SPECIMEN COLLECTION FOR MICRO SAMPLES PRINCIPLE It is critical that complete guidelines for the proper collection and transport of specimens are followed to ensure quality care. All diagnostic information is contingent on the quality of specimen received. Consequences of a poorly collected and/or poorly transported specimen include failure to isolate the causative micro-organism and recovery of contaminants or normal flora, which can lead to improper treatment of the patient. Safety considerations. FOLLOW UNIVERSAL PRECAUTION GUIDELINES (1)

Treat all specimens as potentially hazardous.

(2)

Use appropriate barrier precautions (such as gloves).

(3)

Do not contaminate the external surface of the collection container and/or its accompanying paperwork.

(4)

Minimize direct handling of specimens in transit from the patient to the laboratory. Use plastic sealable bags with separate pouch for lab requisition.

General guidelines for proper specimen collection and transportation. a.

Collect specimen before administering antimicrobial agents when possible.

b.

Collect specimen with as little contamination as possible to ensure that the sample will be representative of the infected site.

c.

Utilize appropriate collection devices. Use sterile equipment and aseptic technique to collect specimens.

d.

Clearly label the specimen container with two patient identifiers, date and time of collection and specimen source. Identify the specimen source and/or specific site correctly so that proper culture media will be selected during processing in the laboratory.

e.

Collect specimens in proper transport media of sturdy, sterile screw cap, leakproof containers with lids.

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Proper transportation of specimens collected in a syringe. Specimens obtained by a physician using needle aspiration should be transferred to a sterile tube or anaerobic transport vial prior to transport of the specimen to the laboratory. If there is little material in the syringe, the physician should draw a small amount of sterile nonbacteriostatic 0.85% NaCl through the syringe and then transfer the specimen to a sterile tube. Alternatively, and only if the specimen will be compromised by transferring it from the syringe, a small amount of sterile 0.85% NaCl may be drawn into the syringe prior to the removal of the needle. The physician should use a protective device while removing the needle to avoid injury and should cap the syringe with a sterile cap prior to transporting it to the laboratory. A syringe should never be sent with the needle attached.

TRANSPORT ALL SPECIMENS TO THE LABORATORY PROMPTLY. Refrigerate most specimens at 2o to 8oC. The following are exceptions: (a) (b) (c) (d)

Blood Cultures - Room temperature. Genital cultures (or any specimen with suspected GC) - Room temperature. Stools for Parasitology Exam (O & P) - Mix stool with preservative (provided by laboratory) and refrigerate. CSF Specimens - Room temperature (unless they are to be cultured for viruses).

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COLLECTION INSTRUCTIONS FOR DIFFERENT ANATOMIC SITES BLOOD CULTURES General Considerations a. b. c.

d.

Correct specimen collection is extremely important when obtaining blood culture specimens. Proper skin disinfection is an essential requirement to reduce the incidence of contamination. If possible, blood samples should be obtained prior to antibiotic therapy. If this is not possible, blood cultures should be drawn immediately before administering next dose. The volume of blood is critical because the concentration of organisms in most cases of bacteremia is low, especially if the patient is on antimicrobial therapy. In infants and children, the concentration may be higher than adults, so less blood is required for culture.

Culture Bottles a.

Mercy Medical Center uses the BacT/Alert system. The bottles are ready for use and should be stored at room temp. Do not use beyond expiration date printed on each bottle label.

Collection Technique a.

b. c. d. e.

f.

After palpation, the venipuncture site should be cleansed with the Blood Culture Prep Kit II. Swab concentrically, starting at the center, with the iodine solution. Repeat with the isopropyl alcohol swab. Remove the plastic flip-top from each bottle and disinfect with isopropyl alcohol. Obtain patient sample in a syringe (10 to 20 ml). Do not change needle before injecting blood into the culture bottle using transfer device. Volume requirements Aerobic bottle up to10 ml Anaerobic bottle up to10 ml Pediatric bottle 1-4 ml Transport the inoculated culture bottles promptly to the laboratory in a biohazard labeled bag. Do not refrigerate.

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CENTRAL NERVOUS SYSTEM (CNS) SPECIMENS CSF Suggested volumes are 1 ml for routine, 1 ml for fungal, and 2 ml for mycobacterial cultures. (1)

Lumbar Puncture Slowly drain the CSF into the sterile leakproof tubes. Three tubes are generally required for microbiology, hematology, and chemistry testing.

(2)

Ommaya Reservoir Fluid a.

b.

Clean the Ommaya reservoir site with antiseptic solution and alcohol prior to removal of Ommaya fluid to prevent introduction of infection. Remove Ommaya fluid via the Ommaya reservoir unit, and place it in sterile tube.

Other CNS Specimens (1)

Brain Abscess A physician aspirates material from a lesion and sends it to the microbiology laboratory in an anaerobic transport system. (See collection guidelines for transport of specimen in a syringe.

CNS specimen collection considerations are outlined in Table 2. GASTROINTESTINAL TRACT The gastrointestinal tract includes the esophagus, stomach, duodenum, small intestine, and colon. 1.

