clinical characteristics of infection, 224

531 A

ActA, Listeria virulence mechanisms, 31 Adenovirus

classification, 217

clinical characteristics of infection, 224

diagnosis, 218–220

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221 Aflatoxin

biosynthetic pathways enzymes, 361 gene clusters, 362

genomics analysis, 363, 366 regulation, 361, 363

diseases, 358, 359 economic impact, 360

food safety and regulation, 360, 361 fungi

development and

aflatoxin production, 363–365 mutant studies, 364

physiology, 356, 357 history of study, 355, 356 toxicology, 357, 358

treatment and control, 359, 360 types, 356, 357

AFLP, see Amplified fragment length polymorphism

Aggregation substance, Enterococcus virulence factor, 161

Aichi virus

classification, 218

clinical characteristics of infection, 224

diagnosis, 218, 220

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221

Ail, Yersinia virulence factor, 91

Amplified fragment

length polymorphism (AFLP), principles, 501

Animal production antimicrobials alternatives

prevention

competitive exclusion, 422–425 immunomodulators, 421, 422 metabolic pathway targeting, 425 vaccines, 420, 421

prospects, 428 rationale, 419, 420 treatment

bacteriophage, 426, 427 programmed cell

death targeting, 426 applications

coccidostats, 406

growth promotion, 406, 407 overview, 405–408

therapeutic use, 406 bans

recommendations, 410 effects, 410, 411

consumption data, 408, 409 development, 426

resistance epidemiology, 411–413 Antibiotic therapy

Enterococcus resistance

food animals, 166, 167 food bacteria strains, 167 gene transfer, 167, 168 humans, 165, 166 prevention, 169 treatment, 163, 164

enterohemorrhagic Escherichia coli resistance, 15, 16

treatment, 12

food animals, see Animal production

antimicrobials

Listeria monocytogenes resistance, 33, 34 treatment, 33 Vibrio

resistance epidemiology, 138, 139 treatment, 137, 138

Yersinia

resistance epidemiology, 97–99 treatment, 96, 97

Antimicrobials, see Animal production antimicrobials; Antibiotic therapy AP-PCR, see Arbitrarily primed PCR Arbitrarily primed PCR

(AP-PCR), principles, 501, 502 Astrovirus

classification, 216, 217 diagnosis, 218–220 B

Bacillus cereus

food irradiation, 473

microbial risk assessment, 449 Bacteriophage, therapeutic prospects,

426, 427

Botulism, see Clostridium botulinum Campylobacter

food irradiation, 465

microbial risk assessments, 449, 450 C

CCF, animal production, 424, 425 CE, see Competitive exclusion CF3, animal production, 424 Cholera, see Vibrio

Cholera toxin, features, 133, 134 Cimetidine, scombroid fish poisoning

management, 378 Clostridium botulinum

botulism toxin

antitoxin therapy, 56 assay in mouse, 43, 44, 497 characteristics and actions, 51–54 immunoassay, 46, 47

mass spectrometry, 46, 47 molecular genetics, 54

polymerase chain reaction detection of gene, 46, 47

types, 42

clinical features of botulism, 54–56

diagnostic criteria, 45, 46 epidemiological typing, 47 foodborne outbreaks, 48–50 food irradiation, 474

identification and isolation, 44, 45 infant botulism, 49, 51, 57

reservoirs, 47, 48 taxonomy, 42 transmission, 41

treatment and control, 56 Clostridium perfringens

β-toxins, 68, 69

clinical features and diagnosis, 69 diseases, 57

enterotoxin detection, 62, 63 features, 67, 68 epidemiology, 58 foodborne outbreaks

food poisoning, 64–67

infectious and antibiotic-associated diarrhea, 67

necrotizing enteritis, 67 food irradiation, 474 history of study, 57, 58 identification, 58, 59 isolation, 60, 61 reservoirs, 63, 64 taxonomy, 58

