Bacteria: Additional Terminology
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
- 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 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
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:
strains of STEC serotypes other than O157:H7
Note the following terms representing Shiga toxins:
Bacteria are often grouped according to reaction to the Gram stain. Note capitalization style in the following (see also 10.3, Capitalization, Proper Nouns):
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.
Microorganism names applied to laboratory media are given lowercase and roman:
bacteroides bile esculin agar
Capitalization indicates a product name:
Haemophilus ID Quad agar
Lactobacillus GG refers to a strain of Lactobacillus rhamnosus named for the authors who isolated it.41
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
the L form of Mycobacterium tuberculosis
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)
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
S enterica subsp salamae
S enterica subsp arizonae
S enterica subsp diarizonae
S enterica subsp houtenae
S enterica subsp indica
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:
When the genus name is repeated, it may be abbreviated:
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 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:
group A β-hemolytic streptococci
group A Streptococcus pyogenes
group B β-hemolytic streptococci (S agalactiae)
group C streptococci
Proteins of Streptococcus pyogenes include the following:
class I M protein
class II M protein
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
1. International Commission on Zoological Nomenclature. International Code of Zoological Nomenclature. 4th ed. London, England: International Trust for Zoological Nomenclature; 1999. Also available at http://www.iczn.org/iczn/. Accessed April 20, 2006.Find this resource:
2. Jeffrey C. Biological Nomenclature. 3rd ed. London, England: Edward Arnold; 1989.Find this resource:
3. Brenner DJ, Staley JT, Krieg NR. Classification of procaryotic organisms and the concept of bacterial speciation. In: Boone DR, Castenholz RW, eds. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Vol 1: The Archaea and the Deeply Branching and Phototrophic Bacteria. New York, NY: Springer-Verlag; 2001:27-31.Find this resource:
4. Sneath PHA. Bacterial nomenclature. In: Boone DR, Castenholz RW, eds. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Vol 1: The Archaea and the Deeply Branching and Phototrophic Bacteria. New York, NY: Springer-Verlag; 2001:83-88.Find this resource:
5. Melville RV. Towards Stability in the Names of Animals: A History of the International Commission on Zoological Nomenclature 1895–1995. London, England: International Trust for Zoological Nomenclature; 1995.Find this resource:
6. Greuter W, McNeill J, Barrie FR, et al, eds. International Code of Botanical Nomenclature (St Louis Code). Vienna, Austria: International Association for Plant Taxonomy; Königstein, Germany: Koeltz Scientific Books; 1999. Also available at http://www.bgbm.org/IAPT/Nomenclature/Code/SaintLouis/0001ICSLContents.htm. Updated February 12, 2001. Accessed April 20, 2006.Find this resource:
7. Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA. International Code of Nomenclature of Bacteria and Statutes of the International Committee on Systematic Bacteriology and Statutes of the Bacteriology and Applied Microbiology Section of the International Union of Microbiological Societies. Washington, DC: International Union of Microbiological Societies, American Society for Microbiology; 1992.Find this resource:
8. Trehane P, Brickell CD, Baum BR, et al, eds. International Code of Nomenclature for Cultivated Plants. Wimborne, England: Quarterjack Publishing; 1995.Find this resource:
9. International Committee on Bionomenclature (ICB). http://www.rom.on.ca/biodiversity/biocode/bioicb1997.html. Accessed September 13, 2005.
10. Ride WDL. Introduction. In: International Commission on Zoological Nomenclature. International Code of Zoological Nomenclature. 4th ed. London, England: International Trust for Zoological Nomenclature; 1999:xix-xxixFind this resource:
11. International Union of Biological Sciences website. http://www.iubs.org. Accessed April 20, 2006.
12. Robinson P, Kommedahl T. Phylocode: a new system of nomenclature. Sci Editor. 2002;25(2):52.Find this resource:
13. Phylocode. http://www.ohiou.edu/phylocode. Modified April 20, 2006. Accessed April 21, 2006.
14. Kolata G. Flu: The Story of the Great Influenza Pandemic of 1918 and the Search for the Virus That Caused It. New York, NY: Touchstone; 1999.Find this resource:
15. Biosis. Index to organism names. http://www.organismnames.com. Accessed April 21, 2006.
16. NCBI Entrez Taxonomy Homepage. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=taxonomy. Accessed April 21, 2006.
