Bacteriology, Mycology, and Mycobacteriology Specimen Collection Guidelines
Specimen Type | Collection | Time and Temp |
Replica limits |
Comment(s) | ||
Guidelines | Device and/or minimum vol | Local Transportb | Courier or local storage | |||
Abscess |
Remove surface exudate by wiping with sterile saline or 70% ETOHa. |
ESwab transport system, sterile tube |
2 h or less, RTa |
24 h or less, RTa |
1/day/source |
Tissue or fluid is always superior to a swab specimen. If swabs must be used, collect two: 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. |
ESwab transport system |
2 h or less, RTa |
24 h or less, RTa |
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 or sterile tube. |
Transport Tube, 1 ml or more, or sterile tube. |
2 h or less, RTa |
24 h or less, RTa |
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 1.5 ml. lysis centrifugation tube. |
16 h or less, RTa if in culture bottle or tube. |
16 h or less, RTa |
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 or less, RTa |
24 h or less, RTa |
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: |
1. Cleanse the skin around the catheter site with alcohol. |
Sterile screw-cap tube or cup |
15 minutes or less, RTa |
24 h or less, 4oC |
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. |
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Not acceptable for culture. |
Cellulitis |
1. Cleanse site by wiping with sterile saline or 70% alcohol. |
Sterile tube (syringe transport not recommended) |
15 minutes or less, RTa |
24 h or less, RTa |
None |
Yield of potential pathogens is only 25-35%. |
CSFa |
1. Disinfect site with 2% iodine tincture. |
Sterile screw-cap tube |
Bacteria: never refrigerate; 15 min or less, RT Virus: transport on ice; 15 min or less, 4oC |
24 h or less, RT
72 h or less, 4oC |
None |
Obtain blood cultures also. If only 1 tube of CSF is collected, it should be submitted to microbiology first; otherwise submit tube 2. |
Decubitus ulcer |
See comment: A swab specimen is not the specimen of choice. |
ESwab or Transport Tube, or sterile tube (for tissue) |
2 h or less, RTa |
24 h or less, RTa |
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: |
Tympanocentesis should be reserved for complicated, recurrent, or chronic persistent otitis media. |
Sterile tube, or Transport Tube. |
2 h or less, RTa |
24 h or less, RTa |
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 crust from the ear canal. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, 4oC |
1/day/ source |
For otitis externa, vigorous swabbing is required since surface swabbing may miss streptococcal cellulitis. |
Eye: |
1. Sample both eyes using separate swabs (premoistened with sterile saline) by rolling over each conjunctiva. |
Direct culture inoculation: BAPa and CHOCa or ESwab transport system. |
Plates: 15 min or less, RTa Swabs: 2 h or less, RTa |
24 h or less, RTa |
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 |
1. Obtain conjunctival swab specimens as described above. |
Direct culture inoculation, blood, CHOCa, and SAB agar |
15 minutes or less, RTa |
24 h or less, RTa |
None |
It is recommended that swabs for culture be taken prior to anesthetic application, whereas corneal scrapings can be obtained afterward. |
Fluid or aspirates |
Prepare eye for needle aspiration of fluid. |
Sterile screw-cap tube or direct inoculate of small amount of fluid onto media. |
15 minutes or less, RTa |
24 h or less, RTa |
1/day |
Include fungal media. Anesthetics may be inhibitory to some etiologic agents. |
Feces: |
1. Pass directly into a clean, dry container. |
Clean, leak-proof, wide-mouth container or a Cary-Blair transport system; 2 g or greater |
Unpreserved: 1 h or less, RT.
