HAI Detection - Demo & Help

Overview

The NHSN HAI Reporting module assists Infection Preventionists in identifying and classifying Healthcare-Associated Infections (HAIs) for NHSN reporting. Currently supported:

• CLABSI - Central Line-Associated Bloodstream Infections
• CAUTI - Catheter-Associated Urinary Tract Infections
• SSI - Surgical Site Infections (Superficial, Deep, Organ/Space)
• VAE - Ventilator-Associated Events (VAC, IVAC, Possible/Probable VAP)
• CDI - Clostridioides difficile Infections (HO-CDI, CO-CDI, CO-HCFA)

The system uses a four-stage workflow:

1. Rule-based screening - Identifies candidates (BSI + line for CLABSI; catheter + positive urine for CAUTI; procedure + infection signals for SSI; ventilator worsening for VAE; positive C. diff test for CDI)
2. LLM fact extraction - Extracts clinical facts from notes (symptoms, alternate sources, wound assessments)
3. Rules engine - Applies deterministic NHSN criteria to extracted facts
4. IP Review - ALL candidates go to IP for final decision

Key principle: The LLM extracts facts and provides a preliminary classification with confidence score, but the Infection Preventionist always makes the final determination. This ensures human oversight on all HAI decisions.

Quick Start - Generate Demo Data

Create CLABSI Candidates

Generate demo patients with CLABSI scenarios for testing:

# Create one CLABSI + one Not CLABSI (random type)
cd /home/david/projects/aegis
python scripts/demo_clabsi.py

# Create all scenario types
python scripts/demo_clabsi.py --all

# Create a specific scenario
python scripts/demo_clabsi.py --scenario clabsi
python scripts/demo_clabsi.py --scenario mbi
python scripts/demo_clabsi.py --scenario secondary-uti
python scripts/demo_clabsi.py --scenario secondary-pneumonia

Create CAUTI Candidates

Generate demo patients with CAUTI (Catheter-Associated UTI) scenarios:

# Create one CAUTI + one Not CAUTI (random type)
cd /home/david/projects/aegis
python scripts/demo_cauti.py

# Create all scenario types
python scripts/demo_cauti.py --all

# Create a specific scenario
python scripts/demo_cauti.py --scenario cauti
python scripts/demo_cauti.py --scenario asymptomatic-bacteriuria
python scripts/demo_cauti.py --scenario not-cauti

Create SSI Candidates

Generate demo patients with SSI (Surgical Site Infection) scenarios:

# Create one SSI + one Not SSI (random type)
cd /home/david/projects/aegis
python scripts/demo_ssi.py

# Create all scenario types
python scripts/demo_ssi.py --all

# Create a specific scenario
python scripts/demo_ssi.py --scenario superficial
python scripts/demo_ssi.py --scenario deep
python scripts/demo_ssi.py --scenario organ-space
python scripts/demo_ssi.py --scenario not-ssi

Create CDI Candidates

Generate demo patients with CDI (C. difficile Infection) scenarios:

# Create one CDI + one Not CDI (random type)
cd /home/david/projects/aegis
python scripts/demo_cdi.py

# Create all scenario types
python scripts/demo_cdi.py --all

# Create a specific scenario
python scripts/demo_cdi.py --scenario ho-cdi
python scripts/demo_cdi.py --scenario co-cdi
python scripts/demo_cdi.py --scenario co-hcfa
python scripts/demo_cdi.py --scenario recurrent
python scripts/demo_cdi.py --scenario not-cdi

Run the Full Pipeline

After creating demo data, run the HAI monitor to detect and classify candidates:

cd /home/david/projects/aegis/hai-detection
python -m src.runner --full

This will:

1. Detect new CLABSI candidates from FHIR
2. Run LLM extraction and rules engine classification
3. Create review entries in the IP Review Queue

Then go to the Dashboard to review and make final decisions on the new cases.

