principles of bacterial detection: biosensors, recognition

Principles of Bacterial Detection:Biosensors, RecognitionReceptors and Microsystems

Edited by

MOHAMMED ZOUROBBiophage Pharma Inc.Montreal, Canada

SOUNA ELWARYConsultant to Biophage Pharma Inc.Montreal, Canada

ANTHONY TURNERCranfield UniversityBedfordshire, UK

fyA Springer

Contents

Part I Introduction

I. Introduction to Pathogenic Bacteria

Tracey Elizabeth Love and Barbara Jones

1. Pathogenic Microorganisms 31.1. Toxins 41.2. Adherence 41.3. Invasion 71.4. Evasion of the Host Immune Response 71.5. Iron Acquisition 81.6. Regulation of Virulence Factors 8

2. Sources and Routes of Infection , 92.1. Natural Infection 92.2. Food and Water 92.3. Hospital Acquired Infections 102.4. Intentional Infection—Biological Warfare 10

3. Detection of Pathogenic Microorganisms 114. Conclusions 12

References 12

2. Sample Preparation: An Essential Prerequisite for High-Quality BacteriaDetection

Jan W. Kretzer, Manfred Biebl and Stefan Miller

1. Introduction 152. The Sample 163. Sampling 17

3.1. Sample drawing 174. Microbiological Examination of Foods 175. Microbiological Examination of Surfaces 176. Microbiological Examination of Air 187. Sample Handling 208. Sample Preparation 219. Sample Preparation for Detection of Intact Bacterial Cells 21

10. Sample Preparation for Detection of Bacterial Nucleic Acids 23II. Conclusions and Future Perspectives 27

References 28

3. Detection of Bacterial Pathogens in Different Matrices: Current Practicesand Challenges

Ahmed E. Yousef

1. Introduction 312. Analytical Tools and Methods: A Historical Perspective 32

vii

viii Contents

3. Defining the Terms 324.'Matrix Complexity and Pathogen Detection 325. Techniques Currently Used in Pathogen Detection Methods 33

5.1. Culture Techniques 335.2. Enzyme-Linked Immunoassay 355.3. Polymerase Chain Reaction (PCR) 36

6. Basics of Pathogen Detection 366.1. Sampling 37

6.1.1. Air Sampling 376.1.2. Surfaces Sampling .- 376.1.3. Bulk Sampling 39

6.2. Sample Preparation 396.3. Pathogen Amplification 396.4. Selection and Screening 406.5. Identification 40

6.5.1. Morphological Characteristics 416.5.2. Biochemical and Physiological Traits 416.5.3. Serological Properties 426.5.4. Genetic Characteristics 42

6.6. Pathogenicity Testing 436.6.1. Koch's Postulates 436.6.2. Mammalian Cell Culture (Tissue Culture) 436.6.3. Virulence Genes and Gene Expression Products 44

6.7. Testing for Specific Traits 447. Challenges to Current Detection Methods 44

7.1. Pathogen Quantification Problems 447.2. Can a Small Bacterial Population be Detected Rapidly and Reliably? 447.3. Which Traits to Analyze, and How Many Tests are Needed for Identifying a Bacterial

Pathogen? 457.4. Real-Time Detection 46References 46

4. Overview of Rapid Microbiological MethodsJeanne Moldenhauer

1. Introduction 492. A History of Rapid Microbiological Methods: Industry Reluctance to Accept

These Methods 503. Types of Microbial Testing Performed 504. Types of Rapid Microbiological Methods 50

4.1. Growth-Based Technologies 504.2. Viability-Based Technologies 504.3. Cellular Component or Artifact-Based Technologies 51

, 4.4. Nucleic Acid-Based Technologies 514.5. Automated Methods 514.6. Combination Methods 51

5. Overview of Rapid Technologies and How They Work 515.1. Adenosine Tri-Phosphate (ATP) Bioluminescence 515.2. Adenylate Kinase 525.3. Autofluorescence 525.4. Biochemical Assays and Physiological Reactions 525.5. Biosensors and Immunosensors 535.6. Carbon Dioxide Detection 535.7. Changes in Headspace Pressure 53

Contents ix

5.8. Colorimetric Detection of Carbon Dioxide Production 535.9. Concentric Arcs of Photovoltaic Detectors with Laser Scanning 54

