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
ClassGenusSpeciesRelated Diseases
GardnerellavaginalisBacterial vaginosis
Micrococcus Opportunistic infections
MycobacteriumbovisTuberculosis, primarily in cattle
MycobacteriumlepraeHansen’s disease
PropionibacteriumacnesAcne, blepharitis, endophthalmitis
Table 2. Phylum Bacteroidetes
ClassGenusSpeciesRelated Diseases
BacteroidiaPorphyromonas Periodontal disease
PrevotellaintermediaPeriodontal disease
Table 3. Phylum Chlamydiae
ClassGenusSpeciesRelated Diseases
ChlamydiatrachomatisSexually transmitted chlamydia
Table 4. Phylum Firmicutes
ClassGenusSpeciesRelated Diseases
BacilluscereusDiarrheal and emetic food poisoning
EnterococcusfaecalisEndocarditis, septicemia, urinary tract infections, meningitis
StaphylococcusaureusSkin infections, sinusitis, food poisoning
StaphylococcusepidermidisNosocomial and opportunistic infections
StaphylococcushominisOpportunistic infections
StaphylococcussaprophyticusUrinary tract infections
StreptococcusagalactiaePostpartum infection, neonatal sepsis
StreptococcusmutansTooth decay
StreptococcuspneumoniaePneumonia, many other infections
StreptococcuspyogenesPharyngitis, scarlet fever, impetigo, necrotizing fasciittis
ClostridiaClostridiumbotulinumBotulinum poisoning
ClostridiumperfringensFood poisoning, gas gangrene
Table 5. Phylum Fusobacteria
ClassGenusSpeciesRelated Diseases
FusobacteriiaFusobacterium Periodontal disease, Lemierre syndrome, skin ulcers
StreptobacillusmoniliformisRat-bite fever
Table 6. Phylum Proteobacteria
ClassGenusSpeciesRelated Diseases
AlphaproteobacteriaAnaplasmaphagocytophilumHuman granulocytic anaplasmosis
BartonellahenselaePeliosis hepatitis, bacillary angiomatosis, endocarditis, bacteremia
BartonellaquintanaTrench fever
BrucellamelitensisOvine brucellosis
EhrlichiachaffeensisHuman monocytic ehrlichiosis
RickettsiaprowazekiiEpidemic typhus
RickettsiarickettsiiRocky Mountain spotted fever
RickettsiatyphiMurine typhus
Eikenella Bite-injury infections
Spirillumminus (alt. minor)Sodoku (rat-bite fever)
EpsilonproteobacteriaCampylobacterjejuniGastroenteritis, Guillain-Barré syndrome
HelicobacterpyloriGastric ulcers
GammaproteobacteriaAeromonashydrophilaDysenteric gastroenteritis
CoxiellaburnetiiQ fever
Enterobacter Urinary and respiratory infections
EscherichiacoliStrains: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
EscherichiacoliStrain:enterotoxigenic E. coli (ETEC)Traveler’s diarrhea
EscherichiacoliStrain:enteropathogenic E. coli (EPEC)Diarrhea, especially in young children
EscherichiacoliStrain:enteroaggregative E. coli (EAEC)Diarrheal disease in children and travelers
EscherichiacoliStrain:diffusely adherent E. coli (DAEC)Diarrheal disease of children
EscherichiacoliStrain:enteroinvasive E. coli (EPEC)Bacillary dysentery, cells invade intestinal epithelial cells
HaemophilusinfluenzaeBacteremia, pneumonia, meningitis
KlebsiellapneumoniaePneumonia, nosocomial infections
LegionellapneumophilaLegionnaire’s disease
MoraxellacatarrhalisOtitis media, bronchitis, sinusitis, laryngitis, pneumonia
Pasteurella Pasteurellosis
Proteus Opportunistic urinary tract infections
PseudomonasaeruginosaOpportunistic, nosocomial pneumonia and sepsis
Serratia Pneumonia, urinary tract infections
VibrioparahemolyticusSeafood gastroenteritis
VibriovulnificusSeafood gastroenteritis, necrotizing wound infections, septicemia
YersiniapseudotuberculosisFar East scarlet-like fever
Table 7. Phylum Spirochaetes
ClassGenusSpeciesRelated Diseases
SpirochaetiaBorreliaburgdorferiLyme disease
BorreliahermsiiTick-borne relapsing fever
BorreliarecurrentisLouse-borne relapsing fever
TreponemapallidumSyphilis, bejel, pinta, yaws
Table 8. Phylum Tenericutes
ClassGenusSpeciesRelated Diseases
MollicutesMycoplasmagenitaliumUrethritis, cervicitis
MycoplasmahominisPelvic inflammatory disease, bacterial vaginosis
MycoplasmapneumoniaeMycoplasma pneumonia
UreaplasmaurealyticumUrethritis, 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.

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