Fecal Specimens a. General Considerations (1) Keep stool specimens cool; do not incubate them. (2) Submit specimen to the lab within 2 hours of collection. (3) Do not use toilet paper to collect stool. b. Have patient obtain stool specimen by one of the following methods: (1) Use stool collection kit supplied by laboratory. (2) Pass stool directly into wide-mouth leakproof container with a tight-fitting lid (such as butter dish). (3) Pass into a clean, dry bedpan, and transfer stool into a leakproof container with a tight-fitting lid.

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(4)

If a diaper must be utilized, place plastic wrap (such as Saran Wrap) inside the diaper to prevent stool from being soaked into the diaper. Never transport a stool in a disposable diaper.

2.

Rectal swabs a. Send the swab in a swab transport.

3.

Gastric Aspirates See specimen transport guide.

4.

Gastric Lavage See specimen transport guide.

5.

Sigmoidoscopy See specimen transport guide.

See Table 3 for collection considerations for gastrointestinal specimens. GENITAL TRACT SPECIMENS Female

2.

1.

Cervix a. Do not use lubricant during procedure. b. Wipe the cervix clean of vaginal secretion and mucus. c. Rotate the sterile swab from an aerobic transport system, and obtain exudate from the endocervical glands. d. If no exudate is seen, insert the sterile swab into the endocervical canal, and rotate the swab. e. Place swab in transport media. DO NOT REFRIGERATE.

1B.

Cervix for CT/NG PCR test (Collection kit available from Micro Lab) a. Use the large sterile swab provided in the collection kit to remove any excess mucus, blood, or examination lubricants. Discard this swab. b. Insert the second, large sterile swab into the endocervical canal. Rotate swab clockwise for 3-5 seconds and withdraw. c. Insert this swab into transport tube of M4 transport media. Break shaft of swab and close tube securely. Leave swab in the transport tube media. Label with two patient identifiers and place specimen in the refrigerator until transported to the lab. d. NOTE: Wooden swabs will not be accepted.

Endometrium Collect endometrium specimens by transcervical aspiration through a telescoping catheter. Use aerobic transport media.

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3.

Rectal Swabs Send the swab in a swab transport or M4 media (for HSV).

4.

Vagina a. Use a speculum without lubricant. b. Collect secretions from the mucosa high in the vaginal canal with sterile pipette or swab. c. Send in an aerobic transport. DO NOT REFRIGERATE.

5.

Vulva a. Clean the surface of the lesion with 0.85% NaCl. If there is a crust on the lesion, remove it. b. Scrape the lesion until serous fluid emerges. c. Wipe away fluid and debris with sterile gauze (try to avoid bleeding). d. Press the base of lesion until clear fluid is expressed. e. Aspirate vesicular fluid with a 26-to-27-gauge needle. Follow guidelines for proper transport of aspirates. f. For HSV detection, unroof the vesicle and collect fluid with a sterile swab. Transport swab in M4 media.

6.

Vaginal Discharge for Trichomonas Vaginalis (Wet Prep) a. Inhouse - Collect specimens on a swab and place in small amount (1 ml or less) of 0.85% NaCl in a sterile tube. Specimen must be received in Microbiology within 30 minutes. b. Outpatient specimens should be collected and transported in aerobic transport media, which will keep Trichomonas viable for approximately 24 hours. Hold all specimens at room temperature. Specimens more than 24 hours old will be rejected. c. Specimens will also be examined for yeast.

Male 1.

Rectal Swab Send in a swab transport.

2.

Epididymis Use a needle and syringe to aspirate material from the epididymis. Follow aspirate transport guidelines.

3.

Penile Lesion

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See procedure for female vulva. 4.

Prostatic Massage Collect the specimen in a sterile tube or on a sterile swab.

5.

e.

Urethra a. Collect specimens at least 2 hours after the patient has urinated. b. Insert a thin urogenital swab 2 to 4 cm into the endourethra, gently rotate it, leave it in place for 1-2 seconds, and withdraw it. Send in aerobic transport. DO NOT REFRIGERATE.

5b.

Urethra swab for CT/NG PCR test (Collection kit available from Micro Lab) a. Patient should not urinate 2 hours prior to sampling. b. Insert the small sterile swab provided in the collection kit 2-4 cm into the urethra. Rotate 3-5 seconds and withdraw. c. Place swab into transport tube of M4 transport media. Break shaft of swab and close tube securely. Leave swab in the transport tube. Label with two patient identifiers and place specimen in the refrigerator until transported to the lab. d. NOTE: Wooden swabs will not be accepted.

6.

Penile Discharge or Prostatic Fluid for Trichomonas Vaginalis See female procedure.

7.

Contact Laboratory for Specific Collection Instructions

See Table 6 for collection considerations for genital tract specimens. OCULAR SPECIMENS Specimen collection guidelines for ocular specimens are summarized in Table 7. Contact laboratory for specific collection instructions. RESPIRATORY SPECIMENS 1.

General Considerations a. b.

c. d.