treatment and control, 69, 70 typing, 61, 62

ComBase, microbial risk assessment, 440

Competitive exclusion (CE), animal production, 422–425 Coronavirus

classification, 217, 218

clinical characteristics of infection, 221 diagnosis, 218, 220

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221 Cryptosporidium

classification, 233–236, 266

clinical features of infection, 263, 264 foodborne outbreaks, 259

identification

enzyme-linked immunosorbent

assay, 240

fecal samples, 240–242 flow cytometry, 242 food assays, 247–250 polymerase chain reaction

inhibitors, 243

oocyst DNA extraction, 244, 245 oocyst assay, 251, 252

sensitivity, 241, 246 targets, 245

immune response, 261, 262 infectious dose, 260 infectivity assays, 252 life cycle, 236–240 oocyst viability assays

molecular assays, 251, 252 morphology, 250, 251 survival, 256–258 pathogenicity, 260, 261 prevention, 267

resistance epidemiology, 265 transmission routes

airborne, 254

animal-to-person, 253, 254 drinking water, 254 food, 254–256 insects, 256

person-to-person, 253 sexual, 256

treatment, 264, 266 virulence, 262, 263 Cyclospora

classification, 277–279

clinical features of infection, 293, 294 foodborne outbreaks, 290–292 identification

fecal detection, 280–284 food detection, 284–287

polymerase chain reaction, 283, 284, 286, 287, 295, 296 immune response, 292, 294 infectious dose, 292 life cycle, 279 oocyst

infectivity assays, 287, 288 survival, 290

viability morphology assay, 287 pathogenicity, 292

transmission routes airborne, 289

animal-to-person, 288 drinking water, 288, 289 food, 289, 290

insects, 290

person-to-person, 288 treatment, 294, 295 virulence, 293

Cytolysin, Enterococcus virulence factor, 161 D

Daraprim, Toxoplasma gondii management, 348 Diphenhydramine,

scombroid fish

poisoning management, 378

DNA microarray,

pathogen identification and characterization, 493, 494 E

ECRA, see Escherichia coli O157:H7 risk assessment

Electron microscopy, gastroenteric virus detection, 219, 220

ELISA, see Enzyme-linked immunosorbent assay Enterococcus classification

and identification, 157, 158 clinical features of infection

bacteremia, 163 endocarditis, 163 rare infections, 163 soft-tissue infection, 163 urinary tract infection, 162, 163 diseases, 157

foodborne outbreaks, 160 reservoirs

animals and insects, 159 foods, 159

humans, 160 probiotics, 159

soil, plants, and water, 159 resistance

epidemiology

food animals, 166, 167 food bacteria strains, 167 humans, 165, 166

gene transfer, 167, 168

prevention, 169 treatment

adjunctive therapy, 164 antimicrobial therapy, 163, 164 virulence factors, 161, 162

Enterohemorrhagic Escherichia coli, see Escherichia coli

Enterotest

, Giardia detection, 309, 310 Enzyme-linked immunosorbent assay

(ELISA)

Clostridium perfringens enterotoxin detection, 62, 63

Cryptosporidium detection, 240 formats, 487, 488

Giardia detection, 307, 308 interference, 488

principles, 487 toxin detection, 496 Escherichia coli

enterohemorrhagic bacteria acid tolerance, 16

antimicrobial resistance, 15, 16 clinical features of infection

sequelae, 11, 12 spectrum, 11 treatment, 12

O157:H7 foodborne outbreaks documented incidences, 7–9 ground beef, 6, 10

juice, 10, 11 produce, 10 water, 11 pathogenesis

infectious dose, 13

susceptible populations, 12, 13 reservoirs

cattle, 5

food animals, 5, 6 humans, 6

pets and wildlife, 6 virulence factors

intimin, 15

loss of enterocyte effacement, 14 p0157, 15

Shiga toxin, 13, 14 Tir, 15

food irradiation beef, 466 juice, 466, 467

overview, 465, 466 poultry, 466 produce, 467, 468 sprouts and seeds, 467 general characteristics, 1, 2

