sepsis-3-cohort

# 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 ```sql 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 ```sql 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 ```sql 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 ```sql 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](../suspicion-of-infection/SKILL.md) - Detailed infection timing - [sofa-score](../sofa-score/SKILL.md) - 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.