INDIGENOUS AND PATHOGENIC MICROORGANISMS BY HUMAN BODY SITE
KEY: (FREQUENCY/PATHOGENICITY)
1 = Rarely 2 = Occasionally 3 = Commonly
The first number tells how frequently the organism can be expected to be found in a clinical specimen.
The second number tells how often the organism is involved in disease production when present (pathogenicity).
Example: 2/3 = Occasionally encountered in clinical specimens/When present, commonly involved in disease production. Example: 1/1 = Rarely encountered in clinical specimens/When present, rarely involved in disease production.
Table 1 lists organisms found in the respiratory, gastrointestinal and genitourinary tracts.
Table 2 lists organisms found in skin, burns, wounds, eyes, and ears.
| TABLE 1 | |||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Absidia spp. | 1/2 | 1/1 | |
| Acidaminococcus fermentans | 1/1 | ||
| Acinetobacter spp. | 2/2 | 2/1 | 2/2 |
| Actinomyces spp. | 3/2 | 2/2 | |
| Adenoviruses | 2/3 | 2/2 | 2/1 |
| Aerococcus viridans | 2/1 | ||
| Aeromonas spp. | 2/2 | ||
| Agrobacterium tumefaciens | 1/2 | ||
| Alcaligenes spp. | 2/2 | 1/2 | |
| Anaerobiospirillum succiniciproducens | 1/2 | ||
| Ancylostoma duodenale | 2/3 | ||
| Angiostrongylus costaricensis | 1/3 | ||
| Anisakis larvae | 1/3 | ||
| Arachnia propionica | 2/1 | ||
| Arcanobacterium haemolyticum | 2/3 | ||
| Ascaris lumbricoides | 2/3 | ||
| Ascaris lumbricoides larvae | 1/3 | ||
| Aspergillus spp . | 2/2 | 1/1 | |
| Astroviruses | 1/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Bacillus anthracis | 1/3 | ||
| Bacillus spp. | 2/1 | 2/2 | 1/1 |
| Bacteroides spp. | 3/2 | 3/2 | 3/2 |
| Balantidium coli | 1/3 | ||
| Bifidobacterium spp. | 2/1 | 2/1 | 1/1 |
| Bilophila wadsworthia | 1/2 | ||
| Bipolaris spp. | 1/2 | ||
| Blastocystis hominis | 2/2 | ||
| Blastomyces dermatitidis | 1/3 | 1/3 | |
| Bordetella pertussis | 2/3 | ||
| Borrelia spp. | 2/1 | ||
| Branhamella (Moraxella) catarrhalis | 2/2 | 2/1 | |
| Brucella spp. | 1/3 | ||
| Brugia malayi | 1/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Caliciviruses | 1/2 | ||
| Calymmatobacterium granulomatis | 1/3 | ||
| Campylobacter spp. | 2/1 | 2/3 | 1/2 |
| Candida spp. | 2/2 | 2/2 | 2/2 |
| Capillaria spp. | 1/3 | ||
| Capnocytophaga spp. | 2/2 | ||
| Cardiobacterium hominis | 2/1 | ||
| Chilomastix mesnili | 2/1 | ||
| Chlamydia spp. | 2/3 | 2/2 | |
| Clonorchis sinensis | 1/3 | ||
| Clostridium spp. | 2/2 | 3/2 | 3/2 |
| Coccidioides immitis | 2/3 | ||
| Coronaviruses | 2/2 | 1/2 | |
| Corynebacterium diphtheriae (toxigenic) | 1/3 | ||
| Corynebacterium spp. | 2/1 | 2/1 | 2/2 |
| Coxiella burnettii | 1/3 | ||
| Cryptococcus neoformans | 1/3 | ||
| Cryptococcus spp. | 1/2 | ||
| Cryptosporidium spp. | 1/1 | 1/3 | |
| Cytomegalovirus | 2/2 | 2/2 | |
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Dicrocoelium dentriticum ova | 1/1 | ||
