D: Taxonomy of Clinically Relevant Microorganisms

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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.¹

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 \(\PageIndex{1}\): Phylum Actinobacteria
Class	Genus	Species	Related Diseases
Actinobacteria	Corynebacterium	diphtheriae	Diphtheria
	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 \(\PageIndex{2}\): Phylum Bacteroidetes
Class	Genus	Species	Related Diseases
Bacteroidia	Porphyromonas		Periodontal disease
Bacteroidia	Prevotella	intermedia	Periodontal disease

Table \(\PageIndex{3}\): Phylum Chlamydiae
Class	Genus	Species	Related Diseases
Chlamydiae	Chlamydia	psittaci	Psittacosis
Chlamydiae	Chlamydia	trachomatis	Sexually transmitted chlamydia

Table \(\PageIndex{4}\): 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 \(\PageIndex{5}\): Phylum Fusobacteria
Class	Genus	Species	Related Diseases
Fusobacteriia	Fusobacterium		Periodontal disease, Lemierre syndrome, skin ulcers
Fusobacteriia	Streptobacillus	moniliformis	Rat-bite fever

Table \(\PageIndex{6}\): 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 \(\PageIndex{7}\): 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 \(\PageIndex{8}\): 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

A table titled “Viral Pathogens (continued)” gives information on order, family, subfamily, genus, species, and related diseases.All entries in this table are unassigned in the order category. For the family flaviviriadae, genus flavivirus, species dengue virus, the related disease is dengue fever. For the family flaviviriadae, genus flavivirus, species Yellow fever virus, the related disease is yellow fever. In the family flaviviriadae, genus hepacivirus, species hepatitis c virus, the related disease is hepatitis C. For the family hepadnaviridae, genus orthohepadnavirus, species hepatitis B virus, the related disease is hepatitis B. For the family Hepeviridae, genus orthohepevirus, species hepatitis E virus, the related disease is hepatitis E. For the family orthomyxoviridae, genus influenzavirus A, species influenza virus A, the related disease is pandemic flu. For the family orthomyxoviridae, genus influenzavirus B, species influenza virus B, the related disease is Flu. For the family orthomyxoviridae, genus influenzavirus C, species influenza virus C, the related disease is Flu. For the family papillomaviridae, genus alphapapillomavirus, species human papillomavirus, the related disease is skin warts. For the family parvoviridae, subfamily parvovirinae, genus erythroparvovirus, species human parvovirus B 19, the related disease is fifth disease (erythema infectosum). For the family poxviridae, subfamily chordopoxvirinae, genus orthopoxvirus, species variola virus, the related diseases are variola major, variola minor (smallpox). For the family poxviridae, subfamily chordopoxvirinae, genus orthopoxvirus, species vaccinia virus, the related disease is cowpox. For the family reoviridae, subfamily sedoreovirinae, genus rotavirus, species eight species, the related disease is gastroenteritis. For the family retroviridae, subfamily orthoretrovirinae, genus lentivirus, species human immunodeficiency virus, the related disease is AIDS. For the family togaviridae, genus alphavirus, species chikungunya virus (CHIKV), the related disease is Chikungunya. For the family togaviridae, genus rubivirus, species rubella virus, the related disease is Rubella (German measles). For an unassigned order, genus deltavirus, species hepatitis D virus, the related disease is hepatitis D. — Figure \(\PageIndex{2}\)

Fungal Pathogens

The Fungi are one of the kingdoms of the domain Eukarya. Fungi are most closely related to the animals and a few other small groups and more distantly related to the plants and other groups that formerly were categorized as protist. At present, the Fungi are divided into seven phyla (or divisions, a hold over from when fungi were studied with plants), but there are uncertainties about some relationships.³ Many groups of fungi, particularly those that were formerly classified in the phylum Zygomycota, which was not monophyletic, have uncertain relationships to the other fungi. The one species listed in this table that falls into this category is Rhizopus arrhizus. Fungal names are governed by the International Code of Nomenclature for Algae, Fungi, and Plants,⁴ but the International Commission on the Taxonomy of Fungi (ICTF) also promotes taxonomic work on fungi. One activity of the ICTF is publicizing name changes for medically and otherwise important fungal species. Many species that formerly had two names (one for the sexual form and one for the asexual form) are now being brought together under one name.

Table \(\PageIndex{9}\): Fungal Pathogens
Division	Genus	Species	Related Diseases
Ascomycota	Aspergillus	flavus	Opportunistic aspergillosis
	Aspergillus	fumigatus	Opportunistic aspergillosis
	Blastomyces	dermatitidis	Blastomycosis
	Candida	albicans	Thrush (candidiasis)
	Coccidioides	immitis	Valley fever (coccidioidomycosis)
	Epidermophyton		Tinea corporis (ringworm), tinea cruris (jock itch), tinea pedis (althlete’s foot), tinea unguium (onychomycosis)
	Histoplasma	capsulatum	Histoplasmosis
	Microsporum		Tinea capitis (ringworm), tinea corpus (ringworm), other dermatophytoses
	Pneumocystis	jirovecii	Opportunistic pneumonia
	Sporothrix	schenckii	Sporotrichosis (rose-handler’s disease)
	Trichophyton	mentagrophytes var. interdigitale	Tinea barbae (barber’s itch), dermatophytoses
	Trichophyton	rubrum	Tinea corporis (ringworm), tinea cruris (jock itch), tinea pedis (althlete’s foot), tinea unguium (onychomycosis)
Basidiomycota	Cryptococcus	neoformans	Opportunistic cryptococcosis, fungal meningitis, encephalitis
Basidiomycota	Malassezia		Dandruff, tinea versicolor
uncertain	Rhizopus	arrhizus	Mucormycosis

Protozoan Pathogens

The relationships among the organisms (and thus their taxonomy) previously grouped under the name Protists are better understood than they were two or three decades ago, but this is still a work in progress. In 2005, the Eukarya were divided into six supergroups.⁵ The latest high-level classification combined two of the previous supergroups to produce a system comprising five supergroups.⁶ This classification was developed for the Society of Protozoologists, but it is not the only suggested approach. One of the five supergroups includes the animals, fungi, and some smaller protist groups. Another contains green plants and three algal groups. The other three supergroups (listed in the three tables below) contain the other protists, many of them which cause disease. In addition, there is a large number of protist groups whose relationships are not understood. In the three supergroups represented here we have indicated the phyla to which the listed pathogens belong.

