include own- ership of data, confidentiality, outbreak control measures, and liability concerns (e.g., what happens when a food product is implicated by Enter-net as a vehi- cle of disease transmission) (14). 2.5. OzFoodNet In Australia, the Commonwealth Department of Health and Ageing estab- lished OzFoodNet in 2000 as a collaborative project with state and territory health authorities to provide better understanding of the causes and incidence of food-borne disease. OzFoodNet provides a network for responding to nationally important new and emerging food-borne diseases, monitoring the burden of these illnesses, and identifying the sources of specific food-borne out- breaks. OzFoodNet reports surveillance data for several bacterial pathogens and summary information from outbreaks potentially related to food and water (15). 2.6. Surveillance of Food-Borne Diseases in Other Countries Except for a few countries such as Japan, China, and Indonesia, relatively lit- tle in the way of surveillance of food-borne disease is carried out in Asia. In 2001 the National Food-Borne Monitoring and Surveillance System was estab- lished in China. Data on acute food-borne diseases were collected from 1992 to 2001. It was found that the microbial food-borne diseases had higher inci-

Surveillance Networks 257 dences, followed by chemical food-borne diseases. Infectious diseases such as cholera, viral hepatitis, bacterial and amoebic diarrhea, typhoid and paraty- phoid, and other infectious diarrhea must be reported. Food poisoning events, with more than 30 cases, or more than one death in an outbreak, or one that hap- pened in a school, must be reported directly to the Ministry of Health (16). The National Institute of Infectious Diseases in Japan under the Ministry of Health, Labor, and Welfare established the Infectious Disease Surveillance Center (IDSC) as the national center for infectious disease surveillance and for exchanging information on infectious diseases with other nations’ surveillance centers. As of January 1999, all patients who visit designated clinics or hospi- tals are reported to health centers (about 600 in the nation), which are then elec- tronically reported to the prefectural/municipal health departments and the IDSC. Most Latin American countries now consider food-borne disease important enough to justify some kind of surveillance scheme and are trying to develop better ways of determining numbers of cases and their causes. 3. Conclusions Twenty years ago, most food-borne outbreaks were local problems that typ- ically resulted from improper food handling practices. Outbreaks were often associated with individual restaurants or social events and often came to the attention of local public health officials through calls from affected persons. These persons, who may have known others who had become ill after eating a shared meal or visiting the same restaurant, provided health officials with much of the information needed to begin an investigation. Today food-borne disease outbreaks involve widely distributed food prod- ucts that are contaminated before distribution, resulting in cases that are spread over several states or countries. It is less common for ill persons to know oth- ers who were ill or to be able to identify a likely source of their infection. For these reasons, it is becoming increasingly important to be able to identify poten- tial common exposures through DNA fingerprinting of patient isolates. Health, food safety, industry, and agricultural agencies should develop closer links to share information about the occurrence of food-borne pathogens. State and ter- ritory health departments should continue to conduct rigorous checks on the quality of surveillance data maintained on surveillance databases. There is a need to establish the global food-borne disease surveillance network, and to share the information. Improvement of surveillance on a worldwide basis is essential to show the extent of the problem of food-borne disease in the many countries and regions with no existing system. Many of the weaknesses of laboratory surveillance programs are overcome by performing prospective, multicenter epidemiological investigations. Such

