AMA Manual of Style - Stacy L. Christiansen, Cheryl Iverson 2020

Organisms and Pathogens
Nomenclature

14.14.1 Biological Nomenclature.

14.14.1.1 Scientific and Vernacular Names.

Scientific names are short terms used in place of lengthy descriptions of species of animals, plants, and organisms. A scientific name is typically derived from Latin and corresponds to a set of formally defined attributes. The meanings of scientific names are internationally understood.¹

In contrast, vernacular names are typically based on the local language, using everyday, “common” words. Examples of vernacular names seen in medical publications include fungi, prokaryotes, meningococcus, and St John’s wort. Vernacular names cannot be assumed to correspond to formally defined sets of attributes and vary by region and language. Table 14.14-1 gives examples of scientific and vernacular names.

Table 14.14-1. Examples of Scientific and Vernacular Names

In scientific writing, scientific names should be used when the labeled entity verifiably corresponds to the set of attributes associated with the scientific name, at least at first mention. Subsequently, vernacular names (including collective genus terms, described later in this section) may be used. Parenthetical mention of the vernacular name when the scientific name is used, and vice versa, is helpful. Table 14.14-2 gives examples of first and subsequent mentions of scientific and vernacular names.

Table 14.14-2. Examples of Scientific and Vernacular Name Usage

14.14.1.2 Biological Nomenclature.

Biological nomenclature is the scientific naming of organisms and is the source of scientific names. Taxonomy comprises the principles and practices of classifying organisms¹ to reflect their relatedness. Nomenclature “is the assignment of names to the taxonomic groups according to international rules.”^2(p27)

Biological nomenclature—the nomenclature of living things—derives from the paradigm of the 18th-century taxonomist Linnaeus, who used 2-word labels to replace the long descriptive Latin phrases appended to the genus name.^3,4 Since Linnaeus’ time, international bodies have continued to formalize biological nomenclature, resulting in the current principal codes (Table 14.14-3).

Table 14.14-3. Biological Nomenclature Principal Codes

The codes contain principles, rules, and recommendations for name derivations, priority, validity, and spelling. For a name to have international standing, the codes stipulate valid publication according to specific requirements.

An effort has been made to unify biological nomenclature for all organisms with a single code, the BioCode, under the auspices of the International Committee for Bionomenclature (a joint committee of the International Union of Microbiological Societies and the International Union of Biological Sciences).^4,10,11,12 Another proposed unifying code is the PhyloCode, which is meant to reflect phylogeny and to be used concurrently with the extant codes, at least initially.^13,14

“The essence of the Linnaean revolution was the recognition that the function of the specific ’name’ was merely to label a concept rather than to describe an entity.”^4(p5) Scientific names change when taxonomy changes but not when new knowledge indicates that the original name is no longer an apt descriptor. (For instance, it was learned several decades after its discovery that the bacterium Haemophilus influenzae did not cause influenza,¹⁵ but the name was not changed.⁸) The stability of names is crucial, and name changes may cause harm.^4(p75) “The International Code of Nomenclature for Algae, Fungi, and Plants aims at the provision of a stable method of naming taxonomic groups, avoiding and rejecting the use of names that may cause error or ambiguity or throw science into confusion.”^7(preamble) (See also “perilous name” in the bacteriologic code.⁸)

14.14.1.3 Resources.

A useful source of names of organisms available on the web, particularly plant and animal names, is the Index to Organism Names.¹⁶ Other resources are available at the National Center for Biotechnology Information Entrez Taxonomy home page.¹⁷

14.14.1.4 Style for Scientific Names.

This section presents style that applies to scientific names. The nomenclature codes differ in some style recommendations, but most publications, when possible, will apply style consistently for all scientific names (eg, will use abbreviations in the same way for animals, plants, and bacteria). Therefore, the recommended style to be applied to animals, plants, and bacteria is presented together in this section (see 14.14.2, Bacteria: Additional Terminology, and 14.14.3, Virus Nomenclature).

Organisms are classified in taxonomic groups, also called taxa (singular: taxon), within different ranks (Table 14.14-4):

Table 14.14-4. Examples of Ranks and Taxa

Major ranks, from most inclusive to most specific, are domain, kingdom, phylum or division, class, order, family, genus, and species.

Stylistic hallmarks of biological nomenclature differentiate scientific names from vernacular names.^1,3 These hallmarks are latinization, italics, and a 2-word term for species: the binomial, also called binary or binominal (eg, Homo sapiens). Within a code, the names of ranks above species usually must be unique; the same species designator, however, can be used with multiple genera, for example, Klebsiella pneumoniae and Streptococcus pneumoniae. Across codes, names may be the same at any rank, for example, the bacterial genus Bacillus and the stick and leaf insect genus Bacillus.

According to the international codes, initial capitals are used for all taxa, except for the second portion of the binomial. That portion is called the specific name in the zoological code and the specific epithet in the botanical and bacteriologic codes. Italics are always used for the genus and species components of the binomial. Diacritical marks (accents) and ligatures (eg, æ) are not used. Hyphens occasionally may be used in the specific epithet (eg, the butterfly Polygonia c-album, which has a c-shaped wing mark).¹

All codes capitalize scientific names of taxa but differ on italicizing higher taxa. The bacterial code recommends italicizing all scientific names but recognizes that journals may wish to style all organism names similarly. Taxa above genus should not be italicized.

Mucormycosis refers to an infection caused by fungi in the order Mucorales, which contains the genera Mucor, Absidia, and Rhizopus. These fungi are ubiquitous in the environment and are opportunistic pathogens that often cause fatal infections.

