Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems Edited by MOHAMMED ZOUROB Biophage Pharma Inc Montreal, Canada SOUNA ELWARY Consultant to Biophage Pharma Inc Montreal, Canada ANTHONY TURNER Cranfield University Bedfordshire, UK 13 Editors Mohammed Zourob Biophage Pharma Inc Montreal Canada m.zourob@biophagepharma.net Souna Elwary Consultant to Biophage Pharma Inc Montreal Canada selwary@yahoo.com Anthony Turner Cranfield University Bedfordshire UK a.p.turner@cranfield.ac.uk ISBN: 978-0-387-75112-2 e-ISBN: 978-0-387-75113-9 Library of Congress Control Number: 2007941938 © 2008 Springer Science+Business Media, LLC All rights reserved This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights Printed on acid-free paper springer.com Preface Bacterial contamination of food and water resources, as well as the increasing incidence of nosocomial infections, has us on our toes, looking for ways of recognizing these elements In addition, the recent and growing threats to personal and territorial securities make this task even more urgent Therefore, accurate assessment of the state of current technologies is a prerequisite for undertaking any course of action towards future improvements In particular, development of new detection and identification technologies for the plethora of bacterial agents has become increasingly important to scientists and to regulatory agencies In recent years, there has been much progress in the field of bacterial agents detection, resulting in the development of more accurate, fast, analyte-specific, robust, and cost effective techniques by incorporating emerging technologies from various disciplines Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems presents a significant and up-to-date review of various integrated approaches for bacterial detection by distinguished engineers and scientists This work is a comprehensive approach to bacterial detection, presenting a thorough knowledge of the subject and an effective integration of disciplines in order to appropriately convey the state-of the-art fundamentals and applications of the most innovative approaches The book consists of four parts The first part (Chapters 1–4) is an introduction to pathogenic bacteria and sampling techniques and provides an overview of the rapid microbiological methods The second part (Chapters 5–20) describes the different transducers used for bacterial detection It covers the theory behind each technique and delivers a detailed stateof-the-art review for all the new technologies used The third part (Chapters 21–29) covers the different recognition receptors used in the latest methods for the detection of bacteria It describes in detail the use of immunoassays, nucleic acids, oligonucleotide microarrays, carbohydrates, aptamers, protein microarrays, bacteriophage, phage display, and molecular imprinted polymers as recognition elements The fourth part (Chapters 30–36) covers the different microsystems used for detection/identification and bacterial manipulations, mainly bacteria lysis in microfluidics, PCR in microfluidics, dielectrophoresis, ultrasonic manipulation techniques, and mass spectrometry We anticipate that the book will be helpful to academicians, practitioners, and professionals working in various fields, including biomedical sciences, physical sciences, microsystems engineering, nanotechnology, veterinary science and medicine, food QA, bioterrorism and security as well as allied health, healthcare and surveillance Since the fundamentals are also reviewed, we believe that the book will appeal to advanced undergraduate and graduate students who study in areas related to bacterial detection We gratefully acknowledge all authors for their participation and contributions, which made this book a reality We give many thanks to Olivier Laczka and Joseph Piliero for the book cover design Mohammed Zourob Souna Elwary Anthony Turner June 2008 v Contents Part I Introduction Introduction to Pathogenic Bacteria Tracey Elizabeth Love and Barbara Jones Pathogenic Microorganisms 1.1 Toxins 1.2 Adherence 1.3 Invasion 1.4 Evasion of the Host Immune Response 1.5 Iron Acquisition 1.6 Regulation of Virulence Factors Sources and Routes of Infection 2.1 Natural Infection 2.2 Food and Water 2.3 Hospital Acquired Infections 2.4 Intentional Infection—Biological Warfare Detection of Pathogenic Microorganisms Conclusions References 4 7 8 9 10 10 11 12 12 Sample Preparation: An Essential Prerequisite for High-Quality Bacteria Detection Jan W Kretzer, Manfred Biebl and Stefan Miller Introduction The Sample Sampling 3.1 Sample drawing Microbiological Examination of Foods Microbiological Examination of Surfaces Microbiological Examination of Air Sample Handling Sample Preparation Sample Preparation for Detection of Intact Bacterial Cells 10 Sample Preparation for Detection of Bacterial Nucleic Acids 11 Conclusions and Future Perspectives References 15 16 17 17 17 17 18 20 21 21 23 27 28 Detection of Bacterial Pathogens in Different Matrices: Current Practices and Challenges Ahmed E Yousef Introduction Analytical Tools and Methods: A Historical Perspective vii 31 32 viii Contents Defining the Terms Matrix Complexity and Pathogen Detection Techniques Currently Used in Pathogen Detection Methods 5.1 Culture Techniques 5.2 Enzyme-Linked Immunoassay 5.3 Polymerase Chain Reaction (PCR) Basics of Pathogen Detection 6.1 Sampling 6.1.1 Air Sampling 6.1.2 Surfaces Sampling 6.1.3 Bulk Sampling 6.2 Sample Preparation 6.3 Pathogen Amplification 6.4 Selection and Screening 6.5 Identification 6.5.1 Morphological Characteristics 6.5.2 Biochemical and Physiological Traits 6.5.3 Serological Properties 6.5.4 Genetic Characteristics 6.6 Pathogenicity Testing 6.6.1 Koch’s Postulates 6.6.2 Mammalian Cell Culture (Tissue Culture) 6.6.3 Virulence Genes and Gene Expression Products 6.7 Testing for Specific Traits Challenges to Current Detection Methods 7.1 Pathogen Quantification Problems 7.2 Can a Small Bacterial Population be Detected Rapidly and Reliably? 7.3 Which Traits to Analyze, and How Many Tests are Needed for Identifying a Bacterial Pathogen? 7.4 Real-Time Detection References 32 32 33 33 35 36 36 37 37 37 39 39 39 40 40 41 41 42 42 43 43 43 44 44 44 44 44 45 46 46 Overview of Rapid Microbiological Methods Jeanne Moldenhauer Introduction A History of Rapid Microbiological Methods: Industry Reluctance to Accept These Methods Types of Microbial Testing Performed Types of Rapid Microbiological Methods 4.1 Growth-Based Technologies 4.2 Viability-Based Technologies 4.3 Cellular Component or Artifact-Based Technologies 4.4 Nucleic Acid-Based Technologies 4.5 Automated Methods 4.6 Combination Methods Overview of Rapid Technologies and How They Work 5.1 Adenosine Tri-Phosphate (ATP) Bioluminescence 5.2 Adenylate Kinase 5.3 Autofluorescence 5.4 Biochemical Assays and Physiological Reactions 5.5 Biosensors and Immunosensors 5.6 Carbon Dioxide Detection 5.7 Changes in Headspace Pressure 49 50 50 50 50 50 51 51 51 51 51 51 52 52 52 53 53 53 Contents 5.8 Colorimetric Detection of Carbon Dioxide Production 5.9 Concentric Arcs of Photovoltaic Detectors with Laser Scanning 5.10 Direct Epifluorescent Filter Technique (DEFT) 5.11 DNA Sequencing 5.12 Endospore Detection 5.13 Enzyme Linked Immunosorbent Assay (ELISA) 5.14 Flow Cytometry 5.15 Fluorescent Probe Detection 5.16 Fatty Acid Profiles (Fatty Acid Methyl Esters, FAMEs) 5.17 Fourier Transformed Infrared Spectroscopy (FTIR) 5.18 Gram Stains (Rapid Method) 5.19 Impedance 5.20 Immunological Methods 5.21 Lab-on-a-Chip (LOC), Arrays, Microarrays and Microchips 5.22 Limulus Amebocyte Lysate (LAL) Endotoxin Testing 5.23 Mass Spectrometry (Matrix-Assisted Laser Desorption-Time of Flight (MALTI-TOF)) 5.24 Microcalorimetry 5.25 Micro-Electro-Mechanical Systems (MEMS) 5.26 Nanotechnology 5.27 Near Infrared Spectroscopy (NIRS) 5.28 Nucleic Acid Probes 5.29 Optical Particle Detection 5.30 Polymerase Chain Reaction (PCR) 5.31 Rep-PCR 5.32 Raman Spectroscopy 5.33 Ribotyping/Molecular Typing 5.34 Solid Phase Laser Scanning Cytometry 5.35 Southern Blotting/Restriction Fragment Length Polymorphism 5.36 Spiral Plating 5.37 Turbidimetry Potential Areas of Application of Rapid Microbiological Methods Disclaimer Conclusions References ix 53 54 54 54 55 55 55 55 56 56 56 57 57 57 58 58 58 59 59 59 59 59 60 60 61 61 61 62 62 62 62 75 75 75 Part II Biosensors Surface Plasmon Resonance (SPR) Sensors for the Detection of Bacterial Pathogens Allen D Taylor, Jon Ladd, Jiˇrí Homola and Shaoyi Jiang Introduction Fundamentals of Surface Plasmon Resonance Biosensing SPR Sensor Instrumentation Surface Chemistries and Molecular Recognition Elements Detection Formats Quantification of Bacteria Cells 6.1 Challenges for the Detection of Whole Bacteria by SPR 6.2 Effect of Bacteria Sample Treatment 6.3 Examples of Bacteria Detection 6.3.1 Escherichia coli 6.3.2 Salmonella spp 6.3.3 Listeria monocytogenes 83 83 85 88 90 91 91 92 92 93 97 98 x Contents 6.3.4 Other Bacteria 6.3.5 Detection of Multiple Bacteria Genetic Markers