| Dientamoeba fragilis | 2/2 | ||
| Dioctophyma renale | 1/3 | ||
| Diphyllobothrium latum | 2/3 | ||
| Dipylidium caninum | 1/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Echinococcus protoscolices or hooklets | 1/3 | ||
| Eikenella corrodens | 2/2 | ||
| Endolimax nana | 2/1 | ||
| Entamoeba coli | 2/1 | ||
| Entamoeba gingivalis | 2/1 | ||
| Entamoeba hartmanni | 2/1 | ||
| Entamoeba histolytica trophozites | 1/3 | ||
| Entamoeba histolytica | 2/3 | 1/3 | |
| Enterobacteriaceae | 2/2 | 3/2 | 3/2 |
| Enterobius vermicularis | 2/3 | 2/2 | |
| Enterococcus spp. | 1/1 | 3/2 | 2/2 |
| Enteromonas hominis | 1/1 | ||
| Enteroviruses | 2/2 | 3/1 | |
| Epstein-Barr virus | 2/2 | ||
| Eubacterium spp. | 3/1 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Fasciola hepatica | 1/3 | ||
| Fasciolopsis buski | 1/3 | ||
| Flavobacterium spp. | 1/2 | 1/2 | |
| Fonsecaea spp. | 1/2 | ||
| Francisella tularensis | 1/3 | ||
| Fusobacterium spp. | 3/2 | 3/2 | 2/1 |
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Gardnerella vaginalis | 2/2 | ||
| Gastrodiscoides hominis | 1/3 | ||
| Gemella spp. | 2/1 | ||
| Geotrichum candidum | 1/1 | 1/1 | |
| Giardia lamblia | 2/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Haemophilus ducreyi | 2/3 | ||
| Haemophilus spp. | 3/2 | ||
| Hepatitis A virus | 2/2 | ||
| Hepatitis B virus | 2/2 | ||
| Helicobacter pylori | 2/3 | ||
| Herpes simplex virus | 2/3 | 2/3 | |
| Heterophyes heterophyes | 1/3 | ||
| Histoplasma capsulatum | 2/3 | 1/3 | 1/3 |
| Human immunodeficiency virus | 1/3 | 2/3 | |
| Hymenolepis spp. | 1/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Influenza viruses | 2/3 | ||
| Iodamoeba butschlii | 2/1 | ||
| Isospora belli | 1/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Kingella spp. | 1/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Lactobacillus spp. | 2/1 | 2/1 | 3/1 |
| Legionella spp. | 2/2 | ||
| Leptospira interrogans | 1/3 | ||
| Leptotrichia buccalis | 2/1 | ||
| Listeria spp. | 1/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Measles virus | 2/3 | ||
| Metagonimus yokogawai | 1/3 | ||
| Micrococcus spp. | 3/1 | ||
| Microsporidian genera (several) | 1/3 | ||
| Mobiluncus spp. | 2/2 | ||
| Molluscum contagiosum virus | 1/3 | ||
| Moraxella spp. | 2/1 | 2/1 | |
| Mucor spp. | 1/2 | 1/2 | |
| Mumps virus | 2/3 | 1/3 | |
| Mycobacterium spp. | 2/2 | 2/2 | 2/2 |
| Mycobacterium tuberculosis group | 2/3 | ||
| Mycoplasma hominis | 2/2 | ||
| Mycoplasma spp. | 1/1 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Necator americanus | 1/3 | 2/3 | |
| Neisseria gonorrhoeae | 1/3 | 1/3 | 2/3 |
| Neisseria meningitidis | 2/2 | 1/3 | |
| Neisseria spp. | 3/1 | 2/1 | 2/1 |
| Nocardia spp. | 2/3 | ||
| Norwalk and Norwalk-like viruses | 2/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Opisthorchis viverrini | 1/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Papillomaviruses | 1/2 | 1/3 | |
