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Molecular Typing and Differentiation
Oakley, B., N. Gonzalez-Escalona, AND M. Molina. Molecular Typing and Differentiation. Chapter 11, Compendium of Methods for the Microbiological Examination of Foods Compendium of Methods for The Microbiological Examination of Foods. American Public Health Association, Washington, DC, , 127-156, (2013).
Book Chapter for Compendium of Methods for the Microbiological Examination of Foods, 5th Edition
In this chapter, general background and bench protocols are provided for a number of molecular typing techniques in common use today. Methods for the molecular typing and differentiation of microorganisms began to be widely adopted following the development of the polymerase chain reaction (PCR) in the 1980s. For the foreseeable future, rapid advances in DNA sequencing will continue to drive the evolution of new molecular typing approaches. In particular, we foresee the increased adoption of whole‐genome based approaches, as described below. Molecular typing methods generally have important advantages of speed and discriminatory power compared to phenotypic characterization methods, but can also change rapidly, given the rapid rate of technological advances. In this chapter, techniques that have either already been superseded by others or are expected to fall out of common usage in the near future are given brief mention for historical purposes, but the more modern technique is given preference. For example, multilocus enzyme electrophoresis (MLEE) has been largely replaced by multilocus sequence typing (MLST),1,92,93 a development which has led to the creation of large databases of MLST profiles—currently for nearly 100 bacterial species and four Candida species. See the MLST section below for more information.