24 hour sputum collections are not recommended for culture. If Corynebacterium diphtheria, Arcanobacterium haemolyticum, Bordetella pertussis, chlamydiae, mycoplasmas, or legionellae are suspected, please see sections dealing with isolation of these organisms. Collect specimen resulting from deep cough in sterile, screw-cap cup or other suitable sterile collection assembly. First morning is best. Specimen must be sputum, not saliva. Saliva specimens will be rejected.

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2.

Induced Sputum Collect the induced sputum in a sterile screw-cap cup or other suitable sterile collection assembly.

3.

Tracheostomy and Endotracheal Aspirations Aspirate the specimen into a sterile sputum trap.

4.

Bronchoscopy Specimens, Bronchial Wash or Bronchoalveolar Lavage See specimen transport guide.

5.

Lung Aspirations See instructions for properly transporting specimens collected in a syringe.

6.

Lung Biopsies a. Obtain a 1-3 cm square piece of tissue if possible. b. Submit in a sterile container without formalin.

Upper Respiratory Tract Infections 1.

Throat (pharyngeal specimens) a. Do not obtain throat samples if epiglottis is inflamed, as sampling may cause serious respiratory obstruction. b. Depress tongue gently with tongue depressor. c. Extend sterile swab to back of throat and sweep back and forth across inflamed or ulcerated areas to obtain sample (avoid touching the cheeks, tongue, uvula, or lips).

2.

Nasal Swabs a. Insert a sterile swab into the nose until resistance is met at the level of the turbinates (approximately 1 in. into the nose). b. Rotate the swab against the nasal mucosa. c. Repeat the process on the other side. d. Send in appropriate transport media.

3.

Nasopharyngeal Suction Suction material from the nasopharynx, and collect in a sterile container.

4.

Nasopharyngeal Swabs

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Carefully insert a flexible-wire calcium alginate-tipped swab through the nose into the posterior nasopharynx and rotate the swab. 5.

Nasal Washings Place the saline wash in an equal volume of viral transport medium, or transport it in a sterile container.

6.

Sinus Aspirates Send specimen in the syringe, or place specimen in sterile tube/cup.

7.

Oral Cultures a. Rinse mouth with sterile saline. b. Wipe the lesion with dry sterile gauze. c. Swab or scrape areas of exudation or ulceration.

Respiratory specimen collection considerations are summarized in Table 8. STERILE BODY FLUIDS (EXCLUDING CSF, URINE, AND BLOOD) a. b. c. d.

Follow guidelines for transporting aspirates. Sterile body fluid collection considerations are summarized in Table 9. Refer to specimen transport guide. Contact laboratory for specific collection procedures.

SUBCUTANEOUS TISSUE AND SKIN SPECIMENS Superficial Wound, Bacterial 1.

Syringe aspiration is preferable to swab collection.

2.

See specimen transport guide and guidelines for transporting aspirates.

Superficial Lesions, Fungal Transport scrapings of the periphery of the lesion border in a sterile container or sterile petri dish that has been securely taped. Ulcers and Nodules Collect in syringe or sterile swab in transport. Subcutaneous Tissue and Skin Specimen Collection Considerations are Summarized in Table 10.

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DEEP WOUNDS, ASPIRATES AND TISSUE SPECIMENS a. b. c.

Deep wound, aspirate and tissue specimen collection considerations are summarized in Table 11. See transport guide. Contact laboratory for specific collection procedures.

URINE General Considerations a. b.

c.

d. e. f. g. h. i.

Never collect urine from a bedpan or urinal. Using the towelette provided by the laboratory (or soap), thoroughly clean the urethral opening (and vaginal vestibule in females) prior to collection procedures to ensure that the specimen obtained is not contaminated with normal flora from this area. Transport specimen to laboratory within 2 hours of collection. If it cannot be transported within 2 hours, the urine specimen should be refrigerated. (Bacterial counts remain stable for at least 24 hours at 4oC.) Do not freeze. Use sterile cups or tubes to transport urine. Also, urine transport kits are available. (See Table 4.) Transport suprapubic bladder aspirates (SPA) specimens for anaerobic culture in an anaerobic transport system. Always transport urine for viral cultures on wet ice in a sterile container. Any urine collection procedure involving catheterization must be done with scrupulous aseptic technique to avoid introducing normal flora. Send the first morning voided urine. Three consecutive first morning urine specimens are recommended for mycobacterial culture. Do not submit 24 hr. urine collections for culture.

Collection Techniques for Urines 1.

Clean Catch Urine Specimens (Female) a. The person obtaining the urine specimen should wash hands with soap and water. If the patient is collecting the specimen, she should be given detailed instructions. b. Cleanse the urethral opening with towelettes supplied by the laboratory or with clean gauze pads soaked with liquid soap. c. If soap is used, rinse the area well with water or wet gauze wipes. d. Hold labia apart during voiding. e. Allow a small amount of urine to pass (do not stop the flow of urine). f. Collect the midstream portion of urine in a sterile container. g. If the patient is menstruating, they should insert a fresh tampon or use

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cotton to stop the flow. 2.

Clean Catch Urine Specimens (Male) a. The person obtaining the urine should wash hands with soap and water. b. Cleanse the penis, retract the foreskin and wash with towelette or soapy water and rinse well with sterile water. c. Keeping the foreskin retracted, collect the midstream portion of the urine in a sterile container.

