Molecular detection of foodborne pathogens edited by dongyou liu

MOLECULAR DETECTION OF FOODBORNE PATHOGENS MOLECULAR DETECTION OF FOODBORNE PATHOGENS EDITED BY DONGYOU LIU Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2010 by Taylor and Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S Government works Printed in the United States of America on acid-free paper 10 International Standard Book Number: 978-1-4200-7643-1 (Hardback) This book contains information obtained from authentic and highly regarded sources Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and 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system of payment has been arranged Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe Library of Congress Cataloging-in-Publication Data Molecular detection of foodborne pathogens / [edited by] Dongyou Liu p ; cm Includes bibliographical references and index ISBN 978-1-4200-7643-1 (hard back : alk paper) Foodborne diseases Molecular diagnosis Food Microbiology I Liu, Dongyou II Title [DNLM: Food Contamination analysis Food Poisoning microbiology Molecular Diagnostic Techniques methods WA 701 M718 2009] QR201.F62M65 2009 615.9’54 dc22 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com 2009017320 This book is dedicated to my parents, Jiaye Liu and Yunlian Li, whose unselfish sacrifice and unrelenting love have been a constant source of inspiration in my pursuit of knowledge and betterment Contents Preface xiii Editor xv Contributors .xvii Chapter Molecular Detection: Principles and Methods Lisa Gorski and Andrew Csordas Section I  Foodborne Viruses Chapter Adenoviruses 23 Charles P Gerba and Roberto A Rodríguez Chapter Astroviruses 33 Edina Meleg and Ferenc Jakab Chapter Avian Influenza Virus 49 Giovanni Cattoli and Isabella Monne Chapter Hepatitis A and E Viruses 63 Hiroshi Ushijima, Pattara Khamrin, and Niwat Maneekarn Chapter Noroviruses 75 Anna Charlotte Schultz, Jan Vinjé, and Birgit Nørrung Chapter Rotaviruses 91 Dongyou Liu, Larry A Hanson, and Lesya M Pinchuk Chapter Sapoviruses 101 Grant S Hansman Chapter Slow Viral Diseases 113 Takashi Onodera, Guangai Xue, Akikazu Sakudo, Gianluigi Zanusso, and Katsuaki Sugiura Section II  Foodborne Gram-Positive Bacteria Chapter 10 Bacillus 129 Noura Raddadi, Aurora Rizzi, Lorenzo Brusetti, Sara Borin, Isabella Tamagnini, and Daniele Daffonchio vii viii Contents Chapter 11 Clostridium 145 Annamari Heikinheimo, Miia Lindström, Dongyou Liu, and Hannu Korkeala Chapter 12 Enterococcus 157 Teresa Semedo-Lemsaddek, Rogério Tenreiro, Paula Lopes Alves, and Maria Teresa Barreto Crespo Chapter 13 Helicobacter 181 Norihisa Noguchi Chapter 14 Kocuria 201 Edoardo Carretto and Daniela Barbarini Chapter 15 Listeria 207 Dongyou Liu and Hans-Jürgen Busse Chapter 16 Micrococcus 221 Friederike Hilbert and Hans-Jürgen Busse Chapter 17 Mycobacterium 229 Irene R Grant and Catherine E.D Rees Chapter 18 Staphylococcus 245 Paolo Moroni, Giuliano Pisoni, Paola Cremonesi, and Bianca Castiglioni Chapter 19 Streptococcus 259 Mark van der Linden, Romney S Haylett, Ralf René Reinert, and Lothar Rink Section III  Foodborne Gram-Negative Bacteria Chapter 20 Aeromonas 273 Germán Naharro, Jorge Riaño, Laura de Castro, Sonia Alvarez, and José María Luengo Chapter 21 Arcobacter 289 Kurt Houf Chapter 22 Bacteriodes 307 Rama Chaudhry, Anubhav Pandey, and Nidhi Sharma Chapter 23 Brucella .317 Sascha Al Dahouk, Karsten Nöckler, and Herbert Tomaso Chapter 24 Burkholderia .331 Karlene H Lynch and Jonathan J Dennis ix Contents Chapter 25 Campylobacter 345 Aurora Fernández Astorga and Rodrigo Alonso Chapter 26 Enterobacter 361 Angelika Lehner, Roger Stephan, Carol Iversen, and Seamus Fanning Chapter 27 Escherichia 369 Devendra H Shah, Smriti Shringi, Thomas E Besser, and Douglas R Call Chapter 28 Klebsiella 391 Beatriz Meurer Moreira, Marco Antonio Lemos Miguel, Angela Christina Dias de Castro, Maria Silvana Alves, and Rubens Clayton da Silva Dias Chapter 29 Plesiomonas 405 Jesús A Santos, Andrés Otero, and María-Luisa García-López Chapter 30 Proteus 417 Antoni Róz∙alski and Paweł Sta˛ czek Chapter 31 Pseudomonas 431 Olga Zaborina and John Alverdy Chapter 32 Salmonella 447 Charlotta Löfström, Jeffrey Hoorfar, Jenny Schelin, Peter Rådström, and Burkhard Malorny Chapter 33 Serratia 459 Zhi-Qing Hu, Wei-Hua Zhao, and Zhuting Hu Chapter 34 Shigella 471 Benjamin R Warren, Keith A Lampel, and Keith R Schneider Chapter 35 Vibrio 485 Asim K Bej Chapter 36 Yersinia 501 Mikael Skurnik, Peter Rådström, Rickard Knutsson, Bo Segerman, Saija Hallanvuo, Susanne Thisted Lambertz, Hannu Korkeala, and Maria Fredriksson-Ahomaa Section IV  Foodborne Fungi Chapter 37 Alternaria 521 Dongyou Liu, Stephen B Pruett, and Cody Coyne Chapter 38 Aspergillus 529 Giancarlo Perrone, Antonia Gallo, and Antonia Susca 867 Index genome arrangement, 34 full-length genomic RNA (gRNA) and sgRNA, 35 HAstV strains isolation, 36 human illness, characteristics of, 36–37 in human, propagation in HEK cells, 35 identification of, 33 image by electron microscopy, 34 immunity for, 37–38 immunocompromised hosts, role in, 37 infections, 36 clinical symptoms associated with, 37 disease, role in, 38 outbreaks for, 38 isolation of, 34 physical and chemical agents, resistance against, 35 sample preparation, 40 mussel sample for RT-PCR detection, 42 for RT-PCR detection, 42 shellfish for RT-PCR detection, 42 sequencing and phylogenetic analysis, 43 star-like morphology, 34 transmission of, 36 treatment and prevention, 40 virus concentration techniques from foods, 41 Avian influenza (AI) viruses and antigen detection, 51–52 classification of, 49 detection procedures H5 HA subtype by qualitative one step real Time RT-PCR, 58–59 one step RT-PCR for detection of H5 subtype, 57 one step RT-PCR for detection of Type A, 56–57 qualitative real time PCR (M gene), Type A, 58 two step RT-PCR for detection of H7 subtype, 57–58 infections caused by, 50, 54 viremia and viral replication, 55 medical importance and zoonotic implication, 50–51 molecular tests for, 53 hemagglutination inhibition test, 52 nucleic acid amplification protocols, 53 PCR-based protocols for detection of, 52–53 RT-PCR based methods, 54 outbreaks in birds, 49 phylogenetic studies, 54 sample collection, 55 sample preparation for PCR testing cloacal and tracheal/oro-pharyngeal swabs, 56 RNA extraction kit, 56 serological methods agar gel immuno-diffusion (AGID) test, 52 surveillance and monitoring programmes, 51 transportation and storage of specimens, 55–56 B Bacillus spp B anthracis detection by RSI-PCR, 136–137 etiological agent of anthrax, 129 toxin genes, 131 whole genome SNP analysis, 131 B cereus abdominal pain and diarrhea, 131 CHO assay, 134 detection by RT-PCR, 138–139 detection techniques by multiplex PCR, 137–138 diarrheal toxins detection, 134 DNA isolation, 136 ecotypes, 130 food and environmental samples, detection of, 134–135 as foodborne pathogen, 129 food poisoning