The following examples of the taxonomic classification according to the 3 codes illustrate style (see 10.3.6, Organisms). The suffixes are typical and specified in each code (eg, family: -idae [animals], -aceae [plants and bacteria]), although exceptions are found (Table 14.14-5).

Table 14.14-5. Examples of Taxonomic Classification

Another scheme for bacterial taxonomic rank uses domain and phylum rather than kingdom and division.³ Subranks and superranks follow the same style, as shown in the examples in Table 14.14-6 (see 14.14.1.6, Subgenus, and 14.14.1.8, Subspecific Ranks, Ternary Names).

Table 14.14-6. Examples of Subranks and Superranks

14.14.1.5 Abbreviation of Genus and Other Abbreviations.

As described in 13.11, Clinical, Technical, and Other Common Terms, treat each manuscript portion (title, abstract, text, etc) separately. After first mention of the binomial species name, abbreviate the genus portion of the name without a period. Do not abbreviate the specific name (eg, use Clostridioides difficile not C diff). Although the JAMA Network journals typically avoid beginning a sentence with an abbreviation, exceptions include a genus name that has already been expanded.

Staphylococcus aureus is a common cause of hospital-acquired infection. Resistant S aureus infection is also a source of community-acquired infection. S aureus can be treated with a range of antibiotics.

When the genus name is repeated but used with a new specific name, do not abbreviate the genus name until subsequent mention.

Staphylococcus aureus and Staphylococcus epidermidis may be components of normal flora or pathogens in clinically significant infections, although S aureus is the more serious pathogen of the two.

Do not abbreviate the specific name, and do not abbreviate the genus name when used alone.

Avoid: S au is the more serious pathogen . . .

Avoid: The more serious pathogen in the genus S . . .

When organisms with genus names that begin with the same letter are mentioned in the same article, genus is abbreviated after first mention, for instance:

community-associated infections caused by Staphylococcus aureus and Streptococcus pneumoniae and bacteremia with S aureus and S pneumoniae

Style variations in such instances are permissible (eg, if the editor thinks there is any possibility of confusing genera), and author requests to expand the genus names should be honored.

Do not use multiletter abbreviations for genus name, for example:

S aureus and S pneumoniae (not Sta aureus or Str pneumoniae)

Do not use 2-letter abbreviations for the binomial; for example, do not use SA for Staphylococcus aureus or SE for S epidermidis. However, longer expressions that include the scientific name may be abbreviated:

Abbreviations such as sp nov (species nova, new species), gen nov (genus novum, new genus), and subsp (subspecies) are used in published proposals of new genus and species designations, for example:

Corynebacterium nigricans sp nov

Roseomonas mucosa sp nov and Roseomonas gilardii subsp rosea subsp nov¹⁸

Wigglesworthia glossinidia sp nov¹⁹

Wigglesworthia gen nov¹⁹

New proposals for higher taxa are indicated as in the following examples^20,21,22,23:

Cycliophora, new phylum

Eucycliophora, new class

Symbiida, new order

Symbiidae, new family

Symbion gen nov

Symbion pandora sp nov

Pfiesteria piscicida gen et sp nov (Pfiesteriaceae fam nov)

Parachlamydiaceae fam nov and Simkaniaceae fam nov

The “nov” abbreviations should be mentioned prominently in the article (eg, in the title) but need not be included with every mention of the organism name.

Synonyms are expressed as follows:

Fugomyces cyanescens (syn Sporothrix cyanescens, Cerinosterus cyanescens)

Mesocestoides vogae (syn M corti)

14.14.1.6 Subgenus.

Subgenus is capitalized, italicized, and placed in parentheses, sometimes with the abbreviation “subgen,” for example:

Mus (Mus) musculus

Moraxella (subgen Branhamella) catarrhalis

14.14.1.7 Parentheses.

For other uses of parentheses within species names, such as name changes, use quotation marks or a qualifier such as “formerly,” for example:

Bartonella (formerly Rochalimaea) henselae

Helicobacter (formerly Campylobacter) pylori

Issatchenkia orientalis (anamorph Candida krusei)

Indicate a change in species name with the entire binomial in parentheses as follows:

Bacteroides ureolyticus (formerly Bacteroides corrodens)

Pneumocystis jiroveci (formerly carinii) pneumonia

Authorship of the scientific name may be indicated by personal names, which are not italicized, following the species name. Sometimes parentheses are used. Within and among codes, conventions for such references vary. Editors should not restyle such terms but rather should verify with authors that the proper form has been used. “L.” alone is the common abbreviation for “Linneaus” (eg, Culex pipiens L.), but “Linnaeus” should be written in full in publications whose readers are unlikely to know of this convention.

Aedes aegypti (Linnaeus)

Culex pipiens Linnaeus

Escherichia coli (Migula) Castellani and Chalmers

Serratia marcescens Bizio

The parentheses indicate that the organism, after initial description, was transferred into another genus by others, in the case of E coli by Castellani and Chalmers. Year of published discovery may be included.

Escherichia coli (Migula 1895) Castellani and Chalmers 1919

Serratia marcescens Bizio 1823

14.14.1.8 Subspecific Ranks, Ternary Names.

Subspecific ranks receive ternary or trinomial names. Subspecific designations are handled differently for animals, plants, and bacteria, as in the examples in Table 14.14-7. (The term var as a synonym for subspecies was removed from the bacterial nomenclature code in 1990.)