3.

Ileal Conduit Urine Collect the urine drained into a sterile container.

4.

Straight Catheter Urine Collect a sample from the mid or later flow of urine in a sterile container.

5.

Indwelling Catheter Urine a. Clean the catheter port with a 70% alcohol wipe. b. Using sterile technique, puncture the collection port with a needle attached to a syringe. (NOTE: DO NOT COLLECT URINE FROM THE COLLECTION BAG.) c. Aspirate the urine, and place it in a sterile container.

6.

Suprapubic Bladder Aspirate (SPA) Send specimen in a sterile container.

Urine Specimen Collection Considerations are Summarized in Table 12. GUIDELINES FOR ANAEROBIC CULTURE Collection and Transport a. b. c.

d. e. f.

The best specimen for anaerobic culture is obtained by using a needle and syringe. Tissue samples and biopsy samples are also very good specimens for anaerobic cultures. When a swab must be used to collect a specimen, use an anaerobic transport tube (available form the laboratory). Aerobic swabs that say they are good for anaerobic transport are not a preferred method. Special care must be taken to sample the active site of infection when a swab is used. Specimen should be transported to the laboratory as soon as possible. Avoid extremes of heat or cold. If delays are unavoidable, hold the specimen at room temperature. Do not refrigerate.

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g.

h.

Do not transport material for culture in the needle and syringe. Place specimens in a sterile tube, leakproof screw-cap cup, or anaerobic transport device. Consult laboratory regarding guidelines for acceptable specimens for anaerobic culture.

LEGIONELLA CULTURES Specimen Transport a. b.

Transport specimens in sterile dry containers. Do not add saline or formalin. Refrigerate specimens.

Acceptable Specimens Sputum, lung exudate, biopsy, tissue, other body tissue, pleural fluid, other body fluid. Urines are not acceptable for culture. Legionella antigen will be done on urines.

MYCOPLASMA CULTURES -Please contact the laboratory before collecting these specimens. Respiratory Tract Specimens (M. pneumoniae) Tracheal Aspirates Collect in sterile container. Throat Swabs Collect by swabbing back and forth or rolling the swab a few times over the mucosal surface. Place the swab in cold transport medium (available from laboratory). Sputum Collect in sterile container. First morning specimen is preferred. Lung Tissue Place in sterile container with sufficient mycoplasma transport medium to prevent drying.

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Refrigerate specimens. GENITAL MYCOPLASMAS (M. hominis and Ureaplasma urealyticum) – Please contact the lab before collecting these specimens. Genitourinary Vaginal Swabs Urethral Swabs (Males) Collect the specimen with a cotton tipped swab and immediately place in mycoplasma transport medium (available from laboratory). Agitate the swab in the medium, express the fluid against the side of the vial and discard the swab. Urine Collect in sterile containers. Urine yields fewer isolates than do genital cultures. Fluids Collect in a sterile container. Blood Anticoagulant is not necessary. Solid Tissues Place into a sterile container with sufficient transport medium to prevent drying. HPV Collection and Transport Use Digene Specimen Collection Kit. Instructions are included with each kit and should be followed carefully. Label specimen with two patient identifiers and indicate specimen source on requisition. Transport to the lab as per instructions in the box. PROCESSING OF SPECIMENS FOR ISOLATION OF UNUSUAL ORGANISMS The causative agents of granuloma inguinale (Calymmatobacterium granulomatis), leptospirosis (Leptospira sp.), Lyme borreliosis (Borrelia burgdorferi), Oroya fever or verruga peruana (Bartibekka bacukkufirnus), rat bite fever (Streptobacillus moniliformis), relapsing fever (Borrelia sp.), tularemia (Francisella tularensis), and whooping cough

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(Bordetella pertussis) are rarely recovered on routine bacteriological media because they have very specific nutrient requirements. The physician must notify the laboratory if any of these organisms are suspected in order to obtain instructions for correct collection and transport of specimens and to alert the laboratory staff of special cultural requirements for optimal isolation of these organisms. The causative agents of brucellosis (Brucella sp.) and plague (Yersinia pestis) can be cultured on routine bacteriological media. If the physician suspects brucellae or Y. Pestis and notifies the laboratory, specific procedures that increase the chances of isolating and identifying these organisms are available. COLLECTION AND TRANSPORT OF CLINICAL SPECIMENS FOR FUNGUS CULTURES a. b.

Collect and transport most specimens as for aerobic cultures. Consult Specimen Transport Guide and Collection considerations for individual specimen types.

In addition, Fungus cultures and/or KOH preps may be done on the following: Hair 1.

No cleaning of scalp is needed.

2. 3. 4. 5.

Select infected areas, and, with forceps, pluck at least 10 hairs. For hairs broken off at the scalp level, use a scalpel or a blade knife. Place hairs between two clean glass slides or in a sterile petri dish. Tape securely or send in screw top container.

1. 2.

