key: cord-0318511-9hzr3001
authors: nan
title: Appendix I Additional Notes on Taxonomy
date: 2012-12-31
journal: nan
DOI: 10.1016/b978-0-12-415895-5.00052-0
sha: b69be33b29de31a987633b3a382a1bee5f18a954
doc_id: 318511
cord_uid: 9hzr3001

Unknown

This section of the book was relegated to the Appendix, because it should only be read by stalwarts, who have studied Chapters 1 through 46, and who hunger for more.

A taxonomy is a theoretical construct. As such, it needs to be constantly tested to determine whether the defined properties of each class actually extend to all of the members of the class, and whether the hierarchies of the classes are true. As new information is acquired, taxonomies will need to change. Some of the recent changes in the taxonomy of living organisms have involved the highest classes in the hierarchy. The first division of the Eukaryotes was assigned to Class Bikonta and Class Unikonta (analogous to dicot and monocot division in Class Angiospermae) [69] . Class Protoctista has been dropped from the formal taxonomy. Class Rhizaria was introduced. Class Microsporidia was moved from Class Protoctista to Class Fungi. Class Chlorophyta was moved from Class Protoctista to Class Archaeplastida.

Troubles also arise on the species level. For example, Enterobius vermicularis is called pinworm in the USA and threadworm in the UK; while Strongyloides stercoralis is just the opposite (threadworm in the USA and pinworm in the UK). The only way to escape this trans-Atlantic confusion is to translate the common name of the organism back to its standard Latin binomial.

Here is a sampling of recent name changes, in species or genus: The organism now called Rhodococcus equi has had more than its share of name changes. These include: Corynebacterium equi, Bacillus hoagii, Corynebacterium purulentus, Mycobacterium equi, Mycobacterium restrictum, Nocardia restricta, and Proactinomyces restrictus. Taxonomic instability impacts negatively on clinical practice. When the name of an organism changes, so must the name of the associated disease. Consider "Allescheria boydii." People infected with this fungal organism were said to suffer from the disease known as allescheriasis. When the organism's name was changed to Petriellidium boydii, the disease name was changed to petriellidosis. When the fungal name was changed, once more, to Pseudallescheria boydii, the disease name was changed to pseudallescheriosis [102] . Changes in the standard names of a fungus, appearing in the International Code of Botanical Nomenclature, should trigger concurrent changes in the standard nomenclatures of medicine, such as the World Health Organization's International Classification of Disease, and the National Library of Medicine's Medical Subject Headings, and a variety of specialized disease nomenclatures. Some of these nomenclatures update infrequently. When disease nomenclatures lag behind official taxonomy, errors in coding and reporting infectious diseases will ensue.

The confusion never ends. Here is a list of obfuscated terminology, guaranteed to mislead all but the most compulsive students.

Chapter 5, The Alpha Proteobacteria À Readers should be careful not to confuse Bartonella with the similar-sounding Bordetella (Beta Proteobacteria, Chapter 6).

Chapter 5, The Alpha Proteobacteria À Readers should be aware that brucellosis has been known by a great number of different names, including Mediterranean fever. Mediterranean fever, an arcane synonym for brucellosis, should not be confused with familial Mediterranean fever (a gene disorder characterized by fever and abdominal pain) or with Mediterranean anemia (a synonym for thalassemia).

Chapter 5, The Alpha Proteobacteria À Readers should be aware that Neorickettsia, despite its name, is not a type of Rickettsia (i.e., not a member of Class Rickettsiaceae). Neorickettsia is a member of Class Anaplasmataceae; hence, the disease it causes is an ehrlichiosis.

Chapter 5, The Alpha Proteobacteria À Readers should not be confused by the term "scrub typhus" for infection by Orientia tsutsugamushi (alternately named Rickettsia tsutsutgamushi). This disease is grouped as a "spotted fever," not a form of typhus.

Chapter 7, Gamma Proteobacteria À The term "dysentery" (from the Latin "dys" and Greek "dus," meaning bad, and the Greek "enterikos" meaning intestine) is often used to connote a specific disease, but dysentery is non-specific term that can be applied to any enteric disorder associated with severe or bloody diarrhea. Because the group of diseases known as "dysentery" are the most frequent cause of childhood morbidity and mortality, it is important to use the term correctly. In developed countries, the term "dysentery" most often refers to salmonellosis, while in less developed countries, "dysentery" usually refers to shigellosis (also called bacillary dysentery, another misnomer) [143] . Other bacterial causes for dysentery are: Vibrio cholerae, Escherichia coli, Clostridium difficile, Salmonella, Campylobacter jejuni, and Yersinia enterocolitica. Viruses that cause dysentery include Rotavirus and Norwalk virus. The term "amoebic dysentery" is usually reserved for gastroenteritis caused by Entamoeba histolytica.

