You are running a temperature of 103 °F, with aches chills and general malaise. A red, puss-filled, welt is present on the sole of your foot and red streaks are starting to appear in the veins of your leg. The microbe growing in the welt has been cultured. Attending physicians know they need to act fast to save you, but what is the identity of the microbe is causing the illness? And what antibiotic do they use to treat it?
You are trying to understand the fate of a pollutant in the environment. You trace its concentration and find it disappears in one plot of land much faster than at any other site. What microbe is doing this?
Reports abound of the mailing of anthrax spores to various media outlets and politicians. The general public is in a panic and worries that every white powder they see is actually anthrax spores. A rapid test is needed to identify actual anthrax spores while calming the public, but what?
Bacterial identification is essential for answering these types of questions. There are several ways to identify microbes and this chapter discusses the most often used methods. The oldest method is biochemical testing. Here the absence or presence of growth of a microbe in a battery of test media is used to create a biochemical fingerprint. By matching the reactions of the test strain to the reactions of known species, it is possible to determine the identity of the microbe. A second method of strain identification is antibody tests. A specially designed antibody, that reacts with an antigen on a test species, is used to probe a sample. If the target species is present, a detectable reaction takes places, usually a color change. A third method of identification is by the use of a DNA probes. When short pieces of DNA are used to amplify a sequence, most often by PCR, they are called a primers. In this case a unique DNA sequence is created that binds specifically to the species being tested for. If the target microbe is present, a detectable reaction takes place. In this chapter we demonstrate these methods for identifying microbes. There are more methods for identification of bacteria, but the three we will describe are commonly in practice.