Holdings: Rapid detection and characterization of foodborne pathogens by molecular techniques

Rapid detection and characterization of foodborne pathogens by molecular techniques:

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Bibliographic Details
Main Author:	Levin, Robert E. (Author)
Format:	Book
Language:	English
Published:	Boca Raton CRC Press 2010
Subjects:	Food > Microbiology Food > Analysis Food Microbiology Food Analysis > methods Food Contamination > prevention & control Food Poisoning > prevention & control Pathogener Mikroorganismus Lebensmittelanalyse
Online Access:	Inhaltsverzeichnis
Item Description:	Includes bibliographical references and index
Physical Description:	XV,592 S. Ill., graph. Darst.
ISBN:	9781420092424

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adam_text	Contents Preface ....................................................................................................................xiii The Author ...............................................................................................................xv Chapter 1 Molecular Techniques for Detecting, Quantifying, and Subspecies Typing of Foodborne Pathogenic Bacteria .................................................................................1 I. The Polymerase Chain Reaction (PCR) ..........................................................1 A. Introduction ............................................................................................1 B. Requirements for PCR ............................................................................1 С Sample Preparation without Enrichment ................................................3 D. Lysing of Cells and Isolation of Bacterial DNA.....................................3 E. PCR for Identification of Pure Cultures .................................................4 F. Quantitative PCR ....................................................................................4 G. Use of an Internal Standard for Quantitative PCR .................................5 H. Construction of an Internal Standard for Quantitative PCR ..................6 I. Construction of a Calibration Curve for Quantitative PCR ...................7 II. Real-Time PCR (Rti-PCR) ..............................................................................8 A. Introduction ............................................................................................8 B. Advantages of Rti-PCR ..........................................................................8 C. Mechanisms of Rti-PCR .......................................................................10 1. SYBR Green ...............................................................................10 2. TaqMan™ Probes ........................................................................11 3. Fluorescent Resonance Energy Transfer (FRET) .......................12 4. Molecular Beacons™ ..................................................................14 5. Unique Fluorogenic Primers .......................................................15 D. Theory of Quantitative Real-Time PCR (QRti-PCR) ...........................16 E. Problems and Limitations of QRti-PCR ...............................................19 III. Nested PCR ...................................................................................................20 A. Introduction ..........................................................................................20 IV. Loop-Mediated Isothermal Amplification (LAMP) Assay ..........................22 A. Introduction ..........................................................................................22 V. Pulsed-Field Gel Electrophoresis (PFGE) ....................................................23 A. Introduction ..........................................................................................23 B. Mechanism of PFGE .............................................................................23 С Interpretation of PFGE Banding Patterns .............................................24 VI. Random Amplification of Polymorphic DNA (RAPD)................................25 A. Introduction ..........................................................................................25 B. Mechanism of RAPD ...........................................................................26 VII. Multilocus Sequence Typing (MLST) ..........................................................27 A. Introduction ..................................-........................................................27 VIII. Restriction Fragment Length Polymorphism (RFLP) and PCR-RFLP ........27 A. Introduction ..........................................................................................27 ^ CONTENTS IX. Amplified Fragment Length Polymorphism (AFLP) ....................................28 A. Introduction ..........................................................................................28 References ................................................................................................................28 Chapter 2 Escherichia coli O157:H7 ........................................................................................33 I. Characteristics of the Organism ....................................................................33 II. Virulence Factors ..........................................................................................33 A. Hemolysins ...........................................................................................33 B. Intimin..................................................................................................34 C. Shiga-Like Toxins .................................................................................34 D. Locus for Enterocyte Effacement .........................................................34 E. Extracellular Serine Protease ...............................................................35 F. Additional Virulence Factors ................................................................35 III. Phenotypic Variation of E. со/г 01 57:H7 ......................................................35 A. Conventional PCR ................................................................................36 B. Multiplex PCR ......................................................................................49 IV. PCR Assays Involving Molecular Probes and Real-Time PCR (Rti-PCR) ......................................................................................................52 