Specimen Collection for Microbiology Specimen Labeling

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Specimen Collection for Microbiology

Specimen Labeling

Information accompanying microbiology specimens must include:

  1. Patient Name, SSN, Date of Birth, sex

  2. Requesting Physician

  3. Tests ordered

  4. Specimen source

  5. Date of specimen collection

Specimen Collection

Blood for Culture

Blood for culture should be collected into bottles provided by Perll Diagnostics (appropriate adapters are also provided):

Aerobic Culture: FA bottle

Anaerobic Culture: FN bottle

Pediatric: PF bottle

Perform venipuncture as recommended by your facility’s approved procedure. Bottle should remain upright while collecting blood. Always collect blood for culture before collecting blood for other tests. If collecting more than one blood culture bottle, collect into the aerobic bottle before the anaerobic bottle. Mark the liquid level on the bottle before drawing blood. Line demarcations on the bottle label indicate sufficient blood volume fill.

Adults: collect 8-10ml of blood

Pediatric: collect 1-4ml of blood

NOTE: the provided adapter insert can be used for collection of blood for other tests if needed.

Endocervical Swabs

The order of testing for specimen collection should be Chlamydia test, Gonorhhea culture/gram stain, pap smear. Since the visible presence of blood may interfere with test results, it is advisable to collect the Pap smear last when using the cytobrush because of induced bleeding that might occur.

Specimens for Chlamydia testing

Specimens are to be collected using the Clearview Female Specimen Collection Kit provided by Perll Diagnostics. Remove excess mucus from the exocervix with a separate swab or cotton ball and discard. Insert the swab into the endocervix and rotate against the surface of the cervical canal for 10 to 30 seconds. Avoid touching any vaginal surface when withdrawing the swab. Return the swab to the transportation.

Specimens for Gonorrhea Culture

Specimens should be collected using an anaerobic Amies swab with charcoal (example: Star Swab SP131X). Rotate swab against the wall of the endocervical canal several times for 20-30 seconds and withdraw without touching the vaginal surface.

Nasal Specimens

NOTE: If Influenza A/B and RSV testing required, one sample may be submitted for both tests.

Nasopharyngeal Swab Method:

For Influenza A/B and RSV

To collect a nasopharyngeal swab sample, carefully insert the swab into the nostril and using gentle rotation, push the swab into the posterior nasopharynx. Gently rotate the swab three times, then remove it from the nasopharynx. Swab should be stored and transported in Universal Transport Media.
For MRSA screening

Swab both anterior nares (inner nose surfaces) utilizing one culture swab. Rotate moistened swab in each nares two to five times clockwise and counterclockwise. The process should gently rub across the nasal mucous membranes about three-fourths of an inch into the nasal passage (adult) so that squamous epithelial cells from the inside of the nose are obtained. Store and transport in Stuarts or Amies media.

Nasopharyngeal Aspirate Method:

For Influenza A/B and RSV

Instill a few drops of sterile saline into the nostril to be suctioned. Insert the flexible plastic tubing along the nostril floor, parallel to the palate. After entering the nasopharynx, aspirate the secretions while removing the tubing. The procedure should be repeated for the other nostril if inadequate secretions were obtained from the first nostril.

Nasal/Nasopharyngeal Wash Method:

For Influenza A/B and RSV

Follow your Institution’s Protocol for obtaining wash specimens. Use the minimal amount of saline that your procedure allows, as excess volume will dilute the amount of antigen in the specimen. The following are examples of procedures used by clinicians:

The child should sit in the parent’s lap facing forward, with the child’s head against the parent’s chest. Fill the syringe or aspiration bulb with the minimal volume of saline required per the subject’s size and age. Instill the saline into one nostril while the head is tilted back. Aspirate the wash specimen back into the syringe or bulb. The aspirated wash sample will likely be at least 1 cc in volume.

Alternatively, following instillation of the saline, tilt the child’s head forward and let the saline drain out into a clean collection cup.

Rectal Swabs

Rectal swabs are not recommended for stool culture except for infants. For Gonorrhea culture insert sterile swab approximately 1-1.5 inches in the anal canal. Move swab from side to side in the anal canal to sample crypts. Allow swab to remain 10-30 seconds for absorption of organisms onto the swab.



Patient should rinse or gargle with water to remove excess oral flora. Patient is then to cough deeply to produce sputum specimen from lower respiratory tract into a sterile container. Specimen should be at least 1ml in volume.


Patient should brush tongue and gums and rinse mouth thoroughly with water. Patient should inhale 25ml of 3-10% sterile saline through a nebulizer. Saline is to be collected in a sterile container. Specimen should be at least 1ml in volume.


Specimen is to be passed into a bedpan or on plastic wrap over a toilet seat. Specimens for culture, C. difficile, and/or vancomycin resistant Enterococcus (VRE) screening should be aseptically transferred to a sterile wide mouth container for transport. Rectal swabs are not recommended except for infants. Specimens for Ova and parasite screening should be transferred into each vial provided using the included spoon, agitate sample with spoon, tighten cap, and shake tube until specimen appears homogeneous.