Antibody Biomarkers Conclusions and Future Perspectives References Bacterial Detection Biosensors Using Evanescent Wave-Based 98 99 101 103 103 104 Fluorescent Kim E Sapsford and Lisa C Shriver-Lake Introduction Current State of Bacterial Fluorescent TIRF Biosensors 2.1 Non-Planar Substrates 2.1.1 Fiber Optics 2.1.2 Capillaries 2.2 Planar Substrates 2.2.1 NRL Array Biosensor 2.2.2 Other Optical Waveguides 2.2.3 TIRF-Microscopy Future Aspects of Bacterial Fluorescent TIRF Biosensors Conclusions References 109 112 112 112 112 112 113 115 116 117 119 120 Fiber Optic Biosensors for Bacterial Detection Ryan B Hayman Fiber Optic Biosensors 1.1 Whole-Cell Detection 1.1.1 Evanescent-Field Sensing 1.1.2 Sandwich Immunoassays 1.2 Bead-Based Arrays 1.3 Nucleic Acid Sandwich Assays 1.4 Nucleic Acid Direct Hybridization 1.5 Extension Reactions Conclusions and Future Perspectives References 125 126 126 127 128 129 131 134 134 135 Integrated Deep-Probe Optical Waveguides for Label Free Bacterial Detection Mohammed Zourob, Nina Skivesen, Robert Horvath, Stephan Mohr, Martin B McDonnell and Nicholas J Goddard Introduction 1.1 Planar Optical Waveguides 1.2 Total Internal Reflection and Evanescent Waves 1.3 Waveguide Modes 1.4 Frustrated Total Internal Reflection, Leaky Modes 1.5 Literature on Waveguides for Bacterial Detection Deep-Probe Optical Waveguide Sensors with Tunable Evanescent Field 2.1 Waveguide Modes, Light Coupling and Sensing Depths of Evanescent Waves 2.1.1 Light Coupling Techniques 139 141 141 143 144 144 145 146 148 Contents 2.2 Waveguide Designs Based on Low-Index Substrates 2.2.1 Bacteria Detection Using Reverse Symmetry Waveguides 2.3 Waveguide Designs Based on Metal- and Dye-Clad Substrates—Leaky Modes 2.3.1 Results Integrated Deep-Probe Optical Waveguides Systems 3.1 Integration with Electric Field 3.2 Integration with Ultrasound Standing Waves (USW) Conclusions and Future Perspectives References xi 150 151 152 156 160 161 163 166 166 Interferometric Biosensors Daniel P Campbell Principles of Optical Interferometry 1.1 Optical Waveguides 1.2 Planar Waveguide Operation 1.3 Types of Waveguides Light Coupling Methods 2.1 Interferometers 2.2 Collinear or Single Channel Interferometers 2.3 Two-Channel Interferometers Interferometric Array Sensors Surface Plasmon Interferometry Other Interferometric Methods and Designs Surface Functionalization Sample Collection Systems Interferometric Applications for Whole-Cell Detection Advantages and Limitations 10 Potential for Improving Current Performance References 169 171 172 175 178 180 183 186 192 195 196 197 198 199 206 206 208 10 Luminescence Techniques for the Detection of Bacterial Pathogens Leigh Farris, Mussie Y Habteselassie, Lynda Perry, S Yanyun Chen, Ronald Turco, Brad Reuhs and Bruce Applegate Beyond Robert Boyle’s Chicken The Bacterial (lux) Luminescent System for Direct Pathogen Detection The Firefly (luc) Luminescent System for Direct Pathogen Detection The Use of Alternative Luciferases in Pathogen Detection Luminescent-Based Immunoassays Chemiluminescence Detection Methods Conclusions and Future Perspectives References 214 215 219 222 222 222 225 226 11 Porous and Planar Silicon Sensors Charles R Mace and Benjamin L Miller Introduction 1.1 Porous Silicon: A Three-Dimensional Matrix for Biosensing 1.2 Effect of PSi Immobilization on Probe Viability: Experiments with GST 1.3 Toward Larger Targets: The First Macroporous Microcavity Structures 1.4 Porous Silicon Bandgap Sensors in Novel Formats: “Smart Bandages” and “Smart Dust” Arrayed Imaging Reflectometry—A Planar Silicon Biosensor 2.1 Theory 231 232 233 235 235 236 236 956 Antibodies (Continued) structure of, 568–569 synthetic peptides and, 571–572 Anticalins, 778 See also Phage display Anti-ferromagnetic dipole moments, alignment of, 447 Antigen detection assay systems, 758 Anti-Listeria monoclonal antibody, 576 Antimicrobial peptides (AMP) and E coli O157:H7 and salmonella detection of, 145 and NRL Array Biosensor, 114 AOAC official method 996.08, 32 AO2 probes multiplexed array response, 130–131 API Systems (bioMerieux), 53 APS-5, chemiluminescent dyes, 586 Aptamers artificial nucleic acid ligands, 356 and bacteria detection, 689–710 nucleic acid tools, 779 properties and targets growing catalogue, 698 ligand interactions, 700 purification and, 701–702 and recognition elements, 700–701 as sensing elements, 702–706 specificity, 698–700 with therapeutic potential, 702 Arenaviruses, 11 Array biosensor, 722 Arrayed imaging reflectometry (AIR) applications of, 242–244 and monochromatic platform, 242 null reflectance condition and, 236–237 and oligonucleotide hybridization, 246–247 pathogen detection, 246 physical rationale and, 236–237 and polychromatic platform, 240–242 probe immobilization and, 244–245 and protein array, 247–250 substrate design and mathematical model, 237–240 Array sensors, interferometric, 192–195 ArrayTube platform, 721 sandwich ELISA and streptavidin HRP-based detection, 591 Artus PCR kit, 615 Attenuated total reflection (ATR), 56 AuD1S probes multiplexed array response, 130–132 Autofluorescence, growth-based technology, 52 Autonomous pathogen detection system (APDS), 494, 500–501 Avidin glycoprotein, 360–361 biotin system, 198 66-kDa glycoprotein, 320–321 AviTag system (Avidity), 777 B Bacillus anthracis (BA), 4, 11, 37, 131 Biohazard Detection System (BDS) for, 500 detection by cantilever sensors, 461–463 DNA characteristics and antigen markers for, 491 endospore-forming pathogen, 485–487 immuno-based flow cytometry detection assays for, 494 Liat Anthrax Assay, 500 lysin, plyG, 513 and NRL Array Biosensor, 113 Index nucleic acid sequence-based amplification (NASBA) method, 509 PCR detection methods, 495 phenotypic tests for presumptive identification of, 490 protective antigen (PA) and botulinum toxin, 493–494 pXO1 and pXO2 plasmids, 498 real-time PCR detection and, 497–498 spores and binding of Gal-SWNTs and Man-SWNTs, 678 sterne detection, 127–128 by TSM sensor, 261 Bacillus cereus, 23 food-borne pathogens, 10 Bacillus genera endospore-producing prokaryotes, 482–483 spores germination study by phase contrast microscopy, 511 spores, SERS fingerprints, 549 Bacillus globigii, 125–126 spores, chip-based detection for analysis of, 844 spores microSERS, 554 Bacillus subtilis, 462 DNA detection of, 499 spores, 461 Bacillus subtilis var niger (BG), 116 Bacillus subtilus and SPR sensors, 98 Bacillus thuringiensis-containing pesticides, 127 Bacillus thuringiensis kurstaki (BTK), 131 BacT/ALERT computer-aided imaging type of system, 51, 53 Bactec (Becton Dickinson and Company) system, 53 Bacteria adhesion of, 661 antigens, physical and chemical stresses effects on expression profile of, 592–594 cells detection immobilization matrices, 159–160 reflection mode, 156–157 scattering mode, 157–159 cells quantification sample treatment effect of, 92 whole bacteria, detection by SPR, 91–92 cells, SPR detection of Escherichia coli, 93–97 Listeria monocytogenes, 98 Salmonella spp., 97–98 cell surface, assembly of C3 convertase on, combination of fiber-optic biosensor with PCR, detection of, 588 in complex samples, analysis of, 544–545 detection by carbohydrate-functionalized carbon nanotubes for, 678–680 carbohydrate microarrays for, 668–670 conjugated fluorescent glycopolymers, 672–676 glyconanoparticles for, 676–677 lectin microarrays for, 670–672 and magnetoelastic sensors, E coli, 449, 450–453 reverse symmetry waveguides, 151–152 detection, real time MS LDI MS, 932 MALDI MS, 932–935 pyrolysis MS, 931–932 whole cell analysis of, 930 dielectrophoresis of, 895 electrokinetics applications for, 901–904 Index fingerprints, impact of growth conditions on, 536–539 immobilization by immunomagnetic separation (IMS), 22 infection, protein expression signatures screening with, 726 magnetic relaxation signal, detection with, 448–449 micropatterning for detection technologies, 855 and monoclonal antibody 8-9H (ligand) interaction sensorgrams, 97 pathogens commercially available immunoassay kits for, 581–582 detection from clinical samples, 604 and pathogenic detection methods, 15 sampling of, 17 surface carbohydrate structures of, 664–668 protein toxin detection, 113–114 See also NRL Array Biosensor sensing and GMR structure, 446–447 sensing and water-soluble fluorescent conjugated glycopoly(p-phenylene)s, 672 SERS fingerprinting of, 535–536 toxins and modes of action, viable/nonviable, 539 and viral surface interactions, fundamentals of, 857 and visible light from biochemical reactions, 216 Bacteria micropatterned surfaces fabrication technologies micromolding (soft lithography) capillary force lithography, 860–861 microcontact printing, 859–860 microtransfer molding, 860 replica molding, 859 photolithography and, 858–859 scanning probe lithography (SPL), 861–862 Bacteria/spore lysis Bench scale methods and, 818–820 microfluidic systems, lysis for chemical, 821–823 electrical, 827–828 laser-based, 826–827 mechanical, 820–821 thermal, 823–825 Bacteriological analytical manual (BAM) method for detection