CLABSI Demo Scenarios

Scenario	Command	Organism	Key Evidence	Classification
Clear CLABSI	--scenario clabsi	S. aureus	Line site infection, negative UA, clear CXR	CLABSI
MBI-LCBI	--scenario mbi	E. coli	BMT patient, ANC 0, Grade 3 mucositis	Not CLABSI - MBI
Secondary (UTI)	--scenario secondary-uti	E. coli	Same organism in blood + urine, pyelonephritis on CT	Not CLABSI - Secondary
Secondary (PNA)	--scenario secondary-pneumonia	Pseudomonas	Same organism in blood + respiratory, VAP on CXR	Not CLABSI - Secondary

CAUTI Demo Scenarios

CAUTI (Catheter-Associated Urinary Tract Infection) detection follows NHSN criteria requiring catheter >2 days, positive culture, and qualifying symptoms:

Scenario	Command	Catheter Days	Key Evidence	Classification
Clear CAUTI	--scenario cauti	5 days	E. coli 10^5 CFU/mL, fever 38.5°C, dysuria	CAUTI
CAUTI (Fever Only, Young)	--scenario cauti-fever	4 days	Klebsiella 10^5 CFU/mL, fever 38.8°C (patient age 50)	CAUTI
Asymptomatic Bacteriuria	--scenario asb	5 days	Positive culture, no symptoms documented	Asymptomatic Bacteriuria
Fever Only (Elderly)	--scenario fever-elderly	2 days	Fever 38.5°C, patient age 75, catheter ≤2 days	Not CAUTI (Age Rule)
Not Eligible (Mixed Flora)	--scenario mixed-flora	5 days	>2 organisms (mixed flora culture)	Not Eligible
Not Eligible (Candida)	--scenario candida	5 days	Candida albicans only (yeast excluded)	Not Eligible

Note: The age-based fever rule requires patients >65 years to have catheter >2 days for fever alone to qualify as a CAUTI symptom.

SSI Demo Scenarios

Scenario	Command	Procedure	Key Evidence	Classification
Superficial SSI	--scenario superficial	Cholecystectomy	Purulent drainage, erythema, positive wound culture	Superficial SSI
Deep SSI	--scenario deep	Colectomy	Fascial dehiscence, fever >38C, deep tissue involved	Deep SSI
Organ/Space SSI	--scenario organ-space	Colectomy	Pelvic abscess on CT, positive drain culture	Organ/Space SSI
Not SSI	--scenario not-ssi	Total Knee	Wound healing well, no infection signs	Not SSI

VAE Demo Scenarios

VAE (Ventilator-Associated Event) detection follows the NHSN tiered classification hierarchy:

Scenario	Command	Ventilator Days	Key Evidence	Classification
VAC Only	--scenario vac	Day 5	FiO2 +25%, no fever, no antibiotics	VAC (Tier 1)
IVAC	--scenario ivac	Day 7	PEEP +4 cmH2O, fever 38.8°C, vancomycin x5 days	IVAC (Tier 2)
Possible VAP	--scenario possible-vap	Day 8	IVAC criteria + positive sputum culture	Possible VAP (Tier 3)
Probable VAP	--scenario probable-vap	Day 10	IVAC criteria + purulent secretions + BAL 10^5 CFU/mL	Probable VAP (Tier 3)
Not VAE	--scenario not-vae	Day 3	Stable ventilator settings, no worsening	Not VAE

Note: VAE detection requires access to ventilator parameter data (FiO2/PEEP) from the EHR.

CDI Demo Scenarios

CDI (Clostridioides difficile Infection) detection follows NHSN LabID Event criteria with time-based onset classification:

Scenario	Command	Specimen Day	Key Evidence	Classification
HO-CDI	--scenario ho-cdi	Day 5	Positive toxin A/B, unformed stool, >3 days after admission	HO-CDI
CO-CDI	--scenario co-cdi	Day 2	Positive toxin A/B, unformed stool, ≤3 days after admission	CO-CDI
CO-HCFA	--scenario co-hcfa	Day 2	CO-CDI + discharged from facility within prior 4 weeks	CO-HCFA
Recurrent CDI	--scenario recurrent	Day 5	Positive test 30 days after prior CDI episode	Recurrent HO-CDI
Duplicate (Not Reported)	--scenario duplicate	Day 3	Positive test 10 days after prior CDI (within 14-day window)	Duplicate
Not CDI (GDH Only)	--scenario gdh-only	Day 4	GDH antigen positive, toxin negative (does not qualify)	Not CDI

Note: CDI classification is time-based. Day 1 = admission date. HO-CDI = specimen day >3. CO-CDI = specimen day ≤3.

