suspicion-of-infection

name	suspicion-of-infection
description	Identify suspected infection events using antibiotic administration plus culture timing. Use as a component of Sepsis-3 definition or for infection research.
tier	validated
category	clinical

Suspicion of Infection

This concept identifies when clinicians suspected infection based on clinical actions: antibiotic administration combined with culture collection within a defined time window.

When to Use This Skill

• Building Sepsis-3 cohorts (infection component)
• Antibiotic stewardship research
• Time-to-treatment studies
• Infection onset timing
• Culture yield research

Pre-computed Table

SELECT
    subject_id,
    stay_id,
    hadm_id,
    ab_id,                     -- Unique antibiotic ID per patient
    antibiotic,                -- Antibiotic name
    antibiotic_time,           -- When antibiotic started
    suspected_infection,       -- 1 if meets criteria, 0 otherwise
    suspected_infection_time,  -- Onset time of suspected infection
    culture_time,              -- When culture was obtained
    specimen,                  -- Culture specimen type
    positive_culture           -- 1 if culture positive, 0 if negative
FROM mimiciv_derived.suspicion_of_infection;

Definition Logic

Suspected infection requires BOTH:

1. Antibiotic administration (systemic, not topical)
2. Culture collection within time window:
   • Culture obtained up to 72h BEFORE antibiotic, OR
   • Culture obtained up to 24h AFTER antibiotic

Suspected Infection Time

The suspected_infection_time is defined as:

• The culture time if culture was obtained BEFORE antibiotic
• The antibiotic time if antibiotic was given BEFORE culture

This represents when infection was first clinically suspected.

Antibiotic Filtering

The query includes systemic antibiotics only:

• Included routes: IV, PO, NG, etc.
• Excluded routes: Topical (OU, OS, OD, AU, AS, AD, TP), eye drops, ear drops
• Excluded formulations: Creams, gels, ophthalmic ointments, desensitization

Culture Matching Logic

Each antibiotic is matched to cultures in two directions:

Culture Before Antibiotic (Primary)

• Culture obtained within 72 hours before antibiotic start
• If multiple cultures, uses the EARLIEST culture before the antibiotic

Culture After Antibiotic (Secondary)

• Culture obtained within 24 hours after antibiotic start
• If multiple cultures, uses the EARLIEST culture after the antibiotic

Priority: Culture-before-antibiotic takes precedence when both exist.

Critical Implementation Notes

1. One Row Per Antibiotic: Each antibiotic prescription gets its own row, potentially matched to one culture.

2. Duplicate Handling: A single culture may be matched to multiple antibiotics. A single antibiotic is matched to at most one culture (the earliest relevant one).

3. ICU Association: The stay_id is populated when antibiotic timing overlaps with an ICU stay. May be NULL for floor patients.

4. Chart Dates vs Times: Microbiology cultures sometimes only have dates (not times). When charttime is null, the query uses chartdate for matching.

5. Positive Culture Flag: Indicates whether organisms grew. Negative cultures still count as suspected infection (clinical suspicion existed).

6. Specimen Types: Include all culture types (blood, urine, sputum, etc.). The specimen column identifies the type.

Example: Infection Events Per Patient

SELECT
    subject_id,
    COUNT(*) AS n_suspected_infections,
    SUM(positive_culture) AS n_positive_cultures
FROM mimiciv_derived.suspicion_of_infection
WHERE suspected_infection = 1
GROUP BY subject_id
ORDER BY n_suspected_infections DESC;

Example: Time from Culture to Antibiotic

SELECT
    ROUND(
        TIMESTAMP_DIFF(antibiotic_time, culture_time, HOUR), 0
    ) AS culture_to_abx_hours,
    COUNT(*) AS n_events
FROM mimiciv_derived.suspicion_of_infection
WHERE suspected_infection = 1
    AND culture_time < antibiotic_time  -- culture first
GROUP BY 1
ORDER BY 1;

Example: Most Common Antibiotics in Suspected Infection

SELECT
    antibiotic,
    COUNT(*) AS n_prescriptions,
    SUM(positive_culture) AS n_positive,
    ROUND(AVG(positive_culture), 2) AS positive_rate
FROM mimiciv_derived.suspicion_of_infection
WHERE suspected_infection = 1
GROUP BY antibiotic
ORDER BY n_prescriptions DESC
LIMIT 20;

Example: Culture Specimen Distribution

SELECT
    specimen,
    COUNT(*) AS n_cultures,
    SUM(positive_culture) AS n_positive,
    ROUND(AVG(positive_culture), 2) AS positive_rate
FROM mimiciv_derived.suspicion_of_infection
WHERE suspected_infection = 1
GROUP BY specimen
ORDER BY n_cultures DESC;

Related Skills

• sepsis-3-cohort - Complete Sepsis-3 definition
• sofa-score - Organ dysfunction component

References

• Singer M et al. "The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3)." JAMA. 2016;315(8):801-810.