of Salmonella spp., 35 Bacteriophage lytic replication cycle of, 734–735 T4, infection cycle, 23 tools for bacterial pathogens detection, 731–750 Bactometer (bioMerieux), 57 BacTrac® commercial impedimetric systems, 57, 354 BAX® Microbial Identification System (Qualicon), 60 BAX® , NAD assays kits, 614 BeadRetriever™ automated IMS systems, 577 B globigii spp detection by sandwich immunoassay format, 145 spores detection by microchip-based flow cell system, 494 BIACore SPR sensors, 87, 582 BioCD single chip interferometer, 197 Biochip affinity studies, Listeria strains, 544 Biohazard Detection System (BDS), 500 Biological warfare (BW), 10–11 agents (BWAs), 131 direct hybridization detection of, 133 BIOLOG Systems (Biolog), 53 957 Bioluminescent enzyme immunoassays (BEIA) for detection of pathogens, 222 BioMag Solo-Sep, 446 Bio-micro-electro-mechanical-systems (Bio-MEMS), 871–872 Biopanning, phage-bearing peptides, 574 Bioparticles, integrated detection system for, 896 Biopesticides Bacillus spp., 488 Biosensor formats biological sensing elements antibodies and, 382–384, 385–387 biosensor transducing element, conducting polymers, 388–390 DNA, 384–387 definition of, 382 Biosensors amperometric, 300–302 DNA based, 306–310 immunosensors, 303–306 microbial metabolism-based, 302–303 applications of, 862–864 charge-transfer resistance, 348–349 constant phase element, 346–347 devices and challenges, 857 double layer and interfacial capacitance, 346 Faradaic parameters, 347–348 geometric capacitance, 346 healthcare and, 864–865 and solution resistance, 345–346 toxins detection of in environment, 865 Warburg impedance, 349–350 based on MIPs, 803 and amino acids detection, 804–805 polymers and, 806–808 toxins and, 805–806 and biological recognition molecule, 110 impedimetric measurement and electrodes, 352–353 tetrapolar configuration and, 352 two and three-electrode configurations, 350–35‘ optical antibody-based microfluidic sensors, 588–589 fiber-optic, 587–588 serodiagnosis, 589–590 surface plasmon resonance (SPR) and, 587 pathogen detection and antibodies (Ab), 355 aptamers, 356 nucleic acids, 355–356 and pathogenic microorganisms, 11 self-doped and non-self-doped Pani conductometric biosensor, 404–406 detection concept of, 398–399 lateral flow conductometric biosensor, 403–404 performance of, 404 preparation and characterization, 392–394 properties of, 394–396, 399–404 testing of, 271 voltammetric, 301 BioTek, 58 Biotin-(Strept) Avidin system, 360–361 Biotin-tagged phages and quantum-dot based detection (QD), bacterial detection, 746 BioVigilant Instantaneous Microbial Detector (IMD), 52 BioWarfare Agent Detection Devices (BADD), 493 Bioweapon, B anthracis, 487 BK multimeter Model AK-2880A, 394 958 Bode plots, impedance plotting, 344 Bordetella pertusis antipeptide antibodies, 572 Bovine serum albumen (BSA), carrier molecule, 571–572 Bragg mirrors/microcavity resonators, 232 Brain-heart infusion broth (BHI) for Listeria isolation and recovery, 593 Branched DNA amplification (bDNA) and in vitro amplification technologies, 615–616 Brevetoxins (895 Da), microSERS studies, 556 Brucella spp., 508, 708 biowarfare agents, 589 Buffered Listeria enrichment broth (BLEB) for Listeria isolation and recovery, 591 Bunyaviruses, Burkholderia spp., 506 biowarfare agents, 591 Butler-Volmer kinetics and electrode-solution interface, 348 C Cadaverine (102 Da), microSERS studies, 555 Calcium dipicolinate [Ca (dpa)] in bacterial endospores, 55 Campylobacter spp., 27 cells in raw milk detection by PCR, 609–610 food-borne pathogens, 10 in food, PCR-based assays, 613 with mono-and polyclonal antibodies detection, 205 and NRL Array Biosensor, 114 and PCR/DNA probe assays, 609 real-time PCR tests for, 617 sandwich immunoassay format detection by, 145 SPR sensors and, 98, 99 Canavalia ensiformis (jack bean), 543 Cantilever sensors for pathogen detection, 459 cells detection and, 461–463 millimeter-sized, 460 physics of, 463–466 resonance modes and, 466–468 Capillary-based systems for PCR, 842–843 Capillary Electrophoresis (CE) based selections, 697 Capillary microbead (spheres) immunoassay for staphylococcal enterotoxins (SEs), 586 Carbohydrate-functionalized carbon nanotubes for bacteria detection, 678–680 Carbohydrate microarrays for bacteria detection, 668–670 covalent approach for, 669 noncovalent approach for, 669 Carbon dioxide detection, growth-based technology, 50 Carbon nanotubes (CNT), 391–392 Cells and inhomogeneous electric field, 898 sorter, 884 See also Large-scale flow cytometer for cell counting and sorting washing, principle of, 920 Centrifugal sampler, 20 See also Air Cepheid GeneXpert® technology, 500 Channel waveguides and Mach-Zehnder interferometers, 177 Chemiluminescence (CL) detection methods, 222–225 Chemiluminescent immunoassay (CLIA), 586 Index Chlamydia trachomatis STI organisms detection, 605 by TSM sensor, 261 Cholera toxin, immunodetection mechanism, 367–368 Clausius-Mossotti factor for dielectric materials, 898 CL-EIS system drawback of, 224–225 Escherichia coli O157:O7 detection of, 224 Clostridium spp., 10, 11, 23, 131, 485 botulinum toxoids A and B, 113 food-borne pathogens, 10 genera, endospore-producing prokaryotes, 482 neurotoxin as chemical weapon, 489 and neurotoxin production, 37 phenotypic identification, 489 spores germination study by phase contrast microscopy, 509–510 tetanus toxin and, 114 vegetative cell, 482 Coformycin (284 Da), microSERS studies, 555 Collinear polarimetric/difference interferometer, 184–186 Comparative genome hybridizations (CGH), 645–646 Competitive assay and SPR sensors, 90–91 Concanavalin A (ConA) from Canavalia ensiformis (jack bean), 543 Conformation-dependent fluorescent sensors, 703 Congen (SureFood® Pathogen Kits), 619 Constant phase element (CPE), 346–347 Continuous-flow PCR, 844–845 Corynebacterium dihtheriae diphtheria toxin, 114 Coupled oscillators model, 286–287 Coupled plasmon-waveguide resonator (CPWR), 146 COVASIAM computer-aided imaging type of system, 51, 52 Cowpea mosaic virus (CPMV), 114 Cross-contaminating organisms, 20 Cryptosporidium parvum oocysts microSERS, 554 protozoan parasite biosensor for, 386 Crystal waveguides, photonic, 176 Curli, pilus type adhesins, Custom-built 8-channel SPR sensor, 99–100 Cyanide, SERS fingerprinting, 555 Cyanine dyes fluorophores, 111 Cy5-labeled polyclonal antibody in sandwich immunoassay format, 589 Cy5-labelled signal antibodies, 127 Cypridina noctiluna, 222 Cytochrome c biochip SERRS fingerprints, 556 D D-Count (AES Chemunex), 55 Deep-probe optical waveguide sensors with tunable evanescent field, 145–146 Dengue-2 virus detection by PCR amplification, 848 3-Deoxy-D-manno-2-octulosonic acid (Kdo), 666 Deoxyribonucleic acid (DNA), 317, 836 amplification, PCR characteristics and applications, 836–837 components of, 837–838 conventional, 839–840 on-chip, 841–846 process of, 833 real-time PCR, apparatus and detection techniques, 840–841 binders, potentiometric detection of, 324 Index biosensor, 306–310 chip/microarray of, 318 Debye length and, 326 genetic analysis, 317–318 immobilization on surfaces of solid substrates, 318–320 microorganisms sequencing and, 54–55 molecular recognition events detection of, 323–326 polymerase and polymerase chain reaction, 692 SAM (self-assembling monolayers)-based strategy for, 321 sequencing of, 331–335 single nucleotide polymorphysms (SNPs) analysis, 327–331 structure of, 317 thiol-gold bionding, 320 threshold voltage shift, 325 Desulfotomaculum genera, endospore-producing prokaryotes, 482–483 4’, 6-Diamidino-2-phenylindole (DAPI), 54 Dielectrophoresis, 895–905 Dipicolinic acid (DPA, 2,6-pyridinedicarboxylic acid) biomarker, 501 Dip-Pen nanolithography, 862 Dip-type MCLW, 154, 157 Direct epifluorescence filter techniques (DEFT), 54, 56 Direct fluorescent antibody (DFA) testing method for vegetative cells, 495 Direct hybridisation methods (Gen-probe), 605 Direct immunoassay detection by magnetic beads, 430 ABICAP column, 432–433 superconducting quantum interference devices (SQUIDs), 431–432 Direct label-free detection systems, 201 Disease state differentiation and identification of diagnostic markers, 724–725 Dissociation enhanced lanthamide fluorescent immunoassay (DELFIA), 585 Disuccinimidyl carbonate (DSC) urea linker, 245 DNASTAR analysis of pVIII phage coat protein, 280 dNTP hybridization, 837 Dodecanal long-chain fatty aldehyde, 216 Dr Food™ , NAD assays kits, 614 Dual phage technology, 749–750 Duopath® Verotoxin tests, 585 Dupont BAX system, 60 DuPont Qualicon, 846 Dye-clad leaky waveguide (DCLW), 152 Dylight fluorophores, 111 Dynabeads® paramagnetic beads, 576 Dynamic-sample systems, 844–846 E Ebola virus, 11 Eckart streaming, 913 E coli O157:H7, 217, 580 bacteriophage and gfp reporter gene, 745 biowarfare agents, 591 cantilever sensors detection by, 459 CL-EIS system for detection of, 224 and 2-dimensional photosensor array, 588 and fluorescent-bacteriophage assay (FBA), 741 food-borne pathogens, 10 in foods detection and identification by PCR assays, 613–614 959 genetic marker