5.10. Direct Epifluorescent Filter Technique (DEFT) 545.11. DNA Sequencing 545.12. Endospore Detection 555.13. Enzyme Linked Immunosorbent Assay (ELISA) 555.14. Flow Cytometry 555.15. Fluorescent Probe Detection 555.16. Fatty Acid Profiles (Fatty Acid Methyl Esters, FAMEs) .• 565.17. Fourier Transformed Infrared Spectroscopy (FTIR).; 565.18. Gram Stains (Rapid Method) 565.19. Impedance 575.20. Immunological Methods 575.21. Lab-on-a-Chip (LOC), Arrays, Microarrays and Microchips 575.22. Limulus Amebocyte Lysate (LAL) Endotoxin Testing 585.23. Mass Spectrometry (Matrix-Assisted Laser Desorption-Time of Flight (MALTI-TOF)) 585.24. Microcalorimetry 585.25. Micro-Electro-Mechanical Systems (MEMS) 595.26. Nanotechnology 595.27. Near Infrared Spectroscopy (NIRS) 595.28. Nucleic Acid Probes 595.29. Optical Particle Detection 595.30. Polymerase Chain Reaction (PCR) 605.31. Rep-PCR : 605.32. Raman Spectroscopy 615.33. Ribotyping/Molecular Typing 615.34. Solid Phase Laser Scanning Cytometry 615.35. Southern Blotting/Restriction Fragment Length Polymorphism 625.36. Spiral Plating 625.37. Turbidimetry 62

6. Potential Areas of Application of Rapid Microbiological Methods 627. Disclaimer 758. Conclusions 75

References 75

Part II Biosensors

5. Surface Plasmon Resonance (SPR) Sensors for the Detection of BacterialPathogens

Allen D. Taylor, Jon Ladd, Jiff Homola and Shaoyi Jiang

1. Introduction 832. Fundamentals of Surface Plasmon Resonance Biosensing 833. SPR Sensor Instrumentation 854. Surface Chemistries and Molecular Recognition Elements 885. Detection Formats 906. Quantification of Bacteria Cells 91

6.1. Challenges for the Detection of Whole Bacteria by SPR 916.2. Effect of Bacteria Sample Treatment 926.3. Examples of Bacteria Detection 92

6.3.1. Escherichia coli 936.3.2. Salmonella spp 976.3.3. Listeria monocytogenes 98

x Contents

6.3.4. Other Bacteria 986.3.5. Detection of Multiple Bacteria 99

7. Genetic Markers 1018. Antibody Biomarkers 1039. Conclusions and Future Perspectives 103

References 104

6. Bacterial Detection Using Evanescent Wave-Based FluorescentBiosensors

Kim E. Saps ford and Lisa C. Shriver-Lake

1. Introduction 1092. Current State of Bacterial Fluorescent TIRF Biosensors 112

2.1. Non-Planar Substrates I 122.1.1. Fiber Optics 1122.1.2. Capillaries 112

2.2. Planar Substrates 1122.2.1. NRL Array Biosensor 1132.2.2. Other Optical Waveguides 1152.2.3. TIRF-Microscopy 116

3. Future Aspects of Bacterial Fluorescent TIRF Biosensors 1174. Conclusions 119

References 120

7. Fiber Optic Biosensors for Bacterial Detection

Ryan B. Hayman

1. Fiber Optic Biosensors 1251.1. Whole-Cell Detection 126

1.1.1. Evanescent-Field Sensing 1261.1.2. Sandwich Immunoassays 127

1.2. Bead-Based Arrays 1281.3. Nucleic Acid Sandwich Assays 1291.4. Nucleic Acid Direct Hybridization 1311.5. Extension Reactions 134

2. Conclusions and Future Perspectives 134References 135

8. Integrated Deep-Probe Optical Waveguides for Label Free BacterialDetection

Mohammed Zourob, Nina Skivesen, Robert Horvath, Stephan Mohr, Martin B. McDonnelland Nicholas J. Goddard

1. Introduction 1391.1. Planar Optical Waveguides 1411.2. Total Internal Reflection and Evanescent Waves 1411.3. Waveguide Modes 1431.4. Frustrated Total Internal Reflection, Leaky Modes 1441.5. Literature on Waveguides for Bacterial Detection 144

2. Deep-Probe Optical Waveguide Sensors with Tunable Evanescent Field 1452.1. Waveguide Modes, Light Coupling and Sensing Depths of Evanescent Waves 146

2.1.1. Light Coupling Techniques 148

Contents xi

2.2. Waveguide Designs Based on Low-Index Substrates 1502.2.1. Bacteria Detection Using Reverse Symmetry Waveguides 151

2.3. Wavlguide Designs Based on Metal- and Dye-Clad Substrates—Leaky Modes 1522.3.1. Results 156

3. Integrated Deep-Probe Optical Waveguides Systems 1603.1. Integration with Electric Field 1613.2. Integration with Ultrasound Standing Waves (USW) 163


9. Interferometric Biosensors

Daniel P. Campbell

1. Principles of Optical Interferometry 1691.1. Optical Waveguides 1711.2. Planar Waveguide Operation 1721.3. Types of Waveguides 175

2. Light Coupling Methods 1782.1. Interferometers 1802.2. Collinear or Single Channel Interferometers 1832.3. Two-Channel Interferometers 186