Table 14.14-7. Examples of Subspecific Designations for Animals, Plants, and Bacteria

Plant names may use var, as above, subsp, f (form), and other subspecific epithets, which are not interchangeable, in ternary names, for example:

Satureja parnassica subsp parnassica

Not all 3-word combinations are ternary names:

Ixodes scapularis larvae

Legionella pneumophila pneumonia

Schistosoma mansoni miracidium

Trypanosoma brucei procyclin

14.14.1.9 Infrasubspecific Subdivisions.

Subdivisions below the subspecies level (infrasubspecific subdivisions) include the serovar (serologically differentiated) and the biovar (biochemically or physiologically differentiated). The suffix -type is most often used in the clinical literature (eg, biotype, serotype). However, to avoid confusion with nomenclatural type (“the element of the taxon with which the name is permanently associated”^8[p17]), the suffix -var is often preferred in microbiological literature.

Infrasubspecific subdivisions are designated with various numbers, letters, or terms; follow author usage:

Brucella suis biovar 4

Cryptococcus neoformans serovar A

Fusarium oxysporum f sp radices-lycopersici [f sp: forma specialis]

Haemophilus influenzae biotype I

Haemophilus influenzae biotype VII

Pseudomonas fluorescens biovar I

Staphylococcus aureus subsp aureus biotype A

Staphylococcus simulans biovar staphylolyticus

Ureaplasma urealyticum parvo biovar

Ureaplasma urealyticum T960 biovar

Yersinia enterocolitica serovar O:8

14.14.1.10 Anglicized and Vernacular (Trivial, Common) Terms.

In medical publications, uncapitalized anglicized forms are often used for taxa in ranks above genus (see 9.5, Microorganisms) (Table 14.14-8).²⁴

Table 14.14-8. Anglicized and Formal Terms of Taxa

14.14.1.11 Collective Genus Terms.

Many organisms possess traditional generic plural designations, which are verifiable in the dictionary. Some also have special adjectival forms. It is also acceptable to add the word organisms or species to the italicized genus name. See the examples in Table 14.14-9.

Table 14.14-9. Examples of Plural and Adjectival Forms of Genus Names

a novel Yersinia species

Loxosceles species (brown recluse) spider venom

group A streptococcal infection

viridans streptococcal endocarditis

Genus names often qualify other terms:

Candida endocarditis

Lactobacillus serogroups

Legionella pneumonia

14.14.1.12 Unspecified Species.

The name of a genus used alone implies the genus as a whole:

Toxocara infections are frequently acquired from household pets.

The term species is used in cases in which the genus is certain but the species cannot be determined. For instance, if an author knew that a skin test reaction indicated the presence of Toxocara organisms but was unsure whether the reaction resulted from Toxocara canis infection or Toxocara cati infection, the author might write:

The source of the patient’s infection was Toxocara species.

In the latter example, Toxocara organisms would also be acceptable, but Toxocara alone would be incorrect.²⁵

14.14.1.13 Name Changes.

Three relatively new names have faced different degrees of acceptance: Chlamydophila (see 14.14.2.3, Chlamydia and Chlamydophila), Clostridioides difficile, and Pneumocystis jirovecii.^26,27,28,29

In 2016, CDC began using Clostridioides difficile instead of Clostridium difficile.³⁰The fungal genus Pneumocystis includes 2 authentic species. The name of the species infective of rats is P carinii. The human pathogen was transitionally named P carinii f sp hominis and is now known as P jirovecii.^26,27 The familiar abbreviation PCP may be retained for Pneumocystis pneumonia in human and nonhuman hosts.²⁶

14.14.1.14 Usage.

In text dealing with infectious conditions, it is important to distinguish between the infectious agent and the condition. Infectious agents, infections, and diseases are not equivalent.

14.14.2 Bacteria: Additional Terminology.

14.14.2.1 General.

For general guidelines on biological nomenclature that apply to bacteria, see 14.14.1, Biological Nomenclature. Rules for bacterial nomenclature are found in the International Code of Nomenclature of Bacteria.⁸ Sources of bacterial names available on the web are the List of Prokaryotic Names With Standing in Nomenclature³¹ and the German Prokaryotic Nomenclature Up-to-Date search page.³² General references consulted in preparation of this section are Jorgensen et al³³ and Carroll et al.³⁴

14.14.2.2 Bacterial Genes.

Bacterial gene nomenclature is covered in 14.6.5, Nonhuman Genetic Terms.

14.14.2.3 Chlamydia and Chlamydophila.

A proposed change in taxonomy resulted in a number of changes, including name changes of 2 medically important organisms.^23,35 Chlamydia pneumoniae became Chlamydophila pneumoniae and Chlamydia psitacci became Chlamydophila psitacci. Chlamydia trachomatis remains so named. The proposal was questioned.^34(p359),36 The new terminology was originally adopted by the Centers for Disease Control and Prevention (CDC) and some major compendia of bacterial names.^32,37 However, this change was dropped, and the CDC today uses Chlamydia (Carolyn M. Black, PhD, director, Division of Scientific Resources, CDC, email, September 14, 2017). Writing in the 2015 Manual of Clinical Microbiology, Gaydos and Essis note, “Although the new taxonomy was validly published, the scientific chlamydia community has consistently rejected the use of the term Chlamydophila, and its use has been abandoned.”^35(p1106)

The TWAR biovar of Chlamydophila pneumoniae was named “after the laboratory designation of the first 2 isolates—TW-183 and AR-39.”^38(p161)-40

14.14.2.4 Escherichia coli.

The O:K:H serotype profile of Escherichia coli is based on the somatic O antigen, capsular K antigen, and flagellar H antigen. The O is a capital letter O, not a zero. The abbreviations O, K, and H within the terms need not be expanded. Expansion of other components is not necessary but can be helpful (NM, nonmotile; NT, not typeable; Orough, O antigen, rough). Note the following examples:

Escherichia coli NM

E coli O157:H7

E coli O6:K13:H1

O157:NM

ONT:NM

Orough:H9

non-O157

O111:NM Prominent serogroups include O26, O103, O111, and O128.