Hazard Analysis and Critical Control Point Program, 388–390, 392, 398, 399

history of study, 1

microbial risk assessments, 450 pathotypes

diffuse-adhering, 2 entero-aggregative, 4, 5 enterohemorrhagic, 5 enteroinvasive, 4 enteropathogemic, 2, 3 enterotoxigenic, 4 Escherichia coli O157:H7

risk assessment (ECRA) conclusions, 447, 448 impact, 447, 448 process, 446, 447 scope, 445, 446

ESP, Giardia virulence factor, 322, 323 Esp, Enterococcus virulence factor,

161, 162 F

Flow cytometry,

Cryptosporidium detection, 242 Fluorescence resonance energy transfer

(FRET), amplicon detection, 490 Food irradiation

allowed uses

arthropod disinfection, 459

dehydrated enzyme preparations, 459 growth and maturation inhibition, 458 poultry, 459

seeds, 459, 460 shell eggs, 459

space-flight programs, 459 spices, 459

Trichinella spiralis, 458 Bacillus cereus control, 473 Campylobacter control, 465 Clostridium control, 474 effectiveness factors, 457, 458 Escherichia coli control

beef, 466

juice, 466, 467 overview, 465, 466 poultry, 466 produce, 467, 468 sprouts and seeds, 467 historical perspective, 457 Listeria control

dairy products, 469

modified atmosphere packaging, 469 overview, 468

poultry, 470, 471

ready-to-eat foods, 469, 470 temperature effects, 468, 469 parasite control, 474, 475 radiation units, 458 regulation, 458 Salmonella control

atmosphere effects, 461 competition and growth rates

of survivors, 461, 462 dose rate, 462

eggs, 463, 464

fruits and vegetables, 464 juice, 464, 465

poultry, 460

serovar differences, 461 substrate effects, 463

temperature effects on radiation resistance, 460, 461

virulence outcomes, 462 water effects, 462, 463 Staphylococcus control, 472, 473 Vibrio control, 471

Yersinia control, 471, 472 Food Safety

and Inspection Service (FSIS) HACCP Program,

see Hazard Analysis and Critical Control Point Program

mission and activities, 383, 384 FRET, see Fluorescence resonance energy

transfer

FSIS, see Food Safety and Inspection Service

G

Gelatinase,

Enterococcus virulence factor, 161 Gel diffusion assay, toxin detection, 497

Giardia

classification, 303–306, 326 clinical features of infection, 323 cyst viabilty assays

molecular assays, 313 morphology, 312, 313 survival in water, 318 economic impact, 315

foodborne outbreaks, 318, 319 identification

Enterotest

, 309, 310

enzyme-linked immunosorbent assay, 307, 308

fecal detection, 307–310 food detection, 310, 311 polymerase chain reaction,

308, 311, 326 immune response, 321, 322 infectious dose, 320 infectivity assays, 313, 314 life cycle, 306, 307

pathogenicity, 320, 321

resistance epidemiology, 324–326 transmission

airborne, 317

animal-to-person, 316 drinking water, 316, 317 food, 317, 318

insects, 318

person-to-person, 316 risk factors, 314, 315 sexual, 318

treatment, 323, 324 vaccination, 324 virulence, 322, 323 H

HACCP Program, see Hazard Analysis and Critical Control Point Program HAV, see Hepatitis A virus

Hazard Analysis and Critical Control Point (HACCP) Program implementation at Food Safety

and Inspection Service, 385, 395 industry

implementation assistance

food safety assessments, 394, 395 in-depth verification teams, 392,

393

intensified verification testing, 393, 394

Technical Assessment Groups, 392 responsibilities, 386, 387

international food safety harmonization, 396, 397 regulation, 396

microbiological testing

Escherichia coli, 388–390, 392, 398, 399 Listeria, 399

National Advisory Committee on Microbiological

Criteria for Foods performance standards evaluation, 389, 390 raw products, 400

ready-to-eat products, 400, 401 Salmonella, 387, 388, 390, 397, 398 origins, 384, 385

