Demo Workflow Guide

Overview

This guide walks through generating and managing ASP alerts. The system monitors three scenarios:

1. Bacteremia Alert - Patient with positive blood culture lacking appropriate antibiotic coverage
2. Antimicrobial Usage Alert - Patient on broad-spectrum antibiotics exceeding the 72-hour threshold
3. No Indication Alert - Patient receiving antibiotics without documented indication (classification: "Never appropriate")

Quick Start Commands

1. Generate a Blood Culture Alert

Create a patient with a positive blood culture (MRSA) without appropriate coverage:

cd /home/david/projects/aegis
python scripts/demo_blood_culture.py --organism mrsa

Then run the bacteremia monitor to detect and alert:

cd asp-bacteremia-alerts
python -m src.monitor

2. Generate an Antimicrobial Usage Alert

Create a patient on meropenem for 5 days (exceeds 72h threshold):

cd /home/david/projects/aegis
python scripts/demo_antimicrobial_usage.py --antibiotic meropenem --days 5

Then run the usage monitor:

cd antimicrobial-usage-alerts
python -m src.runner --once --verbose

3. Generate a No Indication Alert

Create a patient with an antibiotic order but viral diagnosis (no indication for antibiotics):

cd /home/david/projects/aegis
python scripts/demo_indication_alert.py --scenario viral_with_abx

Then run the indication monitor:

cd antimicrobial-usage-alerts
python -m src.runner --indication --once --verbose

Blood Culture Scenarios

Command	Scenario	Alert?
--organism mrsa	MRSA, no antibiotic	Yes
--organism mrsa --antibiotic vancomycin	MRSA with vancomycin	No
--organism mrsa --antibiotic cefazolin	MRSA with wrong antibiotic	Yes
--organism pseudomonas	Pseudomonas, no coverage	Yes
--organism pseudomonas --antibiotic meropenem	Pseudomonas with meropenem	No
--organism candida	Candida, no antifungal	Yes

Antimicrobial Usage Scenarios

Command	Duration	Alert Level
--antibiotic meropenem --days 2	48 hours	None
--antibiotic meropenem --days 4	96 hours	Warning
--antibiotic vancomycin --days 7	168 hours	Critical
--antibiotic ceftriaxone --days 5	120 hours	None (not monitored)

Indication Monitoring Scenarios

The indication monitor classifies antibiotic orders using ICD-10 codes and clinical note extraction. Only "Never appropriate" (N) classifications generate alerts.

Demo Scenarios

Scenario	Description	Alert?
--scenario pneumonia	Bacterial pneumonia (ICD-10 + note)	No (Always appropriate)
--scenario uti	Urinary tract infection	No (Always appropriate)
--scenario viral_uri	Viral upper respiratory infection (no antibiotics)	No (No antibiotics ordered)
--scenario viral_with_abx	Viral URI with unnecessary antibiotics	Yes (Never appropriate)
--scenario no_indication_documented	Antibiotics with no documented indication	Yes (Never appropriate)
--scenario note_contradicts_icd10	ICD-10 says pneumonia, note says viral	Yes (Note overrides ICD-10)

Classification Categories

Category	Meaning	Alert?
A	Always appropriate for antibiotics	No
S	Sometimes appropriate	No
P	Prophylaxis appropriate	No
N	Never appropriate	Yes

Two-Track Classification

The system uses two sources to determine if an antibiotic has an appropriate indication:

1. ICD-10 Classification - Uses Chua et al. pediatric antibiotic indication mappings
2. LLM Note Extraction - Extracts indications from clinical notes using a local LLM

Note Priority: Clinical notes take precedence over ICD-10 codes. If a note explicitly states "viral infection" but the patient has a pneumonia ICD-10 code, the system classifies as "N" (never appropriate) based on the note.

Alert Resolution Workflow

1. View - Click on an alert to see details
2. Acknowledge - Mark as seen (stays in active list)
3. Snooze 4h - Temporarily suppress the alert
4. Resolve - Close with a resolution reason:
   • Acknowledged - No action needed
   • Messaged Team - Contacted the care team
   • Discussed with Team - Had discussion with providers
   • Therapy Changed - Antibiotic regimen was modified
   • Therapy Stopped - Antibiotic was discontinued
   • Patient Discharged - Patient left the hospital

Resolved alerts move to the History tab with a full audit trail.

Interactive Demo Mode

For live demos where the audience can choose scenarios:

# Blood culture - choose organism and antibiotic interactively
python scripts/demo_blood_culture.py --interactive

# Antimicrobial usage - choose drug and duration interactively
python scripts/demo_antimicrobial_usage.py --interactive

Troubleshooting

FHIR server not responding

# Check if container is running
docker ps | grep hapi

# Restart if needed
cd asp-bacteremia-alerts
docker-compose down && docker-compose up -d

Clear all data and start fresh

# Clear FHIR server data
cd asp-bacteremia-alerts
docker-compose down && docker-compose up -d

# Clear alert database
rm -f ~/.aegis/alerts.db

Verify data was uploaded

curl "http://localhost:8081/fhir/Patient?_count=5" | python -m json.tool

Architecture

+-------------------+     +-------------------+
|   Demo Scripts    |---->|  HAPI FHIR        |
|   (add patients)  |     |  Server :8081     |
+-------------------+     +---------+---------+
                                    |
         +--------------------------+--------------------------+
         v                          v                          v
+-------------------+    +-------------------+    +-------------------+
|   Bacteremia      |    |  Broad-Spectrum   |    |   Indication      |
|    Monitor        |    |  Usage Monitor    |    |    Monitor        |
+---------+---------+    +---------+---------+    +---------+---------+
         |                        |                        |
         |                        |               +--------+--------+
         |                        |               v                 v
         |                        |      +-------------+   +-------------+
         |                        |      | ICD-10      |   | LLM Note    |
         |                        |      | (Chua)      |   | Extraction  |
         |                        |      +------+------+   +------+------+
         |                        |             |                 |
         |                        |             +--------+--------+
         |                        |                      |
         +------------------------+----------------------+
                                  v
                        +-------------------+
                        |   Alert Store     |
                        |   (SQLite)        |
                        +---------+---------+
                                  |
                   +--------------+---------------+
                   v              v               v
          +-----------+   +-----------+   +-----------+
          | Dashboard |   |   Teams   |   |   Email   |
          +-----------+   +-----------+   +-----------+