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D: Taxonomy of Clinically Relevant Microorganisms

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    77772
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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
    Prevotella intermedia Periodontal disease

     

    Table \(\PageIndex{3}\): Phylum Chlamydiae
    Class Genus Species Related Diseases
    Chlamydiae Chlamydia psittaci Psittacosis
    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
    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
    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” gives information on order, family, subfamily, genus, species, and related diseases. For order Herpesvirales, family herpesviridae, subfamily betaherpesvirinae, genus human cytomegalovirus group, species human herpesvirus 5, the related disease is Cytomegalovirus hepatitis and other infections in immunocompromised people. For order herpesvirales, family herpesviridae, subfamily gammaherpesvirinae, genus lymphocryptovirus, species human herpesvirus 4(HHV-4; Epstein-Barr virus), the related disease is infectious mononucleosis. For order Herpesvirales, family herpesviridae, subfamily alphaherpesvirinae, genus simplexvirus, species human herpesvirus 1, human herpesvirus 2, the related diseases are herpes simplex virus 1, herpes simplex virus 2. For order herpesvirales, family herpesviridae, subfamily alphaherpesvirinae, genus varicellovirus, species human herpesvirus 3, the related diseases chickenpox, shingles. For order mononegavirales, family filoviridae, subfamily alphaherpesvirinae, genus ebolavirus, species zaire ebolavirus (EBOV), the related disease is Ebola. For order mononegavirales, family filoviridae, genus marburgvirus, species Marburg marburgvirus (MARV), the related disease is Marburg virus disease. For order mononegavirales, family rhabdoviridae, genus lyssavirus, species rabies virus, the related disease is Rabies. For order mononegavirales, family paramyxoviridae, subfamily pneumovirinae, genus pneumovirus, species human respiratory syncytial virus, the related disease is lower respiratory tract infection. For order mononegavirales, family paramyxoviridae, subfamily paramyxovirinae, genus morbillivirus, species measles virus, the related disease is measles (rubeola). For order Nidovirales, family coronaviridae, subfamily coronavirinae, genus coronavirus, the related diseases are common cold, pneumonia, SARS. For order picornavirales, family picornaviridae, genus hepatovirus, species hepatitis A virus, the related disease is hepatitis A. For order picornavirales, family picornaviridae, genus enterovirus, species enterovirus C, the related disease is polio. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus A, the related disease is common cold. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus B, the related disease is common cold. For order picornavirales, family picornaviridae, genus enterovirus, species rhinovirus C, the related disease is common cold. The remaining entries in this table are unassigned in the order category. In the family adenovirus, genus mastadenovirus, the related diseases are respiratory and other infections. In the family arenaviridae, genus mammarenavirus, species lassa mammarenavirus, the related disease is Lassa fever. For the family astroviridae, the related disease is gastroenteritis. For the family bunyaviridae, genus hantavirus, species several species, the related diseases are hantavirus hemorrhagic fever with renal syndrome (HFRS), hantavirus pulmonary syndrome (HPS). For family Bunyaviridae, genus nairovirus, species Crimean-congo hemorrhagic fever virus (CCHF), the related disease is Crimean-Congo hemorrhagic fever. For the family caliciviridae, genus norovirus, species Norwalk virus, the related disease is gastroenteritis.
    Figure \(\PageIndex{1}\)
    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
    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
    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
    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
    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. 1 Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline. 2012. http://www.bergeys.org/outlines.html
    2. 2 International Committee on Taxonomy of Viruses. “ICTV Master Species List.” http://talk.ictvonline.org/files/ict...l/default.aspx
    3. 3 D. S. Hibbett et al. “A Higher-level Phylogenetic Classification of the Fungi.” Mycological Research 111 no. 5 (2007):509–547.
    4. 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. 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. 6 S.M. Adl et al. “The Revised Classification of Eukaryotes.” Journal of Eukaryotic Microbiology 59 no. 5 (2012):429–514.
    7. 7 National Center for Biotechnology Information. “Taxonomy Browser: Nematoda.” http://www.ncbi.nlm.nih.gov/Taxonomy...ax.cgi?id=6231
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