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Bacteria: Additional Terminology 


Harriet S. Meyer

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PRINTED FROM AMA MANUAL OF STYLE ONLINE ( © American Medical Association, 2009. All Rights Reserved. Under the terms of the license agreement, an individual user may print out a PDF of a single chapter of a title in AMA Manual of Style Online for personal use (for details see Privacy Policy).  Subscriber: null; date: 25 November 2015

Bacteria: Additional Terminology

  • There is no “official” classification of bacteria…
  • [B]acterial classifications are devised for micro-
  • biologists, not for the entities being classified.
  • Bacteria show little interest in the matter of their
  • classification.
  •  D. J. Brenner, J. T. Staley, and N. R. Krieg3(p31)
  • … the majority of bacteria in nature have not been
  • grown or characterized.
  •  R. G. E. Murray and John G. Holt30(p2)


For general guidelines on biological nomenclature that apply to bacteria, see 15.14.1, Biological Nomenclature. Rules for bacterial nomenclature are found in the International Code of Nomenclature of Bacteria.7 Sources of bacterial names available on the Web are the List of Prokaryotic Names With Standing in Nomenclature31 and the German Collection of Microorganisms and Cell Cultures bacterial nomenclature search page.32 General references consulted in preparation of this section are Murray et al33 and Brooks et al.34

Bacterial Genes.

Bacterial gene nomenclature is covered in 15.6.5, Genetics, Non-human Genetic Terms.

Chlamydia and Chlamydophila.

A proposed change in taxonomy has resulted in a number of changes, including name changes of 2 medically important organisms.22,35 Chlamydia pneumoniae has become Chlamydophila pneumoniae and Chlamydia psittaci has become Chlamydophila psittaci. Chlamydia trachomatis remains so named. The proposal has been questioned,36 and as of this writing the older terminology persists in medical journals and textbooks. The new terminology is used by the Centers for Disease Control and Prevention and major compendia of bacterial names.31-33,37

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

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 O6:K13:H1

E coli O157:H7





O111:NM (or H-)

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

Diarrheogenic E coli strains are abbreviated as follows (expand at first mention in accordance with 14.11, Abbreviations, Clinical, Technical, and Other Common Terms):


enteroaggregative E coli


enteroinvasive E coli


enteropathogenic E coli


enterotoxigenic E coli


Shiga toxin-producing E coli (also called enterohemorrhagic E coli [EHEC])


verotoxin-producing E coli

Serotype and strain are often mentioned together in various combinations:

O157:H7 STEC

strains of STEC serotypes other than O157:H7


Note the following terms representing Shiga toxins:



Gram-Positive, Gram-Negative.

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

gram-negative bacilli

gram-positive cocci

Gram stain


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 has been shown to be H influenzae biogroup aegyptius; aegypticus is a misspelling.

Laboratory Media.

Microorganism names applied to laboratory media are given lowercase and roman:

bacteroides bile esculin agar

brucella agar

Capitalization indicates a product name:

Haemophilus ID Quad agar

Lactobacillus GG.

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

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

Macrolide Resistance.

Macrolide-resistance phenotypes are expressed as follows:

M phenotype (M: macrolide)

MLSB (L: lincosamide; SB: streptogramin B)

cMLSB (c: constitutive, includes resistance to clindamycin)

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

Mycobacterium avium-intracellulare.

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

Neisseria meningitidis.

Clinically important serogroups of this organism include the following:

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

The vernacular name of this organism is meningococcus.


Nomenclature of salmonellae is complex and evolving.42-45 What had been considered separate species were shown to be strains. The main stylistic change is that the traditional binomial species designation is no longer applied to serotypes, eg:

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:

Species: Salmonella enterica, S bongori (formerly subspecies V)


Subspecies, S enterica:

S enterica subsp enterica

subspecies I

S enterica subsp salamae

subspecies II

S enterica subsp arizonae

subspecies IIIa

S enterica subsp diarizonae

subspecies IIIb

S enterica subsp houtenae

subspecies IV

S enterica subsp indica

subspecies VI

Serotypes (serovars) of subspecies I use italics, roman, and capitals as follows:

Salmonella ser Typhi (equivalent to S enterica subsp enterica ser Typhi)

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. In contrast to E 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 serotype IV 45:g,z51:-

Salmonella serotype IIIa 41:z4z23:-

Salmonella subsp arizonae serovar 50:z4z24:-

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, and F, eg:

Salmonella group E

a group D Salmonella outbreak

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.24

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


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

α-hemolytic streptococci

group A β-hemolytic streptococci

group A Streptococcus pyogenes

group B β-hemolytic streptococci (S 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 S 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 the “Macrolide Resistance” section above) or C polysaccharide with group C streptococci.

The vernacular name of Streptococcus pneumoniae is pneumococcus.


Vibrio cholerae serogroups are expressed as in these examples:

Vibrio cholerae O1

V cholerae O139


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