PCR Methods in Food

Arvanitoyannis, Ioannis S

doi:10.1111/j.1365-2621.2006.01412.x

This book can be characterised as an introductory and easy to use book aiming primarily at providing basic information to non-molecular biologists who would like to get acquainted with the principles behind polymersae chain reaction (PCR), to know how to design, optimise and implement PCR in a food microbiology laboratory, to understand both strengths and limitations of PCR and to understand the basic principles behind microarrays and its potential applications in food microbiology. The contents of this book per chapter are summarized below:

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Chapter 1 – PCR Basics

An introductory but, nevertheless, well-compiled and comprehensive chapter (twenty-five pages) providing basic information on issues like usage of molecular methods towards identifying microbial pathogens, the theory behind PCR, thermocycler technology, detection of the PCR product (amplicon), advanced PCR technologies and microarrays [real-time PCR (RT-PCR), multiplex PCR, terminal restriction fragment length polymorphisms, microarrays], design and optimisation of diagnostic PCR as applicable to food microbiology and access DNA databases to retrieve sequences or search for DNA matches. It contains seven figures out of which three (Figs 5, 6 and 7) are not clear and of very small size (letters in particular) and they should be improved in next edition. The inclusion of 97 references is an extra plus for the chapter.

Chapter 2 – The Mythology of PCR: a warning to the Wise

This rather short (thirteen pages) but solid chapter is focused on very specific issues such as interpretation of conventional PCR and RT-PCR, validation, potential problems and their solutions (false positives and dead vs. live bacterial cell debate, PCR inhibitors, limits of detection and false-negatives). Two figures and seventy-five references are cited in this chapter.

Chapter 3 – Sample Preparation for PCR

A very practical chapter aiming at providing a ‘hands on’ information on crucial questions like: how can one get started?, what conditions affect the success of the PCR?, what are PCR inhibitors? And potential solutions to the challenges of using PCR to detect pathogens in foods. The inclusion of two informative figures and one comprehensive and extensive table and twenty-eight references enhance the importance of this chapter.

Chapter 4 – Making PCR a Normal Routine of the Food Microbiology Laboratory

One of the smallest (eighteen pages) but still quite informative chapter (two figures, two tables, forty-nine references) the contents of which are as follows: setting up your laboratory for PCR, real-time vs. standard format PCR, non-commercial tests for foodborne pathogens and available commercial PCR tests for foodborne pathogens.

Chapter 5 – Molecular Detection of Foodborne Bacterial Pathogens

Although this chapter (twenty-two pages) reports information on topics like conventional PCR detection of foodborne pathogens, multiplex PCR detection of foodborne pathogens, reverse transcriptase PCR detection of foodborne pathogens and RT-PCR detection of foodborne pathogens, its strong points are Table 5.1 (thirteen pages) where representative PCR methods are given for common foodborne bacterial pathogens and the seventy-four references cited.

Chapter 6 – Molecular Approaches for the Detection of Foodborne Viral Pathogens

This very useful chapter (twenty-seven pages) for the average reader chapter contains specific information on topics like virus concentration methods for shellfish and other than shellfish, nucleic acid extraction, RT-PCR detection of viruses in foods, alternative nucleic acid amplification methods and confirmation. The importance of this chapter is further enhanced by the inclusion of three informative figures, two tables (primers used in the detection of noroviruses in foods) and 113 references.

Chapter 7 – Molecular Tools for the Identification of Foodborne Parasites

The final chapter is a well compiled one reporting on DNA extraction procedures, protozoal infections, Cryptosporidium parvum, Cyclospora cayetanensis, Giardia intestinalis, Toxoplasma gondii and Microsporidia (parasite description and identification, molecular detection). However, the presence of just one table (primers used for identification of protozoan parasites) is a disadvantage for this chapter whereas the high number of cited references (148) is advantageous to the average reader who would like to get some extra information on this particular topic.

Chapter 1 – PCR Basics	An introductory but, nevertheless, well-compiled and comprehensive chapter (twenty-five pages) providing basic information on issues like usage of molecular methods towards identifying microbial pathogens, the theory behind PCR, thermocycler technology, detection of the PCR product (amplicon), advanced PCR technologies and microarrays [real-time PCR (RT-PCR), multiplex PCR, terminal restriction fragment length polymorphisms, microarrays], design and optimisation of diagnostic PCR as applicable to food microbiology and access DNA databases to retrieve sequences or search for DNA matches. It contains seven figures out of which three (Figs 5, 6 and 7) are not clear and of very small size (letters in particular) and they should be improved in next edition. The inclusion of 97 references is an extra plus for the chapter.
Chapter 2 – The Mythology of PCR: a warning to the Wise	This rather short (thirteen pages) but solid chapter is focused on very specific issues such as interpretation of conventional PCR and RT-PCR, validation, potential problems and their solutions (false positives and dead vs. live bacterial cell debate, PCR inhibitors, limits of detection and false-negatives). Two figures and seventy-five references are cited in this chapter.
Chapter 3 – Sample Preparation for PCR	A very practical chapter aiming at providing a ‘hands on’ information on crucial questions like: how can one get started?, what conditions affect the success of the PCR?, what are PCR inhibitors? And potential solutions to the challenges of using PCR to detect pathogens in foods. The inclusion of two informative figures and one comprehensive and extensive table and twenty-eight references enhance the importance of this chapter.
Chapter 4 – Making PCR a Normal Routine of the Food Microbiology Laboratory	One of the smallest (eighteen pages) but still quite informative chapter (two figures, two tables, forty-nine references) the contents of which are as follows: setting up your laboratory for PCR, real-time vs. standard format PCR, non-commercial tests for foodborne pathogens and available commercial PCR tests for foodborne pathogens.
Chapter 5 – Molecular Detection of Foodborne Bacterial Pathogens	Although this chapter (twenty-two pages) reports information on topics like conventional PCR detection of foodborne pathogens, multiplex PCR detection of foodborne pathogens, reverse transcriptase PCR detection of foodborne pathogens and RT-PCR detection of foodborne pathogens, its strong points are Table 5.1 (thirteen pages) where representative PCR methods are given for common foodborne bacterial pathogens and the seventy-four references cited.
Chapter 6 – Molecular Approaches for the Detection of Foodborne Viral Pathogens	This very useful chapter (twenty-seven pages) for the average reader chapter contains specific information on topics like virus concentration methods for shellfish and other than shellfish, nucleic acid extraction, RT-PCR detection of viruses in foods, alternative nucleic acid amplification methods and confirmation. The importance of this chapter is further enhanced by the inclusion of three informative figures, two tables (primers used in the detection of noroviruses in foods) and 113 references.
Chapter 7 – Molecular Tools for the Identification of Foodborne Parasites	The final chapter is a well compiled one reporting on DNA extraction procedures, protozoal infections, Cryptosporidium parvum, Cyclospora cayetanensis, Giardia intestinalis, Toxoplasma gondii and Microsporidia (parasite description and identification, molecular detection). However, the presence of just one table (primers used for identification of protozoan parasites) is a disadvantage for this chapter whereas the high number of cited references (148) is advantageous to the average reader who would like to get some extra information on this particular topic.