outbreaks, 131–132 G9241 strains, 131 HBL and NHE, tripartite toxins, 132 INRAAF2 strains, 132 isolation and enumeration, 135–136 MLST schemes, 131 murine hybridoma Ped-2E9 cell model, 133 nausea and vomiting, 132 NVH391/98 and NVH883/00 strains, 132 phylogenetic analysis, 132 sample preparation, 135 species discrimination in, 130 strains isolated from periodontitis in humans, 131 toxin detection, 133 B licheniformis and B pumilus, heat-stable toxin-producing, 133 B mojavensis, cytotoxicity of, 133 B thuringiensis insect pathogen, 129 B weihenstephanensis genome sequencing, 133 psychrotolerant species, 130 ecology of, 130 Bacteroides spp B fragilis biochemical tests, 312 culture, examination of, 312 enterotoxin gene of, 309–310, 314 enterotoxin production, determination of, 312 fecal specimen, collection and transportation of, 311 molecular methods, role of, 310–311 PCR for neuraminidase gene, 314 specimen processing, 312 biological characteristics, 307 CTn9343, map of, 310 detection techniques boiling method, DNA extraction, 313–314 fecal samples, DNA extraction, 314 phenol-chloroform extraction, DNA extraction, 312 epidemiology, 308–309 pathogenesis, 309 PCR reagents for, 311 Bbovine astroviruses (BAstVs) serotypes of astroviruses, 35 Bovine spongiform encephalopathy (BSE), 113 immunohistochemistry of brain tissues from, 118 Brevictenatae, 521 Brucella spp antigen tests brucellin allergic skin test, 321 buffered plate agglutination test (BPAT), 320 complement fixation test (CFT), 320 enzyme-linked immunosorbent assay (ELISA), 320 fluorescence polarization assay (FPA), 320 Rose Bengal test (RBT), 320 Brucella-specific detection targets, 14 brucellosis, 317 in animals, 318 bacteraemia and, 319 geographic distribution, 319 in human, 319 zoonotic disease, 319 detection techniques multiplex PCR, 323 primers for, 323–324 real-time PCR assays, 324–325 diagnosis isolation and identification, 320 serological tests, 320–321 identification and differentiation of, 323 infection, 319–320 transmission of, 318 868 molecular diagnostic techniques molecular typing methods, 322–323 PCR techniques, 321–322 multiplex PCR cycling program, 324 pathogenicity and, 318 primers for, 323–324 real-time PCR assay targeting, 325–327 sample collection and preparation, 323 serological tests antibody detection, 321 primary binding assays for antibody detection, 321 taxonomy, 317–318 Burkholderia spp B mallei, 332 B pseudomallei, 331 Burkholderia cepacia complex (BCC) infections, 332–333 Burkh olderia gladioli pathovar cocovenenans bacterial isolation, 338 biology, 335–336 conventional diagnosis, 336–337 detection techniques, 338–339 epidemiology, 333–334 molecular diagnosis, 337 multiplex PCR with, 339 pathogenesis, 334–335 propagation, 338 storage, 338 strains of, 339 taxonomy of, 333 toxoflavin extraction, 338 reagents and equipment, 337–338 C Campylobacter spp animal models, 348 C jejuni from food, 348 genome of, 346 infection of, 348 life cycle, 346 LOS and flagella, 348 PCR assays, 350 detection techniques duplex real-time PCR amplification for, 355 multiplex PCR, 354–355 and PCR amplification, oligonucleotide primers and probes, 354 flagella and flagellar motility, 347 infection, 346 campylobacteriosis, 345 Guillian–Barré syndrome (GBS), 345 Miller Fisher syndrome (MFS), 345 isolation and detection rapid methods, 349 traditional methods, 348–349 molecular methods DNA-based methods, 349–350 identification of, 351–352 RNA-based methods, 350 whole-genome-based methods, 352 sample preparation and DNA extraction, 353–354 virulence factors adhesion and invasion, 347 chemotaxis and motility, 346–347 cytolethal distending toxin (CDT), 347 glycosylation system, 347 lipooligosaccharide (LOS) and, 347–348 Candida spp., 549–550 C albicans, 550–552, 557 colonial appearance, 550 Index C parapsilosis, 552 detection in food culture process, 554–555 PCR technology, use of, 555–557 detection methods and procedure conventional PCR, 559 real-time PCR, 559–560 sample preparation and extraction, 558–559 diagnosis of candidal infections Candida score, calculation of, 553 colonization index, 553 microscopic or culture detection, 553 nonculture diagnostic techniques, 553, 555 PCR protocols suitable for, 554, 556 diseases caused by, 553–554 geographical distribution of species causing bloodstream infections, 551 growth conditions, 550 incidence rate, for infection, 550–551 morphology of, 550 pathogenicity, study on, 552–553 risk factors, for infection, 551–552 ICU residence as, 551 total parental nutrition (TPN) as, 551 species causing invasive candidal infections, 552 Capsid genes for detection of DNA and RNA viruses, 11 Capsules role in aeromonad virulence, 278 carA gene carbamoyl phosphate synthase in Pseudomonas spp as target, 13 Cereulide by HEp-2 tissue culture assay, 134 Chicken astroviruses (CAstVs) serotypes of astroviruses, 35 Chronic wasting disease (CWD), 113 Clonorchis spp biology of, 771–772 classification and morphology digenea, 769 clonorchiasis chemotherapy for, 772–773 clinical symptoms of, 772 foodborne, diagnosis of, 773 C sinensis adult worms surface and sex, 770 appearance and characteristics, 770 body cavity, 771 CS1/CS2 primers, sensitivity of, 774 distribution of, 769 egg production, 778 excretion system and nervous system, 771 infections with, 772 intestine and eggs, 771 life cycle, 769 light micrographs of, 771 size and shape, 770 detection, eggs in human/animal fecal samples cleanup procedure, 775–776 PCR efficacy of, 776 DNA sequences, 776–777 metacercariae in fish, detection of PCR identification for, 775 sample preparation, 774–775 opisthorchiids, eggs of, 777–778 pathogenesis clonorchiasis, clinical symptoms of, 772 prophylaxis, 772 rediae in snails, detection PCR assay, 773–774 sample collection and preparation, 773 Clostridium spp C botulinum botulinum neurotoxin (BoNT), 146, 148 genetic typing, 151 869 Index molecular identification, 151 PCR assay for distinguish between group I and group II, 152–153 phenotypic identification, 150 primers for differentiation between group I and group II strains, 151 repetitive extragenic palindromes (REP), 151 standard detection and isolation, 150–151 strains producing toxin, 146 C difficile proliferation and infection in human colon, 146 toxin A and B, 146 C perfringens amplified genetic typing methods, 150 antibiotic-associated diarrhea (AAD) and sporadic diarrheas in humans, 146 Clostridium perfringens beta2 toxin (CPB2), 146 Clostridium perfringens enterotoxin (CPE), 146 combination of probe dyes, 149 cpe gene in, 148 food poisoning outbreaks, 148 genetic typing, 150 genome of, 145 molecular identification, 149 multiplex primers for determination of, 147–148 nonamplified genetic typing methods, 150 phenotypic identification, 149 toxin genes, 149 toxinotypes and toxins, 146 toxin producer, 145 type A food poisoning, 146 C septicum alpha toxin, 148 fatal traumatic and nontraumatic myonecrosis, 146 