Clean nail with 70% alcohol. For a specimen of the dorsal plate, scrape the outer surface and discard the scrapings. Then scrape the deeper portion for a specimen. Remove a portion of debris from under the nail with a scalpel. Collect the whole nail or nail clippings. Place all material in a sterile petri dish. Tape securely or send in clean container (urine cup).

Nail

3. 4. 5.

Skin 1. 2. 3. 4.

Wipe lesions and interspaces between the toes with alcohol sponge or sterile water. Scrape the entire lesion(s) and both sides of interspaces with sterile scalpel. Place scrapings between two clean glass slides or in a sterile petri dish. Tape securely or send in a screw top container.

Blood

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1.

Collect 2 Na heparinized tubes.

SPECIMEN COLLECTION AND TRANSPORT FOR MYCOBACTERIUM (AFB) a. b. c. d.

e. f.

Use a sterile leakproof disposable plastic container. Do not use waxed containers. They may produce false positive smear results. Collect initial specimens before antimicrobial therapy is started. Collect specimens aseptically, minimizing contamination. Swabs are not recommended for the isolation of mycobacteria, since they provide limited material. They are acceptable only if a specimen cannot be collected by other means. Collect sufficient material for the tests requested (see individual specimen requirements guides). Do not use any fixatives or preservatives.

Blood Cultures for AFB Patient should be referred to Outpatient Laboratory.

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Table 1

Transport systems for anaerobic specimens

Syringe or needle aspirates

Express excess air from syringe. Replace hub on syringe or using sterile technique, transfer the specimen to a red top Vacutainer. Do Not remove the top of Vacutainer to transfer the specimen. If fairly large vol is collected (2 ml or more), anaerobic bacteria survive for 24 h at room temp (1)a

BD Anaerobic Specimen Collector BD, Div. of Becton Dickinson and Co. Rutherford, N.J.

Sealed, gassed, oxygen-free outer glass tube that contains an inner glass vial fixed within rubbery stopper. Inoculated swab is placed into inner glass vial, and plunger is depressed. Inner vial detaches from rubber stopper and drops into lower portion of outer tube so that tip of swab is exposed to oxygen-free atmosphere during transport. Redox indicator is contained in bottom of outer tube to indicate exposure to oxygen.

Table 2 Culture

Collection considerations for CNS specimens Vol (ml)a

Bacteria

1

Fungi Mycobacteria

2 2

Anaerobes Parasites

NA NA

Virus b CSF can be submitted.

1-2

Table 3 Culture

Comments

Send cloudiest CSF specimen to microbiology laboratory immediately; tube no. 1 is preferred. Rule out Cryptococcus spp, Coccidioides immitis. Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium intracellulare. Brain abscess or CNS biopsy specimens. Brain abscess or CNS biopsy specimens for Entamoeba histolytica, Toxoplasma gondii, Naegleria speciesb. Acanthamoeba sppb. Send to laboratory on ice.

Collection considerations for gastrointestinal specimens Comments

Bacteria

Stools: Three stool specimens recommended. Gram stain for fecal leukocytes only. Gastric biopsy: Rule out Helicobacter pylori (21). Rectal swab: Rule out enteric pathogens (especially Shigella spp.) and Neisseria gonorrhoeae. Fungi Gastric aspirate, gastric biopsy, esophageal brush, esophageal biopsy. Pinworm For pinworm collection kit, contact microbiology laboratory. Swab perianal area when patient gets up in the morning before patient bathes or defecates. Mycobacteria Gastric aspirate or gastric biopsy; feces. Parasites If transport to laboratory is delayed, place stool specimen in preservative. Duodenal aspirates are useful for detecting Giardia spp. and larvae of S. stercoralis and A. lumbricoides. Use rectal biopsy specimens for E. histolytica and B. coli. Use small bowel biopsy specimens for Giardia, Cryptosporidium, and Microsporidium spp. Virus Use esophageal specimens for CMV and HSV and rectal biopsy specimens for HSV. Send to laboratory on ice. Do not freeze. Routine O&P exam is performed only on:  Patients who have AIDS or are immunosuppressed.

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Table 3 Culture

Collection considerations for gastrointestinal specimens Comments  Patients who are residents or recent immigrants from a developing country.  Patients who have traveled to a developing country.  Patients who have persistent undiagnosed diarrhea Travel history or reason listed above must be noted in comments in order for routine O&P to be performed. Giardia and Cryptosporidium antigen testing will be done for standard O&P requests.

Table 4 Transport systems for aerobic specimens System and supplier (references Swab Transport System (example: Culturette) BBL Microbiology Systems, Cockeysville, MD

Comments

Sterile, disposable culture collection and transport system consisting of plastic tube containing two rayon-tipped swabs and transport medium to prevent drying of bacteria and maintain pH. (Note: Always crush ampoule [with protective sleeve over ampoule] after specimen collection.) Note: Many other such transport systems from other manufacturers are available.

Calcium alginate swabs

Can be toxic for some strains of N. Gonorrhoeae, HSV, and Ureaplasma urealyticum and may be toxic for some cell cultures. Useful for collection of Chlamydia cultures.