3. Interferometric Array Sensors 1924. Surface Plasmon Interferometry 1955. Other Interferometric Methods and Designs 1966. Surface Functionalization 1977. Sample Collection Systems 1988. Interferometric Applications for Whole-Cell Detection 1999. Advantages and Limitations 206

10. Potential for Improving Current Performance 206References 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

1. Beyond Robert Boyle's Chicken 2142. The Bacterial (lux) Luminescent System for Direct Pathogen Detection 2153. The Firefly (luc) Luminescent System for Direct Pathogen Detection 2194. The Use of Alternative Luciferases in Pathogen Detection 2225. Luminescent-Based Immunoassays 2226. Chemiluminescence Detection Methods 2227. Conclusions and Future Perspectives 225

References 226

11. Porous and Planar Silicon Sensors

Charles R. Mace and Benjamin L. Miller

1. Introduction 2311.1. Porous Silicon: A Three-Dimensional Matrix for Biosensing 23^1.2. Effect of PSi Immobilization on Probe Viability: Experiments with GST 23;1.3. Toward Larger Targets: The First Macroporous Microcavity Structures 23!1.4. Porous Silicon Bandgap Sensors in Novel Formats: "Smart Bandages" and "Smart Dust" ... 23.

2. Arrayed Imaging Reflectometry—A Planar Silicon Biosensor 23(2.1. Theory 23(

xii Contents

2.1.1. Physical Rationale 2362.1.2. Substrate Design 2372.1.3. Mathematical Model 2382.1.4. Monitoring the Null Reflectance Condition 240

2.2. Applications of AIR Biosensing 2422.2.1. Limitations 2422.2.2. Probe Immobilization 2442.2.3. Pathogen Detection 246

3. Conclusions and Future Perspectives 250References , 251

12. Acoustic Wave (TSM) Biosensors: Weighing Bacteria

Eric Olsen, Arnold Vainrub and Vitaly Vodyanoy

1. Introduction 2552. Historical Perspective, Theory and Background 256

2.1. Piezoelectricity and Acoustic Waves 2562.2. Acoustic Wave Devices 256

3. TSM Biosensors 2593.1. Detection of Microorganisms 2613.2. Measurement in Liquid 2633.3. TSM Biosensor Characteristics 2643.4. Commercial TSM Microbalances 2673.5. Immobilization of Probes onto Sensor Surface 269

3.5.1. Physical Adsorption 2713.5.2. Other Coupling Methods 2723.5.3. Combined Langmuir-Blodgett/Molecular Assembling Method 2723.5.4. Solvent-Free Purified Monolayers 2753.5.5. Immobilization of Monolayers of Phage Coat Proteins 2763.5.6. Immobilization of Molecular Probes onto Porous Substrates 281

4. Problem of "Negative Mass" 2825. Coupled Oscillators Model 2866. Conclusions 290

References 291

13. Amperometric Biosensors for Pathogenic Bacteria Detection

llaria Palchetti and Marco Mascini

1. Introduction 2992. Amperometric Biosensors 300

2.1. Microbial Metabolism-Based Biosensors 3022.2. Immunosensors 3032.3. DNA-Based Biosensors 306

3. Conclusion and Future Perspectives 310References 310

14. Microbial Genetic Analysis Based on Field Effect Transistors

Yuji Miyahara, Toshiya Sakata and Akira Matsumoto

1. Introduction .' 3132. Fundamental Principles of Field Effect Devices 314

2.1. Metal-Insulator-Semiconductor (MIS) Capacitor 3142.2. Principles of Biologically Coupled Field Effect Transistors for Genetic Analysis

(Genetic FETS) 315

Contents xiii

3. Fundamentals of Genetic Analysis 3173.1. DNA 3173.2. Genetic Analysis 3173.3. DNA Chip / DNA Microarray 318

4. Immobilization of DNA Molecules on the Surfaces of Solid Substrates 3184.1. Silanization 3184.2. Thiol-Gold Bonding 3204.3. Avidin, Streptavidin and Biotin 3204.4. Others , 321

5. Genetic Analysis Based on Field Effect Devices 3225.1. Fundamental Characteristics of Genetic Field Effect Devices 322

5.1.1. Detection of DNA Molecular Recognition Events 3225.1.2. Immobilization Density of Oligonucleotide Probes 326

5.2. Single Nucleotide Polymorphisms (SNPs) Analysis 3275.2.1. Controlling Hybridization Temperature for SNPs Analysis 3285.2.2. SNPs Analysis Based on Primer Extension 329

5.3. DNA Sequencing 3316. Conclusions and Future Perspectives 335

References 336

15. Impedance-Based Biosensors for Pathogen Detection

Xavier Munoz-Berbel, Neus Godino, Olivier Laczka, Eva Baldrich, Francesc Xavier Munozand Fco. Javier Del Campo