C tetani tetanus (lockjaw) in humans and animals, 146 detection techniques multiplex PCR, 152 sample preparation DNA rxtraction, 151–152 COX2 mitochondrial gene as target for detection of S cerevisiae, 13 cpn60 gene heat shock protein in bacteria as detection target, 13 CpR1 gene from Cryptosporidium target for food detection systems, 14 Creutzfeldt–Jakob disease (CJD), 113 diagnostic criteria for, 116 immunohistochemical staining with monoclonal antibodies in human brain tissue with, 116 Cryptosporidium spp., 651 as cause of diarrhea, 652 mechanism of infection, 652 classification of, 651–652 detection methods, 655 conventional methods, 655 in drinks, 658–659 in fruit and vegetables, 657 in meat, fish, and shellfish, 658 molecular methods, 655–657 detection procedures nested PCR targeting 587-bp 18S rDNA fragment, 660–661 nested PCR targeting 825-bp 18S rDNA fragment, 660 nested PCR targeting GP60 locus, 661 foodborne outbreaks of, 654 food contamination, sources of, 652–654 foodstuffs, as source of oocysts, 652–653 loci used to detect, 656 oocysts, transmission by, 652 reagents and equipment, for extraction and detection of DNA, 659 recognized species of, 652 sample preparation, 659 Cyclospora spp C cayetanensis clinical presentation and, 668–669 molecular techniques, 669–670 phenotypic techniques, 669 classification and, 667–668 detection techniques multiplex PCR, 672–673 PCR with F1E-R2B, F3E-R4B primers and, 671–672 real-time PCR, 673 RFLP with AluI and, 672 sample processing fast DNA spin prep kit, 671 feces and foods, 671 FTA filter purification, 671 phenol-chloroform extraction, 671 water, 671 Cytochrome oxidase genes from mt DNA as target for detection of helminths, 13 D Debaryomyces spp., 565 characteristics of, 566 classification of, 565 detection methods and procedures, 569 RAPD-PCR, 571–572 reagents and equipment, 569–570 RFLP analysis of mitochondrial DNA, 570–571 sample preparation, 569–570 D hansenii, 565–566 excessive growth, effects of, 567 growth in food, 566–567 infections in humans, 567 molecular methods, for identification, 568 methods based on RFLP, 569 nucleic acid hybridization, 568 PCR techniques, 568–569 physiological and morphological identification, 567–568 structure and reproduction, 565–566 Diphyllobothrium spp biology and pathogenesis, 781–782 classification and morphology, 781 D dendriticum infections of, 782 D ditremum infections of, 782 detection procedure, 785 identification, primers used, 786 diagnostic techniques, 782–783 diphyllobothriasis, 781 Diphyllobothriidae family, 781 D latum infections of, 782 life cycle of, 781 proglottids and plerocercoid, 783 RFLP profiles, 783 DNA extraction from, 785 D nihonkaiense RFLP profiles, 783 D vogeli infections of, 782 internal transcribed spacer (ITS1) and COI gene sequences, 784 molecular diagnostic techniques, 783–784 phylogenetic construction, 784 primers for identification, 786 proglottids and plerocercoid of, 783 reagents and equipments, 785 reported from humans and, 782 sample collection, 785 sequences in Genbank, 782 870 E eap gene in Staphylococcus aureus as detection target, 14 Encephalitozoon, 691 Entamoeba spp E histolytica, 677–678 ALA, intestinal infection, 684 antibody detection, 681 asymptomatic infection, 680 conventional PCR assays for, 682–684 culture techniques, 681 detection technique, 686–687 extraintestinal disease, 680 infect humans, 678 isoenzyme analysis, 681 life cycle of, 678–679 microscopy, 681 pathogenesis, 679–680 real-time PCR (RT-PCR), 684–685 sample collection and preparation, 686 stool antigen assays, 681–682 symptomatic infection, 680 treatment of, 680–681 Enterobacter spp., 361 detection techniques PCR identification, 365 real-time PCR assay identification, 365 diagnosis techniques conventional procedures, 362–363 epidemiology and pathogenesis, 361 Cronobacter infections, 362 necrotizing enterocolitis (NEC), 362 molecular procedures amplified fragment length polymorphisms (AFLP), 364 BOX-PCR and REP-PCR, 364 multi-locus VNTR analysis (MLVA), 364 PFGE method, 364 random amplification of polymorphic DNA (RAPD), 364 ribotypes, 364 species-specific detection and identification, 363 subtyping, 363 sample preparation, 364–365 Enterococci microorganisms, 157 cell isolation and counting without pre-enrichment, 169 detection techniques data analysis, 174 flowchart of multiplex-PCR, 173 genus-and species-specific multiplex PCR, 173 DNA extraction conventional PCR for, 169–170 from fermented cereal-based food, 172 real-time PCR, 170 enrichment procedure, 169 fermented meat products, 158 kits used for extraction from food matrixes, 170–172 molecular approaches for identification and detection atpA gene sequences, 168 bacterial ATP synthase, 168 culture methods, 158 D-alanine:D-alanine ligase (ddl) gene, 161 elongation factor EF-Tu, 161 fluorescent in situ hybridization (FISH) probes, 159 genus-and species-specific PCR primers, 162–167 heat shock proteins, 168 manganese-dependent superoxide dismutase, 168 microarray technology, 159 molecular diagnostic methods, 159 muramidase, 161 nucleic acid based, 158 PCR assays, 158 Index penicillin-binding proteins (PBPs), 161 probes for, 160–161 real-time quantitative PCR (qPCR), 159 rRNA gene sequences, 159 TaqMan system, 159 tuf gene, 161 viable but nonculturable (VBNC) microorganisms and, 158 sample homogenization, 168–169 vegetables and olives, 158 Enterocytozoon, 691 Enzyme linked immunosorbent assay (ELISA), Epidemic keratoconjunctivitis (EKC), 25; see also Adenoviruses Escherichia spp., 369 detection techniques m-PCR assay, sequences, 382 PCR reaction mixture in, 382–383 E coli O157:H7 culture and isolation, 371–373 developed m-PCR assay, 376 ELISA, 374–375 enrichment and IMS, 373–374 infections of, 370–371 latex agglutination test (LAT), 373 microbiological and PCR scheme, 372 nucleic acid microarrays, 380–381 occurrence and, 369–370 PCR, 375–376 phenol chloroform isoamylalcohol (PCI) extraction, 376–377 real-time PCR, 377–380 reverse transcriptase (RT)-based assays, 380 Shiga-toxin producing, 369 tiered microbiological and PCR scheme, 372 reagents and equipment, 382 sample preparation, 382 type III secretion system (TTSS), 371 Esculin hydrolysis, biochemical identification of Aeromonas spp., 279 European Food Safety Association (EFSA), 595 Exotic ungulate encephalopathy (EUE), 115 F Fasciola spp biology, 789–790 detection procedures, 791 fascioliasis, 790 Fasciolidae family, 789 F gigantica distribution of, 789 life cycle of, 790 F hepatica distribution of, 789 life cycle of, 789–790 propensity for liver, 789–790 identification and diagnosis differentiation from definitive hosts, 790 infection in snails by PCR, detection of, 790–791 medical importance, 790 pathogenesis, 790 reagents and equipment, 791 sample preparation and DNA isolation, 791 Feline spongiform encephalopathy (FSE), 115 Fluorescence in situ hybridization (FISH) technique Listeria monocytogenes, detection