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sql/sepsis/sepsis3.sql

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+-- ------------------------------------------------------------------
+-- Title: Sepsis-3 onset
+--
+-- Adapted from the MIMIC-IV upstream
+--   concepts/sepsis/sepsis3.sql
+-- and ported to MIMIC-III v1.3 vanilla PostgreSQL.
+--
+-- Definition (Singer et al., JAMA 2016):
+--   Sepsis-3 = SOFA >= 2 AND suspicion of infection,
+--   where the SOFA window must overlap the suspected-infection time
+--   by at most 48 h before / 24 h after.
+--   The "onset time" is the suspected-infection-time of the earliest
+--   row that satisfies these criteria for each ICU stay.
+--
+-- Implicitly assumes baseline SOFA = 0 prior to ICU admission, since
+-- we do not have premorbid organ-dysfunction data.
+--
+-- Dependencies:
+--   sepsis/suspicion_of_infection.sql
+--   sepsis/sofa_hourly.sql
+-- ------------------------------------------------------------------
+
+DROP TABLE IF EXISTS sepsis3;
+CREATE TABLE sepsis3 AS
+
+WITH sofa AS
+(
+  SELECT icustay_id
+       , starttime
+       , endtime
+       , respiration_24hours    AS respiration
+       , coagulation_24hours    AS coagulation
+       , liver_24hours          AS liver
+       , cardiovascular_24hours AS cardiovascular
+       , cns_24hours            AS cns
+       , renal_24hours          AS renal
+       , sofa_24hours           AS sofa_score
+  FROM   sofa_hourly
+  WHERE  sofa_24hours >= 2
+)
+, s1 AS
+(
+  SELECT soi.subject_id
+       , soi.icustay_id
+       , soi.ab_id
+       , soi.antibiotic
+       , soi.antibiotic_time
+       , soi.culture_time
+       , soi.suspected_infection
+       , soi.suspected_infection_time
+       , soi.specimen
+       , soi.positive_culture
+       , sofa.starttime
+       , sofa.endtime
+       , sofa.respiration
+       , sofa.coagulation
+       , sofa.liver
+       , sofa.cardiovascular
+       , sofa.cns
+       , sofa.renal
+       , sofa.sofa_score
+       , (sofa.sofa_score >= 2 AND soi.suspected_infection = 1) AS sepsis3
+       , ROW_NUMBER() OVER (
+           PARTITION BY soi.icustay_id
+           ORDER BY     soi.suspected_infection_time
+                      , soi.antibiotic_time
+                      , soi.culture_time
+                      , sofa.endtime
+         ) AS rn_sus
+  FROM   suspicion_of_infection soi
+  INNER  JOIN sofa
+         ON  soi.icustay_id = sofa.icustay_id
+         AND sofa.endtime  >= DATETIME_SUB(soi.suspected_infection_time, INTERVAL '48' HOUR)
+         AND sofa.endtime  <= DATETIME_ADD(soi.suspected_infection_time, INTERVAL '24' HOUR)
+  WHERE  soi.icustay_id IS NOT NULL
+    AND  soi.suspected_infection_time IS NOT NULL
+)
+SELECT subject_id
+     , icustay_id
+     , antibiotic_time
+     , culture_time
+     , suspected_infection_time
+     , endtime AS sofa_time
+     , sofa_score
+     , respiration, coagulation, liver, cardiovascular, cns, renal
+     , sepsis3
+FROM   s1
+WHERE  rn_sus = 1;
+
+CREATE INDEX IF NOT EXISTS sepsis3_idx ON sepsis3 (icustay_id);