Chapter 7, Gamma Proteobacteria À Granuloma venereum, caused by Klebsiella granulomatis, can be mistaken clinically with two other diseases that are characterized by genital ulcers: syphilis (Treponema pallidum, Class Spirochaetae, Chapter 9), and chancroid (Haemophilus ducreyi, Class Gamma Proteobacteria, Chapter 7)). Adding to the confusion, the syphilitic genital ulcer is known as a chancre and must be distinguished from chancroid. One last caveat. Granuloma venereum, caused by Klebsiella granulomatis, must not be confused with lymphogranuloma venereum, caused by Chlamydia trachomatis (Class Chlamydiae, Chapter 13).

Chapter 7, Gamma Proteobacteria À Readers should not confuse rhinoscleroma, caused by Klebsiella rhinoscleromatis (Class Gamma Proteobacteria, Chapter 7), with rhinosporidiosis, caused by Rhinosporidium seeberi (Choanozoa, Chapter 23).

Chapter 7, Gamma Proteobacteria À Salmonella typhi and Salmonella paratyphi cause typhoid and paratyphoid, respectively. Neither of these diseases should be confused with typhus, caused by Rickettsia typhi and Rickettsia prowazekii. Both diseases (typhoid and typhus) take their root from a Greek word meaning stupor, referring to the neurologic manifestations of the diseases.

Chapter 7, Gamma Proteobacteria À Species of Genus Shigella are found only in causes of shigellosis. Shigellosis is also called bacillary dysentery. Despite its name, readers should not assume that the cause of bacillary dysentery is a member of Class Bacilli (Chapter 12). The exclusive cause of bacillary dysentery is Shigella species, belonging to the Gamma Proteobacteria (Chapter 7).

Chapter 7, Gamma Proteobacteria À Shigella boydii, one of the causes of shigellosis, should not be confused with Pseudallescheria boydii, a fungus in Class Ascomycota (Chapter 46), one of many fungal organisms associated with the skin infection maduromycosis.

Chapter 7, Gamma Proteobacteria À Readers should not confuse Plesiomonas shigelloides, containing the species name "shigelloides," with the genus name "Shigella".

Chapter 7, Gamma Proteobacteria À Haemophilus influenzae causes pneumonitis, meningitis, conjunctivitis, otitis media, and bacteremia, in infants and young children. Its species name, infuenzae, was assigned when the bacteria was mistakenly thought to be the cause of influenza. Influenza, also known as the flu, is caused exclusively by the influenza virus, a Group V orthomyxovirus (Chapter 43).

Chapter 7, Gamma Proteobacteria À Haemophilus parainfluenzae causes some cases of endocarditis. Despite its name, Haemophilus parainfluenzae is not the cause of the disease known as parainfluenza. Parainfluenza is a type of croup (laryngotracheobronchitis), and about 75% of the cases of croup are caused by the parainfluenza virus, a Group V virus (Chapter 43).

Chapter 7, Gamma Proteobacteria À Haemophilus ducreyi is the cause of chancroid, a sexually transmitted disease. It must not be confused with Klebsiella granulomatus, in Class Enterobacteriaceae, the cause of granuloma inguinale.

Chapter 7, Gamma Proteobacteria À Readers should not confuse Genus Acinetobacter (Gamma Proteobacteria, Chapter 7), with Class Actinobacteria (Chapter 14).

Chapter 9, Spirochaetae À Rat-bite fever is caused by either Spirillum minus or Streptobacillus moniliformus (Class Fusobacteria, Chapter 10) [49] . Regardless of the causative organism, or the phylogenetic classes to which the organisms are assigned, the clinical symptoms are similar, as is the treatment.

Chapter 11, Mollicutes À Erysipelothrix contains one infectious species; Erysipelothrix rhusiopathiae, the cause of erysipeloid, a type of cellulitis (subcutaneous infection). Students should not confuse erysipeloid with the similar-sounding disease, erysipelas. Both erysipeloid and erysipelas produce cellulitis. Erysipelas is more common and, potentially, a more serious disease than erysipeloid. Erysipelas is caused by members of Genus Streptococcus (Class Bacilli, Chapter 12). Two additional similar-sounding skin conditions are erythrasma, characterized by brown scaly skin patches, caused by Corynebacterium minutissimum (Class Actinobacteria, Chapter 14), and erythema infectiosum, caused by Parvovirus B19 (Chapter 40). All four skin conditions are associated with reddened skin, and all four diseases take their root from the Greek, "erusi," meaning red.

Chapter 12, Class Bacilli plus Class Clostridia À The term "bacillary" is misleading. You might think that the adjective "bacillary" would be restricted to members of Class Bacilli, its subclasses, and Genus Bacillus. It seldom does. The word "bacillus" has its root in Latin, from "baculum", a rod or staff, so the name has been applied to the second term in the bionomial name of bacteria that do not belong to Class Bacilli.