of, Fluoroquinolones S marcescens resistance to, mechanisms of active efflux pump, 462–463 gyrA, mutations, 462, 464 Qnr determinants, 464 Foodborne illness, pathogen detection techniques 871 Index assay design and data analysis software, 10 combined detection methods, in complex matrices, sample preparation, immunological assays, 8–9 microfabrication and microfluidics, nucleic acid based, 3–6 targets for, 10–14 typing, validation, 14 Food safety foodborne pathogens, detection of, polymerase chain reaction (PCR) inhibitors, Fusarium spp., 577 classification of, 577–578 F graminearum species complex, 578–579 F oxysporum species, 579 Gibberella fujikuroi species complex, 578 diagnosis of, 581–582 fumonisins-producing species, 582–583 surface plasmon resonance (SPR) biosensors, 585 trichothecenes producing species, 583–585 future research program, 588 molecular detection of fumonisins-producing fusarium spp in maize, 585–586 molecular detection of trichothecenes fusarium spp in wheat, 586–587 quantitative detection of fumonisins-producing fusarium spp in maize, 586–587 spores types, 578 toxic metabolites by, 579–581 fumonisins, 580 trichothecenes, 579–580 G Gerstmann–Sträussler–Scheinker (GSS), 115 Giardia spp antigenic variations, 703 classification of, 702 cyst passage rate, 703 detection techniques DNA sequencing, 712 PCR reaction, 712 sequencing analysis, 712–713 diagnosis EnteroTest, 704 G duodenalis assemblages of, 702 prevalence of, 702 giardiasis, 701 infection outbreaks of, 702–703 life cycle of, 702 molecular methods genotyping tools, 704–708 molecular tools for analysis of environmental samples, 709 PCR assay, 704 reagents and equipment, 710 subtyping tools, 709 in raw vegetables and fruit salad, 702 sample preparation DNA extraction, 711 fecal from, 710 food and water samples, centrifugation of cysts, 711 food and water samples, extraction of cysts, 710–711 transmission, drinking and recreational water, 702 Giardin protein as detection target, 12 Glycerophospholipid cholesterol acyl-transferase (GCAT) role in aeromonad virulence, 278 Granulomatous amoebic encephalitis (GAE), 641–642 H Helicobacter spp cdt pathogenetic gene, 195 cyclodextrin and culture growth, 182 detection methods for, 182 immunological methods, 183–184 LAMP, 186 molecular techniques, 184 multiplex-PCR, 185 nested PCR, 185 PCR, 184 PCR-DGGE, 186 PCR-RFLP, 185–186 reagents and equipment, 186 real-time PCR, 185 RT-PCR, 185 Southern hybridization, 186 16S rRNA gene, 195 standard PCR, 185 TaqMan-PCR, 185 Taq polymerase, 186–187 target genes, 185 urea breath test (UBT), 184 Helicobacter heilmannii culture study, 195 Helicobacter pylori infection with peptic ulcers and gastric cancer, 188 PCR protocols for detection, 189–194 scanning electron micrograph of, 182 host specificity, 195 infection, 181 isolation, 181 sample collection and preparation biopsies and endoscopy of gastric mucosa, 187 DNA extracted from gastric juice, 187 DNA purification and isolation, 188 feces from, 187 mixed infection with clarithromycin-resistant and-susceptible, 187 plaque from oral cavities, 188 species and hosts, 183 structure, 181 Hepatitis A virus (HAV) classification and genetic diversity 3C/3D region junction, 64 subgenotypes, 64 VP1/P2A region junction, 64 VP3/ VP1 region junction, 64 detection techniques nested PCR for, 69 reverse-transcription PCR (RT-PCR), 68–69 sequence analysis and genotype identification, 69–70 diagnosis molecular techniques, 64 genome, 64 genus Hepatovirus within Picornaviridae family, 63 infection foodborne and waterborne, 64 severe and fulminant hepatic failure (FHF), 63 oligonucleotide primers for detection and sequencing from clinical specimens, 65 specimen collection and RNA extraction, 68 Hepatitis E virus (HEV) classification and genetic diversity serotypes, 66 detection and sequencing from clinical specimens oligonucleotide primers for, 67 reagents and equipments, 67–68 detection techniques nested PCR, 70 RT-PCR, 70 872 sequence analysis and genotype identification, 70–71 genome organization, 66 infection diagnosis, 66 foodborne and waterborne, 66 liver abnormalities, viremia and fecal shedding, 65 molecular techniques, 66 route and mechanism, 66 zoonotic foodborne transmission, 66 member of Hepeviridae family, 66 specimen collection and RNA extraction, 68 Heterophyidae family Centrocestus spp fish hosts, 796 infection, 797 clinical manifestations clinical symptoms, degree of, 797 heterophyiasis, intestinal histopathology caused, 797 clinical survey, 797 detection procedures endonuclease digestion, 802 fish-infesting trematodes, PCR assays for, 801–802 interpretation of, 802 PCR amplification, 802 diagnosis amplicons, 798 heterophyid trematode sequences, 799–800 heterphyids rDNA, alignments of, 799–800 molecular tools in, 800 PCR amplification, gene targets for, 799 PCR-based methods, 800–801 precise identification of, 798 probes, 798–799 digenea, life cycle of, 798 Haplorchis spp infection, 797 Heterophyes spp fishborne zoonoses, 795–796 foodborne trematode infections, 796–797 heterophyid trematodes, 796 human trematodiasis, 795 sample collection and preparation, 801 trematodes, 795 heterophyiasis, 796 clinical manifestation of, 797 Phagicola spp metacercariae in heart, 796 Pygidiopsis spp metacercariae in kidney, 796 reagents and equipment, 801 sequences from GenBank, 800 Stellantchasmus spp infection, 797 Human adenovirus illnesses associated with, 24 serotype classification, 24 I Immuno PCR (IPCR), inlA primers for species-specific confirmation of L monocytogenes, 216 Invasins role in aeromonad virulence, 278 Isospora spp clinical manifestations and, 719–720 conventional laboratory diagnosis of duodenal content, 721 histological sample, 721 stool samples, collection and preservation of, 720–721 detection procedure, 727 Index diagnostic techniques histopathology, 723 stool examination, 721–723 extraintestinal tissue cysts of, 719 gametogony, 719 I belli conventional diagnosis of, 718 description of characteristic oocysts of, 717, 719 extraintestinal tissue cysts of, 719 infection with, 719–720 life cycle of, 718 life cycle of, 718–719 molecular diagnosis of, 724 nested PCR amplification, agarose gel electrophoresis of, 727 Oocysts of, 719 RNA cistron, representation of, 727 sample preparation DNA extraction method, 726–727 stool samples, disruption of, 725–726 sporogony, 718 sporozoites, 718–719 transmission of, 719 K Klebsiella spp., 391–392 classification, 392 detection techniques PCR amplification, 398–399 rpoB gene fragments, sequence analysis of, 399 as enteropathogen, 394 as foodborne pathogen, 394 habitat and epidemiology of, 392 healthcare associated infections caused by, 393–394 isolation and biochemical identification, 394 K pneumoniae community acquired pneumonia (CAP), 392–393 infections, 392 molecular identification, 394–395 molecular typing, 395–396 PCR and sequencing methods, 396 PCR DNA fragments, gel