258 Molnar et al. studies allow investigators to clearly define enrollment criteria and obtain detailed clinical data from all patients at selected study centers suspected of having bacterial enteropathogens. References 1. Tauxe, R. V. (2002) Surveillance and investigation of food-borne diseases; roles for public health in meeting objectives for food safety. Food Control 13, 363–369. 2. World Health Organization. (2002) WHO fact sheet 124: Emerging foodborne dis- eases. WHO Geneva. 3. Leclerc, V., Dufour, B., Lombard, B., et al. (2002) Pathogens in meat and milk products: surveillance and impact on human health in France. Livestock Prod. Sci. 76, 195–202. 4. Karras, D. J. (2000) Incidence of foodborne illnesses: preliminary data from the foodborne diseases active surveillance network (FoodNet) [commentary]. Ann. Emerg. Med. 35, 92–93. 5. World Health Organization. Foodborne disease surveillance. www.who.int. 6. Schlundt, J. (2002) New directions in foodborne disease prevention. Int. J. Food Microbiol. 78, 3–17. 7. Centers for Disease Control and Prevention. (1999) Incidence of foodborne ill- nesses: preliminary data from the foodborne diseases active surveillance network (FoodNet)—United States. MMWR Morb. Mortal. Wkly. Rep. 48, 189–194. 8. Mead, P. S., Slutsker, L., Dietz, V., et al. (1999) Food related illness and death in the United States. Emerg. Infect. Dis. 5, 607–624 9. Tauxe, R. V. (1997) Emerging foodborne diseases: an evolving public health chal- lenge. Emerg. Infect. Dis. 3, 425–434. 10. Talan, D. J., Moran, G. J., Mower, W. R., et al. (1998) EMERGEncy ID Net: an emergency department-based emerging infections sentinel network. Ann. Emerg. Med. 32, 703–711. 11. Karras, D. J., Talan, D. A., Morran, G. J., et al. (1999) Characteristics associated with positive stool cultures in emergency department patients with bloody diar- rhoea [abstract]. Ann. Emerg. Med. 34, 52. 12. Swaminathan, B., Barrett, T. J., Hunter, S. B., Tauxe, R. V., and the CDC PulseNet Task Force. (2001) PulseNet the molecular subtyping network for foodborne bac- terial disease surveillance, United States. Emerg. Infect. Dis. 7, 382–389. 13. Yang, S. (1998) FoodNet and Enter-net: emerging surveillance programs for food- borne diseases. Emerg. Infect. Dis. 4, 457–458. 14. Levitt, A. (1998) The U.S.–EU Conference on Extension of the Salm/Enter-net Surveillance System for Human Salmonella and Escherichia coli O157 Infections. Emerg. Infect. Dis. 4, 502–503. 15. Ashbolt, R., Gregory, J., Givney, R., et al. (2002) Enhancing foodborne disease sur- veillance across Australia in 2001: the OzFoodNet Working Group. Comm. Dis. Intell. 26, 375–406. 16. World Health Organization. (2004) The National Surveillance System for Foodborne Disease in China. FAO/WHO Regional Conference on Food Safety for Asia and Pacific, Seremban, Malaysia, May 2004.

Index 259 Index A larval DNA preparation from fish, 223–226, 230 Aeromonas hemolysins, cytotoxicity assay, 10–12 primers, 222 genes, 4 restriction fragment length hemolytic activity assay, 10 polymerase chain reaction detection polymorphism and of genes, electrophoresis, 228, 230 agarose gel electrophoresis of Aspergillus, see Aflatoxin B1 products, 8, 9, 12 amplification reactions, 6, 7, 11 B chromosomal DNA preparation, 5, 6, 11 Bacillus cereus group, materials, 4, 5 identification criteria, 15, 16 primers, 6, 7 isolation, 16, 17 preparation from cultures, 10 species, 15 virulence, 3 sporulation, 17 toxins, Aflatoxin B1, cytotoxicity assay with Vero cells, Aspergillus species, 125 22, 23 high-performance liquid emetic activity assay, 23 chromatography measurement gene detection, with metabolites in rat DNA isolation, 20 hepatocytes, polymerase chain reaction, 20, 23 chromatography, 128–130 hemolytic activity assay, 22 glutathione conjugate standard immunoassay kits for detection, preparation, 128 applications, 91 hepatocyte incubation and toxicity biological activity correlation, 92 assay, 127, 130 kit sources and specificity hepatocyte isolation, 126, 127 comparison, 94–96 materials, 126, 130 nonspecific interference, 94 sample preparation, 127, 128 quality control, 93, 94 toxicity, 125, 126 recovery of toxin and spiked sample testing, 93, 94 Anisakis, reversed passive agglutination distribution and hosts, 218, 219 assay, 92, 93 isolation from fish, 221, 224, 225, 230 sandwich enzyme-linked restriction fragment length immunosorbent assay, 93 polymorphism, immunoassays, 20, 21 polymerase chain reaction, materials for detection, isolation, amplification reactions, 226, and testing, 18, 19 227, 231 purification, 21–23 259

