1. MLAB 2434 – MICROBIOLOGY KERI BROPHY-MARTINEZ
General Concepts in Specimen Collection and Processing

2. General Concepts in Specimen Collection and Processing (cont’d)
Basic Principles of Specimen Collection
Specimen should be taken in acute phase of infection AND before antibiotics are administered
Written order must specify site of culture (example: wound on left arm)

3. General Concepts in Specimen Collection and Processing (cont’d)
Avoid normal flora and colonizing organisms
Collect the appropriate quantity of specimen
Package specimen in correct transport media
Label with patient information & source
Transport the specimen to the lab asap to avoid deterioration

4. General Concepts in Specimen Collection and Processing (cont’d)
Appropriate Collection Techniques
Aspirates and tissues
Aspirates and tissues present few problems, if collected using sterile technique
Lesions, wounds and abscesses; cultures should be from as deep in the wound as possible

5. General Concepts in Specimen Collection and Processing (cont’d)
Swabs
Used only as a last resort. Dacron/polyester swabs preferred
Steps
Clean wound
Explore wound
Obtain fresh and quality culture material
Should be placed in a holding medium to protect pathogens without permitting multiplication during transport

6. General Concepts in Specimen Collection and Processing (cont’d)
Patient Education and Preparation
If patient is responsible for collecting specimen, good instructions are critical
Urine – midstream clean catch first morning specimen
Sputum – collect sputum NOT spit, morning specimens are preferred, deep cough
Stools – usually 3 vials and at least 4 days after barium X-rays, swabs are discouraged

7. General Concepts in Specimen Collection and Processing
Labeling & Requisition
Specimen must have patient name, time, date, source, location
Requisition
must accompany specimen, include diagnosis & antimicrobial history

8. General Concepts in Specimen Collection and Processing
Safety
Standard Precautions
Specimen processing should be conducted in a Class II safety cabinet (hood)

9. General Concepts in Specimen Collection and Processing (cont’d)
Preservation, Storage, and Transport of Specimens
Concerns
Overgrowth
Death of microorganisms: deliver to lab within 30 minutes of collection
Inaccurate quantitation
Loss of organisms from drying
Protection from oxygen
Protection from clotting
Safety of transporter

10. General Concepts in Specimen Collection and Processing (cont’d)
Anticoagulants
Needed in any specimen that might clot (blood, serum, joint fluids)
Sodium polyanethol sulfonate (SPS)
Most common anticoagulant in micro

11. General Concepts in Specimen Collection and Processing (cont’d)
Preservatives
Urine – boric acid for up to 24 hours
Stool – phosphate-buffered saline (PBS) or O & P kit

12. General Concepts in Specimen Collection and Processing (cont’d)
Use of Holding and Transport Media
Media should provide viability without allowing multiplication of bacteria
Media should maintain pH, provide proper atmospheric conditions and prevent drying

13. General Concepts in Specimen Collection and Processing (cont’d)
Types of collection devices

14. General Concepts in Specimen Collection and Processing (cont’d)
Blood culture bottles

15. General Concepts in Specimen Collection and Processing (cont’d)
Sterile container for sputum, urine, and other specimens

16. General Concepts in Specimen Collection and Processing (cont’d)
Aspirates are usually collected and transported in syringes

17. General Concepts in Specimen Collection and Processing(cont’d)
Storage of Specimens
Urine, viral blood specimens, catheters and swabs should be refrigerated (4oC)
Blood and CSF should be processed ASAP
Specimens for fungus cultures can be kept at room temperature
Respiratory and stool cultures should be processed ASAP if at all possible, but refrigerated if immediate processing is not possible
Anaerobes, genital, ear, eye cultures can be held at room temperature

18. General Concepts in Specimen Collection and Processing (cont’d)
Mailing specimens
Regulated by U.S. Dept. of Health and Human Services & U.S. postal Service
National guidelines issued by Department of transportation
Retraining of employees must occur every 2 years

19. Packaging Infectious Substances

20. General Concepts in Specimen Collection and Processing (cont’d)
Unacceptable Specimens
Labels on requisition and on specimen must match (unlabeled, mislabeled)
Noninvasive vs. invasive specimens
Rejected specimens
Leaking
Syringes with needles attached
Stools contaminated with urine or barium
Anaerobic cultures on inappropriate sources
Unpreserved specimens over 2 hours old

21. General Concepts in Specimen Collection and Processing (cont’d)
Unacceptable specimens
Refrigerated blood cultures
Dried-up specimens
Specimens in formalin
Improper collection
Delay in transport
**Do not discard rejected specimen until a new one is submitted, if original specimen is cultured, notate in patients report

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23. General Concepts in Specimen Collection and Processing
Processing of Clinical Samples for Optimal Organism Recovery
Prioritization
Level 1- Critical/invasive ( CSF)
Level 2 – Unpreserved (sputum)
Level 3 – Accuracy of quantitation affected (urine, no preservative)
Level 4 – Protected/Preserved (urine with preservative)

24. General Concepts in Specimen Collection and Processing (cont’d)
Gross Examination of Specimens
Check specimen for:
Volume submitted
Presence of blood or mucous
General appearance: cloudy, clear
Check requisition against sample

25. General Concepts in Specimen Collection and Processing (cont’d)
Direct Examination Techniques
Direct Microscopic Examination
Determine quality of specimen
Diagnose infectious disease
Guide routine culture interpretation
Dictate the need for nonroutine processing
Guide antibiotic therapy

26. General Concepts in Specimen Collection and Processing (cont’d)
Smear Preparation
Tissues
Swabs
Aspirates and body fluids
Single drop smear
Centrifuged sediment smear
Layered smear
Cytocentrifuged smear
Additives

27. General Concepts in Specimen Collection and Processing (cont’d)
Direct Smears NOT useful
Throats, nasopharyngeal swabs
Urine
Female genital tract
Stools

28. References
Engelkirk, P., & Duben-Engelkirk, J. (2008). Laboratory Diagnosis of Infectious Diseases: Essentials of Diagnostic Microbiology . Baltimore, MD: Lippincott Williams and Wilkins.
Mahon, C. R., Lehman, D. C., & Manuselis, G. (2011). Textbook of Diagnostic Microbiology (4th ed.). Maryland Heights, MO: Saunders.