Geisinger Medical Laboratories Microbiology Specimen Collection Instructions



I.  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.


Koneman EW. 1988. Color Atlas and Textbook of Diagnostic Microbiology, 3rd ed., JP Lippincott, Philadelphia.

Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology. ASM Press. Washington DC. 2nd Edition

II. 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.

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

III.  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.


National Committee for Clinical Laboratory Standards, Physician Office Laboratory Procedure Manual; Tentative Guidelines NCCLS Publication Pol 2-T, Villanova, PA, NCCLS 1989.

Miller JM. 1999. A Guide to Specimen Management in Clinical Microbiology. ASM Press. Washington DC. 2nd Edition


NOTE: The patient should be instructed not to take antacids, oily laxatives, or antidiarrheal medication unless prescribed by a physician, prior to the collection of the sample(s). Radiological examinations utilizing contrast chemicals (e.g., bismuth, barium) should be avoided prior to collection of the fecal specimen for parasite analysis.

  1. You have been asked to collect a stool sample for laboratory analysis. The collection set may contain 1, 2, or 3 vials. If multiple specimens must be collected, collect on consecutive days, not on the same day. The vials will contain liquid. NOTE: The liquids are poisonous. Do not drink or pour out liquid. Keep out of the reach of children or pets.

  2. IMPORTANT: Please wash hands before beginning the procedure.
    DO NOT pass the specimen into the toilet.
    DO NOT pass the specimen directly into the collection vial.
    DO NOT urinate on the specimen or into the collection vial.
    DO NOT allow any water to mix with the specimen.

  3. Collect the stool specimen (bowel movement) in any clean, dry wide-mouth container, bedpan, or on a plastic plate or clean newspaper, plastic bag, or clean diaper. This prevents the fecal specimen from falling into the toilet bowl. Collection device (e.g. diaper, newspaper, bedpan) must not be sent to the laboratory. The stool sample must be transferred to the appripriate transport device(s) before being sent to the laboratory.

  4. Carefully open the TotalFix vial (ova and parasite testing only) and/or C&S Medium (Cryptosporidium, Giardia and culture) 

  5. Using the spoon attached to cap, add approximately three spoonfuls of firm stool, or five spoonfuls of soft stool, to each vial. It is important to sample areas of the specimen which appear bloody, slimy, or watery. If the stool is firm, sample small amounts from each end and the middle of the specimen. Fill each vial with enough specimen so that the liquid reaches the “fill line” located on the label.

    NOTE: Hard stools are not acceptable for routine culture.

  6. Thoroughly mix the specimen and the liquid in the vial using the spatula. Fill only one vial at a time and replace the spoon/cap onto the same vial it came from. Do not mix spoons/caps with other vials.
  7. Replace the spoon/cap and close tightly.
  8. Shake each vial until the specimen is well mixed with the liquid in the vial.
  9. Label the vials with:
    1. Patient name, medical record number and/or date of birth.
    2. Date and time specimen was collected.
    3. Specimen number if more than one specimen was taken, for example #1, #2, and #3.
    4. Check the box that best describes your stool sample.
    5. Please note on the label if specimen is bloody.

  10. Place the vial(s) in the original package and seal securely. Store and transport specimens at 2-8oC (refrigerated). Return specimen(s) to the laboratory as soon as possible.

  11. Wash hands thoroughly with soap and water.

  12. IMPORTANT: If any liquid from the vial or stool specimen gets into your eyes or on your skin, rinse the area with plenty of water. If any discomfort or irritation develops, contact a physician.

    ANTIDOTE IF SWALLOWED: Give plenty of milk or water. Follow with a tablespoon of salt in a glass of warm water and repeat until the vomit is clear. Contact a physician or local poison control center IMMEDIATELY.

Alpha-Tec Product Insert. Directions for Stool Specimen Collection Set. 2005.



Pseudomembranous colitis (PMC) related to antimicrobial therapy is caused primarily by Clostridium difficile toxin. C. difficile may also be involved in a similar disease not related to antimicrobial therapy but following the use of methotrexate and other cytotoxic agents, in exacerbations of inflammatory bowel disease, and in complications of strangulation obstruction of the bowel. The C. difficile PCR assay is a rapid method for the detection of C. difficile toxin B gene DNA in human fecal samples, to be used as an aid in the detection of C. difficile associated disease.

Rotavirus is a major cause of acute gastroenteritis, especially in children 6 to 24 months of age. In addition, rotavirus infections can produce severe illness as well as asymptomatic infection in adults. The incubation period of rotavirus infection is usually 1-3 days followed by gastroenteritis with an average duration of 5-8 days. Virus titers are highest shortly after the onset of illness. Rotavirus EIA is a rapid method for detecting rotavirus in stools.

A positive test result for lactoferrin indicates an increased level of fecal lactoferrin and warrants additional testing. Inflammatory diarrheas are caused by pathogens such as Shigella, Salmonella, Capylobacter jejnuii and Clostridium difficile. In inflammatory diarrheas, fecal leukocytes are found in feces in large numbers. This test may not be appropriate for immunocompromised patients.


  1. C. difficile - Stool/feces: Collect a minimum of 2 mL of stool sample in an appropriately labeled sterile container. Specimens should be liquid or soft. (Formed, hardened stool specimens are not acceptable for Clostridium difficile testing.) Store and transport to the laboratory at 2-8°C.

  2. Rotavirus - Stool/Feces: Collect a minimum of 2 mL of stool sample in an appropriately labeled sterile container. Store and transport to the laboratory at 2-8°C.

  3. Lactoferrin EIA - Stool/Feces: Collect a minimum of 1-2 mL of stool sample in an appropriately labeled sterile container. Store and transport to the laboratory at 2-8°C.

Revised: 3/1/2015

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