Specimen collection, transport and methods for specimen collection for diagnosis of anaerobes

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Proper collection of specimens is of utmost importance to avoid contamination of the collected specimen with normal microbial flora and prompt transport to the laboratory for processing is very essential for the diagnosis of infectious diseases.

Isolation of anaerobes from clinical specimens, determination of the numbers of anaerobes in the specimen, and establishing the clinical significance depend on proper collection and transport of the specimen.The laboratory supervisor or head must provide the clinicians with guidelines for the optimal amount and type of specimen required for anaerobic culture and must stress the need and importance of the transport of the properly collected specimen to the laboratory without delay.

Specimen collection for anaerobes

  • The best specimen for anaerobic culture is obtained by using a needle and syringe.
  • Tissue and biopsy specimens are also good for anaerobic culture.
  • Swabs for anaerobic culture should be discouraged or rejected as the specimen volume collected by swab is small; it reduces the probability of isolating the anaerobic pathogens, if present as well as many organisms tend to adhere to the fibers of the swab, which also greatly reduces the recovery of anaerobes.

Specimen transport for anaerobes

  • Transport time depends on the volume and nature of the specimen. Large volumes of purulent material and large pieces of tissue maintain the viability of anaerobes for many hours. Swabs (when necessary) and small volumes of aspirated material, biopsy samples, or curettings should be transported in an anaerobic transport system.
  • Avoid extremes of heat or cold. If delays are unavoidable, hold the specimen at room temperature until further processing.
  • Do not transport material for culture in the needle and syringe. Needle transport is very unsafe because there is always the risk of a needle stick injury, and syringe transport also poses a risk of specimen being expelled during transport, creating a threat to personnel and the environment
  • Transfer aspirated material to an anaerobic transport vial. Large volumes of purulent material may be transported in a sterile screw-cap tube.
  • Provide information regarding specific source, clinical impression, special status of patient, or unusual suspected organisms.
  • Good communication between the clinical microbiology laboratory and the clinicians will ensure the collection and transport of the best possible specimen for anaerobic culture.
  • Place tissue samples, biopsy samples, or curettings into an anaerobic transport device or a sterile tube or petri plate. Place all of this into a sealable plastic bag (Becton Dickinson [BD], Oxoid, Mitsubishi) that generates an anaerobic atmosphere. Large pieces of tissue can be transported in a wide mouthed anaerobic transport device or in a sterile tube or jar.
  • If specimens must be collected by swab, transport swabs in a tube containing anaerobic transport medium

Methods of specimen collection for anaerobes


Prepare the surface first by applying povidone iodine and letting it remain there for at least 1 minute. Aspirate material with needle and syringe. When the use of needle is contraindicated, use a flexible plastic catheter or syringe with no needle to aspirate the material

Sinus tract or deep-wound drainage

Prepare the surface first by applying povidone iodine for one minute. Aspirate the material with a small flexible plastic catheter and syringe or collect curettings of material from deep within the tract or wound.

Decubiti and other surface ulcers

Culture results on specimens from decubiti and other surface ulcers can be very misleading unless special precautions are taken while collecting specimen. Prepare the surface first by applying povidone iodine for 1 minute. Analyze only the specimens obtained from punch biopsy, aspirated material obtained by needle and syringe or on small curettings of material from deep tissue at the wound margin. Swabs from decubiti and other surface ulcers are unacceptable for anaerobic culture.

Pulmonary specimens

Collect lung tissue, transtracheal aspirate, percutaneous aspirate, transcutaneous aspirate, and bronchial brushings via double-lumen catheter. Use shielded catheters to obtain specimens from pulmonary sources to obtain proper specimens. Otherwise the laboratory will identify normal respiratory flora and providing useless information. Bronchial washings and other respiratory specimens not obtained via double-lumen catheters are not appropriate for anaerobic culture.

Female genital tract specimens

Disinfect the cervical opening by swabbing it with povidone-iodine. Sample the upper genital tract by using a double-lumen collector and selfcontained transport system. The Pipelle system obtains cellular material from the uterine wall by suction, and the AccuCulShure uses a double lumen collector that reduces the potential of contamination.  Specimens collected by laparoscopy, culdocentesis, or surgery are appropriate for anaerobic culture.Culture intrauterine devices anaerobically for Actinomyces species or Eubacterium nodatum.

Urinary tract

Obtain urine specimen via suprapubic bladder tap.

In some cases, when aspiration or biopsy is not feasible (e.g., animal bite wounds), an anaerobic swab may be used for anaerobic culture. Anaerobic swabs are the least desirable specimen for a number of reasons, including small volume of specimen, greater chance of contamination with normal microbial flora, excessive dryness, bacterial adherence to cotton fibers, and poor Gram stain quality. There is poor recovery of anaerobic organisms from some swab transport systems beyond 24 hours. If a swab must be used, a swab using polyurethane adsorbing material instead of cotton, with two swabs (one for culture and the other for smear), may provide a useful alternative. An aspirate or biopsy sample or even a very small slice of tissue may often be a better specimen than a swab for anaerobic culture.

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