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Specimen Collection

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Bacteriology, Mycology , and Mycobacteriology Specimen Collection Guidelines^a

Specimen Type	Collection Guidelines Device and/or minimum vol		Time and Temp Local Courier Transport b or local storage		Replica limits	Comment(s)
Abscess	Remove surface exudate by wiping with sterile saline or 70% EtOH.					Tissue or fluid is always superior to a swab specimen. If swabs must be used, collect 1, one for culture and one for Gram staining. Preserve them with Stuart's or Amies medium.
Open	Aspirate if possible, or pass a swab deep into the lesion and firmly sample the lesion's advancing edge.	Aerobic swab transport system	< 2 h, RT	< 24 h, RT	1/day/source	A sample from the base of the lesion and a sample from the abscess wall are most productive.
Closed	Aspirate abscess wall material with needle and syringe. Aseptically transfer all material into anaerobic transport device.	Anaerobic transport system, > 1 ml.	< 2 h, RT	< 24 h, RT	1/day/source	Sampling of the surface area can introduce colonizing bacteria not involved in the infectious process.
Bone marrow	Prepare puncture site as for surgical incision	Inoculate a pediatric l.5 ml. lysis centrifugation tube.	< 16 h, RT if in culture bottle or tube.	< 16 h, RT	1/day	Small volumes of bone marrow may be inoculated directly onto culture media.
Burn	Clean and debride the wound prior to specimen collection.	Tissue placed in a screw-cap container. Aerobic culture. Swab exudate.	< 2 h, RT	< 24 h, RT	1/day/source	A 3- to 4- mm punch biopsy is optimum when quantitative cultures are ordered. Process for aerobic culture only. Quantitative culture may or may not be valuable. Surface cultures of burns may be misleading.
Catheter: I.V.	1. Cleanse the skin around the catheter site with alcohol. 2. Aseptically remove catheter and clip a 5-cm distal tip of the catheter directly into a sterile tube. 3. Transport directly to microbiology to prevent drying.	Sterile screw-cap tube or cup	< 15 min., RT	< 24 h, 4^oC	None	Acceptable i.v. catheters for semiquantitative culture (Maki method): central, CVP, Hickman, Broviac, peripheral, arterial, umbilical, hyperalimentation, Swan-Ganz.
Foley	Do not culture since growth represents distal urethral flora.					Not acceptable for culture.
Cellulitis	1. Cleanse site by wiping with sterile saline or 70% alcohol. 2. Aspirate the area of maximum inflammation (commonly the center rather than the leading edge) with a fine needle and syringe. 3. Draw small amount of sterile saline into syringe and aspirate into sterile screw-cap tube.	Sterile tube (syringe transport not recommended)	< 15 min., RT	< 24 h, RT	None	Yield of potential pathogens is only 25-35%.

Specimen Type	Collection Guidelines Device and/or minimum vol		Time and Temp Local Courier or Transport ^b local storage		Replica limits	Comments
CSF	1. Disinfect site with 2% iodine tincture. 2. Insert a needle with stylet at L3-L4, L4-L5, or L5-S1 interspace. 3. On reaching the subarachnoid space, remove the stylet and collect 1-2 ml. of fluid in each of three leakproof tubes.	Sterile screw-cap tube Minimum amount required: bacteria, > 1 ml; fungi, > 2 ml; AFB, > 2 ml; virus, > 1 ml;	Bacteria: never refrigerate; < 15 min, RT Virus: transport on ice; < 15 min, 4^oC	< 24 h, RT < 72 h, 4^oC	None	Obtain blood cultures also. If only 1 tube of CSF is collected, it should be submitted to microbiology first; otherwise submit tube 2. Aspirate of brain abscess or a biopsy may be necessary to detect anaerobic bacteria or parasites.
Decubitus ulcer	See comment: A swab specimen is not the specimen of choice. 1. Cleanse surface with sterile saline. 2. If a sample biopsy is not available, vigorously swab the base of the lesion. 3. Place the swab in appropriate transport system.	Swab aerobic cultures or anaerobic system (for tissue)	< 2 h, RT	< 24 h, RT	1/day/source	A decubitus swab provides little clinical information; discourage collection of it. A tissue biopsy sample or a needle aspirate is the specimen of choice.
Ear: Inner	Tympanocentesis should be reserved for complicated, recurrent, or chronic persistent otitis media. 1. For an intact ear drum, clean the ear canal with soap solution and collect fluid via the syringe aspiration technique 2. For a ruptured ear drum, collect fluid on a flexible-shaft swab via an auditory speculum.	Sterile tube, or anaerobic system.	< 2 h, RT	< 24 h, RT	1/day/source	Throat or nasopharyngeal cultures are not predictive of agents responsible for otitis media and should not be submitted for that purpose.
Outer	1. Use a moistened swab to remove any debris or cruse from the ear canal. 2. Obtain a sample by firmly rotating the swab in the outer canal.	Aerobic culture	< 2 h, RT	< 24 h, 4^oC	1/day/source	For otitis externa, vigorous swabbing is required since surface swabbing may miss streptococcal cellulitis.
Eye: Conjunctiva	1. Sample both eyes using separate swabs (premoistened with sterile saline) by rolling over each conjunctiva. 2. Inoculate media at time of collection. 3. Smear swabs onto 2 slides for staining.	Direct culture inoculation: BAP and CHOC or aerobic swab transport.	Plates: < 15 min. RT Swabs: < 2 h, RT	< 24 h, RT	None	If possible, sample both conjunctivae, even if only one is infected, to determine the indigenous microflora. The uninfected eye can serve as a control with which to compare the agents isolated from the infected eye.
Corneal Scrapings	1. Obtain conjunctival swab specimens as described above. 2. Instill 2 drops of local anesthetic. 3. Using a sterile spatula, scrape ulcers or lesions and inoculate scraping directly onto media. 4. Apply remaining material to 2 clean glass slides for staining.	Direct culture inoculation, blood, CHOC, and SAB agar	< 15 min. RT	< 24 h, RT	None	It is recommended that swabs for culture be taken prior to anesthetic application, whereas corneal scrapings can be obtained afterward.