Geisinger Medical Laboratories Microbiology Specimen Collection Instructions


Urine Specimens for Culture

Urine Specimen Collection - Male - Clean-Catch Urine Specimens

  1. Wet paper towel and open soap towelette.
  2. Retract the foreskin if uncircumcised, and cleanse end of penis with soap towelette.
  3. Cleanse again with wet paper towel to remove soap.
  4. Urinate small amount into toilet and continue to urinate remainder into specimen container, being careful not to touch the top or inside of container.
  6. Place lid on container and give urine specimen to nurse.
  7. If immediate transport (<1 hour) to the lab is not possible, nursing staff will transfer the specimen to a urine transport device.

1. Koneman EW. 1988. Color Atlas and Textbook of Diagnostic Microbiology, 3rd ed., JP Lippincott, Philadelphia.
2. Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology. ASM Press. Washington DC. 2nd Edition

Urine Specimen Collection - Female - Clean-Catch Urine Specimens

  1. Remove underclothing completely and sit comfortably on seat, swinging one knee to the side as far as you can.
  2. Spread the labial folds with one hand and continue to hold the labial folds apart while you clean and collect the specimen.
  3. Wash. Be sure to wash and rinse well before you collect the urine sample. Using the cleaning materials supplied, wipe from the front of your genital area towards the back. Wash between the folds of the skin as carefully as you can. Repeat.
  4. Rinse. After you have washed with each soap pad, rinse with a water-moistened pad with the same front-to-back motion. Do not use any pad more than once.
  5. Hold yourself apart with one hand and allow the first few drops of urine to pass into the toilet bowl. With the other hand, hold the collection cup on the outside and pass the remaining urine into the cup.
  6. Place the lid on the container and give the urine specimen to the nurse.
  7. If immediate transport (<1 hour) to the lab is not possible, nursing staff will transfer the specimen to a urine transport device.

1. Koneman EN, 1988. Diagnostic Microbiology, 3rd ed., JB Lippincott Company, Philadelphia, PA
2. Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology. ASM Press. Washington DC.  2nd Edition

Urine Specimen Collection - Catheterized

  1. Place patient in a comfortable supine position. If female, have legs drawn up with heels together and knees spread wide apart.
  2. Use aseptic technique.  Wear sterile gloves and work from an appropriate sterile field. Use of a commercially prepared kit that contains all of the necessary materials is recommended.
  3. With sterile soapy cotton balls, or equivalent, cleanse urethral meatus and around the meatus.
  4. Rinse cleansed area beginning at urethra and working away from it with two successive cotton balls.
  5. Pass the sterile catheter (size 10 or 12 French) into the urethra and advance until urine flows freely. The first several milliliters from the catheter should be discarded, then collect the specimen into a sterile specimen cup.
  6. Urine samples can be obtained from indwelling catheters using a #28 needle and syringe. Be sure to disinfect the area where the needle puncture is to be made. Urine can be aspirated through the soft rubber connector between the catheter and collecting tubing.
  7. Do not obtain urine from catheter bags except in the case of neonates or young infants when special precautions have been taken.

1. National Committee for Clinical Laboratory Standards, Physician Office Laboratory Procedure Manual; Tentative Guidelines NCCLS Publication
    Pol 2-T, Villanova, PA, NCCLS 1989.
2. Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology. ASM Press. Washington DC. 2nd Edition

Quantitative urine cultures are indicated 1) at the time of percutaneous nephrostomy to rule out infection, 2) if the patient becomes ill or shows signs of sepsis.1 Culture is not recommended during routine tube changes. Collection of urine from old or used collection bag(s) leads to inaccurate diagnosis. Follow the collection instructions below. 2
ALERT: Do not collect a sample from urine in the existing collecting bag to avoid contaminants.

Specimen labels, new collection bag, sterile urine container, urine transport device, specimen bag, chlorhexidine aqueous solution or 70% isopropyl alcohol wipes, basic dressing pack, towel, or gauze swabs, gloves, securement device or adhesive dressing, waterproof underpad (e.g., Chux), appropriate personal protective equipment (PPE).3


  1. Identify the patient. Two forms of identification are required for proper identification.
  2. Explain procedure to the patient.
  3. Position the patient to in the upright position or a position of comfort.
  4. Position a waterproof underpad to prevent soiling of bed linen and clothing.
  5. Perform hand hygiene.
  6. Don appropriate PPE.
  7. Disconnect the distal tube (away from patient) from the proximal connector.
  8. Scrub the hub with 70% isopropyl alcohol wipes or chlorhexidine swabs. Let the liquid dry (preferably for 15-30 seconds).
  9. Using aseptic technique, carefully insert a new collection bag with a new CTU-30 tubing if needed (position collection bag below the kidney level).
  10. Allow urine to flow freely into the collection bag for 15-30 minutes. Urine allowed to collect or sit in a collection bag for more than 1 hour is considered contaminated and is not to be used as a sterile specimen.
  11. When at least 10 mL of urine has been collected in the new collection bag, open the bag valve over the sterile cup, ensuring the specimen remains sterile. Do not allow the valve or tip of the nephrostomy tube to touch the rim or inside wall of the cup.
  12. With sterile technique, aliquot urine into urine preservative tube using the urine transport device pictured above.
  13. Aseptically replace the lid on the specimen cup.
  14. Label the specimen with 2 patient identifiers and the sample collection date and time.
  15. Repeat the collection on the contralateral side, if applicable.
  16. Discard supplies, doff gloves, and perform hand hygiene.
  17. Place the specimen and its labels into a specimen bag. Immediately send the specimen to the laboratory.
  18. References:


  1. Batura D, Gopal Rao G. A systematic review of the clinical significance of nephrostomy urine cultures. World J Urol. 2020 Jan;38(1):45-55. doi: 10.1007/s00345-019-02663-4. Epub 2019 Feb 7. PMID: 30734071.
  2. Percutaneous nephrostomy (PCN) tube related infections. MD Anderson Cancer Center. Accessed 5/12/23.           
  3. Infection Prevention Policy Number 10008827. Transmission-based Precautions (Isolation Guidelines).

Revised: 8/10/2023

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