| Paracoccidioides brasiliensis | 1/3 | 1/3 | |
| Paragonimus ova | 1/3 | ||
| Paragonimus spp. | 1/3 | ||
| Parainfluenza viruses | 2/2 | ||
| Pasteurella spp. | 1/2 | ||
| Pediococcus spp. | 1/1 | ||
| Penicillium spp. | 1/1 | 1/1 | |
| Peptostreptococcus spp. | 3/2 | 2/2 | 2/1 |
| Plesiomonas shigelloides | 1/2 | ||
| Pneumocystis carinii | 2/2 | ||
| Porphyromonas spp. | 3/2 | 3/2 | |
| Prevotella spp. | 3/2 | 3/2 | |
| Propionibacterium spp. | 2/1 | ||
| Pseudoallescheria boydii | 1/2 | ||
| Pseudomonas spp. | 2/2 | 2/2 | |
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Respiratory syncytial virus | 2/3 | ||
| Retortamonas intestinalis | 1/1 | ||
| Rhinoviruses | 2/2 | ||
| Rhizomucor spp. | 1/2 | 1/1 | |
| Rhizopus spp. | 1/2 | 1/1 | |
| Rhodococcus spp. | 1/2 | ||
| Rhodotorula spp. | 1/1 | 1/1 | |
| Rotavirus | 2/3 | ||
| Rothia dentocariosa | 2/1 | ||
| Rubella virus | 2/3 | ||
| Ruminococcus bromii | 1/1 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Saccharomyces spp. | 2/1 | 1/1 | |
| Sapporo agent | 2/2 | ||
| Sarcinosporon inkin | 2/2 | ||
| Sarcocystis spp. | 1/2 | ||
| Schistosoma haematobium | 1/3 | ||
| Schistosoma spp. | 2/3 | ||
| Selenomonas spp. | 1/1 | 2/1 | |
| Sporothrix schenckii | 1/3 | ||
| Staphylococcus spp. | 3/2 | 2/2 | 3/2 |
| Stomatococcus mucilaginosus | 2/1 | ||
| Streptococcus pneumoniae | 2/2 | ||
| Streptococcus pyogenes | 2/2 | ||
| Streptococcus spp. | 3/2 | 2/2 | 2/2 |
| Strongyloides stercoralis | 2/3 | ||
| Strongyloides stercoralis larvae | 1/3 | ||
| Succinimonas spp. | 2/1 | ||
| Succinivibrio spp. | 2/1 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Taenia spp. | 1/3 | ||
| Torulopsis glabrata | 2/2 | ||
| Treponema pallidum | 2/3 | ||
| Treponema spp. | 2/2 | ||
| Trichinella spiralis larvae | 1/3 | ||
| Trichomonas hominis | 2/1 | ||
| Trichomonas tenax | 2/1 | ||
| Trichomonas vaginalis | 2/3 | ||
| Trichosporon beigelii | 1/1 | ||
| Trichostrongylus spp. | 1/2 | ||
| Trichuris trichiura | 2/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Ureaplasma urealyticum | 2/1 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Varicella-zoster virus | 2/3 | ||
| Veillonella spp. | 3/1 | 2/2 | |
| Vibrio spp. | 2/1 | 2/2 | |
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Wolinella recta | 2/1 | ||
| Wuchereria bancroftii | 1/3 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Xanthomonas maltophilia | 2/2 | ||
| Microorganism | Respiratory Tract | Gastrointestinal Tract | Genitourinary Tract |
| Zygomycetes | 1/1 | ||
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KEY: (FREQUENCY/PATHOGENICITY)
| TABLE 2 | |||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Absidia spp. | 3/1 | 1/2 | |
| Acanthamoeba spp. | 1/3 | ||