V. Loop-Mediated Isothermal Amplification (LAMP) of DNA.......................54 VI. Immunomagnetic Separation and PCR .........................................................54 VII. Restriction Fragment Length Polymorphism ................................................55 VIII. Subspecies Typing of E. coli O157:H7 Isolates .............................................55 References ................................................................................................................56 Chapter 3 Shigella ....................................................................................................................63 I. Characteristics of the Genus .........................................................................63 II. Virulence Factors ..........................................................................................64 III. PCR Detection of Shigellae ..........................................................................65 A. Conventional PCR Assays ....................................................................65 B. Microarrays ...........................................................................................71 C. Multiplex PCR ......................................................................................72 D. Immunocapture PCR ............................................................................73 E. Molecular Typing ..................................................................................73 References ................................................................................................................75 Chapter 4 Salmonella ...............................................................................................................79 I. Characteristics of the Genus .........................................................................79 II. Molecular Techniques ...................................................................................82 A. Conventional PCR ................................................................................82 B. Real-Time PCR (Rti-PCR) .................................................................1 ю CONTENTS vii C. Multiplex PCR (mPCR) ......................................................................115 D. Pulsed Field Gel Electrophoresis (PFGE) ..........................................122 E. Subtracted Restriction Fingerprinting (SFP) ......................................127 F. Random Amplified Polymorphic DNA (RAPD) Analysis .................127 References ..............................................................................................................129 Chapter 5 Vibrio vulnificus ........................................................................................ .............139 I. Characteristics of the Organism ..................................................................139 II. Virulence Factors ........................................................................................140 A. Capsule Production .............................................................................140 B. Extracellular Virulence Factors ..........................................................141 C. Serum-Iron Availability ......................................................................141 III. Enrichment and Isolation Media .................................................................142 A. Alkaline Peptone Salt Broth (APS) ....................................................142 B. Colistin-Polymyxin-ß-Cellobiose (CPC) Agar ...................................142 C. Thiosulfate-Citrate-Bile-Salts Sucrose (TCBS) Agar ........................142 D. Vibrio vulnificus (W) Agar ...............................................................143 E. Sodium Dodecyl Sulfate-Polymyxin-Sucrose (SPS) Agar .................143 F. Cellobiose-Colistin (CC) Agar ...........................................................143 G. Vibrio vulnificus Medium (WM)......................................................143 IV. Identification of V. vulnificus Isolates .........................................................143 A. Biochemical Characteristics ...............................................................143 B. Serotyping and Immunological Techniques .......................................144 V. Typing of V. vulnificus Isolates below the Species Level ............................145 A. Biogroups ............................................................................................145 VI. Viable but Nonculturable (VBNC) V. vulnificus .........................................152 VII. Molecular Methods for Detection and Typing ............................................153 A. Conventional PCR ..............................................................................153 B. Multiplex PCR ....................................................................................154 C. Real-Time PCR (Rti-PCR) .................................................................155 D. RAPD .................................................................................................157 E. Ribotyping ..........................................................................................158 F. 16S rRNA Sequencing ........................................................................159 G. Oligonucleotide Probe ........................................................................159 References ..............................................................................................................161 Chapter 6 Vibrio parahaemolyticus .......................................................................................167 I. Characteristics of the Organism ..................................................................167 II. Clinical Symptoms Due to Infections by V. parahaemolyticus ..................168 III. Ecology of V. parahaemolyticus .................................................................168 IV. Phenotypic Characteristics of V. parahaemolyticus ...................................169 A. General ................................................................................................169 viii CONTENTS B. Flagellation .........................................................................................170 C. Antigenic Properties ...........................................................................171 D. Hemolysins .........................................................................................172 1. General ......................................................................................172 2. Direct Acting Hemolysins .........................................................172 E. H2S Production ...................................................................................179 F. Urease (Uh) Production ......................................................................179 V. Sensitivity of V. parahaemolyticus to Low Temperatures ..........................180 VI. Isolation and Cultivation of V. parahaemolyticus .......................................181 VII. Preservation of V. parahaemolyticus Isolates .............................................182 VIII. Bacteriophage for V. parahaemolyticus ......................................................182 IX. Use of PCR for Detection of V. parahaemolyticus .....................................182 X. Molecular Typing of V. parahaemolyticus Isolates below the Species Level ............................................................................................................188 XI. The O3:K6 Pandemic Clone ........................................................................188 References ..............................................................................................................192 Chapter 7 Vibrio cholerae ......................................................................................................203 I. Characteristics of the Organism ..................................................................203 II. Factors Associated with the Virulence of V. cholerae ................................204 III. PCR Detection, Identification, and Characterization of V. cholerae ..........204 IV. Molecular Typing of V. cholerae Isolates ...................................................223 V. Acquisition of Antibiotic Resistance ...........................................................227 VI. Biotype Conversion by Phage .....................................................................227 References ..............................................................................................................229 Chapter 8 Aeromonas hydrophila ...........................................................................................235 I. Characteristics of the Organism ..................................................................235 II. PCR Detection ............................................................................................236 HI. Distribution of Toxin Genes ........................................................................237 IV. Genotyping Using Hemolysin and Aerolysin Genes ...................................241 V. Restriction Fragment Length Polymorphism (RFLP) ................................241 References ..............................................................................................................242 Chapter 9 Plesiomonas shigelloides .......................................................................................245 I. Characteristics of the Organism ..................................................................245 II. Nomenclature and Taxonomy .....................................................................245 III. Physiological and Biochemical Characteristics ..........................................246 IV. Ecological Distribution ...............................................................................246 V. Toxins and Invasive Factors ........................................................................248 CONTENTS ¡χ VI. ß-Hemolysis................................................................................................249 VII. Isolation.......................................................................................................249 VIII. Serology ......................................................................................................250 IX. Epidemiology and Outbreaks ......................................................................252 X. Application of PCR .....................................................................................252 A. Conventional PCR ..............................................................................252 B. Real-Time PCR (Rti-PCR) .................................................................255 References ..............................................................................................................256 Chapter 10 Campylobacter jejuni ............................................................................................261 I. Characteristics of the Organism ..................................................................261 A. Phenotypic Characteristics of Campylobacters ..................................262 II. Ecological Distribution of Campylobacters ................................................262 A. Environmental Factors ........................................................................262 1. Aquatic Sources of Campylobacters .........................................263 2. Wildlife as a Potential Reservoir for Infection by C. jejuni .....................................................................................264 3. Campylobacters Associated with Farm and Domesticated Animals .....................................................................................266 B. Vertical versus Horizontal Transmission among Poultry ...................269 III. Virulence Factors ........................................................................................269 A. Toxins ..................................................................................................269 B. Cell Adhesion Factors .........................................................................275 C. Lipopolysaccharide (LPS) ..................................................................276 D. Capsule Formation ..............................................................................277 E. Virulence Plasmid ..............................................................................277 IV. Isolation of Campylobacters from Foods ....................................................277 V. Serotyping of Campylobacters and Immunological Detection ...................283 VI. Bacteriophage Typing of С jejuni ..............................................................284 VII. Molecular Methods of Detecting and Typing Campylobacters ..................285 A. Genes Used .........................................................................................285 B. PCR .....................................................................................................285 C. Randomly Amplified Polymorphic DNA (RAPD) Analysis ..............305 1. Pulsed Field Gel Electrophoresis (PFGE) .................................307 2. Restriction Fragment Length Polymorphism (RFLP) Analysis .....................................................................................310 D. Amplified Fragment Length Polymorphism (AFLP) .........................313 1. In Situ Colony Hybridization ....................................................313 E. Multilocus Sequence Typing (MLST) ................................................314 F. Loop-Mediated Isothermal Amplification (LAMP) ...........................315 G. Nucleic Acid Sequence Based Amplification (NASBA) ....................315 H. Restriction Endonuclease Analysis .....................................................316 VIII. The Viable but Nonculturable (VBNC) State of Campylobacters ..............316 x CONTENTS IX. The Coccoid Form of C. jejuni ...................................................................319 X. Immunomagnetic Capture of С jejuni .......................................................319 References ..............................................................................................................320 Chapter 11 Staphylococcus aureus ..........................................................................................337 I. Characteristics of the Organism ..................................................................337 II. Molecular Techniques for Detection and Identification of S. aureus .........338 A. PCR Used to Detect and Identify S. aureus .......................................338 B. Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA ■ FISH) for Detection of S. aureus ........................................................341 C. Conventional and Real-Time PCR (Rti-PCR) Detection of Enterotoxin Genes ..............................................................................341 D. Loop-Mediated Isothermal Amplification (LAMP) Assay for se Toxin Genes ........................................................................................348 E. PCR Detection of the tst Gene in S. aureus Strains ...........................349 F. Molecular Typing of S. aureus Isolates (RAPD, PFGE, RFLP, PCR-RFLP) ........................................................................................349 G. Multilocus Sequence Typing (MLST) of S. aureus Isolates ..............355 H. PCR-Immuno Assays for Detection of S. aureus Exotoxin Genes ..................................................................................................358 I. Exfoliative Toxin (ET) Producing Strains of S. aureus ......................359 J. PCR Detection of Methicillin-Resistant S. aureus Strains ................360 K. Enterotoxin Production by S. intermedius ..........................................362 III. The Role of S. aureus .Bacteriophage (Phage) in Pathogenesis ...................362 References ..............................................................................................................401 Chapter 12 Listeria monocytogenes .........................................................................................411 I. Characteristics of the Organism ..................................................................411 A. Gene Sequences Used in PCR Assays for L. monocytogenes ............412 B. PCR Identification of L. monocytogenes and Other Members of the Genus Listeria...............................................................................413 C. Direct PCR Detection of L. monocytogenes in Foods without Enrichment Cultivation .......................................................................422 D. PCR Detection of L. monocytogenes in Foods Following Enrichment Cultivation .......................................................................424 E. Nested PCR .........................................................................................427 F. Multiplex PCR (mPCR) ......................................................................429 G. Real-Time PCR (Rti-PCR) .................................................................431 H. Application of Random Amplified Polymorphic DNA (RAPD) Analysis toL. monocytogenes Isolates ...............................................432 I. Application of Pulsed Field Gel Electrophoresis (PFGE) to L. monocytogenes Isolates ..................................................................441 CONTENTS xi J. Comparison of RAPD, PFGE, and Other Molecular Methods for Typing L. monocytogenes Isolates ......................................................445 K. M icroarray Technology ......................................................................448 L. PCR Determination of Serotype Divisions ........................................448 References ..............................................................................................................449 Chapter 13 Clostridium botulinum ...........................................................................................457 I. Characteristics of the Organism ..................................................................457 II. Relationship between Botulism and Seafood ..............................................457 III. Infant Botulism ...........................................................................................458 A. Historical Aspects and Incidence .......................................................458 B. Implication of Honey in Infant Botulism ...........................................459 IV. Molecular Techniques Applied to C. botulinum .........................................460 A. PCR Detection of С botulinum .........................................................460 B. Molecular Typing of Clostridium botulinum Strains .........................465 C. Molecular Methods for Differentiating between Group I and Group II Strains ..................................................................................468 D. Molecular Methods for Detection of BoNTs ......................................469 1. Reverse Transcription PCR for Indirect Measurement of BoNT Production ......................................................................469 2. Immunopolymerase Chain Reaction Assays for Ultrasensitive BoNT Detection .................................................470 References ..............................................................................................................481 