IP Review Decisions

When reviewing a CLABSI candidate, you (the Infection Preventionist) make the final determination. The LLM classification and confidence score are shown as decision support, but you always have the final say.

NHSN CLABSI Criteria Quick Reference

Inclusion Criteria

• Patient has a central line at time of BSI OR within 1 calendar day of line removal
• Central line was in place for >2 calendar days on the date of event
• Patient has a laboratory-confirmed bloodstream infection (LCBI)
• BSI is not secondary to an infection at another site

LCBI Criteria

Criterion 1 (Pathogen): Recognized pathogen identified from blood culture not related to infection at another site

Criterion 2 (Contaminant): Common skin contaminant (e.g., CoNS, Corynebacterium) identified from 2+ blood cultures drawn on separate occasions, PLUS patient has fever (>38.0°C), chills, or hypotension

Exclusion: Secondary BSI

A BSI is considered secondary if the same organism is isolated from another site AND:

• The other site infection meets NHSN site-specific criteria, OR
• The clinical presentation is consistent with infection at the other site

NHSN SSI Criteria Quick Reference

Surveillance Window

• 30 days - Standard for most procedures
• 90 days - Procedures with implants (prosthetics, hardware)

Wound Classification

• Class 1 (Clean) - No inflammation, no break in technique, respiratory/GI/GU not entered
• Class 2 (Clean-Contaminated) - Controlled entry into GI/GU/respiratory tract
• Class 3 (Contaminated) - Acute inflammation, gross spillage from GI tract
• Class 4 (Dirty-Infected) - Old traumatic wound, existing infection

Superficial Incisional SSI (any one)

• Purulent drainage from superficial incision
• Organisms from aseptically-obtained culture from superficial incision
• Signs (pain, swelling, erythema, heat) + incision opened by surgeon (unless culture-negative)
• Physician diagnosis of superficial incisional SSI

Deep Incisional SSI (any one)

• Purulent drainage from deep incision (but not organ/space)
• Deep incision spontaneously dehisces OR deliberately opened AND fever (>38°C) or pain
• Abscess in deep incision found on exam, reoperation, imaging, or histopath
• Physician diagnosis of deep incisional SSI

Organ/Space SSI (any one)

• Purulent drainage from drain placed in organ/space
• Organisms from culture of fluid/tissue from organ/space
• Abscess in organ/space found on exam, reoperation, imaging, or histopath
• Physician diagnosis of organ/space SSI

Common Organ/Space Sites

NHSN codes: IAB (intra-abdominal), MED (mediastinitis), BONE (osteomyelitis), DISC (disc space), JNT (joint), MEN (meningitis)

NHSN CAUTI Criteria Quick Reference

Inclusion Criteria

• Indwelling urinary catheter (IUC) in place for >2 calendar days on date of event
• IUC was in place on the date of event OR removed the day before
• Patient has a positive urine culture meeting criteria
• Patient has at least one qualifying symptom (not asymptomatic bacteriuria)

Culture Criteria

• CFU/mL: ≥10⁵ CFU/mL (100,000 colony-forming units per mL)
• Organism count: ≤2 organisms identified (no mixed flora)
• Excluded organisms: Candida species, yeast, and other fungi

Qualifying Symptoms (at least one)

• Fever: Temperature >38.0°C (100.4°F)
• Suprapubic tenderness: Pain/tenderness over the bladder
• CVA pain/tenderness: Costovertebral angle (flank) tenderness
• Urinary urgency: Sudden compelling need to urinate
• Urinary frequency: Increased frequency of urination
• Dysuria: Pain or burning with urination

Age-Based Fever Rule

Special consideration for fever as the only symptom:

• Patient ≤65 years: Fever alone qualifies as a CAUTI symptom
• Patient >65 years: Fever alone requires catheter >2 days; otherwise, another symptom must be present

This rule helps distinguish CAUTI from other causes of fever in elderly catheterized patients.