| Achromobacter xylosoxidans | 1/1 | 1/2 | |
| Acinetobacter spp. | 2/2 | 2/2 | |
| Acremonium spp. | 2/2 | ||
| Actinobacillus actinomycetemcomitans | 1/2 | ||
| Actinomadura madurae | 1/2 | ||
| Actinomyces spp. | 2/2 | 1/2 | |
| Adenoviruses | 2/2 | 2/2 | |
| Aeromonas spp. | 2/2 | ||
| Agrobacterium tumefaciens | 1/2 | ||
| Alternaria spp. | 2/2 | ||
| Ancylostoma spp. | 1/3 | ||
| Arachnia spp. | 2/2 | ||
| Arcanobacterium haemolyticum | 1/2 | ||
| Aspergillus spp . | 2/1 | 2/2 | 2/2 |
| Aureobasidium spp. | 1/1 | ||
| Azotobacter spp. | 1/1 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Bacillus anthracis | 1/3 | ||
| Bacillus spp. | 2/1 | 2/2 | |
| Bacteroides spp. | 2/2 | 1/2 | 1/2 |
| Bartonella bacilliformis | 1/3 | ||
| Basidiobolus ranarum | 1/2 | ||
| Bifidobacterium spp. | 2/2 | 1/2 | 1/2 |
| Bipolaris spp. | 1/2 | ||
| Blastomyces dermatitidis | 2/3 | 2/3 | |
| Branhamella (Moraxella) catarrhalis | 2/2 | ||
| Brucella spp. | 1/3 | ||
| Brugia spp. | 1/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Candida spp. | 3/2 | 2/2 | 2/2 |
| Cephalosporium spp. | 2/2 | ||
| Chlamydia trachomatis | 2/3 | 1/2 | |
| Cladosporium carrionii | 1/2 | ||
| Cladosporium spp. | 2/1 | ||
| Clostridium spp. | 2/2 | 1/2 | 1/2 |
| Coccidioides immitis | 2/3 | 1/3 | |
| Conidiobolus coronatus | 1/2 | ||
| Corynebacterium diphtheriae | 1/3 | 1/3 | 1/3 |
| Corynebacterium spp. | 2/2 | 2/2 | 1/1 |
| Coxsackievirus | 2/2 | ||
| Cryptococcus neoformans | 1/3 | 1/3 | |
| Cryptococcus spp. | 1/1 | ||
| Curvularia spp. | 2/1 | ||
| Cytomegalovirus | 2/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Dematiaceous fungi | 2/2 | ||
| Dirofilaria spp. | 1/3 | ||
| Dracunculus medinensis | 1/3 | ||
| Drechslera spp. | 2/1 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Ehrlichia spp. | 1/3 | ||
| Entamoeba histolytica trophozoites | 1/3 | ||
| Enterobacteriaceae | 2/2 | 2/2 | 2/2 |
| Enterococcus spp. | 2/2 | ||
| Enteroviruses | 2/2 | ||
| Epidermophyton floccosum | 2/3 | ||
| Epstein-Barr virus | 1/3 | ||
| Erysipelothrix spp. | 1/3 | ||
| Eubacterium spp. | 2/2 | 1/1 | |
| Exophiala jeanselmei | 1/1 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Flavobacterium spp. | 2/2 | ||
| Fonsecaea spp. | 1/2 | ||
| Francisella tularensis | 1/3 | ||
| Fusarium spp. | 2/2 | 2/2 | |
| Fusobacterium spp. | 2/2 | 1/2 | 1/2 |
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Geotrichum candidum | 2/1 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Haemophilus influenzae | 2/3 | ||
| Haemophilus influenzae biotype III ( H. aegyptius) | 2/3 | ||
| Herpes simplex virus | 3/3 | 2/3 | 1/2 |
| Histoplasma capsulatum | 2/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Influenzae viruses | 2/2 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Lactobacillus spp. | 1/2 | ||
| Leishmania spp. | 1/3 | ||