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24 h or less, 4oC
48 h or less, RTa or 4oC |
1/day |
Do not perform routine stool cultures on patients whose length of stay was greatter than 3 days and the admitting diagnosis was not gastroenteritis. Culture and toxin tests for Clostridium difficile should be considered in these cases. |
C. difficile |
Pass liquid or soft stool directly into a clean, dry container. Soft stool is defined as stool assuming the shape of its container. |
Sterile, leak-proof, wide-mouth container; 5 ml or greater |
1 h or less, RT; |
2 days, 4oC, for culture; |
1 /2 days |
Patients should be passing 5 or more liquid or soft stools per 24 h. Testing of formed or hard stool is often unproductive and may indicate only commensal carriage. |
Escherichia coli |
Pass liquid or bloody stool into a clean, dry container. |
Sterile, leak-proof wide-mouth container or Cary-Blair transport system |
Unpreserved: |
24 h or less, 4oC 48 h or less, RTa |
1/day |
Bloody or liquid stools collected within 6 days of onset from patients with abdominal cramps have the highest yield. |
Leukocytes |
Pass feces directly into a clean, dry container. Transport specimen to lab within 1 h of collection or transfer to ova and parasite transport system (SAF). |
Sterile, leak-proof, wide-mouth container 2 ml or greater |
Unpreserved: |
24 h or less, 4oC Indefinite, RTa |
1/day |
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Rectal swab |
1. Carefully insert a swab ≈ 1 in. beyond the anal sphincter. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Reserved for detecting Neisseria gonorrhoeae, Shigella spp., Campylobacter spp., HSV, and anal carriage of group B Streptococcus spp. or for patients unable to pass a specimen. |
Fistulas |
See Abscess |
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Fluids: abdominal, amniotic, ascites, bile, joint, paracentesis, pericardial, peritoneal, pleural, synovial, thoracentesis |
1. Disinfect overlying skin with 2% iodine tincture. |
Blood culture bottle for bacteria and yeast or sterile screw-cap tube or Transport Tube. Bacteria, 1 ml or greater; |
15 minutes or less, RTa |
24 h or less, RTa. Pericardial fluid and fluids for fungal cultures: |
None |
Amniotic and culdocentesis fluids should be transported in anaerobic system and need not be centrifuged prior to Gram staining. Other fluids are best examined by Gram staining of a cytocentrifuged preparation. See Table 4. |
Gangrenous tissue |
See Abscess |
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Discourage sampling of surface or superficial tissue; tissue biopsy or aspirates are preferred. |
Gastric: wash or lavage |
Collect early in the morning before patients eat and while they are still in bed. |
Sterile, leak-proof container. |
15 minutes or less, RTa |
24 h or less, 4oC |
1/day |
The specimen must be processed promptly since mycobacteria die rapidly in gastric washings. |
Genital (female): |
1. Aspirate via amniocentesis, cesarean section, or intrauterine catheter. |
Transport Tube or sterile tube, 1 ml or greater |
15 min or greater, RTa |
24 h or greater, RTa |
None |
Swabbing or aspiration of vaginal membrane is not acceptable because of the potential for culture contamination by commensal vaginal flora. |
Bartholin |
1. Disinfect skin with a iodine preparation. |
Transport Tube |
2 h or less, RT |
24 h or less, RTa |
1/day |
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Cervical |
1. Visualize the cervix using a speculum without lubricant. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
See information on virus and chlamydia collection and transport needs. |
Cul-de-sac |
Submit aspirate or fluid |
Transport Tube greater than 1 ml |
2 h or less, RTa |
24 h or less, RTa |
1/day |
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Endometrial |
1. Collect transcervical aspirate via a telescoping catheter. |
Transport Tube 1 ml or greater |
2 h or less, RTa |
24 h or less, RTa |
1/day |
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Products of |
1. Submit a portion of tissue in a sterile container. |
Sterile tube or Transport Tube |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Do not process lochia. Culture of this specimen may or may not provide clinically relevant results, and such results can be misleading. |
Urethral |
Collect 1 h after patient has urinated. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
If no discharge can be obtained, wash the external urethra with betadine soap with rinse with water. Insert a urethrogenital swab 2-4 cm into the urethra; rotate swab for 2 seconds. |
Vaginal |
1. Wipe away an excessive amount of secretion or discharge. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
For intrauterine devices, place entire device in a sterile container and submit at RTa. |
Genital (female or male): |
1. Clean the lesion with sterile saline and remove the surface of the lesion with a sterile scalpel blade. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Specimens for syphilis should not be submitted for culture. |
Genital (male): |