Cotton swabs

Residual fatty acids may inhibit some bacteria and Chlamydia spp. If cotton is glued or spun to wooden applicator stick, wooden stick may inactivate HSV and interfere with some Ureaplasma identification tests.

Dacron swabs

Useful in collection of viral and group A streptococcus specimens.

Nasopharyngeal-urethrogenital swabs (example: Calgiswab type IV; Spectrum Diagnostics, Glenwood, Ill.)

Flexible wire shafts and small tips provide easier specimen collection, especially for collection of nasopharyngeal specimens, B. pertussis, and male urethral specimens of N. gonorrhoeae.

Sterile screw-cap cups

Useful for collection of urine, sputum, stool, bronchoalveolar lavage, and biopsy specimens. If biopsy specimen is small, ad small amount of sterile nonbacteriostatic 0.85% NaCl to cup. Never place biopsy specimen in formalin or wrap in gauze.

Sterile petri dishes

Useful for hair or skin-scraping specimens. Tape petri dish securely prior to transport.

Sterile tubes (screw-cap glass or plastic tubes, sterile Vacutainer tubes without additives)

Useful for collection of sterile fluids, bronchoalveolar lavage, drainage, or brush specimens.

B-D urine tubes BD, Div. of Becton Dickinson & Co., Rutherford, N.J.

Vacutainer tube containing 0.5 ml of freeze-dried boric acid-sodium formate maintenance formula. Maintenance formula holds bacterial population in urine specimen for 48 h at room temp at levels comparable to those in urine specimens without additive but held under refrigeration for same period. Preservative may be toxic to some uropathogens.

Viral transport systems (5)

See procedure for full description of viral transport systems.

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Table 4 Transport systems for aerobic specimens System and supplier (references

Comments

N. gonorrhoeae transport systems - Jembec

Flat plastic petri dish containing culture medium and well for CO 2 -generating tablet. After inoculation of medium, sodium bicarbonate-citric acid tablet is placed in well. Entire dish is placed in zipper lock plastic bag and incubated for 18 to 24 h. Tablet is activated by moisture in medium.

Stool collection kits

Include container for stool cultures, WBC, fecal fat, C. difficile, and preservative for ova and parasites.

Table 5 Specimen transport guide Source and type of specimen Blood

CNS CSF Ommaya fluid Brain fluid CNS biopsy

Gastrointestinal system Feces Rectal swab Gastric lavage or washings Duodenal aspirate Rectal biopsy Sigmoidoscopy specimen

Eye Conjunctival scrapings Corneal scrapings Intraocular fluid

Genital tract, female Amniotic fluid Fallopian tube Bartholin fluid Cervical Urethral Vaginal Endometrial Vulval

Transport method

Blood transport systems or sterile tube with SPS. If Neisseria spp. are suspected, use system without SPS.

Sterile screw-cap tube. Sterile screw-cap tube. Anaerobic transport system. Anaerobic transport system. If specimen is small, send in sterile cup with small amount of nonbacteriostatic 0.85% NaCl. (Never place in formalin.)

Cup or clean container. Swab transport system (For pinworm, use pinworm collection kit.) Sterile screw-cap cup for sputum trap. Sterile screw-cap cup or sputum trap. Sterile screw-cap cup or tube. If specimen is small, send in sterile cup with small amount of nonbacteriostatic 0.85% NaCl. (Never place in formalin.) Sterile screw-cap cup or tube. If specimen is small, send in sterile cup with small amount of nonbacteriostatic 0.85% NaCl. (Never place in formalin.)

Send prepared smears and directly inoculated media. Send prepared smears and directly inoculated media. Send prepared smears and directly inoculated media, anaerobic transport system, or capped syringe without needle with air expelled.

Anaerobic transport system with 1-2 ml of sample. Anaerobic transport system with 1-2 ml of sample. Anaerobic transport system with 1-2 ml of sample. Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system. Swab transport, viral or chlamydial transport, of N. gonorrhoeae transport system. Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system. Sterile screw-cap cup or tube or anaerobic transport system. Sterile screw-cap cup or tube or anaerobic transport system. Capped syringe without needle; slide with coverslip for T. pallidum; swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system.

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Table 5 Specimen transport guide Source and type of specimen Transport method Genital tract, male Anal swab Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system. Urethral Swab transport, viral or chlamydial transport, or N. gonorrhoeae transport system. Epididymis Anaerobic transport system, sterile screw-cap cup. Prostatic massage Sterile screw-cap cup, tube or swab transport system. Semen Sterile screw-cap cup, tube or swab transport system. Penile lesion Capped syringe without needle; slide with coverslip for T. pallidum; swab transport or viral or chlamydial transport system. Specimens for N. gonorrhoeae Anal, cervical, urethral, vaginal Lower respiratory tract Lung biopsy Expectorated sputum Induced sputum. Tracheal or endotracheal aspirate Bronchoalveolar lavage fluid Bronchial washings Transbronchial biopsy Bronchial brush Bronchial lavage fluid Bronchial washings Transbronchial biopsy Bronchial brush Transtracheal aspirate Lung aspirate

Swab transport system or jembec.