E coli strains associated with diarrhea are abbreviated as follows (expand at first mention in accordance with 13.11, Clinical, Technical, and Other Common Terms):

Serotype and strain are often mentioned together in various combinations:

O157:H7 STEC

strains of STEC serotypes other than O157:H7

STEC O103

Note the following terms representing Shiga toxins:

stx1 (Shiga-like toxin 1)

stx2 (Shiga-like toxin 2)

14.14.2.5 Gram-Positive, Gram-Negative.

Bacteria are often grouped according to reaction to the Gram stain. Note capitalization style in the following (see 10.3, Proper Nouns):

gram-negative bacilli

gram-positive cocci

Gram stain

14.14.2.6 Haemophilus.

Haemophilus influenzae strains are defined by capsular antigens, designated types a through f, for instance:

Haemophilus influenzae type b (Hib)

The name of the vaccine should be expanded at first mention:

Haemophilus influenzae type b (Hib) vaccine . . . Hib vaccine

H influenzae type b (Hib) vaccination

Haemophilus aegyptius is closely related to H influenzae biotype III; aegypticus is a misspelling.

14.14.2.7 Laboratory Media.

Microorganism names applied to laboratory media use lowercase and roman letters:

bacteroides bile esculin agar

brucella agar

Capitalization indicates a product name:

Haemophilus ID Quad agar

14.14.2.8 Lactobacillus GG.

Lactobacillus GG refers to a strain of Lactobacillus rhamnosus named for the authors who isolated it.⁴¹

14.14.2.9 L Forms.

L phase variants, or L forms, are forms of various bacteria with deficient or defective cell walls. Examples of usage are as follows:

Helicobacter pylori L-form infection

L-form Bacillus subtilis

L-form bioluminescence

the L form of Mycobacterium tuberculosis

14.14.2.10 Macrolide Resistance.

Macrolide-resistant phenotypes are expressed as follows:

M phenotype (M: macrolide)

MLSB (L: lincosamides; SB: streptogramins B)

cMLSB (c: constitutive, includes resistance to clindamycin)

iMLSB (i: inducible by macrolides but not by clindamycin)

14.14.2.11 Mycobacterium avium-intracellulare.

This term indicates that in a particular context the 2 species M avium and M intracellulare are indistinguishable.

14.14.2.12 Neisseria meningitidis.

Clinically important serogroups of this organism include the following:

serogroups A, B, C, X, Y, and W-135

The vernacular name of this organism is meningococcus.

14.14.2.13 Salmonella.

Nomenclature of salmonellae is complex and evolving.^31,42,43,44 The use of many models presented in the literature and the historical practice of considering different serotypes of Salmonella to be different species made the nomenclature used to describe Salmonella problematic for many years. However, the publication of Judicial Opinion 80 in the International Journal of Systematic and Evolutionary Microbiology in 2005 helped clarify nomenclature issues regarding the genus Salmonella.⁴³

The main stylistic change is that the traditional binomial species designation is no longer applied to serotypes:

Salmonella Typhi, not Salmonella typhi

Editors should query authors if the latter term and its like are used (except, for instance, in discussions of nomenclature) but otherwise should follow author preference and apply style as in the following examples. Note that nearly all Salmonella infections in warm-blooded animals are Salmonella enterica subspecies I.³³

Serotypes (serovars) are set roman, with the first letter capitalized⁴⁵:

Use Salmonella serovar Typhimurium at first mention.

Thereafter, it may be given without the species name: S Typhimurium.

After first mention, ser may be omitted:

Salmonella Enteritidis

Salmonella Typhi

Salmonella Typhimurium

When the genus name is repeated, it may be abbreviated:

S Typhi

Serovars of Salmonella are defined by the O (somatic), Vi (capsular), and H (flagellar) antigens. Clinical diagnostic laboratories submit Salmonella isolates to state and territorial public health laboratories, where they are confirmed and serotyped according to the Kaufmann-White scheme,⁴⁶ using the following typical format (Ferric C. Fang, MD, Department of Laboratory Medicine and Microbiology, University of Washington School of Medicine, email, November 3, 2015):

Subspecies [space] O antigens[colon]phase 1 H antigen [colon] phase 2 H antigens

For example: I 4,5,12:i:1,2′ for S enterica serotype Typhimurium

Mucoid variants, which express a capsule that prevents immunologic detection of the O antigen, contain “Mucoid” instead of O in the antigenic formula: Mucoid:i:1,2. Rough variants are isolates that do not express the O antigen; rather “Rough” is used instead of the O antigen in the antigenic formula: Rough:i:1,2.^45(p23) In contrast to Escherichia coli strains, when Salmonella serotype is expressed with those antigens, the letters O, H, and Vi are not included in the serotype designation. Colons separate the O, Vi, and H designations, which take a variety of forms (letter, numeric, etc):

Salmonella enterica subsp salamae ser 50:z:e,n,x

Salmonella serotype II 50:z:e,n,x

Salmonella enterica serotype IV 48:g,z51:—

Salmonella serotype IIIa 41:z4,z23:—

Salmonella subsp arizonae serovar 50:z4,z24:—

Salmonella Typhimurium 1,4,5,12:1:1,2

Alternatively, geographic or other designations are used:

Salmonella ser Brookfield

Salmonella Typhimurium MR-DT104

Salmonella Typhimurium DT204b

O antigen groups (O groups) are A, B, C₁, C₂, D, E, F, etc:

Salmonella group E

a group D Salmonella outbreak

O antigens have historically been designated by letter, but there are now more than 60 O antigen groups, so letters have been supplanted by numbers (at least by taxonomists; clinicians are still more used to seeing the letters). Numbers refer to subgroups; for example, serogroup D includes D1, D2, and D3. Salmonella Typhi is group D or group D1 if the subgroup is designated (Ferric C. Fang, MD, Department of Laboratory Medicine and Microbiology, University of Washington, email, November 3, 2015).

