Taxonomy of Clinically Relevant Microorganisms

Bacterial Pathogens

The following tables list the species, and some higher groups, of pathogenic Eubacteria mentioned in the text. The classification of Bacteria, one of the three domains of life, is in constant flux as relationships become clearer through sampling of genetic sequences. Many groups at all taxonomic levels still have an undetermined relationship with other members of the phylogenetic tree of Bacteria. Bergey’s Manual of Systematics of Archaea and Bacteria maintains a published list and descriptions of prokaryotic species. The tables here follow the taxonomic organization in the Bergey’s Manual Taxonomic Outline.

We have divided the species into tables corresponding to different bacterial phyla. The taxonomic rank of kingdom is not used in prokaryote taxonomy, so the phyla are the subgrouping below domain. Note that many bacterial phyla not represented by these tables. The species and genera are listed only under the class within each phylum. The names given to bacteria are regulated by the International Code of Nomenclature of Bacteria as maintained by the International Committee on Systematics or Prokaryotes.

Table 1. Phylum Actinobacteria
Class	Genus	Species	Related Diseases
Actinobacteria	Corynebacterium	diphtheriae	Diptheria
	Gardnerella	vaginalis	Bacterial vaginosis
	Micrococcus		Opportunistic infections
	Mycobacterium	bovis	Tuberculosis, primarily in cattle
	Mycobacterium	leprae	Hansen’s disease
	Mycobacterium	tuberculosis	Tuberculosis
	Propionibacterium	acnes	Acne, blepharitis, endophthalmitis

Table 2. Phylum Bacteroidetes
Class	Genus	Species	Related Diseases
Bacteroidia	Porphyromonas		Periodontal disease
Bacteroidia	Prevotella	intermedia	Periodontal disease

Table 3. Phylum Chlamydiae
Class	Genus	Species	Related Diseases
Chlamydiae	Chlamydia	psittaci	Psittacosis
Chlamydiae	Chlamydia	trachomatis	Sexually transmitted chlamydia

Table 4. Phylum Firmicutes
Class	Genus	Species	Related Diseases
Bacilli	Bacillus	anthracis	Anthrax
	Bacillus	cereus	Diarrheal and emetic food poisoning
	Listeria	monocytogenes	Listeriosis
	Enterococcus	faecalis	Endocarditis, septicemia, urinary tract infections, meningitis
	Staphylococcus	aureus	Skin infections, sinusitis, food poisoning
	Staphylococcus	epidermidis	Nosocomial and opportunistic infections
	Staphylococcus	hominis	Opportunistic infections
	Staphylococcus	saprophyticus	Urinary tract infections
	Streptococcus	agalactiae	Postpartum infection, neonatal sepsis
	Streptococcus	mutans	Tooth decay
	Streptococcus	pneumoniae	Pneumonia, many other infections
	Streptococcus	pyogenes	Pharyngitis, scarlet fever, impetigo, necrotizing fasciittis
Clostridia	Clostridium	botulinum	Botulinum poisoning
	Clostridium	difficile	Colitis
	Clostridium	perfringens	Food poisoning, gas gangrene
	Clostridium	tetani	Tetanus

Table 5. Phylum Fusobacteria
Class	Genus	Species	Related Diseases
Fusobacteriia	Fusobacterium		Periodontal disease, Lemierre syndrome, skin ulcers
Fusobacteriia	Streptobacillus	moniliformis	Rat-bite fever