260 Index types and food poisoning, 17, 18 cell lysis, 41, 43 BioMérieux API CAMPY, controls, 41–44 data analysis, 42, 44 Campylobacter biotyping, 31 gel electrophoresis, 41 Biotyping, see Campylobacter; Vibrio materials, 39, 40, 43, 44 botulism forms, 38 cholerae culture, Botulinum toxins, see Clostridium materials, 38, 39, 42, 43 sample collection, 40, 43 botulinum sample preparation, 40 Botulism, see Clostridium botulinum technique, 40, 41, 43 most probable number technique for C cell counting, 42 Cryobank Microbial Preservation Campylobacter, System, Campylobacter dormant phase in culture, 28 preservation, 32–34 infections, 27 Cryptosporidium, isolation, identification, and Cryptosporidium parvum gp60 gene preservation, polymorphism analysis, biotyping, gel electrophoresis of products, 213 BioMérieux API CAMPY, 31 polymerase chain reaction, 211–213 overview, 30, 31 cultivation, 204 catalase test for species detection, identification, 30 DNA extraction, Columbia blood agar preparation, FastDNA spin kit, 206 28, 29, 33 fecal sample preparation, 206, incubation conditions, 29 isolation, 30, 33 207, 213 materials, 28 fish sample preparation, 207 preservation, shellfish sample preparation, Cryobank Microbial Preservation System, 32–34 207, 214 FBP medium preparation, 32 water sample preparation, 207 Preston enrichment broth materials, 205, 206 preparation, 29, 33 overview, 204, 205 sample collection, rRNA gene analysis, swab samples, 29, 30 endonuclease restriction, 208, 209 whole-sample collection, 30 gel electrophoresis of Cathepsin L1, see Fasciola hepatica restriction digests, 209 Cholera, see Vibrio cholerae polymerase chain reaction, 208 Clostridium botulinum, epidemiology, 203–205 botulinum neurotoxins, D assays, 38 classification, 37, 38 DNA extraction, see Anisakis; Bacillus multiplex polymerase chain cereus group; reaction of genes, amplification conditions, 41, 43

Index 261 Cryptosporidium; Pseudoterranova; cell-free culture collection, 108 Trichinella; Vibrio cholerae materials, 102 quantitative analysis of toxin, E 108, 109 ELISA, see Enzyme-linked norovirus detection in food, 147, 148 immunosorbent assay Staphylococcus aureus toxins, see EMERGEncy IDNet, surveillance of Staphylococcus aureus food-borne disease, 255 Escherichia coli O157:H7, Enter-net, surveillance of food-borne diseases, 47 disease, 256 multiplex polymerase chain reaction Enteroviruses, for strain detection, characterization, agarose gel electrophoresis, 50, 53 antigenic characterization, 165 amplification reactions, 50 molecular characterization, 165, 166 interpretation, 51–54 cytopathic effect, 159 materials, 48 detection, primers and genes, 48–50, 53 feces extraction, 157, 158, 166 sample preparation, 50 materials, 154, 155 Shiga toxins, 47, 48 overview, 153, 154 strains in O157:H7 complex, 48 reverse transcriptase-polymerase Event tree analysis, risk assessment, chain reaction, conventional technique, 162, 239, 241 163, 167 nested technique, 163 F overview, 161, 162 real-time technique, 163–165 Fasciola hepatica, RNA extraction, 158, 159 cathepsin-L1 isolation and sample collection, 155, 166 characterization, solid food sample extraction, 158 denaturing gel electrophoresis, virus isolation in cell culture, 196, 197 159–161, 166, 167 enzyme-linked immunosorbent water sample concentration, assay diagnostics, 198, 199 electropositive filters, 155, fluorogenic substrate assay, 196 156, 166 materials, 192–194 ultracentrifugation, 156, 157, 166 parasite culture, 194, 195, 198, 199 Enzyme-linked immunosorbent assay purification from excretory- (ELISA), secretory products, 195, 196, 199 Bacillus cereus toxins, see Bacillus Western blot, 197, 198 cereus group zymography, 197 epidemiology, 191 cathepsin L1 from Fasciola protease secretion, 191, 192 hepatica, 198, 199 Fault tree analysis, risk assessment, GM1 enzyme-linked immunosorbent 237, 239 assay for cholera toxin assay,