14.14.2.14 Strain and Group Designations.

Strains and groups are designated in various ways, sometimes alone, sometimes following the binomial species name. These additional designations are not italicized. Strains are sometimes designated by the abbreviation of a culture collection repository and number. Such abbreviations need not be expanded when used in strain names only but should be otherwise.²⁵

ATCC 27853 strain of Pseudomonas aeruginosa

CDC EO-2 [EO: eugonic oxidizer]

CDC group WO-2 [WO: weak oxidizer]

Escherichia coli ATCC 25922

Staphylococcus aureus NCTC 83

the control strain, NCTC 8325

Geobacillus stearothermophilus (DSMZ 22; equivalent to ATCC 12980)

cultures obtained from the American Type Culture Collection, Manassas, Virginia

14.14.2.15 Streptococci.

Clinically important groups of streptococci are designated in various ways. Capital letters refer to Lancefield serologic groups, for example:

α-hemolytic streptococci

group A β-hemolytic streptococci

group A Streptococcus pyogenes

group B β-hemolytic streptococci (Streptococcus agalactiae)

group C streptococci

viridans streptococci

Proteins of Streptococcus pyogenes include the following:

M protein

class I M protein

class II M protein

P substance

R protein

T substance

The cell wall C polysaccharide of Streptococcus pneumoniae is the basis of the term “C-reactive protein” (an acute-phase inflammatory protein that reacts with the C polysaccharide).

Do not confuse the M protein with the M phenotype of various streptococci and other bacteria (see 14.14.2.10, Macrolide Resistance) or C polysaccharide with group C streptococci.

The vernacular name of Streptococcus pneumoniae is pneumococcus.

14.14.2.16 Vibrio.

Vibrio cholerae serogroups are expressed as in these 2 examples:

Vibrio cholerae O1

V cholerae O139

Principal Author: Cheryl Iverson, MA

Acknowledgment

Thanks to Preeti Malani, MD, MSJ, JAMA, and Department of Internal Medicine, University of Michigan, Ann Arbor, and Ferric C. Fang, MD (Salmonella), University of Washington, Seattle, for reviewing and providing comments.

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22.Steidinger KA, Burkholder JM, Glasgow HB, et al. Pfiesteria piscicida gen. et sp. nov. (Pfiesteriaceae fam. nov.), a new toxic dinoflagellate with a complex life cycle and behavior. J Phycol. 1996;32(1):157-164.

23.Everett KD, Bush RM, Andersen AA. Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int J Syst Bacteriol. April 1999;49:415-440.

24.Piqueras M, Guerrero R. Bacteriologic nomenclature. In: Smart P, Maisonneuve H, Polderman A, eds. Science Editors’ Handbook. 2nd ed. European Association of Science Editors; 2013:59-65.

25.ASM Style Manual for Journals and Books. American Society for Microbiology: 1991.

26.Stringer JR, Beard CB, Miller RF, Wakefield AE. A new name (Pneumocystis jiroveci) for Pneumocystis from humans. Emerg Infect Dis. 2002;8(9):891-896.

27.Cushion MT. Pneumocystis. In: Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of Clinical Microbiology. 11th ed. ASM Press; 2015:2015-2029.

28.Hughes WT. Pneumocystis carinii vs. Pneumocystis jiroveci: another misnomer (response to Stringer et al). Emerg Infect Dis. 2003;9(2):276-277.

29.Stringer JR, Beard CB, Miller RF, Cushion MT. A new name (Pneumocystis jiroveci) for Pneumocystis from humans (response to Hughes). Emerg Infect Dis. 2003;9(2):277-279.

30.Lawson PA, Citron DM, Tyrrell KL, Finegold SM. Reclassification of Clostridium difficile as Clostridioides difficile. Anareobe. August 2016;40:95-99. doi:10.1016/ j.anaerobe.2016.06.008

31.Euzéby JP. List of prokaryotic names with standing in nomenclature. Updated June 18, 2015. Accessed May 24, 2018. http://www.bacterio.net

32.Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures GmbH). Prokaryotic Nomenclature Up-to-Date. Accessed May 24, 2018. http://www.dsmz.de/microorganisms/pnu/bacterial_nomenclature_mm.php

33.Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of Clinical Microbiology. 11th ed. ASM Press; 2015.

34.Carroll KC, Brooks GF, Butel JS, Morse SA, Mietzner TA. Jawetz, Melnick, & Adelberg’s Medical Microbiology. 26th ed. Lange Medical Books/McGraw-Hill; 2013.

35.Gaydos C, Essig A. Chlamydiaceae. In: Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of Clinical Microbiology. 11th ed. ASM Press; 2015:1106-1121.

36.Schachter J, Stephens RS, Timms P, et al. Radical changes to chlamydial taxonomy are not necessary just yet. Int J Syst Evol Microbiol. 2001;51(pt 1):249.

37.Boone DR, Castenholz RW, eds. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Volume 1: The Archaea and the Deeply Branching and Phototropoic Bacteria. Springer-Verlag; 2001.

38.Grayston JT, Kuo C-C, Wang S-P, Altman J. A new Chlamydia psittaci strain, TWAR, isolated in acute respiratory tract infections. N Engl J Med. 1986;315(3):161-168.

39.Grayston JT, Kuo C-C, Campbell LA, Wang SP. Chlamydia pneumoniae sp. nov. for Chlamydia sp: strain TWAR. Int J Syst Bacteriol. 1989;39(1):88-90.

40.Saikku P, Wang SP, Kleemola M, Brander E, Rusanan E, Grayston JT. An epidemic of mild pneumonia due to an unusual strain of Chlamydia psittaci. J Infect Dis. 1985;151(5):832-839.

41.Gorbach SL, Chang TW, Goldin B: Successful treatment of relapsing Clostridium difficile colitis with Lactobacillus GG. Lancet. 1987;2(8574):1519.

42.Forsythe SJ, Abbott SL, Pitout J. Klebsiella, Enterobacter, Citrobacter, Cronobacter, Serratia, Plesiomonas, and Other Enterobacterioceae. In: Jorgensen JH, Pfaller MA, Carroll KC, et al, eds. Manual of Clinical Microbiology. 11th ed. ASM Press; 2015:714-737.

43.Strockbine NA, Bopp CA, Fields PI, Kaper BJ, Nataro JP. Escherichia, Shigella, and Salmonella. In: Jorgensen JH, Pfaller MA, Carroll CK, et al, eds. Manual of Clinical Microbiology. 11th ed. ASM Press; 2015:685-713.

44.Brenner FW, Villar RG, Angulo FJ, Tauxe R, Swaminathan B. Guest commentary: Salmonella nomenclature. J Clin Microbiol. 2000;38(7):2465-2467.

45.Grimont PAD, Weill F-X. Salmonella Serovars. 9th ed. WHO Collaborating Centre for Reference and Research on Salmonella; 2007.

46.Centers for Disease Control and Prevention. National Salmonella Surveillance Overview. US Dept of Health and Human Services; 2011.

14.14.3 Virus Nomenclature.

Most medical articles describe concrete viral entities and, therefore, use the common (vernacular, informal) names of viruses (eg, cytomegalovirus, Hantaan virus, orthopoxviruses). To indicate taxonomic groups, formal virus names are used (eg, Human herpesvirus 5, Hantaan virus, the genus Orthopoxvirus).

14.14.3.1 Style Rules.

A virus term that ends in -virales, -viridae, or -virinae should be capitalized (eg, change paramyxovirinae to Paramyxovirinae). Terms that end in -virus may or may not be formal terms (and may be genera, species, or subspecific entities); editors should follow author usage. Authors should distinguish formal and common terms and style them accordingly. It is useful to give the formal, taxonomic identity of a virus at first mention in an article; afterward the informal name is typically used (unless the article is discussing taxonomy per se). Formal names are used for species and above, so subspecific viral entities (eg, strains, serotypes, isolates) are not capitalized or italicized. Abbreviations may be used for common names.

Reference sources for viral terms include the latest nomenclature reports¹ and online databases.² See Table 14.14-10, which is based on these sources, for formal names, common names, and abbreviations of human (and related) viruses.

Background and further style specifics follow.

Table 14.14-10. Viruses of Humans

^a Entries in this column are not complete listings of all members of the corresponding species. Entries may include species names, strains, serogroups, etc.

^b Use abbreviations in accordance with recommendations in 13.0, Abbreviations.

14.14.3.2 The Viral Code.

International virus taxonomy dates from 1966 and the first published report from 1971. Viral taxonomy and nomenclature are put forth by the International Committee on Taxonomy of Viruses (ICTV) in the International Code of Virus Classification and Nomenclature of ICTV.^1,2,3 (The ICTV is a committee of the Virology Division, International Union of Microbiology Societies.) The code is the work of more than 500 virologists worldwide, including 76 international study groups.⁴ The ninth report was issued in 2012.¹

Official virus names for species and higher taxa are available in book form,^1,3 with updates published in Archives of Virology. Online, official names and updates are available at ICTVdb.² The ICTVdb site also provides information about isolates (eg, serotypes, strains) with links to genome sequence databases. (It is hoped that this linkage will bring needed consistency between official viral nomenclature and viral entries in gene sequence databases.⁴) As with bacterial, animal, and plant nomenclature, viral nomenclature aims for stability and clarity (see 14.14.1, Biological Nomenclature). Names of viral taxa have standing when approved by the members of the full ICTV (https://talk.ictvonline.org).⁵ Proposals for new names or changes should be submitted to the ICTV website.² The viral code applies to the ranks of order, family, subfamily, genus, and species (but not lower ranks). A virus may not yet be classified at each rank (eg, a viral species may belong to a family but not a genus), and a viral genus may not be assigned to a family. The rank of species was added to the code in 1991⁶ and is reflected in the more than 2200 virus and viroid species distributed among 349 genera, 19 subfamilies, 87 families, and 6 orders.⁶ International specialty groups are responsible for viral nomenclature below the rank of species (eg, types, strains). The code does not govern artificially created and laboratory hybrid viruses.

