Microbiology Sample Collection Guidelines and Rejection Criteria

Proper collection and transport of the biological specimens to the laboratory for culture is the most crucial step in the recovery of pathogenic organisms responsible for infectious diseases. A poorly collected specimen may lead to failure to recover the causative organism(s) and/or result in the recovery of contaminating organisms. This will lead to incorrect or harmful therapy if treatment is directed toward commensal or contaminant organisms.

Microbiology Sample Collection Criteria

  1. Collect the specimen from the actual site of infection, avoiding contamination from adjacent tissues, organs, or secretions
  2. Collect the specimen at optimal times (for example, early morning sputum for the culture of acid-fast bacillus) to provide the best chance of recovering causative microorganisms.
  3. Whenever possible, collect specimens prior to administration of antimicrobial agents.
  4. A sufficient quantity of material must be obtained to perform the test.
  5. Properly label the specimen and complete the test request form. Mention the specific source of the specimen.  Each culture container must have a legible label with the following minimum information:
    1. Patient name
    2. Patient identification number
    3. Source of specimen
    4. Name of clinician
    5. Date/hour of collection
  6. To ensure optimal recovery of microorganisms:
    1. Use appropriate collection devices: sterile, leak-proof specimen containers.
    2. Use appropriate transport media (anaerobe transport vials, Cary-Blair media, M4RT for viral and Chlamydia cultures, and urine boric acid transport).
    3. Use appropriate culture media
    4. Minimize transport time. Maintain an appropriate environment between a collection of specimens and delivery to the laboratory.
  7. Ensure that the proper transport system is utilized for orders with more than one test. (For example, anaerobic culture requests need to be submitted in anaerobic transport media; bacteriology requests should not be in viral transport media; AFB requests should not be in anaerobic transport media.)

Microbiology Sample Rejection Criteria

Microbiology lab should have a policy that defines conditions in which a specimen is unacceptable for processing. Specimen rejection criteria should be distributed to all clinical practitioners. Requesting physicians or nursing in charge should always be notified upon receipt of these specimens before discarding them. Such communications should be documented in the laboratory information systems (LIS) with the date and time.

It may be necessary to process some specimens even though they are not clearly identified if they are difficult to repeat. Such  irretrievable specimens include CSF, surgical fluid/tissue/swabs, post mortem specimens, blood cultures/ tips. A notation regarding improper collection should be added to the final report so that physician is able to determine the validity of the results.

This post outlines some of the essential criteria for the rejection of clinical samples for microbiology tests. 

Clerical Errors

  1. Unlabeled or incorrectly labeled specimens: Unlabeled (no identification on the container) or incorrectly marked specimens (when compared with its accompanying request form) should not be accepted for analysis. When a discrepancy is seen between patient identification on the requisition form and specimen container label, request a new specimen or have the requesting physician or nurse correct the error in person in the laboratory (identification of a mislabeled specimen or requisition should not be made over the telephone).
  2. Specimens received without a request form: If a specimen is received without a request form, ask for a correctly completed request. However, if the request form is not received on the same day, do not process the specimen.
  3. Request forms received without specimen: If a matching specimen is not received by the end of the working day, issue a report stating that no specimen was received with the request form.
  4. Specimens received with a request form devoid of any patient demographic details: Request for a correctly completed request form. However, if the correctly completed request form is not received on the same day, do not process the specimen.
  5. Missing vital information in the requisition form: If the specimen source or type or requested test name is not noted in the requisition form, call the physician or charge nurse to ascertain the missing information.

Inappropriate Containers/Conditions

  • Specimens are received in improper or non-sterile containers, leaking containers, or transport media: Leaking or damaged specimens should not be accepted for analysis. Return requisition with appropriate comment. Notify the physician and request a properly handled specimen.
  • Specimen for anaerobes not received in an appropriate container: If specimens for anaerobic bacteria are submitted in aerobic transport, notify the physician or charge nurse. If the physician insists specimen be processed, refer to supervisory personnel or comment in the laboratory record and report form that inappropriate transport may have influenced the recovery of significant anaerobic bacteria.
  • Specimen received in fixative (formalin); exception, stool for parasites and ova: If the specimen is received in a fixative (formalin), it kills any microorganism present in the sample. In such cases, the laboratory should notify the physician and request to send a new proper specimen; record on requisition “specimen unsatisfactory; received in preservative.”

Delay in Transit or Improper transport

  1. Specimens received that have been delayed in transit (specimen transport time exceeds 2 hours post collection and the specimen is not preserved): Reject the samples that have been delayed in transit as unsuitable for processing.
  2. The specimen has been transported at the improper temperature: Reject the sample and request a new specimen.

Inappropriate specimens

  1. Dry swab: Notify physician or charge nurse and request to submit proper specimen in an appropriate transport device. If a physician insists dry swabs be cultured, note on the laboratory record and report with a caveat: “microorganisms recovered may not reflect actual microbiota.”
  2. Foley catheter tip: Processing specimens like Foley catheter tip may produce information of questionable medical value, so the physician should be notified that the specimen is not suitable for microbiological analysis. Note rejection on requisition and return.
  3. Unpreserved urine held in the refrigerator for >24 hours: Notify the physician or nurse in charge and request a new specimen. Return requisition with appropriate comment.
  4. Sputum specimen with 25 < WBC, >10 epithelial cells/lpf: Inform physician or charge nurse that specimen is mostly saliva and is not appropriate for culture. Request a repeat specimen.
  5. 24-h collection of urine or sputum for AFB or fungus culture: Inform physician or nurse that according to laboratory manual, three separate first morning specimens of sputum or of urine are the best samples for analysis; reject 24-h specimens.
  6. Gram stain for Neisseria gonorrhoeae on specimens from cervix, vagina, and anal crypts: As these anatomic locations may harbor nongonococcal Neisseria giving false-positive results, the smear should not be examined. Notify the physician or charge nurse why these smears are unsuitable for processing.
  7. Specimen received for anaerobic culture from a site known to have anaerobes as part of the normal flora such as mouth, vagina, fistula or intestinal contents, samples from ileostomy or colostomy, etc. should not be processed and the physician should be informed accordingly.

Inadequate specimens

Many times laboratory receives an insufficient quantity of specimens for testing; in those cases, the laboratory should seek additional material or test prioritization. For example;

  1. If only one swab is submitted with multiple requests for various organisms (bacteria, AFB, fungi, virus, ureaplasma, etc.), ask the physician to send the additional samples or to prioritize test requests.
  2. If sputum swabs for AFB or fungal culture are received, notify the physician or charge nurse that the specimen is inadequate in quantity for the isolation of these microorganisms. Request properly collected samples.

Excess specimens

  1. If more than one specimen of urine, stool, sputum, wound or routine throat specimens were submitted on the same day from the same source. Notify the physician or charge nurse that, as stated in the laboratory manual, only one specimen will be processed per day.

References and further readings

  1. Andrea J. Linscott, 2016. 2.1. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, Clinical Microbiology Procedures Handbook, 4th Edition. ASM Press, Washington, DC. doi: 10.1128/9781683670438.CMPH.ch2.1
  2. Procop, G. W., & Koneman, E. W. (2016). Koneman’s Color Atlas and Textbook of Diagnostic Microbiology (Seventh, International edition). Lippincott Williams and Wilkins.
  3. Tille, P. (2017). Bailey & Scott’s Diagnostic Microbiology (14 edition). Mosby.

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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