17. Han XY, Pham AS, Tarrand JJ, Rolston KV, Helsel LO, Levett PN. Bacteriologic characterization of 36 strains of Roseomonas species and proposal of Roseomonas mucosa sp nov and Roseomonas gilardii subsp rosea subsp nov. Am J Clin Pathol. 2003;120(2):256-264.Find this resource:
18. Aksoy S. Wigglesworthia gen. nov. and Wigglesworthia glossinidia sp. nov., taxa consisting of the mycetocyte-associated, primary endosymbionts of tsetse flies. Int J Syst Bacteriol. 1995;45(4):848-851.Find this resource:
19. Funch P, Kristensen RM. Cycliophora is a new phylum with affinities to Entoprocta and Ectoprocta. Nature. 1995;378(6558):711-714.Find this resource:
20. Morris SC. A new phylum from the lobster’s lips. Nature. 1995;378(6558):661-662.Find this resource:
21. 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.Find this resource:
22. 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.Find this resource:
23. Ursing JB. Bacteriologic nomenclature. In: Maisonneuve H, Enckell PH, Polderman AKS, Thapa R, Vekony M, eds. Science Editors’ Handbook. West Clandon, England: European Association of Science Editors; 2003;3-4.1:1-4.Find this resource:
24. ASM Style Manual for Journals and Books. Washington, DC: American Society for Microbiology: 1991.Find this resource:
25. Style notes: taxonomic names in microbiology and their adjectival derivatives [editorial]. Ann Intern Med. 1989;110(6):419-420.Find this resource:
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.Find this resource:
27. Cushion MT. Pneumocystis. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, eds. Manual of Clinical Microbiology. 8th ed. Washington, DC: ASM Press; 2003:1712-1725.Find this resource:
28. Hughes WT. Pneumocystis carinii vs. Pneumocystis jiroveci: another misnomer (response to Stringer et al). Emerg Infect Dis. 2003;9(2):276-277.Find this resource:
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.Find this resource:
30. Murray RGE, Holt JG. The history of Bergey’s Manual. In: Boone DR, Castenholz RW, eds. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Vol 1: The Archaea and the Deeply Branching and Phototrophic Bacteria. New York, NY: Springer-Verlag; 2001:1-13.Find this resource:
32. DSMZ. Bacterial nomenclature search page. http://www.dsmz.de/bactnom/bactname. Accessed April 24, 2006.
33. Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, eds. Manual of Clinical Microbiology. 8th ed. Washington, DC: ASM Press; 2003:991-1004.Find this resource:
34. Brooks GF, Butel JS, Morse SA. Jawetz, Melnick, and Adelberg’s Medical Microbiology. 22nd ed. New York, NY: Lange Medical Books/McGraw-Hill; 2001.Find this resource:
35. Mahony JB, Coombes BK, Chernesky MA. Chlamydia and Chlamydophila. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, eds. Manual of Clinical Micro-biology. 8th ed. Washington, DC: ASM Press; 2003:991-1004.Find this resource:
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.Find this resource:
37. Boone DR, Castenholz RW, eds. Bergey’s Manual of Systematic Bacteriology. 2nd ed. Vol 1: The Archaea and the Deeply Branching and Phototropoic Bacteria. New York, NY: Springer-Verlag; 2001.Find this resource:
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.Find this resource:
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.Find this resource:
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.Find this resource:
41. Gorbach SL, Chang TW, Goldin B: Successful treatment of relapsing Clostridium difficile colitis with Lactobacillus GG. Lancet. 1987;2(8574):1519.Find this resource:
42. Euzéby JP. Salmonella nomenclature. http://www.bacterio.cict.fr/salmonellanom.html. Updated March 19, 2005. Accessed September 13, 2005.
43. Farmer JJ III. Enterobacteriaceae: introduction and identification. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, eds. Manual of Clinical Microbiology. 8th ed. Washington, DC: ASM Press; 2003:636-653.Find this resource:
44. Bopp CA, Brenner FW, Fields PI, Wells JG, Strockbine NA. Escherichia, Shigella, and Salmonella. In: Murray PR, Baron EJ, Jorgensen JH, Pfaller MA, Yolken RH, eds. Manual of Clinical Microbiology. 8th ed. Washington, DC: ASM Press; 2003:654-671.Find this resource:
45. Brenner FW, Villar RG, Angulo FJ, Tauxe R, Swaminathan B. Guest commentary: Salmonella nomenclature. J Clin Microbiol. 2000;38(7):2465-2467.Find this resource: