Molecular Methods for the Detection and Characterization of Foodborne and Environmental Pathogens

Suresh D. Pillai, Ph.D., Professor of Microbiology, Texas A&M University, and
Jessica A. McKelvey, M.S., Research Associate, Food Safety and Environmental Microbiology, Texas A&M University

978-1-60595-079-2, ©2017, 163 pages, 6×9, Hardcover or eBook


  • Techniques for the detection and characterization of microbial pathogens in foods and environmental samples
  • Molecular techniques and their underlying theories and protocols laid out step by step
  • Protocols cover: sample processing, DNA extraction, PCR amplification of target genes, methods for quantifying and quality checking DNA/RNA samples
  • Also presents conventional microbiology, DNA, RNA and other genetic techniques using commercially available materials and kits
  • Guidance for examining, recording, and interpreting data

Combining the depth of a textbook and the guidance of a lab manual, this volume introduces contemporary molecular methods that are widely used to identify and characterize microbial populations and specific pathogens. The book is structured to explain the basic theory and the rationale for choosing appropriate approaches and specific methods. This material is supplemented by in-depth descriptions of lab experiments. Step-by-step guidelines are provided for a variety of experimental objectives. The techniques explained in this volume can be used in a variety of instructional settings and have been taught to students in academic disciplines such as food science, nutrition, environmental technology, and animal science.






Chapter 1. Microorganisms: Detection and Characterization

1.1. Microbes on Earth

1.2. Microbes, Humans, and Animal Health

1.3. History of Microbial Detection and Characterization

1.4. Basic Microbiology Techniques

1.5. Challenges Associated with Conventional Microbiology Techniques

1.6. Molecular Detection of Microorganisms

1.7. Detection Specificity and Detection Sensitivity

1.8. Commercial Kits for Microbial Detection and Characterization

1.9. Validation of Commercial Kits

1.10. References

Chapter 1—Laboratory Experiments

Lab 1.1 Introduction/Serial Dilutions/Direct Plating

Lab 1.2 Commercial-Based Tests: Pathogen Detection and MPN Enumeration

Lab 1.3 Selective Enrichment, Isolation, and MPN Enumeration of Fecal Coliforms and Salmonella in Environmental and Food Samples


Chapter 2. Microbial DNA Extraction, Purification, and Quantification

2.1. Nucleic Acid Extraction Principles

2.2. References

Chapter 2—Laboratory Experiments

Lab 2.1 Genomic DNA Extraction from Pure Bacterial Culture and Community DNA from Environmental and Food Samples

Lab 2.2 Purification, Quantification, and Purity Check of Extracted DNA


Chapter 3. Introduction to PCR Amplification

3.1. Conventional PCR Amplification of Target Sequences

3.2. PCR Amplification from Food and Environmental Samples

3.3. References

Chapter 3—Laboratory Experiments

Lab 3.1 Polymerase Chain Reaction (PCR) of Pathogen Targets and Agarose Gel Electrophoresis


Chapter 4. DNA Fingerprinting

4.1. Bacterial Characterization Methods

4.2. Rationale for DNA Fingerprinting

4.3. DNA Fingerprinting Methods

4.4. Non-PCR-Based Methods

4.5. Foodborne Disease Monitoring Programs in the United States

4.6. PCR-Based Methods

4.7. References

Chapter 4—Laboratory Experiments

Lab 4.1 DiversiLab on a Chip: Bacterial Fingerprinting using the DiversiLab System


Chapter 5. Microbial RNA Extraction, Purification, and Quantification

5.1. Stabilization of RNA Molecules

5.2. Extraction of RNA Molecules

5.3. Protection of Extracted RNA Molecules against RNA Degradation

5.4. Storage of RNA Molecules

5.5. Verifying RNA Concentration and RNA Purity

5.6. References

Chapter 5—Laboratory Experiments

Lab 5.1 Pathogen Total RNA Preservation, Extraction, and Quantification

Lab 5.2 Total Extracted RNA Quality Analysis using the Bioanalyzer


Chapter 6. Gene Expression using Real-Time PCR Assay

6.1. Overview of Real-Time PCR Assays

6.2. Quantifying Microbial Gene Expression using RT-PCR Amplifications

Chapter 6—Laboratory Experiments

Lab 6.1 cDNA Synthesis from Extracted RNA

Lab 6.2 Gene Expression Analysis of Bacterial (Salmonella) Virulence Genes Measured by Real-time PCR using SYBR Green Fluorescence


Appendix A

Appendix B


  1. :

    Though traditional microbiological methods, as for example culture media-based techniques, are still essential in the detection, enumeration, and characterisation if microbes, there is a growing demand for methods based on molecular biology. Today, students aquire the skills to perform molecular analyses through independent laboratory research, but textbooks providing step-by-step protocols for these molecular methods are rare. The book “Molecular methods for the detection and characterization of foodborne and environmental pathogens” fills this gap.

    The book contains six chapters: “Microorganisms: Detection and characterization”, “Microbial DNA extraction, purification, and quantification”, Introduction to PCR amplification”, DNA fingerprinting”, Mictobial RNA extraction, purification, and quantification”, and “Gene expression using real-time PCR assay”. As a very useful feature, all chapters have a “Laboratory experiments” section, where detailed protocols and instructions are presented for the everyday laboratory work.

    Based on a graduate level course titled “Molecular methods of microbial detection and characterisation” that Professor Pillai teaches at Texas ACM University, the book targets senior undergraduate and graduate-level students, lecturers, instructors, and all microbiologists who want to keep up with the progress of new technologies.

    Acta Alimentaria

Molecular Methods for the Detection and Characterization of Foodborne and Environmental Pathogens (Entire eBook)
$94.50 Save: $35.00
Chapter 1: Microorganisms: Detection and Characterization
Chapter 2: Microbial DNA Extraction, Purification, and Quantification
Chapter 3: Introduction to PCR Amplification
Chapter 4: DNA Fingerprinting
Chapter 5: Microbial RNA Extraction, Purification, and Quantification
Chapter 6: Gene Expression using Real-Time PCR Assay

978-1-60595-079-2, ©2017, 163 pages, 6×9, Hardcover or eBook

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