Appendix D| 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.[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.

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
Phylum Bacteroidetes
Class Genus Species Related Diseases
Bacteroidia Porphyromonas Periodontal disease
Prevotella intermedia Periodontal disease
Phylum Chlamydiae
Class Genus Species Related Diseases
Chlamydiae Chlamydia psittaci Psittacosis
Chlamydia trachomatis Sexually transmitted chlamydia
Phylum Firmicutes
Class Genus Species Related Diseases
Bacilli Bacillus anthracis Anthrax
Bacillus cereus Diarrheal and emetic food poisoning
Listeria monocytogenes Listeriosis
Enterococcus faecalis Endocarditis, septicaemia, 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
Phylum Fusobacteria
Class Genus Species Related Diseases
Fusobacteriia Fusobacterium Periodontal disease, Lemierre syndrome, skin ulcers
Streptobacillus moniliformis Rat-bite fever
Phylum Proteobacteria
Class Genus Species Related Diseases
Alphaproteobacteria Anaplasma phagocytophilum Human granulocytic anaplasmosis
Bartonella henselae Peliosis hepatitis, bacillary angiomatosis, endocarditis, bacteraemia
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
Helicobacter pylori Gastric ulcers
Gammaproteobacteria Aeromonas hydrophila Dysenteric gastroenteritis
Coxiella burnetii Q fever
Enterobacter Urinary and respiratory infections
Escherichia coli


shiga toxin-producing (STEC) (e.g., O157:H7) also called enterohaemorrhagic E. coli (EHEC) or verocytotoxin-producing E. coli (VTEC)

Foodborne diarrhoea outbreaks, haemorrhagic colitis, hemolytic-uremic syndrome
Escherichia coli


enterotoxigenic E. coli (ETEC)

Traveler’s diarrhoea
Escherichia coli


enteropathogenic E. coli (EPEC)

Diarrhea, especially in young children
Escherichia coli


enteroaggregative E. coli (EAEC)

Diarrheal disease in children and travellers
Escherichia coli


diffusely adherent E. coli (DAEC)

Diarrheal disease of children
Escherichia coli


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, septicaemia
Yersinia enterocolitica Yersiniosis
Yersinia pestis Plague
Yersinia pseudotuberculosis Far East scarlet-like fever
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
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 summarizing viral pathogens.
A table summarizing viral pathogens - continuation

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.

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
Malassezia Dandruff, tinea versicolour
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.

Supergroup Amoebozoa
Phylum Genus Species Related Diseases
Amoebozoa Acanthamoeba Granulomatous amoebic encephalitis, acanthamoebic keratitis
Entamoeba histolytica Enterobiasis
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
Supergroup Excavata
Phylum Genus Species Related Diseases
Metamonada Giardia lamblia Giardiasis
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)

Media Attributions

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  • OSC_Microbio_00_DD_VirPatTBL2

  1. Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline. 2012.
  2. International Committee on Taxonomy of Viruses. “ICTV Master Species List.”
  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.
  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.


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Microbiology: Canadian Edition Copyright © 2019 by Wendy Keenleyside is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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