262 Index FoodNet, surveillance of food-borne L disease, 254, 255 Listeria monocytogenes, G listeriosis epidemiology, 57, 58 subtyping with macrorestriction and Glutathione, aflatoxin B1 conjugation, pulsed-field gel 125, 126, 128 electrophoresis, agarose gel casting and loading, H 67, 68 agarose plug cell lysis and HAV, see Hepatitis A virus washing, 62, 63, 71 Hemolysins, see Aeromonas hemolysins bacteria culture, 60, 61, 70, 71 Hemolytic uremic syndrome, see electrophoresis system setup, 68, 71 materials, 58–60, 70 Escherichia coli O157:H7 overview, 60 Hepatitis A virus (HAV), restriction digestion, buffer preparation, 63, 65, 66 epidemiology, 172 enzyme preparation, 66, 67 nucleic acid sequence-based incubation conditions, 67 plug slice cutting, 66, 71 amplification, running conditions, 68 amplicon analysis, SDS/SeaKem Gold/proteinase K solution preparation, 61, 62, 71 agarose gel electrophoresis, staining and documentation, 68–70 178, 184 Liver fluke disease, see Fasciola microtiter plate hybridization, hepatica 181, 182 M Northern blot, 179, 181 amplification, Monte Carlo simulation, risk characterization, 245, 248 monoplex and biplex reactions, 177, 184 Most probable number (MPN), Clostridium botulinum primers, 176, 177, 184 counting in samples, 42 materials, 173, 174, 184 plaque assay for virus titering, MPN, see Most probable number Multiplex polymerase chain reaction, 175, 176 virus and cell propagation, 175 botulinum neurotoxin genes, High-performance liquid amplification conditions, 41, 43 cell lysis, 41, 43 chromatography (HPLC), controls, 41–44 aflatoxin B1 measurement with data analysis, 42, 44 metabolites in rat hepatocytes, gel electrophoresis, 41 chromatography, 128–130 materials, 39, 40, 43, 44 glutathione conjugate standard preparation, 128 Escherichia coli O157:H7 complex hepatocyte incubation and toxicity strain detection, assay, 127, 130 hepatocyte isolation, 126, 127 agarose gel electrophoresis, 50, 53 materials, 126, 130 sample preparation, 127, 128 HPLC, see High-performance liquid chromatography

Index 263 amplification reactions, 50 O interpretation, 51–54 materials, 48 O157:H7 complex, see Escherichia coli primers and genes, 48–50, 53 O157:H7 sample preparation, 50 Trichinella genotyping, 220, 222, OzFoodNet, surveillance of food-borne disease, 256 223, 228, 231 Vibrio cholerae, P biotyping, 112, 113 PCR, see Polymerase chain reaction detection in food samples, PFGE, see Pulsed-field gel 110–112 electrophoresis Plesiomonas shigelloides, N gastroenteritis, 74, 75 NASBA, see Nucleic acid sequence- geographic distribution, 73, 74 based amplification microbiology, 73 polymerase chain reaction detection Nematodes, see Anisakis; Pseudoterranova; Trichinella of rRNA genes, agarose gel electrophoresis of Noroviruses, classification, 135, 136, 144 products, 77, 79 concentration by filtration, 137, 139, amplification reaction, 77 140, 144, 145 materials, 75, 76, 78 detection in food, overview, 75 capillary isoelectric focusing-whole sensitivity and specificity, 78 column image detection, 148 specimen preparation, 76, 77, 79 enzyme-linked immunosorbent Polymerase chain reaction (PCR), see assay, 147, 148 nucleic acid sequence-based also Multiplex polymerase chain amplification, 148 reaction; Reverse transcriptase- reverse transcriptase-polymerase polymerase chain reaction, chain reaction, 138, 139, 141– Aeromonas hemolysin genes, see 144, 147 Aeromonas hemolysins RNA extraction, 137, 138, 140, Bacillus cereus toxin genes, 20, 23 141, 144, 146, 147 Cryptosporidium detection, see gastroenteritis epidemiology, 136, 172 Cryptosporidium genome open reading frames, 136 Plesiomonas shigelloides detection, isolation, 139, 144, 145 see Plesiomonas shigelloides restriction fragment length Nucleic acid sequence-based polymorphism, see Restriction amplification (NASBA), fragment length polymorphism Vibrio cholerae identification in contamination risks, 184 food samples, see Vibrio hepatitis A virus, see Hepatitis A cholerae Pseudoterranova, virus distribution and hosts, 218, 219 norovirus detection in food, 148 isolation from fish, 221, 224–226, 230 principles, 172 restriction fragment length rotavirus, see Rotavirus

