D: Taxonomy of Clinically Relevant Microorganisms
- Page ID
- 77772
\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)
\( \newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\)
( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\)
\( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)
\( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\)
\( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)
\( \newcommand{\Span}{\mathrm{span}}\)
\( \newcommand{\id}{\mathrm{id}}\)
\( \newcommand{\Span}{\mathrm{span}}\)
\( \newcommand{\kernel}{\mathrm{null}\,}\)
\( \newcommand{\range}{\mathrm{range}\,}\)
\( \newcommand{\RealPart}{\mathrm{Re}}\)
\( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)
\( \newcommand{\Argument}{\mathrm{Arg}}\)
\( \newcommand{\norm}[1]{\| #1 \|}\)
\( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)
\( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\AA}{\unicode[.8,0]{x212B}}\)
\( \newcommand{\vectorA}[1]{\vec{#1}} % arrow\)
\( \newcommand{\vectorAt}[1]{\vec{\text{#1}}} % arrow\)
\( \newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\( \newcommand{\vectorC}[1]{\textbf{#1}} \)
\( \newcommand{\vectorD}[1]{\overrightarrow{#1}} \)
\( \newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}} \)
\( \newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}} \)
\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)
\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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.
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 |
Class | Genus | Species | Related Diseases |
---|---|---|---|
Bacteroidia | Porphyromonas | Periodontal disease | |
Prevotella | intermedia | Periodontal disease |
Class | Genus | Species | Related Diseases |
---|---|---|---|
Chlamydiae | Chlamydia | psittaci | Psittacosis |
Chlamydia | trachomatis | Sexually transmitted chlamydia |
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 |
Class | Genus | Species | Related Diseases |
---|---|---|---|
Fusobacteriia | Fusobacterium | Periodontal disease, Lemierre syndrome, skin ulcers | |
Streptobacillus | moniliformis | Rat-bite fever |
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 |
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 |
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 |
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
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.
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 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.
Phylum | Genus | Species | Related Diseases |
---|---|---|---|
Amoebozoa | Acanthamoeba | Granulomatous amoebic encephalitis, acanthamoebic keratitis | |
Entamoeba | histolytica | Enterobiasis |
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 |
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) |
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.
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 |
Trichuris | trichiura | Trichuriasis (whip worm infection) |
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