January 2019

Do I Choose Aerobic or Anaerobic Culture??

By Tanya Purvis and Amy Burklund

Sometimes it is hard to determine which culture to choose when submitting specimens to the KSVDL Clinical Microbiology Laboratory. A specimen from an inappropriate site, or an improperly collected specimen, may produce false negative results.

As a general guideline, anaerobes are usually collected from a warm, moist environment that is low in oxygen. It is important to avoid shocking the anaerobes by exposing them to oxygen or allowing the sample to become dry.

The following guidelines can be used to determine when it is appropriate to choose an ANAEROBIC culture.

  • Fluid specimens: If the specimen is collected by needle aspiration, all the air must be expelled from the barrel of the syringe prior to collection. The contents then must be transferred to a sterile tube with no additives. Be sure to completely fill the tube, so as to leave no oxygen, which might be toxic to the anaerobes during transport.
  • Tissue specimens: Tissue specimens should be >2-3 cm in diameter. Smaller tissue samples should be placed in an anaerobic transport medium (see acceptable medium at the end of the article) if it will be more than 24 hours until they are received at KSVDL.

Specimens that are suitable for anaerobic culture:

  • Normally sterile body fluids, such as pleural, peritoneal, joint and cerebrospinal fluid, bile, etc.
  • Surgical specimens from sites that normally are sterile
  • Deep abscess contents taken aseptically
  • Aspirates from deep wounds
  • Intestines (Note: Postmortem, some anaerobes of GI origin tend to overgrow in the gut and throughout the carcass, beginning as quickly as 20 minutes post-mortem in the bowel.)

Specimens that are NOT suitable for anaerobic culture:

  • Saliva
  • Vaginal or cervical specimens
  • Feces (unless looking for a particular Clostridial pathogen)
  • Tracheal swabs
  • Naso-tracheal aspirates
  • Colostomy or ileostomy effluents
  • Skin or superficial wound swabs
  • Urine

Clinical Conditions suggestive of anaerobic infections:

  • Foul-smelling discharges
  • Deep infections from penetration of cutaneous or mucosal surfaces
  • Necrotic tissue, gangrene, pseudo membrane formation
  • Gas in tissue or exudate
  • Endocarditis with a negative aerobic culture
  • Infection associated with malignancy or other disease causing tissue destruction and impaired circulation
  • Bite wounds
  • Deep abscesses
  • Septic pleuritis
  • Aspiration pneumonia
  • Fractures associated with trauma to soft tissue
  • Infections following surgery of the gastrointestinal tract
  • Septic processes such as pyometra

The Clinical Microbiology Laboratory accepts swabs, tissue and fluid samples.

If swabs are submitted, the preferred swab is the eSwab™. These eSwabs™ are acceptable swabs for aerobic, anaerobic, Mycoplasma and fungal culture and can be used for other laboratory testing as well. If you would like to have eSwabs™ sent to your clinic, please contact KSVDL Client Care at 866-512-5650 or

Tanya Purvis and Amy Burklund are Microbiologists II in the KSVDL Clinical Microbiology Laboratory.

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