1. Introduction 3412. Fundamentals of Electrochemical Impedance Spectroscopy 342

2.1. Data Analysis: Plotting 3442.2. Data Analysis: Interpretation 344

2.2.1. Non-Faradaic Parameters 3452.2.2. Faradaic Parameters 347

2.3. Measuring at Impedimetric Biosensors 3502.3.1. Measurement Modes 350

2.4. Bacterial Parasitizing Effect on Electrode Surface 3533. Development of an Immunosensor 354

3.1. Biological Recognition Elements in Biosensors for Pathogen Detection 3543.1.1. Antibodies 3553.1.2. Nucleic Acids 3553.1.3. Aptamers 3563.1.4. Other Recognition Strategies 356

3.2. Surface Modification Methods 3573.2.1. Adsorption 3573.2.2. Self-assembled Monolayers 3583.2.3. Silanisation 3593.2.4. Protein A and Protein G 3603.2.5. The Biotin-(Strept)Avidin System 3603.2.6. Chemical Conjugation 3613.2.7. Entrapment 3623.2.8. Microencapsulation 362

3.3. Blocking 3623.4. Signal Amplification 3633.5. The Need for Negative Controls 3643.6. Development of Novel Strategies: Assessing Performance Using ELISA and Microscopy ... 365

4. Current EIS Biosensors for Pathogen Detection 3654.1. Biosensors Based on Interfacial Capacitance Changes 366

xiv Contents

4.2. Biosensors Based on Charge-Transfer Resistance Changes 3674.3. Biosensors Based on Conductivity Changes 3694.4. Other Approaches 370


16. Label-Free Microbial Biosensors Using Molecular Nanowire Transducers

Evangelyn Alocilja and Zarini Muhammad-Tahir

1. Introduction 3771.1. Rationale for Rapid Tests 3771.2. Target Microorganisms and Matrices 378

1.2.1. Escherichia coli 3781.2.2. Salmonella 3791.2.3. Bovine Viral Diarrhea Virus 380

1.3. Food Safety Applications 3812. Biosensor Formats 382

2.1. Definition 3822.2. Antibodies as Biological Sensing Element 3822.3. DNA as Biological Sensing Element 3842.4. DNA-Based Biosensors 3852.5. Antibody-Based Biosensors 3872.6. Biosensor Transducing Element: Conducting Polymer '. 388

2.6.1. Polyaniline 3902.6.2. Self-doped Polyaniline 3912.6.3. Carbon Nanotubes 391

2.7. Conducting Polymer-Based Biosensor for Microbial/Viral Detection 3923. Illustration: Biosensor Using Self-doped and Non-self-doped Pani 392

3.1. Pani Preparation 3923.2. Pani Characterization 392

3.2.1. Conductivity Measurement 3923.2.2. Biosensor Fabrication 3933.2.3. Indium Tin Oxide/Pani Biosensor 3933.2.4. Lateral Flow Conductometric Biosensor 3933.2.5. Signal Measurement 393

3.3. Properties of Pani 3943.4. Detection Concept of the Biosensor 3983.5. Biosensor Properties .• 399

3.5.1. ITO-Pani Biosensor 3993.6. Lateral Flow Conductometric Biosensor 4033.7. Biosensor Performance 404

3.7.1. ITO/Pani Biosensor 4043.8. Conductometric Biosensor 404


17. Magnetic Techniques for Rapid Detection of Pathogens

Yousef Haik, Reyad Sawafta, Irina Ciubotaru, Ahmad Qablan, Ee Lim Tan andKeat Ghee Ong

1. Introduction 4152. Synthesis of Magnetic Particles 417

2.1. Effect of Particle Size 418

Contents xv

2.2. Synthesis Techniques 4232.3. Encapsulation of Magnetic Particles 423

2T3.1. Methods of Preparing Polymer/Protein Coatings 4242.3.2. Examples of Polymer/Protein Encapsulated Particles 426

3. Immobilization Strategies 4263.1. Modification of Particle Surface with a Ligand 430

4. Biological Targets 4305. Magnetic Immunoassays 430

5.1. Direct Immunoassay Detection Using Magnetic Beads 4305.1.1. Superconducting Quantum Interference Devices 4315.1.2. ABICAP Column 432

5.2. Indirect Immunoassay Detection Using Magnetic Beads 4335.2.1. ELISA 433

6. Handling Techniques 4387. Magnetic Separation 439

7.1. Magnetic Force 4397.2. High-Field Electromagnets 4407.3. Permanent Magnets 4417.4. Numerical Analysis for Permanent Magnet Arrangements 442

8. Giant Magnetoresistive (GMR) Devices for Bacterial Detection 4469. Bacteria Detection with Magnetic Relaxation Signal 448