Table \(\PageIndex{10}\): Supergroup Amoebozoa
Phylum	Genus	Species	Related Diseases
Amoebozoa	Acanthamoeba		Granulomatous amoebic encephalitis, acanthamoebic keratitis
Amoebozoa	Entamoeba	histolytica	Enterobiasis

Table \(\PageIndex{11}\): Supergroup SAR (Stramenopiles, Alveolata, Rhizaria)
Phylum	Genus	Species	Related Diseases
Apicomplexa	Babesia		Babesiosis
	Cryptosporidium	hominis	Cryptosporidiosis
	Cryptosporidium	parvum	Cryptosporidiosis
	Cyclospora	cayetanensis	Gastroenteritis
	Plasmodium	falciparum	Malaria
	Plasmodium	malariae	“Benign” or “quartan” (3-day recurrent fever) malaria
	Plasmodium	ovale	“Tertian” (2-day recurrent fever) malaria
	Plasmodium	vivax	“Benign” “tertian” (2-day recurrent fever) malaria
	Plasmodium	knowlesi	Primate malaria capable of zoonosis, quotidian fever
	Toxoplasma	gondii	Toxoplasmosis

Table \(\PageIndex{12}\): Supergroup Excavata
Phylum	Genus	Species	Related Diseases
Metamonada	Giardia	lamblia	Giardiasis
Metamonada	Trichomonas	vaginalis	Trichomoniasis
Euglenozoa	Leishmania	braziliensis	Leishmaniasis
	Leishmania	donovani	Leishmaniasis
	Leishmania	tropica	Cutaneous leishmaniasis
	Trypanosoma	brucei	African sleeping sickness (African trypanosomiasis)
	Trypanosoma	cruzi	Chagas disease
Percolozoa	Naegleria	fowleri	Primary amoebic meningoencephalitis (naegleriasis)

Parasitic Helminths

The taxonomy of parasitic worms, all of which belong to the kingdom Animalia still contains many uncertainties. The pathogenic species are found in two phyla: the Nematoda, or roundworms, and the Platyhelminthes, or flat worms. The Nematoda is tentatively divided into two classes⁷, one of which, Chromadorea, probably contains unrelated groups. The parasitic flatworms are contained within three classes of flatworm, of which two are important to humans, the trematodes and the cestodes.

Table \(\PageIndex{13}\): Phylum Nematoda
Class	Genus	Species	Related Diseases
Chromadorea	Ancylostoma	caninum	Dog hookworm infection
	Ancylostoma	duodenale	Old World hookworm infection
	Ascaris	lumbricoides	Ascariasis
	Enterobius	vermicularis	Enterobiasis (pin worm)
	Loa	loa	Loa loa filariasis (eye worm)
	Necator	americanus	Necatoriasis (New World hookworm infection)
	Strongyloides	stercoralis	Strongyloidiasis
Enoplea	Trichinella	spiralis	Trichinosis
Enoplea	Trichuris	trichiura	Trichuriasis (whip worm infection)

Table \(\PageIndex{14}\): Phylum Platyhelminthes
Class	Genus	Species	Related Diseases
Trematoda	Clonorchis	sinensis	Chinese liver fluke
	Fasciolopsis	buski	Fasciolopsiasis
	Fasciola	gigantica	Fascioliasis
	Fasciola	hepatica	Fascioliasis
	Opisthorchis	felineus	Opisthorchiasis
	Opisthorchis	viverrini	Opisthorchiasis
	Schistosoma	haematobium	Urinary schistosomiasis
	Schistosoma	japonicum	Schistosomiasis
	Schistosoma	mansoni	Intestinal schistosomiasis
Cestoda	Diphyllobothrium	latum	Diphyllobothriosis
	Echinococcus	granulosus	Hydatid cysts (cystic echinococcosis)
	Echinococcus	multilocularis	Echinococcosis
	Taenia	asiatica	Intestinal taeniasis
	Taenia	saginata	Intestinal taeniasis
	Taenia	solium	Intestinal taeniasis, cysticercosis

Footnotes

1 Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline. 2012. http://www.bergeys.org/outlines.html
2 International Committee on Taxonomy of Viruses. “ICTV Master Species List.” http://talk.ictvonline.org/files/ict...l/default.aspx
3 D. S. Hibbett et al. “A Higher-level Phylogenetic Classification of the Fungi.” Mycological Research 111 no. 5 (2007):509–547.
4 J. McNeill et al. International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code). Oberreifenerg, Germany. Koeltz Scientific Books; 2012. http://www.iapt-taxon.org/nomen/main.php?
5 S.M. Adl et al. “The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists.” Journal of Eukaryotic Microbiology 52 no. 5 (2005):399–451.
6 S.M. Adl et al. “The Revised Classification of Eukaryotes.” Journal of Eukaryotic Microbiology 59 no. 5 (2012):429–514.
7 National Center for Biotechnology Information. “Taxonomy Browser: Nematoda.” http://www.ncbi.nlm.nih.gov/Taxonomy...ax.cgi?id=6231