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Sinai Department of Pathology
Pathology Lab Users Guide
Microbiology
Microbiology 7
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LifeBridge Health - Department of Pathology
Microbiology
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Urine |
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- General considerations
a) Never collect urine from a bedpan or urinal.
b) Thoroughly clean the urethral opening (and vaginal vestibule in females) prior to collection procedures to ensure that the specimen obtained is not contaminated with colonizing microorganisms in this area.
c) Soap rather than disinfectants is recommended for cleaning the urethral area. If disinfectants are introduced into the urine during collection, they may be inhibitory to the growth of microorganisms.
d) Transport specimen to laboratory within 2 hours of collection. If it cannot be transported within 2 hours of collection, the urine specimen should be refrigerated. (Bacterial counts remain stable for at least 24 h at 40C.) Do not freeze.
e) Use sterile cups or tubes to transport urine.
f) Transport suprapubic bladder aspirate (SPA) specimens for anaerobic culture in an anaerobic transport system.
g) Always transport urine for viral cultures on wet ice in a sterile container.
h) Any urine collection procedure involving catheterization must be done with scrupulous aseptic technique to avoid introducing microorganisms.
i) Send the first morning voided urine. Three consecutive first morning urine specimens are recommended for mycobacterial culture.
j) Do not submit 24-h urine collections for culture.
- Collection techniques
a) Clean catch urine specimens (female)
1) The person obtaining the urine specimen should wash hands with soap and water, rinse, and dry. If the patient is collecting the specimen, she should be given detailed instructions, including diagrams or a pictorial display.
2) Cleanse the urethral opening and vaginal vestibule area with soapy water or clean gauze pads soaked with liquid soap.
3) Rinse the area well with water or wet gauze wipes.
4) Hold labia apart during voiding.
5) Allow a few milliliters of urine to pass. (Do not stop the flow of urine.)
6) Collect the midstream portion of urine in a sterile container.
b) Clean catch urine specimens (male)
1) The person obtaining the urine should wash hands with soap and water, rinse, and dry. If the patient is collecting the specimen, he should be given detailed instructions, including diagrams or a pictorial display.
2) Cleanse the penis, retract the foreskin (if not circumcised), and wash with soapy water.
3) Rinse the area well with sterile water.
4) Keeping the foreskin retracted, allow a few milliliters of urine to pass. (Do not stop the flow of urine.)
5) Collect the midstream portion of urine in a sterile container.
c) Ileal conduit urine
1) Remove the external urinary appliance, and discard the urine within the appliance.
2) Gently swab and clean the stomal opening with 70% alcohol pad and then with an iodine solution (see 1a. above) disinfect the area.
3) Using sterile technique, insert a double catheter into the stoma. (A double catheter helps to minimize contamination of the specimen with skin flora.)
4) Catheterize the ileal conduit to a depth beyond the fascial level.
5) Collect the urine drained into a sterile container.
d) Straight catheter urine (in/out catheter urine specimens)
In/out catheter urine specimens are useful when clean-catch urines cannot be obtained or when results from clean catch urine specimens are equivocal and a diagnosis is critical.
1) Prior to catheterization, the patient should force fluids until the bladder is full. (Forcing fluids may reduce organism number.)
2) Clean the patients urethral opening (and in females, the vaginal vestibule) with soap, and carefully rinse the area with water.
3) Using sterile technique, pass a catheter into the bladder.
4) Collect the initial 15 to 30 ml of urine, and discard it from the mouth of the catheter.
5) Collect a sample from the mid- or later flow of urine in a sterile container.
e) Indwelling catheter urine
Indwelling catheters are placed in patients who are unable to pass urine.
1) Clean the catheter collection port with a 70% alcohol wipe.
2) Using sterile technique, puncture the collection port with a needle attached to a syringe. Note: Do not collect urine from the collection bag.
3) Aspirate the urine, and place it in a sterile container.
f) SPA of the urinary bladder
SPA is useful in determining urinary infection in adults in whom infection is suspected and for whom results from routine procedures have been equivocal and diagnosis is critical. SPA is also useful in pediatric patients when clean-catch urine specimens are difficult to obtain.
1) Before SPA, the patient should force fluids until the bladder is full. (Forcing fluids may reduce the organism number.)
2) Shave and disinfect the suprapubic site overlying the urinary bladder.
3) The physician will make a small lance wound through the epidermis, just above the symphysis pubis.
4) Aspirate urine from the bladder by using a needle aspiration technique.
g) Bladder washout test (Fairly)
The bladder washout test is useful in determining the site of infection in the urinary tract. Results are equivocal in about 10 to 20% of patients.
1) Prior to test, have the patient force liquids until the bladder is full. (Forcing liquids may reduce organism number.)
2) Clean the urethral area with soapy water, and rinse the area well with water.
3) Insert an indwelling catheter into the bladder through the urethra.
4) Collect an initial urine specimen into a sterile container, and refrigerate it.
5) Empty the bladder through the urethral catheter, and then irrigate it. (Use a sterile nonbacteriostatic 0.85% NaCl solution to irrigate the bladder.)
6) Collect three additional specimens (5 to 10 ml each) at 10 min intervals into separately labeled containers after irrigation of the bladder is performed.
7) Submit the initialed and timed collection samples to the clinical microbiology laboratory for culture. (Note: It is imperative that each specimen container be clearly labeled with the time of specimen collection.)
h) Cystoscopy: bilateral urethral catheterization
1) Bilateral urethral catheterization is useful in determining the site of infection in the urinary tract.
2) Prior to cystoscopy, have the patient force liquids until the bladder is full. (Forcing liquids may reduce the organism number.)
3) Clean the urethral area (and vaginal vestibule in females) with soapy water, and rinse the area well with water.
4) Insert a cystoscope (obruator in place) into the bladder.
5) With sterile technique, collect approximately 5 to 10 ml of urine from open stopcock into a sterile container.
6) Label this sample CB, for catheterized bladder urine, and refrigerate it. Then irrigate the bladder. (Use sterile nonbacteriostatic 0.85% NaCl to irrigate the bladder.)
7) After irrigation of the bladder and insertion of the ureteral catheters, collect irrigating fluid passing from the bladder through the ureteral catheters by holding the ends of both catheters over an opened sterile container.
8) Label this sample WB, for washed bladder urine, and refrigerate it.
9) Pass the ureteral catheters to each midureter or renal pelvis without introducing additional irrigating fluid. Open both stopcocks of the cystoscope to empty the bladder.
10) Discard the first 5 to 10 ml of urine from each ureteral catheter.
11) Collect four consecutive paired cultures (5 to 10 ml each) directly into opened sterile containers.
12) Label these specimens LK-1, RK-1, LK-2, RK-2 (LK for left kidney and RK for right kidney).
- Urine specimen collection considerations are summarized in Table 12.
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Table I Transport systems for anaerobic specimens
| System and Supplier |
Description
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Anaswab system
Scott Laboratories, Inc.
Fiskeville, RI |
Two tube system. Both tubes have been evacuated of oxygen, and air within tubes has been replaced with oxygen free CO2. One tube includes swab attached to rubber stopper. After specimen is obtained, swab is removed from first tube and quickly placed in to second tube, with stopper attached to swab handle becoming final seal for second tube.
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| Port-a-Cult Vial or Port-a-Cult Swab |
Tube is used for transporting swabs, and sealed vial is used for transporting fluid specimens. Both contain semisolid transport medium with reducing agent and redox indicator. Any purple discoloration of medium indicates exposure to air. |
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Bio-Bag Environmental System
BBL Microbiology Systems
Cockeysville, MD. |
Specimen is collected with any swab or tube desired and then placed in gas-impermeable environmental chamber that contains ampoules of indicator. catalyst, and hydrogen-CO2 generator. After bag is sealed, each ampoule is crushed to produce anaerobic conditions. |
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| Syringe or needle aspirates |
Express excess air from syringe, and cap needle or stick needle with rubber stopper. If fairly large volume is collected (2 ml or more), anaerobic bacteria survive for 24 hours at room temp (1).a |
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BD Anaerobic Specimen Collector
BD, Div. of Becton Dickinson and Co.
Rutherford, NJ |
Sealed, gassed, oxygen-free outer glass tube that contains an inner glass vial fixed within rubber 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. |
a 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.
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Table 2 Transport Systems for aerobic specimens.
| System and Supplier |
Comments
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Swab Transport System (example: culturette)
BBL Microbiology Systems
Cockeysville, MD |
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 (with protective sleeve over ampoule) after specimen collection.)
Note: many other such transport systems from other manufacturers are available. |
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| Calcium alginate swabs (2,3,22,31,36) |
Can be toxic for some strains of N. gonorrhoeae, HSV , and Ureaplasma urealtyicum and may be toxic for some cell cultures. Useful for collection of Chlamydia cultures. |
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| Cotton swabs (26) |
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. |
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| Dacron swabs (19) |
Useful in collection of viral and group A streptococcus specimens. |
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Nasopharyngeal-urethrogenital swabs
(example: Calgiswab type IV; Spectrum Diagnostics, Glenwood, IL.) |
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. |
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| Sterile screw-cap cups |
Useful for collection of urine, sputum, stool, bronchoalveolar lavage, and biopsy specimens. If biopsy specimen is small, add small amount of sterile nonbacteriostatic 0.85% NaCl to cup. Never place biopsy specimen in formalin or wrap in gauze. |
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| Sterile petri dishes. |
Useful for hair or skin-scraping specimens. Tape petri dish securely prior to transport. |
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| 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. |
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B-D urine tubes
BD, Div. of Becton Dickinson & CO.
Rutherford, NJ |
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 hrs 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. |
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| Viral transport systems (5) |
See procedure 8.2 for full descriptions of viral transport systems. |
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| N. gonorrohoeae transport systems Jembec |
Flat plastic petri dish containing culture medium and well for C02-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 hrs. Tablet is activated by moisture in medium. |
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Gono-Pak
BBL Microbiology Systems
Cockeysville, Md. |
Modification of Jembec system. Uses 60- or 100 mm petri dish and C02-generating tablet in large zipper lock pouch. |
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Bio-Bag
BBL Microbiology Systems
Cockeysville, Md. |
See Table 1. |
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| Transgrow |
Inner flat surface of flat bottle contains modified Thayer- Martin agar that has been bottled under CO2. Not recommended because of variability in CO2 content, mechanical difficulties in manipulating bottle, and moisture collection on inner surface of bottle that promotes spread of contaminants.
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