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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IFU-10492[A]