Table 6. Phylum Proteobacteria
Class	Genus	Species	Related Diseases
Alphaproteobacteria	Anaplasma	phagocytophilum	Human granulocytic anaplasmosis
	Bartonella	henselae	Peliosis hepatitis, bacillary angiomatosis, endocarditis, bacteremia
	Bartonella	quintana	Trench fever
	Brucella	melitensis	Ovine brucellosis
	Ehrlichia	chaffeensis	Human monocytic ehrlichiosis
	Rickettsia	prowazekii	Epidemic typhus
	Rickettsia	rickettsii	Rocky Mountain spotted fever
	Rickettsia	typhi	Murine typhus
Betaproteobacteria	Bordetella	pertussis	Pertussis
	Eikenella		Bite-injury infections
	Neisseria	gonorrhoeae	Gonorrhea
	Neisseria	meningitidis	Meningitis
	Spirillum	minus (alt. minor)	Sodoku (rat-bite fever)
Epsilonproteobacteria	Campylobacter	jejuni	Gastroenteritis, Guillain-Barré syndrome
Epsilonproteobacteria	Helicobacter	pylori	Gastric ulcers
Gammaproteobacteria	Aeromonas	hydrophila	Dysenteric gastroenteritis
	Coxiella	burnetii	Q fever
	Enterobacter		Urinary and respiratory infections
	Escherichia	coli Strains: shiga toxin-producing (STEC) (e.g., O157:H7) also called enterohemorrhagic E. coli (EHEC) or verocytotoxin-producing E. coli (VTEC)	Foodborne diarrhea outbreaks, hemorrhagic colitis, hemolytic-uremic syndrome
	Escherichia	coli Strain: enterotoxigenic E. coli (ETEC)	Traveler’s diarrhea
	Escherichia	coli Strain: enteropathogenic E. coli (EPEC)	Diarrhea, especially in young children
	Escherichia	coli Strain: enteroaggregative E. coli (EAEC)	Diarrheal disease in children and travelers
	Escherichia	coli Strain: diffusely adherent E. coli (DAEC)	Diarrheal disease of children
	Escherichia	coli Strain: enteroinvasive E. coli (EPEC)	Bacillary dysentery, cells invade intestinal epithelial cells
	Francisella	tularensis	Tularemia
	Haemophilus	ducreyi	Chancroid
	Haemophilus	influenzae	Bacteremia, pneumonia, meningitis
	Klebsiella	pneumoniae	Pneumonia, nosocomial infections
	Legionella	pneumophila	Legionnaire’s disease
	Moraxella	catarrhalis	Otitis media, bronchitis, sinusitis, laryngitis, pneumonia
	Pasteurella		Pasteurellosis
	Plesiomonas	shigelloides	Gastroenteritis
	Proteus		Opportunistic urinary tract infections
	Pseudomonas	aeruginosa	Opportunistic, nosocomial pneumonia and sepsis
	Salmonella	bongori	Salmonellosis
	Salmonella	enterica	Salmonellosis
	Serratia		Pneumonia, urinary tract infections
	Shigella	boydii	Dysentery
	Shigella	dysenteriae	Dysentery
	Shigella	flexneri	Dysentery
	Shigella	sonnei	Dysentery
	Vibrio	cholerae	Cholera
	Vibrio	parahemolyticus	Seafood gastroenteritis
	Vibrio	vulnificus	Seafood gastroenteritis, necrotizing wound infections, septicemia
	Yersinia	enterocolitica	Yersiniosis
	Yersinia	pestis	Plague
	Yersinia	pseudotuberculosis	Far East scarlet-like fever

Table 7. Phylum Spirochaetes
Class	Genus	Species	Related Diseases
Spirochaetia	Borrelia	burgdorferi	Lyme disease
	Borrelia	hermsii	Tick-borne relapsing fever
	Borrelia	recurrentis	Louse-borne relapsing fever
	Leptospira	interrogans	Leptospirosis
	Treponema	pallidum	Syphilis, bejel, pinta, yaws

Table 8. Phylum Tenericutes
Class	Genus	Species	Related Diseases
Mollicutes	Mycoplasma	genitalium	Urethritis, cervicitis
	Mycoplasma	hominis	Pelvic inflammatory disease, bacterial vaginosis
	Mycoplasma	pneumoniae	Mycoplasma pneumonia
	Ureaplasma	urealyticum	Urethritis, fetal infections

Viral Pathogens

There are several classification systems for viruses. The International Committee on Taxonomy of Viruses (ICTV) is the international scientific body responsible for the rules of viral classification. The ICTV system used here groups viruses based on genetic similarity and presumed monophyly. The viral classification system is separate from the classification system for cellular organisms. The ICTV system groups viruses within seven orders, which contain related families. There is, presently, a large number of unassigned families with unknown affinities to the seven orders. Three of these orders infect only Eubacteria, Archaea, or plants and do not appear in this table. Some families may be divided into subfamilies. There are also many unassigned genera. Like all taxonomies, viral taxonomy is in constant flux. The latest complete species list and classification can be obtained on the ICTV website.^[2]

Table 9.

Table 10.