electrophoresis of, 397 phylogenetic analysis, 400 and Raoultella, classification of, 392 rhinoscleroma, 393 sample collection and preparation DNA isolation and, 397–398 sample processing and culture, 397 Kocuria spp catheter-related bacteremia, 202 classification of, 201 clinical relevance, 201 diagnostic methods phenotypic methods, 202 drug susceptibilities of, 202 and food products, 202 identification and susceptibility test systems, 202–203 Kocuria kristinae acute cholecystitis and, 202 phenotypic variability, 202 for standardize quality of fermented sausages, 202 Micrococcaceae family, 201 misidentification of, 203 PCR amplification of 16S RDNA region, 204 16S ± 23S RDNA intergenic region, 204 ribotyping, 203–204 Kuru transmissible agents in dementias, 113 873 Index L β-Lactams in gram-negative bacilli, 462 production by Serratia spp., 463 S marcescens, resistance mechanisms of β-lactamses, 461–462 gram-negative bacteria, outer membrane of, 462 S-Layer proteins role in aeromonad virulence, 278 Lipase-encoding genes role in aeromonad virulence, 278 Lipopolysaccharide role in aeromonad virulence, 278 Listeria spp classification of, 207 detection techniques identities and sequences of internalin gene primers for species-and virulence determination, 216 identities and sequences of primers for serogrouping, 216 identities and sequences of primers for species-specific identification, 215 multipex PCR determination of virulence, 215 multipex PCR identification, 214 multiplex PCR differentiation of serogroups, 215 diagnosis agglutination and enzyme-based immunoassay (EIA), 212–213 biochemical tests, 212 molecular techniques, 213 in vitro culture isolation, 212 in vivo assays, 213 distribution in environment, 208 fish and seafoods, isolation from, 209 genes for virulence-associated proteins, 210 genomes comparison, 211–212 growth of, 208 infection abortion/septicaemia, 209 early-onset fetomaternal/neonatal listeriosis, 210 food related human listeriosis, outbreaks of, 209 granulomatosis infantiseptica, 210 mode of, 210 processed and ready-to-eat (RTE), 209 Listeria primers for species specific identification, 212 Listeria monocytogenes serovars human listeriosis, 208 intracellular mobility and cell-to-cell spread, 210 and relative virulence, 209 Listeria somatic (O)/flagellar (H) antigens and antisera compositions of, 208 serological techniques for interaction between, 207 sample preparation bacterial isolation, 213–214 DNA extraction, 214 whole genome sequences of, 210 Longicatenatae, 521 Loop mediated amplification (LAMP), Lymphoid cell depletion and astroviruses infection, 36 M Map animal pathogen and Crohn’s disease in humans, 230 detection of bacteriophage-based rapid methods, 232 internal amplification control (IAC), 235 microarray technology, 235 NASBA, 235 nested/semi-nested PCR, 233 phenotypic techniques, 231–232 primers for targeting, 234–235 probs for, 236 real-time PCR methods, 233 single PCR, 232–233 detection techniques DNA extraction protocol, 238–239 IS900 single PCR procedure, 239 in food, 231 genome sequence, 229 Johne’s disease in ruminants, 230 reagents and equipment, 237 sample preparation, 237–238 in water, 231 Metagonimus spp detection procedures Karyotyping of, 810 PCR-RFLP, 808–809 RAPD analysis, 809 28S D1 rDNA and mtCOI PCR, sequencing of, 809–810 simple sequence repeat-PCR, 809 Heterophyidae family, 805 identification and diagnosis, 807 medical importance, 807 metagonimiasis, 805 M miyatai biology of, 806 classification and morphology of, 806 M takahashii biology of, 806 classification and morphology of, 806 M yokogawai biology of, 806 classification and morphology of, 806 pathogenicity, 806–807 reagents and equipment, 808 sample collection and preparation DNA extraction, 808 Micrococcus spp aroma and flavor, development of, 222 biogenic amines (BA) production, 222 molecular detection, 225 poisoning, 223 diagnosis, 223 food matrices preparation, 223 dairy products, 224 fish and sea food, 224 meat and meat products, 224 food spoilage by, 222 habitats of, 222 identification of, 221 M luteus biovar II strains, 225–226 characteristics differentiating Kocuria varians and, 225 house-keeping genes, 225–226 PCR detection, 224–225 variability in physiological traits, 221 M lylae isolated from human skin habitat, 221 phenotypic differentiation between, 222 quinone system and peptidoglycan type, 221 Microsporidia organisms, 691 detection techniques multiplex nested PCR protocol, 696 oligonucleotide primers and detection probes, 697–698 real-time PCR method, 696–697 diagnosis microscopy by, 693 serological methods, 694 in vitro culture, 693–694 in vivo assays, 694 E bieneusi genotypes, 693, 697 E cuniculi strain I geographical distribution, 693 874 infection in humans and animals, 692 life cycle, 692 microsporidial spores, 692 molecular techniques, 694 genotyping, 695 species-specific detection, 694 susceptibility testing, 695 sample preparation DNA isolation, 695 Micro total analysis systems (µTAS), Minitek system (BBL), 568 Molecular beacons, 6–7 Molecular Beacon technologies, Multiplex PCR for Listeria monocytogenes speciation and virulence determination, Multiplex PCR method, use of genes in, 537–538 Mycobacterium avium subsp paratuberculosis, IS900 as insertion element, 13 Mycobacterium spp growth rate, 229 identification of, 229 Map-specific PCR targets, 229–230 Mycobacteriaceae family, 229 N NADH dehydrogenase genes from mt DNA as target for detection of helminths, 13 Noncatenatae, 521 Noroviruses (NoVs) classification of, 75 cloning and sequencing of genome, 77 detection in food amplification and detection, 80 amplification and inhibition controls, 85 clarification of water-phase by extracting with chloroform-butanol mixture, 80 elution and concentration, 77 EU legislation, 82 flow chart of, 84 GI and GII assay, 81 mastermix and RT-PCR conditions, 85 quality assurance (QA)/quality control (QC), 82 real-time RT-PCR primers and probes targeting ORF 1-ORF junction, 81 RNA extraction, 80 RT-PCR amplicons, 80 sample processing, 77 in shellfish, 78–79 in soft fruits, 84–85 TaqMan real-time protocol, 84 in vegetables and berries, 78–79 diagnosis, 77 foodborne outbreaks in U.S., 75 genome with open reading frames (ORFs), 76 ORF1–ORF2 junction region, 80 incubation period, 76 infection 1,2-fucosyltransferase FUT2 gene, susceptibility of, 77 human histoblood group antigens (HBGAs) and, 76–77 source of, 76 ready-to-eat (RTE) foods, 75 sample preparation and RNA extraction, 82 reagents and equipments, 83 Nucleic acid based, pathogen detection techniques fluorescence in situ hybridization (FISH), immunological detection methods, 8–9 isothermal amplification, 7–8 microarray detection, polymerase chain reaction (PCR) Index double/single stranded (ss) DNA sequences in vitro, amplification of, multiplex PCR assays, practical considerations for, real-time PCR systems, 6–7 representation and detection protocols, reverse transcriptase PCR, steps used for, Nucleic acid sequence based amplification (NASBA), for detection Hepatitis A virus (HAV), Vibrio cholerae, O OIE Manual for Diagnostic Tests and Vaccines for Terrestrial Animals, 55 Oncosphere-specific protein tso31 as detection target for helminth Taenia, 14 Opisthorchis spp biology and life cycle, 814–815 cholangiocarcinoma (CCA), 813 liver fluke induced, 817–818 nitrative and oxidative DNA damage, 818 classification, 813–814 clinical manifestation and morbidity, 816–817 diagnosis immunological techniques, 820–821 molecular techniques, 821 parasitological techniques, 819–820 epidemiology, 819 geographical distribution, 814 host immune response, 816 opisthorchiasis, 820 praziquantel chemotherapy, 819 Opisthorchiidae family, 813 O viverrini antigens of, 821 commercial kit, DNA preparation, 821–822 CTA B method, DNA preparation, 822 endogenous nitrosation, 818 host, 816 infection, 815 8-oxodG levels and, 818 stool samples PCR detection by pOV-6 primers, 822–823 stool samples PCR detection by trem25-F and OV25-4R primers, 823 pathogenesis and pathology, 815–816 prevention, and control, 819 Orthomyxoviruses, as biological agents of biohazard class 2, 56 Outer membrane proteins (OMP) role in aeromonad virulence, 278 P Paragonimus spp biology and pathogenesis, 829–830 classification and morphology P africanus, 829 P kellicotti, 829 P mexicanus, 829 P skrjabini and P miyazakii, 829 P tuanshanensis, 829 P uterobilateralis, 829 P westermani, 828–829 detection procedures, 833 cycle sequencing, 834 ethanol precipitation of cycle sequencing product, 834–835 PCR amplification, 834 purification of PCR fragment from gel, 834 diagnosing infection enzyme linked immunosorbent assay (ELISA), 832 875 Index immunoblot assays, 832 immunological techniques, 830–832 intradermal test, 831–832 DNA sequence data and phylogenetic analysis, 828 paragonimiasis/endemic hemoptysis, 827 diagnostic methods, 830–831 sample collection, 832–833 DNA extraction from eggs, 833 Penicillium spp., 593 classification of, 594 detection procedures PCR detection of Penicillium species, 599 human diseases and, 595–596 laboratory diagnosis conventional techniques, 596 molecular techniques, 596–598 morphology of, 594 mycotoxinogenic foodborne Penicillia human health and, 595 OTA, 595 patulin, 595 nature and habitat, 594 PCR detection, 599 OTA-producing Penicillium, 599–600 patulin-producing Penicillium, 600 samples preparation culture preparation for toxin detection, 598 DNA extraction from fungal Cultures, 598–599 isolation from air, 598 isolation from food samples, 598 Pharyngoconjunctival fever (PCF), 25; see also Adenoviruses Phenotypic switching”, 552 Plate count technique, 534 Plesiomonas spp equipment and supplies, 411–412 habitat, 406 infection control, 409 pathogenicity and virulence factors, 408 PCR assay and visualization, 412 P shigelloides conventional diagnosis, 409–410 extraintestinal infections, 407 in foods, factors affecting, 406–407 gastroenteritis, 407 hemolytic activity, 409 hugA gene, amplification of, 412 invasiveness, 408–409 molecular diagnosis of, 410–411 PCR assays developed for, 411 plasmids, 409 tetrodotoxin (TTX), 409 toxins, 408 typing, 411 reagents, 411 sample collection, 412 taxonomy of, 405–406 Polymerase chain reaction (PCR) for amplification of double/single stranded (ss) DNA sequences in vitro, amplification efficiency, annealing time, hairpin primers, microchip PCR systems, PCR-RFLP (restriction fragment length polymorphism), thermostable polymerase, use of, in food industry, 555 Prion diseases, see Transmissible spongiform encephalopathies (TSEs) Proteases role in aeromonad virulence, 278 Pseudomonas spp detection techniques, 440 P aeruginosa acquisition of antibiotic resistance in, 432 detection in food products, 436–438 environmental sources of, 431–432 hospitalized patients, risk of acquisition of, 432–436 in human activity environments, selective advantage for, 432 identification in hospitals clinical laboratories, 439 novel nonantibiotic strategies to, 436 virulence potential, assessment of, 439–440 sample preparation bacterial DNA isolation, 440 Pulsed field gel electrophoresis (PFGE), R Real-time PCR (rt-PCR), for fungal detection, 536 Real-time PCR systems nonspecific detection, sequence specific detection, Reverse transcriptase PCR, Rhodotorula spp., 603 affinity for plastic, 605 conventional identification, of yeasts, 606–607 detection methods and procedures DNA extraction, 609 identification and genotyping, by MSP-PCR typing method, 609–610 rDNA sequencing analysis, 611–612 by RFLP-ITS method, 611 sample collection and preparation, 609 by species-specific PCR primers, 610–611 environmental distribution of, 604–605 future research areas, 613 medical importance, 605–606 molecular diagnostic methods, 607–609 occurrence in food and beverages, 605 role in human infections, 605 taxonomy of, 603–604 treatment of infection, 606 type strains of medically relevant Rhodotorula species, 612 Rolling circle amplification (RCA), Rotaviruses detection techniques primers and probes, 97 real-time RT-PCR detection of groups A and C, 96–97 RT-PCR detection of G and P genotypes, 96 VP4 and VP7 primers for, 96 diagnosis acid adsorption–alkaline elution and reconcentration, 95 antigen detection techniques, 94 enzyme immunoassay, 94 molecular procedures, 95 PCR assays, 95 phenotypic techniques, 94 family Reoviridae, 91 genetic changes by sequential point mutations, 93 G-type classification, 92 infection clinical symptoms, 93 gastroenteritis with diarrhea, 93 replication, 93 severity of, 94 transmitted by fecal-oral route via contact with contaminated hands, 93 infectivity of, 92 nonstructural protein (NSP), 91 overlapping reading frames, 91 RNA-binding proteins, 92 876 serogroups, 92 serotypes and genotypes, 91–92 rpsU-dnaG-rpoD region, DNA and RNA synthesis, 13 S Saccharomyces cerevisiae, 619–620 colony formation, 621 detection methods and procedure identification, by restriction of amplified 5.8S-ITS region of ribosomal rRNA operon, 632 microbial cells separation, from bakery dough, 631 reagents and equipment, 627 real-time PCR, detection by, 631–632 sample treatment, 627 typing by microsatellite amplification, 632–633 DNA extraction from human fecal samples, 627, 629–631 pure cultures, 627 from wine, 631 food industry, use in, 620 future investigation approach, 633 genetic typing methods and, 625 life cycle of, 620 molecular techniques for detection and identification, 625–628 microsatellite application, 626 occurrence in nature, 620 as pathogen, 622–624 retrotransposon types, 620 Saccharomyces complex, 619 S boulardii as variant of, 621–622 virulence factor in pathogenic strains, 624 wine fermentation, 620 Salmonella spp biology of serotyping, 447–448 detection TaqMan Real-Time PCR method for, 454–455 diagnostics of biochemical tests and serotyping, 450 culture based method, 450 modified conventional