Classification

Excerpt

Bacteria are classified and identified to distinguish one organism from another and to group similar organisms by criteria of interest to microbiologists or other scientists. The most important level of this type of classification is the species level.

A species name should mean the same thing to everyone. Within one species, strains and subgroups can differ by the disease they produce, their environmental habitat, and many other characteristics. Formerly, species were created on the basis of such criteria, which may be extremely important for clinical microbiologists and physicians but which are not a sufficient basis for establishing a species. Verification of existing species and creation of new species should involve biochemical and other phenotypic criteria as well as DNA relatedness. In numerical or phenetic approaches to classification, strains are grouped on the basis of a large number of phenotypic characteristics. DNA relatedness is used to group strains on the basis of overall genetic similarity.

Species are identified in the clinical laboratory by morphological traits and biochemical tests, some of which are supplemented by serologic assessments (e.g., identification of Salmonella and Shigella species). Because of differences in pathogenicity (Escherichia coli) or the necessity to characterize a disease outbreak (Vibrio cholerae, methicillin-resistant Staphylococcus aureus), strains of medical interest are often classified below the species level by serology or identification of toxins. Pathogenic or epidemic strains also can be classified by the presence of a specific plasmid, by their plasmid profile (the number and sizes of plasmids), or by bacteriophage susceptibility patterns (phage typing). Newer molecular biologic techniques have enabled scientists to identify some species and strains (without the use of biochemical tests) by identifying a specific gene or genetic sequence, sometimes directly from the clinical specimen.

Laboratories have no difficulty in identifying typical strains of common bacteria using commonly available test systems. Problems do arise, however, when atypical strains or rare or newly described species are not in the data base. Such difficulties are compounded when the strains are misidentified rather than unidentified, and so laboratory personnel and physicians (at least infectious diseases specialists) should be familiar with taxonomic reference texts and journals that publish papers on new species. Bacterial nomenclature at the genus and species level changes often, based primarily on the use of newer genetic techniques. A species may acquire more than one name. In some cases the recognition of a new species results in a unique correlation with specific clinical problems. For example, recognition of Porphyromonas gingivalis as a unique species, separate from its previous inclusion within Bacteroides melaninogenicus (now known to be composed of several taxonomic groups of black-pigmenting anaerobic gram-negative bacilli), elucidated its role as a key pathogen in adult periodontitis. It is important to understand why these changes and synonyms exist in taxonomy.

The clinical laboratory is concerned with the rapid, sensitive, and accurate identification of microbes involved in producing disease. The number and types of tests done in such a laboratory depend on its size and the population it serves. Highly specialized or rarely performed tests should be done only by reference laboratories. Physicians, clinical laboratory personnel, and reference laboratory personnel must have a good working relationship if patients are to receive first-rate care.

In addition, the physician and the clinical laboratory personnel must know which diseases and isolates are reportable to public health laboratories and how to report them .