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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Packaging Infectious Substances

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

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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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)

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

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

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

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

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.