Methods and Strategies

rationale for a method of organism identification_

Deciding how to teach microbiology in a manner that is both comprehensive and yet understandable is difficult. Most microbiology text chapters are organized by genus name and provide no obvious approach as to how to work up a clinical isolate. Some texts have flowcharts containing algorithms for organism workup; many of these, however, are either too broad to be helpful (e.g., gram-positive vs. gramnegative bacilli) or too esoteric (e.g., cellular analysis of fatty acids) to be practical in routine clinical practice. Unfortunately, the student ends up simply memorizing seemingly unrelated bits of information about various organisms.

The chapters in Part HI: Bacteriology are arranged to guide the student through the workup of a microorganism. To accomplish this, chapters have been grouped into subsections using results of basic microbiology procedures, such as the Gram stain, oxidase and catalase tests, and growth on common laboratory media, such as blood, chocolate, and MacConkey agars. Each chapter begins with a short description of the organisms covered in the chapter and an assessment of what the' organisms have in common. Because microbiology is ultimately the identification of organisms based on common phenotypic traits shared with known members of the same genus or family, microbiologists "play the odds" every day by finding the best biochemical fit and assigning the most probable identification. For example, the gram-negative rod known as CDC group EF-4a may be considered with either the MacConkey-positive or -negative organisms because it grows on MacConkey agar 50% of the time. Therefore, although CDC group EF-4a has been arbitrarily assigned to the section on oxidase-positive, MacConkey-positive, gram-negative bacilli and coccobacilli in this text, it is also included in the discussion of oxidase-positive, MacConkey-negative, gram-negative bacilli and coccobacilli. This approach to the identification of microorganisms is similar to that used by clinical microbiologists. Internalization of this method allows students entering the workforce to immediately be able" to identify bacteria.

The following chapters help guide the determination of whether a clinical isolate is relevant and provide key biochemical characteristics necessary for organism identification, information on whether susceptibility testing is indicated, and information on the correct antimicrobial agents to use. Most of the procedures described in these chapters can be found at the end of this chapter. In this chapter; each procedure includes a photograph of positive and negative reactions so that the information discussed in the section on expected results can be easily visualized. Chapter 6 includes photographs of some commonly used bacterio-logic stains. In addition. Table 13-1 lists several commonly used commercial identification systems for a variety of the microorganisms discussed in the following pages.

how to use part iii: bacteriology_

In most instances, the first information that a microbiologist uses in the identification process is the macroscopic description of the colony, or colony morphology. This includes the type of hemolysis (if any), pigment (if present), size, texture (opaque, translucent, or transparent), adherence to agar, pitting of agar, and many other characteristics. After careful observation of the colony, the Gram stain is used to separate the organism into one of a variety of broad categories based on Gram reaction and cellular morphology of gram-positive or gram-negative bacteria (e.g., gram-positive cocci, gramnegative rods). For gram-positive organisms, the catalase test should follow the Gram stain, and testing on gram-negative organisms should begin with the oxidase test. These simple tests plus growth on MacConkey agar, if the isolate is a gram-negative rod or coccobacillus, help the microbiologist assign the organism to one of the primary categories (organized here as subsections). Subsequent testing criteria that are outlined in each

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Table 13-1 Examples of Commercial Identification Systems for Various Onanisms

*St Louis, Mo.: tSparks, Md.; ■ *Lenexa, Kan.; www.remelinc.oom , ®West Sacramento, Calif.; f'Westlake, Ohio;

Table 13-1 Examples of Commercial Identification Systems for Various Onanisms

• Organism Group

TVpe of System


Incubation Time



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Bacterial Vaginosis Facts

Bacterial Vaginosis Facts

This fact sheet is designed to provide you with information on Bacterial Vaginosis. Bacterial vaginosis is an abnormal vaginal condition that is characterized by vaginal discharge and results from an overgrowth of atypical bacteria in the vagina.

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