Sample Types and Specimen Quality
Related MOCs: MOC - Diagnostic & Lab Methods · MOC - Clinical Microbiology
Related: DNA Extraction · RNA Extraction · Culture and Isolation · PCR
1. Principle
Pre-analytical choices — which site, which tube, how fast it arrives — dominate diagnostic sensitivity more often than the chemistry of the assay itself.
2. Step-by-Step Procedure (conceptual checklist)
- Match specimen to syndrome (CSF for meningitis, lower respiratory for pneumonia, paired blood cultures for bacteremia).
- Use correct preservative (EDTA/sterile container/viral transport medium/Copan eSwab; avoid heparin for some PCR).
- Collect before antibiotics when possible (culture); document therapy for molecular interpretation.
- Transport under validated conditions (cold chain for RNA viruses).
- Reject/qualify inadequate samples (dry swabs, unlabeled, delayed stool for C. difficile toxins per policy).
3. Interpretation
- Adequate specimen: Anatomically relevant, volume OK, properly preserved.
- Pitfalls: Upper respiratory PCR colonization (PCR note); saliva vs NP for viruses; swabs for WGS outbreaks need isolate cultures when possible.
4. Clinical Use Cases
- Every NAAT/WGS/culture workflow starts here.
- Infection control screens (MRSA nasal, VRE rectal) vs diagnostic specimens — different pretest probability.
5. Comparison with Other Methods
| Issue | Culture impact | Molecular impact |
|---|---|---|
| Antibiotics before draw | May sterilize culture | DNA/RNA may persist |
| Delay at room temp | Overgrowth / death | RNA degradation |
| Wrong site | Misleading flora | Colonization positives |
6. Mnemonic / Visual Aid
Garbage in → genome out (garbage). Preanalytics first.
Related Concepts
Active Recall
- Why might blood culture be negative but plasma microbial cfDNA positive?
- Name one anticoagulant that can inhibit PCR.
- Why document antibiotic exposure on the requisition?