Sterile screw-cap cup; if specimen is small, place it in a small amount of nonbacteriostatic 0.85% NaCl (never place in formalin)> Sterile screw-cap cup. Sterile screw-cap cup. Sputum trap or sterile screw-cap cup or tube. Sputum trap or sterile screw-cap cup or tube. Sputum trap or sterile screw-cap cup or tube. Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Sputum trap or sterile screw-cap cup or tube. Sputum trap or sterile screw-cap cup or tube. Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Sterile screw-cap tube with 1-2 ml of nonbacteriostatic 0.85% NaCl. Anaerobic transport system or sterile screw-cap cup or tube. Anaerobic transport system or sterile screw-cap cup or tube.

Upper respiratory tract Throat swab Nasal swab Oral swab Nasopharyngeal swab Tympanocentesis fluid Sinus aspirate Nasopharyngeal suction Nasal washings

Swab transport or virus transport system. Swab transport or virus transport system. Swab transport or virus transport system. Swab transport or virus transport system. Anaerobic transport system or capped syringe without needleb, Anaerobic transport system or capped syringe without needleb. Sterile screw-cap cup or viral transport system. Sterile screw-cap cup or viral transport system.

Sterile body fluids (excluding CSF, urine, blood) Pleural, peritoneal, ascites, joint and synovial fluids

Sterile screw-cap container, capped syringe without needle, or anaerobic transport system.

Subcutaneous tissue and skin Ulcers or nodules, superficial wound (bacterial) Exudate Biopsy Burn specimens

Capped syringe without needleb, Sterile screw-cap cup (if specimen is small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent drying). Sterile screw-cap container.

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Table 5 Specimen transport guide Source and type of specimen Superficial fungal lesion Sterile screw-cap container. material Deep wounds, aspirates, tissues Site wound Deep wounds or abscesses Soft tissue aspirates Bone Punch skin biopsy

Urine Clean catch Ileal conduit Straight catheter Suprapubic aspirate Bladder washout Bilateral ureteral catheterization

Transport method

Anaerobic transport system. Sterile screw-cap container. Capped syringe without needleb. Sterile screw-cap container (if specimen is small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent drying). Sterile screw-cap container (if specimen is small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent drying).

Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube. Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube. Sterile screw-cap cup or tube, B-D Vacutainer or urine collection tube. Anaerobic transport system or capped syringe without needle. Sterile screw-cap cup or tube (be careful to label specimens with correct times and sites). Sterile screw-cap cup or tube (be careful to label specimens with correct times and sites).

b

Specimens obtained by a physician using needle aspiration should be transferred to a sterile tube or anaerobic transport vial prior to transport of the specimen to the laboratory. If there is little material in the syringe, the physician should draw a small amount of sterile nonbacteriostatic 0.85% NaCl or sterile broth through the syringe and then transfer the specimen to a sterile tube. Alternatively, and only if the specimen will be compromised by transferring it from the syringe, a small amount of sterile 0.85% NaCl or broth may be drawn into the syringe prior to removal of the needle. The physician should use a protective device while removing the needle to avoid injury and should cap the syringe with a sterile cap prior to transporting it to the laboratory.

Table 6 Culture

Collection considerations for genital tract specimens Recommended specimens

N. gonorrhoeae Bacteria Trichomonas vaginalis Fungi Anaerobes HSV C. trachomatis T. pallidum

U. urealyticum LGV H. ducreyi

Cervical, urethral, anal, or vaginal swabs. Prostatic fluid, cervical, vaginal. Vaginal, prostatic fluid. Anal, vaginal, or cervical. Epididymis aspirate, amniotic fluid, abscess fluid. Genital or perianal lesion. Urethral, vulval, cervical. Genital lesion. Note: Secondary lesions of syphilis are most commonly found on mucous membranes and skin (including palms of hands and soles of feet), but any body organ may be involved. Urethral, epididymis or prostatic fluid. Rectal, cervical, urethral, bubo or ulcer material. Material from ulcers of genitalia and perianal areas and from inguinal nodes.

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Table 7 Culture

Collection considerations for ocular specimens Recommended specimens

Bacteria

Inoculate media directly with ocular scrapings. (If N. gonorrhoeae is suspected, inoculate a Thayer-Martin agar plate also.) Inoculate media directly with ocular scrapings. Use anaerobic transport medium, or inoculate medium directly. If inflammation occurs after extracapsular cataract extraction, rule out Propionibacterium spp. (28) Use to detect Acanthamoeba spp. (39) Do not use cotton swabs for specimen collection. Do not use calcium alginate swabs for specimen collection. Inoculate medium directly with ocular scrapings.

Fungi Anaerobes

Parasites Chlamydia Virus Mycobacteria

***Culturettes acceptable for bacteria and fungal cultures.*** ***M4 media required for Chlamydia and virus cultures

Table 8 Culture

Collection considerations for respiratory Vol (ml)a

Bacteria

NA

Fungi

3-5

Anaerobes

Mycobacteria

Pneumocystis spp.