for verotoxin-2 subunit A gene, 101–103 IMS-PCR combinations for detection of, 576 and lateral flow immunoassay (LFI), 305 and LMD-ELISA kit, 580 MALDI MS instrument, 932–935 microfluidics-based antibody biochip-based system, 721–722 multivalent interactions of Gal-SWNTs with, 678–679 and NRL Array Biosensor, 113 QCM sensor, 285 sandwich immunoassay format, 145 serotype, 45 serotyping antibody-based microarrays, 721 SPR sensor detection with, 92 strain and scFv-pIII fusion-encoding phages, 762 and stress conditions by ELISA, 593 SYBR Green-based real-time PCR test, 617 by TSM sensor, 261 and virulent phage PP01, 746 in water detection and identification by QCM and PCR assays, 621 EDC/NHS modified dextran surface, 156 reaction, binding of biomolecules to electrodes, 361 Einstein-Smoluchowski equation for miniaturized systems, 834 EIS biosensors for pathogen detection, 365–366 amplification strategies and second detector biomolecule, 363 charge-transfer resistance changes, 367–369 on conductivity changes, 369 interfacial capacitance changes, 366–367 Electric cell-substrate impedance sensing (ECIS), 357 Electrochemical-immunoassay for bacterial detection, 586 Electrochemical impedance spectroscopy (EIS), 341 fundamentals of, 342–344 Electrode-solution interface, 346 Electrode surface, bacterial parasitizing effect on, 353–354 Electrokinetics, applications for bacteria, 901–904 Electro-wetting-on-dielectric (EWOD) effect, 847 Emeraldine polyaniline (Pani), 390 Emulsion diffusion method, 425 See also Magnetic particles synthesis End-firing, guided mode in waveguide, 178 Endospores bacterium life cycle, 506 as biodosimeters for evaluation of sterilization regimes, 484–485 inactivation by germinability assays, 508–511 metabolic activity assays and, 512–513 lysis, field implementation of, 499–500 pathogenicity of, 485–487 pathogens forming, detection and viability assessment of, 481–514 populations of, 507 resistance and longevity, 482–484 viability assessment and, 505–508 Enterobacter sakazakii, 17 Enzyme immunoassay sandwich (EIS) system, 223 Enzyme linked aptamer assays, 705 Enzyme linked fluorescent assay (ELFA), 585 960 Enzyme-linked immunosorbent assay (ELISA) and antigen-antibody reaction, 577–583 cellular component-based technology, 55 and endospores detection, 492–493 Enzyme-linked sandwich assays, 706 EPEC biosensor, 248 Epoxy coating for substrate for microarray printing, 635 Erwinia spp., 127–128 and handheld advanced nucleic acid analyzer (HANAA), 499 ESP Microbial Detection System (AccuMed), 53 Ethidium bromide (EtBr), intercalator dye, 840 Ethyl-cellulose encapsulation, 426, 428 1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC), 89 Evanescent field sensor illumination, 161 Evanescent wave-based fluorescent biosensors, bacterial detection, 109–111 future aspects of, 117–119 non-planar substrates, 112 planar substrates, 112–116 Evanescent waves sensing depths, 146–148 ExtrAvidin® , 361 F Fabry-Perot interferometer, 170 Fatty acid methyl esters (FAMEs), 56 FDA’s Bacteriological Analytical Manual (BAM), 52 Feces pathogen detection, 32–33 Ferrous ammonium sulphate (FAS), virucidal compound, 733 Fiber optical techniques, 140 Fiber optic biosensors (FOBs), 125, 587–588 bead-based arrays, 128–129 extension reactions, 134 nucleic acid direct hybridization, 131–134 nucleic acid sandwich assays, 129–131 whole-cell detection, 126–127 Fiber-optic interferometers, 183 Fiber optic waveguides, 172 D-Fiber surface plasmon resonance (SPR), 183 Field effect devices genetic analysis based on, 322–326 metal-insulator-semiconductor (MIS) capacitor, 314–315 Field Effect Transistors (FET), 314 biologically coupled genetic analysis (genetic FETS), 315–316 oligonucleotide probes, 316 Filoviruses, 11 FimH adhesin, 661 Firefly luciferase gene luc as reporter, 744 Firefly (luc) luminescent system for direct pathogen detection, 213–221 Firefly (Photuris pyralis) enzyme, 512 Flaviviruses, 11 Flow cytometry, 869–871, 874–875 applications of, 885–886 antibiotic susceptibility testing, 888 bacterial viability, rapid assessment of, 888 blood and urine bacterial detection, 889 environmental monitoring, 886 food bacterial levels in, 888 Bio-MEMS and, 871–872 cell detection, 879 buried optical fiber approach, 882 Index large-scale optical system, 882–883 optical waveguide approach, 881 cell sorting electrokinetic, 885 hydrodynamic, 883–884 magnetic, 885 pneumatic, 884–885 cell transportation and focusing hydrodynamic approach, 875–878 pneumatic and electrokinetic approach, 878–879 immuno-based assays of endospores, 494 viability-based technology, 55 Fluid, electro-hydrodynamic forces of, 900 Fluorescein isothiocyanate (FITC), fluorescent molecules, 585 Fluorescently labeled virus probes (FLVPs) for labeling, 741 Fluorescent probe detection, cellular component and nucleic acid technologies, 55 Fluoroscein fluorophores, 111 Foodborne diseases and bacterial pathogens, 9–10, 567, 731 commercially available PCR and real-time PCR kits, 615 pathogen detection and DNA microarrays, 622 enzyme immunoassay and, 223 Food-borne pathogens, bacterial detection and conventional methods, 607 NAD assays formats of diagnostic biosensors and, 621–622 DNA-probe based detection methods, 620 inter-laboratory validation studies, 616 non-amplified direct DNA probe-based, 620 PCR-ELISA and PCR-DNA probe membrane based assays for Campylobacter and Salmonella, 612 real-time PCR, 617–619 sample preparation for, 609–610 in vitro amplification technologies, 612 outbreaks and, 606–607 rapid nucleic acid diagnostics for food samples and, 609–610 limitations of, 611–612 NAD-based food assay, 608 polymerase chain reaction (PCR), 608–609 RNA target for, 610 sample preparation for, 611 in vitro nucleic acid amplification-based detection, 607–608 Food pathogen detection, NAD assays DNA-probe based detection methods, 620 non-amplified direct DNA probe-based nucleic acid diagnostics, 620 nucleic acid-based diagnostics, 610 nucleic acid diagnostics assays for, 612–616 PCR-ELISA and PCR-DNA probe membrane based assays for Campylobacter and Salmonella, 612 real-time in vitro amplification-based nucleic acid diagnostics, 617–619 in vitro amplification-based NAD assays and Inter-laboratory validation studies standardisation of, 616 Foods microbiological examination of, 17 PCR-based tests for pathogen detection, 609–610 poisoning outbreak and microSERS analysis, 534–535 Index safety and biosecurity applications, 381–382 supply chain and foodborne pathogen contamination, 377–378 Foot and Mouth Disease (FMD) viruses, 508 Four-channel Analyte 2000 system, 127 Fourier Transformed Infrared Spectroscopy (FTIR), cellular component-based technology, 56 F pilus-binding pIII, 762 Franciscella tularensis and NRL Array Biosensor, 113 Francisella tularensis (FT), 11, 131 biowarfare agents, 591 detection of, 127 DNA aptamers, 709–710 by TSM sensor, 261 Fraser broth (FB) for Listeria isolation and recovery, 593 FRET based detection of target analytes, biosensing designs for, 119 Full-width-half-max (FWHM) of Ag-CLW and Ag-SPR resonance, 154–155 Functional antibody fragments (Fab) expression, 573 Functional protein microarrays, 712, 715 G Galabiose-specific P fimbriae, 661 -Galactosidase (B-GAL) enzyme coliform detection, 302 in environmental water samples, 303 Galactosylated single-walled carbon nanotubes (Gal-SWNTs), 678 Ganglioside GM1 cellular receptor, 114 Gaussia princeps, 222 Gel-pads threedimensional microarray systems, 642–643 Gene-Probe Systems (Gene-Probe), 59 Generic/Universal microarrays, 646–647 Genes definition, 835–836 Gene-Trak® commercial NAD assays, 620 Gene-Trak Systems (Gene-Trak), 59 Geobacillus stearothermophilus, 484–485 endospore of, 483 GFP-modified PP01 phage, 746 Giant magnetoresistive (GMR) devices for bacterial detection, 446–448 Giardia waterborne pathogens and parasites, 485 GIII-deleted helper phages, 763(CAPS) Glass impinger, 18–19 See also Air, microbiological examination of -D-Glucuronide glucuronosohydrolase (GUS) enzyme for coliform detection, 302 Glutathione reductase biochip, SERS fingerprints, 555 Glutathione S-transferase (GST) detoxifying enzyme, 234 L-Glycero-D-manno-heptose (Hep), 666 3-Glycidyloxypropyl trimethoxysilane (3-GPS), 319 Glyconanoparticles for bacteria detection, 676–678 Glycopolymers conjugated fluorescent for bacteria detection, 672–676 mannose (polymer A) and -glucose (polymer B) structures of, 674 polydiacetylene liposomes/vesicles, 676 thin films and, 675 Gold nanoparticles and protein analytes detection, 590 Gold screen-printed electrochemical transducer, 307 Goos-Hanchen shift, 142 Graded index waveguide, 175–178 961 Gram-negative bacteria, 708 and gram-positive bacteria, afrimbrial adhesins in, O-antigens of, 664–668 Gram-negative E coli and S typhimurium, SERS fingerprints, 533 Gram-negative infections in animals and humans, 665 Gram-negative Legionella and Escherichia, microSERS studies, 535 Gram negative pilin adhesins, Gram-positive bacteria, 707–708 Gram-positive Listeria and Bacillus, microSERS studies, 535 Gram-positive