AI agent for microbiologists
Culture Contamination Investigation Agent
Find the most likely contamination source and confirm it with tests.
What it does
When plates or flasks turn up contaminated, the cause could be a media batch, an incubator, a hood, a reagent or a person's technique, and tracing it takes days of asking around. This agent collects the logs for every affected and unaffected culture: media lot, incubator, hood, user, date, passage, reagents and any organism identification. It looks for what the affected group shares that the clean group does not, and ranks the suspect sources. It proposes tests for the top ones, such as sterility checks on the media lot or swabs of the incubator, and updates the ranking as results arrive. It keeps testing the next suspect when the top one is cleared. It never takes action. The scientist approves actions. Edge case: contaminants that match skin flora point to technique or handling before equipment.
How it works
Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.
Read the steps as a list
- Contamination reported
- Collect logs for affected and unaffected cultures
- Find what affected cultures share that clean ones do not
- Rank suspect sources using the contaminant type and propose a test for each
- Scientist approves the testsThe agent waits here for your OK.
- Read test results and update the ranking
- Does a tested source explain the pattern in all affected cultures?If not: clear that source and test the next one in the ranking. Back to step 4.
- Propose corrective actions for the confirmed source
- Do new cultures stay clean after the action?If not: reopen the ranking with the new data. Back to step 3.
- Scientist approves the actionsThe agent waits here for your OK.
- Investigation record
How it decides
It ranks a source by how strongly it separates the affected from the unaffected cultures, with extra weight when the contaminant type fits the source.
- Rank a source higher if all affected cultures share it and no clean culture does
- Test the cheapest high-ranked source first
- Point to technique first when the contaminant matches skin flora
- Close the case only after 2 weeks of clean cultures
Make it yours
Every agent is a starting point. You choose these settings for your own situation.
- Logs to include
- Clean period to close (default 14 days)
- Test options available
- Contaminant types to track
- Record template
What keeps you in control
It always asks you first
- Tests to run
- Corrective actions such as discarding media
Hard limits
- Never discard materials or accuse a person
- Keep all ranked sources in the record
It stops when
- Done: source confirmed and cultures stay clean
- Stop: no source separates the groups
Set it up
We guide you through the set-up, step by step
Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.
- One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
- The agent then walks you through connecting your own data, one source at a time
- A downloadable copy with the flow chart, the rules and the full guide
