MLAB 2434 – MICROBIOLOGY KERI BROPHY-MARTINEZ

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. • http://catalog.bd.com/bdCat/search.doCustomer?searchText=urine+culture&typeOfSearch=0&viewPageNum=0&sortByField=Category&x=0&y=0 • http://coe.berkeley.edu/news-center/publications/engineering-news/archive/engineering-news-vol-79-no-9f/need-a-study-break-here-are-a-few-ideas • http://www.firstqualitylaboratory.com/pages/specimenpreparation.html • http://www.lookfordiagnosis.com/images.php?term=Polyanetholesulfonate&lang=1 • Mahon, C. R., Lehman, D. C., & Manuselis, G. (2011). Textbook of Diagnostic Microbiology (4th ed.). Maryland Heights, MO: Saunders.