An example of a species with "bacilla" in its name, that is not a member of Class Bacilli is Bartonella bacilliformis (the cause of verruga peruana). Examples of genera with "bacillus" in their name, that are not members of Class Bacilli, are: Actinobacillus and Streptobacillus. Genus Streptobacillus (Class Fusobacteria, Chapter 10), is a terminologic catastrophe, as it is not a sister genus to Streptococcus, and it is not a member of Class Bacilli.

The subclasses of Class Bacilli were assigned based on phylogeny, not on morphology. Therefore, there are members of Class Bacilli that are not rod-shaped (e.g., Genus Staphylococcus and Streptococcus).

Furthermore, there are diseases containing the term "bacillary" that are not caused by members of Class Bacilli. These include bacillary angiomatosis (caused by Bartonella quintana and Bartonella henselae), and bacillary dysentery (caused by four different Shigella species and by Yersinia enterocolitica).

Chapter 12, Class Bacilli plus Class Clostridia À Listeria monocytogenes is the organism that causes listeriosis. Listeriosis should not be confused with the similar-sounding disease, leptospirosis (Spirochaetae, Chapter 9).

Chapter 13, Chlamydiae À Readers should not confuse trachoma with inclusion conjunctivitis, as each disease is caused by distinct variants of the same species (Chlamydia trachomatis). Trachoma is contracted by exposure to eye secretions from people with trachoma. Inclusion conjunctivitis is caused by ocular exposure to secretions from the sexually transmitted infection.

Chapter 13, Chlamydiae À Chlamydia trachomatis may also cause lymphogranuloma venereum, a disease that usually presents as swollen lymph nodes in the groin. The lymph nodes often have draining abscesses. The disease is rare, with only a few hundred cases occurring in the United States each year. Lymphogranuloma venereum must not be confused with granuloma inguinale, also known as granuloma venereum, caused by the bacterium Klebsiella granulomatis (Chapter 7).

Chapter 14, Actinobacteria À Members of Class Actinobacteria tend to be filamentous, and this morphologic feature led to great confusion. In the past, these filamentous bacteria were mistaken for fungal hyphae, and many of the diseases caused by members of Class Actinobacteria are given fungal names (e.g., actinomycosis, mycetoma, maduromycosis).

Chapter 14, Actinobacteria À Readers should be aware of the highly confusing term, "diphtheroid," from the Greek diphththera, meaning leather membrane, and commonly applied to all the non-pathogenic species within Genus Corynebacterium. As non-pathogens, the diphtheroids do not cause diphtheria. Diphtheria is caused Corynebacterium diphtheriae (i.e., a nondiphtheroid).

Chapter 14, Actinobacteria À Readers should not be confused by the plethora of organisms with "brasiliensis" as the species of the binomen. These include Nocardia brasiliensis, Leishmania brasiliensis (alternately Leishmania braziliensis), Paracoccidioides brasiliensis, and Borrelia brasiliensis.

Chapter 14, Actinobacteria À Readers should not confuse the bacterial genus Tropheryma with the similar-sounding term Taphrinomycotina, the fungal genus that includes Pneumocystis (Class Ascomycota, Chapter 36).

Chapter 19, Apicomplexa À The diseases produced by any of the organisms belonging to Class Coccidia are known collectively as coccidiosis. This term is applied most often to coccidian infections in animals, excluding humans. Coccidiosis must not be confused with the similar-sounding coccidioidomycosis (Ascomycota, Chapter 36).

Chapter 21, Heterokontophyta À Oomycota, a "colorless" class of heterokonts, contains the organisms that produce late blight of potato (Phytophthora infestans), and sudden oak death (Phytophthora ramorum). Oomycota, despite its suffix (mycota, an alternative name for fungus), is not a member of Class Fungi.

Chapter 21, Heterokontophyta À It is important to avoid confusing blastocystis with two similar terms used elsewhere in this book: blastomycosis and blastocyst. Blastomycoses is a fungal disease (Ascomycota, Chapter 36), and blastocyst is the blastula (Overview of Kingdom Animalia, Chapter 25) of mammals. All three terms come from the root word blastos (Greek for bud or embryo). Cystos (as in Blastocystis and blastocyst) is the Greek root meaning sac.

Chapter 22, Amoebozoa À Do not confuse Entamoeba coli (abbreviation E. coli) with Escherichia coli (likewise abbreviated as E. coli). Both live in the colon, and both can be reported in stool specimens. Do not confuse Entamoeba (Class Amoebozoa, Chapter 22) with Dientamoeba (Class Metamonada, Chapter 16).