Throat Swabs

Use of a sterile polyester swab should be used for Gonorrhea culture and Strep A testing. Rayon transport swabs containing modified Stuart's or Amies liquid medium can also be used. Swab the posterior pharynx, tonsils, and other inflamed areas. Avoid touching the tongue, cheeks and teeth with the swab.

Urethral Swabs

Specimens for Gonorrhea culture should be collected using a sterile culturette. Delay obtaining specimens until 2 hrs after patient has last voided. Gently insert the urogenital swab into the urethra (women 1-2 cm, men 2-4 cm). Rotate the swab in one direction for at least one revolution for a minimum of 10 seconds.


Urine may be collected into a wide mouth sterile container or a sterile borate container (see specimen transport conditions)


Specimens for Culture:

Separate the labia and with cotton wool or a sponge moistened with water, wipe the vulva from the front to the back. Disinfectant MUST NOT be used. With the labia still separated allow some urine to pass into the toilet, then, without stopping, allow urine to pass into a container and fill to the line. Pass the remaining urine into the toilet.


Specimens for Culture:

Clean the glans penis with soap and water. Commence urination, and when a few millilitres of urine have been passed introduce a sterile container into the stream and fill the container.

Specimens for Chlamydia and Gonorrhea testing:

The patient should be instructed not to urinate for at least one hour prior to specimen collection. Approximately 20-30mls of first catch urine should be collected into a clean and dry container.

Collection of Catheter Specimens of Urines (CSU’s)

The specimen should not be collected from the drainage bag, only from the sampling port. Using a needle and syringe insert the needle through the latex or plastic port and aspirate urine. Transfer 15ml urine to a red topped sterile container.

Wound Specimens for Culture and/or MRSA screening

Specimens should be collected through aspiration. If direct aspiration is not possible, abscesses and wounds can be irrigated with sterile saline and then aspirated. Wound biopsies are also acceptable specimens. Swab specimens are not optimal, as they contain less material and are more likely to be contaminated by adjacent cutaneous microflora. If wounds or abscesses are to be swabbed, two Amies swabs must be collected for smear and culture.

Specimen Transport

Blood for Culture

Blood culture bottles must be transported to the laboratory as soon as possible for processing. Bottles should be transported at room temperature.

Endocervical Swabs

Swabs for Chlamydia testing should be transported to the test site at refrigeration temperature. Transport media should not be used. If the specimen is not to be tested within 1 day, store at 2-8°C for up to 5 days. Do not freeze

Swabs for Gonorrhea culture should be immediately transported to the laboratory at room temperature due to low organism survival rate.

Nasal Specimens

Transport specimens for Influenza A/B and RSV testing at 4C within eight hours of collection. Specimens stored in M4-RT, Multitrans Media, or Bartels Viratrans only will be accepted up to 48 hours after collection.

Specimens for MRSA testing can be transported at room temperature and should be received within 24 hours.

Rectal Swabs

Specimens should be transported at room temperature. Swabs for culture must be received within 24 hours. Swabs for Gonorrhea culture should be received immediately due to low organism survival rate.


Store/transport specimens at 4°C within 24 hours of collection.


Stool specimens and rectal swabs (infants only) for culture and or C. difficile screening should be transported within 24 hours at 4°C. Stool vials for ova and parasite screening should be placed in the ziplock bag provided and should be transported to the lab within 24 hours at room temperature.

Throat Swabs

Swab specimens may be stored in a clean, dry plastic tube for up to 8 hours at room temperature or 72 hours at 2-8°C. Do not freeze. Swabs for Gonorrhea culture should be transported at room temperature and received immediately due to low organism survival rate.

Urethral Swabs

Swabs for Gonorrhea culture should be transported at room temperature and received immediately due to low organism survival rate.


Unpreserved (no boric acid) samples should be transported to the lab at 4°C within 24 hours of collection. Samples preserved with boric acid can be transported to the lab within 24 hours at room temperature or 4°C.

Wound Specimens

Specimens should be transported within 24 hours at room temperature.

Specimen Acceptability


Any samples received in damaged containers and/or do not have proper labeling will not be accepted for analysis. Samples may also be rejected if the transport criteria are not met accordingly. Additional specimen acceptability criteria are listed below where applicable.


Specimens with large numbers of squamous epithelial cells are considered unacceptable and will not be cultured.


Specimens containing evidence of fecal material will be rejected.


Specimens containing large numbers of squamous epithelial cells (indicating contamination) are considered unacceptable.

Nasal Swabs

Swabs for RSV testing will not be accepted if transported in Amies or M4-3 media. Swabs for Influenza testing will not be accepted if transported in M4, M4-RT, Amies, Stuarts, or Remel M6 media.

Further Testing

Blood Cultures

Initial results will be reported as positive or negative. For positive samples, you may request a Gram stain and/or pathogen isolation.

Pathogen Identification and Susceptibility

Identification is included in testing for positive samples submitted for screening for a specific pathogen (i.e. MRSA, VRE, Gonorrhea).

Susceptibility analysis is included in MRSA and VRE screening.

Identification and susceptibility analysis will be carried out for an additional charge on pathogens isolated form any culture when requested.

NOTE: if ordering susceptibility analysis, you must also order pathogen identification.

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