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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