sepsis-3-cohort

name	sepsis-3-cohort
description	Identify Sepsis-3 patients in MIMIC-IV using the consensus definition (SOFA >= 2 + suspected infection). Use for sepsis cohort studies, outcome research, or quality metrics.
license	Apache-2.0
metadata	{"author":"m4-clinical-extraction","version":"1.0","database":"mimic-iv","category":"cohort-definitions","source":"https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iv/concepts/sepsis","validated":true}

Sepsis-3 Cohort Identification

The Sepsis-3 definition (2016) identifies sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection. Operationalized as:

• Suspected infection (antibiotics + culture within time window) AND
• SOFA score >= 2 (within 48h before to 24h after suspected infection)

When to Use This Skill

• Creating sepsis patient cohorts for research
• Sepsis outcome studies
• Quality improvement and benchmarking
• Comparing sepsis populations across studies
• Validating machine learning models on sepsis data

Pre-computed Table

SELECT
    subject_id,
    stay_id,
    -- Infection details
    antibiotic_time,
    culture_time,
    suspected_infection_time,
    -- SOFA details
    sofa_time,
    sofa_score,
    respiration,
    coagulation,
    liver,
    cardiovascular,
    cns,
    renal,
    -- Sepsis flag
    sepsis3
FROM mimiciv_derived.sepsis3;

Sepsis-3 Definition Details

Suspected Infection Criteria

A patient has suspected infection when:

1. Antibiotics are administered (IV or oral routes, excluding topical) AND
2. Cultures are obtained within a time window:
   • Culture within 72h BEFORE antibiotic, OR
   • Culture within 24h AFTER antibiotic

SOFA Criteria

SOFA >= 2 points, where SOFA is calculated using the 24-hour worst values:

• Must occur within 48h before to 24h after suspected infection time

Important Assumption

Baseline SOFA is assumed to be 0 for all patients. The true Sepsis-3 definition requires acute change of >= 2 points from baseline, but pre-hospital baseline is rarely available.

Critical Implementation Notes

1. ICU-Only Definition: This query identifies sepsis onset WITHIN the ICU. It cannot detect sepsis present at ICU admission or ED sepsis.

2. Time of Sepsis Onset: Defined as the earliest of:

   • suspected_infection_time (when infection was suspected)
   • This is typically the culture time if culture preceded antibiotics

3. Multiple Antibiotics: A patient may have multiple antibiotic-culture pairs. The query returns the first (earliest) suspected infection event.

4. Culture Types: All culture types are included (blood, urine, respiratory, etc.). Each culture specimen is identified.

5. Positive vs Negative Cultures: The positive_culture flag indicates whether the culture grew organisms. Sepsis-3 does not require positive cultures.

6. SOFA Time Window: SOFA must be >= 2 within:

   • 48 hours BEFORE suspected_infection_time, OR
   • 24 hours AFTER suspected_infection_time

Example: Identify Sepsis Cohort

SELECT
    s.stay_id,
    ie.subject_id,
    ie.hadm_id,
    s.suspected_infection_time AS sepsis_onset,
    s.sofa_score,
    adm.hospital_expire_flag AS mortality
FROM mimiciv_derived.sepsis3 s
INNER JOIN mimiciv_icu.icustays ie ON s.stay_id = ie.stay_id
INNER JOIN mimiciv_hosp.admissions adm ON ie.hadm_id = adm.hadm_id
WHERE s.sepsis3 = TRUE;

Example: Sepsis Severity Distribution

SELECT
    CASE
        WHEN sofa_score < 5 THEN 'Mild (SOFA 2-4)'
        WHEN sofa_score < 10 THEN 'Moderate (SOFA 5-9)'
        WHEN sofa_score < 15 THEN 'Severe (SOFA 10-14)'
        ELSE 'Very Severe (SOFA 15+)'
    END AS severity,
    COUNT(*) AS n_patients,
    ROUND(AVG(adm.hospital_expire_flag), 3) AS mortality_rate
FROM mimiciv_derived.sepsis3 s
INNER JOIN mimiciv_icu.icustays ie ON s.stay_id = ie.stay_id
INNER JOIN mimiciv_hosp.admissions adm ON ie.hadm_id = adm.hadm_id
WHERE s.sepsis3 = TRUE
GROUP BY 1
ORDER BY 1;

Example: Time from ICU Admit to Sepsis Onset

SELECT
    ROUND(
        TIMESTAMP_DIFF(s.suspected_infection_time, ie.intime, HOUR), 0
    ) AS hours_to_sepsis,
    COUNT(*) AS n_patients
FROM mimiciv_derived.sepsis3 s
INNER JOIN mimiciv_icu.icustays ie ON s.stay_id = ie.stay_id
WHERE s.sepsis3 = TRUE
GROUP BY 1
ORDER BY 1;

Limitations

1. Baseline SOFA Unknown: Assumes baseline SOFA = 0, may over-classify chronic organ dysfunction as sepsis
2. ICU-Only: Cannot identify ED sepsis or sepsis present on admission
3. Antibiotic-Dependent: Requires antibiotic administration - may miss untreated infections
4. Culture-Dependent: Requires cultures obtained - may miss clinically diagnosed infections

Related Skills

• suspicion-of-infection - Detailed infection timing
• sofa-score - SOFA calculation details

References

• Singer M et al. "The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3)." JAMA. 2016;315(8):801-810.
• Seymour CW et al. "Assessment of Clinical Criteria for Sepsis." JAMA. 2016;315(8):762-774.