Microbiology's new names: a glossary.

This final installment of our three-part glossary brings up to date the nomenclature for mycobacteriology, mycology, parasitology, and virology.

This final article in a three-part series, updating the 1980 taxonomy guide prepared by Dr. Paul Ellner for MLO, covers the microbiology glossary changes in mycobacteriology, mycology, parasitology, and virology.

* Mycobacteriology. The genus Mycobacterium, established by Lehmann and Newmann in 1896, originally included only tubercle (M. tuberculosis) and leprosy (M. leprae) bacilli. These organisms usually are gram-positive and acid- and alcohol-fast. The genus currently comprises 54 approved species; only M. leprae cannot be cultured in vitro'-and is closely related to Nocardia, Rhodococcus, and Corynebacterium.

Although not subdivided into subgenera, the genus is separated into two major groups-the slowgrowing organisms that require seven days or more to yield visible colonies and the rapid growers, whose colonies are discernible in less than seven days. Runyon divided all mycobacteria other than tubercle bacilli (MOTT) into four groups based on growth rate and pigmentation .

Several changes have recently been made in the internal classification of the genus based on numerical taxonomic analyses, immunologic properties, phage susceptibility, chemical nature, pathogenicity, and DNA homology . Of the 54 species, 27 have been associated with humans, and 19 are either obligatory or facultative pathogens. The remaining seven species are environmental organisms that have been isolated from hum n , u their role in human disease has not been established.

The mycobacteriology table groups 26 species into functional and closely related complexes, according to the criteria established by Goodfellow and Wayne. 2 The table also includes an unnamed species isolated from patients with Crohn's disease.

*Mycology. Though more than 100,000 species of fungi have been reported, less than 200 species cause diseases in humans and other animals. We have recently seen a renewed interest in mycology due to increases in opportunistic fungal infections in patients with AIDS or other immune dysfunctions. There has also been an increase in other emerging etiologic agents once considered nonpathogenic. Ultrastructural, genetic, and biochemical studies have changed the classification criteria to distinguish fungi from other organisms-and from each other.

The revised names and new species presented in the mycology table are divided into two groups-hyaline or lightly pigmented fungi and the dematiaceous, olive-to-brown-to-black pigmented fungi.

* Parasitology. Human parasites are classified in five major subdivisions: 1) Protozoa (ameba, flagellates, ciliates, sporozoans, and coccidia); 2) Platyhelminthes or flatworms (cestodes and trematodes); 3) Acanthocephala or thorny-headed worms; 4) Nematoda or round worms; and 5) Arthropoda (insects, spiders, mites, and ticks). Although these categories seem well defined, there is often much confusion in classifying parasitic organisms. The primary reasons are the lack of known specimens and the fact that type specimens must be submitted for study prior to a decision on a legitimate species name.

Reproductive mechanisms are often a valid means of defining species, but there are many exceptions within parasitic groups. Certain organisms are able to alter their morphologic form according to age, host, or nutrition. This often leads to the use of several names for a single organism. Another problem involves the alternation of parasitic and free-living phases in the life cycle; it may be very difficult to recognize these organisms as belonging to the same species. In spite of these problems, it is interesting to note that some of the newer molecular grouping methods confirm the taxonomic conclusions that were reached hundreds of years ago.

As parasite genetics, immunology, and biochemistry continue to evolve, the species designation will tend to be more clearly defined. Earlier species designations were primarily determined by morphologic differences, a phenotypic approach. With the newer and more sophisticated methods, the approach to classification will tend to become more genotypic.

Additionally, as we learn more about microbiology in general, such changing considerations as the role of immunosuppression on the host-parasite interaction will become more of a factor in our review of specific parasites. With this in mind, the organisms listed in the table do not represent all the changes seen during the last 10 years, but those that are most relevant to patient care. New entries include Cryptosporium parvum and various species of Microsporidia implicated in human disease.

* Virology. Viral taxonomy is a relatively new area. It was not until 1966-some 20 years after a bacterial taxonomy was first published-that the International Committee on Nomenclature of Viruses (ICNV) was established. This group became the International Committee on Taxonomy of Viruses (ICTV) in 1973. The ICTV classifies the many viruses isolated from vertebrates, invertebrates, plants, fungi, and bacteria. The hierarchical levels of viral taxonomy consist of family, and, in some cases, subfamily, genus, and species, based on structural, physicochemical, biological, and replicative properties of viruses.

Structural characteristics include size, shape, presence or absence of an envelope, and capsid symmetry. Physicochemical characterization is based on type, strandedness, and the number of segments of nucleic acid, as well as the number and size of proteins and their functional activities. Biological properties include host range, serologic relationships, pathogenicity, and transmission; replicative properties include nucleic acid replication, transcription, and translation. 5-7

The viral taxonomy listing includes viruses that have been recognized, associated with specific diseases, or classified into new or existing families and genera over the last 10 years.

The classification of some of these organisms is not as well defined as for the aerobic and anaerobic bacteria presented in Parts I and II. The table of updated nomenclature that follows represents current usage for organisms implicated in human disease. As with the earlier articles, the table is not intended to be a complete list, but rather a compilation of names of the newer, more clinically significant organisms.