methods, use of, 450 real-time PCR method for, 449 Enterobacteriaceae family, 447 epidemiology cyclic between humans and animals, transmission of, 448 S enteritidis and S typhimurium, 448 S enteritidis, reservoir for, 448–449 infection route, 448 molecular diagnostics, 450 immunological methods, 451–452 nucleic acid-based methods, 452–453 pathogenesis infections, nature and severity of, 448 type III secretion systems (TTSS) for, 448 sample collection and preparation, 453–454 Sapoviruses classification family Caliciviridae, 101 Star-of-David, animal calicivirus morphology, 101 detection techniques ELISA detection system, 107 by EM, 106–107 integrity and morphology, 107 nested PCR, 108 phylogenetic analysis, 109 QIAamp Viral RNA Protocol, 107 real-time RT-PCR method, 108–109 reverse transcription (RT), 107–108 RNA extraction, 107 Index diagnosis enzyme immunoassays (EIAs), 103 nested PCR, 103 real-time RT-PCR methods, 103 genome genogroups (GI–GV), 102 open reading frames (ORFs), 102 phylogenetic analysis, 102 RdRp-capsid junction, 102 SimPlot software, 102 infections gastroenteritis, 101 sporadic cases of acute gastroenteritis, 103 virulence prevalence, 101 molecular detection nested RT-PCR by, 104 reagents and equipments, 105 RT-PCR and identification by sequence analysis, 103–104 sample preparation influent and effluent water, 105–106 oysters, 106 primary-treated domestic wastewater, 105 river water, 106 seawater, 106 secondary-treated effluent and river water, 105 shellfish, 106 stool samples, 106 subgenomic-like construct, expression of, 103 virus-like particles (VLPs), formation of, 103 Sarcocystis spp detection procedures, 734 18S rDNA sequencing, 735 DNA extraction sarcocysts and cell cultures from, 734 single tube extraction from oocysts, 733–734 in vitro excystation method, 734 feeding contaminated meat, 731 mature, excreted oocysts of, 731 sample collection and preparation preliminary visual screening for sporocysts, 732 sporocysts isolation, 732–733 Serratia spp classification of, 460 laboratory identification of, 465 PCR and restriction enzyme digestion PCR amplification, 466 restriction endonuclease digestion, 466 sample preparation, 466 real-time PCR amplification and detection, 466 sample preparation, 466 S marcescens antimicrobial resistance, occurrence of, 461 multidrug efflux pumps identification in, 464 opportunistic pathogen, 460–461 presence of, 459–460 resistance mechanisms, aminoglycosides, 464–465 resistance mechanisms, β-lactams, 461–462 resistance mechanisms, fluoroquinolones, 462–464 Shigella spp actin assembly, 474 contaminations of, 472 detection selected rapid methods for, 477 diagnosis conventional detection in food, 475–476 molecular detection in food, 477–478 FDA investigation of foodborne pathogens, 473 foodborne outbreaks of, 472–473 FoodNet data, 473 hemolytic uremic syndrome (HUS), 475 877 Index icsA (virG) and icsA gene, 474 infection route, 474 macropinocytosis, 474 medical importance, 475 molecular evolutionary relationship between enteroinvasive E coli (EIEC) and, 471–472 nested PCR detection of electrophoresis of, 480 primary PCR, 480 primer solutions, 479–480 outbreaks and foods, 472 pathogenesis, 473 IcsA is distribution, 474–475 intra and intercellular spreading, 474 macropinocytosis involvment, 474 Shiga-like toxin (SLT) production and, 474 Shiga toxin (STX), 475 PCR analyte and bacteriological analysis, preparation of, 478 PCR template, preparation of, 479 sample enrichment, 478 S boydii serotype, 472 S dysenteriae serotype, 472 serogroups of, 473 S flexneri infections, 475 LPS mutant, 474 serotype, 472 shigellosis treatment rehydration and antimicrobial therapy, 475 suspect colonies, identification of, 478–479 Wiskott–Aldrich syndrome protein (N-WASP) and, 474 Slow virus diseases, 113 diagnostic methods enzyme-linked immunosorbent assay (ELISA) techniques, 114 histological and immunohistochemical (IHC) methods, 117 western blot method, 117 virus-induced, 114 Staphylococcus spp coagulase-negative (CNS), 245 colonies of, 245 detection techniques, 253 primer identities, 254 reagents and equipment, 252 sample collection meat sampling, 253 milk sampling, 252–253 sample pretreatment DNA extraction, 253 S aureus coagulase-positive (CPS), 245 endemic strains, 246 in food, 246–247 multiplex PCR, 249–250 nuc gene as thermostable nuclease, 13 real-time PCR, 250–251 reservoirs of, 245 risk assessment in foodstuffs, 247 standard PCR protocols, 247–249 Staphylococcal food poisoning (SFP) in food and food products, 246 outbreaks, 246 symptoms of, 246 virulence factor SE characteristics of, 246 types of, 246 Strand displacement amplification (SDA), Streptococcus spp classification of, 259 Group A streptococci (GAS), 260 Group B streptococci (GBS), 260 Groups D, E, and F streptococci, 260 M-types GAS, 260 serological classification system, 260 dectection techniques composition of primers used in SA g PCR, 267 multiplex PCR for superantigen, 265–266 PCR for emm-typing GAS, 265 diagnosis GAS quick tests, 265 Lancefield agglutination test, 261 molecular techniques, 265 pneumococcus quick test, 265 foodborne infections, 262–264 outbreaks, 261 invasive pneumococcal disease (IPD) in USA, 260 Pneumococcal infections, 260 S agalactiae neonatal infections, 261 perinatal infections, 261 puerperal sepsis, 259 sample collection, 265 scarlet fever, 261 serotype, determination of, 260 skin infection, 261 S mitis mosaic genes and, 260 S oralis mosaic genes and, 260 S pneumoniae colony in human nasopharynx, 261 meningitis and pneumonia, 259 streptococcal superantigens (SAg) infections, 261 streptococcal toxic shock-like syndrome (STSS), 259 streptococcal tonsillopharyngitis, 259 streptolysins O and F, toxins, 261 Superoxide dismutase role in aeromonad virulence, 278 Surface-enhanced Raman scattering (SERS), ssDNA detection, 10 Surface plasmon resonance (SPR) sensors for measurement of refractive index, Systematic evolution of ligands by exponential enrichment (SELEX), 10 T Taenia spp biology and pathogenesis of foodborne, 840 classification, 840 cysticercosis and echinococcosis, 839 detection procedures multiplex PCR, 845–846 PCR product, sequencing of, 846–847 diagnosis, techniques for, 839–840 histopathological specimens for molecular identification, 841 human sparganosis, 839 human taeniid species molecular probes for identification of, 844–845 multiplex PCR for, 846 immunological approaches immunodeficient mice as alternative intermediate hosts, usefulness of, 842 life cycle of, 840 metacestodiases, 839 molecular and immunological techniques, relative performance of, 842–843 molecular tools for prevention of NCC, 840 loop-mediated isothermal amplification (LAMP) tool, 840–841 878 neurocysticercosis (NCC), 839 in humans, 842 racemose cysticercosis, 841 sample collection and preparation, 843, 845 taeniid proglottids expelled from humans, molecular diagnostic techniques, 841 tapeworm infections, 839 T