Chapter 22, Amoebozoa À It is commonly agreed that the term "amoebiasis," with no qualifiers in the name, refers exclusively to the intestinal infection by Entamoeba histolytica. Encephalitides caused by members of Class Amoebozoa (Acanthamoeba and Balamuthia) are named granulomatous amoebic encephalitis. Encephalitis caused by Naegleria fowleri (not an amoeba) is called primary amoebic meningoencephalitis, an accepted misnomer. Naegleria is a member of class Percolozoa (Chapter 18). A better name for the Naeglerian disease would be primary percolozoan meningoencephalitis.

Chapter 24, Archaeplastida À Kleptoplast should not be confused with the similar-sounding word, kinetoplast. A kleptoplast is a chloroplast that has been stolen by another organism. A kinetoplast, uniquely found in members of Class Kinetoplastida, is a clump of DNA composed of copies of the mitochondrial genome, tucked inside a mitochondrion.

Chapter 27, Nematoda À Astute readers will notice that the prefix "trich" appears often within this chapter on Class Nematoda: Trichostrongylus, Trichocephalida, Trichinellidae, Trichinella, and Trichuris. A wide assortment of organisms, diseases, and medical terms contain the root "trich" (pronounced trick) and produce similar-sounding terms (i.e., homonyms). If you want to avoid confusing one disease with another, it is best to "come to terms" with this "trichy" nomenclature. The suffix "trich" comes from the Greek "thrix," meaning hair. Various unrelated organisms with a hair-like appendage, are provided with the "trich" suffix. Likewise, medical conditions of the hair are provided the same suffix: trichosis is any pathologic condition of hair; trichilemmoma is a tumor of hair, trichobezoar is the medical term for a hairball, trichotillomania is compulsive hair pulling. Words that sound somewhat like "trich" include trachoma (caused by the bacteria, Chlamydia trachomatis) and trachea (the windpipe). In addition to Trichomonas, there are several unrelated "trich" organisms that cause disease in humans: Trichinella, Trichomonas, Trichomonad, and Trichophyton. Other "trich" diseases include: Trichostrongylosis trichinosis, trichuriasis, trichomoniasis, trichiasis (everted eyelashes that touching the cornea or conjunctiva, often a post-infectious condition).

Chapter 27, Nematoda À When toxocara migrate through viscera, the condition is called visceral larva migrans. When toxocara migrate through an eye, the condition is called ocular larva migrans. When toxocara migrate through the skin, the condition is NOT called cutaneous larva migrans: this term is reserved for cutaneous manifestations of Ancylostoma brasiliense.

Chapter 27, Nematoda À Readers should not confuse "toxocara" with the similar-sounding "toxoplasma" (Class Apicomplexa, Chapter 19), a problem aggravated when clinicians use the abbreviated form "toxo," referring to "toxoplasmosis."

Chapter 27, Nematoda À Readers should avoid confusion by the layterms for Enterobius infection. In the United States, Enterobius vermicularis is known as pinworm; in the UK, it is known as threadworm. To add to the Chapter 42, Group IV Viruses À Readers should not confuse Rubella virus with the measles virus, Rubeola. Rubeola virus is a paramyxovirus (Group V, Chapter 43), unrelated to Rubella virus.

Chapter 43, Group V Viruses À One member of Class Arenaviridae, Lassa virus, the cause of Lassa fever, should not be confused with Lyssa virus, a member of Class Rhabdoviridae and the cause of rabies.

Chapter 44, Group VI Viruses À Readers should not confuse HTLV-III, a virus discovered in 2005, and which is not known at this time to produce disease in infected humans, with the same name (long since abandoned) that was assigned to the HIV virus.

They are distinguished from other insects by the shape of their mouth parts, which are shaped as a proboscis and covered by a labial sheath. The mouth parts of Class Hemiptera are designed for sucking. Class Hemiptera includes cicadas and aphids. The triatome species that are vectors for Trypanosoma cruzi (Euglenozoa, Chapter 17) are members of Class Hemiptera. Chapter 31, Crustacea À One of the more confusing terms associated with pentastomiasis is "porocephaliasis," named for a pentastome genus, Porocephalus. The genus "Porocephalus" and the infection "porocephaliasis" should not be confused with "porocephaly," a rare developmental disorder in which cysts or cavities are found in the brains of infants. Chapter 36, Ascomycota À Readers should be alerted that the term "Candida" is a source of some taxonomic confusion: candida, in Latin, means white. Many organisms are white, and have taken "candida" as part of a binomial name

Chapter 36, Ascomycota À Readers should remember not to confuse Microsporum with Microspora, a genus in Class Microsporaceae

Microsporidia À It is important not to confuse microsporidiosis with cryptosporidiosis, an apicomplexan disease (Apicomplexa, Chapter 19), that also produces diarrhea in immune-compromised patients