Asymptomatic Bacteriuria

If catheter and culture criteria are met but NO symptoms are documented, the case is classified as:

• Asymptomatic bacteriuria (ASB) - Not reported as CAUTI
• ASB cases require IP review to confirm no symptoms were missed in documentation
• ASB is common in catheterized patients and should not be treated unless symptomatic

Common Uropathogens

Organisms typically associated with CAUTI:

• Escherichia coli (most common)
• Klebsiella pneumoniae
• Enterococcus faecalis
• Pseudomonas aeruginosa
• Proteus mirabilis
• Enterobacter species

NHSN VAE Criteria Quick Reference

VAE Hierarchy (NHSN Tiers)

VAE classifications are hierarchical - higher tiers include all criteria from lower tiers:

Classification	Tier	Requires
VAC (Ventilator-Associated Condition)	1	Baseline period + sustained worsening
IVAC (Infection-related VAC)	2	VAC + temperature/WBC + antimicrobials
Possible VAP	3	IVAC + purulent secretions OR positive culture
Probable VAP	3	IVAC + purulent secretions + quantitative culture

VAC Criteria

Baseline Period (≥2 calendar days):

• Patient on mechanical ventilation
• Stable or decreasing daily minimum FiO2 or PEEP

Worsening Period (≥2 calendar days after baseline):

• Daily minimum FiO2 increased ≥20 percentage points over baseline minimum, OR
• Daily minimum PEEP increased ≥3 cmH2O over baseline minimum

VAC onset date = first day of the worsening period

IVAC Criteria (VAC + all of the following)

• Temperature: >38°C or <36°C
• WBC: ≥12,000 cells/mm³ or ≤4,000 cells/mm³
• Antimicrobials: New qualifying antimicrobial started within ±2 calendar days of VAC onset AND continued for ≥4 calendar days

Possible VAP Criteria (IVAC + one of the following)

• Purulent secretions: ≥25 neutrophils and ≤10 squamous epithelial cells per low power field
• Positive culture: Positive respiratory culture (any growth)

Probable VAP Criteria (IVAC + both of the following)

• Purulent secretions: As defined above
• Quantitative culture meeting threshold:
  • BAL (bronchoalveolar lavage): ≥10⁴ CFU/mL
  • Lung tissue: ≥10⁴ CFU/g
  • PSB (protected specimen brush): ≥10³ CFU/mL
  • ETA (endotracheal aspirate): ≥10⁶ CFU/mL

Qualifying Antimicrobials for IVAC

Includes most IV/PO antibiotics used for respiratory infections:

• Beta-lactams (piperacillin-tazobactam, ceftriaxone, cefepime, meropenem, etc.)
• Fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin)
• Aminoglycosides (gentamicin, tobramycin, amikacin)
• Glycopeptides (vancomycin)
• Oxazolidinones (linezolid)

Excludes: Topical agents, antifungals, antivirals

NHSN CDI Criteria Quick Reference

CDI LabID Event Definition

A positive laboratory test result for:

• C. difficile toxin A and/or B, OR
• Toxin-producing C. difficile by culture or PCR/NAAT

On an unformed stool specimen (including ostomy collections).

Important: GDH (glutamate dehydrogenase) antigen-only results do NOT qualify as a LabID event.

Onset Classification

Classification	Specimen Day	Description
HO-CDI	Day 4+ (>3 days)	Healthcare-Facility-Onset: Specimen collected >3 days after admission
CO-CDI	Days 1-3 (≤3 days)	Community-Onset: Specimen collected ≤3 days after admission
CO-HCFA	Days 1-3	Community-Onset Healthcare Facility-Associated: CO-CDI with discharge from any facility within prior 4 weeks

Day 1 = facility admission date

Recurrence Classification

Days Since Last CDI Event	Classification	Reporting
≤14 days	Duplicate	Not reported (same episode)
15-56 days	Recurrent	Reported as recurrent CDI
>56 days	New Incident	Reported as new CDI event

Test Type Eligibility

For multi-step testing algorithms, the last test performed determines eligibility:

Test Type	Qualifies for LabID Event
Toxin A/B EIA	Yes (if positive)
PCR/NAAT	Yes (if positive)
Toxigenic culture	Yes (if positive)
GDH antigen only	No

Specimen Requirements

• Unformed stool only: Specimen must conform to container shape (Bristol stool types 5-7)
• Formed stool excluded: Solid stool specimens do not qualify
• Ostomy specimens: Acceptable if stool is unformed
• Rectal swabs: Generally not acceptable for CDI surveillance

Common LOINC Codes for C. diff Testing

• 34713-8: C. difficile toxin A
• 34714-6: C. difficile toxin B
• 34712-0: C. difficile toxin A+B
• 82197-9: C. difficile toxin B gene (PCR)
• 80685-5: C. difficile toxin genes (NAAT)

LLM-Assisted Classification

The system uses a two-stage approach: LLM extraction followed by rules engine.