species, SERS fingerprints, 532 Grating coupling, guided mode in waveguide, 178 Gravity settling plate (GSP), 18 See also Air, microbiological examination of Green fluorescent protein (GFP) from jellyfish Aquorea victoria, 745 Griffin.1 and Tomlinson scFv-pIII libraries, 763 Griffin.1 phage, 762 V-Groove technology for fiber alignment, 188 Group A Streptococcus pyogenes (GAS), 470 Growth Direct computer-aided imaging type of system, 51 A guide to fluorescent probes and labeling technologies, 111 H Handheld advanced nucleic acid analyzer (HANAA) for real-time PCR detection, 499–500 Hand-held microflow cytometer, 882 Harmful algae bloom (HAB) spp detection, 129 Hazard analysis critical control point (HACCP) food and feed processing factories, 17 recommendations for, 219 Heat-killed L monocytogenes detection with Biacore 3000 sensor, 98 Helicobacter pylori and SPR sensors, 98 urease epitope, 572 Hemolytic uremic syndrome (HUS), 379 Hemophilus influenzae, 663 Hepatitis B virus, 386 High index waveguide sensors, 140 HiLyte fluorophores, 111 Histamine (111 Da), microSERS studies, 555 Horse radish peroxidase (HRP) enzymes, 302 substrate modifying enzyme, 580 Hospital acquired infections, bacteria and antimicrobial resistance, 604 diarrhea and Clostridium difficile, 487 HRP functionalized liposomes, 368 HSA-encapsulated Gd-Zn-Ferrite nanoparticles, 426, 429 Human IgG-colloidal gold complex, in sandwich assay format, 145 Human immunodeficiency VAP, 857 Human intestinal Caco-2 cell line, 43–44 Human Salmonella infection, 379 Hydrogel-based monoclonal antibody microchip, 723 Hydrogel-immobilized porous silicon sensor, 236 N-Hydroxysuccinimide (NHS), 245 Hydroxyurea, microSERS studies, 555 Hygiena luminometers, 52 Hyperphage, M13KO7 helper phage without gIII gene, 761 962 I IAsys Affinity Sensors, SPR instruments, 587 IAsys instrument, 144–145 IgY antibodies, 572 Immunocard STAT, LFI kits, 584–585 Immunomagnetic electrochemiluminescence (ECL) for antigen detection, 493–494 Immunosensor development biological recognition elements in, 354–357 blocking and, 362–363 negative controls, 364 and signal amplification, 363–364 surface modification methods, 357–362 Impedance-based biosensors for pathogen detection, 341–371 Impedance, growth-based technique, 57 Indirect immunoassay detection by magnetic beads enzyme-linked immunosorbent assay (ELISA), 433–438 Indium tin oxide/Pani biosensor, 393 Inhibition assay and SPR sensors, 90–91 Instantaneous Microbe Detector (IMD) by BioVigilant, 60 Intact bacterial cells, sample preparation for detection of, 21–23 Integrated circuit (IC) biochip, 588–589 Integrated deep-probe optical waveguides for label free bacterial detection, 139–141 integration with electric field, 161–163 ultrasound standing waves (USW), 163–165 Integrated optical waveguides (IOWs), 112 Interdigital electrode transducer (IDT) on piezoelectric plate, 256 Interference phenomena, 170 Interferometric sensors, 140 Internal reflection elements (IRE), 112 Intimins and host cell attachment, Intimin-tir interaction, 248 InvA2 probes arrays, 130 Invitrogen, human recombinant proteins, 719 Ion exchange waveguides, 177 IQuum’s Liat Analyzer portable nucleic acid testing system, 500 Iron and bacterial replication, ITO-Pani biosensor, 399–403 K Keyhole limpet hemocyanine (KLH), carrier molecule, 571–572 Klebsiella pneumoniae, 6, 263, 533 Koch’s postulates, 43 Kratos Analytical Systems, 58 L Label-free microbial biosensors by molecular nanowire transducers, 377–406 Laminar flow filtration, 917 LAMP, see Loop-mediated isothermal AMPlification Langmuir-Blodgett (LB) Langmuir-Schaefer (LS) films and nanostructured PDAs for bacterial sensing, 675 molecular assembling method, 272–274 Large-scale flow cytometer for cell counting and sorting, 870 designs of, 876–877 function of, 870–871 Index Laser-irradiated magnetic bead system (LIMBS) for pathogen analysis, 847 Laser tweezers Raman spectroscopy (LTRS), 528 sorting and identification, 531 Lateral-flow immunoassays (LFIAs) and endospores detection, 493 Latex Agglutination (LA) and Reverse Passive Latex Agglutination (RPLA) detection tests kits, 589 Latex agglutination (LA) for detection of M tuberculosis and Salmonella typhi, 589–590 Lectin microarrays for bacteria detection, 670–672 Lectins, sugar-binding proteins, 720 Legionella spp., 37 SERS fingerprints of, 539 and SPR sensors, 98 by TSM sensor, 261 Leucoemeraldine polyaniline (Pani), 390–391 Liat Bioagent Autonomous Networked Detector (BAND) system, 500 Ligase chain reaction (LCR) and in vitro amplification technologies, 615–616 Light-addressable potentiometric sensors (LAPS), 586 Light coupling techniques, 146, 148–149, 178–180 collinear/single channel interferometers, 183–186 interferometers and, 180–183 two-channel interferometers, 186–192 LightCycler (Roche Molecular Diagnostics), 840 Light-emitting bacteria and quorum sensing, 216 Light ray propagation in waveguide, 173 Limits of detection (LODs) by AMP, 145 Limulus Amebocyte Lysate Endotoxin Testing (LAL), cellular component-based technology, 58 Lipid vesicles monolayer formation, 275–276 Lipopolysaccharide (LPS) (endotoxins), Liposomes for encapsulating strategies, 363 Liquid Arrays, 641–642 See also Microarray technology Liquid trap method, 18 See also Air Listeria spp., 21, 217 CL-EIS system for detection of, 224 SERS fingerprints, 538–544 by TSM sensor, 261 LIVE Bac Light Bacterial Gram Stain Kit, 56 Live spore-forming organisms as food supplements, 488 L monocytogenes, 98 CBD-based magnetic separation (CBD-MS) technique, 739 cells and immunocapture with dielectrophoresis (DEP), 589 cells detection in hot dog and bologna, 127 detection by endolysin Ply118, 736 detection by sandwich immunoassay format, 145 in food, 36 and foodborne listeriosis, 744 food-borne pathogens, 10 in foods detection and identification by PCR assays, 615 identification, 45–46 and NRL Array Biosensor, 114 and PCR/DNA probe assays, 608–609 phage encoded cell wall binding domain CBD500, 739 real time PCR assay for, 847 repair broth (LRB) for Listeria isolation and recovery, 593 and stress conditions by ELISA, 594 Index surface-associated proteins, 572 SYBR Green-based real-time PCR test, 618 L monocytotenes, IMS-PCR combinations for detection of, 576 Locus of enterocyte effacement (LEE), 247 Locus-specific oligo (LSO), 134 Loop-mediated isothermal AMPlification, 839 Lophine [2,4,5-triphenylimidazole] chemiluminescent compounds, 223 LPS O-antigen and C3 convertase assembly, Luciferaseen coding genes lux A and B 216 Luciferase reporter phage (LRP), 743–745 Luciferin/luciferase system, detection of spores, 512 Lucigenin [bis-N-methylacridinium nitrate] chemiluminescent compounds, 223 Luminescent-based immunoassays, 222 Luminescent System (lux ) for direct bacterial pathogen detection, 215–219 Luminex flow cytometry system, 494 Luminex suspension array, 641–642 Luminol [5-amino-2, 3-dihydro-1, 4-phthalazine dione] chemiluminescent compounds, 223 Luminol (3-aminophthalhydrazide), chemiluminescent dyes, 586 LuxAB-encoded luciferase expression, 217 Lux operon from Vibrio fischeri, 743 M MAb2B3-CM5 sensor chip surface, 99 MAb-C11E9, see Anti-Listeria monoclonal antibody Mach-Zehnder interferometer, 180, 189 beamspiltter combination in slab of, 188 with three waveguide output coupler, 189 Magnetic marker technique, handling techniques, 438 Magnetic particles synthesis, 417–418 biological target and, 430 encapsulation of, 423–424 polymer/protein coatings, preparation of, 424–426 particle size, effect of, 418–423 techniques of, 423 Magnetic relaxation signal, bacteria detection, 448–449 Magnetic separation high-field electromagnets, 440–441 magnetic force per unit volume on biological compound, 439–440 permanent magnets, 441–442 Magnetic techniques for rapid detection of pathogens, 415–454 Magnetoelastic sensors, 449–450 MALDI coupled with time-offlight (TOF), 591 Maleimido phenyl butyrate phosphatidylethanolamine (MPB-PE), 276 Malthus Microbial Detection System (Malthus Diagnostics), 57 Malthus® system commercial impedimetric systems, 354 Manning Applied Technologies, 192 -Mannose-functionalized gold glyconanoparticles, 677 Mannose-specific type fimbriae, 661 Mass-associated laser desorbtion/ionization (MALDI), 591 Mass change sensitivity, 468–469 Matrix-Assisted Laser Desorption-Time Of Flight (MALTI-TOF), 58 Matrix components, inhibition of PCR by, 45–46 963 M avium subsp paratuberculosis, affinity molecule-based magnetic separation and PCR detection (IMS-PCR) for detection, 749 Maxtek sensor probe, 269 MB-DNA biosensor, 386 Membrane attack complex (MAC) formation, Membrane-based assays, 115 3-Mercaptopropyl triethoxysilane (3-MPTS), 319 Metal-clad leaky waveguide (MCLW), 116, 139, 146 Metal-Insulator-Semiconductor (MIS) capacitor, 314–315 Metals and free-electron model, 84 Meticillin-resistant S aureus (MRSA), 126, 582, 606 MetriGenix flow-through systems, 643 Michelson interferometer, 170 Microarray technology, 630–631 commercially-available formats, 639–640 marker genes and, 643 microbial diagnostics