10. Magnetoelastic Sensors for Bacterial Detection 44910.1. E. coli Detection 450


18. Cantilever Sensors for Pathogen Detection

Ray Mutharasan

1. Introduction 4592. Millimeter-Sized Cantilever Sensors 4603. Reported Work on Detecting Cells Using Cantilever Sensors 4614. Physics of Cantilever Sensors 4635. Resonance Modes 4666. Characterization of PEMC Sensors 4687. Mass Change Sensitivity 4688. Antibody Immobilization Methods 4699. Detection in Batch and Stagnant Samples 470

10. Detection in Flowing Samples 47311. Selectivity of Detection 47512. Conclusions 477

References 478

19. Detection and Viability Assessment of Endospore-Forming Pathogens

Adrian Ponce, Stephanie A. Connon and Pun To Yung

I. Introduction 4811.1. Historical Perspective 4811.2. Endospore Dormancy, Resistance and Longevity 4821.3. Endospores as Biodosimeters for Evaluating Sterilization Regimes 4841.4. Endospore-Forming Pathogens 4851.5. Bioweapons, Bioinsecticides and Probiotics 487

22. Rapid Nucleic Acid-Based Diagnostics Methods for the Detectionof Bacterial PathogensBarry Glynn

1. Introduction 6031.1. Detection of Pathogenic Bacteria from Clinical Samples 6041.2. NAD Assays for the Detection of Respiratory Infection, Sepsis and Sexually

Transmitted Infection 6041.3. Profiling of Multi-drug Resistance 6061.4. Bioterrorism • 606

2. Detection of Bacterial Food-Borne Pathogens 6062.1. Recent Outbreaks 6062.2. Benefits and Limitations of Conventional Methods 6072.3. Development of Rapid Diagnostics Methods 607

3. Rapid Nucleic Acid Diagnostics for Bacterial Food-Borne Pathogens 6073.1. In Vitro Nucleic Acid Amplification-Based Detection of Food-Borne Pathogens 6073.2. Requirements for a NAD-Based Food Assay 6083.3. Polymerase Chain Reaction (PCR) 6083.4. Application of PCR-Based Tests to Pathogen Detection in Food Samples 6093.5. Use of RNA as an Alternative Nucleic Acid Diagnostic Target 6103.6. Sample Preparation for NAD from Clinical Sample Types 6113.7. Limitations of NAD in Clinical Settings 611

4. Formats of NAD Assays for Food Pathogen Detection 6124.1. Nucleic Acid-Based Diagnostics Based on In Vitro Amplification Technologies 6124.2. PCR-ELISA and PCR-DNA Probe Membrane Based Assays

for Campylobacter and Salmonella 6124.3. Specific Examples of Nucleic Acid Diagnostics Assays for the Detection of Bacterial

Food-Borne Pathogens 6134.3.1. Commercially Available Conventional NAD Assays

for Food-Borne Bacterial Pathogens 6144.3.2. Alternative In Vitro Amplification Technologies 615

4.4. Standardisation of In Vitro Amplification-Based NAD Assaysand Inter-Laboratory Validation Studies 616

4.5. Real-Time In Vitro Amplification-Based Nucleic Acid Diagnostics 6174.5.1. Specific Examples of Real-Time PCR Assays for the Detection of Bacterial

Food-Borne Pathogens 6174.5.2. Alternative Real-Time In Vitro Amplification-Based Diagnostics Technologies 618

4.6. Limitations and Other Considerations for In Vitro Amplification NAD Tests 6194.7. Non-Amplified Direct DNA Probe-Based Nucleic Acid Diagnostics 6204.8. DNA-Probe Based Detection Methods 620

5. Conclusions and Future Perspectives 6215.1. Emerging Nucleic Acid Diagnostic Technologies for Food-Borne Pathogen Detection 621

5.1.1. Biosensors 6215.1.2. Microarrays 622

References 623

23. Oligonucleotide and DNA Microarrays: Versatile Tools for Rapid BacterialDiagnostics

Tanja Kostic, Patrice Francois, Levente Bodrossy and Jacques Schrenzel

1. Introduction 6292. Microarray Technology 6303. Technical Aspects of Microarray Technology 632

3.1. Probes 6323.1.1. Genome Fragments 632

3.1.2. PCR Products 6323.1.3. Oligonucleotide Probes 632

3.2. Substrates for Printing 634^3.2.1. Slides with Poly-L-Lysine Coating 634

3.-2.2. Slides with Amino Silane Coating 6353.2.3. Slides with Aldehyde Coating 6353.2.4. Slides with Epoxy Coating 6353.2.5. Proprietary Surface Chemistries 6363.2.6. Probe Spacers 636

3.3. Targets for Microarray Analysis 6373.3.1. Target Amplifications and Sensitivity Issues 6373.3.2. Labeling of the Targets 6383.3.3. Hybridization and Wash Conditions 638