264 Index polymorphism, gel casting and electrophoresis, polymerase chain reaction, 120, 121 amplification reactions, 226, 227, 231 interpretation, 121, 122 larval DNA preparation from materials, 105, 106 fish, 223–225, 230 overview, 118, 119 primers, 222 plug preparation, 119, 120, 122, 123 restriction fragment length restriction digestion, 120 polymorphism and PulseNet, electrophoresis, 228, 230 bacteria subtyping, 58, 255 formation and aims, 58, 255 Pulsed-field gel electrophoresis (PFGE), outbreak investigations, 255, 256 formats, 82 Listeria monocytogenes subtyping Q after macrorestriction, agarose gel casting and loading, Quantitative risk assessment, see Risk 67, 68 assessment agarose plug cell lysis and washing, 62, 63, 71 R bacteria culture, 60, 61, 70, 71 electrophoresis system setup, 68, 71 Restriction fragment length materials, 58–60, 70 polymorphism (RFLP), overview, 60 restriction digestion, Anisakis, buffer preparation, 63, 65, 66 polymerase chain reaction, enzyme preparation, 66, 67 amplification reactions, 226, incubation conditions, 67 227, 231 plug slice cutting, 66, 71 larval DNA preparation from running conditions, 68 fish, 223–226, 230 SDS/SeaKem Gold/proteinase K primers, 222 solution preparation, 61, 62, 71 restriction fragment length staining and documentation, 68–70 polymorphism and principles, 82, 118, 119 electrophoresis, 228, 230 Salmonella typing for epidemiology, agarose-embedded bacterial DNA Pseudoterranova, preparation, 84, 87 polymerase chain reaction, culture of bacteria, 83, 84, 87 amplification reactions, 226, electrophoresis conditions, 85–88 227, 231 interpretation and statistical larval DNA preparation from analysis, 86, 87 fish, 223–225, 230 materials, 82, 83 primers, 222 overview, 81, 82 restriction fragment length restriction digestion of plugs, 84, 85 polymorphism and sizing of fragments, 86 electrophoresis, 228, 230 Vibrio cholerae pulsotyping, Trichinella, polymerase chain reaction, amplification reactions, 228, 231 larval DNA preparation, 224– 226, 230, 231

Index 265 primers, 222, 223 amplification reaction, 77 restriction fragment length materials, 75, 76, 78 overview, 75 polymorphism and sensitivity and specificity, 78 electrophoresis, 228, 230 specimen preparation, 76, 77, 79 Reverse transcriptase-polymerase chain Ribotyping, Vibrio cholerae, reaction (RT-PCR), agarose gel electrophoresis and enterovirus detection, feces extraction, 157, 158, 166 Southern blot, 116, 117, 122 materials, 154, 155 DNA probe preparation, 114, 115, 122 overview, 153, 154 genomic DNA isolation, 116 reverse transcriptase-polymerase interpretation, 117 chain reaction, materials, 104, 105 conventional technique, 162, plasmid isolation, 113, 114 probe labeling, 115 163, 167 Risk assessment, nested technique, 163 definition, 235 overview, 161, 162 quantitative model development, real-time technique, 163–165 RNA extraction, 158, 159 data collection and accounting for sample collection, 155, 166 uncertainty, 242, 244, 245, 248 solid food sample extraction, 158 virus isolation in cell culture, deterministic risk assessment, 241 159–161, 166, 167 exposure assessment, water sample concentration, electropositive filters, 155, event tree analysis, 239, 241 fault tree analysis, 237, 239 156, 166 hazard characterization, 245 ultracentrifugation, 156, 157, 166 hazard identification, 237 norovirus detection in food, overview of steps, 236, 237, 248 reverse transcriptase-polymerase risk characterization, chain reaction, 138, 139, 141– hazard likelihood and severity 144, 147 RNA extraction, 137, 138, 140, calculation, 246 141, 144, 146, 147 Monte Carlo model running, RFLP, see Restriction fragment length polymorphism 245, 248 Ribosomal RNA (rRNA), sensitivity analysis, 246–248 Cryptosporidium gene analysis, software, 236 endonuclease restriction, 208, 209 stochastic risk assessment, 241, 242 gel electrophoresis of restriction regulatory requirements, 235 digests, 209 Rotavirus, polymerase chain reaction, 208 epidemiology, 172 Plesiomonas shigelloides gene nucleic acid sequence-based detection, amplification, agarose gel electrophoresis of amplicon analysis, products, 77, 79 agarose gel electrophoresis, 178, 184 microtiter plate hybridization, 181, 182