and gene expression studies, 644–645 sequence analysis and, 647–648 substrates for printing, 634–637 targets for amplifications and sensitivity issues, 637–638 labeling and hybridization specificity, 638–639 technical aspects of probes and, 632–634 Microbial diagnostic microarrays (MDMs), 643 Microcalorimetry, viability-based technology, 58–59 Microcantilevers, 92 See also Whole bacteria detection by SPR Microdevice-based thermocyclers, 843 Micro-electromechanical systems (MEMS) microfabrication techniques, 59 technology bulk and surface micromachining technique, 872 and flow cytometer for cell counting and sorting, 870 Micro-EVA principle, 511 Microfabrication techniques bulk and surface micromachining, 872 LIGA, 872–873 polymer-based micromachining, 873 Microflow cytometer with optical waveguides, working principle of, 881 Microfluidics, 834 analysis systems, 834–835 based antibody biochip-based system, 721–722 MicroLog™ system, 607 Microorganisms detection by TSM sensor, 261–263 infection resistance for, 484 and matrices bovine viral diarrhea virus (BVDV), 380–381 E coli O157:H7, 378–379 Salmonella spp., 379–380 pathogenic, detection of, 11 host cell, 3–8 infection and, 9–11 and iron acquisition, toxins and, virulence factors, regulation of, 8–9 principal components analysis (PCA), 533 Micro PRO by AATI, 55 MicroSeq markets, 54 964 MicroSeq 16S rDNA Bacterial Identification System (Applied Biosystems), 61 MicroSERS detection bacterial toxins, 554–558 bacteria of, 535–545 spores of, 545–555 Microsphere-based fiber-optic arrays, 642 Micro-total-analysis-system ( -TAS), 871 MicroVaccum grating platform, 145 Mid Infrared Range (MIR) spectral analysis, 56 Milliflex (Millipore Corporation), luminometers, 52 Miniature Analytical Thermal Cycling Instrument (MATCI) for real-time PCR detection assays, 499 M13KO7 helper phage, 761 Mode’s effective refractive index, 144, 149 Mo-EDTA complex and viable assay method, 22 Molecular imprinting aqueous phase MI hydrogels, 792–795 polyacrylamide gels-hydroMIPs, 793–795 cross-linking, 789 functional monomer, 788–789 (noncovalent) molecular imprinting process, 786–787 polymerization, 790 principles of, 786–787 solid phase extraction for bioagents antibiotics, 795–798 bacterial cells and endospores, 802–803 mycotoxins, 798–799 nano-sized structures, 799–800 peptides and proteins, 800–801 viruses, 801–802 solvent/porogen, 790–791 versatility and template molecule, 787 Molecularly imprinted polymers (MIPs), 785 Monoclonal antibody (MAb) and polyclonal antibody (PAb) for sandwich assay, 93 production, 570–571 Monosaccharides N-acetylneuraminic acid (Neu5Ac), 114 Moraxella sp Pseudomonas putida JS444, 302 Most Probable Number (MPN) techniques, 52 M paratuberculosis sheep with Johne’s disease, screening of, 767 mRNA display, 778 See also Phage display SERS biochip technology, 591 M tuberculosis and Phage TM4, 744 Multilocus sequence typing (MLST) strategy, 134 Multiple antigen peptides (MAPs), 571–572 Multiplex protein expression profiling, 719 Mx3000P (Stratagene), 840 Mycobacterium avium subsp paratuberculosis (MAP), 618 Mycobacterium in milk samples and FAST PlaqueTB test, 734 Mycobacterium tuberculosis, 37, 44 respiratory pathogen, 604–605 by TSM sensor, 261 N NA1S probes multiplexed array response, 130–131 Near Infrared Spectroscopy (NIRS), optical spectroscopic method, 59 Néel relaxation effect, 448 Index Neisseria meningitidis, 590, 724 FASTslides as diagnostic markers, 724 NeutrAvidinTM, 361 N gonorrrhoae, STI organisms detection, 605 NimbleGen’s micromirror device, 640 Nonidet P-40 nonionic detergents, 363 NovaLUM (Charm), luminometers, 52 NRL Array Biosensor, 113 N-type genetic field effect device, 328, 329 Nucleic acids bacterial, sample preparation for detection of, 23–27 based methods for bacteria detection, 23, 28 based tools, immunological tools, 756 diagnostics, 604–606 modifications of, 693 optimizing functional, 697 probes, genotypic technology, 59 properties of, 690–692 sandwich assays, 129–131 selection methods, 694–697 sequence based amplification (NASBA), 60, 386 microorganisms detection of, 508–509 and in vitro amplification technologies, 615–616 Nyquist plot, impedance plotting, 344 O Off-chip beam-combining scheme, 194 Oligo(ethylene glycol) (OEG), 89 Oligonucleotides DNA microarrays tools for rapid bacterial diagnostics, 629–649 probes, 126, 632–634 OmniLog (Biolog), automated systems, 756 On-chip beam-combining scheme, 194 Optical interferometry, 169–171 planar waveguide operation, 172–175 waveguides and, 171–172 waveguides types of, 175–178 Optical sensor systems for bacterial detection, 140 Organism-specific detection methods, 21 Orthopox virus, biowarfare agents, 591 Oxide layer interference spectrum, 239 Oxoid, ELISA-based kit for detection of ST toxins, 580, 583 P Paenibacillus popilliae, biopesticide, 488 PallCheck (The Pall Company), luminometers, 52 PamGene flow-through systems, 643 Panthozyme-TB Complex Plus detection of IgG antibodies, 589–590 PapG adhesin, 663 Para-Amino-phenyl- -D-glucopyranoside (p-AP- -GLU), 306 Partial least squares (PLS) regression, 59 Pathogen detection experiments and continuous flow apparatus, 474 Pathogen detection, immunoassays enzyme immunoassays, 577–580 C botulinum toxins, 584 Escherichia Coli, 580, 583 Listeria monocytogenes, 583 Salmonella, 583 staphylococcal enterotoxin (SE), 583–584 radioimmunoassay (RIA), 577 Index Pathogenicity, definitions of, 3–4 Pathogen identification methods, 34 Pathogen phagocytosis, Pathogens amplification, 39–40 enzyme-linked immunosorbent assay (ELISA) polymerase chain reaction (PCR), 36 label-free fingerprinting of by Raman spectroscopy techniques, 525–560 and matrix complexity, 32–33 methods culture technique, 33, 35 microbial, microSERS for detection and identification of, 535–536 quantification problems, 44 real-time detection, 45 PDS® (Biophage Pharma), 57 Peak-type MCLW, 154, 155, 157 PEG encapsulation, 426 PEI-glutaraldehyde (GA) method, 384 Peltier thermoelectric devices, 847 Penicillium chrysogenum, 59 Peptide biosensor, functional validation of, 273 Permanent magnets arrangements, numerical analysis for, 442–446 and saturation hysteresis curve, 442 Pernigraniline polyaniline (Pani), 390 Perspective Biosystem Voyager, 58 Phage A511::luxAB in detection of Listeria in contaminated foods, 217 Phage amplification assay (PhaB), 733 Phage coat technology, 277–279 Phage-derived tail-fibre proteins, 23 Phage display detection motifs, 765 and high affinity binders, 747 library, 772–775 Phage display methods for bacterial pathogens detection, 755–757 formats for, 764–766 phage M13, 760 and phagemids, 762–764 principles of, 760–762 scFv and peptides genetic modification of phagemid clones, 777 panning methods, 776 screening methods, 777 usage of, 767–769 Phage-encoded affinity molecules detection of pathogen, 738–740 fluorescently labeled phage and, 740–741 Phage M13 genome structure of, 760 principles of, 760–762 Phage-mediated bioluminescent AK assay, 735–736 Phage-mediated cell lysis detection of pathogen ATP release measurement of, 735–736 cytoplasmic markers and, 736–737 impedance measurement, 737 Phage phAE88 reporter, 745 Phagosome-lysosome fusion, Photolithography and patterning technologies, 858–859 Photorhabdus luminescens bacterial lux systems, 215 PickPen magnetic tool, 446 Picoscope, 195 965 Piezoelectric-excited millimetersized cantilever (PEMC) sensors, 459–460 antibody immobilization methods and, 469–470 characterization of, 468 designs of, 464 mass change sensitivity, 468–469 transient response of, 475 Piezoelectricity and acoustic waves, 256 Planar optical waveguides (POW), 141 Planar waveguide Technology (PWT), 641 based TIRF-based biosensors, 112 ray and field models for, 174 refractive index of, 173–175 and TIRF-based biosensors, 112 See also Microarray technology Plasmid-based luxAB cassette in Salmonella host strains, 217 P22::luxAB infection of Salmonella, 217 P-Nitrophenol (PNP), 302 P-Nitrophenyl-b-D-glucuronide (PNPG), 302 Point-of-care analysis, 835 Polyacrylamide Gel Electrophoresis (PAGE) based selections, 696 Polyaniline (Pani), conducting polymers, 388, 390 Polycarbazole, conducting polymers, 388 Polyclonal antibody (PAb), 570 Polyclonal anti-E coli antibodies and magnetic nanoparticle conjugates (MNCs), 576–577 Polydimethyslsiloxane (PDMS) casting process, 873 Poly(3,4-ethylenedioxythiophene), conducting polymers, 388 Polyfuran, conducting polymers, 388 Polyindole, conducting polymers, 388 Poly-L-Lysine coating for substrate for microarray printing, 634 Polymerase Chain Reaction (PCR) bacterial barcodes, 60–61 conventional and microfluidic, 842 genotypic technology, 59 Polymer-based biosensor for microbial/viral detection, 392 Polymer-based micromachining techniques for microfluidic devices, 873 Polymer emulsification process, 425–426 See also Magnetic particles synthesis Polymorphonuclear leukocytes (PMNs), Polysiphonia alga, 204 Polystyrene probes, 127 Position-sensitive photodetector, 87 See also Thin metal film, surface plasmon Premier EHEC