| Leptospira spp. | 1/3 | 1/3 | |
| Listeria spp. | 1/2 | ||
| Loa loa | 1/3 | ||
| Loboa loboi | 1/2 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Madurella spp. | 1/2 | ||
| Malassezia spp. | 2/2 | ||
| Mansonella streptocerca | 1/3 | ||
| Measles virus | 2/3 | ||
| Micrococcus spp. | 3/1 | ||
| Microsporum spp. | 2/3 | ||
| Moraxella ( Branhamella ) catarrhalis | 2/1 | ||
| Moraxella spp. | 2/2 | 2/2 | |
| Mucor spp. | 3/1 | 2/2 | |
| Mumps virus | 2/3 | ||
| Mycobacterium spp. | 2/2 | 1/2 | 1/2 |
| Mycobacterium tuberculosis group | 1/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Neisseria gonorrhoeae | 2/3 | ||
| Neisseria meningitidis | 2/3 | ||
| Neisseria spp. | 2/2 | 2/1 | |
| Neotestudina rosatii | 1/2 | ||
| Nocardia spp. | 1/2 | 1/3 | |
| Nosema spp. | 1/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Oerskovia spp. | 1/2 | ||
| Onchocerca volvulus | 1/3 | 1/3 | |
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Paecilomyces spp. | 2/1 | ||
| Papilloma viruses | 2/3 | ||
| Paracoccidioides basiliensis | 1/3 | ||
| Parainfluenza viruses | 2/2 | ||
| Pasteurella spp. | 1/2 | ||
| Penicillium spp. | 2/1 | ||
| Peptococcus spp. | 1/2 | ||
| Peptostreptococcus spp. | 2/2 | 1/2 | 1/2 |
| Plesiomonas shigelloides | 1/2 | ||
| Poxvirus | 2/3 | 1/3 | |
| Propionibacterium spp. | 3/2 | 2/2 | 2/2 |
| Pseudoallescheria boydii | 1/2 | 1/3 | |
| Pseudomonas aeruginosa | 2/2 | ||
| Pseudomonas spp. | 2/2 | 2/2 | |
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Respiratory syncytial virus | 2/2 | ||
| Rhinocladiella aquaspersa | 1/2 | ||
| Rhizomucor spp. | 2/1 | 2/2 | |
| Rhizopus spp. | 2/1 | 2/2 | |
| Rhodococcus spp. | 1/2 | ||
| Rhodotorula spp. | 2/1 | ||
| Rickettsia spp. | 2/3 | ||
| Rubella virus | 2/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Sarcinosporon inkin | 2/2 | ||
| Scopulariopsis brevicaulis | 2/2 | ||
| Spirillum minus | 1/3 | ||
| Sporothrix schenckii | 2/2 | 1/3 | |
| Staphylococcus spp. | 3/2 | 3/2 | 2/2 |
| Streptobacillus moniliformis | 1/2 | ||
| Streptococcus pneumoniae | 2/3 | ||
| Streptococcus spp. | 2/2 | 2/2 | 2/2 |
| Streptomyces somaliensis | 1/2 | ||
| Strongyloides spp. | 1/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Taenia solium cysticerci | 1/3 | ||
| Taenia solium larvae | 1/3 | ||
| Toxocara spp. | 1/3 | ||
| Toxoplasma gondii | 2/3 | ||
| Treponema pallidum | 2/3 | ||
| Treponema spp. | 2/3 | ||
| Trichophyton spp. | 2/3 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Varicella-zoster virus | 2/3 | 2/3 | 2/2 |
| Veillonella spp. | 2/2 | 1/2 | 1/2 |
| Vibrio spp. | 1/2 | 1/2 | |
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Wangiella dermatitidis | 1/2 | ||
| Microorganism |
Skin, Wound &
Burn Specimens |
Eye
Specimens |
Ear
Specimens |
| Xanthomonas maltophilia | 2/2 | ||
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