Dr. Tessa LeCuyer in the microbiology lab
Virginia Tech Animal Laboratory Services (ViTALS) Microbiology lab

Guidelines for Microbiology Samples and Submissions

  • You may always call the laboratory for assistance with sample collection and transport.
  • In general, keep samples for microbiology testing cold. Exceptions include the following:
    • specimens for dermatophyte culture, blood culture, cerebral spinal fluid, joint fluid, and specimens for which only anaerobic culture will be requested.
  • Submission of tissues and fluids are preferable to the use of swabs for sample collection. When swabs must be used, use appropriate transport media, and submit multiple swabs per site if possible.
  • Anaerobic transport systems are appropriate for most bacteria (facultative and obligate anaerobes).
  • It is very important that specimens for bacteriology stay moist. Swabs and small pieces of tissue may be placed in a small volume of saline or may be transported in a bacterial transport system. It is difficult to recover tissue specimens from transport systems designed for swabs, so wider-neck systems like Port-a-Cul tubes are preferred.
  • Samples in formalin, alcohol, EDTA or heparin are never appropriate for culture.
  • MRSA/MRSP and Strep equi screen tests should be selected when the submitter only wants to rule/in that pathogen. If the diagnosis is open, an aerobic culture should be selected instead, which will include looking for any likely pathogens in the specimen.
  • Let the laboratory know if you have particular bacterial organisms on your differential diagnosis list. Some organisms, such as Nocardia sp., can require prolonged incubation times that can be accommodated if we know a particular organism is a differential diagnosis for a case.

Best Practices for Sample Collection

Source Collection Method(s) Container Temperature Typical Test(s)
Abscess
  • Aspiration of exudate from intact abscess
  • Exudate
  • Section of abscess wall
  • Swab
  • Red top tube
  • Bacterial transport system
  • Sterile bag or jar
  • Refrigerate
  • Aerobic, Anaerobic
Blood
  • Surgical prep
  • 2-3 samples ideal
  • Sample when febrile if possible
  • Blood culture bottle
  • Room
    temperature
  • Blood culture
CSF
  • Surgical prep
  • Larger volume preferable due to bacterial numbers
  • Blood culture bottle
  • Fluid transport vial
  • Sterile container/RTT
  • Room
    temperature
  • Blood culture OR Aerobic, Anaerobic
Dermatophyte
  • Clean lesion with 70% alcohol
  • Pluck hair from lesion edge
  • Toothbrush
  • Sealed bag or envelope
  • Room
    temperature
  • Fungal Culture
Eye
  • Remove crusts prior to sampling
  • Topical dyes and anesthetics may interfere — rinse first
  • Bacterial transport system
  • Refrigerate
  • Aerobic
Feces
  • ~5 g per rectum or immediately after defecation
  • Sealed, leak-proof jar or bag
  • Cary-Blair for Salmonella only
  • Refrigerate
  • Fecal Screen
Joint
  • Surgical prep and collect fluid
  • Synovium
  • Blood culture bottle
  • Fluid transport vial
  • Sterile container
  • Room
    temperature
  • Blood culture OR Aerobic, Anaerobic, Optional: Mycoplasma
Lower Respiratory
  • Transtracheal Wash
  • Bronchoalveolar Lavage
  • Aspirate
  • Avoid upper respiratory tract sampling when possible
  • Submit entire TTW or BAL volume in a sterile container
  • Refrigerate
  • Aerobic, Optional: Mycoplasma
Milk
  • 3-5 ml after teat disinfection and stripping
  • Sterile container
  • Refrigerate or freeze if ³48 hour delay
  • Aerobic, Optional: Mycoplasma
Outer Ear
  • Clean debris from canal with saline
  • Bacterial transport system (gel systems may interfere with Gram stains)
  • Refrigerate
  • Aerobic
Upper Respiratory
  • Biopsy
  • Swab of nasal cavity or nasopharynx
  • Sterile container
  • Bacterial transport system
  • Refrigeration
  • Aerobic
Urine
  • Cystocentesis
  • Clean catheterization
  • Mid-stream free catch
  • Indwelling catheter samples are suboptimal
  • Sterile jar
  • Red top tube
  • Refrigeration
  • Aerobic
Uterine
  • Double guarded swab
  • Biopsy
  • Transport system
  • Sterile container
  • Refrigeration
  • Aerobic, +/- anaerobic
Skin
  • Surgical prep and biopsy
  • Pustule aspiration
  • Swab of affected area after cleaning
  • Sterile container
  • Transport system
  • Refrigeration
  • Aerobic
Necropsy
  • Use sterile instruments
  • Collect samples before opening the GI tract
  • Tissue samples are ideal – should be ~5g
  • Place each tissue in a separate bag
  • Tie off the ends of segment of intestine
  • Whirl-Pak Bags
  • Sterile Container
  • Refrigeration
  • Aerobic