+++ TAXONOMY—THE VOCABULARY OF MEDICAL MICROBIOLOGY ++ One has only to peruse the table of contents of this book to appreciate the diversity of medical pathogens that are associated with infectious diseases. It has been estimated that we currently have the capacity to identify a surprisingly small number of the pathogens responsible for causing human disease. In part this is due to our inability to culture or target these organisms using molecular probes. The diversity of even these identifiable pathogens alone is so great that it is important to appreciate the subtleties associated with each infectious agent. The reason for understanding these differences is significant because each infectious agent has specifically adapted to a particular mode(s) of transmission, the capacity to grow in a human host (colonization), and a mechanism(s) to cause disease (pathology). As such, a vocabulary that consistently communicates the unique characteristics of infectious organisms to students, microbiologists, and health care workers is critical to avoid the chaos that would ensue without the organizational guidelines of bacterial taxonomy (Gk. taxon = arrangement; eg, the classification of organisms in an ordered system that indicates a natural relationship). ++ Identification, classification, and nomenclature are three separate but interrelated areas of bacterial taxonomy. Each area is critical to the ultimate goal of accurately studying the infectious diseases and precisely communicating these to others in the field. ++ Identification is the practical use of a classification scheme (1) to isolate and distinguish specific organisms among the mix of complex microbial flora, (2) to verify the authenticity or special properties of a culture in a clinical setting, and (3) to isolate the causative agent of a disease. The latter may lead to the selection of specific pharmacologic treatments directed toward their eradication, a vaccine mitigating their pathology, or a public health measure (eg, handwashing) that prevents further transmission. ++ Identification schemes are not classification schemes, although there may be some superficial similarity. For example, the popular literature has reported Escherichia coli as the causative agent of hemolytic uremic syndrome (HUS) in infants. There are hundreds of different strains that are classified as E. coli but only a few that are associated with HUS. These strains can be “identified” from the many other E. coli strains by antibody reactivity with their O-, H-, and K-antigens, as described in Chapter 2 (eg, E. coli O157:H7). However, they are more broadly classified as a member of the family Enterobacteriaceae. ++ In a microbiologic context, classification is the categorization of organisms into taxonomic groups. Experimental and observational techniques are required for taxonomic classification. This is because biochemical, physiologic, genetic, and morphologic properties are historically necessary for establishing a taxonomic rank. This area of microbiology is necessarily dynamic as the tools continue to evolve (eg, new methods of microscopy, biochemical analysis, and computational nucleic acid biology). ++ Nomenclature refers to the naming of an organism by an established group ...

+++ OPTICAL METHODS +++ The Light Microscope ++ The resolving power of the light microscope under ideal conditions is about half the wavelength of the light being used. (Resolving power is the distance that must separate two point sources of light if they are to be seen as two distinct images.) With yellow light of a wavelength of 0.4 µm, the smallest separable diameters are thus about 0.2 µm (ie, one-third the width of a typical prokaryotic cell). The useful magnification of a microscope is the magnification that makes visible the smallest resolvable particles. Several types of light microscopes, which are commonly used in microbiology, are discussed as follows. +++ A. Bright-Field Microscope ++ The bright-field microscope is the most commonly used in microbiology courses and consists of two series of lenses (objective and ocular lens), which function together to resolve the image. These microscopes generally employ a 100-power objective lens with a 10-power ocular lens, thus magnifying the specimen 1000 times. Particles 0.2 µm in diameter are therefore magnified to about 0.2 mm and so become clearly visible. Further magnification would give no greater resolution of detail and would reduce the visible area (field). ++ With this microscope, specimens are rendered visible because of the differences in contrast between them and the surrounding medium. Many bacteria are difficult to see well because of their lack of contrast with the surrounding medium. Dyes (stains) can be used to stain cells or their organelles and increase their contrast so that they can be more easily seen in the bright-field microscope. +++ B. Phase-Contrast Microscope ++ The phase-contrast microscope was developed to improve contrast differences between cells and the surrounding medium, making it possible to see living cells without staining them; with bright-field microscopes, killed and stained preparations must be used. The phase-contrast microscope takes advantage of the fact that light waves passing through transparent objects, such as cells, emerge in different phases depending on the properties of the materials through which they pass. This effect is amplified by a special ring in the objective lens of a phase-contrast microscope, leading to the formation of a dark image on a light background (Figure 2-1). ++ FIGURE 2-1

Microbiology is the study of microorganisms, a large and diverse group of microscopic organisms that exist as single cells or cell clusters; it also includes viruses, which are microscopic but not cellular. Microorganisms have a tremendous impact on all life and the physical and chemical makeup of our planet. They are responsible for cycling the chemical elements essential for life, including carbon, nitrogen, sulfur, hydrogen, and oxygen; more photosynthesis is carried out by microorganisms than by green plants. Furthermore, there are 100 million times as many bacteria in the oceans (13 × 1028) as there are stars in the known universe. The rate of viral infections in the oceans is about 1 × 1023 infections per second, and these infections remove 20–40% of all bacterial cells each day. It has been estimated that 5 × 1030 microbial cells exist on earth; excluding cellulose, these cells constitute about 90% of the biomass of the entire biosphere. Humans also have an intimate relationship with microorganisms; 50–60% of the cells in our bodies are microbes (see Chapter 10). The bacteria present in the average human gut weigh about 1 kg, and a human adult will excrete his or her own weight in fecal bacteria each year. The number of genes contained within this gut flora outnumber that contained within our genome by 150-fold; even in our own genome, 8% of the DNA is derived from remnants of viral genomes.