Microorganisms, Body Sites, and Infections

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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 Frequency^a Pathogenicity^b

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

Vagina

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

Respiratory

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

Pneumonia

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

Endocarditis

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

Menigitis

<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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Body Site	Organism	Frequency^a	Pathogenicity^b
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
Eye	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
Vagina	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

Type of Infection		Suspected Organism
Respiratory
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
Pneumonia
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
Endocarditis
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
Menigitis
<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

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)