principles, 385, 386 prospects, 397–401

Hemolysin, Vibrio virulence factor, 132, 133, 135

Hemolytic uremic syndrome, see Escherichia coli

Hemorrhagic colitis, see Escherichia coli Hepatitis A virus (HAV)

biotypes, 175, 176 characteristics, 175

clinical features of infection, 182, 183 diagnosis and detection, 183, 184 epidemiology, 177, 178

outbreaks foodborne

food handlers, 181, 182 fruits and vegetables, 180, 181 shellfish, 180

risk factors, 178, 179 waterborne, 179 pathogenesis, 183 prevention and control

foodborne transmission food handlers, 187 fruits and vegetables, 186 indicator organisms, 187 shellfish, 185, 186 general measures, 184 immunoprophylaxis

active, 184, 185 passive, 185

stability

acid resistance, 176 chlorine resistance, 177 environmental survival, 176 temperature resistance, 176 Hepatitis E virus (HEV)

characteristics, 187, 188 classification, 189

clinical features and pathogenicity humans, 193, 194

nonhuman primates, 194 pigs, 194, 195

diagnosis and detection, 195 epidemiology, 189–191 foodborne infection, 192, 193 reservoirs, 191, 192

treatment and prevention, 195, 196 vaccines, 196

HEV, see Hepatitis E virus

Histamine fish poisoning, see Scombroid fish poisoning

Hyaluronidase, Enterococcus virulence factor, 161

I

Infant botulism,

see Clostridium botulinum

Intimin, enterohemorrhagic Escherichia coli virulence factor, 15

Invasin, Yersinia virulence factor, 91 Irradiation, see Food irradiation Lipopolysaccharide (LPS), Vibrio, 132 Listeria

classification, 27, 28 epidemiology

animals, 34 humans, 34, 355 prevalence in food, 34 food irradiation

dairy products, 469

modified atmosphere packaging, 469 overview, 468

poultry, 470, 471

ready-to-eat foods, 469, 470 temperature effects, 468, 469 Hazard Analysis and Critical Control

Point Program, 399

history of study, 27

identification, 28

Listeria monocytogenes

antimicrobial resistance, 33, 34 clinical features of infection, 31–33 foodborne outbreaks, 29, 30 reservoirs, 28, 29

treatment, 33

microbial risk assessments, 450, 451 mortality, 35, 36

prevention, 35

virulence factors, 30, 31

Listeria monocytogenes risk assessment (LMRA)

conclusions, 444, 445 impact, 444

process, 444 scope, 443 L

Listeriolysin O,

Listeria virulence mechanisms, 31 LMRA, see Listeria monocytogenes risk

assessment Loss of enterocyte

effacement, enterohemorrhagic Escherichia coli virulence factor, 14 LPS, see Lipopolysaccharide

M

Mass spectrometry,

botulism toxin detection, 46, 47 Metronidazole, Giardia management, 324 Microbial risk assessment (MRA)

Escherichia coli O157:H7 risk assessment conclusions, 447, 448 impact, 447, 448 process, 446, 447 scope, 445, 446

expertise requirements, 437, 438 historical perspective, 435, 435 Listeria monocytogenes

risk assessment conclusions, 444, 445 impact, 444

process, 444 scope, 443

outcome applications, 442 process

exposure assessment, 439, 440

hazard characterization, 440, 441 hazard identification, 439 risk characterization, 441, 442 prospects, 448, 452, 453

risk analysis relationship assessment, 437 management, 437 planning, 436, 437 types

geographic assessments, 439 overview, 438

product pathway risk assessments, 438

relative risk rankings, 438, 439 risk-risk assessments, 439 MLST, see Multilocus sequence typing MLVA, see Multilocus variable number

tandem repeat analysis

Molecular beacon, amplicon detection, 491

MRA, see Microbial risk assessment Multilocus sequence typing (MLST)

principles, 503

target genes in pathogens, 504 Vibrio typing, 128

Multilocus variable number tandem repeat analysis (MLVA), principles, 504

Mycotoxins, see Aflatoxin Myf, Yersinia virulence factor, 92 N

NASBA, see Nucleic acid sequence-based assay

Necrotizing enteritis, see Clostridium perfringens

Nitazoxanide (NTZ)