test, sandwich ELISA, 580 Pre-PCR processing methods, 27 Prism coupling and Fresnell’s reflection laws, 149 Prism coupling, guided mode in waveguide, 178 Prism-dielectric system, 84 Probelia System (BioControl Systems), 60 Promega Dual-Luciferase Reporter Assay system, 222 Propagation constant of surface plasmon, 84 Protagen, human recombinant proteins, 719 Protein A-conjugated sepharose bead, 576 Protein/antibody microarrays, 590–591 Protein Chip Arrays, 56 Protein expression signatures screening with bacterial infection, 726 Protein microarrays bacteria detection 966 Protein microarrays (Continued) bacteria and bacterial proteins simultaneous detection of, 723–724 biological toxins, 722 diagnostic markers/vaccine candidates, 724 disease state differentiation and identification of, 724–725 pathogenic organisms of, 721–722 protein expression signatures and, 726 serotyping of, 721 toxin modulators/regulators, 725 definition and classification of, 716 technologies for bacterial and protein analyses detection and identification, 717–726 types of, 717, 718 Proteins based on phage display, 778 ProtoArrays, human and yeast, 725 Pseudomonas spp., 219 SBW25, Raman fingerprints of, 530 by TSM sensor, 261 PSi immobilization effects on probe viability, 233–234 PVA encapsulation, 426 PVIII coat protein, amino acid sequence of 7b1 filamentous bacteriophage, 280–281 PyMS based technology, bio-aerosols detection of, 940–941 Pyrogent Gel Clot (BioWhittaker), 58 Pyrotell (Associates of Cape Cod), 58 Pyruvate orthophosphate dikinase (PPDK) and ATP assays, 220 Q QB replicase and in vitro amplification technologies, 615–616 QD-aptamer sensor, 704 Qiagen Operon format, 639–640 Qiagen (RealArt ™ kits), 618–619 Quantum dots (QDs), 437 as fluorescent probes, 118 sensors, 700–704 Quarter wave resonator, force cells on biosensor surface, 923 Quartz crystal microbalance (QCM), 92, 803 based biosensor for Salmonella spp., 387–388 sensor, 92 See also Whole bacteria detection by SPR Quorum-sensing mechanisms and light-emitting bacteria, 216 R RABIT® commercial impedimetric systems, 354 RABIT (Don Whitley Scientific Ltd), 57 Raman microscopy for whole-organism fingerprinting, 527–531 RAMP System for anthrax spores detection, 493 Random peptide phage display, 770–772 Rapid detect-to-treat sensor systems for endospore-forming pathogens, 492 Rapid Germinability Assays, 508 Rapid method for food-borne pathogen detection and identification, 10 Rapid microbiological methods (RMMs), 49 application of, 62–75 disclaimer, 75 microbial testing types of Index cellular component/artifact-based technologies, 51 growth and viability based technologies, 50 Lab-on-a-Chip (LOC) technologies, 51, 57–58 nucleic acid and automated methods, 51 overview of adenosine tri-phosphate (ATP) bioluminescence, 51–52 adenylate kinase and autofluorescence, 52 biochemical assays and physiological reactions, 52–53 biosensors and immunosensors, 53 carbon dioxide detection, 53 concentric arcs of photovoltaic detectors with laser scanning, 54 direct epifluorescent filter technique (DEFT), 54 and DNA sequencing, 54–55 endospore detection and enzyme linked immunosorbent assay (ELISA), 55 fatty acid profiles, 56 flow cytometry and fluorescent probe detection, 55 Fourier transformed infrared spectroscopy (FTIR), 56 gram stains, 56 headspace pressure, changes in, 53 impedance and immunological methods, 57 limulus amebocyte lysate endotoxin testing (LAL), 58 mass spectrometry, 58 microcalorimetry and micro-electro-mechanical systems (MEMS), 59 near infrared spectroscopy (NIRS), 59 nucleic acid probes and optical particle detection, 59 polymerase chain reaction (PCR), 60 Raman spectroscopy, 61 Rep-PCR, 60–61 ribotyping/molecular typing, 61 solid phase laser scanning cytometry, 61–62 southern blotting/restriction fragment length polymorphism, 62 spiral plating and turbidity, 62 Rapid real-time NAD assays, 605–606 Rapiscreen (Celsis), luminometers, 52 Rayleigh streaming, 913 RBD3000 (AATI), 55 RCA, see Rolling-Circle Amplification Real-time PCR, apparatus and detection techniques on-chip PCR, 841 capillary-based thermocyclers, 842–843 dynamic-sample system, 844–846 microdevice-based thermocyclers, 843 static-sample systems, 843–844 Real-time PCR thermocyclers, 841 Recombinant DNA technology and antibodies, 573 phage display, 573 Reflectometric interference spectroscopy (RiFS), 237 Reichert SR7000 SPR sensor, 97 Renibacterium salmoninarum, 590 Renilla reniformans luciferase, 222 Replicate Organism Detection and Counting (RODAC) method, 17–18 Replicate organism direct agar contact (RODAC), 39 Reporter gene (rep) construction of, 742 luciferase reporter phage (LRP), 743–745 Resonance-Light Scattering (RLS), 641 See also Microarray technology Resonant mirror sensors, 140 Index REVEAL for Listeria, LFI kits, 585 Reverse passive latex agglutination (RPLA) for detection of M tuberculosis and Salmonella typhi, 589 Reverse sample genome probing (RSGP) technique, 632 Reverse symmetry waveguides, bacteria detection, 151 Reynolds number (Re) flow, 92 oscillating cantilever, 460 Rhodamine B, fluorescent molecules, 585 Rhodamine fluorophores, 111 Rhodococcus equi virulence associated protein A (Vap A), 572 Riboflavin mononucleotide (FMNH2 oxidation in bacteria, 216 Riboprinter (DuPont Qualicon), 61 Ribosome display, 780 See also Phage display Ribotyping/Molecular typing, genotypic method, 61 Ricin, biowarfare agents, 591 Ricinus communis, 11 RIDASCREEN, ELISA-based kit, 582 Rifampicin resistance in M tuberculosis, 606 RNA aptamer and flavin mononucleotide (FMN), 691 RNA as target for NAD assay, 611 16S rRNA gene sequencing application, 45 TmRNA in bacterial species, 610 RNA polymerase biochip, SERS fingerprints, 557 Robert Boyle’s chicken, 214–215 Roche Diagnostics “foodproof” real-time PCR assays, 618 Rolling-Circle Amplification, 839 Rolling circle amplification (RCA) and in vitro amplification technologies, 615–664 ROLux whole-cell bioreporter, 218 R353Q locus of factor VII gene, base sequences for oligonucleotide probes, 322 Ruggedized Advanced Pathogen Identification Device (RAPID), 499 S S agalactiae cfb gene, 605 Salmonella spp., 217 and affinity-selected filamentous phages, 749 CL-EIS system for detection of, 224 detection by phage Felix-O1, 732 detection by sandwich immunoassay format, 145 detection, SYBR Green real-time PCR assays, 617 and fimbrial operons, food-borne pathogens, 10 in foods detection and identification by PCR assays, 613–615 genome, 36 IMS-PCR combinations for detection of, 576 LT2 detection by stain phage P22, 741 monoclonal antibodies, 32 NASBA-ECL assay for, 616 and NRL Array Biosensor, 113 outbreak, 568 PCR amplified fragment of InvA gene, 308 and PCR/DNA probe assays, 609 PCR-ELISA assay, 612 phage Felix-O1, 744 phage P22 and ina-recombinant phage, 746 QCM assay, 263 and Salmonellosis, 379–380 sensors with somatic O antibodies, 284 967 serovar Arizonae CRA 1568, 738 strains SuperEpoxy slides, 721 strain (Wood-46), 145 and stress conditions by ELISA, 593 SYBR Green-based real-time PCR test, 618 by TSM sensor, 261 virulence genes, 129 Salmonella Tek ELISA (Organon Teknika), 55 Salmonella Typhimurium detection by RAPTOR, 128 Salting out technique, 424–425 See also Magnetic particles synthesis Sample-shunting PCR, 845–846 Sandwich assay and SPR sensors, 90–91 Scanning probe lithography (SPL) and patterning technologies, 861–862 ScanRDI (AES-Chemunex), 62 ScFv antibody microarray, 726 ScFv libraries, 772–775 ScFv phage display libraries, 772 Schlichting streaming, 913 Scorpion® primers, 498 Screw mechanism, 179 Selective evolution of ligands by exponential enrichment (SELEX), 694 Self-assembled monolayers (SAM), 89, 358 Self-doped polyaniline, 391 Sensor system and sample collection, 198–199 S entrecia, serotyping antibody-based microarrays, 721 Sepsis, bacterial infections, 605 Serodiagnosis, serological identification of antibodies, 589–590 Serratia marcescens subsp sakuensis, 483 Sherlock Microbial Identification System, 56 Shiga-like toxins (Stx) detection, 580 Shigella spp detection by sandwich immunoassay format, 145 food-borne pathogens, 10 and NRL Array Biosensor, 114 Siderophores, See also Iron and bacterial replication Signal amplifying cells, 733 Silicon macroporous microcavity structures, 235 mesoporous microcavity and bacterial lysate, 233 planar biosensor, 236 porous bandgap sensors in novel formats, 235–236 three-dimensional matrix for biosensing, 232–233 Single chain Fv antibody (scFv) antibody of, 573 human antibody fragment Griffin.1 and Tomlinson libraries, 762 phage display library, 748 Single domain antibodies (sdAbs) and domain antibodies (dAbs), 775 Single Nucleotide Polymorphysms (SNPs) analysis, 327 analysis based on primer extension, 329–331 hybridization temperature for, 328–329 Single particle aerosol MS instrument, design of, 941 Singlepath® for E coli O157, 584–585 Single-stranded DNA (ssDNA) surface, 89 Slab waveguides, 177 Smallpox DNA detection experiments, 247 Smart bandage and dust porous silicon, 235 Smart Cycler (Cepheid), 840 