Specimen Source and Potential Pathogens

• Throat, oropharynx

• “Normal” Flora - Alpha Strep, Staph sp., Neiserria sp., Gram + Rods, Anaerobes

• Strep Group A

• Corynebacterium diphtheriae

• Bordetella pertussis

• Haemophilus influenzae

Pseudomembranes when toxin produced

Corynebacterium diphtheriae

Whooping cough; confirm with fluorescent antibody test

Bordetella pertussis

Acute epiglottis in children (Do not attempt throat culture; blood culture best)

Haemophilus influenzae

• Eye

• “Normal” Flora - Same as Throat, oropharynx but in lesser numbers

• Chlamydia

• Neisseria gonorrhoea

Newborns

Chlamydia and Neisseria gonorrhoea

• Ear

• No “Normal Flora”

• Pseudomonas aeruginosa

• H. influenzae

• Streptococcus pnemoniae

• Lower Respiratory Tract (sputum)

• No normal flora

• H. influenzae

• S. aureus

• Streptococcus pneumoniae

• Klebsiella pneumoniae

• Mycoplasma pneumoniae

• Mycobacterium tuberculosis

• Legionella

• Fungi

Early morning sputum specimen best; should have less than 10-15 squamous epithelial cells per LPF

H. influenzae

• Transtrachial Aspirate, Lung Tissue

• Should be sterile

Anaerobes

• Bronchial washing

• Resident oral flora

?

• Gastric specimens

• Rapid urease test

Helicobacter pylori

• Colon

• Profuse flora

• Shigella

• Salomnella

• Campylobacter jejuni

• Yersinia enterocolitica

• Vibrio cholerae

• Toxigenic E. coli

• Clostridium difficile

Selective and differential media on stools (MAC, EMB, HE, XLD, selenite, or GN broth); subculture to selective media after 6-12 hours

Shigella

Microaerophilic at 42^oC

Campylobacter jejuni

MAC after 48 hours at room temperature

Yersinia enterocolitica

TCBS

Vibrio cholerae

Other tests better than culture

Toxigenic E. coli

EIA best

Clostridium difficile

• Urinary Tract

• Normally sterile (may be contaminated with fecal flora)

• E. coli

• Other gram neg rods

• E. faecalis

• Staphylococcus sp.

Midstream catch with proper skin penetration; >100,000 organisms per ml for infection (work up in small numbers if pure culture and white cells present)

E. coli

Genital Tract (7)

• Neisseria gonorrhoea

• Chlamydia trachomatis

• Strep Group B

• Herpes simplex

• Trichomonas vaginalis

• Treponema pallidium

• Gardnerella vaginalis

• Male - purulent discharge, do gram stain

• Female - gram stain sensitive or specific enough, do culture for GC (Thayer-Martin; selective media for GC)

Neisseria gonorrhoea

Serological tests more accurate and faster

Chlamydia trachomatis

Significant in pregnant women

Strep Group B

Parasite, wet mount

Trichomonas vaginalis

Darkfield

Treponema palladium

Implicated in vaginosis; look for “clue” cells

Gardnerella vaginalis

• CSF (6)

• Normally sterile

• H. infleunzae

• Neisseria meningitidis

• E. coli

• Strep Group B

• Cryptococcus

• Listeria

Children under 5

H. influenzae

Neonates

• E. coli

• Strep Group B

Immunocompromised patients

• Cryptococcus

• Listeria

• Deep Wounds/Abcesses

• Bypass normal flora in collection; needle aspirate better than swab

Anaerobes and Aerobes; depends on site

Superficial Wounds (pustules, dermatitis, rashes)

• S. aureus

• Strep Group A

• Pseudomonas aeruginosa

• Blood

• Normally sterile

In immunocompromised and prosthetic heart device patients, ANY organism is considered pathogenic