1. Cleanse the glans with soap and water. |
ESwab transport system or sterile tube |
2 h or less, RTa |
24 h or less, RTa |
1/day |
More relevant results may be obtained by adding a urine specimen immediately before and after massage to indicate urethral and bladder organisms. |
Urethra |
Insert a urethrogenital swab 2-4 cm into the urethral lumen, rotate the swab, and leave it in place for at least 2 seconds to facilitate absorption. |
ESwab transport system. GC selective place |
2 h or less, RTa |
24 h or less, RTa |
1/day |
See information on virus and chlamydia collection and transport needs. |
Hair: |
1. With forceps, collect at least 10-12 affected hairs with the base of the shaft intact. |
Clean container, 10 hairs |
24 h or less, RTa |
1/day/ site |
Collect scalp scales, if present, along with scrapings of active borders of lesions. Note any antifungal therapy taken recently. |
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Nail: |
1. Wipe the nail with 70% alcohol using gauze (not cotton). |
Clean container. |
24 h or less, RTa |
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1 day |
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Pilonidal cyst |
See Abscess |
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Respiratory, lower: |
1. Place aspirate or washing in a sputum trap. |
Sterile container, |
2 h or less, RTa |
24 h or less, 4oC |
1/day |
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Sputum, |
1. Collect the specimen under the direct supervision of a nurse or physician. |
Sterile container, greater than 1 ml. |
2 h or less, RTa |
24 h or less, 4oC |
1/day |
For pediatric patients unable to produce a specimen, a respiratory therapist should collect a specimen via suction. The best specimen should have 10 squamous cells or less per 100x field. |
Sputum, induced |
1. Have the patient rinse mouth with water after brushing the gums and tongue. |
Sterile container |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Histoplasma capsulatum and Blastomyces dermatitidis survive for only short periods of time once a specimen is obtained. Fungal recovery is primarily for Cryptococcus spp. and some filamentous fungi; other yeasts rarely cause lower respiratory tract infection. |
Respiratory, upper: |
1. Remove oral secretions and debris from the surface of the lesion with swab and discard swab. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Discourage sampling of superficial tissue for bacterial evaluation. Tissue biopsy or needle aspirates are the specimens of choice. |
Nasal |
1. Insert a swab, premoistened with sterile saline ≈2 cm into the nares. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Anterior nose cultures should be reserved for detecting staphylococcal and streptococcal carriers or for nasal lesions. |
Throat |
1. Depress the tongue with a tongue depressor. |
ESwab transport system. |
2 h or less, RTa |
24 h or less, RTa |
1/day |
Throat cultures are contraindicated for patients with an inflamed epiglottis. Swabs for N. gonorrhoeae should be inoculated or GC selective plates and transport at RTa. |
Skin: |
1. Cleanse the affected area with 70% alcohol. |
ESwab transport system. |
24 hr or less, RTa |
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1/day/ site |
If the specimen is submitted between glass slides, tape the slides together and submit in an envelope. |
Tissue |
1. Submit in a sterile container. |
Sterile, screw-cap jar. Saline may need to be added. |
15 minutes or less, RTa |
24 h or less, RTa |
None |
Always submit as much tissue as possible. If possible, save an amount of surgical tissue at –70oC in case further studies are needed. |
Urine: |
1. Thoroughly cleanse the urethral area with soap and water. |
Sterile wide-mouth container, 1 ml or greater, or urine transport kit |
Unpreserved: |
24 h or less, 4oC |
1/day |
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Male, |
1. Cleanse the glans with soap and water. |
Sterile wide-mouth container, 1 ml or greater, or urine transport kit |
Unpreserved: |
24 h or less, 4oC |
1/day |
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Straight catheter |
1. Thoroughly cleanse the urethral area with soap and water. |
Sterile, leakproof container |
Unpreserved: |
24 h or less, 4oC |
1/day |
If preparation is inadequate, the procedure may introduce urethral flora into the bladder and increase the risk of iatrogenic infection. |
Indwelling |
1. Disinfect the catheter collection port with 70% alcohol. |
Sterile, leakproof container or urine transport kit |
Unpreserved: |
24 h or less, 4oC |
1/day |
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Wound |
See Abscess |
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a EtoH, ethanol; RT, room temperature; I.V., intravenous; AFB, acid-fast bacilli; CSF, cerebrospinal fluid; BAP, blood agar plate; CHOC, chocolate agar; BHI, brain heart infusion; PVA, polyvinyl alcohol fixative. |
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Reference: Miller, J Michael, A Guide to Specimen Management in Clinical Microbiology, 2nd edition, ASM Press, Washington, D.C., 1999. |