1

5-10

2

Parasites

3-5

Legionella

10

a

Comments

Contact laboratory if Legionella suspected. Submit sputum only; saliva is unacceptable. Collect three early-morning fresh specimens resulting from deep cough or sputum induction. Lung biopsy specimens or lung aspirates are also appropriate. Sinus aspirate, tympanocentesis fluid, transtracheal aspirate, and lung aspirates or biopsy specimens are appropriate. Collect three early-morning fresh specimens resulting from deep cough or sputum induction. Lung biopsy specimens or lung aspirates are also appropriate. Use inducted sputum, bronchoalveolar lavage fluid, or lung biopsy specimen. Can be examined from amoebae, helminth eggs (Paragonimus westermani), hooklets of Echinococcus spp., larvae of hookworm, and Ascaris and Strongyloides spp. Submit sputum

Amounts are guidelines. NA, not applicable.

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Table 9 Culture

Collection considerations for sterile body fluids Vol (ml)a

Bacteria

1-5

Fungi

>10

Anaerobes Mycobacteria

1-5 >10

a

Comments

If gonococcal arthritis is suspected, notify laboratory to add modified Thayer-Martin plate. Blood for Histoplasma capsulatum (AIDS), Cryptococcus spp., Candidaalbicansb, and Candida tropicalisb. Use anaerobic transport system.

Amounts are guidelines. Greater volumes will increase the chance of organism recovery. Can also be recovered in most bacterial cultures.

b

Table 10 Culture

Collection considerations for subcutaneous tissue and skin specimens Comments

Bacteria Anaerobes Fungi Mycobacteria (42) Virus

Syringe aspirates or biopsy specimens are preferable to swab specimens. Uncommon in burn, ulcer, nodules, or superficial skin infections; useful following bites and trauma. Useful in diagnosing dermatophytes, yeast, filamentous fungi, and dimorphic fungi. Useful in diagnosing Mycobacterium marinum, Mycobacterium fortuitum, and Mycobacterium chelonei. Useful in diagnosing HSV and varicella-zoster virus.

a

Rate of recovery of HsV and varicella-zoster virus is highest from the youngest lesions (vesicles), then from pustules, ulcers, and crusted lesions, in that order.

Table 11 Culture

Collection considerations for deep wound, aspirates, and tissue specimens Comments

Bacteria Anaerobes Fungi

Biopsy specimens or aspirates are better than swab specimens. Useful in diagnosing actinomycosis; send in anaerobic transport system. Useful in diagnosing Pseudallescheria boydii, Bipolaris spp., Exophiala spp., and Fusarium spp. Useful in diagnosing Mycobacterium tuberculosis, Mycobacterium bovis, and Mycobacterium kansasii.

Mycobacteria (40)

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Table 12 Culture

Collection considerations for urine specimens Vol (ml)a

Bacteria

0.5-1

Fungi

>20

Mycobacteria

>20

Anaerobes Virus

Parasites

1 10-50

24 h collection

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Comments

Do not collect 24 hour specimen. After proper cleansing of patient, use first morning midstream void. Do not collect 24 hour specimen. First morning void is recommended or cathed specimen. Do not collect 24 hour specimen. First morning three consecutive voided urine specimens are recommended. Use suprapubic aspirate. Send in anaerobic transport system. Do not collect 24 hour specimen. First morning void is recommended. Useful for adenovirus, mumps, and DCMV detection. Send on ice, and transport to laboratory immediately. Use for detecting Schistosoma haematobium eggs, Trichomonas vaginalis trophozoites in males, and Onchocerca volvulus microfilariae.

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CONTAINER TYPES Microbiology BBL Transport System (with double swabs for aerobic cultures) Routine Culture Vaginal Culture Gram Stain Throat Culture Nasal Culture Anaerobic Culturette Anaerobic Culture Jembec Plate GC Screen Ova and Parasite Collection Kit Stool for O & P Special Sterile Container (kits) Available from Micro Acid Fast Culture and Smear Sputum Culture Urine Culture

Virology Chlamydia PCR - for urogenital sources only – kit includes swab(s) & M4 media Male Collection Kit (also used for GC PCR) Female Collection Kit (also used for GC PCR) Chlamydia Culture - for Non-genital sources Includes rectal, eye, respiratory, etc. – liquid media in M4 media tube. Chlamydia Transport Media - liquid media in M4 media tube. Request from virology lab, keep cold. Viral Culture (including Herpes simplex) M4 media

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SPECIMEN REQUIREMENTS FOR BODY FLUIDS (OTHER THAN CSF) TEST

TUBE TYPE

CELL COUNTS.........................................................PURPLE (EDTA) CRYSTAL IDENTIFICATION ................................RED TOP (NO SST)/OR GREEN CHEMISTRY ............................................................RED TOP (NO SST)/OR GREEN CULTURE

............................................................RED TOP (NO SST)- clean top of test tube with alcohol before transferring specimen to tube.

GRAM STAIN...........................................................RED TOP (NO SST) - clean top of test tube with alcohol before transferring specimen to tube. ANAEROBIC CULTURE.........................................Send syringe. Place specimen in sterile tube or cup. IMMUNOLOGY (RA, etc.) ......................................RED TOP (NO SST)

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