asiatica scoleces of, 841 T asisatica cysticercosis in pigs, 842 T saginata bovine cysticercosis in cattle, 842 cysticerci of, 843 distribution of, 840 human taeniasis and cysticercosis of, 840 T solium cysticercosis in, 842 distribution, 840 genotypes of, 841 human taeniasis and cysticercosis of, 840 scoleces of, 841 zoonotic taeniid infections, 842 Targets for detection techniques genes for surface expressed markers, 13–14 insertion elements, 13 mitochondrial genes, 13 nonviral targets cytoskeletal proteins, 12 ribosomal RNA (rRNA) genes, 11–12 RNA targets, 11 unique genes and sequences, 12–13 viral, 10–11 structural genes, 11 virulence and toxin genes, 12 Toxoplasma B1 gene as detection target, 13 Toxoplasma spp bradyzoite, 742–743 cats and mice, bioassay in, 744–745 detection procedures multilocus nested PCR-RFL P genotyping, 749–750 nPCR, 747–748 by real-time PCR, 748–749 diagnosis enzyme-linked immunoabsorbent assay (ELISA), 743–744 indirect fluorescent antibody test (IFA), 743 indirect hemagglutination test (IHA), 743 modified direct agglutination test (MAT), 744 Sabin–Feldman dye test (DT), 743 epidemiology and pathogenesis, 743 molecular techniques multilocus nested PCR-RFLP genotyping, 745–746 nested PCR (nPCR) of repetitive, DNA sequences, 745 reagents and equipment, 746 real-time PCR of repetitive DNA sequences, 745 multilocus nested PCR-RFL P markers, summary of PCR primers for, 750 multilocus PCR-RFL P genotyping results, summary of, 751 PCR-RFLP gel image, 751 sample preparation DNA from animal tissues, extraction, 746–747 oocysts from water samples and extract, purification, 747 T gondii host genetic makeup and parasite genotypes, 745 infectious stages of, 741–742 isolation of, 744 life cycle and, 741–742 oocysts, 742–743 Transmissible spongiform encephalopathies (TSEs), 113 detection techniques, 120–121 abnormal isoform of prion protein, 122 Index diagnostic methods, 117 capillary gel-electrophoresis, 119 conformation-dependent immunoassay (CDI), 119 fluorescence correlation spectroscopy (FCS), 119 modified western blotting method for prion detection, 118 multi-spectral ultraviolet fluorescence spectroscopy (MUFS), 119 tool for, 119 visible and near-infrared (Vis-NIR) spectroscopy, 119 mutations responsible for inherited genetic forms, 114 genes, 115 sample collection and preparation, 120 Trichinella spp amplicon sizes by PCR-RFL P, features of, 852 biology of, 853 detection procedures multiplex PCR, 857 encapsulated clade T britovi, 852 T murrelli, 853 T nativa, 852 T nelsoni, 853 Trichinella T6, 852 Trichinella T8, 852–853 Trichinella T12, 853 expected amplification products, dimension of, 860 hosts for, 852 infection, diagnosing methods for, 854–855 molecular probes, 855 multiplex-PCR, 855 PCR-restriction fragment length polymorphism, 855 random amplified polymorphic DNA (RAPD), 855 reverse line blot hybridization (RLB), 855–856 single-strand conformational polymorphism (SSCP), 855 medical importance, 854 non-encapsulated clade T papuae, 853 T pseudospiralis, 853 T zimbabwensis, 853 pathogenesis, 853 infection pathological picture of, 854 larvae transformation, 854 PCR amplification of single larvae, photograph of, 859 sample collection and preparation DNA purification from single larvae, 857 hosts and preferential muscles, 856 parasite isolation and preservation, 856–857 SSCP approach for, 860 T britovi and Trichinella T8, PCR amplification of single larvae of, 860 and Trichinella T9, PCR-RFLP to distinguish between, 858–859 and Trichinella T8, PCR to distinguish between, 859–860 zoonosis trichinellosis, 851 Trichothecenes, 579 β-Tubulin as targets, 12; see also Targets for detection techniques Turkey astrovirus (TAstV-2) infection, mild crypt hyperplasia, 36 Turkey (TAstVs) serotypes of astroviruses, 35 U U.S foodborne illness outbreaks, statistics, V Vibrio spp biology and pathogenesis, 486 halophilic vibrios, 488 classification of, 486 detection techniques PCR assays, 493 primers and probes, 494 879 Index diagnosis, 488 DNA-DNA colony hybridization in, 489–490 PCR technology, applications of, 490 real-time PCR using, 491 reverse transcriptase PCR (RT-PCR), application of, 491–492 SYBR Green I-based, 491 TaqMan quantitative PCR (qPCR), study, 490–491 V vulnificus in oysters, 491 outbreaks, 485 transmission, source, 485 V cholerae biology and pathogenesis, 487 real-time PCR assays, 493, 495 sample preparation, 492 serotypes, 487 V parahaemolyticus, 489–490 clinical manifestations of, 487 foodborne gastroenteritis, 487 H antigen, 487 Kanagawa phenomenon, 487 outbreaks, 487 pathogenic and nonpathogenic strains, 487 real-time PCR assays, 495 sample preparation, 493 serotype, 487 wound infection and septicemia, 487 V parahaemomlyticus biology and pathogenesis, 487 V vulnificus biology and pathogenesis, 488 liver disease and, 488 prevalence of, 488 real-time PCR assays, 493, 495 sample preparation, 492–493 Voges-Proskauer reaction, biochemical identification of Aeromonas spp., 279 W Waldenstrom’s macroglobulinaemia, 37 Y Yersinia spp., 502 detection methods amplification facilitators, use of, 510 enrichment cultivation step, 510 equipment and materials, 508 procedure, 510 sample preparation, 509–510 YPCE, use of, 510 detection procedure, 510 confirmation of viable target bacteria, 511 DNA extraction, 511 enrichment of food samples, 510–511 pipetting scheme for detection of ail-gene, 512 primers and probes used, 512 quality assurance and control measure, 511 real-time PCR, 511–512 Y enterocolitica, 509–510 Y pestis, 504, 510 Y pseudotuberculosis, 506, 510 genome comparison of Yersinia strains, 502 Y enterocolitica biotypes, 506 characteristics of, 505 detection by culture method and PCR, 507–508 incidences of, 506 isolation of serotypes, 507 molecular detection methods for, 509 pigs, as carriers of pathogenic strains, 507 serotypes, 505 symptoms of infection, 506 transmission of, 507 virulence factors, 506 Y pestis disease caused by, 502–503 epidemiology, 503 isolation and molecular detection methods of, 503–504 life-cycle, 503 plasmids, 503 pneumonic plague, transmission of, 503 Y pseudotuberculosis, 503 epidemiology, 505 incidence and prevalence of, 505 isolation rates from animal sources, 505 O-serotypes, 504–505 PCR-based detection methods for, 505–506 spread of infection, 505 symptoms of infection, 503 virulence factors, 503–504 .. .MOLECULAR DETECTION OF FOODBORNE PATHOGENS MOLECULAR DETECTION OF FOODBORNE PATHOGENS EDITED BY DONGYOU LIU Boca Raton London New York CRC Press is an imprint of the Taylor &... explanation without intent to infringe Library of Congress Cataloging-in-Publication Data Molecular detection of foodborne pathogens / [edited by] Dongyou Liu p ; cm Includes bibliographical references... by manufacturers A detection target is not very useful Molecular Detection of Foodborne Pathogens if a subset of strains of that organism not possess it The best methods have been validated by