Smartcycler, real-time PCR field portable unit, 499 968 SMART-II Anthrax Spore test kit, 493 Soft Lithography and patterning technologies, 858–859 capillary force lithography, 860–861 and microcontact printing, 859–860 microtransfer molding, 860 replica molding and, 859 Sol gel-based TiO2 -SiO2 waveguides, 185 Solid Phase DNA Amplification, 839 Solid phase laser scanning cytometry, 61–62 Solvent displacement method, 422 See also Magnetic particles synthesis Solvent evaporation method, 425 See also Magnetic particles synthesis Southern Blotting/Restriction fragment length polymorphism, 62 SPA, see Solid Phase DNA Amplification SpectroEVA spectroscopy-based endospore viability assay, 510 SpinCon cyclonic collectors, 199 Spiral plating, growth-based technology, 62 3(2-Spiroadamantane) methoxy 4(3 phosphoryloxy) phenyl 1,2 dioxetane (AMPPD) chemiluminescent dyes, 586 Sporeforming pathogens and endospores endospores rapid detection by dipicolinic acid biomarker, 501–505 phenotypic characteristics of, 489–491 rapid immunoassays, 492–494 rapid nucleic acid assays, 495–501 sensor parameters of, 491–492 Sporolactobacillus genera, endospore-producing prokaryotes, 482–483 Sporosarcina genera, endospore-producing prokaryotes, 482 Spreeta, SPR instruments, 587 Spreeta sensor for direct detection of viable E coli O157:H7, 93, 97 SPR-670M, SPR instruments, 587 Staphylococcal enterotoxin B (SEB), 574–575 Staphylococcus spp Cowan-1, 145 enterotoxin B, biowarfare agents, 590 enterotoxin B (SEB), microSERS studies, 554–555 food-borne pathogens, 10 mecA gene, 606 SEB and C2 toxins, 263 SEB toxin, 113–114 and SPR sensors, 98 by TSM sensor, 261 Step index waveguides, 176–177 Stepwise multiple linear regression (SMLR), 59 St Louis encephalitis virus, biowarfare agents, 591 Stomach flu, Strand displacement amplification (SDA) and in vitro amplification technologies, 615–616 Strepomyces fradiae, 59 Streptavidin biotin-binding protein, 385 Streptavidin 60-kDa protein, 320 Streptococcal pyrogenic toxin A (SPEA), 584 Streptococcus pneumoniae, 126 DNA by PCR amplification, 848 S Typhimurium LT2 detection in lettuce suspensions, 218 Succinimidyl 4-(N-maleimidomethyl)-cyclohexane-1carboxylate (SMCC), 361 N-Succinimidyl S-acetylthioacetate (SATA), 361 Index N-Succinimydyl-3(2-pyridyldithio)propionate (SPDP), 276 Sulfosuccinimidyl 6-(biotinamido) hexanoate (NHS-LC-biotin), 321 Superconducting quantum interference devices (SQUIDs), 431–432 Support vector machine technique, 527–528 Surface acoustic wave (SAW), 92 See also Whole bacteria detection by SPR Surface and molecular recognition elements (MREs), 89 Surface enhanced laser desorption ionization time of flight mass spectroscopy (SELDI-TOF-MS), 58 Surface-enhanced Raman scattering (SERS), whole-organism fingerprinting, 531–534 Surface-enhanced Raman spectroscopy (SERS), 61 Surface functionalization, 197–198 Surface modification methods adsorption, 357–358 biotin-(Strept)avidin system, 360–361 chemical conjugation, 361 entrapment, 362 microencapsulation, 362 protein A and G, 360 self-assembled monolayers (SAM), 358–359 silanisation, 359 Surface plasmon resonance imaging (SPRi), 237 Surface plasmon resonance (SPR) based optical sensing, 385 interferometry, 195–196 sensors for detection of bacterial pathogens, 144–145 with angular modulation and four parallel sensing channels, 87 antibody biomarkers, 103 background refractive index, 87 bacteria cells, quantification of, 91–101 biosensor system, 84 detection formats, 90–91 fundamentals of, 83–88 genetic markers, 101–103 instrumentation and, 85–88 portable SPR sensor system, 88 surface chemistries and molecular recognition elements, 88–90 with wavelength division multiplexing, 88 Surfaces microbiological examination of, 17–18 sampling, 35–37 SV1210 Micro-Chip Electrophoresis Analysis System, 848 Swab surface sampling methods, 18 T Taq DNA polymerase, 838 See also Thermus aquaticus and DNA-dependent DNA-polymerase Taq enzyme and PCR, 611 TaqMan® probes, 498, 499 Target antigens (cells) and immunomagnetic separation (IMS), 575–577 TB antigen microarray, 725 Techoic acids of Staphylococcus and Streptococcus spp., TECRA, ELISA-based kit, 582 Tecra Salmonella ELISA (International Bioproducts), 55 Index Terbium dipicolinic acid (Tb-DPA) luminescence assay, 501–503 Thermocyclers and polymerase chain reaction, 841 Thermus aquaticus and DNA-dependent DNA-polymerase, 838 Thin metal film, surface plasmon and angular modulation, 87 attenuated total reflection (ATR) method, excitation by, 85 Three-dimensional microarray formats, 642–643 See also Microarray technology Three-electrode electrochemical cell, 351 Three-layer (substrate-film-cover) structure, eigenmodes of, 146 Three-layer waveguide and mode-power profiles, 148 Thrombotic thrombocytopenic purpura (TTP), 379 Time-resolved fluorescence immunoassay (TRFIA), 585–586 TIRF-based fluorescent microscopy (TIRFM), 116 Tir-IBD probe, 248 TM4 lytic cycle, 744–745 Tn10::luxAB mutagenesis, 743 Total internal reflection (TIR) and evanescent waves, 141–142 Toxic shock syndrome toxin-1 (TSST-1), 584 Toxin modulators/regulators identification, 725 Toxins and microorganisms, Transcription mediated amplification (TMA) and in vitro amplification technologies, 615–616 Transmission electron microscope (TEM) analysis for Pani compounds, 395 Tribonema aequale alga, 204 Trichothecane mycotoxins, 11 Tricorder, 491–492 See also Endospores Trimethylamine (59 Da), microSERS studies, 555 Trinectins, domain (Fn3) of human fibronectin, 779 Triticum vulgaris, wheat germ agglutinin (WGA) from, 543 Triton nonionic detergents, 363 Tuberculosis diagnosis by Mycobacterium tuberculosis, 733 Turbidity, growth-based technology, 62 Tween nonionic detergents, 363 Two-component bacteriophage bioluminescent reporter system, 218 Two-layer PZT transducer on silicon/Pyrex separator, 916 Two-mode interferometer, 184–186 Typhidot® , IgG and IgM antibodies, 590 Tyramide signal amplification (TSA), 648 U Ultrasound and bacterial cells cell viability (MH), 910 cavitation, 914 MCLW instrument, 163–165 and microfluidics, 910 phenomena for acoustic streaming, 913–914 axial radiation forces, 910–911 lateral and secondary radiation forces, 912–913 University of Vermont medium (UVM) for Listeria isolation and recovery, 593 969 V Vaccinia virus (VA), 131 Vancomycin-resistant enterococci, 44 Variola virus, 11 Venezuelan equine encephalitis (VEE), 11 Venezuelan equine encephalitis virus, biowarfare agents, 591 VEROTEST (MicroCarb), ELISA-based kit for detection of ST toxins, 580 V fischeri, N-(3-oxohexanoyl)-homoserine lactone (3-oxo-C6-HSL), 216 Viable but not culturable (VBNC), 62 Viable-but not(yet)-culturable (VBNC), environmental microorganisms, 507 ViaGram Red+ Bacterial Gram Stain and Viability Kit, 56 Vibrio cholerae, 4, 59 cholera toxin, 113 by TSM sensor, 261 Vibrio spp bacterial lux systems, 215 food-borne pathogens, 10 luxAB genes from, 743 O1 and SPR sensors, 99 VIDAS ELISA-based kit, 582 and Mini-VIDAS (bioMerieux), 55 VIP, LFI kits, 584–585 Viral attachment proteins (VAPs), 857 Virulence definitions of, 3–4 as factors, 8–9 microSERS analysis and, 535 Viruses, micropatterning for detection technologies, 858 VITEK system, 607 bioMerieux, 53 VITEK (bioMérieux), automated systems, 756 VT shifts for DNA binders by genetic field effect devices, 323 W Warburg impedance, 349–350 Water pathogen detection, 32–33 Waters MicrobeLynx, 58 Waveguide designs on low-index substrates, 139, 150 on metal-and dye-clad substrates, 152–156 mode in electromagnetic field, calculation from Maxwell’s equations, 146 modes, 143–144, 146 modes in pure dielectric structure, 148 Waveguide excitation fluorescence microscopy (WExFM), 116 Well-based PCR, 844 West Nile virus, biowarfare agents, 591 Wheat germ agglutinin (WGA) from Triticum vulgaris, 543 Whole bacteria detection by SPR, 91–92 Whole-cell detection evanescent-field sensing, 126–127 interferometric applications for, 199–205 sandwich immunoassays, 127–128 970 Whole-organism fingerprinting and Raman microscopy, 527–531 surface-enhanced Raman scattering (SERS), 531–534 Wollaston prism and polarizer, 184 Y Yeast cells detection by PZT/stainless steel cantilever sensor, 463 Yeast cells, Raman fingerprints, 531 Yellow fever virus, biowarfare agents, 591 Yersina spp., 724 biowarfare agents, 591 CL-EIS system for detection of, 224 Index F1 antigen, 113 infection, 660 sequential injection analysis (SIA) for, 494 and SPR sensors, 98 Yersinia spp food-borne pathogens, 10 Young’s interferometer, 170, 186 multi-channel, 193 on planar waveguide, 191 Z Zipper electrode array, 904–905 .. .Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems Edited... analyte-specific, robust, and cost effective techniques by incorporating emerging technologies from various disciplines Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems. .. Simultaneous Detection and Identification of Bacterial Proteins and Bacteria Detection of Diagnostic Markers, Toxin Regulators and Associated Protein Expression Profiles 3.1 Identification of Potential