Chapter 14 Clostridium perfringens ........................................................................................487 I. Characteristics of the Organism ..................................................................487 II. Molecular Methods for Detection of C. perfringens ..................................488 A. PCR .....................................................................................................488 B. Molecular Probes ................................................................................504 III. Molecular Typing of Isolates .......................................................................506 A. Molecular Organization of the CPE Gene ..........................................506 B. Genotyping .........................................................................................510 С Random Amplified Polymorphic DNA (RAPD) Typing ....................514 D. Pulsed Field Gel Electrophoresis (PFGE) Typing ..............................514 E. Amplified Fragment Length Polymorphism (AFLP) .........................515 F. Ribotyping ..........................................................................................516 G. Multiple-Locus Variable Number Tandem Repeat Loci (VNTR) ...............................................................................................517 References ..............................................................................................................517 xü CONTENTS Chapter 15 Bacillus cereus .......................................................................................................523 I. Characteristics of the Organism ..................................................................523 II. Selective Isolation ofß. cereus ...................................................................524 A. Selective Agar Media ..........................................................................524 III. The Emetic Toxin Cereulide .......................................................................525 A. Synthesis of Cereulide and Location of the Responsible Peptide Synthetase ...........................................................................................525 B. Phenotypic Characteristics of Emetic Toxin Producing Strains .........525 C. RAPD Typing of Emetic Strains of B. cereus ....................................525 IV. Enterotoxins ofß. cereus ............................................................................526 A. Major Enterotoxins of B. cereus .........................................................526 V. Molecular Methods for Detection and Confirmation of B. cereus .............526 A. PCR .....................................................................................................526 1. PCR Detection of Emetic Strains of B. cereus .........................526 2. PCR Detection and Confirmation ofß. cereus and Members of the B. cereus Group ..............................................529 VI. Molecular Typing ofß. cereus Isolates .......................................................550 A. Genotyping of B. cereus Isolates ........................................................550 B. Multilocus Sequence Typing (MLST) ofß. cereus Isolates ..............556 С RAPD Typing .....................................................................................556 D. Ribotyping ..........................................................................................556 E. PCR Restriction Fragment Length Polymorphism (PCR-RFLP) ......557 F. Microarrays .........................................................................................557 References ..............................................................................................................559 Index ......................................................................................................................565
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spelling	Levin, Robert E. Verfasser aut Rapid detection and characterization of foodborne pathogens by molecular techniques Robert E. Levin Boca Raton CRC Press 2010 XV,592 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Food Microbiology Food Analysis Food Analysis methods Food Contamination prevention & control Food Poisoning prevention & control Pathogener Mikroorganismus (DE-588)4044890-3 gnd rswk-swf Lebensmittelanalyse (DE-588)4167032-2 gnd rswk-swf Lebensmittelanalyse (DE-588)4167032-2 s Pathogener Mikroorganismus (DE-588)4044890-3 s DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018708286&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Levin, Robert E. Rapid detection and characterization of foodborne pathogens by molecular techniques Food Microbiology Food Analysis Food Analysis methods Food Contamination prevention & control Food Poisoning prevention & control Pathogener Mikroorganismus (DE-588)4044890-3 gnd Lebensmittelanalyse (DE-588)4167032-2 gnd
subject_GND	(DE-588)4044890-3 (DE-588)4167032-2
title	Rapid detection and characterization of foodborne pathogens by molecular techniques
title_auth	Rapid detection and characterization of foodborne pathogens by molecular techniques
title_exact_search	Rapid detection and characterization of foodborne pathogens by molecular techniques
title_full	Rapid detection and characterization of foodborne pathogens by molecular techniques Robert E. Levin
title_fullStr	Rapid detection and characterization of foodborne pathogens by molecular techniques Robert E. Levin
title_full_unstemmed	Rapid detection and characterization of foodborne pathogens by molecular techniques Robert E. Levin
title_short	Rapid detection and characterization of foodborne pathogens by molecular techniques
title_sort	rapid detection and characterization of foodborne pathogens by molecular techniques
topic	Food Microbiology Food Analysis Food Analysis methods Food Contamination prevention & control Food Poisoning prevention & control Pathogener Mikroorganismus (DE-588)4044890-3 gnd Lebensmittelanalyse (DE-588)4167032-2 gnd
topic_facet	Food Microbiology Food Analysis Food Analysis methods Food Contamination prevention & control Food Poisoning prevention & control Pathogener Mikroorganismus Lebensmittelanalyse
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018708286&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT levinroberte rapiddetectionandcharacterizationoffoodbornepathogensbymoleculartechniques

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