Microbiology — Sources (culture specimen sources) master file
Use the Sources master file to predefine the specimen sources available during microbiology result entry. Linking specific sources to each microbiology test reduces selection errors, speeds data entry, and ensures accurate reporting and interpretation. For example, if a Blood Culture test is linked only to “Blood,” users won’t see unrelated sources like “Urine” when entering results. If needed, users can switch to view all system sources (permission/config dependent).
Why standardize specimen sources
- Accuracy and safety: Correct source drives appropriate comments and may affect interpretation.
- Speed and simplicity: Short, curated lists mean fewer clicks and fewer mistakes.
- Consistency: Standardized names across benches and reports.
- Interoperability: Stable mapping to HL7/SNOMED supports clean interfaces to EHRs and middleware.
Examples of common sources
- Blood, CSF, Synovial fluid, Pleural fluid, Peritoneal fluid
- Urine (clean-catch, catheterized, suprapubic)
- Respiratory (sputum, tracheal aspirate, BAL, nasopharyngeal swab)
- Wound/abscess, Tissue, Bone, Catheter tip
- Stool, Throat swab, Nasal swab, Eye/ear swab
What you can configure
- Source name and internal code (required)
- Short name/abbreviation and display order
- Active status (activate/deactivate to control availability)
- Interface mappings (optional): HL7 specimen fields (e.g., SPM/OBR), SNOMED codes
Link sources to tests (scoping)
After you create a microbiology test, use the Sources (Advanced) button in Test Setup to associate specific specimen sources to that test. During result entry:
- The Source dropdown shows only the associated sources for that test.
- Users can optionally switch to “All system sources” if configured to allow exceptions.
Tip: You can also set a default source for a test to further speed up entry.
📘 Instructions: Add sources
Follow the steps below to add sources.
- Click Microbiology.
- Click Sources.
- When the form opens, fill in the fields marked with asterisks (e.g., Source Name/Code).
- Click Add to save.
Best practices
- Keep the list concise and use clear, clinician-friendly names.
- Use categories (e.g., Urine, Respiratory, Sterile fluid) to aid filtering and reporting.
- Scope sources to tests to avoid misclassification (e.g., “Blood” for Blood Culture only).
- Maintain mappings (HL7/SNOMED) for clean downstream integration.
- Deactivate obsolete sources.
- Where helpful, define variants (e.g., “Urine—clean catch,” “Urine—catheterized”) aligned with SOPs.
Troubleshooting
- Source not visible during entry: Ensure it’s Active and associated with the test via Sources (Advanced).
- Wrong or long list showing: Verify the test’s source associations; remove non-applicable sources.
- Interface mismatch in EHR: Review HL7/SNOMED mappings and update the source record accordingly.
- Users need to pick outside the scoped list: Allow “All system sources” as a temporary override (policy-permitting) and review whether the source should be added to the test’s list.