Geisinger Medical Laboratories
Microbiology Specimen Collection Instructions



  1. Special collection procedures are essential to recovery of anaerobic bacteria since even brief exposure to oxygen may be detrimental to their survival. The anaerobic specimen collector protects anaerobic bacteria from exposure to toxic amounts of oxygen until the specimen is inoculated on appropriate medium in an anaerobic environment.
  2. Use the Anaerobic Transport Media for collection and transportation of anaerobic specimens for up to 72 hours.
  3. There are several kinds of specimens that usually should not be cultured for anaerobes. These include coughed sputum, gastric contents, skin/ulcers/decubiti/superficial wounds, feces, urine, nasopharynx secretions, vaginal secretions, cervical, uterine, seminal fluid, perirectal, BALs, and small bowel contents.
  4. Principle
    1. ATM is a mineral salt base semisolid agar with reducing agents to maintain anaerobic conditions. It also contains a chemical indicator. In the absence of oxygen, this indicator will remain clear; in the presence of oxygen, the indicator turns purple.
    2. The air space in the ATM is filled with CO2 , a gas that is heavier than air.
  5. Precautions/Warning:  Observe the following precautions in connection with the anaerobic specimen collector:
    1. Do not use if the tube is opened or damaged.
    2. Do not use if the indicator is purple.


Anaerobic Transport Media (ATM): Order from GML Client Services. Store at room temperature. Do not expose to sunlight. Observe expiration date.

  1. Collection of liquid or purulent specimens.
  1. Collect specimen from deep within the wound with sterile syringe and needle. If possible, the skin should be disinfected before needle puncture. Air trapped in syringe should be expelled by holding syringe and needle upright. Expel air at tip of syringe into alcohol saturated sponge. Set aside with sponge or shield on needle.
  2. Peel apart package and remove transport. Do not touch or contaminate rubber port in the lid.
  3. Inject up to 5 ml of fluid into the transport media through the rubber port. If greater than 5 ml of fluid is obtained, place the entire volume (up to 50 ml) in a sterile screw-cap specimen cup.
  4. Transport to the laboratory.
  5. Fluid is submitted in the ATM , sterile cup or sterile tubes. This is also acceptable for routine aerobic culture, fungal, and AFB culture.

B.  Collection of Tissue

  1. If a tissue is small enough to easily fit inside the ATM  tube, simply uncap the tube and, while holding the tube upright, drop the tissue onto the agar surface and replace the tube cap.
  2. If a tissue is too large to fit into the ATM, place it on a piece of sterile gauze moistened with physiolologic saline inside a sterile screw cap collection cup.
  3. Tissue submitted in ATM  or in a sterile cup is also acceptable for routine aerobic, fungal and AFB culture.

C.  Collection by ESwab (Swabs are not the preferred collection method for anaerobic culture).

  1. Peel apart package and remove the swab.
  2. Using the swab, obtain specimen using aseptic technique to avoid superficial contaminants. It may be necessary to separate the wound margins or make a small lance in a closed abscess before extending the tip of the swab deeply into the wound. Take care not to touch the adjacent skin margins.
  3. Remove the tube cap while holding the tube upright.
  4. Place the swab into the tube and break it off at the score line.
  5. Place the cap back on the tube and tighten the cap.
  6. Do not place more than one swab in each ESwab tube.
  7. Do not remove the liquid media from the tube. 

Be sure to label all specimens properly and take to laboratory immediately.


  1. Within hospital: Transport as soon as possible to the Microbiology lab. If
       sent through the tube system, be sure to adequately cushion the ATM to
       prevent breakage.
  2. Via the courier: Transport as soon as possible. Store the specimen at room
       temperature for up to 72 hours if same-day transport is not possible.

Koneman EW, 1988. Color Atlas and Textbook of Diagnostic Microbiology. JD Lippincott, Philadelphia.

Revised: 3/4/2011

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