AN INTRODUCTION TO THE HOWS AND WHYS OF MOLECULAR TYPING

Until recently, the relatedness of bacterial isolates has been determi ned solely by testing for one or several phenotypic markers, using met hods such as serotyping, phage typing, biotyping, antibiotic susceptib ility testing, and bacteriocin typing. However, there are problems in the use of many of these phenotype-based methods. For example, phage a nd bacteriocin typing systems are not available for all bacterial spec ies and serotyping can be labor-intensive and costly. In addition, phe notypic markers may not be stably expressed under certain environmenta l or culture conditions. In contrast, some of the newer molecular typi ng methods involving the analysis of DNA offer many advantages over tr aditional techniques. One of the more important advantages is that sin ce DNA can always be extracted from bacteria, all bacteria should be t ypeable. Another is that the discriminatory power of DNA-based methods is greater than that of phenotypic procedures. This review focuses on the basics of molecular typing along with the advantages and disadvan tages of several of the newer genotypic typing techniques. This includ es methods such as plasmid typing, pulsed-field gel electrophoresis, r ibotyping and its variations, and polymerase chain reaction-based meth ods such as random amplified polymorphic DNA analysis. Molecular typin g of microorganisms has made great strides in the last decade, and man y food microbiology laboratories have become more knowledgeable and be tter equipped to carry out these new molecular techniques. Molecular t yping procedures can be broadly defined as methods used to differentia te bacteria, based on the composition of biological molecules such as proteins, fatty acids, carbohydrates, etc., or nucleic acids. The latt er can also be more specifically defined as genotyping, and is the sub ject of this review.