sepsis-3-cohort

name	sepsis-3-cohort
description	Identify Sepsis-3 patients using the consensus definition (SOFA >= 2 + suspected infection). Use for sepsis cohort studies, outcome research, or quality metrics.
tier	validated
category	clinical

Sepsis-3 Cohort Identification

The Sepsis-3 definition (Singer et al. 2016) identifies sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection. This is a conceptual definition; the operationalization is a proxy:

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

Related Sepsis-3 Constructs

• qSOFA (quick SOFA): Bedside screening tool for patients outside the ICU (RR >= 22, altered mentation, SBP <= 100). Not a diagnostic criterion — meant to prompt further assessment. Sensitivity is limited; a negative qSOFA does not rule out sepsis.
• Septic Shock: Sepsis with vasopressor requirement to maintain MAP >= 65 mmHg AND lactate > 2 mmol/L despite adequate fluid resuscitation. Carries substantially higher mortality than sepsis alone.

M4Bench Use

In M4Bench, target concept tables listed in the task configuration are removed or unavailable in the agent database. Use this skill as procedural guidance and derive the requested output from available source or intermediate tables; do not rely on a precomputed target table or bundled SQL script.

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

Sepsis-3 Definition Details

Suspected Infection Criteria

A patient has suspected infection when:

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

See suspicion-of-infection for detailed matching logic.

SOFA Criteria

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

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

See sofa-score for SOFA component details.

Baseline SOFA Assumption

Baseline SOFA is assumed to be 0 for all patients. The true Sepsis-3 definition requires an acute change of >= 2 points from baseline, but pre-hospital baseline organ function is rarely available in retrospective data. This assumption may over-classify patients with chronic organ dysfunction (e.g., chronic kidney disease, cirrhosis) as having sepsis.

Critical Implementation Notes

1. ICU-Only by Design: SOFA requires ICU-level monitoring data (vasopressors, mechanical ventilation status, hourly urine output). This inherently limits Sepsis-3 operationalization to ICU stays. ED sepsis and floor sepsis are not captured.

2. Time of Sepsis Onset: Defined as the earliest suspected_infection_time. This is typically the culture time if culture preceded antibiotics, or the antibiotic time if antibiotics came first.

3. First Event: A patient may have multiple antibiotic-culture pairs. Implementations typically return the first (earliest) suspected infection event per ICU stay.

4. Culture Positivity Not Required: Sepsis-3 does not require positive cultures. Clinical suspicion (antibiotics ordered + cultures sent) is sufficient.

5. SOFA Time Window: The [-48h, +24h] window around suspected infection time is the Seymour et al. operationalization. Some studies use narrower windows.

General Limitations

1. Baseline SOFA Unknown: Assumes baseline SOFA = 0. Patients with pre-existing organ dysfunction (CKD, cirrhosis, chronic respiratory failure) may be over-classified as septic.

2. ICU-Only: Cannot identify ED sepsis, floor sepsis, or sepsis present on ICU admission. This systematically excludes patients who die before ICU transfer or are managed on the floor.

3. Antibiotic-Dependent: Requires antibiotic administration — may miss untreated infections or patients who die before antibiotics are started.

4. Culture-Dependent: Requires cultures obtained — may miss clinically diagnosed infections where cultures were not sent (e.g., empiric treatment of pneumonia without sputum culture).

5. Does Not Capture Septic Shock: Sepsis-3 cohort identification captures sepsis only. Septic shock identification requires additional vasopressor and lactate criteria.

Dataset-Specific Implementation Notes

MIMIC-IV

MIMIC-IV implementation details:

• Combines a suspected-infection component with a SOFA organ-dysfunction component.
• Returns one row per ICU stay (earliest suspected infection event with SOFA >= 2).
• The sepsis3 boolean flag is TRUE when both criteria are met.
• SOFA uses 24-hour worst values aligned to the suspected infection window.

MIMIC-IV limitations:

• Depends on the quality of both upstream concepts. Any limitations in infection timing or SOFA component extraction propagate here.
• SOFA components draw from ICU charting tables — onset timing is relative to ICU admission, not hospital admission.

eICU

Building Sepsis-3 in eICU requires constructing both components from raw tables:

Suspected infection component:

eICU Table	Columns	Maps to MIMIC
medication	drugname, routeadmin, drugstartoffset	prescriptions / derived antibiotic
microlab	culturetakenoffset, culturesite, organism	microbiologyevents

SOFA component sources:

SOFA Component	eICU Table	Column(s)
Respiration (PaO2/FiO2)	lab	labname = 'paO2', 'FiO2'
Coagulation (Platelets)	lab	labname = 'platelets x 1000'
Liver (Bilirubin)	lab	labname = 'total bilirubin'
Cardiovascular (MAP)	vitalperiodic	systemicmean; also vitalaperiodic.noninvasivemean
Cardiovascular (Vasopressors)	infusiondrug	drugname, infusionrate
CNS (GCS)	nursecharting	nursingchartcelltypevalname (Eyes, Motor, Verbal)
Renal (Creatinine)	lab	labname = 'creatinine'
Renal (Urine Output)	intakeoutput	celllabel (filter for urine-related entries)

eICU limitations:

• Center variability in missingness: Charting practices, medication naming, and data completeness vary substantially across the 208 hospitals. Missingness is not random — it correlates with hospital size, teaching status, and EHR system. This affects both infection identification and SOFA computation.
• Medication naming: medication.drugname is free-text and varies across sites. The same antibiotic may appear as "Vancomycin", "VANCOMYCIN", "vancomycin 1g IV", etc. Antibiotic identification requires extensive text matching.
• Culture timing: microlab.culturetakenoffset provides timing in minutes from unit admission. The antibiotic-culture pairing logic must be rebuilt for the eICU offset-based time system.
• SOFA computation: Each component comes from a different table with different naming conventions. The eicu-code repository provides pivoted tables (pivoted_lab, pivoted_bg, pivoted_score, pivoted_uo) that can simplify extraction.
• APACHE IV alternative: eICU provides APACHE IV scores in apachepatientresult, which includes a severity/mortality prediction. While not the same as Sepsis-3, APACHE IV combined with an infection flag may serve as a pragmatic alternative for eICU sepsis studies.

Related Skills

• suspicion-of-infection — Infection component (antibiotic + culture timing)
• sofa-score — Organ dysfunction component
• sirs-criteria — Historical pre-Sepsis-3 inflammatory response criteria

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.
• Shankar-Hari M et al. "Developing a New Definition and Assessing New Clinical Criteria for Septic Shock." JAMA. 2016;315(8):775-787.