14.14.3.3 Formal vs Vernacular Virus Names.

Formal virus names are used for taxonomic groups (order, family, subfamily, genus, and species) in the abstract state.^1,7,8,9 Use of the formal name indicates that the group has official standing according to the ICTV code. Vernacular (common, informal) virus species names are used for actual entities (eg, laboratory material or outbreak specimens): “concrete viral objects that cause diseases. . . .”^9(p2247)

14.14.3.4 Style of Virus Names.

For examples of the typographic conventions described in this section, see Table 14.14-11.^1,6,10,11

Typical endings for order, family, subfamily, genus, and species are listed in Table 14.14-11.

Table 14.14-11. Examples of Typical Endings for Order, Family, Subfamily, Genus, and Species

14.14.3.5 Latin and English Forms.

Formal names of viral genus and above are latinized. English, the scientific lingua franca during the era of viral discovery, is used for formal virus species names no matter what the language of publication.

14.14.3.6 Initial Capitals.

Formal virus names at each rank have initial capital letters. Other capitals are used when a proper noun is part of the name:

St Louis encephalitis virus

West Nile virus

Vernacular names do not use initial capitals unless a proper noun is part of the name:

La Crosse virus

14.14.3.7 Italics.

Although the viral nomenclature code recommends italicizing all scientific virus names (ie, species through order), codes for other organisms differ on using italics for names of higher taxa. For example, for reasons of internal consistency, the JAMA Network journals do not italicize names of viral taxa above genus. The JAMA Network journals italicize formal viral genus and species names. The ICTVdb² recommends italic for species, with initial cap. It is consistent with style in other areas of biological nomenclature. Vernacular names are never italicized.

14.14.3.8 How to Style a Virus Term.

If a term ends in -virales, -viridae, or —virinae, the term would have an initial capital letter. For example, parvoviridae would be changed to Parvoviridae. Context will often determine whether a term ending in -virus is a formal or vernacular name and can be revised as necessary, querying the author. For instance, the term poliovirus might be left as is or might be changed to the formal species term Poliovirus. Terms for strains, types, serogroups, isolates, etc are never italicized or capitalized (see the section on those entities below). In figure legends in which actual viral entities are depicted (eg, electron micrographs), italics and capital letters would not be used for the actual entity depicted.¹² Legends to schematic depictions of viruses, however, probably refer to classes of virus, and formal style should be used.

14.14.3.9 Formal and Vernacular Names in Articles.

Formal names are used for abstract entities, vernacular names for physical entities:

West Nile virus is a member of the genus Flavivirus. The presence of West Nile virus was confirmed in mosquitoes and dead crows.

Polymerase chain reaction assays were used to detect RNA of West Nile virus (family Flaviviridae, genus Flavivirus, species West Nile virus).

It is useful, for purposes of identification, to include the formal name initially in an article that discusses actual viral entities (with the vernacular name used thereafter)^1,7,8,10:

Hepatitis C virus . . . hepatitis C virus

Human herpesvirus 4 . . . Epstein-Barr virus

Human herpesvirus 3 . . . varicella-zoster virus

Human immunodeficiency virus 1 . . . HIV-1

In such articles, the virus and its higher taxonomic classification may be usefully included early on:

Most disease seen in the United States is caused by the Sin Nombre virus (family Bunyaviridae, genus Hantavirus, species Sin Nombre virus).

The formal name remains in English, the vernacular name in the language of publication^9,10:

Measles virus . . . virus de la rougeole . . .

Hepatitis B virus . . . el virus de la hepatitis B

14.14.3.10 Abbreviations.

Formal viral species names should not be abbreviated. Common names of viral species names may be abbreviated. Recommended abbreviations are given in the international code (see Table 14.14-10).¹ Note that related gene symbols and virus abbreviations may differ (see 14.6.2, Human Gene Nomenclature):

The viral code recommends that rank always be specified with formal names and that it precede the virus name:

the family Paramyxoviridae

the genus Respirovirus (formerly the genus Paramyxovirus)

the species Human parainfluenzavirus 1

Virus names used as adjectives are not italicized¹²:

HIV infection

murine leukemia virus polymerase

vaccinia immune globulin

West Nile virus surveillance

Ebola virus

Official style calls for temporary names (recognized taxa whose names are not yet formally approved) to be presented in roman type within quotation marks:

Sapovirus (formerly “Sapporo-like virus”)

“T4-like viruses”

Formal style is unambiguous. Vernacular style can be ambiguous because the ending -virus occurs in common names at all taxonomic ranks and in other informal designations (eg, arboviruses, which includes several families). It is therefore helpful for authors to specify rank with vernacular terms as well:

the family of retroviruses

Hantaan virus, a species of the genus Hantavirus

the paramyxovirus family

the paramyxovirus subfamily

14.14.3.11 Plant Virus Alternative.

Many plant virologists favor a different style for formal species names, which uses a binomial term that includes species and genus.^3,8,13 (Despite the designation “binomial,” it may contain more than 2 words.) Plant virus names in this style consist of an English species name followed by the genus name:

14.14.3.12 Binomial Proposal.

Formal virus species names do not currently follow the binomial style typical of other organisms (see 14.14.1, Biological Nomenclature), which includes the genus name and a specific epithet. Confusion exists between terms for abstract virus species and actual virus entities, which often are distinguished only typographically. Some virologists have indicated a preference for a binomial style for official virus species names.^7,9 Such a style would resemble the plant style described above, giving species and then genus. (For instance, Measles virus would become Measles morbillivirus. The vernacular term measles virus would remain in use for actual measles virus entities.) These differing ideas about scientific (vs common) names of viruses have long been a source of disagreement among virologists. After discussion of the proposal, the ICTV Executive Committee “overwhelmingly ascribe to the view that the disadvantages of renaming virus species on a large scale to conform to the NLBS [Non-Latinized Binomial System] or any other nomenclatural system greatly outweighs the potential advantages.”¹⁴

14.14.3.13 Derivations.

For derivations of virus names, consult the reports of the ICTV.²

Some virus names are combinations of words; such names are known as sigla. Examples include echovirus (enteric cytopathic human orphan virus) and picornavirus (pico-, RNA virus). Variant capitalization (eg, ECHOvirus, picoRNAvirus) is not used.

