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Microorganisms, Body Sites, and Infections
by Scott Toste, Pharm.D., R.Ph.
Copyright © 1996-2002

Bacteria play an important part in human disease. The development of an infection depends on the complex interactions of the host's susceptibility to infection, the organism's virulence potential, and the opportunity for interaction between host and organism. To better understand the dynamics of infectious disease, I have compiled three tables that cross reference microorganisms with the body areas they usually colonize and the type of infection they cause. Table 1 lists the different types of microorganisms that commonly colonize the human body, their frequency of occurrence, and their propensity to cause disease. Table 2 list different types of infections and the commonly associated pathogens. Table 3 lists many of the common disease causing microorganisms and the types of infections that each can produce.


Table 1: Microbial Flora In & On The Human Body
Body Site Organism Frequencya Pathogenicityb
Mouth & Oropharynx Actinomyces 2+ M
Bacteroides 2+ L
Candida 2+ L
Corynebacterium 2+ L
Eikenella corrodens 1+ L
Enterobacteriaceae 1+ L
Fusobacterium 3+ M
Haemophilus influenzae 1+ M
Haemophilus, other species 3+ L
Kingella 1+ M
Lactobacillus 1+ L
Moraxella catarrhalis 2+ M
Moraxella, other species  1+ L
Mycoplasma 1+ L
Neisseria 3+ L
Peptostreptococcus 3+ L
Staph. aureus 2+ M
Staph. epidermidis 3+ L
Strep. viridams 3+ L
Strep. pyogenes 2+ H
Strep. Non-group A 3+ L
Strep pneumoniae 2+ M
Treponema 2+ L
Nasopharynx Haemophilus 1+ L
Neisseria 1+ L
Staph. aureus 1+ M
Staph. epidermidis 3+ L
Strep. viridans 2+ L
Strep. pneumoniae 1+ M
Outer Ear Enterobacteriaceae 1+ M
Pseudomonas 1+ M
Staph. epidermidis 3+ L
Strep. pneumoniae 1+ M
Eye Haemophilus 1+ L
Staph. Epidermidis 3+ L
Stomach Helicobacter pylori 1+ H
Lactobacillus 1+ L
Streptococcus 1+ L
Small Intestine Bacteroides 2+ M
Candida 1+ M
Clostridium 1+ M
Enterobacteriaceae 1+ M
Enterococcus 2+ M
Fusobacterium 2+ L
Lactobacillus 3+ L
Peptostreptococcus 2+ L
Staphylococcus 1+ L
Streptococcus 2+ L
Large Intestine Bacteroides 3+ H
Candida 1+ M
Clostridium 3+ M
Corynebacterium 1+ L
Enterobacteriaceae 3+ M
Enterococcus 3+ M
Fusobacterium 3+ M
Lactobacillus 2+ L
Mycobacterium 1+ L
Peptostreptococcus 3+ M
Pseudomonas 1+ L
Staphylococcus 1+ L
Streptococcus 1+ L
Anterior Urethra Candida 1+ M
Corynebacterium 3+ L
Enterobacteriaceae 1+ M
Enterococcus 1+ L
Gardneralla vaginalis 1+ L
Lactobacillus 3+ L
Mycoplasma 1+ M
nonpathogenic Neisseria 1+ L
Staph. epidermidis 2+ L
Streptococcus 1+ L
Ureaplasma 1+ M
Actinomyces 2+ M
Bacteroides 2+ M
Candida 2+ M
Clostridium 1+ M
Enterobacteriaceae 2+ M
Enterococcus 2+ L
Fusobacterium 2+ M
Gardneralla vaginalis 3+ L
Lactobacillus 3+ L
Mobiluncus 2+ H
Mycoplasma 2+ M
nonpathogenic Neisseria 2+ L
Staphylococcus 3+ L
Streptococcus 2+ L
Torulopsis 2+ M
Ureaplasma 2+ M
Skin Candida 1+ M
Clostridium 1+ L
Corynebacterium 3+ L
Proprionibacterium 3+ L
Staph. aureus 1+ H
Staph. epidermidis 3+ M
Strep. pyogenes 1+ L
 aFrequency of recovery from healthy individuals: 1+, rare; 2+, frequently isolated; 3+, commonly present.
 bCause of disease: H. high; M, moderate; L, low.