266 Index Northern blot, 179, 181 sandwich enzyme-linked amplification, immunosorbent assay, 93 monoplex and biplex reactions, Surveillance, food-borne disease, 177, 184 Asia, 256, 257 EMERGEncy IDNet, 255 primers, 176, 177, 184 Enter-net, 256 immunofluorescence for virus FoodNet, 254, 255 goals, 251, 252 titering, 176 Latin America, 257 materials, 173, 174, 184 OzFoodNet, 256 virus and cell propagation, 175 prospects, 257, 258 rRNA, see Ribosomal RNA PulseNet, 255, 256 RT-PCR, see Reverse transcriptase- World Health Organization, 252–254 polymerase chain reaction T S Trichinella, distribution and hosts, 219, 220 Salmonella, isolation from muscle, 221, 222, 225, diseases and transmission, 81 226, 230, 231 pulsed-field gel electrophoresis multiplex polymerase chain reaction typing for epidemiology, genotyping, 220, 222, 223, agarose-embedded bacterial DNA 228, 231 preparation, 84, 87 restriction fragment length culture of bacteria, 83, 84, 87 polymorphism, electrophoresis conditions, 85–88 polymerase chain reaction, interpretation and statistical amplification reactions, analysis, 86, 87 228, 231 materials, 82, 83 larval DNA preparation, 224– overview, 81, 82 226, 230, 231 restriction digestion of plugs, 84, 85 primers, 222, 223 sizing of fragments, 86 restriction fragment length polymorphism and Sensitivity analysis, risk electrophoresis, 228, 230 characterization, 246–248 transmission, 219 Southern blot, Vibrio cholerae V ribotyping, 116, 117, 122 Vibrio cholerae, Staphylococcus aureus, immunoassay cholera toxin mechanism of action, 100 kits for toxin detection, cholera transmission, 100 comparative genomics, 100 applications, 91 food analysis, biological activity correlation, 92 culture, kit sources and specificity/sensitivity biochemical characterization, 106, 107 comparison, 96 nonspecific interference, 94 quality control, 93, 94 recovery of toxin and spiked sample testing, 93, 94 reversed passive agglutination assay, 92, 93

Index 267 enrichment, isolation, and overview, 118, 119 presumptive identification, 106 plug preparation, 119, 120, media, 100, 101, 122 122, 123 sample processing, 106 restriction digestion, 120 GM1 enzyme-linked ribotyping, immunosorbent assay for agarose gel electrophoresis and cholera toxin, cell-free culture collection, 108 Southern blot, 116, 117, 122 materials, 102 DNA probe preparation, 114, quantitative analysis of toxin, 115, 122 108, 109 genomic DNA isolation, 116 polymerase chain reaction for interpretation, 117 materials, 104, 105 detection, plasmid isolation, 113, 114 biotyping, 112, 113 probe labeling, 115 materials, 103, 104, 122 serotyping, 102, 107, 108 multiplex polymerase chain microbiology and serogroups, 99, 100 reaction, 110–112 W overview, 109, 110 template preparation, 110 Western blot, cathepsin L1 from pulsed-field gel electrophoresis, Fasciola hepatica, 197, 198 gel casting and electrophoresis, WHO, see World Health Organization 120, 121 World Health Organization (WHO), interpretation, 121, 122 materials, 105, 106 surveillance of food-borne disease, 252–254