3.4. Classical Commercially-Available Microarray Formats 6393.4.1. Spotting Approaches 6393.4.2. In Situ Synthesis 639

3.5. Alternative Methods for Improving Microarray-Based Detection Sensitivity 6413.5.1. Resonance-Light Scattering (RLS) 6413.5.2. Planar-Waveguide Technology (PWT) 6413.5.3. Liquid Arrays 6413.5.4. Three-Dimensional Microarray Formats 642

3.6. Marker Genes Used on Microbial Diagnostic Microarrays (MDMs) 6434. Analysis and QC Aspects 6435. Applications of Microarray Technology in Microbial Diagnostics .• 644

5.1. Gene Expression Studies 6445.2. Comparative Genome Hybridizations (CGH) 6455.3. Generic or Universal Microarrays 6465.4. Microarrays for Sequence Analysis 6475.5. Microbial Diagnostic Microarrays 648

6. Conclusions 649References 649

24. Pathogenic Bacterial Sensors Based on Carbohydrates as SensingElements

Haiying Liu

1. Introduction 6602. Bacterial Surface Lectins 6613. Surface Carbohydrate Structures of Pathogenic Bacteria 6644. Carbohydrate Microarrays for Detection of Bacteria 6685. Lectin Microarrays for Detection of Bacteria 6706. Conjugated Fluorescent Glycopolymers for Detection of Bacteria 6727. Glyconanoparticles for Detection of Bacteria 6768. Carbohydrate-Functionalized Carbon Nanotubes for Detection of Bacteria 6789. Conclusions and Future Perspectives 680

References 681

25. Aptamers and Their Potential as Recognition Elements for the Detectionof BacteriaCasey C. Fowler, Naveen K. Navani, Eric D. Brown and Yingfu Li

1. Functional Nucleic Acids 6891.1. Properties of Nucleic Acids 6901.2. Synthesizing, Sequencing and Modifying Nucleic Acids 692

xx Contents

1.2.1. DNA Polymerase and Polymerase Chain Reaction 6921.2.2. RNA Polymerase and In Vitro Transcription 6921.2.3^ Reverse Transcription 6931.2.4. Other Modifications 693

2. Isolation of Functional Nucleic Acids 6942.1. Introduction to SELEX 6942.2. Selection Methods 694

2.2.1. Bead and Column Based Selections 6962.2.2. Polyacrylamide Gel Electrophoresis (PAGE) Based Selections 6962.2.3. Capillary Electrophoresis (CE) Based Selections..". 697

2.3. Optimizing Functional Nucleic Acids 6973. Aptamers: Properties and Targets 697

3.1. The Growing Aptamer Catalogue 6983.2. Aptamer Specificity 6983.3. Aptamer-Ligand Interactions 7003.4. Aptamers vs. Other Recognition Elements 700

4. Applications of Aptamers 7014.1. Aptamers for Purification 7014.2. Aptamers with Therapeutic Potential 7024.3. Aptamers as Sensing Elements 702

4.3.1. Conformation-Dependent Fluorescent Sensors 7034.3.2. Quantum Dot Sensors 7034.3.3. Target Detection by Fluorescence Anisotropy '. 7044.3.4. Enzyme Linked Aptamer Assays 7054.3.5. Acoustic Sensors 7054.3.6. Electrochemical Sensors 706

5. Aptamers for Detection of Pathogenic Bacteria 7065.1. Categories of Microbial Agents to be Detected 707

5.1.1. Gram-Positive Bacteria 7075.1.2. Gram-Negative Bacteria 708

5.2. Traditional Pathogen Detection Methods 7085.3. Aptamers in Pathogen Detection 709


26. Protein Microarray Technologies for Detection and Identificationof Bacterial and Protein Analytes

Christer Wingren and Carl AK Borrebaeck

1. Introduction 7151.1. Definition and Classification of Protein Microarrays 7161.2. Functional Protein Microarrays 7161.3. Affinity Protein Microarrays 7191.4. Alternative Microarray Setups 720

2. Detection of Bacteria and Bacterial Protein Analytes 7212.1. Serotyping of Bacteria 7212.2. Detection of Pathogenic Organisms 7212.3. Detection of Multiple Toxins 7222.4. Simultaneous Detection and Identification of Bacterial Proteins and Bacteria 723

3. Detection of Diagnostic Markers, Toxin Regulators and Associated Protein Expression Profiles. 7243.1. Identification of Potential Diagnostic Markers and/or Vaccine Candidates 7243.2. Disease State Differentiation and Identification of Diagnostic Markers 7243.3. Identification of Potential Toxin Modulators/Regulators 7253.4. Screening of Protein Expression Signatures Associated with Bacterial Infection 726