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Table 2: Various Infections & Suspected Organisms
Type of Infection Suspected Organism
Pharyngitis Strep. pyogenes
Bronchitis, Otitis Haemophilus influenza, Strep. pneumoniae, Moraxella catarrhalis
Acute Sinusitis Strep. pneumoniae, Haemophilus influenza, Moraxella catarrhalis
Chronic Sinusitis anaerobes, Staph. aureus
Epiglotis Haemophilus influenza
Community Acquired Normal host Strep. pneumoniae, viral, Mycoplasma
Aspiration Normal aerobic & anaerobic mouth flora
Pediatric, COPD Strep. pneumoniae, Haemophilus influenza
Alcoholic Strep. pneumoniae, Klebsiella
Hospital Acquired Aspiration Mouth anaerobes, Gram ( - ) rods, Staph. aureus
Neutropenic Fungi, Gram ( - ) rods, Staph. aureus
AIDS Fungi, pneumocystis, Legionella, Nocardia, Strep. pneumoniae
Urinary Tract
Community Acquired E. coli, other Gram ( - ) rods, Staph. aureus, Staph. epidermidis, Enterococcus
Hospital Acquired Resistant Gram ( - ) rods, Enterococcus
Skin/Soft Tissue
Cellulitis Strep. pyogenes, Staph. aureus
IV Catheter Site Staph. aureus, Staph. epidermidis
Surgical Wound Staph. aureus, Gram ( - ) rods
Diabetic Ulcer Staph. aureus, Gram ( - ) rods, anaerobes
Furuncle Staph. aureus
Intra-Abdominal Bacteroides fragilis, E. coli, Enterococcus
Gastroenteritis Salmonella, Shigella, Helicobactr, Clostridium, Amoeba, Giardia, viral, E. coli
Subacute Strep. viridans
Acute IV Drug Abuser Staph. aureus, Gram ( - ) rods, Enterococcus, fungi
Prosthetic Valve Staph. epidermidis
Osteomyelitis/ Septic Arthritis Staph. aureus, Strep, Gram ( - ) rods
<2 Months Old E. coli, group B Strep, Listeria
2 Months -12 Years Haemophilus influenzae, Strep.pneumoniae, Neisseria meningitids
Adults Strep. pneumoniae, Neisseria meningitids, Gram ( - ) rods
Post-neurosurgery Staph. aureus, Gram ( - ) rods
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Table 3: Pathogenic Organisms & Associated Infections
Organism Infection
Acinetobacter oppurtunistic infections
Actinomyces cervicofacial, pulmonary, abdominal, pelvic or CNS (brain abscess) actinomycosis
Bacillus anthracis anthrax
Bacillus cereus food poisoning, bacteremia
Bacteroides abscess infection, bacteremia, endocarditis, soft tissue infection, gangrene
Bordetella pertussis pertussis (whooping cough)
Borrelia burgdorferi Lyme disease
Brucella Brucellosis (Malta fever)
Campylobacter jejuni enteritis, bacteremia, septic abortion, reactive arthritis
Chlamydia pneumoniae atypical pneumonia, bronchitis, pharyngitis, sinusitis
Chlamydia trachomatis nongonococcal urethritis, pelvic inflammatory disease, proctocolitis, epididymitis
Clostridium botulinum infant botulism, food borne botulism, wound botulism
Clostridium difficile antibiotic-associated diarrhea, pseudomembranous colitis
Clostridium perfringens bacteremia, gas gangrene, soft tissue infections, food poisoning
Clostridium tetani tetanus
Citrobacter lower respiratory tract infection, UTI, hospital associated bacteremia, neonatal CNS infection
Corynebacterium jeikeium septecemia, endocarditis, foreign body infection
Corynebacterium other than jeikeium UTI, skin infections, bacteremia, pharyngitis, pneumonia, diphtheria (C. diphtheria)
Enterobacter lower respiratory tract infection, UTI, hospital associated bacteremia, burn wound infections
Enterocoocus bacteremia, endocarditis, osteomyelitis, UTI, intraabdominal infection
Escherichia coli UTI, hemorrhagic colitis, hemolytic uremic syndrome, septicemia, neonatal meningitis, gastroenteritis
Gardnerella vaginalis bacterial vaginosis, UTI, bacteremia
Haemophilus ducreyi genital ulceration with regional adenopathy
Haemophilus influenza pneumonia, meningitis, epiglotitis, otitis
Klebsiella pneumonia, bronchitis, UTI, bacteremia, wound infection, billiary tract infection
Legionella Legionaire's Disease (pneumonia), Pontiac fever
Leptospira leptospirosis, Weil's Disease
Listeria monocytogenes meningitis, bacteremia, endocarditis, cerebritis, listerosis in pregnancy, granulomatosis infantiseptica
Moraxella catarrhalis sinusitis, otisitis media, acute urethritis, respiratory tract infections
Mycobacterium tuberculosis, opportunistic systemic infections
Mycoplasma community acquired pneumonia, tracheobronchitis, pharyngitis
Neisseria gonorrhae gonorrhea
Neisseria menigitidis meningitis, urethritis, arthritis, pneumonia
Nocradia pneumonia, brain abscess, disseminated nocardial infection, mycetoma, cellulitis, lymphocutaneous nodules, keratitis
Pasteurella animal bite wound infections, respiratory tract infection, oppotunistic infection
Proteus pneumonia, UTI, wound infection, chronic destructive ear infection, septicemia
Pseudomonas aeruginosa bacteremia, endocarditis, pulmonary infection, ear infection, burn wound infection, UTI, gastroenteritis, eye infection, musculoskeletal infection
Pseudomonas cepacia pulmonary infection in cystic fibrosis
Rickettsia Rocky Mountain Spotted Fever
Salmonella enteritis, septicemia, enteric fever, typhoid fever
Serratia lower respiratory tract infection, UTI, bacteremia, wound infection
Shigella Shigellosis dysentery), reactive arthritis
Staph. aureus scaled skin syndrome, cutaneous infections, toxic shock syndrome, endocarditis, pneumonia, food poisoning, septic arthritis, osteomyelitis, septicemia
Staph. epidermidis endocarditis, foreign body infection, osteomyelitis, UTI
Strep. pneumoniae pneumonia, sinusitis, otitis media, meningitis, bacteremia
Strep. pyogenes pharyngitis, scarlet fever, streptococcal toxic shock syndrome, erysipelas, pyoderma, rheumatic fever, glomerular nephritis
Strep. viridans bacteremia, endocarditis, dental caries
Strep. Group B neonatal infections (bacteremia, menigitis, pneumonia, postpartum sepsis)
Treponema pallidum syphilis
Ureaplasma nongonococcal urethritis, postpartum bacteremia, urethroprostatitis, epdidymitis, septic arthritis, chorioamnionitis, respiratory infection in newborns, newborn meningitis
Vibrio cholerae cholera
Yersinia enterocolitica enterocolitis, polyarthritis, liver abscess, septicemia
Yersinia pestis plague (Bubonic, Speticemic, Pneumonic)
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Copyright © 1996-2002, Scott Toste, Pharm.D. R.Ph.