14.14.3.14 Strains, Types, and Isolates.

In clinical and laboratory articles that deal with actual entities, most terms will refer to strains, serotypes, serogroups, or viral isolates (ie, ranks below species). Such terms are not capitalized (unless they include proper nouns) or italicized. Such terms often contain numbers, letters, or names:

coxsackievirus A1, coxsackievirus A24

Desert Shield virus (a strain of Norwalk virus)

enterovirus D68

human adenovirus 2 (a strain of Human adenovirus C)

human astrovirus 3, Berlin isolate

human coronavirus 229E

Hantaan virus 76-118 (a serotype of Hantaan virus)

hepatitis C virus (HCV) genotype 1

HCV subtype (or genotype) 3a

hepatitis D virus genotype 1

human poliovirus 1, poliovirus 1, or poliovirus type 1

human poliovirus 2, poliovirus 2, or poliovirus type 2

human poliovirus 3, poliovirus 3, or poliovirus type 3

human respiratory syncytial virus A2

La Crosse virus (a serotype of California encephalitis virus)

Norwalk virus (a strain of Norwalk virus)

rotavirus B strain IDIR

tick-borne encephalitis virus European subtype

Formal species names may also include numbers or letters (eg, Human herpesvirus 1, hepatitis B virus; see Table 14.14-10).¹⁵

14.14.3.15 Hepatitis Terms.

Antigens of hepatitis B virus and antibodies to hepatitis B virus are expressed as given in Table 14.14-12.

Table 14.14-12. Antigens and Antibodies of Hepatitis B Virus

Do not confuse hepatitis e antigen with hepatitis E virus or anti-HBe with anti—hepatitis E virus (anti-HEV).

14.14.3.16 Influenza Types and Strains.

Strains of influenza A virus are identified by antigenic subtypes, defined by the surface proteins hemagglutinin (H) and neuraminidase (N):

influenza A(H3N2)

There are 18 different hemagglutinin subtypes (H1-H18) and 11 different neuraminidase subtypes (N1-N11).¹⁵

The H,N suffix is used only for influenza A, but the 3 species of influenza virus may also contain suffixes with terms for the host of origin (if nonhuman), geographic origin (or a proper name in older strains), laboratory strain number, and year of isolation, separated by virgules (forward slashes) and, in the case of influenza A, followed by the H and N designations in parentheses:

influenza A/New York/55/2004 (H3N2)

influenza A/chicken/Hong Kong/317.5/01 (H5N1)

influenza B/Jiangsu/10/2003

influenza C/California/78

avian influenza A(H7N9)

avian influenza A/Anhui/01/2005 (H5N1)

novel influenza A (H1N1)

A virus that normally circulates in swine is called a variant virus when it is found in humans and is designated with “v”: influenza A H3N2v.¹⁶

Influenza B viruses are not divided into subtypes but may be broken down into lineages and strains. Currently, circulating influenza B viruses belong to B/Yamagata and B/Victoria.

14.14.3.17 Phages.

Phages are viruses that infect bacteria. The term phage is shortened from “bacteriophage.” Although the current ICTV nomenclature code prohibits Greek letters in new virus names, older names with Greek letters have not been changed. Spelled-out Greek letters are also found, and letters may be uppercase or lowercase; follow author style. Vernacular terms often include the word phage:

phage T4 or T4 phage

Phage groups or genera are sometimes referred to with general terms, such as the following: T-even phages, actinophages, coliphages, and T7 phage group.

Examples of formal phage names are given in Table 14.14-13.

Table 14.14-13. Examples of Formal Phage Names

All the above phage viruses have identically named strains, and many more strains belong to species of similar names. Follow author usage.

Enterobacteria phages Qβ and M11 are strains of Enterobacteria phage Qβ.

(For phage cloning vectors, see 14.6.1.4.4, Cloning Vectors.)

14.14.3.18 Genes.

For genes related to human viruses, see 14.6.2, Human Gene Nomenclature. For retrovirus gene terms, see 14.6.3, Oncogenes and Tumor Suppressor Genes, and 14.6.5, Nonhuman Genetic Terms.

14.14.4 Prions.

Disease names and abbreviations of spongiform encephalopathies are given in Table 14.14-14.^1,17,18,19

Table 14.14-14. Disease Names and Abbreviations of Spongiform Encephalopathies

(Do not confuse “kudu” and “kuru.”)

The infectious agents of transmissible spongiform encephalopathies (TSEs) are known as TSE agents or prions. The term prion (from “proteinaceous infectious particle”) reflects the agents’ proposed association or identity with spongiform encephalopathy—related pathologic proteins. Follow author preference for the terms TSE agent and prion.

Proteins related to spongiform encephalopathies in humans are designated as follows:

The last term refers to a transgenic mouse line with a proline to leucine mutation at residue 101 (see 14.6.1, Nucleic Acids and Amino Acids).

For prion-related genes, see 14.6.2, Human Gene Nomenclature.

Principal Author: Cheryl Iverson, MA

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