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Fluorescence in situ hybridization (FISH) is a technique using a tagged nucleic acid probe on cultures or fixed tissue to identify the DNA of the suspected organism ( Figure 34). Molecular methods overall tend to be very sensitive and specific. Detection of an organism's nucleic acid does not require a viable organism, which is a big advantage. The use of molecular techniques in microbial identification has increased dramatically over the past decade and there is still a rapid rate of introduction of new and revised methods and applications. What is important, when making a selection, is to go back to basics and consider: what is the purpose of the identification? what does the microbiologist need to know? and what does the result tell the microbiologist? These questions can help with selecting and implementing the appropriate microbial identification test.
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Most routine testing laboratories select phenotypic test kits and use established contract test facilities where genotypic testing is required. This is, however, far too time consuming and too prohibitively expensive for standard laboratories. Some microbiologists are of the view that the only way to characterize a microorganism correctly is through a “polyphasic approach” that is a combination of phenotypic testing methods and genotypic testing methods. In terms of selecting between methods, this will depend on costs and resources, the time that the microbiologist is prepared to wait for and what level of identification is required. It is additionally important to understand that any systems used to identify bacteria, whether phenotypic or genotypic, will have limitations, because no single test methodology will provide results that are 100% accurate. It is important to note that groupings established by phenetic and phylogenetic systems do not always agree and within each grouping the methodological differences and varying contents of different databases will sometimes lead to conflicting analyses. The techniques described have been divided between phenotypic and genotypic methods. This chapter has outlined some of the microbial identification techniques undertaken. Tim Sandle, in Pharmaceutical Microbiology, 2016 9.7 Conclusion