Cryptosporidium management, 264–266

Giardia management, 324 Norovirus

classification, 216

clinical characteristics of infection, 223, 224

diagnosis, 218, 219, 225

foodborne outbreaks, 221, 222

pathogenicity, 222, 223

reservoirs, 220, 221

NTZ, see Nitazoxanide

Nucleic acid sequence-based assay (NASBA),

pathogen detection, 492 O

O157:H7, see Escherichia coli

Oocyst, see Cryptosporidium; Cyclospora;

Giardia; Toxoplasma gondii P

PCD, see Programmed cell death PCR, see Polymerase chain reaction Peptide nucleic acid (PNA), probes

for amplicon detection, 491, 492 PFGE,

see Pulsed-field gel electrophoresis Phage typing, principles, 498, 499 Picobirnavirus

classification, 218 diagnosis, 218, 220

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221

Plasmid typing, principles, 499

PlcB, Listeria virulence mechanisms, 31 PNA, see Peptide nucleic acid

Polymerase chain reaction (PCR) botulism toxin gene detection, 46 Clostridium perfringens enterotoxin

gene detection, 63, 69 Cryptosporidium detection

inhibitors, 243 oocyst assay, 251, 252

oocyst DNA extraction, 244, 245 sensitivity, 241, 246

targets, 245

Cyclospora detection, 283, 284, 286, 287, 295, 296

gastroenteric virus detection, 219, 220 Giardia detection, 308, 311, 326 hepatitis A virus detection, 184 hepatitis E virus detection, 195 multiplexed assays, 489, 492 principles, 489

prospects, 502, 503

real-time polymerase chain reaction, 490–493

reverse transcriptase-polymerase chain reaction, 493

toxin gene detection, 494–496 typing

arbitrarily primed PCR, 501, 502 random amplified polymorphic

DNA PCR, 501, 502 repetitive element PCR, 502 Vibrio identification, 122–125 Programmed cell death

(PCD), therapeutic targeting, 426 Pulsed-field gel electrophoresis (PFGE)

principles, 500

Vibrio typing, 126–128 Pyrimethamine,

Toxoplasma gondii management, 348

R

Radiation pasteurization, see Food irradiation

Random amplified polymorphic DNA PCR (RAPD-PCR), principles, 501, 502

RAPD-PCR,

see Random amplified polymorphic DNA PCR

Rep-PCR, see Repetitive element PCR Repetitive element PCR

(Rep-PCR), principles, 502 Resistance,

see Animal production antimicrobials;

Antibiotic therapy

Restriction fragment length polymorphism (RFLP)

principles, 499, 500 Vibrio typing, 126

Reverse passive latex agglutination (RPLA) Clostridium perfringens enterotoxin

detection, 62, 63 toxin detection, 496

RFLP, see Restriction fragment length polymorphism

Risk assessment,

see Microbial risk assessment Rotavirus

classification, 216

clinical characteristics of infection, 224

diagnosis, 218–220

foodborne outbreaks, 221, 222

pathogenicity, 222, 223 reservoirs, 220, 221 RPLA, see Reverse passive

latex agglutination Salmonella

food irradiation atmosphere effects, 461 competition and growth

rates of survivors, 461, 462 dose rate, 462

eggs, 463, 464

fruits and vegetables, 464 juice, 464, 465

poultry, 460

serovar differences, 461 substrate effects, 463 temperature effects

on radiation resistance, 460, 461 virulence outcomes, 462

water effects, 462, 463

Hazard Analysis and Critical Control Point Program, 387, 388, 390, 397, 398

microbial risk assessments, 451, 452 S

Sapovirus

classification, 216

clinical characteristics of infection, 223, 224

diagnosis, 218, 219

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221 SARS, see Coronavirus Scombroid fish poisoning