Stage 1: LLM Fact Extraction

A local LLM (Ollama llama3.1) reads clinical notes and extracts structured facts:

• Alternate infection sources - Pneumonia, UTI, SSTI, intra-abdominal
• Symptoms - Fever, WBC changes, hypotension
• MBI factors - Neutropenia, mucositis, HSCT status, GVHD
• Line assessment - Exit site findings, clinical suspicion
• Contamination signals - Team treating as contaminant

The LLM answers factual questions about documentation - it does NOT make classification decisions.

Stage 2: Rules Engine

Deterministic NHSN criteria are applied to the extracted facts:

1. Basic eligibility check (line days, timing)
2. MBI-LCBI criteria evaluation
3. Secondary BSI check (same organism at other site)
4. Contamination check (single commensal culture)
5. Default to CLABSI if no exclusions apply

IP Makes Final Decision

ALL candidates are routed to IP review regardless of confidence score. The LLM classification and confidence are displayed as decision support, but IP always makes the final determination.

This approach ensures:

• Human oversight on all HAI determinations
• Transparency - Every decision can be traced to specific criteria
• Override tracking - When IP disagrees with LLM, it's logged for quality assessment

Privacy: All PHI stays on-premise. The Ollama LLM runs locally and no data is sent to external services.

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 HAI data and start fresh

# Clear HAI/NHSN database (shared database)
rm -f ~/.aegis/nhsn.db

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

LLM classification not running

# Check if Ollama is running
curl http://localhost:11434/api/tags

# If not running, start Ollama
ollama serve

Check available Ollama models

ollama list

Architecture

+-------------------+     +-------------------+
|   Demo Scripts    |---->|  HAPI FHIR        |
| demo_clabsi.py    |     |  Server :8081     |
| demo_ssi.py       |     |                   |
| demo_vae.py       |     |                   |
| demo_cdi.py       |     |                   |
+-------------------+     +---------+---------+
                                    |
                                    v
                         +-------------------+
                         |  HAI Monitor      |
                         |  (Rule-based      |
                         |   Screening)      |
                         +---------+---------+
                                   |
       +----------+----------+----------+----------+----------+
       |          |          |          |          |          |
+----------+ +----------+ +----------+ +----------+ +----------+
|CLABSI    | |CAUTI     | |SSI       | |VAE       | |CDI       |
|Detector  | |Detector  | |Detector  | |Detector  | |Detector  |
|(BSI+Line)| |(Cath+UCx)| |(Procedure| |(Vent     | |(C.diff   |
+----------+ +----------+ +----------+ +----------+ +----------+
       |          |          |          |          |
       +----------+----------+----------+----------+
                                   |
              +--------------------+--------------------+
              v                                        v
    +-------------------+                    +-------------------+
    |  LLM Extraction   |                    |   Rules Engine    |
    |  (Ollama llama3.1)|---> Facts ------->|  (NHSN Criteria)  |
    +-------------------+                    +---------+---------+
                                                       |
                                                       v
                                             +-------------------+
                                             |   IP Review       |
                                             | (Final Decision)  |
                                             +---------+---------+
                                                       |
                         +-----------------------------+
                         v                             v
               +-------------------+          +-------------------+
               |  Confirmed HAI    |          | Confirmed Not HAI |
               |  (NHSN Events)    |          |    (Rejected)     |
               +-------------------+          +-------------------+
        

Links

• Dashboard - Active cases awaiting IP review
• History - Completed reviews (confirmed HAI and confirmed not HAI)
• Reports & Analytics - LLM quality metrics and override tracking
• NHSN Submission - Export or submit confirmed events to NHSN
• ASP Alerts Help - Help for bacteremia and antimicrobial usage alerts