Contents


27. Bacteriophage: Powerful Tools for the Detection of Bacterial Pathogens

Mathias Schmelcher and Martin J. Loessner

1. Introduction 7312. Detection by Phage Amplification 7323. Detection Through Phage-Mediated Cell Lysis 734

3.1. Measurement of ATP Release 7353.2. Detection of Other Cytoplasmic Markers 7363.3. Measurement of Impedance 737

4. Detection Through Cell Wall Recognition, Phage Adsorption and DNA Injection 7384.1. Immobilized Phage 7384.2. Detection Through Phage-Encoded Affinity Molecules 7384.3. Fluorescently Labeled Phage 740

5. Detection by Reporter Phage 7415.1. Luciferase Reporter Phage (LRP) 7435.2. Fluorescent Protein Reporter Phage 7455.3. Other Reporter Phages 746

6. Other Detection Methods Using Phage 7476.1. Phage Display for Production of Highly Specific Binding Molecules 7476.2. Dual Phage Technology '. 749


28. Phage Display Methods for Detection of Bacterial Pathogens

Paul A. Gulig, Julio L. Martin, Harald G. Messer, Beverly L. Deffense andCrystal J. Harpley

1. Introduction 7561.1. Why Detect Bacteria and What Tools Are Available? 7561.2. Immunological Tools 7561.3. Nucleic Acid-Based Tools 758

2. What Types of Antigen Detection Methods Are Being Developed? 7583. Phage Display 759

3.1. Phage M13 7603.2. Principles of Phage Display 7603.3. Phages Versus Phagemids 7623.4. Phage Display Formats 764

3.4.1. Random Peptides 7643.4.2. Antibody Fragments 764

3.5. The Phages Themselves Are Not the Ultimate Tool 7673.6. Using Phage Display 767

4. Review of Literature on Phage Display Against Bacterial Pathogens 7694.1. Random Peptide Phage Display 7704.2. scFv Libraries 7724.3. Single Domain Antibodies (sdAbs) and Domain Antibodies (dAbs) 775

5. Summary of Our Results Using and Developing Phage Display scFv and Peptides 7755.1. Panning Methods 7765.2. Screening Methods 7775.3. Genetic Modification of Phagemid Clones 7775.4. Random Peptide Phage Libraries 777

xxii Contents

6. New Directions 7786.1. Proteins Based on Phage Display 778

6.\.{. Affibodies 7786.1.2. Anticalins 7786.1-.3. Ankyrins 7786.1.4. Trinectins 779

6.2. Alternatives to Phage Display 7796.2.1. Aptamers 7796.2.2. Ribosome Display 7796.2.3. mRNA Display ! 780


29. Molecular Imprinted Polymers for Biorecognition of Bioagents

Keith Warriner, Edward P.C. Lai, Azadeh Namvar, Daniel M. Hawkinsand Subrayal M. Reddy

1. Introduction 7852. Principles of Molecular Imprinting 786

2.1. Imprinting Considerations 7872.1.1. Versatility 7872.1.2. Template Molecule 7882.1.3. Functional Monomer •. 7882.1.4. Cross-Linking 7892.1.5. Polymerization 7902.1.6. Solvent 790

2.2. Aqueous Phase MIP 7912.2.1. Hydrogels 7922.2.2. MIP Within Hydrogels 7932.2.3. Polyacrylamide Gels—HydroMIPs 793

3. Solid Phase Extraction Based on MIPs for Concentrating Bioagents 7953.1. Antibiotics 7953.2. Mycotoxins 7983.3. Nano-Sized Structures 7993.4. Peptides and Proteins 8003.5. Viruses 8013.6. Bacterial Cells and Endospores 802

4. Biosensors Based on MIPs 8034.1. MlP-based Sensors for Detection of Amino Acids 8044.2. Molecular-Imprinted Films for Toxins 8054.3. Microbial Imprinted Polymers 806


Part IV Microsystems

30. Microfluidics-Based Lysis of Bacteria and Spores for Detectionand Analysis

Ning Bao and Chang Lu

1. Introduction 8172. Bench Scale Methods for Bacteria/Spore Lysis 8183. Bacteria/Spore Lysis Based on Microfluidic Systems 820

Contents xxiii

3.1. Mechanical Lysis 8203.2. Chemical Lysis 8213.3. Thermal Lysis 8233.4. Laser-Based Lysis 8263.5. Electrical Lysis 827


31. Detection of Pathogens by On-Chip PCR *

Pierre-Alain Auroux

1. Introduction 8332. Microfluidics 834

2.1. History of Miniaturized Total Analysis System (|xTAS) 8342.2. Advantages of Miniaturized Analysis Systems 834

3. DNA Amplification 8353.1. A Brief History of DNA 8353.2. PCR Characteristics and Applications 8363.3. Components to Perform PCR 8373.4. PCR Process 8383.5. Conventional PCR 8393.6. Real-Time PCR: Apparatus and Detection Techniques : 8403.7. On-Chip PCR 841