barrier disruption hypothesis, 376, 377

clinical features, 377, 378 diamine oxidase inhibitors

in pathogenesis, 376 dose effects, 378

etiology, 375

foodborne outbreaks, 375, 376

histamine potentiator hypothesis, 376 reservoirs, 375

resistance epidemiology, 378 treatment, 378

Seed, irradiation treatment, 459, 467

Serotyping, principles, 498 Shiga toxin,

enterohemorrhagic Escherichia coli virulence factor, 13, 14

Skin permeable factor (SPF), Vibrio virulence factor, 133 SPF, see Skin permeable factor

Staphylococcus, food irradiation, 472, 473 Strand displacement

amplification (SDA), pathogen detection, 492, 493

Sulfadiazine,

Toxoplasma gondii management, 348

T

Tir, enterohemorrhagic Escherichia coli virulence factor, 15

TLRs, see Toll-like receptors Toll-like receptors (TLRs),

innate immunity, 422 Torovirus

classification, 217, 218 diagnosis, 218, 220

foodborne outbreaks, 221, 222 pathogenicity, 222, 223 reservoirs, 220, 221 Toxoplasma gondii

characteristics, 337, 339 classification, 337, 342 clinical features, 345–348 food irradiation, 475 life cycle, 339, 341 pathogenicity, 344, 345 prevention and control, 348 transmission, 342–344 treatment, 348

ToxR, Vibrio virulence factor, 134 Trichinella spiralis, food irradiation,

457, 458, 475

Trimethoprim-sulfamethoxazole, Cyclospora management, 294 U

Urease, Yersinia virulence factor, 92, 93 USDA,

see Food Safety and Inspection Service; Hazard Analysis

and Critical Control Point Program

V Vaccines

animal production DNA vaccines, 421

live-attenuated vaccines, 421 overview, 420, 421

subunit vaccines, 421 Giardia, 324

hepatitis E virus, 196 Vibrio

cholera toxin features, 133, 134 classification, 115, 116

clinical features of infection, 136, 137 decontamination from food, 139,

140

diseases, 115, 136, 137

foodborne outbreaks, 129–132 food irradiation, 471

identification biochemical

and growth characteristics, 117–119

isolation, 116 kits, 117, 120

polymerase chain reaction, 122–125

serotyping, 117, 120, 121 microbial risk assessments, 452 molecular typing

multilocus sequence typing, 128 pulsed-field gel electrophoresis,

126–128 restriction fragment

length polymorphism, 126 pathogenicity and virulence factors,

132–136

phylogenetic analysis, 125–127 prevention and control, 140, 141 reservoirs, 128, 129

resistance epidemiology, 138, 139 treatment, 137, 138

VM-ST, Vibrio virulence factor, 134

Y

YadA, Yersinia virulence factor, 90, 91 Yersinia enterocolitica

biotypes and strains, 79, 80 clinical features, 93–96 foodborne outbreaks, 87–89 food irradiation, 471, 472 history of study, 79 phage typing, 82 reservoirs, 83–87

resistance epidemiology, 97–99 serotypes, 81

treatment, 96, 97 virulence factors

Ail, 91 Invasin, 91 Myf, 92 urease, 92, 93 YadA, 90, 91 Yops, 90, 91 Yst, 92

Yersinia pseudotuberculosis biotypes, 80

clinical features, 93–96 foodborne outbreaks, 87–89 food irradiation, 471, 472 history of study, 79 reservoirs, 83–87

resistance epidemiology, 97–99 serotypes, 81–83

treatment, 96, 97 virulence factors

Ail, 91 Invasin, 91 Myf, 92 urease, 92, 93 YadA, 90, 91 Yops, 90, 91 YPM, 93

Yops, Yersinia virulence factor, 90, 91

YPM, Yersinia virulence factor, 93

Yst, Yersinia virulence factor, 92