3.7.1. Capillary-Based Thermocyclers 8423.7.2. Microdevice-Based Thermocyclers 8433.7.3. Static-Sample Systems 8433.7.4. Dynamic-Sample Systems 844

4. Minireview 8465. Conclusions 848

References 849

32. Micro- and Nanopatterning for Bacteria- and Virus-BasedBiosensing ApplicationsDavid Morrison, Kahp Y. Suh and All Khademhosseini

1. Introduction 8552. Fundamentals of Bacterial and Viral Surface Interactions 8573. Technologies for Patterning 858

3.1. Overview 8583.2. Photolithography 8583.3. Micromolding (Soft Lithography) 859

3.3.1. Replica Molding 8593.3.2. Microcontact Printing 8593.3.3. Microtransfer Molding 8603.3.4. Capillary Force Lithography 860

3.4. Scanning Probe Lithography 8614. Biosensing Applications and Examples 862

4.1. Overview 8624.2. Healthcare Applications 8644.3. Detection of Toxins in the Environment 8654.4. Real Devices and Challenges 866


xxiv Contents

33. Microfabricated Flow Cytometers for Bacterial Detection

Sung-Yi Yang and Gwo-Bin Lee

1. Introduction 8691.1. Bio-MEMS 8711.2. Review of Microfabrication Techniques 872

1.2.1. Bulk Micromachining Technique 8721.2.2. Surface Micromachining Technique 8721.2.3. LIGA 8721.2.4. Polymer-Based Micromachining Techniques for Microfluidic Devices 873

2. Operation Principles 8742.1. Cell Transportation and Focusing 875

2.1.1. Hydrodynamic Approach 8752.1.2. Pneumatic Approach 8782.1.3. Electrokinetic Approach 879

2.2. Cell Detection '. 8802.2.1. Optical Waveguide Approach 8812.2.2. Buried Optical Fiber Approach 8822.2.3. Large-Scale Optical System Approach 882

2.3. Cell Sorting 8832.3.1. Hydrodynamic Sorting 8832.3.2. Pneumatic Sorting 8842.3.3. Electrokinetic Sorting 8852.3.4. Magnetic Sorting 885

3. Applications 8853.1. Environmental Monitoring 8863.2. Rapid Assessment of Bacterial Viability 8883.3. Rapid Analysis of Bacteria Levels in Food 8883.4. Antibiotic Susceptibility Testing 8893.5. Bacterial Detection in Blood and Urine 889


34. Bacterial Concentration, Separation and Analysis by Dielectrophoresis

Michael Pycraft Hughes and Kai Friedrich Hoettges

1. Introduction 8952. Theory 8973. Applications of Electrokinetics to Bacteria 9014. Toward an Integrated Detection System 9045. Conclusions and Future Perspectives 905

References 906

35. Ultrasonic Microsystems for Bacterial Cell Manipulation

Martyn Hill and Nicholas R. Harris

1. Introduction 9091.1. Ultrasound and Bacterial Cells 910

1.1.1. Cell Viability 9101.2. Ultrasound and Microfluidics 910

2. Relevant Ultrasonic Phenomena 9102.1. Axial Radiation Forces 9102.2. Lateral and Secondary Radiation Forces 912

Contents xxv

2.3. Acoustic Streaming 9132.4. Cavitation 914

3. Applications of Ultrasonic Particle Manipulation 9143.1. Practical Considerations 914

3.1.1. Transduction 9143.1.2. Mechanical Effects 9153.1.3. Construction 916

3.2. Filtration and Fractionation of Cells 9173.2.1. Filtration and Concentration 9173.2.2. Fractionation of Cells : 9203.2.3. Trapping of Cells 921

3.3. Biosensor Enhancement by Forcing Cells to a Surface 9224. Conclusions and Future Perspectives 924

References 924

36. Recent Advances in Real-Time Mass SpectrometryDetection of Bacteria

/Aryan L van Wuijckhuijse and Ben L.M. van Baar

1. Introduction 9291.1. General 9291.2. Scope 9301.3. MS in the Whole Cell Analysis of Bacteria 930

1.3.1. The Definition of 'Identity' of Bacteria 9301.3.2. Mass Spectrometry of Bacteria 931

1.4. Aerosol MS 9361.4.1. MS of Deposited Aerosols 9361.4.2. Direct MS of aerosols 938

2. Current State of the Technology 9392.1. Considerations on Aerosol MS of Bacteria 9392.2. Deposition and PyMS Based Technology 9402.3. Deposition and MALDI MS Based Technology 9412.4. Single Particle LDI MS Technology 9412.5. Single Particle MALDI MS Technology 943


Index 955

principles of bacterial detection: biosensors, recognition

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